03:02:2018 10:23 ECO (https://github.com/evidenceontology/evidenceontology) is released into the public domain under CC0 1.0 Universal (CC0 1.0). Anyone is free to copy, modify, or distribute the work, even for commercial purposes, without asking permission. Please see the Public Domain Dedication (https://creativecommons.org/publicdomain/zero/1.0/) for an easy-to-read description of CC0 1.0 or the full legal code (https://creativecommons.org/publicdomain/zero/1.0/legalcode) for more detailed information. To get a sense of why ECO is CC0 as opposed to licensed under CC-BY, please read this thoughtful discussion (https://github.com/OBOFoundry/OBOFoundry.github.io/issues/285) on the OBO Foundry GitHub site. eco OBO-Edit 2.3.1 rctauber 1.2 Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. Really of interest to developers only BFO OWL specification label Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 Person:Alan Ruttenberg Really of interest to developers only BFO CLIF specification label editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label example A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> IAO example of usage example of usage has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 has curation status definition definition definition textual definition textual definition The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> IAO definition definition definition textual definition textual definition editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obfoundry.org/obo/obi> editor note term editor Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> IAO term editor term editor alternative term An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> alternative term definition source formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> IAO definition source definition source curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note The 'term requester' can credit the person, organization or project who request the ontology term.,The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. IAO ontology term requester imported from For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from elucidation person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms elucidation has associated axiom(nl) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language has associated axiom(nl) has associated axiom(fol) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax has associated axiom(fol) ISA alternative term An alternative term used by the ISA tools project (http://isa-tools.org). Requested by Alejandra Gonzalez-Beltran https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178 Person: Alejandra Gonzalez-Beltran Person: Philippe Rocca-Serra ISA tools project (http://isa-tools.org) ISA alternative term IEDB alternative term An alternative term used by the IEDB. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IEDB alternative term temporal interpretation https://github.com/oborel/obo-relations/wiki/ROAndTime Grouping classes used by GO GO biological process terms should be used in the GO with/from field GO cellular component terms should be used in the GO with/from field Chemical entity IDs should be used in the GO with/from field Gene IDs should be used in the GO with/from field GO molecular function terms should be used in the GO with/from field Protein IDs should be used in the GO with/from field Protein complex IDs should be used in the GO with/from field Transcript IDs should be used in the GO with/from field Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content. An account of the content of the resource. Description Description The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system. A reference to a resource from which the present resource is derived. Source Source A legal document giving official permission to do something with the resource. DC license subset_property has_alternative_id has_broad_synonym database_cross_reference has_exact_synonym has_narrow_synonym has_obo_format_version has_obo_namespace has_related_synonym in_subset shorthand label label has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part has part realizes this disease course realizes this disease this investigation realizes this investigator role this shattering realizes this fragility to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes A relation connecting a piece of evidence to an assertion method, where that assertion method is supported by the evidence. mchibucos 2010-12-09T05:00:20Z ECO:9000000 eco used_in used_in In the future we may use a more generic relation with weaker domain and range constraints taken from IAO, RO or OBI. used_in A relation connecting a piece of evidence to an assertion method, where that assertion method is supported by the evidence. GOC:cjm ECO:9000001 eco uses uses uses This document is about information artifacts and their representations is_about is a (currently) primitive relation that relates an information artifact to an entity. 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about has_specified_input has_specified_input see is_input_of example_of_usage A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot has_specified_input is_specified_output_of is_specified_output_of A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_output_of participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in participates in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. concretizes material MaterialEntity a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic the undetached arm of a human being An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] material entity A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] A type of information that is used to support an assertion. eco evidence code evidence_code ECO:0000000 evidence A type of information that is used to support an assertion. ECO:MCC A type of curator inference where conclusions are drawn based on the background scientific knowledge of the curator. eco ECO:0000001 inference from background scientific knowledge A type of curator inference where conclusions are drawn based on the background scientific knowledge of the curator. ECO:SN A type of experimental evidence resulting from the direct measurement of some aspect of a biological feature. ECO:0005006 eco ECO:0000002 direct assay evidence A type of experimental evidence resulting from the direct measurement of some aspect of a biological feature. ECO:SN A type of direct assay evidence based on reconstructing a biological sample from its disassociated state to its original state. eco ECO:0000003 reconstitution assay evidence A type of direct assay evidence based on reconstructing a biological sample from its disassociated state to its original state. ECO:KAV PMID:26029343 A type of fractionation evidence where sub-cellular components are separated based on their physical properties such as density in a sucrose density gradient. eco IDA: cell fractionation ECO:0000004 If using this term for Gene Ontology annotation, it would be used most typically for annotations to the cellular component ontology. cell fractionation evidence A type of fractionation evidence where sub-cellular components are separated based on their physical properties such as density in a sucrose density gradient. ECO:KIM TAIR:TED A type of protein assay evidence where the catalytic activity of an enzyme is determined. ECO:0005001 MI:0415 eco IDA: enzyme assays ECO:0000005 enzyme assay evidence A type of protein assay evidence where the catalytic activity of an enzyme is determined. url:http://www.sciencedirect.com/science/article/pii/S2213020914000068 MI:0415 enzymatic study A type of evidence resulting from manipulation of variables in order to discover cause and effect. ECO:0005023 eco ECO:0000006 experimental evidence A type of evidence resulting from manipulation of variables in order to discover cause and effect. url:http://holah.co.uk/page/experimental/ A type of protein detection assay evidence where a fluorescently labeled antibody is used to detect the presence or localization of a biomolecule within a cell. eco IDA: immunofluorescence ECO:0000007 immunofluorescence evidence A type of protein detection assay evidence where a fluorescently labeled antibody is used to detect the presence or localization of a biomolecule within a cell. ECO:MCC TAIR:TED A type of experimental evidence that is based on characterization of gene expression. eco ECO:0000008 Use this evidence type when the annotation is inferred from the timing or location of expression of a gene. It may be difficult to determine whether the expression pattern truly indicates that a gene plays a role in a given process. expression pattern evidence A type of experimental evidence that is based on characterization of gene expression. ECO:MCC GO:IEP A type of expression pattern evidence where abundance of a transcript is analyzed. ECO:0000048 transcript expression level evidence eco ECO:0000009 transcript expression evidence A type of expression pattern evidence where abundance of a transcript is analyzed. ECO:RCT A type of expression pattern evidence resulting from protein abundance quantification techniques. eco ECO:0000010 protein expression evidence A type of expression pattern evidence resulting from protein abundance quantification techniques. PMC:4029002 url:https://www.thermofisher.com/us/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/pierce-protein-methods/overview-protein-expression-systems.html A type of experimental phenotypic evidence resulting from the effect that a given gene has on another gene or genes, and the products. TAIR:TED eco ECO:0000011 genetic interaction evidence A type of experimental phenotypic evidence resulting from the effect that a given gene has on another gene or genes, and the products. ECO:RCT PMID:11822023 A type of genetic interaction evidence where a wild-type copy of the gene in question is inserted into a mutant cell to see if it restores the wild-type phenotype in the mutant background. eco IGI: functional complementation ECO:0000012 functional complementation evidence A type of genetic interaction evidence where a wild-type copy of the gene in question is inserted into a mutant cell to see if it restores the wild-type phenotype in the mutant background. PMID:27403640 A type of functional complementation evidence resulting from the introduction of a transgene to prevent, or "rescue" an organism from a condition. eco ECO:0000013 transgenic rescue experiment evidence A type of functional complementation evidence resulting from the introduction of a transgene to prevent, or "rescue" an organism from a condition. url:http://www.mdpi.com/1420-3049/19/9/13932/pdf url:http://www.nature.com/gt/journal/v11/n15/full/3302282a.html A type of experimental phenotypic evidence derived from the difference in two alleles of a corresponding gene that result from one or more changes in the genome. eco ECO:0000015 mutant phenotype evidence A type of experimental phenotypic evidence derived from the difference in two alleles of a corresponding gene that result from one or more changes in the genome. GO:IMP A type of mutant phenotype evidence where a phenotype is associated with altered gene product which lacks the molecular function of the wild-type gene. eco ECO:0000016 loss-of-function mutant phenotype evidence A type of mutant phenotype evidence where a phenotype is associated with altered gene product which lacks the molecular function of the wild-type gene. SO:0002054 A type of experimental phenotypic evidence where a transgenic strain carrying the construct of a promoter cDNA fusion in which a gene of interest is driven by a defined promoter or enhancer is ectopically expressed in the defined pattern to characterize potential cellular properties and functions of a protein of interest. eco IMP: analysis of overexpression/ectopic expression phenotype ECO:0000017 ectopic expression evidence A type of experimental phenotypic evidence where a transgenic strain carrying the construct of a promoter cDNA fusion in which a gene of interest is driven by a defined promoter or enhancer is ectopically expressed in the defined pattern to characterize potential cellular properties and functions of a protein of interest. PMID:10948520 PMID:19301619 A type of mutant phenotype evidence where a phenotype is observed while expressing an anti-sense version of a gene product in a wild-type (for that gene product) background. eco IMP: anti-sense experiments ECO:0000018 anti-sense experiment evidence A type of mutant phenotype evidence where a phenotype is observed while expressing an anti-sense version of a gene product in a wild-type (for that gene product) background. ECO:SN A type of mutant phenotype evidence where an RNA construct is introduced into a cell and the expression of the gene bearing its complementary sequence is suppressed. eco IMP: RNAi experiment ECO:0000019 RNAi evidence A type of mutant phenotype evidence where an RNA construct is introduced into a cell and the expression of the gene bearing its complementary sequence is suppressed. ECO:MCC A type of protein assay evidence based on the inhibition of the molecular function of a protein. eco ECO:0000020 specific protein inhibition evidence A type of protein assay evidence based on the inhibition of the molecular function of a protein. ECO:MCC A type of experimental evidence that is based on characterization of an interaction between a gene product and another molecule. ECO:0005025 MI:0045 eco ECO:0000021 Molecules interacted with might include protein, nucleic acid, ion, or complex. physical interaction evidence A type of experimental evidence that is based on characterization of an interaction between a gene product and another molecule. ECO:SN MI:0045 experimental interaction detection A type of physical interaction evidence where a cellular component subunit is isolated as part of purification of its larger complex. MI:0025 eco IPI: co-purification ECO:0000022 co-purification evidence A type of physical interaction evidence where a cellular component subunit is isolated as part of purification of its larger complex. TAIR:TED MI:0025 copurification A type of physical interaction evidence that depends on the strength of the interaction between two entities. MI:0400 ligand binding evidence eco ECO:0000023 affinity evidence A type of physical interaction evidence that depends on the strength of the interaction between two entities. ECO:MCC PSI-MI:MI:0400 MI:0400 affinity technology A type of affinity evidence resulting from the binding of a molecule to a protein or protein complex. eco ECO:0000024 protein binding evidence A type of affinity evidence resulting from the binding of a molecule to a protein or protein complex. GO:0005515 url:https://en.wikipedia.org/wiki/Mutation A type of affinity evidence where proteins of interest (bait and prey) are covalently linked to incomplete fragments of a third protein (reporter) and expressed in vivo, at which time interaction between bait and prey proteins brings reporter fragments in close enough proximity to allow them to reform and become a functional reporter protein. MI:0090 eco ECO:0000025 Typically enzymes which confer resistance to antibiotics, such as Dihydrofolate reductase or Beta-lactamase, or proteins that give colorimetric or fluorescent signals are used. The Bait protein is generally the protein under study and the methods are readily adaptable to highthroughput mode. hybrid interaction evidence A type of affinity evidence where proteins of interest (bait and prey) are covalently linked to incomplete fragments of a third protein (reporter) and expressed in vivo, at which time interaction between bait and prey proteins brings reporter fragments in close enough proximity to allow them to reform and become a functional reporter protein. ECO:MCC PSI-MI:MI:0090 MI:0090 protein complementation assay A type of experimental genomic evidence resulting from a process in which single stranded nucleic acids are allowed to interact so that complexes, or hybrids, are formed by molecules with sufficiently similar, complementary sequences. eco ECO:0000026 nucleic acid hybridization evidence A type of experimental genomic evidence resulting from a process in which single stranded nucleic acids are allowed to interact so that complexes, or hybrids, are formed by molecules with sufficiently similar, complementary sequences. OBI:0302903 A type of similarity evidence based on structural similarity of an annotated gene or gene product to another gene or group of genes. eco ECO:0000027 For GO annotation, in the case of a single gene, an accession for the related gene's sequence is entered in the evidence_with field. structural similarity evidence A type of similarity evidence based on structural similarity of an annotated gene or gene product to another gene or group of genes. ECO:MCC TAIR:TED A type of match to sequence model evidence that is based on the presence of a recognized domain or motif in a gene product's (usually protein) primary sequence. eco ISS: recognized domains ECO:0000028 motif similarity evidence A type of match to sequence model evidence that is based on the presence of a recognized domain or motif in a gene product's (usually protein) primary sequence. ECO:SN A type of match to sequence model evidence resulting from a positive match of a protein, or set of proteins to a predictive model (signature) in the InterPro database. eco ECO:0000029 match to InterPro member signature evidence A type of match to sequence model evidence resulting from a positive match of a protein, or set of proteins to a predictive model (signature) in the InterPro database. PMC:2686546 url:http://www.ncbi.nlm.nih.gov/mesh?term=Nucleic+Acid+Hybridization A type of BLAST evidence that is used in a manual assertion. eco curated BLAST analysis ECO:0000030 BLAST evidence used in manual assertion true true A type of BLAST evidence that is used in a manual assertion. ECO:MCC A type of protein BLAST evidence that is used in a manual assertion. GO_REF:0000012 GO_REF:0000027 eco curated protein BLAST analysis ECO:0000031 protein BLAST evidence used in manual assertion true true A type of protein BLAST evidence that is used in a manual assertion. ECO:SN GO_REF:0000012 Pairwise alignment (TIGR) GO_REF:0000027 BLAST search criteria for ISS assignment in PAMGO_GAT A type of nucleotide BLAST evidence that is used in a manual assertion. eco curated nucleic acid BLAST analysis ECO:0000032 nucleotide BLAST evidence used in manual assertion true true A type of nucleotide BLAST evidence that is used in a manual assertion. ECO:SN A type of author statement that is based on a cited reference. eco ECO:0000033 The traceable author statement (TAS) evidence code covers author statements that are attributed to a cited source. Typically this type of information comes from review articles. Material from the introductions and discussion sections of non-review papers may also be suitable if another reference is cited as the source of experimental work or analysis. When annotating with this code the curator should use caution and be aware that authors often cite papers dealing with experiments that were performed in organisms different from the one being discussed in the paper at hand. Thus a problem with the TAS code is that it may turn out from following up the references in the paper that no experiments were performed on the gene in the organism actually being characterized in the primary paper. For this reason we recommend (when time and resources allow) that curators track down the cited paper and annotate directly from the experimental paper using the appropriate experimental evidence code. When this is not possible and it is necessary to annotate from reviews, the TAS code is the appropriate code to use for statements that are associated with a cited reference. Once an annotation has been made to a given term using an experimental evidence code, we recommend removing any annotations made to the same term using the TAS evidence code. traceable author statement A type of author statement that is based on a cited reference. ECO:MCC GO:TAS A type of author statement that is not associated with results presented or a cited reference. eco ECO:0000034 The non-traceable author statement evidence code should be used in all cases where the author makes a statement that a curator wants to capture but for which there are neither results presented nor a specific reference cited in the source used to make the annotation. The source of the information may be peer reviewed papers, textbooks, database records or vouchered specimens. non-traceable author statement A type of author statement that is not associated with results presented or a cited reference. ECO:SN A curator inference that results from research where no information about a biological feature was found in the scientific literature, at biological databases, or within other resources. eco ECO:0000035 An assertion of "no biological data found" carries the assumption that a more-or-less exhaustive search has been conducted. no biological data found A curator inference that results from research where no information about a biological feature was found in the scientific literature, at biological databases, or within other resources. ECO:SN An evidence that reflects an annotation was made before curators began tracking evidence types. NR not recorded eco ECO:0000037 The evidence not_recorded appears in some legacy annotations; it should not be used for new annotations. not_recorded true An evidence that reflects an annotation was made before curators began tracking evidence types. ECO:MCC GO:NR NR GO:NR not recorded GO:NR eco ECO:0000038 transient rescue experiment evidence A type of direct assay evidence resulting from determining the presence, abundance, structure, function, or activity of proteins. ECO:0005022 eco ECO:0000039 protein assay evidence A type of direct assay evidence resulting from determining the presence, abundance, structure, function, or activity of proteins. PMID:18429326 A type of affinity evidence resulting from quantitation of the analyte which depends on the reaction of an antigen (analyte) and an antibody. ECO:0005018 eco ECO:0000040 immunological assay evidence A type of affinity evidence resulting from quantitation of the analyte which depends on the reaction of an antigen (analyte) and an antibody. ERO:0001362 url:http://www.ncbi.nlm.nih.gov/books/NBK21589/,http://cores.ucsf.edu/protein-assay.html A type of evidence resulting from comparing likeness of distinct biological entities. IS eco inferred from similarity ECO:0000041 similarity evidence A type of evidence resulting from comparing likeness of distinct biological entities. ECO:SN A type of mutant phenotype evidence resulting from a phenotype that is associated with the altered gene product which possesses a new molecular function or a new pattern of gene expression. eco ECO:0000042 gain-of-function mutant phenotype evidence A type of mutant phenotype evidence resulting from a phenotype that is associated with the altered gene product which possesses a new molecular function or a new pattern of gene expression. SO:0002053 url:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3614608/ A type of similarity based on biomolecular sequence. eco ECO:0000044 A sequence similarity analysis may involve a gene or a gene product, and it could be based on similarity to a single other gene or to a group of other genes. sequence similarity evidence A type of similarity based on biomolecular sequence. ECO:MCC TAIR:TED eco ECO:0000045 spatial pattern of protein expression evidence A type of protein expression evidence resulting from the quantification of protein production in a sample. eco ECO:0000046 protein expression level evidence A type of protein expression evidence resulting from the quantification of protein production in a sample. NBK:22011 url:http://www.informatics.jax.org/glossary/gain-of-function eco ECO:0000047 spatial pattern of transcript expression evidence A type of experimental phenotypic evidence that is based on the expression pattern of a reporter gene. eco IEP: expression of a reporter gene ECO:0000049 reporter gene assay evidence A type of experimental phenotypic evidence that is based on the expression pattern of a reporter gene. TAIR:TED A type of phenotypic evidence based on an author's phenotypic description of a species or higher level group explicitly referencing an observation of a voucher specimen, a specimen with a permanent museum catalog. IVS eco ECO:0000050 voucher specimen analysis evidence A type of phenotypic evidence based on an author's phenotypic description of a species or higher level group explicitly referencing an observation of a voucher specimen, a specimen with a permanent museum catalog. TAIR:TED A type of similarity based on genotype without respect to expression. IGTS eco inferred from genetic similarity ECO:0000051 A genetic similarity analysis might consider genetic markers, polymorphisms, alleles, or other characteristics sometimes considered as part of the field of traditional genetics. Although an attempt has been made to treat as distinct the concepts of "genetic", "genotypic", "genomic", and "sequence", there is considerable overlap in usage throughout the field of biology. genetic similarity evidence A type of similarity based on genotype without respect to expression. ECO:MCC PhenoScape:IGTS A type of genetic interaction evidence resulting from a second mutation that either suppresses or enhances the phenotype expressed from an original mutation. TAIR:TED eco IGI: 'traditional' genetic interactions (e.g. suppressors, synthetic lethals) ECO:0000052 suppressor/enhancer interaction evidence A type of genetic interaction evidence resulting from a second mutation that either suppresses or enhances the phenotype expressed from an original mutation. url:http://biorxiv.org/content/early/2015/10/03/021592 url:http://www.wormbook.org/chapters/www:geneticsuppression/geneticsuppression.html A type of combinatorial analysis where data are combined and evaluated by an algorithm. TAIR:TED eco ECO:0000053 Combinatorial analyses could include experimental or computational results. Examples include: (i) large-scale experiment such as a genome-wide two-hybrid or genome-wide synthetic interactions; (ii) integration of large-scale data sets of various types; and (iii) text-based-computation, e.g. text-mining. For simple sequence comparisons, one should use the sequence similarity analysis evidence type. For microarray results alone, expression pattern analysis is appropriate; whereas, large-scale computational analysis should be used when microarray results are combined with the results of other types of large-scale experiments. computational combinatorial evidence A type of combinatorial analysis where data are combined and evaluated by an algorithm. ECO:MCC ECO:go A type of genetic interaction evidence that is based on the phenotypic outcome of two mutations in unrelated genetic loci. eco IGI: double mutant analysis ECO:0000054 double mutant phenotype evidence A type of genetic interaction evidence that is based on the phenotypic outcome of two mutations in unrelated genetic loci. ECO:RCT A type of expression pattern evidence resulting from the hybridization of a target with a probe which is attached to the microarray surface. eco ECO:0000055 array experiment evidence true A type of expression pattern evidence resulting from the hybridization of a target with a probe which is attached to the microarray surface. url:http://www.premierbiosoft.com/tech:notes/microarray.html A type of genetic interaction evidence that is based on the suppression of one allelic effect by an allele at another genetic locus. eco IGI: epistatic interactions ECO:0000056 Epistasis' can be used in different contexts in different areas of genetics. It is sometimes used to mean 'genetic interaction', whereas other times it may be specific to mutations that block the effects of other mutations. epistatic interaction evidence A type of genetic interaction evidence that is based on the suppression of one allelic effect by an allele at another genetic locus. PMID:18852697 A type of similarity based on the expression of a genotype in an environment. IPTS phenotype similarity evidence eco inferred from phenotypic similarity ECO:0000057 Phenotype is defined as the outcome of the expression of a genotype in a given environment. A comparison might involve whole organisms or sub-parts of organisms. phenotypic similarity evidence A type of similarity based on the expression of a genotype in an environment. ECO:MCC PhenoScape:IPTS A type of transcript expression evidence resulting from simultaneous profiling of the expression levels of thousands of genes in a single experiment allowing analysis of genes and their networks. ECO:0000356 differential gene expression evidence from microarray experiment eco ECO:0000058 expression microarray evidence A type of transcript expression evidence resulting from simultaneous profiling of the expression levels of thousands of genes in a single experiment allowing analysis of genes and their networks. url:http://www.illumina.com/techniques/microarrays/gene-expression-arrays.html url:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2435252/ A type of experimental evidence that is based on the expression of a genotype in an environment. ECO:0000014 ECO:0005017 eco inferred from phenotype ECO:0000059 experimental phenotypic evidence A type of experimental evidence that is based on the expression of a genotype in an environment. ECO:SN A type of phenotypic similarity evidence based on the similarity of stucture locations or arrangements. IPS eco ECO:0000060 positional similarity evidence A type of phenotypic similarity evidence based on the similarity of stucture locations or arrangements. TAIR:TED A type of phenotypic evidence that is based on a gene product that is associated with a quantitative trait locus, but has not been cloned. QTL analysis evidence eco IGI: quantitative trait analysis ECO:0000061 quantitative trait analysis evidence A type of phenotypic evidence that is based on a gene product that is associated with a quantitative trait locus, but has not been cloned. TAIR:TED A type of expression microarray evidence where expression level is quantified by sample biotin-labeled cRNA (transcribed from an unknown RNA sample) hybridized to DNA oligonuclotides immoblized on a solid surface. genomic microarray evidence eco ECO:0000062 cRNA to DNA expression microarray evidence A type of expression microarray evidence where expression level is quantified by sample biotin-labeled cRNA (transcribed from an unknown RNA sample) hybridized to DNA oligonuclotides immoblized on a solid surface. url:https://link.springer.com/chapter/10.1007/978-94-017-9716-0_30 A type of phenotypic similarity evidence based on the similarity of the histological makeup of structures. ICS eco ECO:0000063 compositional similarity evidence A type of phenotypic similarity evidence based on the similarity of the histological makeup of structures. TAIR:TED A type of functional complementation evidence that is based on the insertion of a wild-type copy of a gene into a heterologous organism, with the mutation occurring in a homologous gene. eco IGI: functional complementation in heterologous system ECO:0000064 functional complementation in heterologous system evidence A type of functional complementation evidence that is based on the insertion of a wild-type copy of a gene into a heterologous organism, with the mutation occurring in a homologous gene. TAIR:TED A type of hybrid interaction evidence that is based on a protein-DNA complementation assay where a single promoter acts as bait and is screened against a library of prey transcription factors. MI:0432 eco IPI: yeast one-hybrid assay ECO:0000066 The assay involves screening a library of candidate proteins for the ability bind to a target, cis-regulatory element or any other short, DNA binding sequence placed 5' to a yeast reporter gene (TAIR:TED). yeast one-hybrid evidence A type of hybrid interaction evidence that is based on a protein-DNA complementation assay where a single promoter acts as bait and is screened against a library of prey transcription factors. ECO:MCC PSI-MI:MI:0432 TAIR:TED MI:0432 one hybrid A type of phenotypic similarity evidence based on the similarity of embryological or post-embryonic orgin of structures. IDS eco ECO:0000067 developmental similarity evidence A type of phenotypic similarity evidence based on the similarity of embryological or post-embryonic orgin of structures. TAIR:TED A type of hybrid interaction evidence that is based on detection of protein-protein interaction by activation of a yeast reporter gene after a bait protein fused to a DNA-binding domain (which has been transfected into a yeast cell) is used to screen a cDNA library of clones fused to an activation domain. eco IPI: yeast two-hybrid assay ECO:0000068 yeast 2-hybrid evidence A type of hybrid interaction evidence that is based on detection of protein-protein interaction by activation of a yeast reporter gene after a bait protein fused to a DNA-binding domain (which has been transfected into a yeast cell) is used to screen a cDNA library of clones fused to an activation domain. PMID:12734586 A type of nucleic acid hybridization evidence where methylation-sensitive restriction enzymes are utilized to analyze methylated DNA fragments by hybridizing them to a CpG island microarray. ECO:0000065 CpG island microarray evidence eco ECO:0000069 differential methylation hybridization evidence A type of nucleic acid hybridization evidence where methylation-sensitive restriction enzymes are utilized to analyze methylated DNA fragments by hybridizing them to a CpG island microarray. PMID:18987809 A type of immunoprecipitation evidence that involves precipitating two or more proteins via binding to an antibody specific to a single protein, followed by protein identification. MI:0019 eco IPI: co-immunoprecipitation ECO:0000070 If performing GO annotation, the interacting protein is referenced in the evidence_with column. co-immunoprecipitation evidence A type of immunoprecipitation evidence that involves precipitating two or more proteins via binding to an antibody specific to a single protein, followed by protein identification. ECO:MCC MI:0019 coimmunoprecipitation A type of phenotypic similarity evidence based on the similarity of shape, structure, or configuration in structures. IMS eco ECO:0000071 morphological similarity evidence A type of phenotypic similarity evidence based on the similarity of shape, structure, or configuration in structures. TAIR:TED A type of physical interaction evidence that is based on a genetic screening system that detects protein-protein interactions and is not based on a transcriptional readout. eco IPI: Sos-recruitment assay ECO:0000072 Sos-recruitment assay evidence true A type of physical interaction evidence that is based on a genetic screening system that detects protein-protein interactions and is not based on a transcriptional readout. TAIR:TED A type of experimental evidence that is based on the characterization of an attribute of the genome underlying a gene product. inferred from genomic analysis eco ECO:0000073 experimental genomic evidence A type of experimental evidence that is based on the characterization of an attribute of the genome underlying a gene product. ECO:MCC A type of physical interaction evidence that is based on detection of protein-protein interaction between a bait and prey protein by in vivo reconstitution of split-ubiquitin (when bait and prey interact) and release of a reporter protein. MI:0112 eco IPI: split-ubiquitin assay ECO:0000074 The bait protein is fused to the C-terminal ubiquitin (Cub) domain followed by a reporter protein, and the prey protein is fused to a mutated N terminal ubiquitin (NubG) domain. If bait and prey interact, their interaction brings the NubG and Cub domains close enough to reconstitute.TAIR:TED split-ubiquitin assay evidence A type of physical interaction evidence that is based on detection of protein-protein interaction between a bait and prey protein by in vivo reconstitution of split-ubiquitin (when bait and prey interact) and release of a reporter protein. PMID:15064465 MI:0112 ubiquitin reconstruction A type of phenotypic similarity evidence that is based on the categorization of genes by the similarity of expression profiles. IGES eco ECO:0000075 gene expression similarity evidence A type of phenotypic similarity evidence that is based on the categorization of genes by the similarity of expression profiles. PMID:19958477 A type of physical interaction evidence that is based on detection of protein-protein interactions by separation of target proteins by SDS-PAGE which are blotted to a membrane, followed by denaturation and renaturation, probing with purified bait proteins, and detection of the target-bait complexes. MI:0047 eco IPI: far-Western analysis ECO:0000076 The interacting protein is referenced in the evidence_with column. far-Western blotting evidence A type of physical interaction evidence that is based on detection of protein-protein interactions by separation of target proteins by SDS-PAGE which are blotted to a membrane, followed by denaturation and renaturation, probing with purified bait proteins, and detection of the target-bait complexes. PMID:18079728 A type of polymerase chain reaction evidence resulting from initial modification of DNA by sodium bisulfite, converting all unmethylated cytosines to uracil, and subsequent amplification with primers specific for methylated versus unmethylated DNA. methylation-specific PCR evidence eco ECO:0000077 methylation-specific polymerase chain reaction evidence A type of polymerase chain reaction evidence resulting from initial modification of DNA by sodium bisulfite, converting all unmethylated cytosines to uracil, and subsequent amplification with primers specific for methylated versus unmethylated DNA. PMC:38513 A type of DNA detection assay evidence that is based on detection of a specific DNA sequence by hybridization of labeled probes to any immobilized DNA fragment with sequence similarity. Southern blot eco ISS: Southern blotting ECO:0000078 The DNA fragments are prepared through gel electrophoresis then transferred to a filter membrane. southern hybridization evidence A type of DNA detection assay evidence that is based on detection of a specific DNA sequence by hybridization of labeled probes to any immobilized DNA fragment with sequence similarity. PMID:18432697 A type of affinity evidence that results from separation of biochemical mixtures by selective binding of a compound to an immobilized compound on a polymeric matrix, subsequent removal of unattached components, and then displacement of the bond compound. MI:0004 eco IDA: affinity chromatography ECO:0000079 "Used when an annotation is made based on affinity chromatography, which is a selective separation technique by which a compound (e.g., an antibody) is immobilized on a polymeric matrix and used to bind selectively other compounds. Following removal of the unattached components, the bound compound is displaced by changing the concentration of protons, salts, or cofactors in the eluent" (from original definition by TAIR:TED). Types of highly specific interaction might include those of antigen and antibody, enzyme and substrate, or receptor and ligand. affinity chromatography evidence A type of affinity evidence that results from separation of biochemical mixtures by selective binding of a compound to an immobilized compound on a polymeric matrix, subsequent removal of unattached components, and then displacement of the bond compound. ECO:MCC TAIR:TED MI:0004 affinity chromatography technology A type of similarity that indicates common ancestry. IP eco ECO:0000080 phylogenetic evidence A type of similarity that indicates common ancestry. ECO:MCC PhenoScape:IP IP PhenoScape:IP A type of motif similarity evidence that is based on detection of a targeting sequence in the primary sequence of a protein through computational prediction and/or a manual examination of the sequence. eco ISS: targeting sequence prediction ECO:0000081 targeting sequence prediction evidence A type of motif similarity evidence that is based on detection of a targeting sequence in the primary sequence of a protein through computational prediction and/or a manual examination of the sequence. ECO:RCT TAIR:TED A type of experimental genomic evidence where DNA polymerase is used to synthesize new strand of DNA complementary to the offered template strand. PCR evidence eco ECO:0000082 polymerase chain reaction evidence A type of experimental genomic evidence where DNA polymerase is used to synthesize new strand of DNA complementary to the offered template strand. OBI:0000415 A type of motif similarity evidence that is based on detection of one, or more, transmembrane domains in the primary sequence of a protein through computational prediction and/or a manual examination of the sequence. eco ISS: transmembrane domain prediction ECO:0000083 transmembrane domain prediction evidence A type of motif similarity evidence that is based on detection of one, or more, transmembrane domains in the primary sequence of a protein through computational prediction and/or a manual examination of the sequence. ECO:RCT TAIR:TED A type of genomic context evidence in which a gene product's identity is supported on the basis of the identity of neighboring genes. mgiglio 2009-03-20T11:55:18Z GO_REF:0000025 inferred from genome cluster eco ICL ECO:0000084 Genomic cluster analyses include synteny and operon structure. gene neighbors evidence A type of genomic context evidence in which a gene product's identity is supported on the basis of the identity of neighboring genes. ECO:MCC GOC:MG GO_REF:0000025 Operon structure as IGC evidence A type of protein assay evidence that involves precipitation of a multivalent antigen by a bivalent antibody for protein isolation. CollecTF eco IDA: immunoprecipitation ECO:0000085 Transcription factors isolated in this way can be incubated with a radiolabeled probe to demonstrate binding. immunoprecipitation evidence A type of protein assay evidence that involves precipitation of a multivalent antigen by a bivalent antibody for protein isolation. ECO:MCC ECO:SW TAIR:TED A type of experimental genomic evidence resulting from a genome-wide estimate of DNA methylation by differential enzymatic digestion of genomic DNA with methylation-sensitive and methylation-insensitive isoschizomers followed by restrained PCR amplification of methylated sequences. eco ECO:0000086 intermethylated site amplification evidence A type of experimental genomic evidence resulting from a genome-wide estimate of DNA methylation by differential enzymatic digestion of genomic DNA with methylation-sensitive and methylation-insensitive isoschizomers followed by restrained PCR amplification of methylated sequences. PMID:18987810 url:https://www.ncbi.nlm.nih.gov/probe/docs/techpcr/ A type of microscopy evidence where antibodies are used to detect the location of molecules or other structures within cells or tissues. eco IDA: immunolocalization ECO:0000087 immunolocalization evidence A type of microscopy evidence where antibodies are used to detect the location of molecules or other structures within cells or tissues. ECO:MCC ECO:SN A type of evidence that is based on a combination of experimental evidences or existing models of that system in a related species used for the reconstruction of a biological system. mgiglio 2009-03-20T12:00:17Z eco ISR inferred from system reconstruction ECO:0000088 The biological system in question might be a multi-step process or pathway or a physical complex comprising several components. The components in the experimental evidence can come from the same species or a mix of species. The experimental evidences may be only partial or weak. biological system reconstruction evidence A type of evidence that is based on a combination of experimental evidences or existing models of that system in a related species used for the reconstruction of a biological system. ECO:MCC GOC:mg A type of DNA detection assay evidence resulting from the use of restriction enzymes for direct end-labeling of DNA (creating landmarks), followed by high-resolution two-dimensional electrophoresis to visualize the landmarks. SIB:PG ECO:0001125 RLGS evidence restriction landmark genome scanning evidence eco ECO:0000089 restriction landmark genomic scanning evidence A type of DNA detection assay evidence resulting from the use of restriction enzymes for direct end-labeling of DNA (creating landmarks), followed by high-resolution two-dimensional electrophoresis to visualize the landmarks. PMID:8388788 A type of immunolocalization evidence where the antibodies are labeled with colloidal gold particles whose location is then detected via microscopy. eco IDA: immunogold labelling ECO:0000090 immunogold labelling evidence A type of immunolocalization evidence where the antibodies are labeled with colloidal gold particles whose location is then detected via microscopy. ECO:MCC A type of immunolocalization evidence in which recombinant proteins fused with epitopes are recognized by antibodies. eco IDA: immunolocalization of epitope-tagged protein ECO:0000092 epitope-tagged protein immunolocalization evidence A type of immunolocalization evidence in which recombinant proteins fused with epitopes are recognized by antibodies. TAIR:TED A type of experimental genomic evidence where gene sequence or variation is determined or detected by fluorescently-labeled DNA fragments hybridized to sequence-specific oligonucleotides immobilized on an array. DNA microarray oligonucleotide microarray evidence SNP array evidence single nucleotide polymorphism array evidence eco ECO:0000093 array-based sequence capture evidence A type of experimental genomic evidence where gene sequence or variation is determined or detected by fluorescently-labeled DNA fragments hybridized to sequence-specific oligonucleotides immobilized on an array. PMID:21049075 A type of direct assay evidence based on the effect of a substance, factor, or condition as measured in a living organism. eco IDA: bioassay ECO:0000094 biological assay evidence A type of direct assay evidence based on the effect of a substance, factor, or condition as measured in a living organism. ECO:MCC TAIR:TED A type of in vivo assay evidence that measures one or more aspects of cell growth over a specified time period to indicate an induced or repressed regulatory effect. CollecTF mchibucos 2014-10-15T00:58:50Z eco growth curve analysis ECO:0000095 Cell growth aspects can include growth rate and extent of growth. A cell growth curve acts as a natural reporter. cell growth assay evidence A type of in vivo assay evidence that measures one or more aspects of cell growth over a specified time period to indicate an induced or repressed regulatory effect. ECO:SW PomBase:MAH A type of direct assay evidence based on an electrophoretic mobility shift of macromolecules, compounds, and proteins where solutions of protein and nucleic acid are combined and the resulting mixtures are electrophoresed under native conditions through polyacrylamide or agarose gel to detect protein-nucleic acid interactions. CollecTF MI:0413 EMSA: electrophoretic mobility shift assay eco Gel retardation assay IDA: electrophoretic mobility shift assay ECO:0000096 EMSA is often used for assessing TF-binding with fluorophore labelling. Protein-nucleic acid complexes generally migrate at a slower rate than the corresponding non-bonded nucleic acid. electrophoretic mobility shift assay evidence A type of direct assay evidence based on an electrophoretic mobility shift of macromolecules, compounds, and proteins where solutions of protein and nucleic acid are combined and the resulting mixtures are electrophoresed under native conditions through polyacrylamide or agarose gel to detect protein-nucleic acid interactions. ECO:KIM ECO:SW PMID:17703195 TAIR:TED MI:0413 electrophoretic mobility shift assay Gel retardation assay PMID:17703195 A type of expression microarray evidence where expression level is quantified by fluroescently-labeled cDNA (reverse transcribed from an unknown RNA sample) hybridized to DNA immobilized on a solid surface. CollecTF ECO:0001041 ECO:0005524 eco DNA microarray RNA microarray ECO:0000097 cDNA to DNA expression microarray evidence A type of expression microarray evidence where expression level is quantified by fluroescently-labeled cDNA (reverse transcribed from an unknown RNA sample) hybridized to DNA immobilized on a solid surface. ECO:RCT A type of nucleic acid hybridization evidence based on localization of a specific segment of DNA or RNA by the application of a complementary strand of nucleic acid to which a reporter molecule is attached. eco IDA: in situ hybridization ECO:0000098 in situ hybridization evidence A type of nucleic acid hybridization evidence based on localization of a specific segment of DNA or RNA by the application of a complementary strand of nucleic acid to which a reporter molecule is attached. url:https://www.ncbi.nlm.nih.gov/probe/docs/techish/ A type of direct assay evidence resulting from the separation of various cell components while preserving their individual functions. eco ECO:0000100 fractionation evidence A type of direct assay evidence resulting from the separation of various cell components while preserving their individual functions. NBK:26936 url:https://www.ncbi.nlm.nih.gov/books/NBK26936/ A type of cRNA to DNA expression microarray evidence resulting from the use of a proprietary Affymetrix GeneChip System for analyzing complex genetic information. Affymetrix array experiment evidence eco ECO:0000101 Affymetrix GeneChip evidence A type of cRNA to DNA expression microarray evidence resulting from the use of a proprietary Affymetrix GeneChip System for analyzing complex genetic information. ERO:0001265 A type of fractionation evidence resulting from a protein fractionated with other compounds, factors, or macromolecules. eco IDA: co-fractionation ECO:0000102 co-fractionation evidence A type of fractionation evidence resulting from a protein fractionated with other compounds, factors, or macromolecules. TAIR:TED A type of expression microarray evidence where expression levels are quantified by hybridization of fluorescently-labeled DNA to cDNA (reverse transcribed from an unknown RNA sample) immobilized on a solid surface. REM evidence RNA expression microarray evidence microarray RNA expression level evidence eco IEP: transcript levels (e.g. microarray data) ECO:0000104 REM is a 'reverse-format' microarray, where the unknown sample is immoblized to a surface and known DNA is hybridized to that. DNA to cDNA expression microarray evidence A type of expression microarray evidence where expression levels are quantified by hybridization of fluorescently-labeled DNA to cDNA (reverse transcribed from an unknown RNA sample) immobilized on a solid surface. ECO:RCT PMID:15329382 REM is a 'reverse-format' microarray, where the unknown sample is immoblized to a surface and known DNA is hybridized to that. PMID:15329382 A type of cDNA to DNA expression microarray evidence resulting from the use of a proprietary NimbleGen array to measure expression levels. eco ECO:0000105 Nimblegen array evidence A type of cDNA to DNA expression microarray evidence resulting from the use of a proprietary NimbleGen array to measure expression levels. PMID:15607417 url:https://roche-biochem.jp/pdf/products/microarray/user_guide/SeqCap/SeqCap_UserGuide_Delivery_ver3.0.pdf A type of transcript expression evidence based on electrophoresis and probing to determine levels of RNA expression using a complementary hybridization probe on the separated RNA samples. CollecTF RNA blot evidence northern assay evidence eco IEP: transcript levels (e.g. Northerns) ECO:0000106 northern blot evidence A type of transcript expression evidence based on electrophoresis and probing to determine levels of RNA expression using a complementary hybridization probe on the separated RNA samples. ECO:SW TAIR:TED A type of transcript expression evidence in which expression levels are determined through RT-PCR (quantitative or otherwise). RT-PCR transcription evidence eco IEP: transcript levels (e.g. RT-PCR) ECO:0000108 reverse transcription polymerase chain reaction transcription evidence A type of transcript expression evidence in which expression levels are determined through RT-PCR (quantitative or otherwise). TAIR:TED A type of polymerase chain reaction evidence where RNA is reverse transcribed into cDNA and amplified for product measurement in real time for transcription analysis i.e. qPCR. CollecTF RT-PCR evidence qRT-PCR eco ECO:0000109 The starting product for PCR, and therefore amplification volume, is directly correlated to the transcription rate. reverse transcription polymerase chain reaction evidence A type of polymerase chain reaction evidence where RNA is reverse transcribed into cDNA and amplified for product measurement in real time for transcription analysis i.e. qPCR. ECO:SW PMID:11013345 PMID:12901609 qRT-PCR PMID:12901609 A type of nuclease protection assay evidence where mRNA is hybridized with radiolabeled RNA probes after which RNAse is added to digest the unbound, nonresistant single-stranded