1.2 10:05:2016 15:33 For more details, see https://github.com/evidenceontology/evidenceontology OBO-Edit 2.3.1 eco snadendla definition 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 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 used_in 2010-12-09T05:00:20Z A relation connecting a piece of evidence to an assertion method, where that assertion method is supported by the evidence. ECO:9000000 In the future we may use a more generic relation with weaker domain and range constraints taken from IAO, RO or OBI. eco mchibucos used_in used_in A relation connecting a piece of evidence to an assertion method, where that assertion method is supported by the evidence. GOC:cjm uses ECO:9000001 eco uses uses evidence A type of information that is used to support an assertion. ECO:0000000 eco evidence code evidence_code A type of information that is used to support an assertion. ECO:MCC inference from background scientific knowledge A curator inference that links the current annotation to a different evidence-based annotation via background knowledge of the curator. ECO:0000001 eco A curator inference that links the current annotation to a different evidence-based annotation via background knowledge of the curator. ECO:MCC ECO:go direct assay evidence ECO:0000002 Experimental evidence that is based on direct measurement of some aspect of a biological feature. eco ECO:MCC Experimental evidence that is based on direct measurement of some aspect of a biological feature. reconstitution assay evidence A type of direct assay evidence based on reconstructing a biological sample from its disassociated state to its original state. ECO:0000003 eco A type of direct assay evidence based on reconstructing a biological sample from its disassociated state to its original state. ECO:KAV PMID:26029343 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:0000004 IDA: cell fractionation If using this term for Gene Ontology annotation, it would be used most typically for annotations to the cellular component ontology. eco 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 enzyme assay evidence ECO:0000005 IDA: enzyme assays PSI-MI:MI:0415 Used when an annotation is made based on assays that determine the catalytic activity of enzymes. eco enzymatic study PSI-MI:MI:0415 TAIR:TED Used when an annotation is made based on assays that determine the catalytic activity of enzymes. experimental evidence An evidence type that is based on the results of a laboratory assay. ECO:0000006 eco An evidence type that is based on the results of a laboratory assay. ECO:MCC GOC:ecd 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:0000007 IDA: immunofluorescence eco 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 expression pattern evidence A type of experimental evidence that is based on characterization of gene expression. 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. eco A type of experimental evidence that is based on characterization of gene expression. ECO:MCC GO:IEP transcript expression evidence ECO:0000009 eco protein expression evidence ECO:0000010 eco genetic interaction evidence ECO:0000011 TAIR:TED:0000006 eco functional complementation evidence ECO:0000012 IGI: functional complementation Used when an annotation is made based on a functional complementation assay in which a wild-type copy of the gene in question is inserted into a mutant background in the organism of the gene's origin or a heterologous organism with a mutation in the homologous gene. eco TAIR:TED Used when an annotation is made based on a functional complementation assay in which a wild-type copy of the gene in question is inserted into a mutant background in the organism of the gene's origin or a heterologous organism with a mutation in the homologous gene. transgenic rescue experiment evidence ECO:0000013 eco mutant phenotype evidence ECO:0000015 The IMP evidence code covers those cases when the function, process or cellular localization of a gene product is inferred based on differences in the function, process, or cellular localization between two different alleles of the corresponding gene. The IMP code is used for cases where one allele may be designated 'wild-type' and another as 'mutant'. It is also used in cases where allelic variation occurs naturally and no specific allele is designated as wild-type or mutant. Caution should be used when making annotations from gain-of-function mutations as it may be difficult to infer a gene's normal function from a gain of function mutation, although it is sometimes possible. eco GO:IMP The IMP evidence code covers those cases when the function, process or cellular localization of a gene product is inferred based on differences in the function, process, or cellular localization between two different alleles of the corresponding gene. The IMP code is used for cases where one allele may be designated 'wild-type' and another as 'mutant'. It is also used in cases where allelic variation occurs naturally and no specific allele is designated as wild-type or mutant. Caution should be used when making annotations from gain-of-function mutations as it may be difficult to infer a gene's normal function from a gain of function mutation, although it is sometimes possible. loss-of-function mutant phenotype evidence ECO:0000016 eco ectopic expression evidence ECO:0000017 IMP: analysis of overexpression/ectopic expression phenotype Used when an annotation is made based on the analysis of the phenotype of a wild-type or mutant transgenic organism that has been engineered to overexpress or ectopically express the gene product in question. eco TAIR:TED Used when an annotation is made based on the analysis of the phenotype of a wild-type or mutant transgenic organism that has been engineered to overexpress or ectopically express the