overhang regions, later the remaining probe target hybrids are purified and resolved on denaturing polyacrylamide gel, and quantified by autoradiography. CollecTF ribonuclease protection assay RPA eco IEP: RNA protection assay RNAse protection assay ECO:0000110 RNA protection assay evidence A type of nuclease protection assay evidence where mRNA is hybridized with radiolabeled RNA probes after which RNAse is added to digest the unbound, nonresistant single-stranded overhang regions, later the remaining probe target hybrids are purified and resolved on denaturing polyacrylamide gel, and quantified by autoradiography. ECO:SW PMID:23457339 TAIR:TED A type of gel electrophoresis evidence where proteins are separated using gel electrophoresis and then they are blotted on a nitrocellulose or polyvinylidene difluoride (PVDF) membrane, later an antibody with a dye or an enzyme is added to the solution which is able to bind to its specific protein and this product is detected either by chemiluminescent detection technique or fluorescence imaging technique. CollecTF eco IEP: protein levels (e.g. Western blots) Western blot expression analysis protein immunoblot ECO:0000112 Western blot is used for protein detection and analysis. A mixed protein sample is separated through polyacrylamide gel electrophoresis then transferred to a membrane, such as polyvinylidene fluoride (PVDF), and labeled with protein-specific antibodies. western blot evidence A type of gel electrophoresis evidence where proteins are separated using gel electrophoresis and then they are blotted on a nitrocellulose or polyvinylidene difluoride (PVDF) membrane, later an antibody with a dye or an enzyme is added to the solution which is able to bind to its specific protein and this product is detected either by chemiluminescent detection technique or fluorescence imaging technique. ECO:SW PMID:23050259 TAIR:TED A type of protein expression evidence where a protein of interest is isolated on the basis of its hybridization to an antibody raised to a homologous protein. eco IEP: expression library screening ECO:0000114 expression library screen evidence A type of protein expression evidence where a protein of interest is isolated on the basis of its hybridization to an antibody raised to a homologous protein. ECO:MCC TAIR:TED A type of nucleic acid hybridization evidence in which preferential or exclusive expression of genes in one cell type or tissue is compared to another cell type or tissue when mRNA from each sample is reverse transcribed, labeled, and hybridized to a cDNA library to compare hybridization patterns. eco IEP: differential hybridization ECO:0000116 Differential hybridization identifies differentially expressed cloned genes. Two different mRNA-derived probes are used to demonstrate RNA expression under a specific condition. differential hybridization evidence A type of nucleic acid hybridization evidence in which preferential or exclusive expression of genes in one cell type or tissue is compared to another cell type or tissue when mRNA from each sample is reverse transcribed, labeled, and hybridized to a cDNA library to compare hybridization patterns. PMID:14668817 A type of nucleic acid hybridization evidence in which preferential or exclusive expression of genes in one cell type or tissue are compared to another cell type or tissue when denatured ds-cDNA from the two samples are hybridized, and the common sequences are 'subtracted'. eco IEP: subtractive hybridization ECO:0000118 Subtractive hybridization is used for isolation and identification of transcripts involving the removal of any sequences present in the control from the test probe to detect only transcripts present in the sample. The method is PCR-based for the comparison of two cDNA libraries. subtractive hybridization evidence A type of nucleic acid hybridization evidence in which preferential or exclusive expression of genes in one cell type or tissue are compared to another cell type or tissue when denatured ds-cDNA from the two samples are hybridized, and the common sequences are 'subtracted'. PMID:11298187 A type of experimental phenotypic evidence in which a gene and/or gene product is investigated in a transgenic organism that has been engineered to overexpress that gene product. eco IMP: analysis of overexpression/ectopic expression phenotype ECO:0000120 over expression analysis evidence A type of experimental phenotypic evidence in which a gene and/or gene product is investigated in a transgenic organism that has been engineered to overexpress that gene product. PMID:22419077 A type of protein assay evidence where sub-cellular localization of a protein within a cell is determined. eco ECO:0000122 protein localization evidence A type of protein assay evidence where sub-cellular localization of a protein within a cell is determined. GO:0008104 url:http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019937 A type of protein localization evidence resulting from the fusion of a protein of interest to a labeling protein which has enzymatic activity or fluorescence properties. eco ECO:0000124 fusion protein localization evidence A type of protein localization evidence resulting from the fusion of a protein of interest to a labeling protein which has enzymatic activity or fluorescence properties. MI:0240 A type of fusion protein localization evidence resulting from the labeling of a protein of interest with green fluorescent protein (GFP) from the jellyfish Aequorea victoria. GFP fusion protein localization evidence eco IDA: localization of GFP/YFP fusion protein ECO:0000126 green fluorescent protein fusion protein localization evidence A type of fusion protein localization evidence resulting from the labeling of a protein of interest with green fluorescent protein (GFP) from the jellyfish Aequorea victoria. PMID:9759496 A type of fusion protein localization evidence resulting from the labeling of a protein of interest with yellow fluorescent protein (YFP), which was created by mutating green fluorescent protein (GFP) of the Aequorea victoria. YFP fusion protein localization evidence eco IDA: localization of GFP/YFP fusion protein ECO:0000128 yellow fluorescent protein fusion protein localization evidence A type of fusion protein localization evidence resulting from the labeling of a protein of interest with yellow fluorescent protein (YFP), which was created by mutating green fluorescent protein (GFP) of the Aequorea victoria. MI:0368 url:http://www.jbc.org/content/276/31/29188.long A type of fusion protein localization evidence resulting from the targeted insertion of the beta-glucuronidase (GUS) coding gene as a reporter gene for the localization of a particular gene product. GUS fusion protein localization evidence GUS staining evidence eco IDA: localization of GUS fusion protein ECO:0000130 beta-glucuronidase fusion protein localization evidence A type of fusion protein localization evidence resulting from the targeted insertion of the beta-glucuronidase (GUS) coding gene as a reporter gene for the localization of a particular gene product. ECO:RCT A type of fusion protein localization evidence resulting from the targeted insertion of the beta-galactosidase coding gene (lacZ) into a specific gene to create a beta-galactosidase-tagged fusion protein. LacZ fusion protein localization evidence eco ECO:0000132 beta-galactosidase fusion protein localization evidence A type of fusion protein localization evidence resulting from the targeted insertion of the beta-galactosidase coding gene (lacZ) into a specific gene to create a beta-galactosidase-tagged fusion protein. PMID:23681629 A type of direct assay evidence resulting from the activity assessment of transport proteins. eco IDA: transport assay ECO:0000134 transport assay evidence A type of direct assay evidence resulting from the activity assessment of transport proteins. PMID:18401524 A type of affinity evidence resulting from the binding of a molecule to a nucleic acid. eco ECO:0000136 nucleic acid binding evidence A type of affinity evidence resulting from the binding of a molecule to a nucleic acid. GO:0003676 A type of nucleic acid binding evidence resulting from an enzyme displaying binding activity to specific ribohomopolymer. eco IDA: ribohomopolymer binding assay ECO:0000138 ribohomopolymer binding assay evidence A type of nucleic acid binding evidence resulting from an enzyme displaying binding activity to specific ribohomopolymer. PMC:102612 A type of chromatography evidence that uses a thin layer of adsorbent (such as silica gel, alumina, or cellulose) on a flat, inert substrate. TLC evidence eco IDA: thin layer chromatography ECO:0000140 thin layer chromatography evidence A type of chromatography evidence that uses a thin layer of adsorbent (such as silica gel, alumina, or cellulose) on a flat, inert substrate. ECO:MCC A type of protein binding evidence resulting from a metal ion binding to a protein at a specific binding site. eco ECO:0000142 protein:ion binding evidence A type of protein binding evidence resulting from a metal ion binding to a protein at a specific binding site. PMID:2377604 A type of nucleic acid binding evidence in which DNA-protein binding is detected using labeled DNA as probes, hybridized to electrophoretically separated proteins. eco IDA: Southwestern analysis ECO:0000144 Southwestern blot evidence A type of nucleic acid binding evidence in which DNA-protein binding is detected using labeled DNA as probes, hybridized to electrophoretically separated proteins. ECO:RCT TAIR:TED A type of nucleic acid binding evidence in which RNA-protein binding is detected using labeled RNA as probes, hybridized to electrophoretically separated proteins. eco IDA: Northwestern analysis ECO:0000146 Northwestern blot evidence A type of nucleic acid binding evidence in which RNA-protein binding is detected using labeled RNA as probes, hybridized to electrophoretically separated proteins. ECO:RCT TAIR:TED eco IDA: in vitro binding assay ECO:0000148 in vitro binding evidence true A type of reconstitution assay evidence resulting from the use of reconstituted polymerase transcription systems to investigate RNA synthesis. eco IDA: in vitro reconstitution assay with recombinant protein ECO:0000150 in vitro transcription reconstitution assay evidence A type of reconstitution assay evidence resulting from the use of reconstituted polymerase transcription systems to investigate RNA synthesis. PMID:9237163 A type of in vitro transcription reconstitution assay evidence resulting from the use of recombinant proteins in preparation of a fully-defined transcription system. eco IDA: in vitro reconstitution assay with recombinant protein ECO:0000152 in vitro recombinant protein transcription reconstitution assay evidence A type of in vitro transcription reconstitution assay evidence resulting from the use of recombinant proteins in preparation of a fully-defined transcription system. PMID:9237165 A type of protein expression evidence where a gene from one cell is inserted into a cell that does not typically contain that gene and heterologous protein expression is assessed. eco IDA: protein expression in heterologous system ECO:0000154 heterologous protein expression evidence A type of protein expression evidence where a gene from one cell is inserted into a cell that does not typically contain that gene and heterologous protein expression is assessed. ECO:KAV A type of fractionation evidence resulting from the isolation of a single type of protein from a complex mixture. eco ECO:0000156 protein separation evidence A type of fractionation evidence resulting from the isolation of a single type of protein from a complex mixture. ERO:0000526 eco IDA: protein separation and direct sequencing ECO:0000158 protein separation followed by direct sequencing evidence eco IDA: protein separation and fragment identification ECO:0000160 protein separation followed by fragment identification evidence A type of transport assay evidence in which the uptake mechanism of a transporter is investigated in a cell that does not normally express that protein. eco IDA: uptake assay in heterologous system ECO:0000162 The transporter is a recombinant protein. heterologous system uptake evidence A type of transport assay evidence in which the uptake mechanism of a transporter is investigated in a cell that does not normally express that protein. ECO:RCT doi:10.1146/annurev.pp.46.060195.002223 A type of direct assay evidence where electrical properties of cells or tissues are studied. eco ECO:0000164 The scale of electrophysiology assays can range from small, e.g. a single ion channel, to large, e.g. an entire organ such as a heart. electrophysiology assay evidence A type of direct assay evidence where electrical properties of cells or tissues are studied. ECO:KAV A type of voltage clamp recording evidence which involves using two electrodes inserted into a large cell (often a xenopus oocyte) where one electrode is used to measure the internal potential (voltage) of the cell and the other electrode is used to clamp the current. eco IDA: two-electrode voltage clamp technique ECO:0000166 two-electrode voltage clamp recording evidence A type of voltage clamp recording evidence which involves using two electrodes inserted into a large cell (often a xenopus oocyte) where one electrode is used to measure the internal potential (voltage) of the cell and the other electrode is used to clamp the current. ECO:SN PMID:23529422 A type of direct assay evidence resulting from the detection and quantification of transcribed RNA. eco ECO:0000168 transcription assay evidence A type of direct assay evidence resulting from the detection and quantification of transcribed RNA. MeSH:D014158 url:https://bmcmolbiol.biomedcentral.com/articles/10.1186/1471-2199-15-7 A type of transcription assay evidence in which sequence-specific binding proteins that increase transcription of a specific target gene or genes are identified, quantified, and/or analyzed. eco IDA: transcriptional activation assay ECO:0000170 transcriptional activation assay A type of transcription assay evidence in which sequence-specific binding proteins that increase transcription of a specific target gene or genes are identified, quantified, and/or analyzed. url:http://smcg.ccg.unam.mx/enp-unam/05-TranscripYRegulacion/transcription.pdf A type of experimental phenotypic evidence in which the biochemical aspect of a mutation is analyzed. eco IMP: analysis of biochemical trait ECO:0000172 For example, the accumulation of a biosynthetic intermediate. biochemical trait analysis evidence A type of experimental phenotypic evidence in which the biochemical aspect of a mutation is analyzed. ECO:RCT A type of mutant phenotype evidence in which the physiological response of a mutant when presented with an external stimulus is determined. eco IMP: analysis of physiological response ECO:0000174 Examples include: abnormal growth of the root in response to gravity, delay in flowering in response to varying light conditions. mutant physiological response evidence A type of mutant phenotype evidence in which the physiological response of a mutant when presented with an external stimulus is determined. ECO:RCT A type of mutant phenotype evidence in which traits arising from a mutation are visually examined. eco IMP: analysis of visible trait ECO:0000176 mutant visible phenotype evidence A type of mutant phenotype evidence in which traits arising from a mutation are visually examined. ECO:RCT A type of evidence in which the location of the gene within the genome provides insight into its function, or provides evolutionary insight. eco ECO:0000177 This type of evidence might include identity of neighboring genes, operon structure, synteny, phylogenetic analysis, or other whole-genome analysis. genomic context evidence A type of evidence in which the location of the gene within the genome provides insight into its function, or provides evolutionary insight. PMID:21609955 A type of biological assay evidence resulting from an assay performed on or in an organism. eco ECO:0000178 in vivo assay evidence A type of biological assay evidence resulting from an assay performed on or in an organism. ECO:RCT url:https://www.cancer.gov/publications/dictionaries/cancer-terms?cdrid=46352 A type of experimental evidence arising from the investigation of an animal model system. eco ECO:0000179 animal model system study evidence A type of experimental evidence arising from the investigation of an animal model system. ECO:MCC A type of experimental evidence arising from a controlled investigation that uses human subjects. eco ECO:0000180 clinical study evidence A type of experimental evidence arising from a controlled investigation that uses human subjects. ECO:MCC A type of biological assay evidence resulting from an assay performed outside the living organism, in an artificial setting. ECO:0005013 eco ECO:0000181 in vitro assay evidence A type of biological assay evidence resulting from an assay performed outside the living organism, in an artificial setting. ECO:RCT url:https://www.cancer.gov/publications/dictionaries/cancer-terms?cdrid=45733 A type of biological assay evidence resulting from a sample of microorganisms or living tissue grown in a medium. eco ECO:0000182 in vitro culture assay evidence A type of biological assay evidence resulting from a sample of microorganisms or living tissue grown in a medium. ECO:RCT A type of in vitro assay evidence resulting from studies in which the components are derived from resting, nonstimulated cells, therefore all reactions occur in vitro. in vitro assay eco ECO:0000183 cell-free assay evidence A type of in vitro assay evidence resulting from studies in which the components are derived from resting, nonstimulated cells, therefore all reactions occur in vitro. PMID:18453125 A type of specific protein inhibition evidence where the protein under study is an enzyme. eco ECO:0000184 enzyme inhibition evidence A type of specific protein inhibition evidence where the protein under study is an enzyme. ECO:MCC A type of sequence similarity evidence in which an annotation is made based on a manually-reviewed or published sequence alignment mchibucos 2010-03-18T12:21:31Z ECO:00000057 eco ECO:0000200 Such alignments may be pairwise alignments or multiple alignments. sequence alignment evidence A type of sequence similarity evidence in which an annotation is made based on a manually-reviewed or published sequence alignment url:http://www.geneontology.org/GO.evidence.shtml A type of sequence similarity evidence in which orthology is established by multiple criteria, including amino acid and/or nucleotide sequence comparisons and one or more of the following: phylogenetic analysis, coincident expression, conserved map location, functional complementation, immunological cross-reaction, similarity in subcellular localization, subunit structure, substrate specificity, and response to specific inhibitors. mchibucos 2010-03-18T12:30:06Z ECO:00000060 eco ortholog evidence ECO:0000201 Orthology is a relationship between genes in different species indicating that the genes derive from a common ancestor. sequence orthology evidence A type of sequence similarity evidence in which orthology is established by multiple criteria, including amino acid and/or nucleotide sequence comparisons and one or more of the following: phylogenetic analysis, coincident expression, conserved map location, functional complementation, immunological cross-reaction, similarity in subcellular localization, subunit structure, substrate specificity, and response to specific inhibitors. url:http://www.geneontology.org/GO.evidence.shtml A type of sequence similarity evidence in which the function of a gene product is predicted based on a sequence-based statistical model. mchibucos 2010-03-18T12:32:30Z ECO:00000063 eco ECO:0000202 Used when evidence from any kind of statistical model of a sequence or group of sequences is used to make a prediction about the function of a protein or RNA. Examples of relevant evidence are: Hidden Markov Models, PROSITE motifs, and tools such as tRNASCAN. match to sequence model evidence A type of sequence similarity evidence in which the function of a gene product is predicted based on a sequence-based statistical model. ECO:MCC url:http://www.geneontology.org/GO.evidence.shtml An assertion method that does not involve human review. mchibucos 2010-03-18T12:36:04Z ECO:00000067 eco ECO:0000203 An automatic assertion is based on computationally generated information that is not reviewed by a person prior to making the assertion. For example, one common type of automatic assertion involves creating an association of evidence with an entity based on commonness of attributes of that entity and another entity for which an assertion already exists. The commonness is determined algorithmically. automatic assertion An assertion method that does not involve human review. ECO:MCC An evidence type that is based on an assertion by the author of a paper, which is read by a curator. mchibucos 2010-06-21T11:17:21Z eco ECO:0000204 author statement An evidence type that is based on an assertion by the author of a paper, which is read by a curator. ECO:MCC A type of inferential evidence that is based on a conclusion drawn by a curator. mchibucos 2010-08-18T05:55:12Z eco ECO:0000205 curator inference A type of inferential evidence that is based on a conclusion drawn by a curator. ECO:MCC A type of pairwise sequence alignment evidence obtained with basic local alignment search tool (BLAST). mchibucos 2010-08-06T04:48:24Z eco ECO:0000206 BLAST evidence A type of pairwise sequence alignment evidence obtained with basic local alignment search tool (BLAST). ECO:MCC A type of BLAST evidence in which nucleotide sequences are aligned. mchibucos 2010-08-06T04:49:58Z eco ECO:0000207 nucleotide BLAST evidence A type of BLAST evidence in which nucleotide sequences are aligned. ECO:MCC A type of BLAST evidence in which amino acid or translated nucleotide sequences are aligned. mchibucos 2010-08-06T04:50:45Z eco ECO:0000208 protein BLAST evidence A type of BLAST evidence in which amino acid or translated nucleotide sequences are aligned. ECO:MCC A type of BLAST evidence that is used in an automatic assertion. mchibucos 2010-08-06T04:55:21Z eco ECO:0000209 BLAST evidence used in automatic assertion true true A type of BLAST evidence that is used in an automatic assertion. ECO:MCC A type of nucleotide BLAST evidence that is used in an automatic assertion. mchibucos 2010-08-06T05:09:51Z eco ECO:0000210 nucleotide BLAST evidence used in automatic assertion true true A type of nucleotide BLAST evidence that is used in an automatic assertion. ECO:RCT A type of protein BLAST evidence that is used in an automatic assertion. mchibucos 2010-08-06T05:11:04Z eco ECO:0000211 protein BLAST evidence used in automatic assertion true true A type of protein BLAST evidence that is used in an automatic assertion. ECO:RCT A type of evidence that arises out of the integration of more than one line of evidence. mchibucos 2010-08-06T05:24:57Z ECO:0000036 ECO:0000043 eco inferred from in-silico analysis ECO:0000212 A key aspect of this type of evidence is that two or more pieces of information are combined to generate an emergent type of evidence not possible with the constituent pieces of evidence alone. A combinatorial analysis typically involves incorporation of different types of evidence. combinatorial evidence A type of evidence that arises out of the integration of more than one line of evidence. ECO:MCC A type of combinatorial analysis that is used in an automatic assertion. mchibucos 2010-08-06T05:28:33Z eco ECO:0000213 Combinatorial analyses could include experimental or computational results. Examples include: (i) large-scale experiment such as a genome-wide two-hybrid or genome-wide synthetic interactions; (ii) integration of large-scale data sets of various types; and (iii) text-based-computation, e.g. text-mining. For simple sequence comparisons, one should use the sequence similarity analysis evidence type. For microarray results alone, expression pattern analysis is appropriate; whereas, large-scale computational analysis should be used when microarray results are combined with the results of other types of large-scale experiments. combinatorial evidence used in automatic assertion true true A type of combinatorial analysis that is used in an automatic assertion. ECO:MCC A type of phylogenetic evidence whereby an aspect of an ancestral gene is inferred through the characterization of an aspect of a descendant gene. mchibucos 2010-10-05T11:16:50Z eco ECO:0000214 This type of evidence can be used in support of both positive and "not" GO annotations. It should be used to annotate ancestral genes but not extant ones. biological aspect of descendant evidence A type of phylogenetic evidence whereby an aspect of an ancestral gene is inferred through the characterization of an aspect of a descendant gene. ECO:MCC A type of phylogenetic evidence characterized by long phylogenetic tree branch lengths following a duplication event. mchibucos 2010-10-05T03:41:34Z eco ECO:0000215 Long branch lengths indicate that descendant sequences may have acquired different or additional functions than the ancestral sequence. rapid divergence from ancestral sequence evidence A type of phylogenetic evidence characterized by long phylogenetic tree branch lengths following a duplication event. ECO:MCC A type of phylogenetic evidence characterized by the absence of key sequence residues. mchibucos 2010-10-05T03:43:17Z eco ECO:0000216 The loss of certain residues important for function can indicate that a sequence lacks a particular function. phylogenetic determination of loss of key residues evidence A type of phylogenetic evidence characterized by the absence of key sequence residues. ECO:MCC A means by which a statement is made about an entity. mchibucos 2010-11-12T04:17:37Z eco ECO:0000217 assertion method A means by which a statement is made about an entity. ECO:MCC An assertion method that involves human review. mchibucos 2010-11-12T04:20:02Z eco ECO:0000218 A manual assertion could be based on evidence that is generated by and interpreted by a human or it could involve human review of computationally generated information. manual assertion An assertion method that involves human review. ECO:MCC A type of sequencing assay that determines the sequence of a biopolymer comprised of nucleotides. mchibucos 2010-11-15T12:22:40Z eco DNA sequencing ECO:0000219 nucleotide sequencing assay evidence A type of sequencing assay that determines the sequence of a biopolymer comprised of nucleotides. ECO:MCC DNA sequencing OBI:0000626 A type of experimental evidence where the order of molecules that constitute a biopolymer is determined. mchibucos 2010-11-15T01:44:45Z eco ECO:0000220 sequencing assay evidence A type of experimental evidence where the order of molecules that constitute a biopolymer is determined. ECO:MCC OBI:0600047 A type of nucleotide sequencing assay evidence in which a sequence is derived from a parallelized sequencing technique. mchibucos 2010-11-15T02:19:34Z eco next generation sequencing evidence ECO:0000221 Typically thousands to millions of reads are produced in parallel. high throughput nucleotide sequencing assay evidence A type of nucleotide sequencing assay evidence in which a sequence is derived from a parallelized sequencing technique. ECO:MCC A type of high throughput nucleotide sequencing evidence in which sequence is determined through hybridization of adaptor-ligated DNA to a glass slide on which each fragment is simultaneously clonally amplified, followed by progressive rounds of base incorporation with fluorescently-tagged nucleotides, washing, imaging, and cleavage. mchibucos 2010-11-15T02:38:03Z eco Solexa sequencing result ECO:0000222 In Illumina sequencing technology, adapters are ligated onto the ends of randomly fragmented DNA. After single-stranded fragments are bound to the inside surface of a flow cell channel, they undergo in-place bridge PCR amplification. To begin the sequencing cycle, labeled reversible terminators, primers and DNA polymerase are added, followed by laser excitation of the fluorescent label and high resolution scanning. After non-incorporated nucleotides are washed away and the dye is chemically removed, the next cycle repeats with four labeled reversible terminators, primers and DNA polymerase, again followed by imaging. Illumina sequencing evidence A type of high throughput nucleotide sequencing evidence in which sequence is determined through hybridization of adaptor-ligated DNA to a glass slide on which each fragment is simultaneously clonally amplified, followed by progressive rounds of base incorporation with fluorescently-tagged nucleotides, washing, imaging, and cleavage. OBI:0000724 PMID:26000844 Solexa sequencing result OBI:0000724 A type of high throughput nucleotide sequencing evidence in which the sequence for a ssDNA is determined by addition of primers and then nucleotides, one base pair at a time (which generate a specific fluorescence), to the target strand. mchibucos 2010-11-15T03:50:14Z pyrosequencing eco ECO:0000223 454 pyrosequencing technology amplifies individual DNA fragments inside water droplets within an oil solution (emulsion PCR). Within each droplet, a single DNA template is attached to a single primer-coated bead. Each bead is subsequently captured in a picolitre well within the sequencing machine. A luciferase-based readout system is used to identify individual nucleotides added to the nascent DNA. The target strand is usually prepared by fragmentation, adaptor ligation, and amplification by emulsion PCR. 454 pyrosequencing evidence A type of high throughput nucleotide sequencing evidence in which the sequence for a ssDNA is determined by addition of primers and then nucleotides, one base pair at a time (which generate a specific fluorescence), to the target strand. EFO:0005016 pyrosequencing OBI:0000730 A type of high throughput nucleotide sequencing evidence in which sequence is determined through rounds of ligation-based sequencing with fluorescently-labeled Di-base probes and cleavage, after which the template is reset, with a primer offset by one base, for subsequent rounds of ligation. mchibucos 2010-11-15T04:17:41Z eco ECO:0000224 SOLiD sequencing technology is based on sequencing by ligation. After library preparation, emulsion PCR and bead enrichment are performed, including 3' modification of templates on selected beads to allow covalent bonding to a slide. 3' modified beads are attached to a glass slide and primers are added. Four fluorescently labeled di-base probes are added and multiple cycles of ligation, detection and cleavage are performed. The number of cycles determines read length. After a number of ligation cycles, the extension product is removed and another round of ligation cycles is performed with a new primer complimentary to the n-1 position of the template. Five rounds of primer reset are performed for each sequence tag. Samples are prepared by fragmentation of a sample library, adaptor ligation, emulsion PCR, and attachment of resultant beads to glass slides. SOLiD sequencing evidence A type of high throughput nucleotide sequencing evidence in which sequence is determined through rounds of ligation-based sequencing with fluorescently-labeled Di-base probes and cleavage, after which the template is reset, with a primer offset by one base, for subsequent rounds of ligation. OBI:0000706 A type of nucleotide sequencing assay in which DNA sequence is determined by addition of a primed DNA template to a reaction mixture, followed by addition of DNA polymerase, deoxynucleosidetriphosphates (dNTPs - one of which may be radiolabeled), and one of four di-deoxynucleotidetriphosphates (ddNTPs), after which DNA elongation is terminated and the DNA is separated by size and imaged. mchibucos 2010-11-15T04:46:31Z Sanger sequencing dye terminator sequencing eco ECO:0000225 Chain termination sequencing, also called Sanger sequencing after its developer, uses dideoxynucleotide triphosphates (ddNTPs) as DNA chain terminators. Single-stranded DNA template, DNA primer, DNA polymerase, fluorescently or radioactively labeled nucleotides, and one of four ddNTPs are added together in each of four separate sequencing reactions. The synthesized and labeled DNA fragments from each of the four reactions are denatured, separated by size by gel electrophoresis, and visualized by autoradiography or UV light. The ddNTPs lack an OH group so the next dNTP cannot be attached, causing chain termination. chain termination sequencing evidence A type of nucleotide sequencing assay in which DNA sequence is determined by addition of a primed DNA template to a reaction mixture, followed by addition of DNA polymerase, deoxynucleosidetriphosphates (dNTPs - one of which may be radiolabeled), and one of four di-deoxynucleotidetriphosphates (ddNTPs), after which DNA elongation is terminated and the DNA is separated by size and imaged. OBI:0000695 A type of immunoprecipitation evidence that is used to identify a protein binding site on a genomic DNA sequence. mchibucos 2010-11-16T01:29:08Z MI:0402 ChIP evidence eco ECO:0000226 Chromatin immunoprecipitation (ChIP) is used to investigate protein-DNA interactions in vivo. DNA and proteins are chemically cross-linked in vivo to form chromatin complexes, followed by cell lysis and DNA shearing. Fragmented DNA-protein complexes are selectively enriched for a protein of interest using a specific antibody (immunoprecipitation). Protein digestion and DNA purification are performed prior to DNA detection via molecular cloning and sequencing, polymerase chain reaction (PCR), microarray analysis (ChIP-on-chip), or direct high-throughput sequencing (ChIP-seq). chromatin immunoprecipitation evidence A type of immunoprecipitation evidence that is used to identify a protein binding site on a genomic DNA sequence. ECO:MCC MI:0402 chromatin immunoprecipitation assay A type of chromatin immunoprecipitation evidence that uses polymerase chain reaction (PCR) where specific primers are used on the pulled-down DNA for DNA detection. CollecTF mchibucos 2010-11-16T05:02:00Z ChIP-PCR evidence eco ECO:0000227 ChIP-PCR is often used to validate ChIP-chip results and less frequently,ChIP-Seq results. chromatin immunoprecipitation-PCR evidence A type of chromatin immunoprecipitation evidence that uses polymerase chain reaction (PCR) where specific primers are used on the pulled-down DNA for DNA detection. ECO:MCC ECO:SW PMID:18388953 A type of chromatin immunoprecipitation evidence in which protein-DNA interactions are investigated at known genomic binding sites through a process of ChIP, DNA purification, and finally quantitative polymerase chain reaction (qPCR) for DNA detection. mchibucos 2010-11-16T05:26:47Z ChIP-qPCR evidence eco ECO:0000228 chromatin immunoprecipitation-qPCR evidence A type of chromatin immunoprecipitation evidence in which protein-DNA interactions are investigated at known genomic binding sites through a process of ChIP, DNA purification, and finally quantitative polymerase chain reaction (qPCR) for DNA detection. url:https://www.diagenode.com/applications/chip-qpcr A type of chromatin immunoprecipitation evidence that uses high-throughput sequencing where immunoprecipitated DNA fragments are funnelled into a massively parallel sequencer to produce multiple short reads for locating binding sites of DNA-associated proteins. CollecTF mchibucos 2010-11-16T05:30:41Z ChIP-SEQ evidence ChIP-seq evidence eco ECO:0000229 ChIP-Seq experiments often use the input as a control to eliminate biases. To obtain similar results, ChIP-chip with high-density tiling arrays can be used. chromatin immunoprecipitation-seq evidence A type of chromatin immunoprecipitation evidence that uses high-throughput sequencing where immunoprecipitated DNA fragments are funnelled into a massively parallel sequencer to produce multiple short reads for locating binding sites of DNA-associated proteins. ECO:MCC ECO:SW OBI:0000716 PMID:22955991 ChIP-SEQ evidence OBI:0000716 ChIP-seq evidence PMID:22955991 A type of chromatin immunoprecipitation evidence that uses a tiling microarray for the detection of protein-bound DNA regions where chromatin is immunoprecipitated for protein tagging and DNA is sheared from the cross-linked protein-DNA complex to be arrayed revealing the protein-bound genomic regions. CollecTF mchibucos 2010-11-16T05:43:55Z MI:0225 ChIP-chip evidence ChIP-on-chip evidence eco ECO:0000230 A fixating agent such as formaldehyde is used to cross link proteins and DNA. Sonication is applied for DNA shearing. For transcription factor tagging, an antibody or epitope is employed. After cross-linking is reversed, the DNA is amplified and labeled with a flourophore for microarray which produces a resolution of aproximately 500 bp. chromatin immunoprecipitation-chip evidence A type of chromatin immunoprecipitation evidence that uses a tiling microarray for the detection of protein-bound DNA regions where chromatin is immunoprecipitated for protein tagging and DNA is sheared from the cross-linked protein-DNA complex to be arrayed revealing the protein-bound genomic regions. ECO:MCC ECO:SW PMID:18388953 PMID:19381927 MI:0225 chromatin immunoprecipitation array A type of polymerase chain reaction evidence where the reaction product is quantified in real-time across cycles by means of fluorescent dyes for detection and quantification of specific sequences in a DNA sample. CollecTF mchibucos 2010-11-16T05:57:20Z Q-PCR evidence quantitative PCR evidence real-time PCR evidence real-time polymerase chain reaction evidence eco qRT-PCR evidence ECO:0000231 Quantitative PCR enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample. The dye is activated upon binding double-stranded DNA. Although qRT-PCR is commonly found in literature synonymous to qPCR, it is preferable not to use this synonym as it is the accepted abbreviation for reverse transcription PCR. qPCR should be used instead (ISBN 978-0-470-68386-6 page 173). quantitative polymerase chain reaction evidence A type of polymerase chain reaction evidence where the reaction product is quantified in real-time across cycles by means of fluorescent dyes for detection and quantification of specific sequences in a DNA sample. ECO:MCC ECO:SW A type of experimental evidence that is based on a five-step technique of cross-linking DNA in vivo, restriction digestion, intramolecular ligation, reversing DNA cross-links, and DNA processing and quantitation. mchibucos 2010-11-17T12:27:14Z 3C chromosome conformation capture eco ECO:0000232 Chromosome conformation capture technologies are used to study the structural properties and spatial organization of chromosomes inside cells. All types of chromosome conformation capture technology involve five primary steps: cross-linking of DNA in vivo, restriction digestion, intramolecular ligation, reversing cross-linkages, and DNA enrichment and quantitation. The last step is different for each type of chromosome conformation capture technology, and may include PCR (3C), inverse PCR (4C), or ligation-mediated amplification (5C). Methods for product quantitation can include agarose gel detection or real-time quantitative PCR in the case of 3C, or high-throughput sequencing or microarray analysis for 4C and 5C. chromosome conformation capture-based evidence A type of experimental evidence that is based on a five-step technique of cross-linking DNA in vivo, restriction digestion, intramolecular ligation, reversing DNA cross-links, and DNA processing and quantitation. ECO:MCC A type of chromosome conformation capture-based evidence that is derived by performing a type of polymerase chain reaction (PCR) in the final product quantitation step. mchibucos 2010-11-17T12:46:15Z 3C eco ECO:0000233 3C is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 3C differs only in the fifth step, which involves performing either standard polymerase chain reaction (PCR) or quantitative PCR (qPCR) for product quantitation. chromosome conformation capture evidence A type of chromosome conformation capture-based evidence that is derived by performing a type of polymerase chain reaction (PCR) in the final product quantitation step. ECO:MCC A type of chromosome conformation capture-based evidence that is derived by inverse polymerase chain reaction (inverse PCR) on a prior circularized 3C library followed by product quantitation with a microarray. mchibucos 2010-11-19T01:20:28Z 4C chromosome conformation capture on chip circularized 3C eco ECO:0000234 4C is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 4C differs only in the fifth step, which involves inverse polymerase chain reaction (inverse PCR) on a circularized 3C library prior to product quantitation. circularized chromosome conformation capture evidence A type of chromosome conformation capture-based evidence that is derived by inverse polymerase chain reaction (inverse PCR) on a prior circularized 3C library followed by product quantitation with a microarray. ECO:MCC A type of chromosome conformation capture-based evidence that is derived by performing ligation-mediated amplification (LMA) prior to product quantitation. mchibucos 2010-11-19T01:22:20Z 5C carbon-copy 3C eco ECO:0000235 5C is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 5C differs only in the fifth step, which involves ligation-mediated amplification (LMA) followed by product quantitation. carbon-copy chromosome conformation capture evidence A type of chromosome conformation capture-based evidence that is derived by performing ligation-mediated amplification (LMA) prior to product quantitation. ECO:MCC A type of chromosome conformation capture evidence that is derived by performing polymerase chain reaction (PCR) in the quantitation step. mchibucos 2010-11-19T03:00:47Z 3C 3C-PCR eco ECO:0000236 chromosome conformation capture-PCR evidence A type of chromosome conformation capture evidence that is derived by performing polymerase chain reaction (PCR) in the quantitation step. ECO:MCC A type of chromosome conformation capture evidence that is derived by performing quantitative polymerase chain reaction (qPCR) in the quantitation step. mchibucos 2010-11-19T03:06:47Z 3C-qPCR 3C-quantitative PCR 3C-real-time PCR eco ECO:0000237 chromosome conformation capture-qPCR evidence A type of chromosome conformation capture evidence that is derived by performing quantitative polymerase chain reaction (qPCR) in the quantitation step. ECO:MCC A type of chromosome conformation capture-based evidence that is derived by performing immunoprecipitation enrichment of ligated fragments events prior to product quantitation. mchibucos 2010-11-19T04:24:03Z eco ECO:0000238 Hi-C is used to study the structural properties and spatial organization of chromosomes inside cells. Hi-C is similar to other types of chromosome conformation capture technology, but involves the addition of biotinylated nucleotides during the second or fourth step and enrichment for ligated fragments using immunoprecipitation after the fourth step. Hi-C evidence A type of chromosome conformation capture-based evidence that is derived by performing immunoprecipitation enrichment of ligated fragments events prior to product quantitation. ECO:MCC A type of chromosome conformation capture-based evidence that is derived by inverse polymerase chain reaction (inverse PCR) on a circularized 3C library prior to product quantitation with high-throughput (HT) sequencing. mchibucos 2010-11-30T03:22:25Z 3C sequencing 3C-seq 4C sequencing 4C-seq circularized 3C sequencing circularized 3C-seq eco ECO:0000239 3C-seq is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 3C-seq differs only in the fifth step, which involves inverse polymerase chain reaction (PCR) on a circularized 3C library prior to product quantitation. chromosome conformation capture sequencing evidence A type of chromosome conformation capture-based evidence that is derived by inverse polymerase chain reaction (inverse PCR) on a circularized 3C library prior to product quantitation with high-throughput (HT) sequencing. ECO:MCC A type of experimental phenotypic evidence in which the phenotype of an organism is observed after the disruption of a structural feature. mchibucos 2010-12-06T12:24:16Z eco ECO:0000240 anatomical perturbation evidence A type of experimental phenotypic evidence in which the phenotype of an organism is observed after the disruption of a structural feature. ECO:MCC A type of experimental phenotypic evidence in which the phenotype of an organism is observed after modification of the extra-organismal context. mchibucos 2010-12-06T12:33:58Z eco mechanical constraint evidence ECO:0000241 Many environmental factors are subject to modification, such as temperature, pressure, humidity, radiation, and so forth. environmental perturbation evidence A type of experimental phenotypic evidence in which the phenotype of an organism is observed after modification of the extra-organismal context. ECO:MCC A type of anatomical perturbation that is based on disruption of tissue. mchibucos 2010-12-06T12:33:58Z ablated tissue evidence eco ECO:0000242 A tissue ablation experiment involves observing the phenotype of an entity whose tissues have been disrupted through genetic or biochemical manipulation, physical destruction, or some other means. tissue ablation evidence A type of anatomical perturbation that is based on disruption of tissue. ECO:MCC A type of anatomical perturbation that is based on adding tissue to an organism through a graft procedure. mchibucos 2010-12-06T12:33:58Z eco ECO:0000243 tissue grafting evidence A type of anatomical perturbation that is based on adding tissue to an organism through a graft procedure. ECO:MCC A type of combinatorial analysis that is used in a manual assertion. mchibucos 2010-12-09T02:02:12Z eco ECO:0000244 Combinatorial analyses could include experimental or computational results. Examples include: (i) large-scale experiment such as a genome-wide two-hybrid or genome-wide synthetic interactions; (ii) integration of large-scale data sets of various types; and (iii) text-based-computation, e.g. text-mining. For simple sequence comparisons, one should use the sequence similarity analysis evidence type. For microarray results alone, expression pattern analysis is appropriate; whereas, large-scale computational analysis should be used when microarray results are combined with the results of other types of large-scale experiments. combinatorial evidence used in manual assertion true true A type of combinatorial analysis that is used in a manual assertion. ECO:MCC A type of computational combinatorial analysis that is used in a manual assertion. mchibucos 2010-12-09T02:37:54Z GOECO:RCA RCA inferred from reviewed computational analysis eco ECO:0000245 computational combinatorial evidence used in manual assertion http://geneontology.org/page/rca-inferred-reviewed-computational-analysis true true A type of computational combinatorial analysis that is used in a manual assertion. ECO:MCC GOECO:RCA inferred from reviewed computational analysis RCA GOECO:RCA inferred from reviewed computational analysis GOECO:RCA A type of computational combinatorial analysis that is used in an automatic assertion. mchibucos 2010-12-09T02:37:54Z eco ECO:0000246 computational combinatorial evidence used in automatic assertion true true A type of computational combinatorial analysis that is used in an automatic assertion. ECO:MCC A type of sequence alignment evidence that is used in a manual assertion. mchibucos 2010-12-09T05:12:27Z GOECO:ISA ISA inferred from sequence alignment eco ECO:0000247 sequence alignment evidence used in manual assertion http://geneontology.org/page/isa-inferred-sequence-alignment true true A type of sequence alignment evidence that is used in a manual assertion. ECO:RCT GOECO:ISA inferred from sequence alignment ISA GOECO:ISA inferred from sequence alignment GOECO:ISA A type of sequence alignment evidence that is used in an automatic assertion. mchibucos 2010-12-09T05:12:27Z eco ECO:0000248 sequence alignment evidence used in automatic assertion true true A type of sequence alignment evidence that is used in an automatic assertion. ECO:RCT A type of sequence similarity evidence that is used in an automatic assertion. mchibucos 2010-12-09T05:22:30Z eco ECO:0000249 sequence similarity evidence used in automatic assertion true true A type of sequence similarity evidence that is used in an automatic assertion. ECO:RCT A type of sequence similarity evidence that is used in a manual assertion. mchibucos 2010-12-09T05:22:30Z GOECO:ISS ISS inferred from sequence or structural similarity eco ECO:0000250 sequence similarity evidence used in manual assertion http://geneontology.org/page/iss-inferred-sequence-or-structural-similarity true true A type of sequence similarity evidence that is used in a manual assertion. ECO:MCC GOECO:ISS inferred from sequence or structural similarity ISS GOECO:ISS inferred from sequence or structural similarity GOECO:ISS A type of similarity evidence that is used in an automatic assertion. mchibucos 2010-12-09T05:28:12Z eco ECO:0000251 similarity evidence used in automatic assertion true true A type of similarity evidence that is used in an automatic assertion. ECO:RCT A type of similarity evidence that is used in a manual assertion. mchibucos 2010-12-09T05:28:12Z eco ECO:0000252 similarity evidence used in manual assertion true true A type of similarity evidence that is used in a manual assertion. ECO:RCT A type of genetic similarity evidence that is used in a manual assertion. mchibucos 2010-12-10T01:42:44Z eco ECO:0000253 genetic similarity evidence used in manual assertion true true A type of genetic similarity evidence that is used in a manual assertion. ECO:RCT A type of genetic similarity evidence that is used in an automatic assertion. mchibucos 2010-12-10T01:42:44Z eco ECO:0000254 genetic similarity evidence used in automatic assertion true true A type of genetic similarity evidence that is used in an automatic assertion. ECO:RCT A type of match to sequence model evidence that is used in a manual assertion. mchibucos 2010-12-10T02:26:35Z GOECO:ISM GO_REF:0000011 ISM inferred from sequence model eco ECO:0000255 match to sequence model evidence used in manual assertion http://geneontology.org/page/ism-inferred-sequence-model true true A type of match to sequence model evidence that is used in a manual assertion. ECO:RCT GOECO:ISM inferred from sequence model GO_REF:0000011 Hidden Markov Models (TIGR) ISM GOECO:ISM inferred from sequence model GOECO:ISM A type of match to sequence model evidence that is used in an automatic assertion. mchibucos 2010-12-10T02:26:35Z GO_REF:0000002 GO_REF:0000107 eco ECO:0000256 match to sequence model evidence used in automatic assertion true true A type of match to sequence model evidence that is used in an automatic assertion. ECO:RCT GO_REF:0000002 Gene Ontology annotation through association of InterPro records with GO terms. GO_REF:0000107 Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl A type of motif similarity evidence that is used in a manual assertion. mchibucos 2010-12-10T02:44:34Z eco ECO:0000257 motif similarity evidence used in manual assertion true true A type of motif similarity evidence that is used in a manual assertion. ECO:RCT A type of motif similarity evidence that is used in an automatic assertion. mchibucos 2010-12-10T02:44:34Z eco ECO:0000258 motif similarity evidence used in automatic assertion true true A type of motif similarity evidence that is used in an automatic assertion. ECO:RCT A type of match to InterPro member signature evidence that is used in an automatic assertion. mchibucos 2010-12-10T02:54:51Z eco ECO:0000259 match to InterPro member signature evidence used in automatic assertion true true A type of match to InterPro member signature evidence that is used in an automatic assertion. ECO:RCT A type of match to InterPro member signature evidence that is used in a manual assertion. mchibucos 2010-12-10T02:54:51Z eco ECO:0000260 match to InterPro member signature evidence used in manual assertion true true A type of match to InterPro member signature evidence that is used in a manual assertion. ECO:RCT A type of targeting sequence prediction that is used in an automatic assertion. mchibucos 2010-12-10T03:02:49Z eco ECO:0000261 targeting sequence prediction evidence used in automatic assertion true true A type of targeting sequence prediction that is used in an automatic assertion. ECO:RCT A type of targeting sequence prediction that is used in a manual assertion. mchibucos 2010-12-10T03:02:49Z eco ECO:0000262 targeting sequence prediction evidence used in manual assertion true true A type of targeting sequence prediction that is used in a manual assertion. ECO:RCT A type of transmembrane domain prediction that is used in an automatic assertion. mchibucos 2010-12-10T03:28:35Z eco ECO:0000263 transmembrane domain prediction evidence used in automatic assertion true true A type of transmembrane domain prediction that is used in an automatic assertion. ECO:RCT A type of transmembrane domain prediction that is used in a manual assertion. mchibucos 2010-12-10T03:28:35Z eco ECO:0000264 transmembrane domain prediction evidence used in manual assertion true true A type of transmembrane domain prediction that is used in a manual assertion. ECO:RCT A type of sequence orthology evidence that is used in an automatic assertion. mchibucos 2010-12-10T03:39:41Z GO_REF:0000019 GO_REF:0000020 GO_REF:0000035 GO_REF:0000049 eco Ortholog evidence ECO:0000265 sequence orthology evidence used in automatic assertion true true A type of sequence orthology evidence that is used in an automatic assertion. ECO:RCT GO_REF:0000019 Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara GO_REF:0000020 Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins. GO_REF:0000035 Automatic transfer of experimentally verified manual GO annotation data to plant orthologs using Ensembl Compara GO_REF:0000049 Automatic transfer of experimentally verified manual GO annotation data to fungal orthologs using Ensembl Compara A type of sequence orthology evidence that is used in a manual assertion. mchibucos 2010-12-10T03:39:41Z GOECO:ISO ISO inferred from sequence orthology eco Ortholog evidence ECO:0000266 sequence orthology evidence used in manual assertion http://geneontology.org/page/iso-inferred-sequence-orthology true true A type of sequence orthology evidence that is used in a manual assertion. ECO:MCC GOECO:ISO inferred from sequence orthology ISO GOECO:ISO inferred from sequence orthology GOECO:ISO A type of protein detection assay evidence where an antigen is bound to a substrate, and an antibody directly or indirectly linked to an enzyme is utilized to determine the amount of bound antigen which is visualized with a color change in the substrate. CollecTF mchibucos 2010-12-14T01:57:13Z MI:0411 ELISA evidence enzyme-linked immunosorbent assay eco ECO:0000267 ELISA is sometimes used in the study of transcriptional regulation to identify a produced protein, especially secreted protein. enzyme-linked immunoabsorbent assay evidence A type of protein detection assay evidence where an antigen is bound to a substrate, and an antibody directly or indirectly linked to an enzyme is utilized to determine the amount of bound antigen which is visualized with a color change in the substrate. ECO:MCC ECO:SW PMID:23949770 MI:0411 enzyme linked immunosorbent assay A type of direct assay evidence in which cells or particles are characterized by passing them through a light source and monitoring the resultant light scatter or fluorochrome excitation. mchibucos 2010-12-14T02:07:08Z FCM eco ECO:0000268 flow cytometry evidence A type of direct assay evidence in which cells or particles are characterized by passing them through a light source and monitoring the resultant light scatter or fluorochrome excitation. ECO:MCC A type of experimental evidence that is used in a manual assertion. mchibucos 2010-12-20T05:36:49Z GOECO:EXP EXP inferred from experiment eco ECO:0000269 experimental evidence used in manual assertion http://geneontology.org/page/exp-inferred-experiment true true A type of experimental evidence that is used in a manual assertion. ECO:MCC GOECO:EXP inferred from experiment EXP GOECO:EXP inferred from experiment GOECO:EXP A type of expression pattern evidence that is used in a manual assertion. mchibucos 2010-12-20T05:46:39Z GOECO:IEP IEP inferred from expression pattern eco ECO:0000270 expression evidence used in manual assertion http://geneontology.org/page/iep-inferred-expression-pattern true true A type of expression pattern evidence that is used in a manual assertion. ECO:MCC GOECO:IEP inferred from expression pattern IEP GOECO:IEP inferred from expression pattern GOECO:IEP A type of array experiment evidence that is used in a manual assertion. mchibucos 2010-12-20T05:51:58Z eco ECO:0000271 array experiment evidence used in manual assertion true A type of array experiment evidence that is used in a manual assertion. ECO:MCC A type of Affymetrix GeneChip evidence that is used in a manual assertion. mchibucos 2010-12-20T05:53:36Z eco ECO:0000272 Affymetrix GeneChip evidence used in manual assertion true true A type of Affymetrix GeneChip evidence that is used in a manual assertion. ECO:MCC A type of cDNA to DNA expression microarray evidence that is used in a manual assertion. mchibucos 2010-12-20T05:55:49Z ECO:0001178 ECO:0005525 eco ECO:0000273 cDNA to DNA expression microarray evidence used in manual assertion true true A type of cDNA to DNA expression microarray evidence that is used in a manual assertion. ECO:MCC A type of differential methylation hybridization evidence that is used in a manual assertion. mchibucos 2010-12-20T05:58:44Z CpG island microarray evidence used in manual assertion eco ECO:0000274 differential methylation hybridization evidence used in manual assertion true true A type of differential methylation hybridization evidence that is used in a manual assertion. ECO:RCT A type of expression microarray evidence that is used in a manual assertion. mchibucos 2010-12-20T06:01:26Z eco ECO:0000275 expression microarray evidence used in manual assertion true true A type of expression microarray evidence that is used in a manual assertion. ECO:MCC A type of cRNA to DNA expression microarray evidence that is used in a manual assertion. mchibucos 2010-12-20T06:03:28Z genomic microarray evidence used in manual assertion eco ECO:0000276 cRNA to DNA expression microarray evidence used in manual assertion true true A type of cRNA to DNA expression microarray evidence that is used in a manual assertion. ECO:RCT A type of evidence arising from a Nimblegen array experiment that is used in a manual assertion. mchibucos 2010-12-20T06:05:20Z eco ECO:0000277 Nimblegen array evidence used in manual assertion true true A type of evidence arising from a Nimblegen array experiment that is used in a manual assertion. ECO:MCC A type of array-based sequence capture evidence that is used in a manual assertion. mchibucos 2010-12-20T06:09:45Z oligonucleotide microarray evidence used in manual assertion eco ECO:0000278 array-based sequence capture evidence used in manual assertion true true A type of array-based sequence capture evidence that is used in a manual assertion. ECO:MCC A type of Western blot assay that is used in a manual assertion. mchibucos 2010-12-20T06:20:01Z eco ECO:0000279 western blot evidence used in manual assertion true true A type of Western blot assay that is used in a manual assertion. ECO:MCC A type of protein expression level analysis that is used in a manual assertion. mchibucos 2010-12-20T06:21:54Z eco ECO:0000280 protein expression level evidence used in manual assertion true true A type of protein expression level analysis that is used in a manual assertion. ECO:MCC A type of expression library screen evidence that is used in a manual assertion. mchibucos 2010-12-20T06:24:05Z eco ECO:0000281 expression library screen evidence used in manual assertion true true A type of expression library screen evidence that is used in a manual assertion. ECO:MCC A type of heterologous protein expression analysis that is used in a manual assertion. mchibucos 2010-12-20T06:27:04Z eco ECO:0000282 heterologous protein expression evidence used in manual assertion true true A type of heterologous protein expression analysis that is used in a manual assertion. ECO:MCC A type of protein expression spatial pattern analysis that is used in a manual assertion. mchibucos 2010-12-20T06:31:44Z eco ECO:0000283 spatial pattern of protein expression evidence used in manual assertion true true A type of protein expression spatial pattern analysis that is used in a manual assertion. ECO:MCC A type of protein expression analysis that is used in a manual assertion. mchibucos 2010-12-20T06:33:46Z eco ECO:0000284 protein expression evidence used in manual assertion true true true A type of protein expression analysis that is used in a manual assertion. ECO:MCC A type of DNA to cDNA expression microarray evidence that is used in a manual assertion. mchibucos 2010-12-20T06:41:33Z eco ECO:0000285 DNA to cDNA expression microarray evidence used in manual assertion true true A type of DNA to cDNA expression microarray evidence that is used in a manual assertion. ECO:MCC A type of differential hybridization experiment that is used in a manual assertion. mchibucos 2010-12-20T06:55:14Z eco ECO:0000287 differential hybridization evidence used in manual assertion true true A type of differential hybridization experiment that is used in a manual assertion. ECO:MCC A type of RNA protection assay that is used in a manual assertion. mchibucos 2010-12-20T06:57:33Z eco ECO:0000288 RNA protection assay evidence used in manual assertion true true A type of RNA protection assay that is used in a manual assertion. ECO:MCC A type of spatial pattern of transcript expression analysis that is used in a manual assertion. mchibucos 2010-12-20T06:59:18Z eco ECO:0000289 spatial pattern of transcript expression evidence used in manual assertion true true A type of spatial pattern of transcript expression analysis that is used in a manual assertion. ECO:MCC A type of subtractive hybridization experiment that is used in a manual assertion. mchibucos 2010-12-20T07:00:48Z eco ECO:0000290 subtractive hybridization evidence used in manual assertion true true A type of subtractive hybridization experiment that is used in a manual assertion. ECO:MCC A type of transcript expression evidence that is used in a manual assertion. mchibucos 2010-12-20T07:02:08Z ECO:0000286 eco ECO:0000291 transcript expression evidence used in manual assertion true true A type of transcript expression evidence that is used in a manual assertion. ECO:MCC A type of mutant phenotype evidence that uses anti-sense by introducing morpholino oligonucleotides into the cytosol of a cell. mchibucos 2011-01-10T03:36:25Z anti-sense eco ECO:0000292 Morpholino oligonucleotides modify gene expression by blocking access of other molecules to specific, approximately 25-base-long regions of the base-pairing surfaces of ribonucleic acid (RNA). To achieve this anti-sense knockdown technique, delivery of the morpholino can be achieved via microinjection, electroporation, or another method. morpholino experiment evidence A type of mutant phenotype evidence that uses anti-sense by introducing morpholino oligonucleotides into the cytosol of a cell. ECO:MCC A type of evidence arising from a physical interaction analysis where a combinatorial chemistry technique is used to identify oligonucleotides that bind to a target ligand. mchibucos 2011-01-10T04:23:50Z MI:0657 SELEX evidence in vitro selection evidence eco in vitro evolution evidence ECO:0000293 SELEX begins with the synthesis of a large oligonucleotide library, either single-stranded DNA or RNA, which consists of random fixed-length sequences flanked by constant 5' and 3' ends that serve as primers. The library is exposed to a target ligand, typically a protein or small organic compound. Unbound sequences are removed, typically with affinity chromatography. Bound sequences are eluted and the nucleic acid is extracted, followed by PCR amplification (RNA is first reverse transcribed). PCR product is converted to single stranded (DNA) or transcribed (RNA). Oligonucleotides are bound to the ligand again and the process is repeated with increasing elution stringency. After several rounds of the process, recovered oligonucleotides are sequenced and analyzed to reveal the binding specificity of the protein. systematic evolution of ligands by exponential amplification evidence A type of evidence arising from a physical interaction analysis where a combinatorial chemistry technique is used to identify oligonucleotides that bind to a target ligand. ECO:MCC url:http://en.wikipedia.org/wiki/Systematic_Evolution_of_Ligands_by_Exponential_Enrichment MI:0657 systematic evolution of ligands by exponential enrichment A type of hybrid interaction evidence that uses bacterial transformation with two plasmids to assess in vivo binding of a DNA-binding domain (bait) and DNA target site (prey). mchibucos 2011-01-10T06:16:20Z B1H evidence eco ECO:0000294 Bacterial one-hybrid assay is a method for screening a library of candidate proteins (prey plasmid) for the ability to bind to a target, cis-regulatory element or any other short, DNA binding sequence placed 5' to reporter genes (bait plasmid). Transformation of a bacterial host with two different plasmids is required: One is designed to express the "bait". The other plasmid contains a "prey" which, if bound to by the chimeric fusion product, drives expression of downstream reporter genes. bacterial one-hybrid evidence A type of hybrid interaction evidence that uses bacterial transformation with two plasmids to assess in vivo binding of a DNA-binding domain (bait) and DNA target site (prey). ECO:MCC A type of transcript evidence based on high-throughput (HT) sequencing of fragmented cDNA molecules. mchibucos 2011-01-11T12:54:50Z ECO:0000357 WTSS whole transcriptome shotgun sequencing differential gene expression evidence from RNA-seq experiment eco RNA sequencing ECO:0000295 Total RNA is isolated from cells and mRNA is purified by targeting the 3' polyadenylated (poly(A)) tail with poly(T) oligos covalently attached to a substrate. Next, cDNA fragments are generated either by hydrolysis of RNA into 200-300 base oligonucleotides, preceded by reverse transcription, or by reverse transcription initiated by random primers. The cDNA second strand is synthesized, fragments are adapter ligated and high-throughput sequencing is performed by Roche 454, Illumina, ABI-SOLiD, or another HT sequencing technology. Resulting sort reads are aligned against a reference genome, and downstream analysis is performed. RNA-seq evidence A type of transcript evidence based on high-throughput (HT) sequencing of fragmented cDNA molecules. ECO:MCC whole transcriptome shotgun sequencing PMID:18611170 A type of transcriptional activation assay evidence that is based on transcriptional activation of a green fluorescent protein (GFP) reporter gene. mchibucos 2011-01-11T02:31:19Z localization of GFP transcript eco ECO:0000296 This term describes transcriptional activation; to describe immunolocalization of the protein, use the term "immunolocalization of green fluorescent protein". green fluorescent protein transcript localization evidence A type of transcriptional activation assay evidence that is based on transcriptional activation of a green fluorescent protein (GFP) reporter gene. ECO:MCC ECO:RCT A type of transcriptional activation assay evidence that is based on transcriptional activation of a LacZ reporter gene. mchibucos 2011-01-11T02:53:19Z eco ECO:0000297 This term describes transcriptional activation; to describe immunolocalization of the protein, use the term "immunolocalization of LacZ protein". LacZ transcript localization evidence A type of transcriptional activation assay evidence that is based on transcriptional activation of a LacZ reporter gene. ECO:MCC A type of experimental phenotypic evidence where embryonic development proceeds although cytokinesis is blocked. mchibucos 2011-01-11T03:28:49Z eco ECO:0000298 In the embryos of some organisms, inhibition of cytokinesis blocks neither the cell cycle nor the unfolding of the developmental program. As such, embryonic morphology can be frozen, allowing analysis of the developmental fate of each cell present at the time of cleavage arrest. cleavage arrested development evidence A type of experimental phenotypic evidence where embryonic development proceeds although cytokinesis is blocked. ECO:MCC A type of cleavage arrested development that arises after treatment with cytochalasin. mchibucos 2011-01-11T03:30:29Z eco ECO:0000299 Cytochalasin inhibits cytokinesis by blocking the formation of contractile microfilaments. cytochalasin experiment evidence A type of cleavage arrested development that arises after treatment with cytochalasin. ECO:MCC A type of immunolocalization evidence data that was generated using green fluorescent protein (GFP) as a marker. mchibucos 2011-01-11T03:48:50Z GFP immunolocalization evidence eco ECO:0000300 This term describes immunolocalization of the protein; to describe transcriptional activation, use the term "localization of green fluorescent protein transcript". green fluorescent protein immunolocalization evidence A type of immunolocalization evidence data that was generated using green fluorescent protein (GFP) as a marker. ECO:MCC A type of immunolocalization evidence that was generated using LacZ protein as a marker. mchibucos 2011-01-11T04:06:40Z LacZ protein immunolocalization evidence eco ECO:0000301 This term describes immunolocalization of the protein; to describe transcriptional activation, use the term "localization of LacZ transcript". beta-galactosidase protein immunolocalization evidence A type of immunolocalization evidence that was generated using LacZ protein as a marker. ECO:MCC A type of author statement that is used in a manual assertion. mchibucos 2011-01-20T02:26:47Z eco ECO:0000302 author statement used in manual assertion true true A type of author statement that is used in a manual assertion. ECO:MCC A type of non-traceable author statement that is used in a manual assertion. mchibucos 2011-01-20T02:29:50Z GOECO:NAS NAS non-traceable author statement eco ECO:0000303 non-traceable author statement used in manual assertion http://geneontology.org/page/nas-non-traceable-author-statement true true A type of non-traceable author statement that is used in a manual assertion. ECO:MCC GOECO:NAS non-traceable author statement NAS GOECO:NAS non-traceable author statement GOECO:NAS A type of traceable author statement that is used in a manual assertion. mchibucos 2011-01-20T02:31:03Z GOECO:TAS TAS traceable author statement eco ECO:0000304 traceable author statement used in manual assertion http://geneontology.org/page/tas-traceable-author-statement true true A type of traceable author statement that is used in a manual assertion. ECO:MCC GOECO:TAS traceable author statement TAS GOECO:TAS traceable author statement GOECO:TAS A type of curator inference that is used in a manual assertion. mchibucos 2011-01-20T02:33:32Z GOECO:IC IC inferred by curator eco ECO:0000305 curator inference used in manual assertion http://geneontology.org/page/ic-inferred-curator true true A type of curator inference that is used in a manual assertion. ECO:MCC GOECO:IC inferred by curator IC GOECO:IC inferred by curator GOECO:IC A type of inference from background scientific knowledge that is used in a manual assertion. mchibucos 2011-01-20T02:35:11Z eco ECO:0000306 inference from background scientific knowledge used in manual assertion true true A type of inference from background scientific knowledge that is used in a manual assertion. ECO:MCC A type of no biological data found that is used in a manual assertion. mchibucos 2011-01-20T02:43:18Z GOECO:ND ND no biological data available eco ECO:0000307 no biological data found used in manual assertion http://geneontology.org/page/nd-no-biological-data-available true true A type of no biological data found that is used in a manual assertion. ECO:MCC GOECO:ND no biological data available ND GOECO:ND no biological data available GOECO:ND A type of phylogenetic evidence whereby an aspect of a descendant gene is inferred through the characterization of an aspect of an ancestral gene. mchibucos 2011-02-04T05:41:26Z eco ECO:0000308 First, a characteristic of the most recent common ancestor (MRCA) is inferred from experimental evidence in descendants; this is followed by inferring a characteristic of a descendant of the MRCA. This type of evidence can be used in support of both positive and "not" GO annotations. biological aspect of ancestor evidence A type of phylogenetic evidence whereby an aspect of a descendant gene is inferred through the characterization of an aspect of an ancestral gene. ECO:MCC A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by a cap-trapper system. mchibucos 2011-02-17T01:33:09Z CAGE eco ECO:0000309 Complementary DNA (cDNA) is synthesized from microgram quantities of mRNA using first-strand cDNA primer (oligo dT12-18) and reverse transcriptase in the presence of trehalose and sorbitol, followed by selection of full-length cDNA with biotinylated cap-trapper. Linkers are attached to the 5' ends of full-length enriched cDNAs to introduce a recognition site for the restriction endonuclease MmeI, which creates a two base overhang. After amplification, sequencing tags are concatenated for high-throughput sequencing. Resulting sort reads are aligned against a reference genome, and downstream analysis is performed. cap analysis of gene expression evidence A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by a cap-trapper system. ECO:MCC CAGE PMID:16489339 A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by reverse transcriptase template switching. mchibucos 2011-02-17T01:33:34Z eco nanoCAGE ECO:0000310 NanoCAGE captures the 5' ends of molecules by template switching. When polymerizing the cDNA of a capped mRNA, the reverse transcriptase adds extra cytosines that are complementary to the cap. Each 5' full length cDNAs is extended upon hybridization of the riboguanosine-tailed template switching oligonucleotides to these extra cytosines. In semisuppressive PCR, the short templates fold intramolecularly and prevent the binding of primers, which precludes amplification; longer molecules are less likely to fold and are thus amplified. Templates derived from reaction artifacts form stable homoduplexes, also precluding amplification. After template switching, semisuppressive PCR, and EcoP151 cleavage, 25-bp tags are ligated to bar code-containing oligonucleotide adaptors. After PCR amplification, the nanoCAGE tags are sequenced by synthesis. NanoCAGE requires as little as 10 nanograms of total RNA. nano-cap analysis of gene expression evidence A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by reverse transcriptase template switching. ECO:MCC nanoCAGE PMID:20543846 A type of evidence that is based on work performed by a person or group prior to a use by a different person or group. mchibucos 2011-03-02T05:24:13Z eco ECO:0000311 imported information A type of evidence that is based on work performed by a person or group prior to a use by a different person or group. ECO:MCC A type of imported information that is used in a manual assertion. mchibucos 2011-03-02T05:29:44Z eco ECO:0000312 imported information used in manual assertion true true A type of imported information that is used in a manual assertion. ECO:MCC A type of imported information that is used in an automatic assertion. mchibucos 2011-03-02T05:33:43Z eco ECO:0000313 imported information used in automatic assertion true true A type of imported information that is used in an automatic assertion. ECO:MCC A type of direct assay evidence that is used in a manual assertion. mchibucos 2011-10-28T04:59:31Z GOECO:IDA inferred from direct assay eco IDA ECO:0000314 direct assay evidence used in manual assertion http://geneontology.org/page/ida-inferred-direct-assay true true A type of direct assay evidence that is used in a manual assertion. ECO:MCC GOECO:IDA inferred from direct assay inferred from direct assay GOECO:IDA IDA GOECO:IDA A type of mutant phenotype evidence that is used in a manual assertion. mchibucos 2011-10-28T05:12:49Z GOECO:IMP eco IMP inferred from mutant phenotype ECO:0000315 mutant phenotype evidence used in manual assertion http://geneontology.org/page/imp-inferred-mutant-phenotype true true A type of mutant phenotype evidence that is used in a manual assertion. ECO:MCC GOECO:IMP inferred from mutant phenotype IMP GOECO:IMP inferred from mutant phenotype GOECO:IMP A type of genetic interaction experiment evidence that is used in a manual assertion. mchibucos 2011-10-28T05:14:42Z GOECO:IGI IGI inferred from genetic interaction eco ECO:0000316 genetic interaction evidence used in manual assertion http://geneontology.org/page/igi-inferred-genetic-interaction true true A type of genetic interaction experiment evidence that is used in a manual assertion. ECO:MCC GOECO:IGI inferred from genetic interaction IGI GOECO:IGI inferred from genetic interaction GOECO:IGI A type of genomic context evidence that is used in a manual assertion. mchibucos 2011-10-28T05:22:53Z GOECO:IGC IGC inferred from genomic context eco ECO:0000317 genomic context evidence used in manual assertion http://geneontology.org/page/igc-inferred-genomic-context true true A type of genomic context evidence that is used in a manual assertion. ECO:MCC GOECO:IGC inferred from genomic context IGC GOECO:IGC inferred from genomic context GOECO:IGC A type of biological aspect of ancestor evidence that is used in a manual assertion. mchibucos 2011-10-28T05:23:51Z GOECO:IBA IBA inferred from biological aspect of ancestor eco ECO:0000318 biological aspect of ancestor evidence used in manual assertion http://geneontology.org/page/iba-inferred-biological-aspect-ancestor true true A type of biological aspect of ancestor evidence that is used in a manual assertion. ECO:MCC GOECO:IBA inferred from biological aspect of ancestor IBA GOECO:IBA inferred from biological aspect of ancestor GOECO:IBA A type of biological aspect of descendant evidence that is used in a manual assertion. mchibucos 2011-10-28T05:25:09Z GOECO:IBD IBD inferred from biological aspect of descendant eco ECO:0000319 biological aspect of descendant evidence used in manual assertion http://geneontology.org/page/ibd-inferred-biological-aspect-descendent true true A type of biological aspect of descendant evidence that is used in a manual assertion. ECO:MCC GOECO:IBD inferred from biological aspect of descendant IBD GOECO:IBD inferred from biological aspect of descendant GOECO:IBD A type of phylogenetic determination of loss of key residues evidence that is used in a manual assertion. mchibucos 2011-10-28T05:25:48Z GOECO:IKR GOECO:IMR IKR IMR inferred from key residues inferred from missing residues eco ECO:0000320 phylogenetic determination of loss of key residues evidence used in manual assertion http://geneontology.org/page/ikr-inferred-key-residues true true A type of phylogenetic determination of loss of key residues evidence that is used in a manual assertion. ECO:MCC GOECO:IKR inferred from key residues GOECO:IMR inferred from missing residues IKR GOECO:IKR IMR GOECO:IKR inferred from key residues GOECO:IKR inferred from missing residues GOECO:IKR A type of rapid divergence from ancestral sequence evidence that is used in a manual assertion. mchibucos 2011-10-28T05:26:42Z GOECO:IRD IRD inferred from rapid divergence eco ECO:0000321 rapid divergence from ancestral sequence evidence used in manual assertion http://geneontology.org/page/ird-inferred-rapid-divergence true true A type of rapid divergence from ancestral sequence evidence that is used in a manual assertion. ECO:MCC GOECO:IRD inferred from rapid divergence IRD GOECO:IRD inferred from rapid divergence GOECO:IRD Evidence that was initially used in manual assertion by one person or group, which is imported by a second person or group and used in automatic assertion. mchibucos 2011-12-13T12:04:48Z GO_REF:0000037 GO_REF:0000039 GO_REF:0000041 eco ECO:0000322 imported manually asserted information used in automatic assertion Evidence that was initially used in manual assertion by one person or group, which is imported by a second person or group and used in automatic assertion. ECO:MCC GO_REF:0000037 Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries. GO_REF:0000039 Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries. GO_REF:0000041 IEA (UniProt UniPathway) A type of imported information used in automatic assertion that was initially used in automatic assertion by one person or group, which is imported by a second person or group and used in automatic assertion. mchibucos 2011-12-13T02:06:25Z GO_REF:0000038 GO_REF:0000040 eco ECO:0000323 imported automatically asserted information used in automatic assertion A type of imported information used in automatic assertion that was initially used in automatic assertion by one person or group, which is imported by a second person or group and used in automatic assertion. ECO:MCC GO_REF:0000038 Gene Ontology annotation based on automatic assignment of UniProtKB keywords in UniProtKB/TrEMBL entries. GO_REF:0000040 Gene Ontology annotation based on the automatic assignment of UniProtKB Subcellular Location terms in UniProtKB/TrEMBL entries. A type of direct assay evidence in which an image is created and analyzed. mchibucos 2012-02-23T12:01:43Z ECO:0001122 ECO:0005024 ECO:MCC radiologic test evidence eco ECO:0000324 imaging assay evidence A type of experimental evidence that is based on separation of constituent parts of a mixture (the mobile phase) as they pass differentially through a stationary phase due to differences in partition coefficient and retention on the stationary phase. mchibucos 2012-05-16T11:46:27Z chromatographic evidence eco ECO:0000325 chromatography evidence A type of experimental evidence that is based on separation of constituent parts of a mixture (the mobile phase) as they pass differentially through a stationary phase due to differences in partition coefficient and retention on the stationary phase. ECO:MCC A type of sequence alignment evidence that is based on comparing the position of exon junctions, relative to a reference genome, for a transcript annotation and a supporting transcript. mchibucos 2012-06-08T11:03:59Z eco ECO:0000326 transcript splice pattern evidence A type of sequence alignment evidence that is based on comparing the position of exon junctions, relative to a reference genome, for a transcript annotation and a supporting transcript. ECO:MCC A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features. mchibucos 2012-06-08T11:11:24Z eco ECO:0000327 This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that have the same splice pattern as a RefSeq transcript. If such full transcript information is not available, RefSeq reports sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, supported by the evidence term ECO:0000328 or a child. whole transcript splice pattern evidence A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features. ECO:MCC A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript. mchibucos 2012-06-08T11:21:57Z eco ECO:0000328 This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, but for which full transcript information is unavailable. For sequences that have the same splice pattern as a whole RefSeq transcript, use the evidence term ECO:0000327 or a child. coding sequence splice pattern evidence A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript. ECO:MCC A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features, and is used in manual assertion. mchibucos 2012-06-08T11:40:03Z eco ECO:0000329 This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that have the same splice pattern as a RefSeq transcript. If such full transcript information is not available, RefSeq reports sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, supported by the evidence term ECO:0000328 or a child. whole transcript splice pattern evidence used in manual assertion true true A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features, and is used in manual assertion. ECO:MCC A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript, and is used in manual assertion. mchibucos 2012-06-08T11:43:47Z eco ECO:0000330 This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, but for which full transcript information is unavailable. For sequences that have the same splice pattern as a whole RefSeq transcript, use the evidence term ECO:0000327 or a child. coding sequence splice pattern evidence used in manual assertion true true A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript, and is used in manual assertion. ECO:MCC A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript, and is used in automatic assertion. mchibucos 2012-06-08T11:48:09Z eco ECO:0000331 This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, but for which full transcript information is unavailable. For sequences that have the same splice pattern as a whole RefSeq transcript, use the evidence term ECO:0000327 or a child. coding sequence splice pattern evidence used in automatic assertion true true A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript, and is used in automatic assertion. ECO:MCC A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features, and is used in automatic assertion. mchibucos 2012-06-08T11:49:17Z eco ECO:0000332 This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that have the same splice pattern as a RefSeq transcript. If such full transcript information is not available, RefSeq reports sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, supported by the evidence term ECO:0000328 or a child. whole transcript splice pattern evidence used in automatic assertion true true A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features, and is used in automatic assertion. ECO:MCC A type of gel electrophoresis evidence where proteins are separated according to their electrophoretic mobility. mchibucos 2012-07-31T02:56:43Z SDS-PAGE evidence eco ECO:0000333 Electrophoretic mobility is a function of both the length and charge of a protein. The protein sample is linearized with sodium dodecyl sulfate (SDS), an anionic detergent. Typically, polypeptides bound with SDS possess an even distribution of charge per unit mass, and subsequent fractionation is by size. sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence A type of gel electrophoresis evidence where proteins are separated according to their electrophoretic mobility. ECO:MCC PubMed:4861258 url:http://www.nature.com/nmeth/journal/v2/n1/full/nmeth0105-83.html url:http://www.ncbi.nlm.nih.gov/Class/NAWBIS/Modules/Protein/protein18.html A type of direct assay evidence resulting from an assay where both the size of and number of particles in a sample are determined. mchibucos 2012-07-31T03:19:32Z eco ECO:0000334 An example of an instrument used to analyze particle sizes and counts is the Beckman Coulter® Z Series system. particle size and count assay evidence A type of direct assay evidence resulting from an assay where both the size of and number of particles in a sample are determined. ECO:MCC A type of direct assay evidence where the quantity of a substance used as part of an assay is measured. mchibucos 2012-07-31T03:52:46Z eco ECO:0000335 Two examples of substance quantification assay are (i) measuring how much of a radiolabelled compound is taken up by a cell and (ii) measuring how much of a substrate is turned over by a given enzyme. substance quantification evidence A type of direct assay evidence where the quantity of a substance used as part of an assay is measured. ECO:MCC A type of biological assay evidence in which a mutated strain of a microorganism, such as a yeast or bacterium, is grown competitively with wild-type cells and the relative fitness of the strains is assessed. mchibucos 2012-08-24T12:03:58Z fitness profiling eco ECO:0000336 competitive growth assay evidence A type of biological assay evidence in which a mutated strain of a microorganism, such as a yeast or bacterium, is grown competitively with wild-type cells and the relative fitness of the strains is assessed. GOC:MAH PMID:14718172 PMID:20537132 fitness profiling GOC:MAH PMID:20537132 A type of direct assay evidence where molecules have been sorted according to their size and charge by moving through a gel in the presence of an electric field. mchibucos 2012-08-24T12:11:51Z ECO:0005026 eco ECO:0000337 Molecules typically separated include DNA, RNA, or protein. The gel is typically made of agarose, polyacrylamide, or starch. gel electrophoresis evidence A type of direct assay evidence where molecules have been sorted according to their size and charge by moving through a gel in the presence of an electric field. ECO:MCC wikipedia:Gel_electrophoresis A type of gel electrophoresis evidence in which large DNA molecules are separated on agarose gel by alternately pulsed, perpendicularly oriented electrical fields, at least one of which is inhomogeneous. mchibucos 2012-08-24T12:34:01Z PFGE eco ECO:0000338 pulsed-field gel electrophoresis evidence A type of gel electrophoresis evidence in which large DNA molecules are separated on agarose gel by alternately pulsed, perpendicularly oriented electrical fields, at least one of which is inhomogeneous. PMID:6373014 A type of gel electrophoresis evidence where DNA molecules are electrophoresed on a low percentage agarose gel followed by high voltage electrophoresis on a higher percentage agarose gel in the presence of ethidium bromide. mchibucos 2012-08-24T12:42:37Z 2-D agarose gel electrophoresis eco ECO:0000339 The first dimension gel is intentionally run at low voltage in low percentage agarose to separate DNA molecules in proportion to their mass. The second dimension is run at high voltage in a gel of higher agarose concentration in the presence of ethidium bromide so that the mobility of a non-linear molecule is drastically influenced by its shape. two-dimensional agarose gel electrophoresis evidence A type of gel electrophoresis evidence where DNA molecules are electrophoresed on a low percentage agarose gel followed by high voltage electrophoresis on a higher percentage agarose gel in the presence of ethidium bromide. PMID:16118435 PMID:8594382 A type of experimental evidence in which retention of an introduced plasmid is determined when a mitotically stable plasmid (or minichromosome) is introduced into cells, which are grown without selection for several generations. mchibucos 2012-08-24T01:27:58Z minichromosome maintenance assay evidence eco ECO:0000340 Loss per generation is determined by comparing colony numbers on selective and non-selective media. plasmid maintenance assay evidence A type of experimental evidence in which retention of an introduced plasmid is determined when a mitotically stable plasmid (or minichromosome) is introduced into cells, which are grown without selection for several generations. ECO:MCC PMID:6323245 minichromosome maintenance assay evidence PMID:6323245 A type of specific protein inhibition evidence where the molecular function of a protein is inhibited by an antibody. mchibucos 2012-08-24T01:48:24Z eco ECO:0000341 specific protein inhibition by antibody evidence A type of specific protein inhibition evidence where the molecular function of a protein is inhibited by an antibody. ECO:MCC A type of RNA-seq evidence where intron locations in predicted transcripts are compared to intron locations supported by RNA-seq evidence. mchibucos 2013-04-03T04:22:05Z eco ECO:0000342 RNA-seq alignment intron location evidence is used by NCBI RefSeq (http://www.ncbi.nlm.nih.gov/refseq). Exon-exon boundaries (or intron locations) of a RefSeq transcript, as determined by aligning the transcript to a reference chromosome, are compared to intron locations supported by RNAseq data. Support of intron position by RNA-seq alignment evidence A type of RNA-seq evidence where intron locations in predicted transcripts are compared to intron locations supported by RNA-seq evidence. ECO:MCC A type of support of intron position by RNA-seq alignment evidence where RNA-seq alignment from a single sample supports all of the intron positions (exon pairs) predicted for a transcript. mchibucos 2013-04-03T04:41:48Z eco ECO:0000343 Full support entails that all exon pairs represented in the transcript are supported. For example, for a transcript containing five exons, if liver RNA-seq reads support all four introns but brain RNA-seq supports only three introns, then the liver data fully support the transcript exons whereas the brain data do not. Full support of intron position by RNA-seq alignment evidence A type of support of intron position by RNA-seq alignment evidence where RNA-seq alignment from a single sample supports all of the intron positions (exon pairs) predicted for a transcript. ECO:MCC A type of support of intron position by RNA-seq alignment evidence where RNA-seq alignment to a genome supports only some of the intron positions (exon pairs) predicted for a transcript. mchibucos 2013-04-03T04:50:46Z eco ECO:0000344 Partial support can occur in two ways. First, one or more exon-exon pair (intron) is not supported by any RNA-seq sample included in the analysis. Second, no single RNA-seq sample provides support for all exon-exon pairs (introns) represented in a transcript, but all represented exons are supported by at least one sample. Partial support of intron position by RNA-seq alignment evidence A type of support of intron position by RNA-seq alignment evidence where RNA-seq alignment to a genome supports only some of the intron positions (exon pairs) predicted for a transcript. ECO:MCC mchibucos 2013-04-03T05:10:34Z eco ECO:0000345 single exon transcript confirmation via alignment evidence A type of support of intron position by RNA-seq alignment evidence that is used in a manual assertion. mchibucos 2013-04-04T04:37:35Z eco ECO:0000346 Support of intron position by RNA-seq alignment evidence used in manual assertion true true A type of support of intron position by RNA-seq alignment evidence that is used in a manual assertion. ECO:MCC A type of support of intron position by RNA-seq alignment evidence that is used in an automatic assertion. mchibucos 2013-04-04T04:38:45Z eco ECO:0000347 Support of intron position by RNA-seq alignment evidence used in automatic assertion true true A type of support of intron position by RNA-seq alignment evidence that is used in an automatic assertion. ECO:MCC A type of full support of intron position by RNA-seq alignment evidence that is used in an automatic assertion. mchibucos 2013-04-04T04:40:19Z eco ECO:0000348 Full support of intron position by RNA-seq alignment evidence used in automatic assertion true true A type of full support of intron position by RNA-seq alignment evidence that is used in an automatic assertion. ECO:MCC A type of full support of intron position by RNA-seq alignment evidence that is used in a manual assertion. mchibucos 2013-04-04T04:41:34Z eco ECO:0000349 Full support of intron position by RNA-seq alignment evidence used in manual assertion true true A type of full support of intron position by RNA-seq alignment evidence that is used in a manual assertion. ECO:MCC A type of partial support of intron position by RNA-seq alignment evidence that is used in an automatic assertion. mchibucos 2013-04-04T04:42:53Z eco ECO:0000350 Partial support of intron position by RNA-seq alignment evidence used in automatic assertion true true A type of partial support of intron position by RNA-seq alignment evidence that is used in an automatic assertion. ECO:MCC A type of partial support of intron position by RNA-seq alignment evidence that is used in a manual assertion. mchibucos 2013-04-04T04:43:56Z eco ECO:0000351 Partial support of intron position by RNA-seq alignment evidence used in manual assertion true true A type of partial support of intron position by RNA-seq alignment evidence that is used in a manual assertion. ECO:MCC A type of evidence that is used in an manual assertion. mchibucos eco ECO:0000352 evidence used in manual assertion true true A type of evidence that is used in an manual assertion. ECO:MCC A type of physical interaction evidence that is used in a manual assertion. mchibucos 2013-10-31T21:01:27Z GOECO:IPI IPI inferred from physical interaction eco ECO:0000353 physical interaction evidence used in manual assertion http://geneontology.org/page/ipi-inferred-physical-interaction true true A type of physical interaction evidence that is used in a manual assertion. ECO:MCC GOECO:IPI inferred from physical interaction IPI GOECO:IPI inferred from physical interaction GOECO:IPI A type of gene neighbors evidence that is used in a manual assertion. mchibucos 2013-11-19T13:37:24Z GO_REF:0000025 eco ECO:0000354 gene neighbors evidence used in manual assertion true true A type of gene neighbors evidence that is used in a manual assertion. ECO:MCC GO_REF:0000025 operon structure as IGC evidence A type of phylogenetic evidence characterized by the mapping of the character states of living organisms onto phylogenies using the method of maximum parsimony. mchibucos 2014-04-22T17:02:31Z eco ECO:0000355 Example of use: "The presence of paired evaginated hemispheres and olfactory bulbs in both agnathan and gnathostome radiations suggests that such hemispheres were also present in the common ancestor." PMID: 7013637. Northcutt RG. (1981) Evolution of the telencephalon in nonmammals. Ann. Rev. Neurosci. phylogenetic distribution evidence A type of phylogenetic evidence characterized by the mapping of the character states of living organisms onto phylogenies using the method of maximum parsimony. ECO:MCC PMID:21238344 A type of transcript expression evidence resulting from a microarray analysis with the use of the Gene Set Enrichment Analysis (GSEA) method or the Fisher's-Exact (FE) method to assess the differential expression. mchibucos 2014-09-26T16:25:47Z eco ECO:0000358 differential geneset expression evidence from microarray experiment (GSEA, Fisher-exact) A type of transcript expression evidence resulting from a microarray analysis with the use of the Gene Set Enrichment Analysis (GSEA) method or the Fisher's-Exact (FE) method to assess the differential expression. PMID:19725948 A type of transcript expression evidence resulting from the use of the Gene Set Enrichment Analysis (GSEA) method or Fisher's-Exact (FE) method to assess an RNA-seq dataset for differential gene expression. mchibucos 2014-09-26T16:26:48Z eco ECO:0000359 differential geneset expression evidence from RNA-seq experiment (GSEA, Fisher-exact) A type of transcript expression evidence resulting from the use of the Gene Set Enrichment Analysis (GSEA) method or Fisher's-Exact (FE) method to assess an RNA-seq dataset for differential gene expression. PMC:2881125 mchibucos 2014-09-26T16:39:11Z eco ECO:0000360 biological target-disease association via drug A type of evidence where an assertion is derived from another assertion via logical inference or some non-logical but rational means. mchibucos 2015-07-14T11:19:37Z eco ECO:0000361 Inference is the process of deriving logical conclusions from premises known or assumed to be true, or alternatively, arriving at conclusions via some non-logical means of observation of patterns of facts, which can result in identifying new meanings and contexts for understanding. Given the evidence provided by a set of premises, deductive reasoning involves drawing conclusions that necessarily follow, i.e. are certain, whereas inductive reasoning generates conclusions that are likely to be, but are not necessarily, true. inferential evidence A type of evidence where an assertion is derived from another assertion via logical inference or some non-logical but rational means. ECO:MCC A type of inferential evidence based on a computationally derived unary inference or an inference chain in which at least one step is computationally derived. mchibucos 2015-07-14T11:24:27Z eco ECO:0000362 evidence based on computational logical inference A type of inferential evidence based on a computationally derived unary inference or an inference chain in which at least one step is computationally derived. ECO:MCC GOC:MC A type of evidence based on computational logical inference that is used in automatic assertion. mchibucos 2015-07-14T11:35:08Z GO_REF:0000108 eco ECO:0000363 evidence based on computational logical inference used in automatic assertion true true A type of evidence based on computational logical inference that is used in automatic assertion. ECO:MCC GO_REF:0000108 Automatic assignment of GO terms using logical inference, based on on inter-ontology links A type of evidence based on logical inference from a manually curated annotation that is used in an automatic assertion. mchibucos 2015-07-14T11:44:19Z eco ECO:0000364 evidence based on logical inference from manual annotation used in automatic assertion A type of evidence based on logical inference from a manually curated annotation that is used in an automatic assertion. ECO:MCC A type of evidence based on logical inference from an automatically curated annotation that is used in an automatic assertion. mchibucos 2015-07-14T11:45:25Z eco ECO:0000366 evidence based on logical inference from automatic annotation used in automatic assertion A type of evidence based on logical inference from an automatically curated annotation that is used in an automatic assertion. ECO:MCC A type of evidence that is used in an automatic assertion. cjm GOECO:IEA GO_REF:0000003 GO_REF:0000004 GO_REF:0000023 IEA inferred from electronic annotation eco ECO:0000501 evidence used in automatic assertion http://geneontology.org/page/automatically-assigned-evidence-codes true true A type of evidence that is used in an automatic assertion. ECO:cjm GOECO:IEA inferred from electronic annotation GO_REF:0000003 Gene Ontology annotation based on Enzyme Commission mapping. GO_REF:0000004 Gene Ontology annotation based on Swiss-Prot keyword mapping. GO_REF:0000023 Gene Ontology annotation based on Swiss-Prot Subcellular Location vocabulary mapping. IEA GOECO:IEA inferred from electronic annotation GOECO:IEA A type of in vitro cell based assay evidence resulting from the growth of cells in a micro-environment that mimics real tissue and establishes physiological cell-cell and cell-substrate interactions that regulate proliferation and differentiation. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001001 3D cell culture evidence A type of in vitro cell based assay evidence resulting from the growth of cells in a micro-environment that mimics real tissue and establishes physiological cell-cell and cell-substrate interactions that regulate proliferation and differentiation. PMID:21042962 url:http://volttecnologia.com.br/wp-content/uploads/2016/03/Drug-discovery.pdf A type of in vitro cell based assay evidence resulting from labeling cells with [3H]arachidonic acid and subsequently determining the release of the arachidonic acid by the cells. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001002 [3H]arachidonic acid release assay evidence A type of in vitro cell based assay evidence resulting from labeling cells with [3H]arachidonic acid and subsequently determining the release of the arachidonic acid by the cells. ISBN:0323152295 PMID:20693009 A type of DNA synthesis cell proliferation assay evidence resulting from the measurement of cell proliferation rate by determining the incorporation of [3H]-thymidine into cellular nucleic acids. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001003 [3H]-thymidine incorporation assay evidence A type of DNA synthesis cell proliferation assay evidence resulting from the measurement of cell proliferation rate by determining the incorporation of [3H]-thymidine into cellular nucleic acids. OBI:0000669 url:http://www.scientistsolutions.com/forum/cell-culture-and-tissue-culture-proliferationapoptosis/3h-thymidine-incorporation-assay-rat-1a A type of cytotoxicity assay evidence resulting from the measurement of the amount of radioactive 51Cr released in the supernatant of a sample of 51Cr pre-labeled cells via cytolysis by effector cells (cytotoxic T-cells). SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001004 51Cr release assay evidence A type of cytotoxicity assay evidence resulting from the measurement of the amount of radioactive 51Cr released in the supernatant of a sample of 51Cr pre-labeled cells via cytolysis by effector cells (cytotoxic T-cells). PMC:3929704 url:http://www4.mpbio.com/ecom/docs/proddata.nsf/5f64ffd4f38c2fda8525645d00769d68/53d2a75653615bab852568cb00572ff3?OpenDocument A type of apoptotic assay evidence resulting from the use of 7-aminoactinomycin D (7-AAD) to distinguish viable, apoptotic, and dead cells, using the fact that permeability of the cell membrane, and fluorescence intensity, is low in early apoptotic cells and high in late apoptotic and dead cells. SIB:PG mchibucos 2014-03-16T11:30:54Z 7-AAD staining evidence 7-amino-actinomycin D staining evidence eco ECO:0001005 7-aminoactinomycin staining evidence A type of apoptotic assay evidence resulting from the use of 7-aminoactinomycin D (7-AAD) to distinguish viable, apoptotic, and dead cells, using the fact that permeability of the cell membrane, and fluorescence intensity, is low in early apoptotic cells and high in late apoptotic and dead cells. ECO:RCT A type of in vitro cell based assay evidence resulting from the analysis of cell binding either to extracellular matrix proteins or other cells. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001006 adhesion assay evidence A type of in vitro cell based assay evidence resulting from the analysis of cell binding either to extracellular matrix proteins or other cells. PMID:15576904 PMID:21909903 A type of ex vivo assay evidence derived by ex vivo selection of tumor-reactive lymphocytes, and their activation and numerical expansion before re-infusion to the autologous tumor-bearing host. SIB:PG mchibucos 2014-03-16T11:30:54Z Adoptive immunotherapy passive immunization eco ECO:0001007 adoptive cell transfer evidence A type of ex vivo assay evidence derived by ex vivo selection of tumor-reactive lymphocytes, and their activation and numerical expansion before re-infusion to the autologous tumor-bearing host. ECO:SN url:http://jco.ascopubs.org/content/23/10/2346.full.pdf+html url:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2305722/pdf/nihms42807.pdf A type of cell viability assay evidence resulting from the continuous measurement of fluorescence intensity from the viable cells, where cell permeable compound, resazurin in Alamar blue is reduced to fluorescent resorufin. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001008 Alamar blue assay evidence A type of cell viability assay evidence resulting from the continuous measurement of fluorescence intensity from the viable cells, where cell permeable compound, resazurin in Alamar blue is reduced to fluorescent resorufin. PMC:3478843 url:https://www.thermofisher.com/us/en/home/references/protocols/cell-and-tissue-analysis/cell-profilteration-assay-protocols/cell-viability-with-alamarblue.html A type of anatomical perturbation evidence where an organ or tissue is transplanted from one individual to another of the same species with a different genotype. SIB:PG mchibucos 2014-03-16T11:30:54Z Allotransplantation allografting tissue grafting eco ECO:0001009 allograft transplantation experiment evidence A type of anatomical perturbation evidence where an organ or tissue is transplanted from one individual to another of the same species with a different genotype. ECO:SN url:http://www.nature.com/subjects/allograft url:http://www.organdonor.gov/about/terms_and_topics/ A type of chromatography evidence where a positively charged ion exchange resin with an affinity for molecules having net negative surface charges is used to separate the molecules. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001010 anion-exchange chromatography evidence A type of chromatography evidence where a positively charged ion exchange resin with an affinity for molecules having net negative surface charges is used to separate the molecules. ECO:SN PMID:20978968 url:http://www.bio-rad.com/en-us/applications-technologies/anion-exchange-chromatography url:http://www.uta.edu/faculty/sawasthi/Enzymology-4351-5324/Class%20Syllabus%20Enzymology/Ion%20Exchange%20Chromatography-1.pdf A type of apoptotic assay evidence resulting from the addition and subsequent binding of Annexin V to phosphatidylserine in cells to detect if they are viable, apoptotic, or necrotic. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001011 annexin-V staining evidence A type of apoptotic assay evidence resulting from the addition and subsequent binding of Annexin V to phosphatidylserine in cells to detect if they are viable, apoptotic, or necrotic. PMC:3169266 A type of experimental phenotypic evidence resulting from behavioral phenotyping and analysis to assess cognitive functioning. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001012 behavioral assay evidence A type of experimental phenotypic evidence resulting from behavioral phenotyping and analysis to assess cognitive functioning. PMID:24462904 A type of immunological assay evidence resulting from inhibitory effect of monoclonal antibody combining with an antigen over other antibodies. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001013 blocking monoclonal antibody evidence A type of immunological assay evidence resulting from inhibitory effect of monoclonal antibody combining with an antigen over other antibodies. PMID:11292349 url:http://www.sciencedirect.com/science/article/pii/S0140673600034966 A type of immunological assay evidence resulting from the use of peptides to block antibodies from binding to their targets. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001014 blocking peptide evidence A type of immunological assay evidence resulting from the use of peptides to block antibodies from binding to their targets. ECO:RCT SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001015 blocking polyclonal antibody evidence A type of direct assay evidence where a blood sample is extracted from an organism to analyze different blood components. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001016 blood test evidence A type of direct assay evidence where a blood sample is extracted from an organism to analyze different blood components. ECO:SN url:https://www.nhlbi.nih.gov/health/health-topics/topics/bdt A type of chemotaxis assay evidence resulting from the analysis of the number of cells that migrate from the upper compartment of a chamber (separated by a micro-porous membrane) to the lower compartment, in which chemotactic agents are present. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001017 Boyden chamber assay evidence A type of chemotaxis assay evidence resulting from the analysis of the number of cells that migrate from the upper compartment of a chamber (separated by a micro-porous membrane) to the lower compartment, in which chemotactic agents are present. PMID:13872176 PMID:15576901 A type of nucleotide analog incorporation evidence resulting from the incorporation of bromodeoxyuridine (BrdU) as a thymidine analog into nuclear DNA, resulting in a label that can be tracked using antibody probes. SIB:PG mchibucos 2014-03-16T11:30:54Z 5-bromo-2'-deoxyuridine incorporation assay evidence BUdR incorporation assay evidence BrdU incorporation assay evidence BrdUrd incorporation assay evidence eco ECO:0001018 bromodeoxyuridine incorporation assay evidence A type of nucleotide analog incorporation evidence resulting from the incorporation of bromodeoxyuridine (BrdU) as a thymidine analog into nuclear DNA, resulting in a label that can be tracked using antibody probes. PMID:23690005 A type of apoptotic assay evidence resulting from the detection of caspase activation, which results in the cleaving of intracellular substrates during apoptosis. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001019 caspase assay evidence A type of apoptotic assay evidence resulting from the detection of caspase activation, which results in the cleaving of intracellular substrates during apoptosis. PMID:18314058 PMID:25086023 A type of in vitro cell based assay evidence resulting from the quantification of a sample of cells. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001020 cell counting evidence A type of in vitro cell based assay evidence resulting from the quantification of a sample of cells. ECO:RCT A type of in vitro cell based assay evidence resulting from the quantification of cell permeability. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001021 cell permeability assay evidence A type of in vitro cell based assay evidence resulting from the quantification of cell permeability. PMID:16962665 A type of staining evidence resulting from monitoring division by the use of carboxyfluorescein diacetate succinimidyl ester (CFSE) to label intracellular molecules with carboxyfluorescein; when a labeled cell divides, the number of carboxyfluorescein-tagged molecules is split. SIB:PG mchibucos 2014-03-16T11:30:54Z CFDA-SE staining evidence CFSE-staining evidence eco ECO:0001022 carboxyfluorescein diacetate succinimidyl ester staining evidence A type of staining evidence resulting from monitoring division by the use of carboxyfluorescein diacetate succinimidyl ester (CFSE) to label intracellular molecules with carboxyfluorescein; when a labeled cell divides, the number of carboxyfluorescein-tagged molecules is split. PMC:3185625 A type of protein detection assay evidence resulting from a complex (a chemiluminescent compound, protein and a steroidal hapten) utilized as a labeled antigen, which emits light when treated with hydrogen peroxide and copper acetate at a high pH. SIB:PG mchibucos 2014-03-16T11:30:54Z CLIA evidence eco ECO:0001023 chemiluminescence-linked immunoassay evidence A type of protein detection assay evidence resulting from a complex (a chemiluminescent compound, protein and a steroidal hapten) utilized as a labeled antigen, which emits light when treated with hydrogen peroxide and copper acetate at a high pH. PMID:659901 A type of mutant phenotype evidence resulting from the fusion of two or more different genes to create one protein product. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001024 chimeric protein evidence A type of mutant phenotype evidence resulting from the fusion of two or more different genes to create one protein product. PMID:22588898 PMID:25832756 A type of gel electrophoresis evidence resulting from the electrophoresis of two substances together, allowing for the characterization of ligand/nucleic acid binding interactions. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001025 co-electrophoresis evidence A type of gel electrophoresis evidence resulting from the electrophoresis of two substances together, allowing for the characterization of ligand/nucleic acid binding interactions. PMID:7668395 A type of imaging assay evidence resulting from the limited observation of the co-occurrence of molecules in a subcellular location. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001026 co-localization evidence A type of imaging assay evidence resulting from the limited observation of the co-occurrence of molecules in a subcellular location. PMC:3074624 A type of direct assay evidence resulting from the counting of microbial colonies that arise from viable cells grown on a plate or dish. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001027 colony counting evidence A type of direct assay evidence resulting from the counting of microbial colonies that arise from viable cells grown on a plate or dish. PMID:16558698 PMID:23457446 A type of physical interaction evidence resulting from the separation of a mixture of molecules under the influence of a force such as artificial gravity, where molecules sedimenting together are assumed to interact. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001028 co-sedimentation assay evidence A type of physical interaction evidence resulting from the separation of a mixture of molecules under the influence of a force such as artificial gravity, where molecules sedimenting together are assumed to interact. MI:0027 A type of gel electrophoresis evidence resulting in the assessment of DNA breakage in a cell, based on size and shape of DNA migration. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001029 comet assay evidence A type of gel electrophoresis evidence resulting in the assessment of DNA breakage in a cell, based on size and shape of DNA migration. OBI:0302736 PMID:10737956 A type of knockout evidence resulting from a temporally-restricted and/or tissue-specific targeted gene removal. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001030 conditional knockout evidence A type of knockout evidence resulting from a temporally-restricted and/or tissue-specific targeted gene removal. PMC:3572410 A type of knockin evidence resulting from the targeted introduction of a temporally-restricted and/or tissue-specific mutation. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001031 conditional knockin evidence A type of knockin evidence resulting from the targeted introduction of a temporally-restricted and/or tissue-specific mutation. PMID:16832820 A type of experimental phenotypic evidence resulting from a constitutively active mutant (CAM), resulting in mutant proteins that remain active in the absence of upstream signals. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001032 constitutively active mutant evidence A type of experimental phenotypic evidence resulting from a constitutively active mutant (CAM), resulting in mutant proteins that remain active in the absence of upstream signals. PMID:12217490 A type of protein binding evidence resulting from the identification of two interacting proteins (that exist in close proximity) by linking through covalent bonds followed by identification SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001033 cross-linking evidence A type of protein binding evidence resulting from the identification of two interacting proteins (that exist in close proximity) by linking through covalent bonds followed by identification PMID:15530987 PMID:19241040 A type of structure determination evidence resulting from the use of a narrow beam of x-rays to identify molecular structures by creating a diffraction pattern. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001034 crystallography evidence A type of structure determination evidence resulting from the use of a narrow beam of x-rays to identify molecular structures by creating a diffraction pattern. MI:0114 A type of histochemistry evidence resulting from localizing chemical components of cells and organelles on histological sections. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001035 cytochemistry evidence A type of histochemistry evidence resulting from localizing chemical components of cells and organelles on histological sections. PMID:11597006 A type of apoptotic assay evidence resulting from the identification of an accumulation of Cytochrome c in the cytoplasm after its release from the mitochondria, an early event in apoptosis. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001036 cytochrome C release assay evidence A type of apoptotic assay evidence resulting from the identification of an accumulation of Cytochrome c in the cytoplasm after its release from the mitochondria, an early event in apoptosis. PMID:10914021 PMID:12815469 A type of staining evidence resulting from 4',6-diamidino-2-phenylindole (DAPI) binding to AT regions of DNA and emitting a blue fluorescence. SIB:PG mchibucos 2014-03-16T11:30:54Z DAPI staining evidence eco ECO:0001037 4',6-diamidino-2-phenylindole staining evidence A type of staining evidence resulting from 4',6-diamidino-2-phenylindole (DAPI) binding to AT regions of DNA and emitting a blue fluorescence. PMID:8580206 url:https://www.thermofisher.com/us/en/home/references/protocols/cell-and-tissue-analysis/protocols/dapi-imaging-protocol.html A type of experimental phenotypic evidence resulting from a mutation in which there is a removal of one or more contiguous nucleotides. SIB:PG mchibucos 2014-03-16T11:30:54Z ECO:0005510 eco ECO:0001038 deletion mutation evidence A type of experimental phenotypic evidence resulting from a mutation in which there is a removal of one or more contiguous nucleotides. SO:0000159 A type of apoptotic assay evidence resulting from the visualization of the DNA ladder (apoptotic DNA fragmentation) in gel electrophoresis. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001039 DNA laddering assay evidence A type of apoptotic assay evidence resulting from the visualization of the DNA ladder (apoptotic DNA fragmentation) in gel electrophoresis. PMC:4401164 A type of RNA detection assay evidence based on the direct application of a RNA mixture in a circular motion on a matrix for hybridization with labeled DNA fragments. CollecTF SIB:PG mchibucos 2014-03-16T11:30:54Z eco RNA dot blot ECO:0001040 RNA dot blot assay evidence A type of RNA detection assay evidence based on the direct application of a RNA mixture in a circular motion on a matrix for hybridization with labeled DNA fragments. ECO:SW PMID:21424648 A type of experimental phenotypic evidence resulting from the analysis of a mutated gene producing mutant polypeptides that disrupt the activity of the wild-type genes. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001042 dominant-negative mutant evidence A type of experimental phenotypic evidence resulting from the analysis of a mutated gene producing mutant polypeptides that disrupt the activity of the wild-type genes. PMC:2217636 PMID:8018332 A type of Edman degradation evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:59:00Z eco ECO:0001043 Edman degradation evidence used in manual assertion true true A type of Edman degradation evidence that is used in a manual assertion. ECO:MCC A type of protein detection assay evidence resulting from labeling a termonal amino acid residue and cleaving it from a peptide by sequentially removing one residue at a time from the amino end of the peptide, without disrupting the bonds. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001044 Edman degradation evidence A type of protein detection assay evidence resulting from labeling a termonal amino acid residue and cleaving it from a peptide by sequentially removing one residue at a time from the amino end of the peptide, without disrupting the bonds. OBI:0000705 doi:10.3891/acta.chem.scand.04-0283 A type of affinity evidence resulting from the quantitative analysis of gene and protein expression monitored by proprietary eTag reporters. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001045 eTag assay evidence A type of affinity evidence resulting from the quantitative analysis of gene and protein expression monitored by proprietary eTag reporters. PMID:15137949 A type of physical interaction evidence resulting from a mixture of two molecules passed through a nitrocellulose filter, where one may be immobilized on the filter, and if the immobilized molecule is capable of binding to the other, it will be retained on the filter as well. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001046 filter binding assay evidence A type of physical interaction evidence resulting from a mixture of two molecules passed through a nitrocellulose filter, where one may be immobilized on the filter, and if the immobilized molecule is capable of binding to the other, it will be retained on the filter as well. PMID:23028069 A type of expression pattern evidence and in situ hybridization evidence resulting from the use of fluorescent probes to detect complementary sequences of nucleic acids. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001047 fluorescence in situ hybridization evidence A type of expression pattern evidence and in situ hybridization evidence resulting from the use of fluorescent probes to detect complementary sequences of nucleic acids. PMC:346675 PMID:6812046 A type of physical interaction evidence resulting from the measurement of the proximity of two fluorophores, where the energy from an excited molecular fluorophore to another fluorophore can only occur within ~10nm. SIB:PG mchibucos 2014-03-16T11:30:54Z FRET eco ECO:0001048 fluorescence resonance energy transfer evidence A type of physical interaction evidence resulting from the measurement of the proximity of two fluorophores, where the energy from an excited molecular fluorophore to another fluorophore can only occur within ~10nm. PMID:11516318 PMID:15696158 A type of chromatography evidence resulting from the exclusion of proteins based on molecular size by filtration through a porous matrix (swollen gel), from which larger molecules are excluded. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001049 gel-filtration evidence A type of chromatography evidence resulting from the exclusion of proteins based on molecular size by filtration through a porous matrix (swollen gel), from which larger molecules are excluded. CHMO:0001011 doi:10.1038/nmeth0506-410 A type of histology evidence resulting from the identification of chemical components in cells and tissues. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001050 histochemistry evidence A type of histology evidence resulting from the identification of chemical components in cells and tissues. MMO:0000497 A type of imaging assay evidence resulting from the qualitative microscopic examination of cells or tissues. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001051 histology evidence A type of imaging assay evidence resulting from the qualitative microscopic examination of cells or tissues. OBI:0600020 A type of chromatography evidence resulting from the separation of molecules in a solute by forcing the solvent containing the sample through a column packed with nonporous particles at high pressure. mchibucos 2014-03-16T11:30:54Z HPLC evidence eco ECO:0001052 high-performance liquid chromatography evidence A type of chromatography evidence resulting from the separation of molecules in a solute by forcing the solvent containing the sample through a column packed with nonporous particles at high pressure. PMID:16376355 A type of protein detection assay evidence resulting from the use of antibodies linked to coloring agents to localize structures in cell cultures to identify proteins. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001053 immunocytochemistry evidence A type of protein detection assay evidence resulting from the use of antibodies linked to coloring agents to localize structures in cell cultures to identify proteins. MI:1200 OBI:0001986 A type of immunological assay evidence resulting from the use of antibodies to remove specific proteins from a sample. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001054 immunodepletion evidence A type of immunological assay evidence resulting from the use of antibodies to remove specific proteins from a sample. BAO:0002505 A type of protein detection assay evidence resulting from the use of antibodies to detect proteins in localized cells of tissue sections. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001055 immunohistochemistry evidence A type of protein detection assay evidence resulting from the use of antibodies to detect proteins in localized cells of tissue sections. OBI:0001986 A type of genetic transformation evidence resulting from a mutation induced by a mutagenic compounds or irradiation. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001056 induced mutation evidence A type of genetic transformation evidence resulting from a mutation induced by a mutagenic compounds or irradiation. OBI:0001154 A type of in vitro assay evidence where acetylated residues are detected in a compound (such as a protein or a nucleic acid) in an in vitro experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001057 in vitro acetylation assay evidence A type of in vitro assay evidence where acetylated residues are detected in a compound (such as a protein or a nucleic acid) in an in vitro experiment. ECO:SN SIB:PG url:http://www.perkinelmer.com/resources/technicalresources/applicationsupportknowledgebase/radiometric/acetylation.xhtml A type of in vitro assay evidence that is based on the detection protein fragements from the cleavage of a protein by a protease in vitro. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001058 in vitro cleavage assay evidence A type of in vitro assay evidence that is based on the detection protein fragements from the cleavage of a protein by a protease in vitro. PMID:21121091 A type of in vitro assay evidence where the removal of ubiquitin groups on a protein is detected in vitro. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001059 in vitro deubiquitination assay evidence A type of in vitro assay evidence where the removal of ubiquitin groups on a protein is detected in vitro. ECO:SN PMID:19692941 SIB:PG A type of in vitro assay evidence where the removal of acetyl groups from a compound is detected in an in vitro experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001060 in vitro deacetylation assay evidence A type of in vitro assay evidence where the removal of acetyl groups from a compound is detected in an in vitro experiment. ECO:SN SIB:PG url:http://www.perkinelmer.com/resources/technicalresources/applicationsupportknowledgebase/radiometric/acetylation.xhtml A type of in vitro assay evidence where the removal of farnesyl groups from a protein is detected in an in vitro experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001061 in vitro defarnesylation assay evidence A type of in vitro assay evidence where the removal of farnesyl groups from a protein is detected in an in vitro experiment. ECO:SN PMID:16126733 SIB:PG A type of in vitro assay evidence where the removal of methyl groups from a compound is detected in an in vitro experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001062 in vitro demethylation assay evidence A type of in vitro assay evidence where the removal of methyl groups from a compound is detected in an in vitro experiment. ECO:SN SIB:PG url:http://en.wikipedia.org/wiki/Demethylation A type of in vitro assay evidence where the removal of sumo groups is detected on a protein in vitro. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001063 in vitro desumoylation assay evidence A type of in vitro assay evidence where the removal of sumo groups is detected on a protein in vitro. ECO:SN SIB:PG url:http://www.enzolifesciences.com/BML-UW8955/sumoylation-kit/ A type of in vitro assay evidence where farnesylated residues in proteins are detected in an in vitro experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001064 in vitro farnesylation assay evidence A type of in vitro assay evidence where farnesylated residues in proteins are detected in an in vitro experiment. ECO:SN SIB:PG url:http://en.wikipedia.org/wiki/Farnesyltransferase A type of in vitro assay evidence where methylated residues are detected in a compound (such as a protein or a nucleic acid) in an in vitro experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001065 in vitro methylation assay evidence A type of in vitro assay evidence where methylated residues are detected in a compound (such as a protein or a nucleic acid) in an in vitro experiment. ECO:SN SIB:PG url:http://en.wikipedia.org/wiki/Methylation A type of in vitro assay evidence where palmitoylated residues in proteins are detected in an in vitro experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001066 in vitro palmitoylation assay evidence A type of in vitro assay evidence where palmitoylated residues in proteins are detected in an in vitro experiment. ECO:SN PMID:17077383 SIB:PG A type of in vitro assay evidence where the removal of phosphatase groups on a protein is detected in an in vitro experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001067 in vitro phosphatase assay evidence A type of in vitro assay evidence where the removal of phosphatase groups on a protein is detected in an in vitro experiment. ECO:SN SIB:PG url:http://en.wikipedia.org/wiki/Phosphatase A type of in vitro assay evidence where phosphorylated residues in a protein are detected in an in vitro experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001068 in vitro protein kinase assay evidence A type of in vitro assay evidence where phosphorylated residues in a protein are detected in an in vitro experiment. ECO:SN SIB:PG url:http://en.wikipedia.org/wiki/Protein_kinase url:http://en.wikipedia.org/wiki/Protein_phosphorylation A type of in vitro assay evidence where ADP-ribosylated residues in proteins are detected in an in vitro experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001069 in vitro polyADP-ribosylation assay evidence A type of in vitro assay evidence where ADP-ribosylated residues in proteins are detected in an in vitro experiment. ECO:SN PMID:21870253 SIB:PG A type of in vitro assay evidence where sumoylated residues are detected on a protein in an in vitro experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001070 in vitro sumoylation assay evidence A type of in vitro assay evidence where sumoylated residues are detected on a protein in an in vitro experiment. ECO:SN SIB:PG url:http://www.enzolifesciences.com/BML-UW8955/sumoylation-kit/ A type of in vitro assay evidence where transcription is detected in vitro to validate the activation or repression ablity of a transcription factor in the absence of other proteins present in in vivo conditions. CollecTF SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001071 in vitro transcription assay evidence A type of in vitro assay evidence where transcription is detected in vitro to validate the activation or repression ablity of a transcription factor in the absence of other proteins present in in vivo conditions. ECO:SN ECO:SW PMID:21125481 SIB:PG A type of in vitro assay evidence where de novo protein synthesis is detected in an in vitro experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001072 in vitro translation assay evidence A type of in vitro assay evidence where de novo protein synthesis is detected in an in vitro experiment. ECO:SN PMID:18230759 SIB:PG A type of in vitro assay evidence where ubiquitinated residues are detected on a protein in an in vitro experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001073 in vitro ubiquitination assay evidence A type of in vitro assay evidence where ubiquitinated residues are detected on a protein in an in vitro experiment. ECO:SN PMID:19692941 SIB:PG A type of in vivo assay evidence where acetylated residues are detected in a compound (such as a protein or a nucleic acid) in cells in vivo. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001074 in vivo acetylation assay evidence A type of in vivo assay evidence where acetylated residues are detected in a compound (such as a protein or a nucleic acid) in cells in vivo. ECO:SN SIB:PG url:http://www.perkinelmer.com/resources/technicalresources/applicationsupportknowledgebase/radiometric/acetylation.xhtml A type of in vivo assay evidence that is based on the detection of protein fragments from the cleavage of a protein by a protease in vivo. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001075 in vivo cleavage assay evidence A type of in vivo assay evidence that is based on the detection of protein fragments from the cleavage of a protein by a protease in vivo. ECO:SN PMID:22154596 A type of in vivo assay evidence where the removal of acetyl groups from a compound is detected in cells in vivo. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001076 in vivo deacetylation assay evidence A type of in vivo assay evidence where the removal of acetyl groups from a compound is detected in cells in vivo. ECO:SN SIB:PG url:http://www.perkinelmer.com/resources/technicalresources/applicationsupportknowledgebase/radiometric/acetylation.xhtml A type of in vivo assay evidence where removal of farnesyl groups from a protein is detected in cells in vivo. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001077 in vivo defarnesylation assay evidence A type of in vivo assay evidence where removal of farnesyl groups from a protein is detected in cells in vivo. ECO:SN PMID:15556768 PMID:16507103 SIB:PG A type of in vivo assay evidence where the removal of methyl groups from a compound is detected in cells in vivo. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001078 in vivo demethylation assay evidence A type of in vivo assay evidence where the removal of methyl groups from a compound is detected in cells in vivo. ECO:SN SIB:PG url:http://en.wikipedia.org/wiki/Demethylation A type of in vivo assay evidence where the removal of ubiquitin groups on a protein is detected in cells in vivo. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001079 in vivo deubiquitination assay evidence A type of in vivo assay evidence where the removal of ubiquitin groups on a protein is detected in cells in vivo. ECO:SN PMID:19692941 SIB:PG A type of in vivo assay evidence where the removal of sumo groups on a protein is detected in cells in vivo. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001080 in vivo desumoylation assay evidence A type of in vivo assay evidence where the removal of sumo groups on a protein is detected in cells in vivo. ECO:SN SIB:PG url:http://www.enzolifesciences.com/BML-UW8955/sumoylation-kit/ A type of in vivo assay evidence where farnesylated residues in proteins are detected in cells in vivo. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001081 in vivo farnesylation assay evidence A type of in vivo assay evidence where farnesylated residues in proteins are detected in cells in vivo. ECO:SN PMID:9030603 SIB:PG A type of in vivo assay evidence where methylated residues are detected in a compound (such as a protein or a nucleic acid) in vivo. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001082 in vivo methylation assay evidence A type of in vivo assay evidence where methylated residues are detected in a compound (such as a protein or a nucleic acid) in vivo. ECO:SN SIB:PG url:http://en.wikipedia.org/wiki/Methylation A type of in vivo assay evidence where palmitoylated residues in proteins are detected in cells in vivo. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001083 in vivo palmitoylation assay evidence A type of in vivo assay evidence where palmitoylated residues in proteins are detected in cells in vivo. ECO:SN PMID:10329400 SIB:PG A type of in vivo assay evidence where the removal of phosphate groups on a protein is detected in cells in vivo. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001084 in vivo phosphatase assay evidence A type of in vivo assay evidence where the removal of phosphate groups on a protein is detected in cells in vivo. ECO:SN SIB:PG url:http://en.wikipedia.org/wiki/Phosphatase A type of in vivo assay evidence where phosphorylated residues in a protein are detected in cells in vivo. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001085 in vivo protein kinase assay evidence A type of in vivo assay evidence where phosphorylated residues in a protein are detected in cells in vivo. ECO:SN SIB:PG url:http://en.wikipedia.org/wiki/Protein_kinase url:http://en.wikipedia.org/wiki/Protein_phosphorylation A type of in vivo assay evidence where sumoylated residues are detected on a protein in cells in vivo. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001086 in vivo sumoylation assay evidence A type of in vivo assay evidence where sumoylated residues are detected on a protein in cells in vivo. ECO:SN SIB:PG url:http://www.enzolifesciences.com/BML-UW8955/sumoylation-kit/ A type of in vivo assay evidence where transcription is detected in cells in vivo. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001087 in vivo transcription assay evidence A type of in vivo assay evidence where transcription is detected in cells in vivo. ECO:SN PMID:12181418 SIB:PG A type of in vivo assay evidence where de novo protein synthesis is detected in cells in vivo. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001088 in vivo translation assay evidence A type of in vivo assay evidence where de novo protein synthesis is detected in cells in vivo. ECO:SN PMID:24901308 SIB:PG A type of in vivo assay evidence where ubiquitinated residues on a protein are detected in cells in vivo. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001089 in vivo ubiquitination assay evidence A type of in vivo assay evidence where ubiquitinated residues on a protein are detected in cells in vivo. ECO:SN PMID:19692941 SIB:PG A type of genetic transformation evidence resulting from the targetted replacement of a wild-type DNA sequence with a different sequence. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001090 knockin evidence A type of genetic transformation evidence resulting from the targetted replacement of a wild-type DNA sequence with a different sequence. PMID:18077807 PMID:21800101 A type of genetic transformation evidence resulting from the removal of a particular gene (or genes), disrupting the function and allowing for functional analysis. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001091 knockout evidence A type of genetic transformation evidence resulting from the removal of a particular gene (or genes), disrupting the function and allowing for functional analysis. PMC:2782548 A type of physical interaction evidence resulting from the qualitative and quantitative analysis of the affinity with which a protein binds to a lipid. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001092 lipid binding assay evidence A type of physical interaction evidence resulting from the qualitative and quantitative analysis of the affinity with which a protein binds to a lipid. PMID:22848065 PMID:23681540 A type of physical interaction evidence resulting from the analysis of protein-protein interactions by use of a luciferase enzyme fused to a particular protein (or proteins), which are coexpressed with epitope-tagged partners in mammalian cells. SIB:PG mchibucos 2014-03-16T11:30:54Z LUMIER assay eco ECO:0001093 luminescence-based mammalian interactome mapping assay evidence A type of physical interaction evidence resulting from the analysis of protein-protein interactions by use of a luciferase enzyme fused to a particular protein (or proteins), which are coexpressed with epitope-tagged partners in mammalian cells. MI:0729 PMID:15761153 SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001094 macroscopy evidence A type of hybrid interaction evidence resulting from the analysis of proteins of interest attached to two portions of the transcriptional activator, and in interaction bring the two portions together to increase expression of the reporter gene. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001095 mammalian 2-hybrid assay evidence A type of hybrid interaction evidence resulting from the analysis of proteins of interest attached to two portions of the transcriptional activator, and in interaction bring the two portions together to increase expression of the reporter gene. ECO:RCT PMID:9043710 A type of spectrometry evidence resulting from identifying the amount and type of material entities present in a sample by fragmenting it and measuring the mass-to-charge ratio of the resulting particles. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001096 mass spectrometry evidence A type of spectrometry evidence resulting from identifying the amount and type of material entities present in a sample by fragmenting it and measuring the mass-to-charge ratio of the resulting particles. OBI:0000470 A type of imaging assay evidence resulting from the use of technology to visualize and provide information about the body to diagnose, treat, or monitor medical conditions. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001097 medical imaging evidence A type of imaging assay evidence resulting from the use of technology to visualize and provide information about the body to diagnose, treat, or monitor medical conditions. url:http://www.fda.gov/Radiation-EmittingProducts/RadiationEmittingProductsandProcedures/MedicalImaging/ucm2005914.htm A type of direct assay evidence where a microscope was used to view a sample. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001098 microscopy evidence A type of direct assay evidence where a microscope was used to view a sample. ECO:MCC SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001099 motility wound healing assay evidence A type of metabolic cell proliferation assay evidence resulting from 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) in combination with phenazine methyl sulfate (PMS) as an intermediate electron acceptor reagent to produce a soluble formazan dye in viable cells. SIB:PG mchibucos 2014-03-16T11:30:54Z 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium eco ECO:0001100 MTS assay evidence A type of metabolic cell proliferation assay evidence resulting from 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) in combination with phenazine methyl sulfate (PMS) as an intermediate electron acceptor reagent to produce a soluble formazan dye in viable cells. NBK:144065 PMID:1867954 A type of metabolic cell proliferation assay evidence resulting from the reduction of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) to its insoluble purple formazan dye in viable cells. SIB:PG mchibucos 2014-03-16T11:30:54Z 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide eco ECO:0001101 MTT assay evidence A type of metabolic cell proliferation assay evidence resulting from the reduction of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) to its insoluble purple formazan dye in viable cells. NBK:144065 PMID:6606682 A type of protein detection assay evidence resulting from determination of analyte concentration by fluorescent bead sets attached to an antibody (to a specific analyte) with a fluorescent reporter dye label attached to a second antibody (to a specific analyte). SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001102 multiplex bead-based immunoassay evidence A type of protein detection assay evidence resulting from determination of analyte concentration by fluorescent bead sets attached to an antibody (to a specific analyte) with a fluorescent reporter dye label attached to a second antibody (to a specific analyte). PMC:1534009 A type of experimental phenotypic evidence resulting from the observation of the impact of a natural mutation on the expressed traits. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001103 natural variation mutant evidence A type of experimental phenotypic evidence resulting from the observation of the impact of a natural mutation on the expressed traits. ECO:RCT A type of apoptotic assay evidence resulting from the nuclei fragmenting into smaller pieces during programmed cell death. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001104 nuclear fragmentation evidence A type of apoptotic assay evidence resulting from the nuclei fragmenting into smaller pieces during programmed cell death. PMID:16738861 A type of structure determination evidence resulting from the use of an MRI to provide chemical information about tissue metabolites. SIB:PG mchibucos 2014-03-16T11:30:54Z NMR spectroscopy eco ECO:0001105 nuclear magnetic resonance spectroscopy evidence A type of structure determination evidence resulting from the use of an MRI to provide chemical information about tissue metabolites. PMID:16428685 A type of RNA detection assay evidence resulting from the detection and quantitation of specific RNAs (from a sample of total cellular RNA) that are bound by antisense RNA or DNA probes and therefore protected from nucleases. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001106 nuclease protection assay evidence A type of RNA detection assay evidence resulting from the detection and quantitation of specific RNAs (from a sample of total cellular RNA) that are bound by antisense RNA or DNA probes and therefore protected from nucleases. PMID:17486122 PMID:18428580 A type of DNA synthesis cell proliferation assay evidence resulting from the analysis and measurement of the incorporation of nucleotide analog(s) into the DNA. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001107 nucleotide analog incorporation evidence A type of DNA synthesis cell proliferation assay evidence resulting from the analysis and measurement of the incorporation of nucleotide analog(s) into the DNA. PMC:3149870 A type of protein binding evidence resulting from the panning of a phage library where the individual phage displayed a different peptide or protein by fusion to coat proteins on the capsid. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001108 phage display evidence A type of protein binding evidence resulting from the panning of a phage library where the individual phage displayed a different peptide or protein by fusion to coat proteins on the capsid. MI:0084 PMID:11680867 A type of protein assay evidence resulting from the identification of the phosphorylated residue in a protein by amino acid analysis. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001109 phosphoamino acid analysis evidence A type of protein assay evidence resulting from the identification of the phosphorylated residue in a protein by amino acid analysis. PMID:11680867 PMID:18429115 SIB:PG mchibucos 2014-03-16T11:30:54Z phosphopeptide affinity enrichment evidence eco ECO:0001110 peptide affinity enrichment evidence A type of direct assay evidence resulting from the physical examination and measurement of the feature of a subject or sample. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001111 physical examination evidence A type of direct assay evidence resulting from the physical examination and measurement of the feature of a subject or sample. ECO:RCT A type of protein assay evidence resulting from protein-bound peptides detected from a collection of peptides arranged as an array and incubated with the partner protein in order to map protein-protein interaction sites. SIB:PG mchibucos 2014-03-16T11:30:54Z phosphopeptide array evidence eco ECO:0001112 peptide array evidence A type of protein assay evidence resulting from protein-bound peptides detected from a collection of peptides arranged as an array and incubated with the partner protein in order to map protein-protein interaction sites. PMID:21243154 A type of experimental phenotypic evidence resulting from the change in a single nucleotide. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001113 point mutation evidence A type of experimental phenotypic evidence resulting from the change in a single nucleotide. SO:1000008 A type of staining evidence resulting from the binding and labeling of DNA (during apoptosis, when there is a loss of nuclear DNA content) with propidium iodide (PI) to identify the cells from which it originated. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001114 propidium iodide staining evidence A type of staining evidence resulting from the binding and labeling of DNA (during apoptosis, when there is a loss of nuclear DNA content) with propidium iodide (PI) to identify the cells from which it originated. PMID:17406435 A type of direct assay evidence resulting from the analysis of a molecule by its intrinsic fluorescence, or by attaching it with a fluorophore. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001115 fluorescence evidence A type of direct assay evidence resulting from the analysis of a molecule by its intrinsic fluorescence, or by attaching it with a fluorophore. url:http://www.nature.com/subjects/biological-fluorescence A type of protein detection assay evidence resulting from protein samples immobilized on a membrane, then subsequently incubated and imaged. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001116 protein dot blot assay evidence A type of protein detection assay evidence resulting from protein samples immobilized on a membrane, then subsequently incubated and imaged. doi:10.1007/978-94-009-0951-9_24 A type of protein detection assay evidence resulting from proteins immobilized to prepare protein chips, or microwells, that can be utilized to determine presence of proteins, monitor differential expression profiles, and/or study protein interactions. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001117 protein microarray evidence A type of protein detection assay evidence resulting from proteins immobilized to prepare protein chips, or microwells, that can be utilized to determine presence of proteins, monitor differential expression profiles, and/or study protein interactions. PMC:1828913 A type of sequencing assay evidence resulting from determining the sequence of amino acids in a protein. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001118 protein sequencing assay evidence A type of sequencing assay evidence resulting from determining the sequence of amino acids in a protein. ERO:0001287 A type of mass spectrometry evidence resulting from quantitative analysis of peptides, proteins, and proteomes. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001119 quantitative mass spectrometry evidence A type of mass spectrometry evidence resulting from quantitative analysis of peptides, proteins, and proteomes. PMID:22665296 A type of direct assay evidence resulting from the assessment of biological reactions by use of a radioactive isotope to label the reactant. SIB:PG mchibucos 2014-03-16T11:30:54Z radioassay radioisotopic assay eco ECO:0001120 radioisotope assay evidence A type of direct assay evidence resulting from the assessment of biological reactions by use of a radioactive isotope to label the reactant. ISBN:978-3-642-50036-7 A type of protein detection assay evidence resulting from the use of a radioligand to measure the binding of a substance to a specific antibody or other receptor system. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001121 radioimmunoassay evidence A type of protein detection assay evidence resulting from the use of a radioligand to measure the binding of a substance to a specific antibody or other receptor system. MeSH:D011863 A type of direct assay evidence from the analysis of the real-time interaction between an analyte in solution and its interactant linked to the surface of the resonant mirror. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001123 resonant mirror biosensor evidence A type of direct assay evidence from the analysis of the real-time interaction between an analyte in solution and its interactant linked to the surface of the resonant mirror. PMID:19151938 A type of DNA detection assay evidence resulting from homologous DNA fragments digested by restriction enzymes, and the resulting restriction fragments are sorted by length to illustrate differences. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001124 restriction fragment detection evidence A type of DNA detection assay evidence resulting from homologous DNA fragments digested by restriction enzymes, and the resulting restriction fragments are sorted by length to illustrate differences. doi:10.1007/978-94-009-0951-9_24 url:http://www.ncbi.nlm.nih.gov/probe/docs/techrflp/ A type of spectrometry evidence resulting from the evaluation of a molecule in a fluid by its ability to alter the transmission of light at specific wavelengths. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001126 spectrophotometry evidence A type of spectrometry evidence resulting from the evaluation of a molecule in a fluid by its ability to alter the transmission of light at specific wavelengths. MMO:0000173 A type of physical interaction evidence based on real-time, rapid plasmon generation on the interface between a planar surface and vacuum that measures changes in refractive index close to the sensor surface when an analyte and its immobilized ligand bind to observe and characterize molecular interaction. SIB:PG mchibucos 2014-03-16T11:30:54Z SPR evidence eco ECO:0001127 Plasmons are generated by an incident light beam. surface plasmon resonance evidence A type of physical interaction evidence based on real-time, rapid plasmon generation on the interface between a planar surface and vacuum that measures changes in refractive index close to the sensor surface when an analyte and its immobilized ligand bind to observe and characterize molecular interaction. ECO:SW PMID:11578932 PMID:19151937 PMID:8574707 SPR evidence PMID:11578932 A type of experimental phenotypic evidence resulting from a transplantation in which the transplanted material (stem cells) is from an individual's identical twin. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001128 syngeneic transplantation experiment evidence A type of experimental phenotypic evidence resulting from a transplantation in which the transplanted material (stem cells) is from an individual's identical twin. PMID:18469352 A type of enzyme assay evidence resulting from the analysis of tumor necrosis factor (TNF)-a converting enzyme (TACE), which releases a soluble TNF-a from the membrane-bound precursor protein. SIB:PG mchibucos 2014-03-16T11:30:54Z Tumor necrosis factor - alpha converting enzyme activity assay eco ECO:0001129 TACE activity assay evidence A type of enzyme assay evidence resulting from the analysis of tumor necrosis factor (TNF)-a converting enzyme (TACE), which releases a soluble TNF-a from the membrane-bound precursor protein. PMC:1808921 A type of cytochemistry evidence resulting from the analysis of section(s) of a paraffin block containing embedded tissues cores arranged in an array pattern. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001130 tissue microarray evidence A type of cytochemistry evidence resulting from the analysis of section(s) of a paraffin block containing embedded tissues cores arranged in an array pattern. PMID:11770905 A type of genetic transformation evidence resulting from an organism that has had its expressed phenotype altered by modification. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001131 transgenic organism evidence A type of genetic transformation evidence resulting from an organism that has had its expressed phenotype altered by modification. OBI:1000048 A type of mass spectrometry evidence resulting from the analysis of prepared phosphopeptides separated in two dimensions on a TLC plate. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001132 tryptic phosphopeptide mapping assay evidence A type of mass spectrometry evidence resulting from the analysis of prepared phosphopeptides separated in two dimensions on a TLC plate. PMID:18429120 A type of apoptotic assay evidence resulting from the visualization of DNA fragmentation by detection of exposed 3'-OH ends, localized by terminal deoxynucleotidyl transferase (TdT) which then catalyzes the addition of labeled dUTPs. SIB:PG mchibucos 2014-03-16T11:30:54Z TUNEL assay evidence TdT-mediated dUTP-biotin nick end labeling assay terminal deoxynucleotidyl transferase-dUTP nick end labeling assay evidence eco ECO:0001133 terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence A type of apoptotic assay evidence resulting from the visualization of DNA fragmentation by detection of exposed 3'-OH ends, localized by terminal deoxynucleotidyl transferase (TdT) which then catalyzes the addition of labeled dUTPs. PMID:22566045 A type of direct assay evidence resulting from the analysis of a urine sample. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001134 urine test evidence A type of direct assay evidence resulting from the analysis of a urine sample. ECO:RCT A type of in vitro assay evidence resulting from the creation of a wound in a cell monolayer, then capturing images at regular intervals to observe directional cell migration during the closure of the wound. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001135 wound healing assay evidence A type of in vitro assay evidence resulting from the creation of a wound in a cell monolayer, then capturing images at regular intervals to observe directional cell migration during the closure of the wound. PMID:15576902 A type of metabolic cell proliferation assay evidence resulting from the assessment of metabolic activity from a water-soluble tetrazolium salt WST-1 being reduced outside the cell (by reacting with mitochondrial succinate-tetrazolium reductase) to form a formazan dye. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001136 WST-1 assay evidence A type of metabolic cell proliferation assay evidence resulting from the assessment of metabolic activity from a water-soluble tetrazolium salt WST-1 being reduced outside the cell (by reacting with mitochondrial succinate-tetrazolium reductase) to form a formazan dye. PMID:18417231 A type of anatomical perturbation evidence where live cells, tissues, or organs from a non-human animal source are transplanted, implanted or infused into a human recipient. SIB:PG mchibucos 2014-03-16T11:30:54Z Xenograft transplantation Xenografting Xenotransplantation tissue grafting eco ECO:0001137 xenotransplantation experiment evidence A type of anatomical perturbation evidence where live cells, tissues, or organs from a non-human animal source are transplanted, implanted or infused into a human recipient. ECO:SN url:http://ilarjournal.oxfordjournals.org/content/37/1/16.full.pdf+html url:http://www.fda.gov/BiologicsBloodVaccines/Xenotransplantation/ A type of 3D cell culture evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T15:18:35Z eco ECO:0001138 3D cell culture evidence used in manual assertion true true A type of 3D cell culture evidence that is used in a manual assertion. ECO:MCC A type of 51Cr release assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T15:20:55Z eco ECO:0001139 51Cr release assay evidence used in manual assertion true true A type of 51Cr release assay evidence that is used in a manual assertion. ECO:MCC A type of 7-aminoactinomycin staining evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T15:22:01Z eco ECO:0001140 7-aminoactinomycin staining evidence used in manual assertion true true A type of 7-aminoactinomycin staining evidence that is used in a manual assertion. ECO:MCC A type of [3H]-thymidine incorporation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T15:31:52Z eco ECO:0001141 [3H]-thymidine incorporation assay evidence used in manual assertion true true A type of [3H]-thymidine incorporation assay evidence that is used in a manual assertion. ECO:MCC A type of [3H]arachidonic acid release assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T15:32:44Z eco ECO:0001142 [3H]arachidonic acid release assay evidence used in manual assertion true true A type of [3H]arachidonic acid release assay evidence that is used in a manual assertion. ECO:MCC A type of adhesion assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T15:33:38Z eco ECO:0001143 adhesion assay evidence used in manual assertion true true A type of adhesion assay evidence that is used in a manual assertion. ECO:MCC A type of adoptive cell transfer evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T15:36:19Z eco ECO:0001144 adoptive cell transfer evidence used in manual assertion true true A type of adoptive cell transfer evidence that is used in a manual assertion. ECO:MCC A type of Alamar blue assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T15:37:21Z eco ECO:0001145 Alamar blue assay evidence used in manual assertion true true A type of Alamar blue assay evidence that is used in a manual assertion. ECO:MCC A type of allograft transplantation experiment evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T15:38:22Z eco ECO:0001146 allograft transplantation experiment evidence used in manual assertion true true A type of allograft transplantation experiment evidence that is used in a manual assertion. ECO:MCC A type of anion-exchange chromatography evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T15:44:30Z eco ECO:0001147 anion-exchange chromatography evidence used in manual assertion true true A type of anion-exchange chromatography evidence that is used in a manual assertion. ECO:MCC A type of annexin-V staining evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T15:52:01Z eco ECO:0001148 annexin-V staining evidence used in manual assertion true true A type of annexin-V staining evidence that is used in a manual assertion. ECO:MCC A type of behavioral assay evidence used that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T15:53:38Z eco ECO:0001149 behavioral assay evidence used in manual assertion true true A type of behavioral assay evidence used that is used in a manual assertion. ECO:MCC A type of blocking monoclonal antibody evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T15:54:44Z eco ECO:0001150 blocking monoclonal antibody evidence used in manual assertion true true A type of blocking monoclonal antibody evidence that is used in a manual assertion. ECO:MCC A type of blocking peptide evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T15:55:33Z eco ECO:0001151 blocking peptide evidence used in manual assertion true true A type of blocking peptide evidence that is used in a manual assertion. ECO:MCC A type of blocking polyclonal antibody evidence tthat is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:01:39Z eco ECO:0001152 blocking polyclonal antibody evidence used in manual assertion true true A type of blocking polyclonal antibody evidence tthat is used in a manual assertion. ECO:MCC A type of blood test evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:02:47Z eco ECO:0001153 blood test evidence used in manual assertion true true A type of blood test evidence that is used in a manual assertion. ECO:MCC A type of Boyden chamber assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:03:53Z eco ECO:0001154 Boyden chamber assay evidence used in manual assertion true true A type of Boyden chamber assay evidence that is used in a manual assertion. ECO:MCC A type of BrdU incorporation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:04:49Z eco ECO:0001155 bromodeoxyuridine incorporation assay evidence used in manual assertion true true A type of BrdU incorporation assay evidence that is used in a manual assertion. ECO:MCC A type of caspase assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:06:06Z eco ECO:0001156 caspase assay evidence used in manual assertion true true A type of caspase assay evidence that is used in a manual assertion. ECO:MCC A type of cell counting evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:07:13Z eco ECO:0001157 cell counting evidence used in manual assertion true true A type of cell counting evidence that is used in a manual assertion. ECO:MCC A type of cell permeability assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:07:58Z eco ECO:0001158 cell permeability assay evidence used in manual assertion true true A type of cell permeability assay evidence that is used in a manual assertion. ECO:MCC A type of carboxyfluorescein diacetate succinimidyl ester staining evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:08:54Z eco ECO:0001159 carboxyfluorescein diacetate succinimidyl ester staining evidence used in manual assertion true true A type of carboxyfluorescein diacetate succinimidyl ester staining evidence that is used in a manual assertion. ECO:MCC A type of chemiluminescence-linked immunoassay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:09:55Z eco ECO:0001160 chemiluminescence-linked immunoassay evidence used in manual assertion true true A type of chemiluminescence-linked immunoassay evidence that is used in a manual assertion. ECO:MCC A type of chimeric protein evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:10:40Z eco ECO:0001161 chimeric protein evidence used in manual assertion true true A type of chimeric protein evidence that is used in a manual assertion. ECO:MCC A type of co-electrophoresis evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:11:22Z eco ECO:0001162 co-electrophoresis evidence used in manual assertion true true A type of co-electrophoresis evidence that is used in a manual assertion. ECO:MCC A type of co-localization evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:12:04Z eco ECO:0001163 co-localization evidence used in manual assertion true true A type of co-localization evidence that is used in a manual assertion. ECO:MCC A type of co-sedimentation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:12:55Z eco ECO:0001164 co-sedimentation assay evidence used in manual assertion true true A type of co-sedimentation assay evidence that is used in a manual assertion. ECO:MCC A type of colony counting evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:14:57Z eco ECO:0001165 colony counting evidence used in manual assertion true true A type of colony counting evidence that is used in a manual assertion. ECO:MCC A type of comet assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:16:01Z eco ECO:0001166 comet assay evidence used in manual assertion true true A type of comet assay evidence that is used in a manual assertion. ECO:MCC A type of conditional knockin evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:17:22Z eco ECO:0001167 conditional knockin evidence used in manual assertion true true A type of conditional knockin evidence that is used in a manual assertion. ECO:MCC A type of conditional knockout evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:17:58Z eco ECO:0001168 conditional knockout evidence used in manual assertion true true A type of conditional knockout evidence that is used in a manual assertion. ECO:MCC A type of constitutively active mutant evidence that is used a in manual assertion. SIB:PG mchibucos 2014-03-17T16:20:23Z eco ECO:0001169 constitutively active mutant evidence used in manual assertion true true A type of constitutively active mutant evidence that is used a in manual assertion. ECO:MCC A type of cross-linking evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:21:29Z eco ECO:0001170 cross-linking evidence used in manual assertion true true A type of cross-linking evidence that is used in a manual assertion. ECO:MCC A type of crystallography evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:22:20Z eco ECO:0001171 crystallography evidence used in manual assertion true true A type of crystallography evidence that is used in a manual assertion. ECO:MCC A type of cytochemistry evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:23:10Z eco ECO:0001172 cytochemistry evidence used in manual assertion true true A type of cytochemistry evidence that is used in a manual assertion. ECO:MCC A type of cytochrome C release assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:23:53Z eco ECO:0001173 cytochrome C release assay evidence used in manual assertion true true A type of cytochrome C release assay evidence that is used in a manual assertion. ECO:MCC A type of 4',6-diamidino-2-phenylindole staining evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:25:03Z eco ECO:0001174 4',6-diamidino-2-phenylindole staining evidence used in manual assertion true true A type of 4',6-diamidino-2-phenylindole staining evidence that is used in a manual assertion. ECO:MCC A type of deletion evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:25:54Z eco ECO:0001175 deletion mutation evidence used in manual assertion true true A type of deletion evidence that is used in a manual assertion. ECO:MCC A type of DNA laddering assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:26:46Z eco ECO:0001176 DNA laddering assay evidence used in manual assertion true true A type of DNA laddering assay evidence that is used in a manual assertion. ECO:MCC A type of RNA dot blot assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:45:52Z eco ECO:0001177 RNA dot blot assay evidence used in manual assertion true true A type of RNA dot blot assay evidence that is used in a manual assertion. ECO:MCC A type of dominant-negative mutant evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:47:44Z eco ECO:0001179 dominant-negative mutant evidence used in manual assertion true true A type of dominant-negative mutant evidence that is used in a manual assertion. ECO:MCC A type of eTag assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:59:39Z eco ECO:0001180 eTag assay evidence used in manual assertion true true A type of eTag assay evidence that is used in a manual assertion. ECO:MCC A type of filter binding assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:03:28Z eco ECO:0001181 filter binding assay evidence used in manual assertion true true A type of filter binding assay evidence that is used in a manual assertion. ECO:MCC A type of fluorescence in situ hybridization evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:04:20Z eco ECO:0001182 fluorescence in situ hybridization evidence used in manual assertion true true A type of fluorescence in situ hybridization evidence that is used in a manual assertion. ECO:MCC A type of fluorescence resonance energy transfer evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:05:22Z eco ECO:0001183 fluorescence resonance energy transfer evidence used in manual assertion true true A type of fluorescence resonance energy transfer evidence that is used in a manual assertion. ECO:MCC A type of gel-filtration evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:06:14Z eco ECO:0001184 gel-filtration evidence used in manual assertion true true A type of gel-filtration evidence that is used in a manual assertion. ECO:MCC A type of histochemistry evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:07:19Z eco ECO:0001185 histochemistry evidence used in manual assertion true true A type of histochemistry evidence that is used in a manual assertion. ECO:MCC A type of immunocytochemistry evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:12:39Z eco ECO:0001186 immunocytochemistry evidence used in manual assertion true true A type of immunocytochemistry evidence that is used in a manual assertion. ECO:MCC A type of histology evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:09:50Z eco ECO:0001187 histology evidence used in manual assertion true true A type of histology evidence that is used in a manual assertion. ECO:MCC A type of immunodepletion evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:16:19Z eco ECO:0001188 immunodepletion evidence used in manual assertion true true A type of immunodepletion evidence that is used in a manual assertion. ECO:MCC A type of immunohistochemistry evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:17:22Z eco ECO:0001189 immunohistochemistry evidence used in manual assertion true true A type of immunohistochemistry evidence that is used in a manual assertion. ECO:MCC A type of in vitro acetylation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:19:24Z eco ECO:0001190 in vitro acetylation assay evidence used in manual assertion true true A type of in vitro acetylation assay evidence that is used in a manual assertion. ECO:MCC A type of in vitro cleavage assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:21:22Z eco ECO:0001191 in vitro cleavage assay evidence used in manual assertion true true A type of in vitro cleavage assay evidence that is used in a manual assertion. ECO:MCC A type of in vitro deacetylation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:23:42Z eco ECO:0001192 in vitro deacetylation assay evidence used in manual assertion true true A type of in vitro deacetylation assay evidence that is used in a manual assertion. ECO:MCC A type of in vitro defarnesylation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:25:45Z eco ECO:0001193 in vitro defarnesylation assay evidence used in manual assertion true true A type of in vitro defarnesylation assay evidence that is used in a manual assertion. ECO:MCC A type of in vitro demethylation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:27:00Z eco ECO:0001194 in vitro demethylation assay evidence used in manual assertion true true A type of in vitro demethylation assay evidence that is used in a manual assertion. ECO:MCC A type of in vitro desumoylation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:29:01Z eco ECO:0001195 in vitro desumoylation assay evidence used in manual assertion true true A type of in vitro desumoylation assay evidence that is used in a manual assertion. ECO:MCC A type of in vitro deubiquitination assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:29:48Z eco ECO:0001196 in vitro deubiquitination assay evidence used in manual assertion true true A type of in vitro deubiquitination assay evidence that is used in a manual assertion. ECO:MCC A type of in vitro farnesylation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:30:50Z eco ECO:0001197 in vitro farnesylation assay evidence used in manual assertion true true A type of in vitro farnesylation assay evidence that is used in a manual assertion. ECO:MCC A type of in vitro methylation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:31:54Z eco ECO:0001198 in vitro methylation assay evidence used in manual assertion true true A type of in vitro methylation assay evidence that is used in a manual assertion. ECO:MCC A type of in vitro palmitoylation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:32:57Z eco ECO:0001199 in vitro palmitoylation assay evidence used in manual assertion true true A type of in vitro palmitoylation assay evidence that is used in a manual assertion. ECO:MCC A type of in vitro phosphatase assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:34:16Z eco ECO:0001200 in vitro phosphatase assay evidence used in manual assertion true true A type of in vitro phosphatase assay evidence that is used in a manual assertion. ECO:MCC A type of in vitro polyADP-ribosylation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:34:57Z eco ECO:0001201 in vitro polyADP-ribosylation assay evidence used in manual assertion true true A type of in vitro polyADP-ribosylation assay evidence that is used in a manual assertion. ECO:MCC A type of in vitro protein kinase assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:39:57Z eco ECO:0001202 in vitro protein kinase assay evidence used in manual assertion true true A type of in vitro protein kinase assay evidence that is used in a manual assertion. ECO:MCC A type of in vitro sumoylation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:41:25Z eco ECO:0001203 in vitro sumoylation assay evidence used in manual assertion true true A type of in vitro sumoylation assay evidence that is used in a manual assertion. ECO:MCC A type of in vitro transcription assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:44:40Z eco ECO:0001204 in vitro transcription assay evidence used in manual assertion true true A type of in vitro transcription assay evidence that is used in a manual assertion. ECO:MCC A type of in vitro translation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:46:30Z eco ECO:0001205 in vitro translation assay evidence used in manual assertion true true A type of in vitro translation assay evidence that is used in a manual assertion. ECO:MCC A type of in vitro ubiquitination assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:47:18Z eco ECO:0001206 in vitro ubiquitination assay evidence used in manual assertion true true A type of in vitro ubiquitination assay evidence that is used in a manual assertion. ECO:MCC A type of in vivo acetylation assay evidence that is used in manual assertion. SIB:PG mchibucos 2014-03-17T17:48:56Z eco ECO:0001207 in vivo acetylation assay evidence used in manual assertion true true A type of in vivo acetylation assay evidence that is used in manual assertion. ECO:MCC A type of in vivo cleavage assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:49:43Z eco ECO:0001208 in vivo cleavage assay evidence used in manual assertion true true A type of in vivo cleavage assay evidence that is used in a manual assertion. ECO:MCC A type of in vivo deacetylation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:50:47Z eco ECO:0001209 in vivo deacetylation assay evidence used in manual assertion true true A type of in vivo deacetylation assay evidence that is used in a manual assertion. ECO:MCC A type of in vivo defarnesylation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:52:41Z eco ECO:0001210 in vivo defarnesylation assay evidence used in manual assertion true true A type of in vivo defarnesylation assay evidence that is used in a manual assertion. ECO:MCC A type of in vivo demethylation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:53:40Z eco ECO:0001211 in vivo demethylation assay evidence used in manual assertion true true A type of in vivo demethylation assay evidence that is used in a manual assertion. ECO:MCC A type of in vivo desumoylation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:54:36Z eco ECO:0001212 in vivo desumoylation assay evidence used in manual assertion true true A type of in vivo desumoylation assay evidence that is used in a manual assertion. ECO:MCC A type of in vivo deubiquitination assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:56:28Z eco ECO:0001213 in vivo deubiquitination assay evidence used in manual assertion true true A type of in vivo deubiquitination assay evidence that is used in a manual assertion. ECO:MCC A type of in vivo farnesylation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:57:18Z eco ECO:0001214 in vivo farnesylation assay evidence used in manual assertion true true A type of in vivo farnesylation assay evidence that is used in a manual assertion. ECO:MCC A type of in vivo methylation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T18:03:16Z eco ECO:0001215 in vivo methylation assay evidence used in manual assertion true true A type of in vivo methylation assay evidence that is used in a manual assertion. ECO:MCC A type of in vivo palmitoylation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T18:04:07Z eco ECO:0001216 in vivo palmitoylation assay evidence used in manual assertion true true A type of in vivo palmitoylation assay evidence that is used in a manual assertion. ECO:MCC A type of in vivo phosphatase assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T18:06:08Z eco ECO:0001217 in vivo phosphatase assay evidence used in manual assertion true true A type of in vivo phosphatase assay evidence that is used in a manual assertion. ECO:MCC A type of in vivo protein kinase assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T18:07:58Z eco ECO:0001218 in vivo protein kinase assay evidence used in manual assertion true true A type of in vivo protein kinase assay evidence that is used in a manual assertion. ECO:MCC A type of in vivo sumoylation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T18:09:49Z eco ECO:0001219 in vivo sumoylation assay evidence used in manual assertion true true A type of in vivo sumoylation assay evidence that is used in a manual assertion. ECO:MCC A type of in vivo transcription assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T18:11:20Z eco ECO:0001220 in vivo transcription assay evidence used in manual assertion true true A type of in vivo transcription assay evidence that is used in a manual assertion. ECO:MCC A type of in vivo translation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T18:42:50Z eco ECO:0001221 in vivo translation assay evidence used in manual assertion true true A type of in vivo translation assay evidence that is used in a manual assertion. ECO:MCC A type of in vivo ubiquitination assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T18:44:11Z eco ECO:0001222 in vivo ubiquitination assay evidence used in manual assertion true true A type of in vivo ubiquitination assay evidence that is used in a manual assertion. ECO:MCC A type of induced mutation evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T18:45:56Z eco ECO:0001223 induced mutation evidence used in manual assertion true true A type of induced mutation evidence that is used in a manual assertion. ECO:MCC A type of knockin evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T18:49:35Z eco ECO:0001224 knockin evidence used in manual assertion true true A type of knockin evidence that is used in a manual assertion. ECO:MCC A type of knockout evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T18:51:31Z eco ECO:0001225 knockout evidence used in manual assertion true true A type of knockout evidence that is used in a manual assertion. ECO:MCC A type of lipid binding assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T18:52:19Z eco ECO:0001226 lipid binding assay evidence used in manual assertion true true A type of lipid binding assay evidence that is used in a manual assertion. ECO:MCC A type of LUMIER assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T18:55:16Z eco ECO:0001227 luminescence-based mammalian interactome mapping assay evidence used in manual assertion true true A type of LUMIER assay evidence that is used in a manual assertion. ECO:MCC A type of macroscopy evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T18:56:21Z eco ECO:0001228 macroscopy evidence used in manual assertion true true A type of macroscopy evidence that is used in a manual assertion. ECO:MCC A type of mammalian 2-hybrid assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T18:57:25Z eco ECO:0001229 mammalian 2-hybrid assay evidence used in manual assertion true true A type of mammalian 2-hybrid assay evidence that is used in a manual assertion. ECO:MCC A type of mass spectrometry evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T18:59:50Z eco ECO:0001230 mass spectrometry evidence used in manual assertion true true A type of mass spectrometry evidence that is used in a manual assertion. ECO:MCC A type of medical imaging evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T19:04:43Z eco ECO:0001231 medical imaging evidence used in manual assertion true true A type of medical imaging evidence that is used in a manual assertion. ECO:MCC A type of microscopy evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T19:05:37Z eco ECO:0001232 microscopy evidence used in manual assertion true true A type of microscopy evidence that is used in a manual assertion. ECO:MCC A type of motility wound healing assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T19:08:13Z eco ECO:0001233 motility wound healing assay evidence used in manual assertion true true A type of motility wound healing assay evidence that is used in a manual assertion. ECO:MCC A type of MTS assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T19:08:51Z eco ECO:0001234 MTS assay evidence used in manual assertion true true A type of MTS assay evidence that is used in a manual assertion. ECO:MCC A type of MTT assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T19:13:17Z eco ECO:0001235 MTT assay evidence used in manual assertion true true A type of MTT assay evidence that is used in a manual assertion. ECO:MCC A type of multiplex bead-based immunoassay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T19:14:03Z eco ECO:0001236 multiplex bead-based immunoassay evidence used in manual assertion true true A type of multiplex bead-based immunoassay evidence that is used in a manual assertion. ECO:MCC A type of natural variation mutant evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T19:15:48Z eco ECO:0001237 natural variation mutant evidence used in manual assertion true true A type of natural variation mutant evidence that is used in a manual assertion. ECO:MCC A type of nuclear magnetic resonance spectroscopy evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T19:18:50Z eco ECO:0001238 nuclear magnetic resonance spectroscopy evidence used in manual assertion true true A type of nuclear magnetic resonance spectroscopy evidence that is used in a manual assertion. ECO:MCC A type of nuclear fragmentation evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T19:19:55Z eco ECO:0001239 nuclear fragmentation evidence used in manual assertion true true A type of nuclear fragmentation evidence that is used in a manual assertion. ECO:MCC A type of nuclease protection assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T19:23:41Z eco ECO:0001240 nuclease protection assay evidence used in manual assertion true true A type of nuclease protection assay evidence that is used in a manual assertion. ECO:MCC A type of nucleotide analog incorporation evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T19:25:17Z eco ECO:0001241 nucleotide analog incorporation evidence used in manual assertion true true A type of nucleotide analog incorporation evidence that is used in a manual assertion. ECO:MCC A type of phage display evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T19:27:17Z eco ECO:0001242 phage display evidence used in manual assertion true true A type of phage display evidence that is used in a manual assertion. ECO:MCC A type of phosphoamino acid analysis evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T19:28:59Z eco ECO:0001243 phosphoamino acid analysis evidence used in manual assertion true true A type of phosphoamino acid analysis evidence that is used in a manual assertion. ECO:MCC A type of peptide affinity enrichment evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T19:30:13Z eco ECO:0001244 peptide affinity enrichment evidence used in manual assertion true true A type of peptide affinity enrichment evidence that is used in a manual assertion. ECO:MCC A type of peptide array evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:16:45Z eco ECO:0001245 peptide array evidence used in manual assertion true true A type of peptide array evidence that is used in a manual assertion. ECO:MCC A type of physical examination evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:17:27Z eco ECO:0001246 physical examination evidence used in manual assertion true true A type of physical examination evidence that is used in a manual assertion. ECO:MCC A type of point mutation evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:18:10Z eco ECO:0001247 point mutation evidence used in manual assertion true true A type of point mutation evidence that is used in a manual assertion. ECO:MCC A type of propidium iodide staining evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:18:58Z eco ECO:0001248 propidium iodide staining evidence used in manual assertion true true A type of propidium iodide staining evidence that is used in a manual assertion. ECO:MCC A type of protein detection by fluorescence evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:19:35Z eco ECO:0001249 fluorescence evidence used in manual assertion true true A type of protein detection by fluorescence evidence that is used in a manual assertion. ECO:MCC A type of protein dot blot assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:20:30Z eco ECO:0001250 protein dot blot assay evidence used in manual assertion true true A type of protein dot blot assay evidence that is used in a manual assertion. ECO:MCC A type of protein microarray evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:21:11Z eco ECO:0001251 protein microarray evidence used in manual assertion true true A type of protein microarray evidence that is used in a manual assertion. ECO:MCC A type of protein sequencing assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:22:08Z eco ECO:0001252 protein sequencing assay evidence used in manual assertion true true A type of protein sequencing assay evidence that is used in a manual assertion. ECO:MCC A type of quantitative mass spectrometry evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:23:15Z eco ECO:0001253 quantitative mass spectrometry evidence used in manual assertion true true A type of quantitative mass spectrometry evidence that is used in a manual assertion. ECO:MCC A type of radioisotope assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:27:05Z eco ECO:0001254 radioisotope assay evidence used in manual assertion true true A type of radioisotope assay evidence that is used in a manual assertion. ECO:MCC A type of radioimmunoassay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:28:04Z eco ECO:0001255 radioimmunoassay evidence used in manual assertion true true A type of radioimmunoassay evidence that is used in a manual assertion. ECO:MCC A type of imaging assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:29:00Z eco ECO:0001256 imaging assay evidence used in manual assertion true true A type of imaging assay evidence that is used in a manual assertion. ECO:MCC A type of restriction fragment detection evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:29:05Z eco ECO:0001257 restriction fragment detection evidence used in manual assertion true true A type of restriction fragment detection evidence that is used in a manual assertion. ECO:MCC A type of spectrophotometry evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:29:09Z eco ECO:0001258 spectrophotometry evidence used in manual assertion true true A type of spectrophotometry evidence that is used in a manual assertion. ECO:MCC A type of syngeneic transplantation experiment evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:29:13Z eco ECO:0001259 syngeneic transplantation experiment evidence used in manual assertion true true A type of syngeneic transplantation experiment evidence that is used in a manual assertion. ECO:MCC A type of xenotransplantation experiment evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:29:18Z eco ECO:0001260 xenotransplantation experiment evidence used in manual assertion true true A type of xenotransplantation experiment evidence that is used in a manual assertion. ECO:MCC A type of WST-1 assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:29:22Z eco ECO:0001261 WST-1 assay evidence used in manual assertion true true A type of WST-1 assay evidence that is used in a manual assertion. ECO:MCC A type of wound healing assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:29:26Z eco ECO:0001262 wound healing assay evidence used in manual assertion true true A type of wound healing assay evidence that is used in a manual assertion. ECO:MCC A type of urine test evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:29:30Z eco ECO:0001263 urine test evidence used in manual assertion true true A type of urine test evidence that is used in a manual assertion. ECO:MCC A type of TUNEL assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:29:34Z eco ECO:0001264 terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence used in manual assertion true true A type of TUNEL assay evidence that is used in a manual assertion. ECO:MCC A type of tryptic phosphopeptide mapping assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:29:38Z eco ECO:0001265 tryptic phosphopeptide mapping assay evidence used in manual assertion true true A type of tryptic phosphopeptide mapping assay evidence that is used in a manual assertion. ECO:MCC A type of transgenic organism evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:29:41Z eco ECO:0001266 transgenic organism evidence used in manual assertion true true A type of transgenic organism evidence that is used in a manual assertion. ECO:MCC A type of tissue microarray evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:29:45Z eco ECO:0001267 tissue microarray evidence used in manual assertion true true A type of tissue microarray evidence that is used in a manual assertion. ECO:MCC A type of TACE activity assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:29:49Z eco ECO:0001268 TACE activity assay evidence used in manual assertion true true A type of TACE activity assay evidence that is used in a manual assertion. ECO:MCC A type of surface plasmon resonance evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:29:54Z eco ECO:0001269 surface plasmon resonance evidence used in manual assertion true true A type of surface plasmon resonance evidence that is used in a manual assertion. ECO:MCC A type of restriction landmark genome scanning evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:29:58Z eco ECO:0001270 restriction landmark genomic scanning evidence used in manual assertion true true A type of restriction landmark genome scanning evidence that is used in a manual assertion. ECO:MCC A type of resonant mirror biosensor evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:30:02Z eco ECO:0001271 resonant mirror biosensor evidence used in manual assertion true true A type of resonant mirror biosensor evidence that is used in a manual assertion. ECO:MCC A type of high-performance liquid chromatography evidence that is used in a manual assertion. mchibucos 2014-03-16T20:49:54Z eco ECO:0001272 high-performance liquid chromatography evidence used in manual assertion true true A type of high-performance liquid chromatography evidence that is used in a manual assertion. ECO:MCC A type of ectopic expression evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T22:34:56Z eco ECO:0001273 ectopic expression evidence used in manual assertion true true A type of ectopic expression evidence that is used in a manual assertion. ECO:MCC A type of protein-binding evidence that detects binding of a tagged protein to an array of oligonucleotide probes representing potential binding sites. swolfish 2015-06-05T14:36:00Z PBM evidence eco ECO:0001601 protein-binding microarray evidence A type of protein-binding evidence that detects binding of a tagged protein to an array of oligonucleotide probes representing potential binding sites. PMID:22146299 A type of in vivo assay evidence in which living cells are stained with a vital stain, i.e. dye that can be used on living cells without causing cell death. swolfish 2015-06-08T11:51:37Z eco vital staining evidence ECO:0001603 in vivo cell staining evidence A type of in vivo assay evidence in which living cells are stained with a vital stain, i.e. dye that can be used on living cells without causing cell death. GOC:MAH vital staining evidence GOC:MAH A type of reporter gene assay evidence based on the fusion of selected genes with the phoA gene to express alkaline phosphatase in periplasmic space for protein tracing. CollecTF swolfish 2015-10-29T15:53:45Z eco SEAP reporter assay Secreted Embryonic Alkaline Phosphatase reporter assay ECO:0001801 Alkaline phosphatase reporter assay produces a hybrid protein with alkaline phosphatase activity following transportation across the cellular membrane. alkaline phosphatase reporter gene assay evidence A type of reporter gene assay evidence based on the fusion of selected genes with the phoA gene to express alkaline phosphatase in periplasmic space for protein tracing. ECO:SW PMID:11823238 A type of reporter gene assay evidence based on the fusion of the lacZ gene to a specific promoter for the expression of beta-galactosidase which will appear blue when grown on a X-gal medium. CollecTF swolfish 2015-10-29T15:57:10Z beta-gal reporter gene assay eco lacZ reporter gene assay ECO:0001802 The assay is often performed using a plasmid borne construction on a lacZ strain. beta-galactosidase reporter gene assay evidence A type of reporter gene assay evidence based on the fusion of the lacZ gene to a specific promoter for the expression of beta-galactosidase which will appear blue when grown on a X-gal medium. ECO:SW PMID:20439410 A type of reporter gene assay evidence based on the fusion of the CAT gene to a specific promoter for the expression of chloramphenicol acetyltransferase which confers resistance to the chloramphenicol antibiotic. CollecTF swolfish 2015-10-29T16:06:42Z CAT reporter gene assay eco ECO:0001803 The amount of acetylated chloramphenicol is directly proportional to the amount of CAT enzyme present. chloramphenicol acetyltransferase reporter gene assay evidence A type of reporter gene assay evidence based on the fusion of the CAT gene to a specific promoter for the expression of chloramphenicol acetyltransferase which confers resistance to the chloramphenicol antibiotic. ECO:SW PMID:1630936 CAT reporter gene assay PMID:1630936 A type of reporter gene assay evidence where the beta-glucuronidase enzyme from Escherichia coli is used as the reporter to transform non-fluorescent substrates into fluorescents for detection. CollecTF swolfish 2015-10-29T16:11:02Z GUS reporter gene assay eco ECO:0001804 beta-glucuronidase reporter gene assay evidence A type of reporter gene assay evidence where the beta-glucuronidase enzyme from Escherichia coli is used as the reporter to transform non-fluorescent substrates into fluorescents for detection. ECO:SW A type of reporter gene assay evidence where luciferase, an oxidative enzyme, is used as the reporter to detect a gene product with bioluminescence. CollecTF swolfish 2015-10-29T16:15:39Z eco ECO:0001805 luciferase reporter gene assay evidence A type of reporter gene assay evidence where luciferase, an oxidative enzyme, is used as the reporter to detect a gene product with bioluminescence. ECO:SW PMID:17623934 A type of chromatin immunoprecipitation evidence that uses gama-exonuclease to digest TF-unbound DNA after ChIP for the identification of transcription factor binding site locations with high-resolution data. CollecTF swolfish 2015-10-29T16:37:36Z ChIP-exo eco ECO:0001806 chromatin immunoprecipitation- exonuclease evidence A type of chromatin immunoprecipitation evidence that uses gama-exonuclease to digest TF-unbound DNA after ChIP for the identification of transcription factor binding site locations with high-resolution data. ECO:SW PMID:25249628 ChIP-exo PMID:25249628 A type of electrophoretic mobility shift that is used in a manual assertion. swolfish 2015-11-03T12:13:17Z eco ECO:0001807 electrophoretic mobility shift assay evidence used in manual assertion true true A type of electrophoretic mobility shift that is used in a manual assertion. ECO:SW A type of reverse transcription polymerase chain reaction evidence that is used in a manual assertion. swolfish 2015-11-03T12:22:46Z eco ECO:0001808 reverse transcription polymerase chain reaction evidence used in manual assertion true true A type of reverse transcription polymerase chain reaction evidence that is used in a manual assertion. ECO:SW A type of chromatography evidence where immobilized promoter DNA is labeled and bound to a matrix through which a protein mixture is poured and then eluted to purify specific DNA binding proteins. CollecTF swolfish 2015-11-03T13:48:49Z eco DNA affinity purification ECO:0001809 Biotinylation is commonly used for labeling and beads are commonly used as the matrix. Bound protein will remain attached to the beads. Results can be detected through gel electrophoresis and then sequenced by mass-spectrometry. This technique can be used to demonstrate binding of a purified protein, or to purify the binding protein from crude extract or protein mixture. DNA affinity chromatography evidence A type of chromatography evidence where immobilized promoter DNA is labeled and bound to a matrix through which a protein mixture is poured and then eluted to purify specific DNA binding proteins. ECO:SW PMID:11694305 PMID:11725488 A type of nucleic acid binding evidence where proteins that have been bound to DNA protect a binding site from enzymatic cleavage with DNAse, thereby detecting protein-DNA interactions. CollecTF swolfish 2015-11-03T13:55:15Z eco DNase protection ECO:0001810 In DNAse footingprinting amplified DNA combined with TF and DNAse is electrophoresed for fragment comparison with a non-TF control sample. TF-bound fragments do not appear in the gel. Such fragments can be isolated, purified, and sequenced. This technique is often used to identify the binding motif of a TF resolving the protected region to 50-100 bp which can be further examined for TF-binding sites. DNAse footprinting evidence A type of nucleic acid binding evidence where proteins that have been bound to DNA protect a binding site from enzymatic cleavage with DNAse, thereby detecting protein-DNA interactions. ECO:SW PMID:212715 PMID:22194258 A type of fluorescence evidence based on rapid and quantitative analysis of diverse molecular interactions, enzyme activities, and nucleic acid hybridization which uses a fluorophore to measure the binding constants and kinetics of reactions that cause a change in the rotational time of the molecules. CollecTF swolfish 2015-11-03T14:01:36Z FA eco FP Fluorescence polarization ECO:0001811 The degree of polarization of a fluorophore is inversely related to its molecular rotation. When the fluorophore is bound to a small molecule, the rate at which it tumbles can decrease significantly from when it is bound tightly to a large protein. If the fluorophore is attached to the larger protein in a binding pair, the difference in polarization between bound and unbound states will be smaller and less accurate. The degree of binding is calculated by using the difference in anisotropy of the partially bound, free, and fully bound states measured by titrating the two binding partners. Fluorescence polarixation assays are homogeneous. fluorescence anisotropy evidence A type of fluorescence evidence based on rapid and quantitative analysis of diverse molecular interactions, enzyme activities, and nucleic acid hybridization which uses a fluorophore to measure the binding constants and kinetics of reactions that cause a change in the rotational time of the molecules. ECO:SW PMID:20232898 FP PMCID:3277431 PMID:20232898 Fluorescence polarization PMCID:3277431 PMID:20232898 A type of systematic evolution of ligands by exponential amplification evidence based on a restricted genomic DNA library to identify naturally occurring genomic aptamers and RNA-protein interaction networks with RNA-binding protein as bait and high-throughput sequencing. CollecTF swolfish 2015-11-03T14:05:37Z genomic SELEX eco ECO:0001812 The reported sequences should always be verified for presence in the genome sequence. genomic systematic evolution of ligands by exponential amplification evidence A type of systematic evolution of ligands by exponential amplification evidence based on a restricted genomic DNA library to identify naturally occurring genomic aptamers and RNA-protein interaction networks with RNA-binding protein as bait and high-throughput sequencing. ECO:SW PMID:20541015 PMID:21720957 genomic SELEX PMID:20541015 A type of nuclear magnetic resonance spectroscopy evidence based on two-dimensional NMR for elucidation of the chemical structure of an isolated or synthesized chemical compound where the characteristic transfer magnetization of a proton to a nitrogen or carbon isotope is monitored by NMR, generating a specific peak in the spectrum. CollecTF swolfish 2015-11-03T14:11:06Z HSQC eco ECO:0001813 Chemical shifts in the spectrum indicating binding can be detected from analysis of a protein spectrum in the presence or absence of its cognate DNA binding site. heteronuclear single quantum coherence spectroscopy evidence A type of nuclear magnetic resonance spectroscopy evidence based on two-dimensional NMR for elucidation of the chemical structure of an isolated or synthesized chemical compound where the characteristic transfer magnetization of a proton to a nitrogen or carbon isotope is monitored by NMR, generating a specific peak in the spectrum. ECO:SW PMID:19856946 HSQC PMID:19856946 A type of nucleic acid binding evidence where the synthetic molecule methidiumpropyl-EDTA (MPE) is used to cleave ligand-protected DNA, followed by analysis of the restriction fragments to generate a footprint (i.e. size and location) of small molecule binding sites on the DNA. CollecTF swolfish 2015-11-03T14:24:04Z eco MPE Fe(II) footprinting MPE-EDTA Fe(II) footprinting Methidiumpropyl-EDTA Fe(II) footprinting ECO:0001814 methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence A type of nucleic acid binding evidence where the synthetic molecule methidiumpropyl-EDTA (MPE) is used to cleave ligand-protected DNA, followed by analysis of the restriction fragments to generate a footprint (i.e. size and location) of small molecule binding sites on the DNA. ECO:SW PMID:6225070 MPE Fe(II) footprinting PMID:6225070 MPE-EDTA Fe(II) footprinting PMID:6225070 Methidiumpropyl-EDTA Fe(II) footprinting PMID:6225070 A type of nucleic acid binding evidence where nucleic acid that has been bound to protein is cleaved with 1,10-phenanthroline-copper complex resulting in a high-resolution footprint of sequence-specific protein-DNA contacts. CollecTF swolfish 2015-11-04T08:37:51Z 1,10-Phenanthroline-copper footprinting eco OP-Cu Complex ECO:0001815 copper-phenanthroline footprinting evidence A type of nucleic acid binding evidence where nucleic acid that has been bound to protein is cleaved with 1,10-phenanthroline-copper complex resulting in a high-resolution footprint of sequence-specific protein-DNA contacts. ECO:SW PMID:11691942 1,10-Phenanthroline-copper footprinting PMID:1384472 OP-Cu Complex PMID:1384472 A type of reporter gene assay evidence based on the fusion of select genes with the green fluorescent protein (GFP) gene for detection with bioluminescence of the gene product when exposed to blue ultraviolet light. CollecTF swolfish 2015-11-04T08:58:42Z GFP reporter gene assay eco GFP promoter fusion green fluorescent protein promoter fusion ECO:0001816 green fluorescent protein reporter gene assay evidence A type of reporter gene assay evidence based on the fusion of select genes with the green fluorescent protein (GFP) gene for detection with bioluminescence of the gene product when exposed to blue ultraviolet light. ECO:SW PMID:11989662 GFP reporter gene assay PMID:11989662 A type of protein binding evidence where a gene is fused with the GST gene and the resulting recombinant bait protein is captured on an immobilized Glutathione affinity ligand and incubated with prey protein to identify and characterize protein-protein interactions. CollecTF swolfish 2015-11-04T09:05:56Z GST pull-down assay eco ECO:0001817 The recombinant protein can also be eluted following the pull-down and analyzed further with qPCR or sequencing. glutathione S-transferase pull-down assay evidence A type of protein binding evidence where a gene is fused with the GST gene and the resulting recombinant bait protein is captured on an immobilized Glutathione affinity ligand and incubated with prey protein to identify and characterize protein-protein interactions. ECO:SW PMID:26096507 GST pull-down assay PMID:26096507 A type of nucleic acid binding evidence used to identify protein-binding sites on the DNA molecule where DNA that has been bound to protein is digested with hydroxyl radical produced by reduction of hydrogen peroxide with iron (II), followed by separating the cleavage products on a denaturing electrophoresis gel. CollecTF swolfish 2015-11-04T09:20:26Z eco ECO:0001818 hydroxyl-radical footprinting evidence A type of nucleic acid binding evidence used to identify protein-binding sites on the DNA molecule where DNA that has been bound to protein is digested with hydroxyl radical produced by reduction of hydrogen peroxide with iron (II), followed by separating the cleavage products on a denaturing electrophoresis gel. ECO:SW PMID:18546600 PMID:19378159 PMID:3090544 A type of transcript expression evidence used to determine expression levels of mRNA where a radiolabeled synthetic oligonucleotide primer is annealed to mRNA at the transcription start site of a gene and the mRNA is extended with reverse transcriptase producing cDNA which is electrophoresed on a polyacrylamide gel and autoradiographed, and the band size is proportional to the initial RNA. CollecTF swolfish 2015-11-04T09:33:18Z eco ECO:0001819 The most commonly used radiolabel is 32P. primer extension assay evidence A type of transcript expression evidence used to determine expression levels of mRNA where a radiolabeled synthetic oligonucleotide primer is annealed to mRNA at the transcription start site of a gene and the mRNA is extended with reverse transcriptase producing cDNA which is electrophoresed on a polyacrylamide gel and autoradiographed, and the band size is proportional to the initial RNA. ECO:SW PMID:23378648 A type of polymerase chain reaction evidence where a mRNA primer is used for RT-PCR and terminal deoxynucleotidyl transferase (TdT) is used to add identical nucleotides to the 3' end of the cDNA after which PCR with a different primer and TdT-oligomer are performed in the other sense to obtain the full length sequence of a RNA transcript. CollecTF swolfish 2015-11-04T09:48:38Z RACE PCR eco ECO:0001820 RACE PCR is frequently used to verify transcription start sites relevant to the function of transcription factor binding sites such as repression. rapid amplification of cDNA ends polymerase chain reaction evidence A type of polymerase chain reaction evidence where a mRNA primer is used for RT-PCR and terminal deoxynucleotidyl transferase (TdT) is used to add identical nucleotides to the 3' end of the cDNA after which PCR with a different primer and TdT-oligomer are performed in the other sense to obtain the full length sequence of a RNA transcript. ECO:SW PMID:17498297 RACE PCR PMI:17498297 A type of nucleotide sequencing assay evidence where RNA is extracted from a cell, reverse transcribed to cDNA for a snapshot of an organism's transcriptome with precise measurement of transcript levels and their isoforms. CollecTF swolfish 