gene product in question. anti-sense experiment evidence ECO:0000018 IMP: anti-sense experiments Used when an annotation is based on a phenotype observed when expressing an anti-sense version of a gene product in a wild-type (for that gene product) background. eco TAIR:TED Used when an annotation is based on a phenotype observed when expressing an anti-sense version of a gene product in a wild-type (for that gene product) background. RNAi evidence ECO:0000019 IMP: RNAi experiment Inference based on a phenotype observed when expressing an RNAi construct that includes a fragment of the gene product in a wild-type (for that gene product) background. A double-stranded RNA specifically suppresses the expression of the gene bearing its complementary sequence. eco Inference based on a phenotype observed when expressing an RNAi construct that includes a fragment of the gene product in a wild-type (for that gene product) background. A double-stranded RNA specifically suppresses the expression of the gene bearing its complementary sequence. TAIR:TED specific protein inhibition evidence A type of protein assay evidence based on the inhibition of the molecular function of a protein. ECO:0000020 eco A type of protein assay evidence based on the inhibition of the molecular function of a protein. ECO:MCC physical interaction evidence ECO:0000021 Experimental evidence that is based on characterization of an interaction between a gene product and another molecule. Molecules interacted with might include protein, nucleic acid, ion, or complex. PSI-MI:MI:0045 eco experimental interaction detection PSI-MI:MI:0045 ECO:MCC Experimental evidence that is based on characterization of an interaction between a gene product and another molecule. co-purification evidence A type of physical interaction evidence where a cellular component subunit is isolated as part of purification of its larger complex. ECO:0000022 IPI: co-purification PSI-MI:MI:0025 eco copurification PSI-MI:MI:0025 A type of physical interaction evidence where a cellular component subunit is isolated as part of purification of its larger complex. TAIR:TED affinity evidence A type of physical interaction evidence that depends on the strength of the interaction between two entities. ECO:0000023 PSI-MI:MI:0400 eco ligand binding evidence A type of physical interaction evidence that depends on the strength of the interaction between two entities. ECO:MCC PSI-MI:MI:0400 affinity technology PSI-MI:MI:0400 protein binding evidence ECO:0000024 eco 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:0000025 PSI-MI:MI:0090 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. eco protein complementation assay PSI-MI:MI:0090 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 nucleic acid hybridization evidence ECO:0000026 eco 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: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. eco 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 motif similarity evidence ECO:0000028 ISS: recognized domains Used when an annotation is made based on the presence of a recognized domain or motif in a gene product's (usually protein) primary sequence. eco TAIR:TED Used when an annotation is made based on the presence of a recognized domain or motif in a gene product's (usually protein) primary sequence. match to InterPro member signature evidence ECO:0000029 eco BLAST evidence used in manual assertion A type of BLAST evidence that is used in a manual assertion. ECO:0000030 curated BLAST analysis eco true true A type of BLAST evidence that is used in a manual assertion. ECO:MCC protein BLAST evidence used in manual assertion ECO:0000031 GO_REF:0000012 GO_REF:0000027 Protein BLAST evidence that is used in a manual assertion. curated protein BLAST analysis eco BLAST search criteria for ISS assignment in PAMGO_GAT GO_REF:0000027 true true Pairwise alignment (TIGR) GO_REF:0000012 ECO:MCC Protein BLAST evidence that is used in a manual assertion. nucleotide BLAST evidence used in manual assertion ECO:0000032 Nucleotide BLAST evidence that is used in a manual assertion. curated nucleic acid BLAST analysis eco ECO:MCC Nucleotide BLAST evidence that is used in a manual assertion. true true traceable author statement A type of author statement that is based on a cited reference. 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. eco A type of author statement that is based on a cited reference. ECO:MCC GO:TAS non-traceable author statement An author statement that is not associated with results presented or a cited reference. 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. eco An author statement that is not associated with results presented or a cited reference. ECO:MCC 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. An assertion of "no biological data found" carries the assumption that a more-or-less exhaustive search has been conducted. ECO:0000035 eco 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:MCC GO:ND not_recorded An evidence that reflects an annotation was made before curators began tracking evidence types. ECO:0000037 NR The evidence not_recorded appears in some legacy annotations; it should not be used for new annotations. eco not recorded true GO:NR NR An evidence that reflects an annotation was made before curators began tracking evidence types. ECO:MCC GO:NR GO:NR not recorded transient rescue experiment evidence ECO:0000038 eco protein assay evidence ECO:0000039 eco immunological assay evidence ECO:0000040 eco similarity evidence An evidence type that is based on comparing likeness of distinct biological entities. ECO:0000041 IS eco inferred from similarity An evidence type that is based on comparing likeness of distinct biological entities. ECO:MCC PhenoScape:IS gain-of-function mutant phenotype evidence ECO:0000042 eco sequence similarity evidence 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. A type of similarity based on biomolecular sequence. ECO:0000044 eco A type of similarity based on biomolecular sequence. ECO:MCC TAIR:TED spatial pattern of protein expression evidence ECO:0000045 eco protein expression level evidence ECO:0000046 eco spatial pattern of transcript expression evidence ECO:0000047 eco transcript expression level evidence ECO:0000048 eco reporter gene assay evidence ECO:0000049 IEP: expression of a reporter gene Used when an annotation is made on the basis of the expression pattern of a reporter gene. The reporter gene may consist of the native promoter of the gene in question that drives the expression of a readily assayable gene product such as GUS or GFP. The reporter gene may also be a marker of a particular type of physiological response. eco TAIR:TED Used when an annotation is made on the basis of the expression pattern of a reporter gene. The reporter gene may consist of the native promoter of the gene in question that drives the expression of a readily assayable gene product such as GUS or GFP. The reporter gene may also be a marker of a particular type of physiological response. voucher specimen analysis evidence ECO:0000050 IVS Used when an annotation is made on the basis of for a phenotype description for a species or higher level group that given by an author who explicitly references an observation of a voucher specimen(s). Voucher specimens are defined as those specimens with permanent museum catalog numbers. Thus it would be possible for a person to examine this particular specimen and observe the annotated phenotype. eco PhenoScape:DOA Used when an annotation is made on the basis of for a phenotype description for a species or higher level group that given by an author who explicitly references an observation of a voucher specimen(s). Voucher specimens are defined as those specimens with permanent museum catalog numbers. Thus it would be possible for a person to examine this particular specimen and observe the annotated phenotype. genetic similarity evidence 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. A type of similarity based on genotype without respect to expression. ECO:0000051 IGTS eco inferred from genetic similarity A type of similarity based on genotype without respect to expression. ECO:MCC PhenoScape:IGTS suppressor/enhancer interaction evidence ECO:0000052 IGI: 'traditional' genetic interactions (e.g. suppressors, synthetic lethals) TAIR:TED:0000063 eco computational combinatorial evidence A type of combinatorial analysis where data are combined and evaluated by an algorithm. 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. ECO:0000053 TAIR:TED:0000004 eco A type of combinatorial analysis where data are combined and evaluated by an algorithm. ECO:MCC ECO:go double mutant phenotype evidence ECO:0000054 IGI: double mutant analysis Used when an annotation is made based on the phenotype of double mutant organism that contains a mutation in the gene product of interest in addition to a second mutation at an unrelated locus. eco TAIT:TED Used when an annotation is made based on the phenotype of double mutant organism that contains a mutation in the gene product of interest in addition to a second mutation at an unrelated locus. array experiment evidence ECO:0000055 eco epistatic interaction evidence ECO:0000056 IGI: epistatic interactions Used when an annotation is based on results of epistatis analysis of an allele of the gene in question and a mutant allele at another locus. eco TAIR:TED Used when an annotation is based on results of epistatis analysis of an allele of the gene in question and a mutant allele at another locus. phenotypic similarity evidence A type of similarity based on the expression of a genotype in an environment. ECO:0000057 IPTS 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. eco inferred from phenotypic similarity A type of similarity based on the expression of a genotype in an environment. ECO:MCC PhenoScape:IPTS expression microarray evidence ECO:0000058 eco experimental phenotypic evidence ECO:0000014 ECO:0000059 Experimental evidence that is based on the expression of a genotype in an environment. eco inferred from phenotype ECO:MCC Experimental evidence that is based on the expression of a genotype in an environment. positional similarity evidence ECO:0000060 IPS Used when an annotation is made based on the similarity of the location and or arrangement of structures. eco PhenoScape:IPS Used when an annotation is made based on the similarity of the location and or arrangement of structures. quantitative trait analysis evidence A type of experimental phenotypic evidence where an annotation is made for a gene product that has not been cloned but is associated with a quantitative trait locus. ECO:0000061 IGI: quantitative trait analysis eco A type of experimental phenotypic evidence where an annotation is made for a gene product that has not been cloned but is associated with a quantitative trait locus. TAIR:tn genomic microarray evidence ECO:0000062 eco compositional similarity evidence ECO:0000063 ICS Used when an annotation is made based on the similarity of the histological makeup of structures. eco PhenoScape:ICS Used when an annotation is made based on the similarity of the histological makeup of structures. functional complementation in heterologous system evidence ECO:0000064 IGI: functional complementation in heterologous system Used when an annotation is made based on a functional complementation assay in which a wild-type copy of the gene in question is inserted into a heterologous organism with a mutation in the homologous gene. eco TAIR:TED Used when an annotation is made based on a functional complementation assay in which a