2015-11-04T10:15:57Z RNA-Seq WTTS Whole Transcriptome Shotgun Sequencing eco ECO:0001821 Use ECO:0000295 (RNA-seq evidence) in place of this term. RNA sequencing assay evidence true A type of nucleotide sequencing assay evidence where RNA is extracted from a cell, reverse transcribed to cDNA for a snapshot of an organism's transcriptome with precise measurement of transcript levels and their isoforms. ECO:SW PMID:19015660 RNA-Seq PMID:23851085 Whole Transcriptome Shotgun Sequencing PMID:23851085 A type of knockout evidence based on the survival of an organism in a particular environment where a gene for an enzyme or regulator is knocked out and results are used as a natural reporter. CollecTF swolfish 2015-11-04T10:48:59Z eco ECO:0001822 survival rate analysis evidence A type of knockout evidence based on the survival of an organism in a particular environment where a gene for an enzyme or regulator is knocked out and results are used as a natural reporter. ECO:SW A type of crystallography evidence where a purified sample at high concentration is crystallised and the crystals are exposed to an x ray beam to obtain three dimensional molecular structure of proteins and biological macromolecules. CollecTF swolfish 2015-11-04T10:56:22Z eco ECO:0001823 X-ray crystallography can be used for a crystal used to probe at the tridimensional structure of proteins. In some cases, it is possible to co-crystallize the protein bound to its DNA binding site, providing detail on the particular arrangement of the two components. x-ray crystallography evidence A type of crystallography evidence where a purified sample at high concentration is crystallised and the crystals are exposed to an x ray beam to obtain three dimensional molecular structure of proteins and biological macromolecules. ECO:SW PMID:23135450 PMID:24648090 A type of affinity evidence used to identify DNA binding sites in eukaryotes where Escherichia coli DNA adenine methyltransferase (Dam) is fused to a transcription factor, co-factor, chromatin-associated protein, or nuclear-associated protein, followed by a methyl-dependent PCR to localize methyltransferase in the region of the binding site. CollecTF swolfish 2015-11-05T15:56:13Z DamID eco ECO:0001824 The methylation tag is detected with methylation-sensitive restriction enzymes, DpnI and DpnII. DNA adenine methyltransferase identification evidence A type of affinity evidence used to identify DNA binding sites in eukaryotes where Escherichia coli DNA adenine methyltransferase (Dam) is fused to a transcription factor, co-factor, chromatin-associated protein, or nuclear-associated protein, followed by a methyl-dependent PCR to localize methyltransferase in the region of the binding site. ECO:SW PMID:16938559 PMID:17545983 PMID:19588092 DamID PMID:19588092 A type of affinity evidence where the absorbed or released heat of a biomolecular binding event is directly measured in a reference cell and sample cell after the addition of a ligand using a microcalorimeter for a complete thermodynamic profile of the molecular interaction. CollecTF swolfish 2015-11-05T16:06:20Z ITC eco ECO:0001825 When ITC is used to study TF, the temperature of two identical cells containing a known concentration of TF is monitored. After the ligand is added to the cells in precisely measured aliquots, the temperature difference in each cell is observed to determine target binding. This value can be used to compute the energetics of the reaction and hence, binding affinity of the TF for the DNA fragment. The thermodynamic profile that is measured includes the values of binding constant (K(a)), stoichiometry (n), and the enthalpy of binding (DeltaH(b)). isothermal titration calorimetry evidence A type of affinity evidence where the absorbed or released heat of a biomolecular binding event is directly measured in a reference cell and sample cell after the addition of a ligand using a microcalorimeter for a complete thermodynamic profile of the molecular interaction. ECO:SW PMID:10527727 ITC PMID:10527727 A type of nucleic acid binding evidence where DNA is non-specifically fragmented with ultraviolet light while protein-bound regions are protected from UV damage and strand breakage patterns are analyzed by PAGE and sequenced to detect protein-DNA contacts. CollecTF swolfish 2015-11-05T16:13:36Z eco UV footprinting ultraviolet footprinting ECO:0001826 ultraviolet light footprinting evidence A type of nucleic acid binding evidence where DNA is non-specifically fragmented with ultraviolet light while protein-bound regions are protected from UV damage and strand breakage patterns are analyzed by PAGE and sequenced to detect protein-DNA contacts. ECO:SW PMID:2842760 PMID:7602584 A type of nucleic acid binding evidence used to identify protein binding sites on the DNA molecule where multiple copies of a DNA fragment containing a putative TF-binding site are randomly methylated with dimethyl sulfate (DMS) and cleaved at the methyl group, followed by separating the cleavage products on a denaturing electrophoresis gel. CollecTF swolfish 2015-11-05T16:16:27Z eco methylation interference footprinting ECO:0001827 premethylation interference footprinting evidence A type of nucleic acid binding evidence used to identify protein binding sites on the DNA molecule where multiple copies of a DNA fragment containing a putative TF-binding site are randomly methylated with dimethyl sulfate (DMS) and cleaved at the methyl group, followed by separating the cleavage products on a denaturing electrophoresis gel. ECO:SW PMID:1583685 A type of inference from background scientific knowledge used in manual assertion where a visual inspection of promoter region is made to identify putative binding sites. swolfish 2015-11-10T14:40:16Z eco ECO:0001828 visual sequence inspection evidence A type of inference from background scientific knowledge used in manual assertion where a visual inspection of promoter region is made to identify putative binding sites. ECO:SW A type of reporter gene assay evidence used to locate and isolate Fur sites where a plasmid library is created and cloned into a cell line with a ferric uptake regulator (Fur)-repressed reporter and the Fur protein is titrated away from its binding site on the reporter, after which the cell is isolated and plasmid extracted for further sequence analysis. CollecTF swolfish 2015-11-10T14:55:36Z FURTA eco Fluorescence polarization ECO:0001829 ferric uptake regulator titration assay evidence A type of reporter gene assay evidence used to locate and isolate Fur sites where a plasmid library is created and cloned into a cell line with a ferric uptake regulator (Fur)-repressed reporter and the Fur protein is titrated away from its binding site on the reporter, after which the cell is isolated and plasmid extracted for further sequence analysis. ECO:SW PMID:10713425 PMID:7642488 PMID:8107138 FURTA PMID:10713425 Fluorescence polarization PMID:15689115 A type of in vitro cell based assay evidence resulting from analyzing the difference between the number (estimation) of cells at the start and the remaining viable cells at the end of the assay. snadendla 2015-02-13T12:08:01Z eco ECO:0005004 cell viability assay evidence A type of in vitro cell based assay evidence resulting from analyzing the difference between the number (estimation) of cells at the start and the remaining viable cells at the end of the assay. NBK:144065 A type of in vitro cell based assay evidence resulting from the measurement of cell proliferation. snadendla 2015-02-11T16:27:13Z eco ECO:0005007 cell proliferation assay evidence A type of in vitro cell based assay evidence resulting from the measurement of cell proliferation. ECO:RCT A type of cell proliferation assay evidence resulting from the measure of proliferation by estimation of DNA synthesis. snadendla 2015-02-11T16:30:10Z eco ECO:0005008 DNA synthesis cell proliferation assay evidence A type of cell proliferation assay evidence resulting from the measure of proliferation by estimation of DNA synthesis. PMC:3908118 A type of cell proliferation assay resulting from the assessment of metabolic activity. snadendla 2015-02-11T16:36:33Z eco ECO:0005009 metabolic cell proliferation assay evidence A type of cell proliferation assay resulting from the assessment of metabolic activity. ECO:RCT snadendla 2015-02-11T16:37:23Z eco ECO:0005010 cell proliferation marker detection assay evidence A type of cell proliferation assay evidence resulting from the analysis of ATP concentration (light intensity) when luciferase catalyzes the oxidation of luciferin in the presence of ATP, magnesium ions and molecular oxygen. snadendla 2015-02-11T16:47:30Z eco ECO:0005011 ATP bioluminescence assay evidence A type of cell proliferation assay evidence resulting from the analysis of ATP concentration (light intensity) when luciferase catalyzes the oxidation of luciferin in the presence of ATP, magnesium ions and molecular oxygen. PMID:15344559 snadendla 2015-02-12T11:39:35Z eco ECO:0005012 cytotoxicity assay evidence A type of in vitro assay evidence resulting from the use of live cells. snadendla 2015-02-12T13:26:55Z eco ECO:0005014 in vitro cell based assay evidence A type of in vitro assay evidence resulting from the use of live cells. ECO:RCT A type of direct assay evidence resulting from the use of stains or dyes to aid in analysis of a microscopic image. snadendla 2015-02-19T11:48:57Z eco ECO:0005019 staining evidence A type of direct assay evidence resulting from the use of stains or dyes to aid in analysis of a microscopic image. ECO:RCT A type of in vitro cell based assay evidence resulting from a given chemical substance causing a movement response, or not, in the sample cells or organisms. snadendla 2015-02-19T13:10:20Z eco ECO:0005021 chemotaxis assay evidence A type of in vitro cell based assay evidence resulting from a given chemical substance causing a movement response, or not, in the sample cells or organisms. PMC:3667641 A type of mutant phenotype evidence resulting from the conversion of one genotype into another by the introduction of exogenous DNA. snadendla 2015-03-16T15:33:50Z eco ECO:0005027 genetic transformation evidence A type of mutant phenotype evidence resulting from the conversion of one genotype into another by the introduction of exogenous DNA. ECO:RCT A type of experimental evidence resulting from the visualization and examination of chemical and/or molecular structures. snadendla 2015-03-20T12:16:17Z eco ECO:0005031 structure determination evidence A type of experimental evidence resulting from the visualization and examination of chemical and/or molecular structures. ECO:RCT A type of microscopy evidence and structure determination evidence resulting from an electron beam utilized to create an image. snadendla 2015-03-20T12:21:48Z eco ECO:0005033 electron microscopy evidence A type of microscopy evidence and structure determination evidence resulting from an electron beam utilized to create an image. ECO:RCT A type of in vitro cell based assay evidence resulting from the occurrence, visualization, and/or analysis of apoptosis. snadendla 2015-04-07T21:58:24Z eco ECO:0005034 apoptotic assay evidence A type of in vitro cell based assay evidence resulting from the occurrence, visualization, and/or analysis of apoptosis. ECO:RCT A type of in vivo assay evidence where ADP-ribosylated residues in proteins are detected in cells in vivo. snadendla 2015-06-15T15:35:05Z eco ECO:0005500 in vivo polyADP-ribosylation assay evidence A type of in vivo assay evidence where ADP-ribosylated residues in proteins are detected in cells in vivo. ECO:SN PMID:2820766 SIB:PG A type of in vivo polyADP-ribosylation assay evidence that is used in a manual assertion. snadendla 2015-06-15T15:37:23Z eco ECO:0005501 in vivo polyADP-ribosylation assay evidence used in manual assertion true true A type of in vivo polyADP-ribosylation assay evidence that is used in a manual assertion. ECO:SN A type of biological assay evidence derived by studying an organ, tissues, or cells taken from an organism in an external environment with the minimum alteration of natural conditions. snadendla 2015-06-26T11:46:15Z eco ECO:0005502 ex vivo assay evidence A type of biological assay evidence derived by studying an organ, tissues, or cells taken from an organism in an external environment with the minimum alteration of natural conditions. ECO:SN PMID:16305312 url:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2305722/pdf/nihms42807.pdf A type of gel electrophoresis evidence that involves one dimension electrophoresis where biomolecules are electrophoresed on a low percentage polyacrylamide gel to be separated in proportion to their mass or isoelectric point, followed by high voltage electrophoresis on a higher percentage gel in the presence of ethidium bromide to alter non-linear molecular shape. CollecTF snadendla 2015-10-01T16:23:20Z 2D PAGE 2D-PAGE eco ECO:0005503 Two-dimensional polyacrylamide gel electrophoresis is commonly employed to establish a proteome for an organism and demonstrate expression changes. two-dimensional polyacrylamide gel electrophoresis evidence A type of gel electrophoresis evidence that involves one dimension electrophoresis where biomolecules are electrophoresed on a low percentage polyacrylamide gel to be separated in proportion to their mass or isoelectric point, followed by high voltage electrophoresis on a higher percentage gel in the presence of ethidium bromide to alter non-linear molecular shape. ECO:SW url:http://www.nature.com/nmeth/journal/v2/n1/full/nmeth0105-83.html A type of experimental evidence resulting from the use of a spectrometer. snadendla 2015-08-14T15:48:08Z eco ECO:0005504 spectrometry evidence A type of experimental evidence resulting from the use of a spectrometer. ECO:RCT A type of motif similarity evidence where the motif, a local alignment of sequences, is represented by a regular expression, which captures the variability of nucleotides at each position in a discrete form and can then be used to search genetic sequences by identifying matches to the regular expression. CollecTF snadendla 2015-10-09T13:51:52Z eco ECO:0005505 Regular expression is a computational tool used for determining whether a given genome contains a DNA region resembling a transcription factor binding motif. For example A/T=W indicates A or T may be present in a column of the alignment. (PMID: 20708667). regular expression motif search evidence A type of motif similarity evidence where the motif, a local alignment of sequences, is represented by a regular expression, which captures the variability of nucleotides at each position in a discrete form and can then be used to search genetic sequences by identifying matches to the regular expression. ECO:SW PMID:17337630 A type of point mutation evidence resulting from a change in a base (or bases) causing the substitution of one amino acid for another. snadendla 2015-09-18T16:52:34Z eco ECO:0005506 missense mutation evidence A type of point mutation evidence resulting from a change in a base (or bases) causing the substitution of one amino acid for another. SO:0001583 A type of point mutation evidence resulting in an incomplete and usually nonfunctional protein product because of a premature stop codon. snadendla 2015-09-18T16:55:32Z eco ECO:0005507 nonsense mutation evidence A type of point mutation evidence resulting in an incomplete and usually nonfunctional protein product because of a premature stop codon. url:https://ghr.nlm.nih.gov/primer/mutationsanddisorders/possiblemutations A type of point mutation evidence resulting from the change of a DNA nucleotide that does not cause any changes in the amino acid sequence. snadendla 2015-09-18T17:01:12Z eco ECO:0005508 silent mutation evidence A type of point mutation evidence resulting from the change of a DNA nucleotide that does not cause any changes in the amino acid sequence. url:http://www.sciencemag.org/news/2006/12/sound-silent-mutation A type of experimental phenotypic evidence resulting from a mutation in which there is an insertion of an additional nucleotide, or nucleotides. snadendla 2015-09-18T17:02:03Z eco ECO:0005509 insertion mutation evidence A type of experimental phenotypic evidence resulting from a mutation in which there is an insertion of an additional nucleotide, or nucleotides. GO:0070705 A type of experimental phenotypic evidence resulting from a mutation in which inserted nucleotide(s) have a sequence identical to, or derived from, adjacent nucleotides. snadendla 2015-09-18T17:03:25Z eco ECO:0005511 duplication mutation evidence A type of experimental phenotypic evidence resulting from a mutation in which inserted nucleotide(s) have a sequence identical to, or derived from, adjacent nucleotides. SO:1000035 A type of experimental phenotypic evidence resulting from any mutation that causes a shift in bases and therefore changes the code for the amino acids. snadendla 2015-09-18T17:05:49Z eco ECO:0005512 frameshift mutation evidence A type of experimental phenotypic evidence resulting from any mutation that causes a shift in bases and therefore changes the code for the amino acids. url:https://ghr.nlm.nih.gov/primer/mutationsanddisorders/possiblemutations A type of experimental phenotypic evidence resulting from a mutation that increases the number of times that a DNA sequence is repeated. snadendla 2015-09-18T17:06:34Z eco ECO:0005513 repeat expansion mutation evidence A type of experimental phenotypic evidence resulting from a mutation that increases the number of times that a DNA sequence is repeated. PMID:9397685 url:https://ghr.nlm.nih.gov/primer/mutationsanddisorders/possiblemutations A type of experimental phenotypic evidence resulting from a mutation in which there is a change in nucleotides at a splice site snadendla 2015-09-18T17:07:29Z eco ECO:0005514 splice site mutation evidence A type of experimental phenotypic evidence resulting from a mutation in which there is a change in nucleotides at a splice site ECO:RCT A type of experimental phenotypic evidence resulting from a mutation in which a region of a chromosome is transferred to a nonhomologous chromosome snadendla 2015-09-18T17:08:01Z eco ECO:0005515 translocation mutation evidence A type of experimental phenotypic evidence resulting from a mutation in which a region of a chromosome is transferred to a nonhomologous chromosome ECO:RCT A type of experimental evidence resulting from the detection and analysis of molecular markers. snadendla 2015-09-24T15:54:21Z eco ECO:0005516 molecule detection assay evidence A type of experimental evidence resulting from the detection and analysis of molecular markers. ECO:RCT A type of molecule detection assay evidence resulting from the detection and quantification of a protein, or multiple proteins. snadendla 2015-09-25T14:27:40Z eco ECO:0005517 protein detection assay evidence A type of molecule detection assay evidence resulting from the detection and quantification of a protein, or multiple proteins. ECO:RCT A type of molecule detection assay evidence resulting from the detection of specific RNAs. snadendla 2015-09-25T14:43:53Z eco ECO:0005518 RNA detection assay evidence A type of molecule detection assay evidence resulting from the detection of specific RNAs. ECO:RCT A type of molecule detection assay evidence resulting from the detection and visualization of a sequence of DNA. snadendla 2015-09-25T19:33:25Z eco ECO:0005519 DNA detection assay evidence A type of molecule detection assay evidence resulting from the detection and visualization of a sequence of DNA. ECO:RCT A type of molecule detection assay evidence based on changes in surface-reflected light due to ligand binding on the surface of a semi-transparent substrate to detect proteins, DNA, and other biological material in a multiplexed, high-throughput microarray format without labels. CollecTF snadendla 2015-09-28T16:01:01Z IRIS SRIB Spectral Reflectance Imaging Biosensor eco ECO:0005520 Differences in the optical path lengths between a surface layer and a buried silica layer can be measured very precisely allowing optical height information to be converted to accumulated mass on the surface. For the purpose of TF-binding site identification, IRIS is coupled with DNA-arrays with immobilized potential binding regions exposed to the protein of interest and eluted. Protein-bound fragments exhibit changes in reflectance that can be used to gauge binding quantitatively. interferometric reflectance imaging sensor evidence A type of molecule detection assay evidence based on changes in surface-reflected light due to ligand binding on the surface of a semi-transparent substrate to detect proteins, DNA, and other biological material in a multiplexed, high-throughput microarray format without labels. ECO:SW PMID:21587155 PMID:24271115 A type of nuclease protection assay evidence where RNA is hybridized with complementary DNA probes and exposed to S1 nuclease for unbound RNA degradation after which the intact RNA is run on a gel for probe size determination and RNA identification to detect and map specific RNAs in a complex mixture of total cellular RNA. CollecTF snadendla 2015-09-28T17:16:56Z eco ECO:0005521 S1 nuclease protection assay evidence A type of nuclease protection assay evidence where RNA is hybridized with complementary DNA probes and exposed to S1 nuclease for unbound RNA degradation after which the intact RNA is run on a gel for probe size determination and RNA identification to detect and map specific RNAs in a complex mixture of total cellular RNA. ECO:SW PMID:21390683 A type of DNA detection assay evidence resulting from evaluation of the relative abundance of target sequences hybridizing to DNA samples that are immobilized on a nitrocellulose or nylon membrane. snadendla 2015-09-30T10:03:03Z eco ECO:0005522 DNA dot blot assay evidence A type of DNA detection assay evidence resulting from evaluation of the relative abundance of target sequences hybridizing to DNA samples that are immobilized on a nitrocellulose or nylon membrane. PMID:18265189 A type of DNA dot blot assay evidence that is used in a manual assertion. snadendla 2015-09-30T10:04:00Z eco ECO:0005523 DNA dot blot assay evidence used in manual assertion true true A type of DNA dot blot assay evidence that is used in a manual assertion. ECO:SN ECO:SW A type of protein detection assay evidence where soft ionization is used for the analysis of biomolecules for mass determination in a three step process of plate preparation, radiation, and ionization with high throughput technology. CollecTF snadendla 2015-09-30T10:51:56Z MALDI-TOF Mass Spectrometry MALDI-TOF-MS eco ECO:0005526 MALDI-TOF MS is commonly used for protein identification in constructing a proteome where protein fingerprints obtained by microbial cells are compared with a database of reference spectra by means of various algorithms integrated in systems recently made commercially available. matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence A type of protein detection assay evidence where soft ionization is used for the analysis of biomolecules for mass determination in a three step process of plate preparation, radiation, and ionization with high throughput technology. ECO:SW PMID:21964792 PMID:25354905 A type of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence that is used in a manual assertion. snadendla 2015-09-30T10:58:51Z eco ECO:0005527 matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence used in manual assertion true true A type of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence that is used in a manual assertion. ECO:SN ECO:SW A type of experimental phenotypic evidence based on target-specified mutagenesis for the characterization of various gene and protein interactions, structures, and functions where oligonucleotide primers are used to alter a nucleotide sequence. CollecTF snadendla 2015-09-30T11:34:41Z site directed mutagenesis eco ECO:0005528 Site-directed mutagenesis is often performed in tandem with EMSA. It is often implemented only in conserved motif positions or serially through all positions of a site. site-directed mutagenesis evidence A type of experimental phenotypic evidence based on target-specified mutagenesis for the characterization of various gene and protein interactions, structures, and functions where oligonucleotide primers are used to alter a nucleotide sequence. ECO:SW PMID:21204030 PMID:24011050 PMID:3541892 A type of experimental phenotypic evidence where radiation or a DNA-damaging agent in vivo, or PCR with degenerate primers in vitro are used for non-targeted mutagenesis. CollecTF snadendla 2015-09-30T11:55:03Z eco ECO:0005529 Random mutagenesis is not often used in TF-binding site determination; however, it is sometimes used to investigate the effect of mutations in TF binding domains in conjunction with expression assays. Random mutations can also be introduced via chemicals, error-prone PCR (EP-PCR), degenerate oligonucleotides-Pfu(DOP), UV irradiation, mutator strains, nucleotide analogs, or DNA recombination. random mutagenesis evidence A type of experimental phenotypic evidence where radiation or a DNA-damaging agent in vivo, or PCR with degenerate primers in vitro are used for non-targeted mutagenesis. ECO:SW PMID:15153637 PMID:18265275 A type of random mutagenesis evidence that is used in a manual assertion. snadendla 2015-09-30T11:57:00Z eco ECO:0005530 random mutagenesis evidence used in manual assertion true true A type of multiple sequence alignment evidence based on a set of algorithms that infer over-represented motifs from a set of biological sequences returning one or more local multiple sequence alignment defining the inferred motifs. CollecTF snadendla 2015-09-30T15:04:45Z eco ECO:0005531 Relationship type between sequences (e.g. orthologs from multiple genomes or co-expressed genes in the same genome) is not necessarily assumed. The local multiple sequence alignment is typically ungapped. A common application of motif discovery is to infer the binding motif of a given transcription factor (TF). This can be based on the results of a whole-genome expression analysis, assuming that co-expressed genes are co-regulated by the same TF, from peaks in ChIP-seq experiments with the TF, or from the comparative genomics analysis of the promoter regions of orthologs. motif discovery evidence A type of multiple sequence alignment evidence based on a set of algorithms that infer over-represented motifs from a set of biological sequences returning one or more local multiple sequence alignment defining the inferred motifs. ECO:SW PMID:10812473 PMID:16845028 PMID:8211139 Relationship type between sequences (e.g. orthologs from multiple genomes or co-expressed genes in the same genome) is not necessarily assumed. The local multiple sequence alignment is typically ungapped. A common application of motif discovery is to infer the binding motif of a given transcription factor (TF). This can be based on the results of a whole-genome expression analysis, assuming that co-expressed genes are co-regulated by the same TF, from peaks in ChIP-seq experiments with the TF, or from the comparative genomics analysis of the promoter regions of orthologs. PMID:19892760 PMID:23032607 A type of motif similarity evidence where the motif is represented by a consensus sequence which incorporates the most frequent nucleotide at each position acting as a generic representative for the sequences in the alignment, and is compared to the genetic sequence for a perfect or imperfect match. CollecTF snadendla 2015-10-09T14:12:54Z eco ECO:0005532 This technique is used to identify transcription factor binding sites by searching a bacterial genome for DNA regions resembling a given TF-binding motif. PMID: 17085555. consensus search evidence A type of motif similarity evidence where the motif is represented by a consensus sequence which incorporates the most frequent nucleotide at each position acting as a generic representative for the sequences in the alignment, and is compared to the genetic sequence for a perfect or imperfect match. ECO:SW PMID:15130839 A type of motif discovery evidence based on a set of algorithms that infer motifs in non-coding DNA sequences from the conservation of functional regulatory sites through evolution at a higher rate than their local surroundings for the identification of an evolutionary 'footprint'. CollecTF snadendla 2015-09-30T16:23:02Z eco ECO:0005533 The name derives to experimental footprinting techniques where transcription factor (TF)-binding sites are identified by sequencing the region of DNA protected from biochemical agents by the bound TF. This technique is used to identify or verify transcription factor-binding motifs, most commonly in the Eukaryota (PMID: 11997340). phylogenetic footprinting evidence A type of motif discovery evidence based on a set of algorithms that infer motifs in non-coding DNA sequences from the conservation of functional regulatory sites through evolution at a higher rate than their local surroundings for the identification of an evolutionary 'footprint'. ECO:SW PMID:16477324 PMID:3199442 A type of motif similarity evidence based on comparative genomics which uses a search method to scan a set of genomes for instances of a specific motif, and then applies a comparative criterion to analyze the collective strength of these predictions, based on the assumption that functional instances of the motif will be preserved by natural selection and their prediction will therefore be consistent across genomes. CollecTF snadendla 2015-10-09T14:30:38Z eco ECO:0005534 This technique is used to predict transcription factor binding sites in gene promoter regions by identifying conserved DNA regions across multiple genomes. PMID: 22305460. Orthology is a typical comparative criterion used. comparative genomics motif search evidence A type of motif similarity evidence based on comparative genomics which uses a search method to scan a set of genomes for instances of a specific motif, and then applies a comparative criterion to analyze the collective strength of these predictions, based on the assumption that functional instances of the motif will be preserved by natural selection and their prediction will therefore be consistent across genomes. ECO:SW PMID:10854408 A type of match to sequence model evidence which captures the application of a broad suite of supervised and unsupervised machine learning algorithms trained on known motif instances and applied to the prediction of novel putative instances of a motif in a set of biological sequences. CollecTF snadendla 2015-10-01T11:58:36Z eco ECO:0005535 Machine learning algorithms include, but are not limited to artificial neural networks, random-forest, k-means clustering, hidden Markov models. This suite of methods can be used to identify or verify transcription factor-binding sites in genomic sequences (PMID: 15703297). machine learning prediction of motif instance evidence A type of match to sequence model evidence which captures the application of a broad suite of supervised and unsupervised machine learning algorithms trained on known motif instances and applied to the prediction of novel putative instances of a motif in a set of biological sequences. ECO:SW PMID:17117497 PMID:2014171 A type of motif similarity evidence where the motif is represented by a position-specific frequency matrix (PSFM) that specifies the frequency of each base at each position of the motif, from which a position-specific scoring matrix (PSSM) can be derived under the framework of a log-likelihood ratio providing a scoring system based on the likelihood of a sequence given the motif, versus a genomic-frequency based null hypothesis. CollecTF snadendla 2015-10-09T15:04:35Z PSSM motif search PSSM eco ECO:0005536 This technique is used to predict transcription factor binding sites in gene promoter regions by using a position weight matrix approach. (PMID: 15604457). position-specific scoring matrix motif search evidence A type of motif similarity evidence where the motif is represented by a position-specific frequency matrix (PSFM) that specifies the frequency of each base at each position of the motif, from which a position-specific scoring matrix (PSSM) can be derived under the framework of a log-likelihood ratio providing a scoring system based on the likelihood of a sequence given the motif, versus a genomic-frequency based null hypothesis. ECO:SW PMID:10812473 A type of reporter gene assay evidence based on the fusion of the xylE gene to a specific promoter for the expression of catechol 2,3-dioxygenase that converts the colorless catechol substrate to yellow 2-hydroxymuconic semialdehyde for identification of the expression of a particular gene. CollecTF snadendla 2015-10-28T15:31:28Z eco ECO:0005537 xylE reporter gene assay evidence A type of reporter gene assay evidence based on the fusion of the xylE gene to a specific promoter for the expression of catechol 2,3-dioxygenase that converts the colorless catechol substrate to yellow 2-hydroxymuconic semialdehyde for identification of the expression of a particular gene. ECO:SW PMID:2592344 snadendla 2015-11-17T15:15:50Z eco ECO:0005538 computationally derived logical inference true snadendla 2015-11-17T15:17:47Z eco ECO:0005539 computationally derived logical inference used in automatic assertion true snadendla 2015-11-17T15:24:42Z eco ECO:0005540 computationally derived logical inference from automatic assertion used in automatic assertion true snadendla 2015-11-17T15:32:03Z eco ECO:0005541 computationally derived logical inference from manual assertion used in automatic assertion true A type of biological system reconstruction evidence by experimental evidence from single species that is used in a manual assertion. snadendla 2015-12-16T15:32:41Z eco ECO:0005542 Processes, pathways and complexes shown by a single experiment should not be annotated with this term but with ECO:0000353 or a child thereof. biological system reconstruction evidence by experimental evidence from single species used in manual assertion true true A type of biological system reconstruction evidence by experimental evidence from single species that is used in a manual assertion. ECO:SN PMID:19450514 A type of biological system reconstruction evidence by experimental evidence from mixed species that is used in a manual assertion. snadendla 2015-12-16T15:45:01Z eco ECO:0005543 Inference is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. The evidence may originate from a combination of several experiments. biological system reconstruction evidence by experimental evidence from mixed species used in manual assertion true true A type of biological system reconstruction evidence by experimental evidence from mixed species that is used in a manual assertion. ECO:SN PMID:22232657 A type of biological system reconstruction evidence based on orthology evidence that is used in a manual assertion. snadendla 2015-12-18T16:20:49Z eco ECO:0005544 Inference is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. Evidence may originate from a combination of several experiments. biological system reconstruction evidence based on orthology evidence used in manual assertion true A type of biological system reconstruction evidence based on orthology evidence that is used in a manual assertion. ECO:SN A type of biological system reconstruction evidence based on homology evidence where the evidence is inferred by orthology from an existing experimentally supported model to a process, pathway or complex in another species. snadendla 2015-12-16T15:57:37Z eco ECO:0005545 Inference is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. Evidence may originate from a combination of several experiments. biological system reconstruction evidence based on orthology evidence A type of biological system reconstruction evidence based on homology evidence where the evidence is inferred by orthology from an existing experimentally supported model to a process, pathway or complex in another species. ECO:SN PMID:15660128 A type of biological system reconstruction evidence based on paralogy evidence that is used in a manual assertion. snadendla 2015-12-16T16:05:15Z eco ECO:0005546 Inference is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. Evidence may originate from a combination of several experiments. biological system reconstruction evidence based on paralogy evidence used in manual assertion true A type of biological system reconstruction evidence based on paralogy evidence that is used in a manual assertion. ECO:SN PMID:15660128 A type of biological system reconstruction evidence based on inference from background scientific knowledge that is used in a manual assertion. snadendla 2015-12-16T16:07:42Z eco ECO:0005547 Functional studies or ligand binding evidence are often used for the reconstruction of biological systems. It does not provide physical interaction evidence but uses proxies such a ligand binding evidences to infer the presence or absence of the complex components. biological system reconstruction evidence based on inference from background scientific knowledge used in manual assertion true true A type of biological system reconstruction evidence based on inference from background scientific knowledge that is used in a manual assertion. ECO:SN PMID:17876790 A type of biological system reconstruction based solely on background scientific knowledge of that biological system. snadendla 2015-12-18T15:32:15Z eco ECO:0005548 The available knowledge is usually a combination of partial or weak experimental evidence where either some components are missing or no physical interaction evidence can be found but the system is inferred by similarity to related systems in taxonomically-disparate organisms with experimental evidence. Functional studies or ligand binding evidence are often used for the reconstruction of biological systems. It does not provide physical interaction evidence but uses proxies such a ligand binding evidences to infer the presence or absence of the complex components. biological system reconstruction evidence based on inference from background scientific knowledge A type of biological system reconstruction based solely on background scientific knowledge of that biological system. ECO:SN PMID:17876790 A type of biological system reconstruction where the evidence is inferred by homology based on conservation of sequence, function, and composition from an existing experimentally supported model to a process, pathway, or complex. snadendla 2015-12-18T15:49:46Z eco ECO:0005549 Inference may be based on paralogy and/or orthology of the genome-encoded components and is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. Evidence may originate from a combination of several experiments in the same or another species. biological system reconstruction evidence based on homology evidence A type of biological system reconstruction where the evidence is inferred by homology based on conservation of sequence, function, and composition from an existing experimentally supported model to a process, pathway, or complex. ECO:SN PMID:15660128 A type of biological system reconstruction evidence based on homology evidence where the evidence is inferred by paralogy from an existing experimentally supported model to a process, pathway, or complex in the same species. snadendla 2015-12-18T16:24:08Z eco ECO:0005550 Inference is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. Evidence may originate from a combination of several experiments. biological system reconstruction evidence based on paralogy evidence A type of biological system reconstruction evidence based on homology evidence where the evidence is inferred by paralogy from an existing experimentally supported model to a process, pathway, or complex in the same species. ECO:SN PMID:15660128 A type of biological system reconstruction evidence that uses experimental evidence as support. snadendla 2015-12-18T16:34:13Z eco ECO:0005551 biological system reconstruction evidence by experimental evidence A type of biological system reconstruction evidence that uses experimental evidence as support. ECO:SN PMID:19450514 PMID:22232657 A type of biological system reconstruction evidence where the experimental evidence is derived by using a mix of species used in the same experiment. snadendla 2015-12-18T16:35:13Z eco ECO:0005552 Inference is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. The evidence may originate from a combination of several experiments. biological system reconstruction evidence by experimental evidence from mixed species A type of biological system reconstruction evidence where the experimental evidence is derived by using a mix of species used in the same experiment. ECO:SN PMID:22232657 A type of biological system reconstruction where the experimental evidence is derived by using multiple experiments in a single species. snadendla 2015-12-18T16:36:44Z eco ECO:0005553 Processes, pathways and complexes shown by a single experiment should not be annotated with this term but with ECO:0000353 or a child thereof. biological system reconstruction evidence by experimental evidence from single species A type of biological system reconstruction where the experimental evidence is derived by using multiple experiments in a single species. ECO:SN A type of sequence alignment evidence where two sequences are aligned to identify regions of similarity that may indicate functional, structural and/or evolutionary relationships between two biological sequences (protein or nucleic acid). snadendla 2016-02-08T14:30:46Z eco ECO:0005554 pairwise sequence alignment evidence A type of sequence alignment evidence where two sequences are aligned to identify regions of similarity that may indicate functional, structural and/or evolutionary relationships between two biological sequences (protein or nucleic acid). ECO:SN url:http://www.ebi.ac.uk/Tools/psa/ A type of sequence alignment evidence where three or more biological sequences (protein or nucleic acid) of similar length are aligned to infer homology and the evolutionary relationships between the sequences studied. CollecTF snadendla 2016-02-08T14:31:24Z eco ECO:0005555 multiple sequence alignment evidence A type of sequence alignment evidence where three or more biological sequences (protein or nucleic acid) of similar length are aligned to infer homology and the evolutionary relationships between the sequences studied. ECO:SN url:http://www.ebi.ac.uk/Tools/msa/ A type of multiple sequence alignment evidence that is used in a manual assertion. snadendla 2016-02-08T14:59:18Z eco ECO:0005556 multiple sequence alignment evidence used in manual assertion true true A type of multiple sequence alignment evidence that is used in a manual assertion. ECO:SN A type of multiple sequence alignment evidence that is used in an automatic assertion. snadendla 2016-02-08T15:00:50Z eco ECO:0005557 multiple sequence alignment evidence used in automatic assertion true true A type of multiple sequence alignment evidence that is used in an automatic assertion. ECO:SN A type of motif discovery evidence that is used in a manual assertion. snadendla 2016-02-08T15:07:47Z eco ECO:0005558 motif discovery evidence used in manual assertion true true A type of motif discovery evidence that is used in a manual assertion. ECO:SN A type of motif discovery evidence that is used in an automatic assertion. snadendla 2016-02-08T15:08:19Z eco ECO:0005559 motif discovery evidence used in automatic assertion true true A type of motif discovery evidence that is used in an automatic assertion. ECO:SN A type of pairwise sequence alignment evidence that is used in a manual assertion. snadendla 2016-02-08T15:17:05Z eco ECO:0005560 pairwise sequence alignment evidence used in manual assertion true true A type of pairwise sequence alignment evidence that is used in a manual assertion. ECO:SN A type of pairwise sequence alignment evidence that is used in an automatic evidence. snadendla 2016-02-08T15:17:52Z eco ECO:0005561 pairwise sequence alignment evidence used in automatic assertion true true A type of pairwise sequence alignment evidence that is used in an automatic evidence. ECO:SN A type of in vitro assay evidence resulting from the evaluation of the phosphorylation activity of kinase on a gel-incorporated substrate. snadendla 2016-02-09T12:05:29Z eco ECO:0005562 in gel protein kinase assay evidence A type of in vitro assay evidence resulting from the evaluation of the phosphorylation activity of kinase on a gel-incorporated substrate. PMID:12372853 A type of voltage clamp recording evidence that involves recording trace of the current (pA) going through the analyzed ion channels determined from voltage clamp current recording. snadendla 2016-02-09T12:40:03Z eco ECO:0005563 macroscopic current trace evidence A type of voltage clamp recording evidence that involves recording trace of the current (pA) going through the analyzed ion channels determined from voltage clamp current recording. ECO:SN PMID:17938230 url:http://www.utdallas.edu/~tres/microelectrode/microelectrodes_ch03.pdf A type of electrophysiology assay evidence that involves measuring the amount of current (pA) going through the ion channels per unit of membrane. snadendla 2016-02-09T12:43:07Z eco ECO:0005564 current density evidence A type of electrophysiology assay evidence that involves measuring the amount of current (pA) going through the ion channels per unit of membrane. ECO:SN url:http://circres.ahajournals.org/content/102/11/1298.full url:http://www.bem.fi/book/04/04.htm snadendla 2016-02-09T12:45:42Z eco ECO:0005565 single channel conductance evidence true A type of electrophysiology assay evidence that involves the measurement of the current that persists after the fast and slow inactivation of the analyzed channels. snadendla 2016-02-09T12:46:54Z eco ECO:0005566 sustained current evidence A type of electrophysiology assay evidence that involves the measurement of the current that persists after the fast and slow inactivation of the analyzed channels. ECO:SN url:http://www.nature.com/ncomms/journal/v3/n2/full/ncomms1717.html snadendla 2016-02-09T12:48:17Z eco ECO:0005567 steady state activation curve evidence true snadendla 2016-02-09T12:50:45Z eco ECO:0005568 steady state inactivation curve evidence true snadendla 2016-02-09T12:57:16Z eco ECO:0005569 window current trace evidence true A type of electrophysiology assay evidence in which the amount of current remaining after a series of depolarization at different frequencies described as the normalized current related to the time course. snadendla 2016-02-09T12:58:18Z eco ECO:0005570 use dependence of inactivation evidence A type of electrophysiology assay evidence in which the amount of current remaining after a series of depolarization at different frequencies described as the normalized current related to the time course. ECO:SN url:http://circres.ahajournals.org/content/89/8/700.full A type of electrophysiology assay evidence that involves recording the change in membrane potential caused by applying specific current to the cell. snadendla 2016-02-12T13:58:32Z birnlex:2278 current clamp voltage recording evidence eco ECO:0005571 current clamp recording evidence A type of electrophysiology assay evidence that involves recording the change in membrane potential caused by applying specific current to the cell. ECO:SN url:http://www.nature.com/nprot/journal/v4/n8/full/nprot.2009.91.html birnlex:2278 current clamp voltage recording protocol A type of voltage clamp recording evidence that involves direct measurement of ionic current across a membrane while controlling the membrane potential by maintaining the voltage. snadendla 2016-02-12T14:06:40Z birnlex:2281 eco ECO:0005572 whole-cell voltage clamp recording evidence A type of voltage clamp recording evidence that involves direct measurement of ionic current across a membrane while controlling the membrane potential by maintaining the voltage. ECO:SN url:http://circres.ahajournals.org/content/72/1/91.full.pdf birnlex:2281 whole-cell voltage clamp recording protocol A type of patch-clamp recording evidence that involves isolation of a patch of membrane electrically from the external solution and to record current flowing into the patch and this is achieved by pressing a fire-polished glass pipette, which has been filled with a suitable electrolyte solution, against the surface of a cell and applying light suction. snadendla 2016-02-12T14:07:39Z birnlex:2283 cell-attached patch-clamp recording evidence eco ECO:0005573 cell-attached single-channel recording evidence A type of patch-clamp recording evidence that involves isolation of a patch of membrane electrically from the external solution and to record current flowing into the patch and this is achieved by pressing a fire-polished glass pipette, which has been filled with a suitable electrolyte solution, against the surface of a cell and applying light suction. ECO:SN url:http://www.utdallas.edu/~tres/microelectrode/microelectrodes_ch04.pdf birnlex:2283 cell-attached single-channel recording protocol A type of patch-clamp recording evidence that involves study of individual ion channels by gently pulling the patch of membrane away from the cell, and the patch remains attached to the pipette with its cytoplasmic surface exposed to the bathing solution. snadendla 2016-02-12T14:16:53Z birnlex:2286 cell-detached inside-out patch-clamp recording evidence eco ECO:0005574 cell-detached inside-out single-channel recording evidence A type of patch-clamp recording evidence that involves study of individual ion channels by gently pulling the patch of membrane away from the cell, and the patch remains attached to the pipette with its cytoplasmic surface exposed to the bathing solution. ECO:SN url:http://www.acnp.org/g4/GN401000005/CH005.html birnlex:2286 cell-detached inside-out single-channel recording protocol A type of patch-clamp reocrding evidence that involves ion channel analysis by incorporating the ion channels into liposomes suitable for patch-clamping which allows isolation and study of a specific population of channels into that bilayer membrane. snadendla 2016-02-12T14:17:46Z birnlex:2287 eco ECO:0005575 reconstituted bilayer single-channel patch recording evidence A type of patch-clamp reocrding evidence that involves ion channel analysis by incorporating the ion channels into liposomes suitable for patch-clamping which allows isolation and study of a specific population of channels into that bilayer membrane. ECO:SN url:http://nanion.de/images/stories/papers/Bilayers_lab-on-a-chip08.pdf birnlex:2287 reconstituted bilayer single-channel patch recording protocol A type of electrophysiology assay evidence that involves recording membrane potential by controlling the membrane voltage and measuring the transmembrane current required to maintain that voltage. snadendla 2016-02-12T14:18:36Z birnlex:2279 voltage clamp current recording evidence eco ECO:0005576 voltage clamp recording evidence A type of electrophysiology assay evidence that involves recording membrane potential by controlling the membrane voltage and measuring the transmembrane current required to maintain that voltage. ECO:SN url:http://neurobio.drexelmed.edu/GaoWeb/Resources/Recording%20_Techniques.pdf url:http://www.acnp.org/g4/GN401000005/CH005.html birnlex:2279 voltage clamp current recording protocol A type of electrophysiology assay evidence that involves recording the electrical activity of the brain by means of electrodes placed on the surface of the head. snadendla 2016-02-12T14:19:21Z birnlex:2293 eco ECO:0005577 electroencephalography recording evidence A type of electrophysiology assay evidence that involves recording the electrical activity of the brain by means of electrodes placed on the surface of the head. ECO:SN url:http://www.jove.com/science-education/5420/electro-encephalography-eeg birnlex:2293 electroencephalography recording protocol A type of microscopy evidence where the images are taken with a higher resolution than the diffraction limit that help in studying nanoscopic sub-cellular structures. snadendla 2016-02-12T15:20:47Z eco ECO:0005578 super-resolution microscopy evidence A type of microscopy evidence where the images are taken with a higher resolution than the diffraction limit that help in studying nanoscopic sub-cellular structures. ECO:SN url:http://journal.frontiersin.org/article/10.3389/fncel.2015.00007/full A type of immunogold labelling evidence that is used in a manual assertion. snadendla 2016-02-12T15:38:03Z eco ECO:0005579 immunogold labelling evidence used in manual assertion true true A type of immunogold labelling evidence that is used in a manual assertion. ECO:SN A type of flow cytometry evidence that is used in a manual assertion. snadendla 2016-02-12T16:04:23Z eco ECO:0005580 flow cytometry evidence used in manual assertion true true A type of flow cytometry evidence that is used in a manual assertion. ECO:SN A type of enzyme-linked immunoabsorbent assay evidence that is used in a manual assertion. snadendla 2016-02-12T16:23:38Z eco ECO:0005581 enzyme-linked immunoabsorbent assay evidence used in manual assertion true true A type of enzyme-linked immunoabsorbent assay evidence that is used in a manual assertion. ECO:SN A type of patch-clamp recording evidence where a part of cellular membrane is detached from the cell and whose external face is exposed to the extracellular medium which allows isolating and