wild-type copy of the gene in question is inserted into a heterologous organism with a mutation in the homologous gene. CpG island microarray evidence ECO:0000065 eco 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:0000066 IPI: yeast one-hybrid assay PSI-MI:MI:0432 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). eco 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 one hybrid PSI-MI:MI:0432 developmental similarity evidence ECO:0000067 IDS Used when an annotation is made based on the similarity of embryological and/or post-embryonic origin of structures. eco PhenoScape:IDS Used when an annotation is made based on the similarity of embryological and/or post-embryonic origin of structures. yeast 2-hybrid evidence ECO:0000068 IPI: yeast two-hybrid assay Used when an annotation is based on the interaction between two proteins in a yeast two-hybrid assay. The assay involves screening a trap-tagged library with a bait-tagged vector. The library is tagged with a DNA-binding domain (trap) and the bait is tagged with a transcriptional activation domain. Interaction between a library-trap protein and the bait results in activation of a yeast reporter gene whose transcription can be experimentally assayed. eco TAIR:TED Used when an annotation is based on the interaction between two proteins in a yeast two-hybrid assay. The assay involves screening a trap-tagged library with a bait-tagged vector. The library is tagged with a DNA-binding domain (trap) and the bait is tagged with a transcriptional activation domain. Interaction between a library-trap protein and the bait results in activation of a yeast reporter gene whose transcription can be experimentally assayed. differential methylation hybridization evidence ECO:0000069 eco 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:0000070 IPI: co-immunoprecipitation If performing GO annotation, the interacting protein is referenced in the evidence_with column. PSI-MI:MI:0019 eco 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 coimmunoprecipitation PSI-MI:MI:0019 morphological similarity evidence ECO:0000071 IMS Used when an annotation is made based on the similarity of the shape, structure or overall configuration of structures. eco PhenoScape:IMS Used when an annotation is made based on the similarity of the shape, structure or overall configuration of structures. Sos-recruitment assay evidence 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:0000072 IPI: Sos-recruitment assay eco 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 experimental genomic evidence ECO:0000073 Experimental evidence that characterizes an attribute of the genome underlying a gene product. eco inferred from genomic analysis ECO:MCC Experimental evidence that characterizes an attribute of the genome underlying a gene product. split-ubiquitin assay evidence ECO:0000074 IPI: split-ubiquitin assay PSI-MI:MI:0112 Used when an annotation is based on the interaction of two proteins in a split-ubiquitin assay. 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 ubiquiting (NubG) domain. If bait and prey interact, their interaction brings the NubG and Cub domains close enough together to reconstitute split-ubiquitin, resulting in the release of the reporter protein by the action of the UBPs. eco TAIR:TED Used when an annotation is based on the interaction of two proteins in a split-ubiquitin assay. 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 ubiquiting (NubG) domain. If bait and prey interact, their interaction brings the NubG and Cub domains close enough together to reconstitute split-ubiquitin, resulting in the release of the reporter protein by the action of the UBPs. ubiquitin reconstruction PSI-MI:MI:0112 gene expression similarity evidence ECO:0000075 IGES Used when an annotation is made based on the similarity of expression of genes in structures. eco PhenoScape:IGES Used when an annotation is made based on the similarity of expression of genes in structures. far-Western blotting evidence ECO:0000076 IPI: far-Western analysis PSI-MI:MI:0047 Used when an annotation is based on the interaction of protein with another in a far-Western assay. The assay involves separating target proteins on an SDS-PAGE gel, blotting to a membrane, hybridization with a protein probe and visualization using a probe-directed antibody. The interacting protein is referenced in the evidence_with column. eco TAIR:TED Used when an annotation is based on the interaction of protein with another in a far-Western assay. The assay involves separating target proteins on an SDS-PAGE gel, blotting to a membrane, hybridization with a protein probe and visualization using a probe-directed antibody. The interacting protein is referenced in the evidence_with column. methylation-specific polymerase chain reaction evidence ECO:0000077 eco methylation-specific PCR evidence southern hybridization evidence ECO:0000078 ISS: Southern blotting Southern blot Used when an annotation is based on the hybridization of a probe derived from the gene in question with a gene of known function/process/component. Can also be used when a probe derived from a gene of known function/process/component hybridizes with the gene in question. eco TAIR:TED Used when an annotation is based on the hybridization of a probe derived from the gene in question with a gene of known function/process/component. Can also be used when a probe derived from a gene of known function/process/component hybridizes with the gene in question. affinity chromatography evidence "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. 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:0000079 IDA: affinity chromatography PSI-MI:MI:0004 eco 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 affinity chromatography technology PSI-MI:MI:0004 phylogenetic evidence A type of similarity that indicates common ancestry. ECO:0000080 IP eco A type of similarity that indicates common ancestry. ECO:MCC PhenoScape:IP IP PhenoScape:IP targeting sequence prediction evidence ECO:0000081 ISS: targeting sequence prediction Used when a component annotation is made based on the presence of a targeting sequence in a protein's primary sequence. The presence of the targeting sequence may be detected by computational prediction and/or the author's manual examination of the sequence. eco TAIR:TED Used when a component annotation is made based on the presence of a targeting sequence in a protein's primary sequence. The presence of the targeting sequence may be detected by computational prediction and/or the author's manual examination of the sequence. polymerase chain reaction evidence ECO:0000082 PCR evidence eco transmembrane domain prediction evidence ECO:0000083 ISS: transmembrane domain prediction Used when a component annotation is made based on the presence of one or more transmembrane domains in a protein's primary sequence. The presence of the transmembrane domains may be detected by computational prediction and/or the author's manual examination of the sequence. eco TAIR:TED Used when a component annotation is made based on the presence of one or more transmembrane domains in a protein's primary sequence. The presence of the transmembrane domains may be detected by computational prediction and/or the author's manual examination of the sequence. gene neighbors evidence 2009-03-20T11:55:18Z ECO:0000084 Evidence that supports the identity of a gene product on the basis of the identity of neighboring genes. GO_REF:0000025 Genomic cluster analyses include synteny and operon structure. ICL eco inferred from genome cluster mgiglio ECO:MCC Evidence that supports the identity of a gene product on the basis of the identity of neighboring genes. GOC:mg Operon structure as IGC evidence GO_REF:0000025 immunoprecipitation evidence A type of protein assay evidence that involves precipitation of a multivalent antigen by a bivalent antibody for protein isolation. ECO:0000085 IDA: immunoprecipitation Transcription factors isolated in this way can be incubated with a radiolabeled probe to demonstrate binding. eco 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 intermethylated site amplification evidence ECO:0000086 eco 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:0000087 IDA: immunolocalization eco 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 biological system reconstruction evidence 2009-03-20T12:00:17Z 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:0000088 ISR 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. eco inferred from system reconstruction mgiglio 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 restriction landmark genomic scanning evidence ECO:0000089 ECO:0001125 RLGS evidence eco restriction landmark genome scanning evidence 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:0000090 IDA: immunogold labelling eco A type of immunolocalization evidence where the antibodies are labeled with colloidal gold particles whose location is then detected via microscopy. ECO:MCC epitope-tagged protein immunolocalization evidence ECO:0000092 IDA: immunolocalization of epitope-tagged protein Used when an annotation is made based on immunolocalization of recombinant proteins fused with epitopes that are recognized by antibodies. eco TAIR:TED Used when an annotation is made based on immunolocalization of recombinant proteins fused with epitopes that are recognized by antibodies. oligonucleotide microarray evidence ECO:0000093 eco biological assay evidence Direct assay evidence that is derived by using a living organism to measure the effect of a substance, factor, or condition. ECO:0000094 IDA: bioassay eco Direct assay evidence that is derived by using a living organism to measure the effect of a substance, factor, or condition. ECO:MCC TAIR:TED cell growth assay evidence 2014-10-15T00:58:50Z 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. Cell growth aspects can include growth rate and extent of growth. A cell growth curve acts as a natural reporter. ECO:0000095 eco growth curve analysis mchibucos 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 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: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. EMSA: electrophoretic mobility shift assay Gel retardation assay IDA: electrophoretic mobility shift assay PSI-MI:MI:0413 eco electrophoretic mobility shift assay PSI-MI:MI:0413 Gel retardation assay PMID:17703195 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 cDNA microarray evidence ECO:0000097 eco in situ hybridization evidence ECO:0000098 IDA: in situ hybridization Used when an annotation is made based on a method that hybridizes a labeled nucleic acid probe to a tissue or cell specimen in which the cellular structures are still intact. Depending on the label and protocol used, the probe may detect complementary DNA or RNA by hybridizing specifically to that gene or sequence. eco TAIR:TED Used when an annotation is made based on a method that hybridizes a labeled nucleic acid probe to a tissue or cell specimen in which the cellular structures are still intact. Depending on the label and protocol used, the probe may detect complementary DNA or RNA by hybridizing specifically to that gene or sequence. fractionation evidence ECO:0000100 eco Affymetrix array experiment evidence ECO:0000101 eco co-fractionation evidence ECO:0000102 IDA: co-fractionation Used when an annotation is made based on fractionation of a protein with other compounds, factors, or macromolecules. eco TAIR:TED Used when an annotation is made based on fractionation of a protein with other compounds, factors, or macromolecules. microarray