studying a single or at least a small number of channels into that fragment (patch). snadendla 2016-03-02T10:47:25Z cell-detached outside-out patch-clamp evidence eco ECO:0005582 cell-detached outside-out single-channel recording evidence A type of patch-clamp recording evidence where a part of cellular membrane is detached from the cell and whose external face is exposed to the extracellular medium which allows isolating and studying a single or at least a small number of channels into that fragment (patch). ECO:SN url:http://www.nature.com/nprot/journal/v2/n11/full/nprot.2007.403.html A type of voltage clamp recording evidence that involves inserting the oocyte in a chamber that separates the surface into 3 regions where the top portion of the oocyte membrane is the region that is clamped from which currents are actually recorded while the bottom portion is the region of the oocyte that is cut-open, making it possible to inject current intracellularly through a low resistance pathway. snadendla 2016-03-02T11:29:32Z eco ECO:0005583 cut-open oocyte voltage clamp recording evidence A type of voltage clamp recording evidence that involves inserting the oocyte in a chamber that separates the surface into 3 regions where the top portion of the oocyte membrane is the region that is clamped from which currents are actually recorded while the bottom portion is the region of the oocyte that is cut-open, making it possible to inject current intracellularly through a low resistance pathway. ECO:SN PMID:9711615 A type of voltage clamp recording evidence where recording is done on a fragment of the cell membrane (attached to or detached from the cell) using a large tip diameter pipette that allows isolating and studying a small number of channels into that fragment (patch). snadendla 2016-03-02T11:33:48Z eco ECO:0005584 macropatch voltage clamp recording evidence A type of voltage clamp recording evidence where recording is done on a fragment of the cell membrane (attached to or detached from the cell) using a large tip diameter pipette that allows isolating and studying a small number of channels into that fragment (patch). ECO:SN url:http://jxb.oxfordjournals.org/content/50/Special_Issue/1037.full.pdf A type of mass spectrometry evidence where mass-to-charge ratio (m/z) of gas-phase ions is measured which is used to identify and quantify molecules in complex solutions within the framework of high throughput studies. snadendla 2016-03-02T12:33:07Z eco ECO:0005585 There are significant differences in data analysis and data evaluation if to compare a HTP mass-spec and a regular mass-spec. The regular mass spec method is quite a reliable technique for identifying a protein molecular weight and analysing its post-modifications, other mass-spec applications might require the additional quality controls and more stringent data evaluation. More complex sample mixture is processed, more quality questions should be addressed, such as a sample contamination and sensitivity of the mass spectrometer while using HTP mass-spec. For HTP mass-spec, the analysis of the small data sets allows to manually assign the spectra to proteins or peptides, but for large data sets only the statistical tools can be used instead. high throughput mass spectrometry evidence A type of mass spectrometry evidence where mass-to-charge ratio (m/z) of gas-phase ions is measured which is used to identify and quantify molecules in complex solutions within the framework of high throughput studies. ECO:SN PMID:20805795 A type of high throughput mass spectrometry evidence that is used in a manual assertion. snadendla 2016-03-02T12:50:02Z eco ECO:0005586 high throughput mass spectrometry evidence used in manual assertion true A type of high throughput mass spectrometry evidence that is used in a manual assertion. ECO:SN A type of microscopy evidence where sharp images are taken by excluding most of the light from the specimen that is not from the microscope's focal plane, thus allowing better contrast and less haze, which makes it possible to build three-dimensional reconstructions of a volume of the specimen by assembling a series of thin slices taken along the vertical axis. snadendla 2016-03-17T12:29:45Z eco ECO:0005587 confocal microscopy evidence A type of microscopy evidence where sharp images are taken by excluding most of the light from the specimen that is not from the microscope's focal plane, thus allowing better contrast and less haze, which makes it possible to build three-dimensional reconstructions of a volume of the specimen by assembling a series of thin slices taken along the vertical axis. ECO:SN url:http://www.physics.emory.edu/faculty/weeks//lab/papers/ebbe05.pdf A type of microscopy evidence where imaging of a thin cell or a tissue specimen is performed by full aperture emission of light gathered by the microscope's objective, which maximizes the recorded signal and simultaneously minimizes the required exposure times. snadendla 2016-03-17T12:30:27Z eco ECO:0005588 wide-field microscopy evidence A type of microscopy evidence where imaging of a thin cell or a tissue specimen is performed by full aperture emission of light gathered by the microscope's objective, which maximizes the recorded signal and simultaneously minimizes the required exposure times. ECO:SN url:http://jcb.rupress.org/content/172/1/9.full url:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3048960/ url:http://zeiss-campus.magnet.fsu.edu/articles/livecellimaging/techniques.html A type confocal microscopy evidence that is used in a manual assertion. snadendla 2016-03-17T12:32:24Z eco ECO:0005589 confocal microscopy evidence used in manual assertion true true A type confocal microscopy evidence that is used in a manual assertion. ECO:SN A type of wide-field microscopy evidence that is used in a manual assertion. snadendla 2016-03-17T12:34:42Z eco ECO:0005590 wide-field microscopy evidence used in manual assertion true true A type of wide-field microscopy evidence that is used in a manual assertion. ECO:SN A type of immunogold labelling evidence where electron microscopy technique is used to detect the location of the antibodies labeled with colloidal gold particles. snadendla 2016-03-17T15:43:00Z eco ECO:0005591 immunogold labelling electron microscopy assay evidence A type of immunogold labelling evidence where electron microscopy technique is used to detect the location of the antibodies labeled with colloidal gold particles. ECO:SN PMID:4110101 A type of immunogold labelling electron microscopy assay evidence that is used in a manual assertion. snadendla 2016-03-17T16:39:37Z eco ECO:0005592 immunogold labelling electron microscopy assay evidence used in manual assertion true true true A type of immunogold labelling electron microscopy assay evidence that is used in a manual assertion. ECO:SN A type of direct assay evidence that involves the use of antibodies to detect biomolecules. snadendla 2016-03-17T17:07:33Z eco ECO:0005593 immunodetection assay evidence A type of direct assay evidence that involves the use of antibodies to detect biomolecules. ECO:SN A type of immunolocalization evidence involving enzymatic detection of a peroxidase tagged antibody. snadendla 2016-03-17T17:11:34Z eco ECO:0005594 immunoperoxidase immunolocalization evidence A type of immunolocalization evidence involving enzymatic detection of a peroxidase tagged antibody. ECO:SN A type of immunoperoxidase immunolocalization evidence that is used in a manual assertion. snadendla 2016-03-17T17:14:05Z eco ECO:0005595 immunoperoxidase immunolocalization evidence used in manual assertion true true A type of immunoperoxidase immunolocalization evidence that is used in a manual assertion. ECO:SN A type of immunoperoxidase immunolocalization evidence where electron microscopy technique is used for enzymatic detection of a peroxidase tagged antibody. snadendla 2016-03-17T17:16:38Z Immunoperoxidase labelling electron microscopy eco ECO:0005596 immunoperoxidase immunolocalization electron microscopy evidence A type of immunoperoxidase immunolocalization evidence where electron microscopy technique is used for enzymatic detection of a peroxidase tagged antibody. ECO:SN A type of immunoperoxidase immunolocalization electron microscopy evidence that is used in a manual assertion. snadendla 2016-03-17T17:23:56Z eco ECO:0005597 immunoperoxidase immunolocalization electron microscopy evidence used in manual assertion true true true A type of immunoperoxidase immunolocalization electron microscopy evidence that is used in a manual assertion. ECO:SN A type of wide-field microscopy evidence where pure white and ultraviolet light are produced by a mercury lamp, passed through an optical filter (excitation filter), and directed to a sample via a dichroic mirror, followed by detection of the fluorescent light by a camera after it passes through an emission filter. snadendla 2016-03-18T11:53:56Z eco ECO:0005598 The optical filter is used to select the wavelength of excitation light. The detection camera is typically a CCD camera. Both topographical and dynamic information of a sample are obtained. wide-field fluorescence microscopy evidence A type of wide-field microscopy evidence where pure white and ultraviolet light are produced by a mercury lamp, passed through an optical filter (excitation filter), and directed to a sample via a dichroic mirror, followed by detection of the fluorescent light by a camera after it passes through an emission filter. ECO:SN url:http://www.bristol.ac.uk/synaptic/research/techniques/widefield.html A type of wide-field fluorescence microscopy evidence where fluorescently tagged antibodies are imaged that are used to bind to their antigens. snadendla 2016-03-18T11:55:40Z wide-field epifluorescence microscopy eco ECO:0005599 immunofluorescence wide-field microscopy evidence A type of wide-field fluorescence microscopy evidence where fluorescently tagged antibodies are imaged that are used to bind to their antigens. ECO:SN url:http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0057135 A type of confocal microscopy evidence where light passes through immunofluorescent-stained tissue sections or cells and then the emitted light passes through the dichroic mirror and is focused onto the pinhole for subsequent detection. snadendla 2016-03-18T12:48:42Z eco ECO:0005600 This allows visualization of sub cellular distribution of biomolecules of interest. immunofluorescence confocal microscopy evidence A type of confocal microscopy evidence where light passes through immunofluorescent-stained tissue sections or cells and then the emitted light passes through the dichroic mirror and is focused onto the pinhole for subsequent detection. ECO:SN url:http://www.physics.emory.edu/faculty/weeks/confocal/ url:https://www.hycultbiotech.com/media/wysiwyg/protocol_Immunofluorescence.pdf A type of immunofluorescence confocal microscopy evidence that is used in a manual assertion. snadendla 2016-03-18T12:52:04Z eco ECO:0005601 immunofluorescence confocal microscopy evidence used in manual assertion true true true A type of immunofluorescence confocal microscopy evidence that is used in a manual assertion. ECO:SN A type of protein expression level evidence where the level of expression of a protein is determined in a cell or tissue extract by western blot technique. snadendla 2016-03-18T13:02:29Z eco ECO:0005602 protein expression level evidence based on western blot A type of protein expression level evidence where the level of expression of a protein is determined in a cell or tissue extract by western blot technique. ECO:SN A type of mass spectrometry evidence where one or more protein analyses are performed. snadendla 2016-03-18T13:11:37Z eco ECO:0005603 protein mass spectrometry evidence A type of mass spectrometry evidence where one or more protein analyses are performed. ECO:SN A type of experimental evidence where the investigated organism or a potential antagonist is inoculated so as to grow along the diameter line of the agar medium in a Petri dish, then, potentially susceptible microbes (usually bacteria) are streaked perpendicularly to the growth line and inhibition of growth of a test microbe in the vicinity of that line suggests that the antagonist secretes one or more diffusible antibiotics. snadendla 2016-03-29T15:40:54Z eco ECO:0005604 cross-streak test evidence A type of experimental evidence where the investigated organism or a potential antagonist is inoculated so as to grow along the diameter line of the agar medium in a Petri dish, then, potentially susceptible microbes (usually bacteria) are streaked perpendicularly to the growth line and inhibition of growth of a test microbe in the vicinity of that line suggests that the antagonist secretes one or more diffusible antibiotics. ECO:SN url:www.jstor.org/stable/3792785 A type of experimental evidence where sensitivity/resistance to an antimicrobial agent is tested by impregnating small filter disks with a known concentration of antimicrobial agent which is then placed on a Mueller-Hinton agar plate inoculated with the test organism. snadendla 2016-03-29T16:02:22Z zone of inhibition evidence eco ECO:0005605 disk diffusion test evidence A type of experimental evidence where sensitivity/resistance to an antimicrobial agent is tested by impregnating small filter disks with a known concentration of antimicrobial agent which is then placed on a Mueller-Hinton agar plate inoculated with the test organism. ECO:SN url:http://www.cdc.gov/nczved/resources/cholera/ch9.pdf A type of experimental evidence where a foreign genetic material is introduced into the cell for study of gene function and regulation and protein function. snadendla 2016-03-29T16:59:17Z eco ECO:0005606 cell transfection experiment evidence A type of experimental evidence where a foreign genetic material is introduced into the cell for study of gene function and regulation and protein function. ECO:SN url:http://ch.promega.com/resources/product-guides-and-selectors/protocols-and-applications-guide/transfection/ url:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2911531/ A type of chemotaxis assay evidence where the presence or absence of positive or negative chemotaxis in swimming organisms is determined by observing the rotational behavior of the organism tethered to a coverslip by their flagella. snadendla 2016-03-31T15:51:10Z eco ECO:0005607 tethered cell assay evidence A type of chemotaxis assay evidence where the presence or absence of positive or negative chemotaxis in swimming organisms is determined by observing the rotational behavior of the organism tethered to a coverslip by their flagella. ECO:SN PMID:1103143 A type of chemotaxis assay evidence where the presence or absence of positive or negative chemotaxis in swimming organisms is determined by measuring chemotaxis in response to sudden concentration changes from one uniform spatial environment to another. snadendla 2016-03-31T16:42:35Z Temporal assay eco ECO:0005608 tumble frequency assay evidence A type of chemotaxis assay evidence where the presence or absence of positive or negative chemotaxis in swimming organisms is determined by measuring chemotaxis in response to sudden concentration changes from one uniform spatial environment to another. ECO:SN PMID:4576832 A type of chemotaxis assay evidence where the presence or absence of positive or negative chemotaxis in swimming organisms is determined (typically bacteria or archaea) by measuring the rate of accumulation of the organism into a capillary. snadendla 2016-03-31T16:45:29Z eco ECO:0005609 To determine the presence of positive chemotaxis, an attractant is placed in the capillary and the presence of positive chemotaxis is determined based on the amount of organism that accumulated in the capillary. To determine the presence of negative chemotaxis, a repellent is added to the organismal suspension (but not in the capillary) and the organisms that fled into the capillary are measured. capillary assay evidence A type of chemotaxis assay evidence where the presence or absence of positive or negative chemotaxis in swimming organisms is determined (typically bacteria or archaea) by measuring the rate of accumulation of the organism into a capillary. ECO:SN PMID:4632978 A type of biological system reconstruction evidence based on homology evidence that is used in a manual assertion. snadendla 2016-03-31T17:00:03Z eco ECO:0005610 Inference may be based on paralogy and/or orthology of the genome-encoded components and is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. Evidence may originate from a combination of several experiments in the same or another species. biological system reconstruction evidence based on homology evidence used in manual assertion true true A type of biological system reconstruction evidence based on homology evidence that is used in a manual assertion. ECO:SN A type of direct assay evidence used in manual assertion where phenotype or disease association is made with the gene because of involvement in the molecular mechanism of disease or involvement in a pathway known to contribute to a disease. snadendla 2016-04-12T16:55:16Z IED inferred from experimental data eco ECO:0005611 inference from experimental data evidence A type of direct assay evidence used in manual assertion where phenotype or disease association is made with the gene because of involvement in the molecular mechanism of disease or involvement in a pathway known to contribute to a disease. ECO:SN A type of mutant phenotype evidence used in manual assertion where variations or changes, such as mutations or abnormal levels of the product(s) of a single gene of interest, including non-mutational changes such as inhibition with antibodies or other inhibitors are determined. snadendla 2016-04-12T17:09:43Z IPM inferred from phenotype manipulation eco ECO:0005612 Changes can include any gene mutation/knockout, over-expression or ectopic expression of wild-type or mutant genes, anti-sense experiments, RNAi experiments, specific protein inhibitors. inference from phenotype manipulation evidence A type of mutant phenotype evidence used in manual assertion where variations or changes, such as mutations or abnormal levels of the product(s) of a single gene of interest, including non-mutational changes such as inhibition with antibodies or other inhibitors are determined. ECO:SN A type of natural variation mutant evidence used in manual assertion where alleles are directly linked to phenotype and Mendelian diseases as a result of various experiments. snadendla 2016-04-12T17:24:00Z IAGP inferred by association of genotype from phenotype eco ECO:0005613 Used for 1) polymorphism or segregation of genetic markers (SNPs, mutations, RFLPs, microsatellites); 2) polymorphism or segregation of physical markers (FISH, centromeric or heterochromatic regions, chromosomal banding patterns); 3) detection of polymorphisms in inbred stock. inference by association of genotype from phenotype A type of natural variation mutant evidence used in manual assertion where alleles are directly linked to phenotype and Mendelian diseases as a result of various experiments. ECO:SN A type of two-dimensional polyacrylamide gel electrophoresis evidence that is used in a manual assertion. snadendla 2016-05-06T11:03:08Z eco ECO:0005614 two-dimensional polyacrylamide gel electrophoresis evidence used in manual assertion true true A type of two-dimensional polyacrylamide gel electrophoresis evidence that is used in a manual assertion. ECO:SN A type of alkaline phosphatase reporter gene assay evidence that is used in a manual assertion. snadendla 2016-05-06T11:05:59Z eco ECO:0005615 alkaline phosphatase reporter gene assay evidence used in manual assertion true true A type of alkaline phosphatase reporter gene assay evidence that is used in a manual assertion. ECO:SN A type of beta-galactosidase reporter gene assay evidence that is used in a manual assertion. snadendla 2016-05-06T11:08:57Z eco ECO:0005616 beta-galactosidase reporter gene assay evidence used in manual assertion true true A type of beta-galactosidase reporter gene assay evidence that is used in a manual assertion. ECO:SN A type of chloramphenicol acetyltransferase reporter gene assay evidence that is used in a manual assertion. snadendla 2016-05-06T11:11:07Z eco ECO:0005617 chloramphenicol acetyltransferase reporter gene assay evidence used in manual assertion true true A type of chloramphenicol acetyltransferase reporter gene assay evidence that is used in a manual assertion. ECO:SN A type of chromatin immunoprecipitation-chip evidence that is used in an automatic assertion. snadendla 2016-05-06T11:17:04Z eco ECO:0005618 chromatin immunoprecipitation-chip evidence used in automatic assertion true true A type of chromatin immunoprecipitation-chip evidence that is used in an automatic assertion. ECO:SN A type of chromatin immunoprecipitation- exonuclease evidence that is used in an automatic assertion. snadendla 2016-05-06T11:22:25Z eco ECO:0005619 chromatin immunoprecipitation- exonuclease evidence used in automatic assertion true true A type of chromatin immunoprecipitation- exonuclease evidence that is used in an automatic assertion. ECO:SN A type of chromatin immunoprecipitation-PCR evidence that is used in a manual assertion. snadendla 2016-05-06T11:25:01Z eco ECO:0005620 chromatin immunoprecipitation-PCR evidence used in manual assertion true true A type of chromatin immunoprecipitation-PCR evidence that is used in a manual assertion. ECO:SN A type of chromatin immunoprecipitation-seq evidence that is used in an automatic assertion. snadendla 2016-05-06T11:29:13Z eco ECO:0005621 chromatin immunoprecipitation-seq evidence used in automatic assertion true true A type of chromatin immunoprecipitation-seq evidence that is used in an automatic assertion. ECO:SN A type of comparative genomics motif search evidence that is used in a manual assertion. snadendla 2016-05-06T14:49:36Z eco ECO:0005622 comparative genomics motif search evidence used in manual assertion true true A type of comparative genomics motif search evidence that is used in a manual assertion. ECO:SN A type of comparative genomics motif search evidence that is used in an automatic assertion. snadendla 2016-05-06T14:52:21Z eco ECO:0005623 comparative genomics motif search evidence used in automatic assertion true true A type of comparative genomics motif search evidence that is used in an automatic assertion. ECO:SN A type of consensus search evidence that is used in a manual assertion. snadendla 2016-05-06T14:54:53Z eco ECO:0005624 consensus search evidence used in manual assertion true true A type of consensus search evidence that is used in a manual assertion. ECO:SN A type of consensus search evidence that is used in an automatic assertion. snadendla 2016-05-06T14:58:22Z eco ECO:0005625 consensus search evidence used in automatic assertion true true A type of consensus search evidence that is used in an automatic assertion. ECO:SN A type of copper-phenanthroline footprinting evidence that is used in a manual assertion. snadendla 2016-05-06T15:01:25Z eco ECO:0005626 copper-phenanthroline footprinting evidence used in manual assertion true true A type of copper-phenanthroline footprinting evidence that is used in a manual assertion. ECO:SN A type of DNA adenine methyltransferase identification evidence that is used in a manual assertion. snadendla 2016-05-06T15:05:14Z eco ECO:0005627 DNA adenine methyltransferase identification evidence used in manual assertion true true A type of DNA adenine methyltransferase identification evidence that is used in a manual assertion. ECO:SN A type of DNA adenine methyltransferase identification evidence that is used in an automatic assertion. snadendla 2016-05-06T15:06:46Z eco ECO:0005628 DNA adenine methyltransferase identification evidence used in automatic assertion true true A type of DNA adenine methyltransferase identification evidence that is used in an automatic assertion. ECO:SN A type of DNA affinity chromatography evidence that is used in a manual assertion. snadendla 2016-05-06T15:08:40Z eco ECO:0005629 DNA affinity chromatography evidence used in manual assertion true true A type of DNA affinity chromatography evidence that is used in a manual assertion. ECO:SN A type of cDNA to DNA expression microarray evidence that is used in an automatic assertion. snadendla 2016-05-06T15:31:51Z eco ECO:0005630 cDNA to DNA expression microarray evidence used in automatic assertion true true A type of cDNA to DNA expression microarray evidence that is used in an automatic assertion. ECO:SN A type of DNAse footprinting evidence that is used in a manual assertion. snadendla 2016-05-06T15:35:41Z eco ECO:0005631 DNAse footprinting evidence used in manual assertion true true A type of DNAse footprinting evidence that is used in a manual assertion. ECO:SN A type of fluorescence anisotropy evidence that is used in a manual assertion. snadendla 2016-05-06T15:45:40Z eco ECO:0005632 fluorescence anisotropy evidence used in manual assertion true true A type of fluorescence anisotropy evidence that is used in a manual assertion. ECO:SN A type of ferric uptake regulator titration assay evidence that is used in a manual assertion. snadendla 2016-05-06T15:49:18Z eco ECO:0005633 ferric uptake regulator titration assay evidence used in manual assertion true true A type of ferric uptake regulator titration assay evidence that is used in a manual assertion. ECO:SN A type of genomic systematic evolution of ligands by exponential amplification evidence that is used in a manual assertion. snadendla 2016-05-06T16:41:30Z eco ECO:0005634 genomic systematic evolution of ligands by exponential amplification evidence used in manual assertion true true A type of genomic systematic evolution of ligands by exponential amplification evidence that is used in a manual assertion. ECO:SN A type of genomic systematic evolution of ligands by exponential amplification evidence that is used in an automatic assertion. snadendla 2016-05-06T16:43:03Z eco ECO:0005635 genomic systematic evolution of ligands by exponential amplification evidence used in automatic assertion true true A type of genomic systematic evolution of ligands by exponential amplification evidence that is used in an automatic assertion. ECO:SN A type of green fluorescent protein reporter gene assay evidence that is used in a manual assertion. snadendla 2016-05-06T16:46:32Z eco ECO:0005636 green fluorescent protein reporter gene assay evidence used in manual assertion true true A type of green fluorescent protein reporter gene assay evidence that is used in a manual assertion. ECO:SN A type of green fluorescent protein reporter gene assay evidence that is used in an automatic assertion. snadendla 2016-05-06T16:48:29Z eco ECO:0005637 green fluorescent protein reporter gene assay evidence used in automatic assertion true true A type of green fluorescent protein reporter gene assay evidence that is used in an automatic assertion. ECO:SN A type of cell growth assay evidence that is used in a manual assertion. snadendla 2016-05-06T16:52:15Z eco ECO:0005638 cell growth assay evidence used in manual assertion true true A type of cell growth assay evidence that is used in a manual assertion. ECO:SN A type of cell growth assay evidence that is used in an automatic assertion. snadendla 2016-05-06T16:53:28Z eco ECO:0005639 cell growth assay evidence used in automatic assertion true true A type of cell growth assay evidence that is used in an automatic assertion. ECO:SN A type of glutathione S-transferase pull-down assay evidence that is used in a manual assertion. snadendla 2016-05-06T16:56:39Z eco ECO:0005640 glutathione S-transferase pull-down assay evidence used in manual assertion true true A type of glutathione S-transferase pull-down assay evidence that is used in a manual assertion. ECO:SN A type of beta-glucuronidase reporter gene assay evidence that is used in a manual assertion. snadendla 2016-05-06T16:58:29Z eco ECO:0005641 beta-glucuronidase reporter gene assay evidence used in manual assertion true true A type of beta-glucuronidase reporter gene assay evidence that is used in a manual assertion. ECO:SN A type of heteronuclear single quantum coherence spectroscopy evidence that is used in a manual assertion. snadendla 2016-05-06T23:10:13Z eco ECO:0005642 heteronuclear single quantum coherence spectroscopy evidence used in manual assertion true true A type of heteronuclear single quantum coherence spectroscopy evidence that is used in a manual assertion. ECO:SN A type of hydroxyl-radical footprinting evidence that is used in a manual assertion. snadendla 2016-05-06T23:14:48Z eco ECO:0005643 hydroxyl-radical footprinting evidence used in manual assertion true true A type of hydroxyl-radical footprinting evidence that is used in a manual assertion. ECO:SN A type of immunoprecipitation evidence that is used in a manual assertion. snadendla 2016-05-06T23:20:49Z eco ECO:0005644 immunoprecipitation evidence used in manual assertion true true A type of immunoprecipitation evidence that is used in a manual assertion. ECO:SN A type of interferometric reflectance imaging sensor evidence that is used in a manual assertion. snadendla 2016-05-06T23:27:58Z eco ECO:0005645 interferometric reflectance imaging sensor evidence used in manual assertion true true A type of interferometric reflectance imaging sensor evidence that is used in a manual assertion. ECO:SN A type of interferometric reflectance imaging sensor evidence that is used in an automatic assertion. snadendla 2016-05-06T23:29:23Z eco ECO:0005646 interferometric reflectance imaging sensor evidence used in automatic assertion true true A type of interferometric reflectance imaging sensor evidence that is used in an automatic assertion. ECO:SN A type of isothermal titration calorimetry evidence that is used in a manual assertion. snadendla 2016-05-06T23:36:26Z eco ECO:0005647 isothermal titration calorimetry evidence used in manual assertion true true A type of isothermal titration calorimetry evidence that is used in a manual assertion. ECO:SN A type of luciferase reporter gene assay evidence that is used in a manual assertion. snadendla 2016-05-06T23:44:52Z eco ECO:0005648 luciferase reporter gene assay evidence used in manual assertion true true A type of luciferase reporter gene assay evidence that is used in a manual assertion. ECO:SN A type of machine learning prediction of motif instance evidence that is used in a manual assertion. snadendla 2016-05-06T23:51:30Z eco ECO:0005649 machine learning prediction of motif instance evidence used in manual assertion true true A type of machine learning prediction of motif instance evidence that is used in a manual assertion. ECO:SN A type of machine learning prediction of motif instance evidence that is used in an automatic assertion. snadendla 2016-05-06T23:54:00Z eco ECO:0005650 machine learning prediction of motif instance evidence used in automatic assertion true true A type of machine learning prediction of motif instance evidence that is used in an automatic assertion. ECO:SN A type of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence that is used in an automatic assertion. snadendla 2016-05-06T23:57:30Z eco ECO:0005651 matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence used in automatic assertion true true A type of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence that is used in an automatic assertion. ECO:SN A type of methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence that is used in a manual assertion. snadendla 2016-05-09T14:42:28Z eco ECO:0005652 methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence used in manual assertion true true A type of methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence that is used in a manual assertion. ECO:SN A type of northern assay evidence that is used in a manual assertion. snadendla 2016-05-09T14:48:03Z eco ECO:0005653 northern assay evidence used in manual assertion true true A type of northern assay evidence that is used in a manual assertion. ECO:SN A type of phylogenetic footprinting evidence that is used in a manual assertion. snadendla 2016-05-09T14:50:52Z eco ECO:0005654 phylogenetic footprinting evidence used in manual assertion true true A type of phylogenetic footprinting evidence that is used in a manual assertion. ECO:SN A type of phylogenetic footprinting evidence that is used in an automatic assertion. snadendla 2016-05-09T14:51:55Z eco ECO:0005655 phylogenetic footprinting evidence used in automatic assertion true true A type of phylogenetic footprinting evidence that is used in an automatic assertion. ECO:SN A type of premethylation interference footprinting evidence that is used in a manual assertion. snadendla 2016-05-09T14:55:25Z eco ECO:0005656 premethylation interference footprinting evidence used in manual assertion true true A type of premethylation interference footprinting evidence that is used in a manual assertion. ECO:SN A type of primer extension assay evidence that is used in a manual assertion. snadendla 2016-05-09T14:58:38Z eco ECO:0005657 primer extension assay evidence used in manual assertion true true A type of primer extension assay evidence that is used in a manual assertion. ECO:SN A type of position-specific scoring matrix motif search evidence that is used in a manual assertion. snadendla 2016-05-09T15:01:31Z eco ECO:0005658 position-specific scoring matrix motif search evidence used in manual assertion true true A type of position-specific scoring matrix motif search evidence that is used in a manual assertion. ECO:SN A type of position-specific scoring matrix motif search evidence that is used in an automatic assertion. snadendla 2016-05-09T15:02:31Z eco ECO:0005659 position-specific scoring matrix motif search evidence used in automatic assertion true true A type of position-specific scoring matrix motif search evidence that is used in an automatic assertion. ECO:SN A type of quantitative polymerase chain reaction evidence that is used in a manual assertion. snadendla 2016-05-09T15:09:01Z eco ECO:0005660 quantitative polymerase chain reaction evidence used in manual assertion true true A type of quantitative polymerase chain reaction evidence that is used in a manual assertion. ECO:SN A type of rapid amplification of cDNA ends polymerase chain reaction evidence that is used in a manual assertion. snadendla 2016-05-09T15:19:20Z eco ECO:0005661 rapid amplification of cDNA ends polymerase chain reaction evidence used in manual assertion true true A type of rapid amplification of cDNA ends polymerase chain reaction evidence that is used in a manual assertion. ECO:SN A type of regular expression motif search evidence that is used in a manual assertion. snadendla 2016-05-09T16:13:55Z eco ECO:0005662 regular expression motif search evidence used in manual assertion true true A type of regular expression motif search evidence that is used in a manual assertion. ECO:SN A type of regular expression motif search evidence that is used in an automatic assertion. snadendla 2016-05-09T16:15:03Z eco ECO:0005663 regular expression motif search evidence used in automatic assertion true true A type of regular expression motif search evidence that is used in an automatic assertion. ECO:SN A type of RNA sequencing assay evidence that is used in a manual assertion. snadendla 2016-05-09T16:18:35Z eco ECO:0005664 Use ECO:0006068 (RNA-seq evidence used in manual assertion) in place of this term. RNA sequencing assay evidence used in manual assertion true A type of RNA sequencing assay evidence that is used in a manual assertion. ECO:SN A type of RNA sequencing assay evidence that is used in an automatic assertion. snadendla 2016-05-09T16:19:38Z eco ECO:0005665 Use ECO:0006069 (RNA-seq evidence used in automatic assertion) in place of this term. RNA sequencing assay evidence used in automatic assertion true A type of RNA sequencing assay evidence that is used in an automatic assertion. ECO:SN A type of S1 nuclease protection assay evidence that is used in a manual assertion. snadendla 2016-05-09T16:22:58Z eco ECO:0005666 S1 nuclease protection assay evidence used in manual assertion true true A type of S1 nuclease protection assay evidence that is used in a manual assertion. ECO:SN A type of site-directed mutagenesis evidence that is used in a manual assertion. snadendla 2016-05-09T16:29:13Z eco ECO:0005667 site-directed mutagenesis evidence used in manual assertion true true A type of site-directed mutagenesis evidence that is used in a manual assertion. ECO:SN A type of survival rate analysis evidence that is used in a manual assertion. snadendla 2016-05-09T16:31:08Z eco ECO:0005668 survival rate analysis evidence used in manual assertion true true A type of survival rate analysis evidence that is used in a manual assertion. ECO:SN A type of ultraviolet light footprinting evidence that is used in a manual assertion. snadendla 2016-05-09T16:33:44Z eco ECO:0005669 ultraviolet light footprinting evidence used in manual assertion true true A type of ultraviolet light footprinting evidence that is used in a manual assertion. ECO:SN A type of x-ray crystallography evidence that is used in a manual assertion. snadendla 2016-05-10T11:53:00Z eco ECO:0005670 x-ray crystallography evidence used in manual assertion true true A type of x-ray crystallography evidence that is used in a manual assertion. ECO:SN A type of x-ray crystallography evidence that is used in an automatic assertion. snadendla 2016-05-10T11:54:03Z eco ECO:0005671 x-ray crystallography evidence used in automatic assertion true true A type of x-ray crystallography evidence that is used in an automatic assertion. ECO:SN A type of xylE reporter gene assay evidence that is used in a manual assertion. snadendla 2016-05-10T11:57:15Z eco ECO:0005672 xylE reporter gene assay evidence used in manual assertion true true A type of xylE reporter gene assay evidence that is used in a manual assertion. ECO:SN A type of experimental phenotypic evidence where a non-standard trait (e.g. natural competence) is assessed qualitatively (e.g. presence/absence) and used as a natural reporter to conclude that some genes or pathways are regulated by the transcription factor. CollecTF snadendla 2016-05-10T12:57:41Z eco ECO:0005673 ad-hoc qualitative phenotype observation evidence A type of experimental phenotypic evidence where a non-standard trait (e.g. natural competence) is assessed qualitatively (e.g. presence/absence) and used as a natural reporter to conclude that some genes or pathways are regulated by the transcription factor. ECO:SN PMID:15150239 A type of ad-hoc qualitative phenotype observation that is used in a manual assertion. snadendla 2016-05-10T14:28:47Z eco ECO:0005674 ad-hoc qualitative phenotype observation evidence used in manual assertion true true A type of ad-hoc qualitative phenotype observation that is used in a manual assertion. ECO:SN A type of experimental phenotypic evidence where a quantifiable phenotypic trait (e.g. glucose intake) is assessed in a quantitative manner after induction of the regulatory mechanism and used as a natural reporter to conclude that some genes or pathways are regulated by the transcription factor. CollecTF snadendla 2016-05-10T14:30:50Z eco ECO:0005675 ad-hoc quantitative phenotype observation evidence A type of experimental phenotypic evidence where a quantifiable phenotypic trait (e.g. glucose intake) is assessed in a quantitative manner after induction of the regulatory mechanism and used as a natural reporter to conclude that some genes or pathways are regulated by the transcription factor. ECO:SN PMID:15150239 A type of ad-hoc quantitative phenotype observation evidence that is used in a manual assertion. snadendla 2016-05-10T14:34:50Z eco ECO:0005676 ad-hoc quantitative phenotype observation evidence used in manual assertion true true A type of ad-hoc quantitative phenotype observation evidence that is used in a manual assertion. ECO:SN A direct assay evidence where the activity of a solution is determined by exposing an indicator culture or organism to a series of dilutions and determining the lowest concentration that elicits a biological response. critical dilution assay spot assay For chemicals, bacteriocins, or phage, the indicator culture is typically present in a soft-agar layer on top of nutrient agar and a small quantity of each dilution is spotted onto the soft agar overlay. dilution assay evidence A direct assay evidence where the activity of a solution is determined by exposing an indicator culture or organism to a series of dilutions and determining the lowest concentration that elicits a biological response. http://www.sciencedirect.com/science/article/pii/016770129400068I A type of enzyme assay evidence that is used in a manual assertion. eco ECO:0005801 enzyme assay evidence used in manual assertion true A type of enzyme assay evidence that is used in a manual assertion. ECO:SN A type of cell transfection experiment evidence that is used in a manual assertion. eco ECO:0005802 cell transfection experiment evidence used in manual assertion true A type of cell transfection experiment evidence that is used in a manual assertion. ECO:SN A type of direct assay evidence where the motility of a cell or cells is determined. eco ECO:0005803 motility assay evidence A type of direct assay evidence where the motility of a cell or cells is determined. ECO:SN A type of immunofluorescence evidence that is used in a manual assertion. eco ECO:0005804 immunofluorescence evidence used in manual assertion true A type of immunofluorescence evidence that is used in a manual assertion. ECO:SN A type of yeast 2-hybrid evidence that is used in a manual assertion. eco ECO:0005805 yeast 2-hybrid evidence used in manual assertion true A type of yeast 2-hybrid evidence that is used in a manual assertion. ECO:SN A type of evidence derived from exploiting the CyaA (calmodulin-activated adenylate cyclase toxin) secreted by Bordatella pertussis to synthesize cAMP and alter cellular physiology in a host cell for various biological applications. rctauber 2016-06-15T08:42:16Z eco ECO:0006001 Cya fusion reporter assay evidence A type of evidence derived from exploiting the CyaA (calmodulin-activated adenylate cyclase toxin) secreted by Bordatella pertussis to synthesize cAMP and alter cellular physiology in a host cell for various biological applications. PMID:10217833 PMID:14702323 A type of Cya fusion reporter assay evidence that is used in a manual assertion. CollecTF rctauber 2010-06-15T08:44:10Z eco ECO:0006002 Cya fusion reporter assay evidence used in manual assertion true A type of Cya fusion reporter assay evidence that is used in a manual assertion. ECO:RCT A type of electron microscopy evidence that is used in a manual assertion. rctauber 2016-10-12T12:32:29Z eco ECO:0006003 electron microscopy evidence used in manual assertion true A type of electron microscopy evidence that is used in a manual assertion. ECO:RCT A type of super-resolution microscopy evidence that is used in a manual assertion. rctauber 2016-10-12T12:32:29Z eco ECO:0006004 super-resolution microscopy evidence used in manual assertion true A type of super-resolution microscopy evidence that is used in a manual assertion. ECO:RCT A type of fractionation evidence that is used in a manual assertion. rctauber 2016-10-12T12:32:29Z eco ECO:0006005 fractionation evidence used in manual assertion true A type of fractionation evidence that is used in a manual assertion. ECO:RCT A type of electrophysiology assay evidence that is used in a manual assertion. rctauber 2016-10-12T12:32:29Z eco ECO:0006006 electrophysiology assay evidence used in manual assertion true A type of electrophysiology assay evidence that is used in a manual assertion. ECO:RCT A type of chromatin immunoprecipitation-chip evidence that is used in a manual assertion. rctauber 2016-10-21T11:55:53Z eco ECO:0006007 chromatin immunoprecipitation-chip evidence used in manual assertion true A type of chromatin immunoprecipitation-chip evidence that is used in a manual assertion. ECO:RCT A type of chromatin immunoprecipitation- exonuclease evidence that is used in a manual assertion. rctauber 2016-10-21T11:55:53Z eco ECO:0006008 chromatin immunoprecipitation- exonuclease evidence used in manual assertion true A type of chromatin immunoprecipitation- exonuclease evidence that is used in a manual assertion. ECO:RCT A type of chromatin immunoprecipitation-seq evidence that is used in a manual assertion. rctauber 2016-10-21T11:55:53Z eco ECO:0006009 chromatin immunoprecipitation-seq evidence used in manual assertion true A type of chromatin immunoprecipitation-seq evidence that is used in a manual assertion. ECO:RCT A type of nucleic acid binding evidence in which RNA-binding proteins are identified through cross-linking RNA and proteins by UV light, capturing RNA-protein complexes on oligo(dT) beads, and finally identifying by mass spectrometry. rctauber 2016-10-21T12:28:17Z ultraviolet light cross-linking RNA binding evidence eco ECO:0006010 mRNA interactome capture evidence A type of nucleic acid binding evidence in which RNA-binding proteins are identified through cross-linking RNA and proteins by UV light, capturing RNA-protein complexes on oligo(dT) beads, and finally identifying by mass spectrometry. PMID:27729395 A type of mRNA interactome capture evidence that is used in a manual assertion. rctauber 2016-10-21T12:28:17Z eco ECO:0006011 mRNA interactome capture evidence used in manual assertion true A type of mRNA interactome capture evidence that is used in a manual assertion. ECO:RCT A type of electrophysiology assay evidence in which a glass micropipette is sealed to the surface of a cell membrane (patch) to study ion channels. rctauber 2016-11-28T11:44:05Z eco ECO:0006012 patch-clamp recording evidence A type of electrophysiology assay evidence in which a glass micropipette is sealed to the surface of a cell membrane (patch) to study ion channels. ECO:RCT A type of patch-clamp recording evidence that is used in a manual assertion. rctauber 2016-11-28T11:44:05Z eco ECO:0006013 patch-clamp recording evidence used in manual assertion A type of patch-clamp recording evidence that is used in a manual assertion. ECO:RCT A type of patch-clamp recording evidence in which a glass micropipette filled with a prepared solution is used to form a seal with the cell membrane followed by rupture of membrane to provide accurate and high resolution electrical property measurements of the whole cell. rctauber 2016-11-28T11:44:05Z eco ECO:0006014 whole-cell patch-clamp recording evidence A type of patch-clamp recording evidence in which a glass micropipette filled with a prepared solution is used to form a seal with the cell membrane followed by rupture of membrane to provide accurate and high resolution electrical property measurements of the whole cell. PMID:27341060 A type of whole-cell patch-clamp recording evidence that is used in a manual assertion. rctauber 2016-11-28T11:44:05Z eco ECO:0006015 whole-cell patch-clamp recording evidence used in manual assertion A type of whole-cell patch-clamp recording evidence that is used in a manual assertion. ECO:RCT A type of traceable author statement that is based on a publication about a clinical study. rctauber 2016-11-30T09:44:47Z published clinical study evidence eco ECO:0006016 traceable author statement from published clinical study A type of traceable author statement from published clinical study that is used in a manual assertion. rctauber 2016-11-30T09:44:47Z PCS eco ECO:0006017 Created and used by the Human Phenotype Ontology (HPO) Annotations group. Here it is used when evidence for an HPO annotation is information extracted from articles in the medical literature. traceable author statement from published clinical study used in manual assertion http://human-phenotype-ontology.github.io/documentation.html#annot true PCS HPO:PCS A type of curator inference that is based on the individual clinical experience of a clinician rctauber 2016-11-30T09:44:47Z individual clinical experience evidence eco ECO:0006018 inference based on individual clinical experience A type of inference based on individual clinical experience that is used in a manual assertion. rctauber 2016-11-30T09:44:47Z ICE eco ECO:0006019 Created and used by the Human Phenotype Ontology (HPO) Annotations group. Here it is used for annotating disorders with a limited amount of published data, and is accompanied by a reference to the individual or center performing the annotation. inference based on individual clinical experience used in manual assertion http://human-phenotype-ontology.github.io/documentation.html#annot true ICE HPO:ICE A type of in vitro culture assay evidence in which biofilm growth is monitored and detected from attachment to development. rctauber 2016-12-05T09:33:18Z eco ECO:0006020 biofilm formation assay evidence A type of in vitro culture assay evidence in which biofilm growth is monitored and detected from attachment to development. PMID:10547784 A type of biofilm formation assay evidence that is used in a manual assertion. rctauber 2016-12-05T09:33:18Z eco ECO:0006021 biofilm formation assay evidence used in manual assertion true A type of biofilm formation assay evidence that is used in a manual assertion. ECO:RCT A type of biofilm formation assay evidence in which microtiter dishes or tubes are inoculated and incubated to promote biofilm formation, and then biofilms are detected by staining with crystal violet or safranin to observe phenotypes. rctauber 2016-12-05T09:33:18Z eco ECO:0006022 microtiter plate biofilm assay evidence A type of biofilm formation assay evidence in which microtiter dishes or tubes are inoculated and incubated to promote biofilm formation, and then biofilms are detected by staining with crystal violet or safranin to observe phenotypes. PMID:10547784 A type of microtiter plate biofilm assay evidence that is used in a manual assertion. rctauber 2016-12-05T09:33:18Z eco ECO:0006023 microtiter plate biofilm assay evidence used in manual assertion true A type of microtiter plate biofilm assay evidence that is used in a manual assertion. ECO:RCT A type of biofilm formation assay evidence in which biofilm formation is analyzed, without staining, over 4 to 48 hours by growth on a tilted multiwell plate. rctauber 2016-12-05T09:33:18Z ALI biofilm assay evidence eco ECO:0006024 Tilting of the plate positions the air-liquid interface on a clear portion to improve visability. air-liquid interface assay evidence A type of biofilm formation assay evidence in which biofilm formation is analyzed, without staining, over 4 to 48 hours by growth on a tilted multiwell plate. PMID:18770545 A type of air-liquid interface assay evidence that is used in a manual assertion. rctauber 2016-12-05T09:33:18Z eco ECO:0006025 air-liquid interface assay evidence used in manual assertion true A type of air-liquid interface assay evidence that is used in a manual assertion. ECO:RCT A type of biofilm formation assay evidence in which a colony is grown on a semipermeable membrane on an agar plate to continously supply nutrients by relocating to fresh plates. rctauber 2016-12-05T09:33:18Z eco ECO:0006026 The plates commonly contain different carbon sources or antibiotic treatments to observe properties of the cells. colony biofilm assay evidence A type of biofilm formation assay evidence in which a colony is grown on a semipermeable membrane on an agar plate to continously supply nutrients by relocating to fresh plates. PMID:18770545 A type of colony biofilm assay evidence that is used in a manual assertion. rctauber 2016-12-05T09:33:18Z eco ECO:0006027 colony biofilm assay evidence used in manual assertion true A type of colony biofilm assay evidence that is used in a manual assertion. ECO:RCT A type of biofilm formation assay evidence in which mature bacterial biofilms are grown in a multiwell plate that has a growth medium continually pumped through the wells while waste is continually pumped out. rctauber 2016-12-05T09:33:18Z eco ECO:0006028 Kadouri drip-fed biofilm assay evidence A type of biofilm formation assay evidence in which mature bacterial biofilms are grown in a multiwell plate that has a growth medium continually pumped through the wells while waste is continually pumped out. PMID:18770545 A type of Kadouri drip-fed biofilm assay evidence that is used in a manual assertion. rctauber 2016-12-05T09:33:18Z eco ECO:0006029 Kadouri drip-fed biofilm assay evidence used in manual assertion true A type of Kadouri drip-fed biofilm assay evidence that is used in a manual assertion. ECO:RCT A type of co-immunoprecipitation evidence that is used in a manual assertion. rctauber 2016-01-13T11:32:26Z eco ECO:0006030 co-immunoprecipitation evidence used in manual assertion true true A type of co-immunoprecipitation evidence that is used in a manual assertion. ECO:RCT A type of immunolocalization evidence that is used in a manual assertion. rctauber 2017-01-23T07:54:37Z eco ECO:0006031 immunolocalization evidence used in manual assertion true A type of immunolocalization evidence that is used in a manual assertion. ECO:RCT A type of experimental phenotypic evidence arising from experiment in which neuronal activity is manipulated using genetically encoded, optically activated neuronal actuators. rctauber 2017-01-23T11:58:48Z optogenetic actuator evidence eco ECO:0006032 optogenetic evidence A type of experimental phenotypic evidence arising from