RNA expression level evidence ECO:0000104 IEP: transcript levels (e.g. microarray data) Used when an annotation is made based on levels of RNA expression determined by microarray experiment. eco TAIR:TED Used when an annotation is made based on levels of RNA expression determined by microarray experiment. Nimblegen array evidence ECO:0000105 eco northern assay evidence A type of transcript expression level evidence based on electrophoresis and probing to determine levels of RNA expression using a complementary hybridization probe on the separated RNA samples. ECO:0000106 IEP: transcript levels (e.g. Northerns) Northern blot eco A type of transcript expression level 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 reverse transcription polymerase chain reaction transcription evidence ECO:0000108 IEP: transcript levels (e.g. RT-PCR) RT-PCR transcription evidence Used when an annotation is made based on levels of RNA expression determined by an RT-PCR experiment (quantitative or otherwise). eco TAIR:TED Used when an annotation is made based on levels of RNA expression determined by an RT-PCR experiment (quantitative or otherwise). 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:0000109 RT-PCR evidence The starting product for PCR, and therefore amplification volume, is directly correlated to the transcription rate. eco qRT-PCR PMID:12901609 qRT-PCR 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 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:0000110 IEP: RNA protection assay RNAse protection assay RPA eco ribonuclease protection assay 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 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:0000112 IEP: protein levels (e.g. Western blots) Western blot expression analysis 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. eco protein immunoblot 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 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:0000114 IEP: expression library screening eco 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 differential hybridization evidence ECO:0000116 IEP: differential hybridization Used when an annotation is made based on results of a differential hybridization experiment that demonstrates expression of an RNA under one condition and not another. eco TAIR:TED Used when an annotation is made based on results of a differential hybridization experiment that demonstrates expression of an RNA under one condition and not another. subtractive hybridization evidence ECO:0000118 IEP: subtractive hybridization Used when an annotation is made based on results of a subtractive hybridization experiment that demonstrates expression of an RNA under one condition and not another. eco TAIR:TED Used when an annotation is made based on results of a subtractive hybridization experiment that demonstrates expression of an RNA under one condition and not another. over expression analysis evidence ECO:0000120 IMP: analysis of overexpression/ectopic expression phenotype Used when an annotation is made based on the analysis of the phenotype of a wild-type or mutant transgenic organism that has been engineered to overexpress the gene product in question. eco TAIR:TED Used when an annotation is made based on the analysis of the phenotype of a wild-type or mutant transgenic organism that has been engineered to overexpress the gene product in question. protein localization evidence ECO:0000122 eco fusion protein localization evidence ECO:0000124 eco green fluorescent protein fusion protein localization evidence ECO:0000126 GFP fusion protein localization evidence IDA: localization of GFP/YFP fusion protein eco yellow fluorescent protein fusion protein localization evidence ECO:0000128 IDA: localization of GFP/YFP fusion protein YFP fusion protein localization evidence eco beta-glucuronidase fusion protein localization evidence ECO:0000130 GUS fusion protein localization evidence GUS staining evidence IDA: localization of GUS fusion protein eco beta-galactosidase fusion protein localization evidence ECO:0000132 LacZ fusion protein localization evidence eco transport assay evidence ECO:0000134 IDA: transport assay eco nucleic acid binding evidence ECO:0000136 eco ribohomopolymer binding assay evidence ECO:0000138 IDA: ribohomopolymer binding assay eco 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:0000140 IDA: thin layer chromatography TLC evidence eco 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 protein:ion binding evidence ECO:0000142 eco Southwestern blot evidence ECO:0000144 IDA: Southwestern analysis Used when an annotation is made based on a Southwestern blot analysis, which detects DNA binding of proteins using labeled DNA as probe hybridizing to electrophoretically separated proteins. eco TAIR:TED Used when an annotation is made based on a Southwestern blot analysis, which detects DNA binding of proteins using labeled DNA as probe hybridizing to electrophoretically separated proteins. Northwestern blot evidence ECO:0000146 IDA: Northwestern analysis Used when an annotation is made based on a Northwestern blot analysis, which detects RNA binding of proteins using labeled RNA as probe hybridizing to electrophoretically separated proteins. eco TAIR:TED Used when an annotation is made based on a Northwestern blot analysis, which detects RNA binding of proteins using labeled RNA as probe hybridizing to electrophoretically separated proteins. in vitro binding evidence ECO:0000148 IDA: in vitro binding assay eco true in vitro transcription reconstitution assay evidence ECO:0000150 IDA: in vitro reconstitution assay with recombinant protein eco in vitro recombinant protein transcription reconstitution assay evidence ECO:0000152 IDA: in vitro reconstitution assay with recombinant protein eco 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:0000154 IDA: protein expression in heterologous system eco 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 protein separation evidence ECO:0000156 eco protein separation followed by direct sequencing evidence ECO:0000158 IDA: protein separation and direct sequencing eco protein separation followed by fragment identification evidence ECO:0000160 IDA: protein separation and fragment identification eco heterologous system uptake evidence ECO:0000162 IDA: uptake assay in heterologous system Used when an annotation is made based on small molecule update assays carried out in a heterologous system that contains a recombinant protein. eco TAIR:TED Used when an annotation is made based on small molecule update assays carried out in a heterologous system that contains a recombinant protein. electrophysiology assay evidence A type of direct assay evidence where electrical properties of cells or tissues are studied. 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. eco A type of direct assay evidence where electrical properties of cells or tissues are studied. ECO:KAV two-electrode voltage clamp experiment evidence A type of electrophysiology assay 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:0000166 IDA: two-electrode voltage clamp technique eco A type of electrophysiology assay 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 transcription assay ECO:0000168 eco transcriptional activation assay ECO:0000170 IDA: transcriptional activation assay Used when an annotation is made based on assays that show transcriptional activation of a specific target reporter gene. eco TAIR:TED Used when an annotation is made based on assays that show transcriptional activation of a specific target reporter gene. biochemical trait analysis evidence ECO:0000172 IMP: analysis of biochemical trait Used when an annotation is made based on the analysis of a biochemical aspect of a mutant phenotype; for example, the accumulation of a biosynthetic intermediate. eco TAIR:TED Used when an annotation is made based on the analysis of a biochemical aspect of a mutant phenotype; for example, the accumulation of a biosynthetic intermediate. mutant physiological response evidence ECO:0000174 IMP: analysis of physiological response Used when an annotation is made based on the physiological response of a mutant to an external stimulus; for example, abnormal growth of the root in response to gravity, delay in flowering in response to varying light conditions. eco TAIR:TED Used when an annotation is made based on the physiological response of a mutant to an external stimulus; for example, abnormal growth of the root in response to gravity, delay in flowering in response to varying light conditions. mutant visible phenotype evidence ECO:0000176 IMP: analysis of visible trait Used when an annotation is made based on the visual examination of a mutant phenotype; for example, abnormalities in organism morphology. eco TAIR:TED Used when an annotation is made based on the visual examination of a mutant phenotype; for example, abnormalities in organism morphology. genomic context evidence An evidence type that is based on the location of a gene, which gives rise to a gene product, within the genome. ECO:0000177 This type of evidence might include identity of neighboring genes, operon structure, synteny, phylogenetic analysis, or other whole-genome analysis. eco An evidence type that is based on the location of a gene, which gives rise to a gene product, within the genome. ECO:MCC ECO:go in vivo assay evidence ECO:0000178 eco animal model system study evidence A type of experimental evidence arising from the investigation of an animal model system. ECO:0000179 eco A type of experimental evidence arising from the investigation of an animal model system. ECO:MCC clinical study evidence A type of experimental evidence arising from a controlled investigation that uses human subjects. ECO:0000180 eco A type of experimental evidence arising from a controlled investigation that uses human subjects. ECO:MCC in vitro assay evidence ECO:0000181 eco in vitro culture assay evidence ECO:0000182 eco cell-free assay evidence ECO:0000183 eco in vitro assay enzyme inhibition evidence A type of specific protein inhibition evidence where the protein under study is an enzyme. ECO:0000184 eco A type of specific protein inhibition evidence where the protein under study is an enzyme. ECO:MCC sequence alignment evidence 2010-03-18T12:21:31Z A type of sequence similarity evidence where a sequence alignment is the basis for making an annotation, but only when the alignment has been manually reviewed; or if the information is in a published paper, the authors have manually reviewed the evidence. Such alignments may be pairwise alignments or multiple alignments. ECO:00000057 ECO:0000200 eco mchibucos A type of sequence similarity evidence where a sequence alignment is the basis for making an annotation, but only when the alignment has been manually reviewed; or if the information is in a published paper, the authors have manually reviewed the evidence. Such alignments may be pairwise alignments or multiple alignments. url:http://www.geneontology.org/GO.evidence.shtml sequence orthology evidence 2010-03-18T12:30:06Z ECO:00000060 ECO:0000201 Orthology is a relationship between genes in different species indicating that the genes derive from a common ancestor. Orthology is established by multiple criteria generally 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. eco mchibucos ortholog evidence Orthology is a relationship between genes in different species indicating that the genes derive from a common ancestor. Orthology is established by multiple criteria generally 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 match to sequence model evidence 2010-03-18T12:32:30Z ECO:00000063 ECO:0000202 Sequence similarity evidence that is based on a sequence-based statistical model that predicts the function of a gene product. 