experiment in which neuronal activity is manipulated using genetically encoded, optically activated neuronal actuators. GOC:DOS PMID:17035522 A type of optogenetic evidence that is used in a manual assertion. rctauber 2017-01-23T11:58:48Z eco ECO:0006033 optogenetic evidence used in manual assertion true A type of optogenetic evidence that is used in a manual assertion. ECO:RCT A type of fluorescence evidence that is based on direct, quantitative measurement of some cellular property using a fluorescent sensor. rctauber 2017-01-23T11:58:48Z eco ECO:0006034 Examples include sensors for ion concentration and potential difference across a membrane. fluorescent sensor evidence A type of fluorescence evidence that is based on direct, quantitative measurement of some cellular property using a fluorescent sensor. GOC:DOS A type of fluorescent sensor evidence that is used in a manual assertion. rctauber 2017-01-23T11:58:48Z eco ECO:0006035 fluorescent sensor evidence used in manual assertion true A type of fluorescent sensor evidence that is used in a manual assertion. ECO:RCT A type of fluorescent sensor evidence that is based on direct, quantitative measurement of some cellular property using a genetically encoded fluorescent sensor. rctauber 2017-01-23T11:58:48Z optogenetic sensor evidence eco ECO:0006036 genetically encoded fluorescent sensor evidence A type of fluorescent sensor evidence that is based on direct, quantitative measurement of some cellular property using a genetically encoded fluorescent sensor. GOC:DOS A type of genetically encoded fluorescent sensor evidence that is used in a manual assertion. rctauber 2017-01-23T11:58:48Z eco ECO:0006037 genetically encoded fluorescent sensor evidence used in manual assertion true A type of genetically encoded fluorescent sensor evidence that is used in a manual assertion. ECO:RCT A type of fluorescent sensor evidence and electrophysiology assay evidence where the electrical properties of cells or tissues are studied using fluorescent sensors. rctauber 2017-01-23T11:58:48Z electrophysiology - optical assay evidence eco ECO:0006038 Examples include genetically encoded sensors that detect potential difference across plasma membrane. genetically encoded fluorescent electrophysiology assay evidence A type of fluorescent sensor evidence and electrophysiology assay evidence where the electrical properties of cells or tissues are studied using fluorescent sensors. GOC:DOS A type of genetically encoded fluorescent electrophysiology assay evidence that is used in a manual assertion. rctauber 2017-01-23T11:58:48Z eco ECO:0006039 genetically encoded fluorescent electrophysiology assay evidence used in manual assertion true true A type of genetically encoded fluorescent electrophysiology assay evidence that is used in a manual assertion. ECO:RCT A type of genetically encoded fluorescent electrophysiology assay evidence that is based on direct, quantitative measurement of ion concentration using a genetically encoded fluorescent sensor. rctauber 2017-01-23T11:58:48Z eco ECO:0006040 Examples include the genetically encoded calcium indicator GCaMP. genetically encoded fluorescent ion concentration sensor assay evidence A type of genetically encoded fluorescent electrophysiology assay evidence that is based on direct, quantitative measurement of ion concentration using a genetically encoded fluorescent sensor. GOC:DOS A type of genetically encoded fluorescent ion concentration sensor assay evidence that is used in a manual assertion. rctauber 2017-01-23T11:58:48Z eco ECO:0006041 genetically encoded fluorescent ion concentration sensor assay evidence used in manual assertion true A type of genetically encoded fluorescent ion concentration sensor assay evidence that is used in a manual assertion. ECO:RCT A type of cell fractionation evidence that is used in a manual assertion. rctauber 2017-02-21T07:26:28Z eco ECO:0006042 cell fractionation evidence used in manual assertion true A type of cell fractionation evidence that is used in a manual assertion. ECO:RCT A type of electrophysiology assay evidence resulting from the use of electrodes to measure in vivo electrical activity coming from adjacent neurons. rctauber 2017-02-21T07:26:28Z eco ECO:0006043 extracellular recording evidence A type of electrophysiology assay evidence resulting from the use of electrodes to measure in vivo electrical activity coming from adjacent neurons. url:http://www.nature.com/subjects/extracellular-recording A type of extracellular recording evidence that is used in a manual assertion. rctauber 2017-02-21T07:26:28Z eco ECO:0006044 extracellular recording evidence used in manual assertion true A type of extracellular recording evidence that is used in a manual assertion. ECO:RCT A type of extracellular recording evidence in which an extracellular microelectrode is used to measure the electrical activity of a single neuron. rctauber 2017-02-21T07:26:28Z eco ECO:0006045 single-unit extracellular recording evidence A type of extracellular recording evidence in which an extracellular microelectrode is used to measure the electrical activity of a single neuron. doi:10.1385/0-89603-185-3:1 A type of single-unit extracellular recording evidence that is used in a manual assertion. rctauber 2017-02-21T07:26:28Z eco ECO:0006046 single-unit extracellular recording evidence used in manual assertion true A type of single-unit extracellular recording evidence that is used in a manual assertion. ECO:RCT A type of extracellular recording evidence in which electrical activity is measured in either tissue or at a cellular level with microelectrodes. rctauber 2017-02-21T07:26:28Z local field potential recording evidence eco ECO:0006047 field potential recording evidence A type of extracellular recording evidence in which electrical activity is measured in either tissue or at a cellular level with microelectrodes. ECO:RCT A type of field potential recording evidence that is used in a manual assertion. rctauber 2017-02-21T07:26:28Z eco ECO:0006048 field potential recording evidence used in manual assertion true A type of field potential recording evidence that is used in a manual assertion. ECO:RCT A type of genetic transformation evidence that is used in a manual assertion rctauber 02-21-2017T18:98:58Z eco ECO:0006049 genetic transformation evidence used in manual assertion true A type of genetic transformation evidence that is used in a manual assertion ECO:RCT A type of anti-sense experiment evidence that is used in a manual assertion. rctauber 02-21-2017T18:98:58Z eco ECO:0006050 anti-sense experiment evidence used in manual assertion true A type of anti-sense experiment evidence that is used in a manual assertion. ECO:RCT A type of morpholino experiment evidence that is used in a manual assertion. rctauber 02-21-2017T18:98:58Z eco ECO:0006051 morpholino experiment evidence used in manual assertion true A type of morpholino experiment evidence that is used in a manual assertion. ECO:RCT A type of RNAi evidence that is used in a manual assertion. rctauber 02-21-2017T18:98:58Z eco ECO:0006052 RNAi evidence used in manual assertion true A type of RNAi evidence that is used in a manual assertion. ECO:RCT A type of experimental phenotypic evidence that arises from assaying the response of a cell, tissue, organ or organism following exposure to a receptor agonist or antagonist. dosumis 2017-03-07T08:51:02Z eco ECO:0006053 pharmacological assay evidence A type of experimental phenotypic evidence that arises from assaying the response of a cell, tissue, organ or organism following exposure to a receptor agonist or antagonist. GOC:DOS A type of experimental phenotypic evidence used in a manual assertion that arises from assaying the response of a cell, tissue, organ or organism following exposure to a receptor agonist or antagonist. rctauber 2017-03-07T08:51:02Z eco ECO:0006054 pharmacological assay evidence used in manual assertion true A type of experimental phenotypic evidence used in a manual assertion that arises from assaying the response of a cell, tissue, organ or organism following exposure to a receptor agonist or antagonist. GOC:DOS A type of evidence where data generation is automated with equipment to allow for assaying samples or molecules in parallel. mchibucos 2017-03-28T14:48:39Z HT evidence high-throughput evidence high throughput cell biology evidence high throughput screening evidence eco ECO:0006055 Some relevant articles include: PMID: 23340846, doi:10.1038/nmeth0607-523 high throughput evidence A type of evidence where data generation is automated with equipment to allow for assaying samples or molecules in parallel. ECO:MCC A type of evidence that is used in a manual assertion where data generation is automated with equipment to allow for assaying large numbers of samples or molecules in parallel. rctauber 2017-03-28T14:48:39Z GOECO:HTP HTP inferred from high throughput experiment eco ECO:0006056 high throughput evidence used in manual assertion true A type of evidence that is used in a manual assertion where data generation is automated with equipment to allow for assaying large numbers of samples or molecules in parallel. ECO:RCT GOECO:HTP inferred from high throughput experiment HTP GOECO:HTP inferred from high throughput experiment GOECO:HTP A type of evidence that is used in an automatic assertion where data generation is automated with equipment to allow for assaying samples or molecules in parallel. rctauber 2017-03-28T14:48:39Z eco ECO:0006057 high throughput evidence used in automatic assertion true A type of evidence that is used in an automatic assertion where data generation is automated with equipment to allow for assaying samples or molecules in parallel. ECO:RCT A type of high throughput evidence where a classical cell biology technique is automated with equipment to allow for assaying biomolecules in parallel. mchibucos 2017-03-28T14:48:39Z eco omics experiment ECO:0006058 HT methodologies may incorporate techniques from optics, chemistry, biology or image analysis (https://en.wikipedia.org/wiki/High_throughput_biology) high throughput cell biology evidence A type of high throughput evidence where a classical cell biology technique is automated with equipment to allow for assaying biomolecules in parallel. ECO:MCC A type of high throughput evidence used in a manual assertion where a classical cell biology technique is automated with equipment to allow for assaying biomolecules in parallel. rctauber 2017-03-28T14:48:39Z eco ECO:0006059 high throughput cell biology evidence used in manual assertion true A type of high throughput evidence used in a manual assertion where a classical cell biology technique is automated with equipment to allow for assaying biomolecules in parallel. ECO:RCT A type of high throughput evidence used in an automatic assertion where a classical cell biology technique is automated with equipment to allow for assaying biomolecules in parallel. rctauber 2017-03-28T14:48:39Z eco ECO:0006060 high throughput cell biology evidence used in automatic assertion true A type of high throughput evidence used in an automatic assertion where a classical cell biology technique is automated with equipment to allow for assaying biomolecules in parallel. ECO:RCT A type of wide-field fluorescence microscopy evidence used in a manual assertion where fluorescently tagged antibodies are imaged that are used to bind to their antigens. rctauber 2017-05-15T08:57:07Z eco ECO:0006061 immunofluorescence wide-field microscopy evidence used in manual assertion true true A type of wide-field fluorescence microscopy evidence used in a manual assertion where fluorescently tagged antibodies are imaged that are used to bind to their antigens. ECO:SN url:http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0057135 A type of wide-field microscopy evidence that is used in a manual assertion where pure white and ultraviolet light are produced by a mercury lamp, passed through an optical filter (excitation filter), and directed to a sample via a dichroic mirror, followed by detection of the fluorescent light by a camera after it passes through an emission filter. rctauber 2017-05-15T09:01:19Z eco ECO:0006062 wide-field fluorescence microscopy evidence used in manual assertion true A type of wide-field microscopy evidence that is used in a manual assertion where pure white and ultraviolet light are produced by a mercury lamp, passed through an optical filter (excitation filter), and directed to a sample via a dichroic mirror, followed by detection of the fluorescent light by a camera after it passes through an emission filter. ECO:SN url:http://www.bristol.ac.uk/synaptic/research/techniques/widefield.html A type of experimental phenotypic evidence that is used in a manual assertion where a gene and/or gene product is investigated in a transgenic organism that has been engineered to overexpress that gene product. rctauber 2017-05-15T09:03:49Z eco ECO:0006063 over expression analysis evidence used in manual assertion true A type of experimental phenotypic evidence that is used in a manual assertion where a gene and/or gene product is investigated in a transgenic organism that has been engineered to overexpress that gene product. PMID:22419077 A type of in vitro assay evidence that is used in a manual assertion where components are derived from resting, nonstimulated cells, therefore all reactions occur in vitro. rctauber 2017-05-15T09:08:17Z eco ECO:0006064 cell-free assay evidence used in manual assertion true A type of in vitro assay evidence that is used in a manual assertion where components are derived from resting, nonstimulated cells, therefore all reactions occur in vitro. PMID:18453125 A type of in vitro assay evidence that is used in a manual assertion where live cells are used. rctauber 2017-05-15T09:11:13Z eco ECO:0006065 in vitro cell based assay evidence used in manual assertion true A type of in vitro assay evidence that is used in a manual assertion where live cells are used. ECO:RCT A type of fluorescence evidence where quantitative information on the diffusion properties of a sample is produced from the measurement of diffusion of fluorescent probes over time into an area that has been photobleached by a high-intensity laser pulse. dosumis rctauber 2017-05-16T10:55:40Z FRAP evidence eco ECO:0006066 FRAP is a fluorescence microscopy-based technique. fluorescence recovery after photobleaching evidence A type of fluorescence evidence where quantitative information on the diffusion properties of a sample is produced from the measurement of diffusion of fluorescent probes over time into an area that has been photobleached by a high-intensity laser pulse. PMID:26314367 FRAP is a fluorescence microscopy-based technique. PMID:26314367 A type of fluorescence evidence that is used in a manual assertion where quantitative information on the diffusion properties of a sample is produced from the measurement of diffusion of fluorescent probes over time into an area that has been photobleached by a high-intensity laser pulse. rctauber 2017-05-16T10:55:40Z eco ECO:0006067 fluorescence recovery after photobleaching evidence used in manual assertion true A type of high throughput nucleotide sequencing assay evidence used in a manual assertion based on high-throughput (HT) sequencing of fragmented cDNA molecules. rctauber 2017-06-28T10:37:02Z eco ECO:0006068 RNA-seq evidence used in manual assertion true A type of high throughput nucleotide sequencing assay evidence used in a manual assertion based on high-throughput (HT) sequencing of fragmented cDNA molecules. ECO:MCC A type of high throughput nucleotide sequencing assay evidence used in an automatic assertion based on high-throughput (HT) sequencing of fragmented cDNA molecules. rctauber 2017-06-28T10:37:02Z eco ECO:0006069 RNA-seq evidence used in automatic assertion true A type of high throughput nucleotide sequencing assay evidence used in an automatic assertion based on high-throughput (HT) sequencing of fragmented cDNA molecules. ECO:MCC A type of electron microscopy evidence resulting from the use of antibodies to identify the localization of antigens in cells and tissues. dosumis rctauber 2017-07-05T09:59:10Z immunolabelling electron microscopy evidence eco ECO:0006070 immuno-labelling electron microscopy evidence A type of electron microscopy evidence resulting from the use of antibodies to identify the localization of antigens in cells and tissues. PMID:25151300 A type of electron microscopy evidence used in a manual assertion resulting from the use of antibodies to identify the localization of antigens in cells and tissues. PMID:25151300 dosumis rctauber 2017-07-05T09:59:10Z eco ECO:0006071 immuno-labelling electron microscopy evidence used in manual assertion true A type of electron microscopy evidence used in a manual assertion resulting from the use of antibodies to identify the localization of antigens in cells and tissues. PMID:25151300 A type of super-resolution microscopy evidence resulting from the use of fluorescently-tagged antibodies to identify the localization of antigens in cells and tissue. dosumis rctauber 2017-07-05T09:59:10Z eco ECO:0006072 immunofluorescence super resolution microscopy evidence A type of super-resolution microscopy evidence resulting from the use of fluorescently-tagged antibodies to identify the localization of antigens in cells and tissue. PMID:19245833 A type of super-resolution microscopy evidence used in a manual assertion resulting from the use of fluorescently-tagged antibodies to identify the localization of antigens in cells and tissue. dosumis rctauber 2017-07-05T09:59:10Z eco ECO:0006073 immunofluorescence super resolution microscopy evidence used in manual assertion true A type of super-resolution microscopy evidence used in a manual assertion resulting from the use of fluorescently-tagged antibodies to identify the localization of antigens in cells and tissue. PMID:19245833 A type of physical interaction evidence that is used in manual assertion where a cellular component subunit is isolated as part of purification of its larger complex. rctauber 2017-09-14T09:19:19 eco ECO:0006074 co-purification evidence used in manual assertion true A type of physical interaction evidence that is used in manual assertion where a cellular component subunit is isolated as part of purification of its larger complex. TAIR:TED A type of physical interaction evidence that is used in manual assertion that depends on the strength of the interaction between two entities. rctauber 2017-09-14T09:19:20 eco ECO:0006075 affinity evidence used in manual assertion true A type of physical interaction evidence that is used in manual assertion that depends on the strength of the interaction between two entities. ECO:MCC A type of affinity evidence that is used in manual assertion resulting from the binding of a molecule to a protein or protein complex. rctauber 2017-09-14T09:19:21 eco ECO:0006076 protein binding evidence used in manual assertion true true A type of affinity evidence that is used in manual assertion resulting from the binding of a molecule to a protein or protein complex. GO:0005515 A type of affinity evidence that is used in manual assertion where proteins of interest (bait and prey) are covalently linked to incomplete fragments of a third protein (reporter) and expressed in vivo, at which time interaction between bait and prey proteins brings reporter fragments in close enough proximity to allow them to reform and become a functional reporter protein. rctauber 2017-09-14T09:19:22 eco ECO:0006077 hybrid interaction evidence used in manual assertion true A type of affinity evidence that is used in manual assertion where proteins of interest (bait and prey) are covalently linked to incomplete fragments of a third protein (reporter) and expressed in vivo, at which time interaction between bait and prey proteins brings reporter fragments in close enough proximity to allow them to reform and become a functional reporter protein. ECO:MCC A type of affinity evidence that is used in manual assertion resulting from quantitation of the analyte which depends on the reaction of an antigen (analyte) and an antibody. rctauber 2017-09-14T09:19:23 eco ECO:0006078 immunological assay evidence used in manual assertion true A type of affinity evidence that is used in manual assertion resulting from quantitation of the analyte which depends on the reaction of an antigen (analyte) and an antibody. ERO:0001362 A type of hybrid interaction evidence that is used in manual assertion that is based on a protein-DNA complementation assay where a single promoter acts as bait and is screened against a library of prey transcription factors. rctauber 2017-09-14T09:19:24 eco ECO:0006079 yeast one-hybrid evidence used in manual assertion true A type of hybrid interaction evidence that is used in manual assertion that is based on a protein-DNA complementation assay where a single promoter acts as bait and is screened against a library of prey transcription factors. ECO:MCC A type of physical interaction evidence that is used in a manual assertion that is based on detection of protein-protein interaction between a bait and prey protein by in vivo reconstitution of split-ubiquitin (when bait and prey interact) and release of a reporter protein. rctauber 2017-09-14T09:19:25 eco ECO:0006080 split-ubiquitin assay evidence used in manual assertion true A type of physical interaction evidence that is used in a manual assertion that is based on detection of protein-protein interaction between a bait and prey protein by in vivo reconstitution of split-ubiquitin (when bait and prey interact) and release of a reporter protein. PMID:15064465 A type of physical interaction evidence that is used in a manual assertion that is based on detection of protein-protein interactions by separation of target proteins by SDS-PAGE which are blotted to a membrane, followed by denaturation and renaturation, probing with purified bait proteins, and detection of the target-bait complexes. rctauber 2017-09-14T09:19:26 eco ECO:0006081 far-Western blotting evidence used in manual assertion true A type of physical interaction evidence that is used in a manual assertion that is based on detection of protein-protein interactions by separation of target proteins by SDS-PAGE which are blotted to a membrane, followed by denaturation and renaturation, probing with purified bait proteins, and detection of the target-bait complexes. PMID:18079728 A type of affinity evidence that is used in a manual assertion that results from separation of biochemical mixtures by selective binding of a compound to an immobilized compound on a polymeric matrix, subsequent removal of unattached components, and then displacement of the bond compound. rctauber 2017-09-14T09:19:27 eco ECO:0006082 affinity chromatography evidence used in manual assertion true A type of affinity evidence that is used in a manual assertion that results from separation of biochemical mixtures by selective binding of a compound to an immobilized compound on a polymeric matrix, subsequent removal of unattached components, and then displacement of the bond compound. ECO:MCC A type of affinity evidence that is used in a manual assertion resulting from the binding of a molecule to a nucleic acid. rctauber 2017-09-14T09:19:28 eco ECO:0006083 nucleic acid binding evidence used in manual assertion true A type of affinity evidence that is used in a manual assertion resulting from the binding of a molecule to a nucleic acid. GO:0003676 A type of nucleic acid binding evidence that is used in a manual assertion resulting from an enzyme displaying binding activity to specific ribohomopolymer. rctauber 2017-09-14T09:19:29 eco ECO:0006084 ribohomopolymer binding assay evidence used in manual assertion true A type of nucleic acid binding evidence that is used in a manual assertion resulting from an enzyme displaying binding activity to specific ribohomopolymer. PMC:102612 A type of protein binding evidence that is used in a manual assertion resulting from a metal ion binding to a protein at a specific binding site. rctauber 2017-09-14T09:19:30 eco ECO:0006085 protein:ion binding evidence used in manual assertion true A type of protein binding evidence that is used in a manual assertion resulting from a metal ion binding to a protein at a specific binding site. PMID:2377604 A type of nucleic acid binding evidence that is used in a manual assertion in which DNA-protein binding is detected using labeled DNA as probes, hybridized to electrophoretically separated proteins. rctauber 2017-09-14T09:19:31 eco ECO:0006086 Southwestern blot evidence used in manual assertion true A type of nucleic acid binding evidence that is used in a manual assertion in which DNA-protein binding is detected using labeled DNA as probes, hybridized to electrophoretically separated proteins. ECO:RCT A type of nucleic acid binding evidence that is used in a manual assertion in which RNA-protein binding is detected using labeled RNA as probes, hybridized to electrophoretically separated proteins. rctauber 2017-09-14T09:19:32 eco ECO:0006087 Northwestern blot evidence used in manual assertion true A type of nucleic acid binding evidence that is used in a manual assertion in which RNA-protein binding is detected using labeled RNA as probes, hybridized to electrophoretically separated proteins. ECO:RCT A type of evidence that is used in a manual assertion arising from a physical interaction analysis where a combinatorial chemistry technique is used to identify oligonucleotides that bind to a target ligand. rctauber 2017-09-14T09:19:33 eco ECO:0006088 systematic evolution of ligands by exponential amplification evidence used in manual assertion true A type of evidence that is used in a manual assertion arising from a physical interaction analysis where a combinatorial chemistry technique is used to identify oligonucleotides that bind to a target ligand. ECO:MCC A type of hybrid interaction evidence that is used in a manual assertion that uses bacterial transformation with two plasmids to assess in vivo binding of a DNA-binding domain (bait) and DNA target site (prey). rctauber 2017-09-14T09:19:34 eco ECO:0006089 bacterial one-hybrid evidence used in manual assertion true A type of hybrid interaction evidence that is used in a manual assertion that uses bacterial transformation with two plasmids to assess in vivo binding of a DNA-binding domain (bait) and DNA target site (prey). ECO:MCC A type of oligonucleotide microarray evidence that is used in a manual assertion that detects binding of a tagged protein to an array of oligonucleotide probes representing potential binding sites. rctauber 2017-09-14T09:19:35 eco ECO:0006090 protein-binding microarray evidence used in manual assertion true true A type of oligonucleotide microarray evidence that is used in a manual assertion that detects binding of a tagged protein to an array of oligonucleotide probes representing potential binding sites. PMID:22146299 A type of genetic interaction evidence that is used in a manual assertion where a wild-type copy of the gene in question is inserted into a mutant cell to see if it restores the wild-type phenotype in the mutant background. rctauber 2017-09-14T09:19:36 eco ECO:0006091 functional complementation evidence used in manual assertion true A type of genetic interaction evidence that is used in a manual assertion where a wild-type copy of the gene in question is inserted into a mutant cell to see if it restores the wild-type phenotype in the mutant background. PMID:27403640 A type of functional complementation evidence that is used in a manual assertion that is used in manual assertion resulting from the introduction of a transgene to prevent, or "rescue" an organism from a condition. rctauber 2017-09-14T09:19:37 eco ECO:0006092 transgenic rescue experiment evidence used in manual assertion true A type of functional complementation evidence that is used in a manual assertion that is used in manual assertion resulting from the introduction of a transgene to prevent, or "rescue" an organism from a condition. url:http://www.nature.com/gt/journal/v11/n15/full/3302282a.html A type of transient rescue experiment evidence that is used in a manual assertion. rctauber 2017-09-14T09:19:38 eco ECO:0006093 transient rescue experiment evidence used in manual assertion true A type of transient rescue experiment evidence that is used in a manual assertion. ECO:RCT A type of genetic interaction evidence that is used in a manual assertion resulting from a second mutation that either suppresses or enhances the phenotype expressed from an original mutation. rctauber 2017-09-14T09:19:39 eco ECO:0006094 suppressor/enhancer interaction evidence used in manual assertion true A type of genetic interaction evidence that is used in a manual assertion resulting from a second mutation that either suppresses or enhances the phenotype expressed from an original mutation. url:http://www.wormbook.org/chapters/www:geneticsuppression/geneticsuppression.html A type of genetic interaction evidence that is used in a manual assertion that is based on the phenotypic outcome of two mutations in unrelated genetic loci. rctauber 2017-09-14T09:19:40 eco ECO:0006095 double mutant phenotype evidence used in manual assertion true A type of genetic interaction evidence that is used in a manual assertion that is based on the phenotypic outcome of two mutations in unrelated genetic loci. ECO:RCT A type of genetic interaction evidence that is used in a manual assertion that is based on the suppression of one allelic effect by an allele at another genetic locus. rctauber 2017-09-14T09:19:41 eco ECO:0006096 epistatic interaction evidence used in manual assertion true A type of genetic interaction evidence that is used in a manual assertion that is based on the suppression of one allelic effect by an allele at another genetic locus. PMID:18852697 A type of functional complementation evidence that is used in a manual assertion that is based on the insertion of a wild-type copy of a gene into a heterologous organism, with the mutation occurring in a homologous gene. rctauber 2017-09-14T09:19:42 eco ECO:0006097 functional complementation in heterologous system evidence used in manual assertion true A type of functional complementation evidence that is used in a manual assertion that is based on the insertion of a wild-type copy of a gene into a heterologous organism, with the mutation occurring in a homologous gene. TAIR:TED A type of mutant phenotype evidence based on the analysis of a mutation that allows normal function of the organism at low temperatures, but altered function at higher temperatures. pgaudet rctauber 2017-09-18T07:58:28 Ts mutation evidence eco ECO:0006098 temperature-sensitive mutant phenotype evidence A type of mutant phenotype evidence based on the analysis of a mutation that allows normal function of the organism at low temperatures, but altered function at higher temperatures. GOC:PG PMID:19596904 A type of mutant phenotype evidence that is used in a manual assertion based on the analysis of a mutation that allows normal function of the organism at low temperatures, but altered function at higher temperatures. pgaudet rctauber 2017-09-18T07:58:28 eco ECO:0006099 temperature-sensitive mutant phenotype evidence used in manual assertion true A type of mutant phenotype evidence that is used in a manual assertion based on the analysis of a mutation that allows normal function of the organism at low temperatures, but altered function at higher temperatures. GOC:PG PMID:19596904 A type of mutant phenotype evidence based on the analysis of a mutation which, in diploid organisms, must be present in both alleles for a phenotype to manifest itself. pgaudet rctauber 2017-09-18T07:58:28 eco ECO:0006100 recessive mutant phenotype evidence A type of mutant phenotype evidence based on the analysis of a mutation which, in diploid organisms, must be present in both alleles for a phenotype to manifest itself. GOC:PG NBK:21578 A type of mutant phenotype evidence that is used in a manual assertion based on the analysis of a mutation which, in diploid organisms, must be present in both alleles for a phenotype to manifest itself. pgaudet rctauber 2017-09-18T07:58:28 eco ECO:0006101 recessive mutant phenotype evidence used in manual assertion true A type of mutant phenotype evidence that is used in a manual assertion based on the analysis of a mutation which, in diploid organisms, must be present in both alleles for a phenotype to manifest itself. GOC:PG NBK:21578 A type of high throughput evidence derived from high throughput analysis of differences in alleles of a corresponding gene. GOC rctauber 2017-10–05T07:39:47Z eco ECO:0007000 high throughput mutant phenotype evidence A type of high throughput evidence derived from high throughput analysis of differences in alleles of a corresponding gene. GO:IMP A type of high throughput evidence that is used in a manual assertion derived from high throughput analysis of differences in alleles of a corresponding gene. GOC rctauber 2017-10–05T07:39:47Z GOECO:HMP HMP inferred from high throughput mutant phenotype eco ECO:0007001 When using the HMP evidence code, the guidelines for IMP should be adhered to (http://geneontology.org/page/imp-inferred-mutant-phenotype) high throughput mutant phenotype evidence used in manual assertion true true A type of high throughput evidence that is used in a manual assertion derived from high throughput analysis of differences in alleles of a corresponding gene. GO:IMP GOECO:HMP inferred from high throughput mutant phenotype HMP GOECO:HMP inferred from high throughput mutant phenotype GOECO:HMP A type of high throughput evidence derived from the high throughput analysis of the effect that a given gene has on another gene or genes, and products. GOC rctauber 2017-10–05T07:39:47Z eco ECO:0007002 high throughput genetic interaction evidence A type of high throughput evidence derived from the high throughput analysis of the effect that a given gene has on another gene or genes, and products. PMID:11822023 A type of high throughput evidence that is used in a manual assertion derived from the high throughput analysis of the effect that a given gene has on another gene or genes, and products. GOC rctauber 2017-10–05T07:39:47Z GOECO:HGI HGI inferred from high throughput genetic interaction eco ECO:0007003 When using the HGI evidence code, the guidelines for IGI should be adhered to (http://geneontology.org/page/igi-inferred-genetic-interaction) high throughput genetic interaction evidence used in manual assertion true true A type of high throughput evidence that is used in a manual assertion derived from the high throughput analysis of the effect that a given gene has on another gene or genes, and products. PMID:11822023 GOECO:HGI inferred from high throughput genetic interaction HGI GOECO:HGI inferred from high throughput genetic interaction GOECO:HGI A type of high throughput evidence derived from the high throughput direct measurement of some aspect of a biological feature. GOC rctauber 2017-10–05T07:39:47Z eco ECO:0007004 high throughput direct assay evidence A type of high throughput evidence derived from the high throughput direct measurement of some aspect of a biological feature. ECO:MCC A type of high throughput evidence that is used in a manual assertion derived from the high throughput direct measurement of some aspect of a biological feature. GOC rctauber 2017-10–05T07:39:47Z GOECO:HDA HDA inferred from high throughput direct assay eco ECO:0007005 When using the HDA evidence code, the guidelines for IDA should be adhered to (http://geneontology.org/page/ida-inferred-direct-assay) high throughput direct assay evidence used in manual assertion true true A type of high throughput evidence that is used in a manual assertion derived from the high throughput direct measurement of some aspect of a biological feature. ECO:MCC GOECO:HDA inferred from high throughput direct assay HDA GOECO:HDA inferred from high throughput direct assay GOECO:HDA A type of high throughput evidence derived from the high throughput characterization of gene expression. GOC rctauber 2017-10–05T07:39:47Z eco ECO:0007006 high throughput expression pattern evidence A type of high throughput evidence derived from the high throughput characterization of gene expression. GO:IEP A type of high throughput evidence that is used in a manual assertion derived from the high throughput characterization of gene expression. GOC rctauber 2017-10–05T07:39:47Z GOECO:HEP HEP inferred from high throughput expression pattern eco ECO:0007007 When using the HEP evidence code, the guidelines for EXP should be adhered to (http://geneontology.org/page/iep-inferred-expression-pattern) high throughput expression pattern evidence used in manual assertion true true A type of high throughput evidence that is used in a manual assertion derived from the high throughput characterization of gene expression. GO:IEP GOECO:HEP inferred from high throughput expression pattern HEP GOECO:HEP inferred from high throughput expression pattern GOECO:HEP A type of protein binding evidence in which radioactive ligands are used to measure receptor-ligand interactions, such as in determining selectivity for a particular ligand. fjungo rctauber 2017-12-15T10:46:19Z radioactive ligand binding assay evidence radiometric ligand-binding assay evidence competitive binding assay evidence eco ECO:0007008 radioligand binding assay evidence A type of protein binding evidence in which radioactive ligands are used to measure receptor-ligand interactions, such as in determining selectivity for a particular ligand. PMID:27471749 A type of radioligand binding assay evidence that is used in a manual assertion. rctauber 2017-12-15T10:48:44Z eco ECO:0007009 radioligand binding assay evidence used in manual assertion true A type of radioligand binding assay evidence that is used in a manual assertion. ECO:RCT A type of inferential evidence resulting from a conclusion drawn by the author of the publication. rctauber 2018-02-08T09:11:07Z eco ECO:0007010 author inference A type of inferential evidence resulting from a conclusion drawn by the author of the publication. ECO:RCT A type of combinatorial evidence in which the author draws a conclusion based on a combination of prior scientific background knowledge and evidence from one or more experiments. sbello rctauber 2018-02-15T11:17:11Z eco ECO:0007011 combinatorial evidence from author knowledge and experimental evidence true true A type of combinatorial evidence in which the author draws a conclusion based on a combination of prior scientific background knowledge and evidence from one or more experiments. ECO:RCT A type of combinatorial evidence in which the curator draws a conclusion based on a combination of prior scientific background knowledge and evidence from one or more experiments. ZFIN rctauber 2018-02-15T11:17:11Z eco ECO:0007012 combinatorial evidence from curator knowledge and experimental evidence true true A type of combinatorial evidence in which the curator draws a conclusion based on a combination of prior scientific background knowledge and evidence from one or more experiments. ECO:RCT A type of combinatorial evidence from author knowledge and experimental evidence that is used in a manual assertion. rctauber 2018-02-15T11:22:10Z eco ECO:0007013 combinatorial evidence from author knowledge and experimental evidence used in manual assertion true true A type of combinatorial evidence from author knowledge and experimental evidence that is used in a manual assertion. ECO:RCT A type of combinatorial evidence from curator knowledge and experimental evidence that is used in a manual assertion. rctauber 2018-02-15T11:22:10Z eco ECO:0007014 combinatorial evidence from curator knowledge and experimental evidence used in manual assertion true true true A type of combinatorial evidence from curator knowledge and experimental evidence that is used in a manual assertion. ECO:RCT A type of substance quantification evidence where an electrical gradient potential is applied to analyze an analyte of interest, resulting in a measurement amount of electrical current across the potential range applied. SynGO rctauber 2018-02-28T12:11:00Z eco ECO:0007015 voltammetry evidence A type of substance quantification evidence where an electrical gradient potential is applied to analyze an analyte of interest, resulting in a measurement amount of electrical current across the potential range applied. ECO:JBM PMID:28127962 A type of voltammetry evidence that is used in a manual assertion. rctauber 2018-02-28T12:12:34Z eco ECO:0007016 voltammetry evidence used in manual assertion true A type of voltammetry evidence that is used in a manual assertion. ECO:RCT A type of fluorescence evidence where a molecule tagged with a fluorescent protein is exposed to ultraviolet or blue light to shift the spectral emission properties for visualization. SynGO rctauber 2018-03-02T09:01:00Z eco ECO:0007017 photoconversion evidence A type of fluorescence evidence where a molecule tagged with a fluorescent protein is exposed to ultraviolet or blue light to shift the spectral emission properties for visualization. ECO:RCT PMID:28574633 A type of photoconversion evidence that is used in a manual assertion. rctauber 2018-03-02T09:05:04Z eco ECO:0007018 photoconversion evidence used in manual assertion true A type of photoconversion evidence that is used in a manual assertion. ECO:RCT Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. janelomax 2012-09-19T15:05:24Z GO:0000004 GO:0007582 GO:0044699 Wikipedia:Biological_process biological process physiological process biological_process single organism process single-organism process GO:0008150 Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. Note that when this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. biological_process Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. GOC:go_curators GOC:isa_complete The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. janelomax 2012-10-17T15:46:40Z GO:0044710 Wikipedia:Metabolism metabolism metabolic process resulting in cell growth metabolism resulting in cell growth biological_process single-organism metabolic process GO:0008152 Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. metabolic process The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. GOC:go_curators ISBN:0198547684 The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. Reactome:REACT_100537 Reactome:REACT_101147 Reactome:REACT_101952 Reactome:REACT_105649 Reactome:REACT_108313 Reactome:REACT_29068 Reactome:REACT_34240 Reactome:REACT_71 Reactome:REACT_78136 Reactome:REACT_78959 Reactome:REACT_79662 Reactome:REACT_85241 Reactome:REACT_85359 Reactome:REACT_86357 Reactome:REACT_89816 Reactome:REACT_91657 Reactome:REACT_91965 Reactome:REACT_93586 Reactome:REACT_93968 Reactome:REACT_94814 Reactome:REACT_98256 Wikipedia:Gene_expression biological_process GO:0010467 gene expression The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. GOC:dph GOC:tb Reactome:REACT_100537 Gene Expression, Xenopus tropicalis Reactome:REACT_101147 Gene Expression, Danio rerio Reactome:REACT_101952 Gene Expression, Sus scrofa Reactome:REACT_105649 Gene Expression, Drosophila melanogaster Reactome:REACT_108313 Gene Expression, Caenorhabditis elegans Reactome:REACT_29068 Gene Expression, Escherichia coli Reactome:REACT_34240 Gene Expression, Staphylococcus aureus N315 Reactome:REACT_71 Gene Expression, Homo sapiens Reactome:REACT_78136 Gene Expression, Mus musculus Reactome:REACT_78959 Gene Expression, Taeniopygia guttata Reactome:REACT_79662 Gene Expression, Plasmodium falciparum Reactome:REACT_85241 Gene Expression, Oryza sativa Reactome:REACT_85359 Gene Expression, Gallus gallus Reactome:REACT_86357 Gene Expression, Canis familiaris Reactome:REACT_89816 Gene Expression, Mycobacterium tuberculosis Reactome:REACT_91657 Gene Expression, Arabidopsis thaliana Reactome:REACT_91965 Gene Expression, Rattus norvegicus Reactome:REACT_93586 Gene Expression, Dictyostelium discoideum Reactome:REACT_93968 Gene Expression, Bos taurus Reactome:REACT_94814 Gene Expression, Schizosaccharomyces pombe Reactome:REACT_98256 Gene Expression, Saccharomyces cerevisiae The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GO:0043283 biopolymer metabolic process macromolecule metabolism biological_process GO:0043170 macromolecule metabolic process The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. CHEBI:33694 GOC:mah biopolymer metabolic process GOC:mtg_chebi_dec09 The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. midori 2010-03-08T03:32:18Z organic molecular entity metabolic process organic molecular entity metabolism organic substance metabolism biological_process GO:0071704 organic substance metabolic process The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. CHEBI:50860 GOC:mah processed material Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples Is a material entity that is created or changed during material processing. PERSON: Alan Ruttenberg processed material assay Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation. PlanAndPlannedProcess Branch measuring scientific observation OBI branch derived study assay any method assay cDNA library PMID:6110205. collection of cDNA derived from mouse splenocytes. Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process. ALT DEF (PRS):: a cDNA library is a collection of host cells, typically E.Coli cells but not exclusively. modified by transfer of plasmid DNA molecule used as vector containing a fragment or totality of cDNA molecule (the insert) . cDNA library may have an array of role and applications. PERSON: Luisa Montecchi PERSON: Philippe Rocca-Serra GROUP: PSI PRS: 22022008. class moved under population, modification of definition and replacement of biomaterials in previous definition with 'material' addition of has_role restriction cDNA library extract Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923 an extract is a material entity which results from an extraction process PERSON: Philippe Rocca-Serra extracted material GROUP: OBI Biomatrial Branch extract transcription profiling assay Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis. BMC Genomics. 2008 Jul 31;9:364. PMID: 18671858 An assay which aims to provide information about gene expression and transcription activity using ribonucleic acids collected from a material entity using a range of techniques and instrument such as DNA sequencers, DNA microarrays, Northern Blot Philippe Rocca-Serra gene expression profiling OBI transcription profiling transcription profiling assay analyte assay example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant. 2013-09-23: simplify equivalent axiom Note: is_realization of some analyte role isn't always true, for example when there is none of the analyte in the evaluant. For the moment we are writing it this way, but when the information ontology is further worked out this will be replaced with a condition discussing the measurement. logical def modified to remove expression below, as some analyte assays report below the level of detection, and therefore not a scalar measurement datum, replaced by measurement datum and ('has measurement unit label' some 'measurement unit label') and ('is quality measurement of' some 'molecular concentration')) PERSON:Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Alan Ruttenberg PERSON:Bjoern Peters PERSON:Helen Parkinson PERSON:Philippe Rocca-Serra PERSON:Alan Ruttenberg GROUP:OBI Planned process branch analyte assay recombinant vector A recombinant vector is created by a recombinant vector cloning process, and contains nucleic acids that can be amplified. It retains functions of the original cloning vector. recombinant vector northern blot analysis PMID: 18428227. Analysis of RNA by northern blot hybridization. Brown T, Mackey K. Curr Protoc Hum Genet. 2001 Nov;Appendix 3:Appendix 3K. a northern blot analysis is an assay allowing monitoring presence of gene transcripts by hybridizing labeled RNA or DNA probes against messenger RNAs isolated from tissue or cell cultures, resolved on denaturing agarose gel, transfered by blotting procedure to a nitrocellulose or nylon membrane and immobilized by cross linking or baking to the membrane. Detection of hybridization signals is carried out by immunofluorescence or radioactivity measurements using photographic films or digital imaging devices such as Phosphor Imager 2010-01-31: Philippe Rocca-Serra: Need to add a restriction taking into account probe and transcript information Person: Philippe Rocca-Serra northern blot northern blot analysis RNA extract an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen. PERSON: Chris Stoeckert PERSON: Jie Zheng Group: UPenn Group RNA extract processed specimen A tissue sample that has been sliced and stained for a histology study. A blood specimen that has been centrifuged to obtain the white blood cells. A specimen that has been intentionally physically modified. Bjoern Peters Bjoern Peters A tissue sample that has been sliced and stained for a histology study. processed specimen nucleic acid extract An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. PERSON: Jie Zheng UPenn Group nucleic acid extract transcription profiling by high thoughput sequencing design A study design in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and/or to quantitate transcript abundance Person: Chris Stoeckert, Jie Zheng Group: ArrayExpress production team transcription profiling by high throughput sequencing design RNA-seq assay An assay in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and or to quantitate transcript abundance PERSON: James Malone transcription profiling by high throughput sequencing EFO_0002770 transcription profiling by high throughput sequencing JZ: should be inferred as 'DNA sequencing'. Will check in the future. an assay that uses high-throughput sequencing technologies to sequence cDNA in order to get information about a sample's RNA content. RNA-Seq provides researchers with efficient ways to measure transcriptome data experimentally, allowing them to get information such as how different alleles of a gene are expressed, detect post-transcriptional mutations or identify gene fusions. WEB: http://en.wikipedia.org/wiki/RNA-Seq RNA-seq assay transcription profiling by array design A study design that identifies forms and abundance of transcripts in the genome using microarray technology. Person: Chris Stoeckert, Jie Zheng MO_533 transcript_identification_design transcription profiling by array design transcription profiling by RT-PCR design A study design which aims to examine the transcriptome of a biological sample by reverse transcription PCR (RT-PCR). Person: Chris Stoeckert, Jie Zheng Group: ArrayExpress production team transcription profiling by RT-PCR design transcription profiling by RT-PCR assay An assay in which the transcriptome of a biological sample is analysed by reverse transcription PCR (RT-PCR) Person: Anna Farne EFO_0002943: transcription profiling by RT-PCR transcription profiling by RT-PCR assay transcription profiling design A study design that identifies forms and abundance of transcripts in the genome. Person: Chris Stoeckert, Jie Zheng MO_533 transcript_identification_design transcription profiling design transcription profiling by array assay An assay in which the transcriptome of a biological sample is analysed using array technology. JZ: add alternative term: 'RNA profiling by array assay' requested by ENCODE developer. See tracker: https://sourceforge.net/p/obi/obi-terms/757/ Person: James Malone RNA profiling by array assay EFO_0002768: transcription profiling by array transcription profiling by array assay nano-cap analysis of gene expression Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. PMID:20543846 nano-CAGE is a type of CAGE developed to work from very low amount (nanogram scale) of mRNA samples PERSON:Philippe Rocca-Serra; Marcus Chibucos nano-CAGE PMID: 20543846 nano-cap analysis of gene expression cap analysis of gene expression 5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing. Takahashi H, Lassmann T, Murata M, Carninci P. Nat Protoc. 2012 Feb 23;7(3):542-61. doi: 10.1038/nprot.2012.005. PMID: 22362160 An assay which aims at monitoring RNA transcript abundances in biological samples by extracting 5' ends of capped transcripts, RTPCR and sequence those. Copy numbers of CAGE tags provide a way of quantification and provide a measure of expression of the transcriptome PERSON:Philippe Rocca-Serra; Marcus Chibucos CAGE PMID:14663149 cap analysis of gene expression specimen Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. A material entity that has the specimen role. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. PERSON: James Malone PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch specimen study design a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design. A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available. PERSON: Chris Stoeckert experimental design rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol. study design sequencing assay The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template the use of a chemical or biochemical means to infer the sequence of a biomaterial has_output should be sequence of input; we don't have sequence well defined yet PlanAndPlannedProcess Branch OBI branch derived sequencing assay