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. eco mchibucos ECO:MCC Sequence similarity evidence that is based on a sequence-based statistical model that predicts the function of a gene product. url:http://www.geneontology.org/GO.evidence.shtml automatic assertion 2010-03-18T12:36:04Z An assertion method that does not involve human review. 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. ECO:00000067 ECO:0000203 eco mchibucos An assertion method that does not involve human review. ECO:MCC author statement 2010-06-21T11:17:21Z An evidence type that is based on an assertion by the author of a paper, which is read by a curator. ECO:0000204 eco mchibucos An evidence type that is based on an assertion by the author of a paper, which is read by a curator. ECO:MCC curator inference 2010-08-18T05:55:12Z A type of inferential evidence that is based on a conclusion drawn by a curator. ECO:0000205 eco mchibucos A type of inferential evidence that is based on a conclusion drawn by a curator. ECO:MCC BLAST evidence 2010-08-06T04:48:24Z A type of pairwise sequence alignment evidence obtained with basic local alignment search tool (BLAST). ECO:0000206 eco mchibucos A type of pairwise sequence alignment evidence obtained with basic local alignment search tool (BLAST). ECO:MCC nucleotide BLAST evidence 2010-08-06T04:49:58Z BLAST evidence from aligning nucleotide sequence with nucleotide sequence. ECO:0000207 eco mchibucos BLAST evidence from aligning nucleotide sequence with nucleotide sequence. ECO:MCC protein BLAST evidence 2010-08-06T04:50:45Z BLAST evidence from aligning amino acid or translated nucleotide sequence with amino acid or translated nucleotide sequence. ECO:0000208 eco mchibucos BLAST evidence from aligning amino acid or translated nucleotide sequence with amino acid or translated nucleotide sequence. ECO:MCC BLAST evidence used in automatic assertion 2010-08-06T04:55:21Z A type of BLAST evidence that is used in an automatic assertion. ECO:0000209 eco mchibucos true true A type of BLAST evidence that is used in an automatic assertion. ECO:MCC nucleotide BLAST evidence used in automatic assertion 2010-08-06T05:09:51Z ECO:0000210 Nucleotide BLAST evidence that is used in an automatic assertion. eco mchibucos true true ECO:MCC Nucleotide BLAST evidence that is used in an automatic assertion. protein BLAST evidence used in automatic assertion 2010-08-06T05:11:04Z ECO:0000211 Protein BLAST evidence that is used in an automatic assertion. eco mchibucos true true ECO:MCC Protein BLAST evidence that is used in an automatic assertion. combinatorial evidence 2010-08-06T05:24:57Z 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. A type of evidence that arises out of the integration of more than one line of evidence. ECO:0000036 ECO:0000043 ECO:0000212 eco inferred from in-silico analysis mchibucos A type of evidence that arises out of the integration of more than one line of evidence. ECO:MCC combinatorial evidence used in automatic assertion 2010-08-06T05:28:33Z A type of combinatorial analysis that is used in an automatic assertion. 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. ECO:0000213 eco mchibucos true A type of combinatorial analysis that is used in an automatic assertion. ECO:MCC true biological aspect of descendant evidence 2010-10-05T11:16:50Z 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: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. eco mchibucos 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 rapid divergence from ancestral sequence evidence 2010-10-05T03:41:34Z A type of phylogenetic evidence characterized by long phylogenetic tree branch lengths following a duplication event. ECO:0000215 Long branch lengths indicate that descendant sequences may have acquired different or additional functions than the ancestral sequence. eco mchibucos A type of phylogenetic evidence characterized by long phylogenetic tree branch lengths following a duplication event. ECO:MCC phylogenetic determination of loss of key residues evidence 2010-10-05T03:43:17Z A type of phylogenetic evidence characterized by the absence of key sequence residues. ECO:0000216 The loss of certain residues important for function can indicate that a sequence lacks a particular function. eco mchibucos A type of phylogenetic evidence characterized by the absence of key sequence residues. ECO:MCC assertion method 2010-11-12T04:17:37Z A means by which a statement is made about an entity. ECO:0000217 eco mchibucos A means by which a statement is made about an entity. ECO:MCC manual assertion 2010-11-12T04:20:02Z 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. An assertion method that involves human review. ECO:0000218 eco mchibucos An assertion method that involves human review. ECO:MCC nucleotide sequencing assay evidence 2010-11-15T12:22:40Z A sequencing assay result for a biopolymer that comprises nucleotides. DNA sequencing ECO:0000219 eco mchibucos DNA sequencing OBI:0000626 A sequencing assay result for a biopolymer that comprises nucleotides. ECO:MCC sequencing assay evidence 2010-11-15T01:44:45Z A type of experimental evidence where the order of molecules that constitute a biopolymer is determined. ECO:0000220 eco mchibucos A type of experimental evidence where the order of molecules that constitute a biopolymer is determined. ECO:MCC OBI:0600047 high throughput nucleotide sequencing assay evidence 2010-11-15T02:19:34Z A nucleotide sequencing assay result that is derived from a parallelized sequencing technique. ECO:0000221 Typically thousands to millions of reads are produced in parallel. eco mchibucos A nucleotide sequencing assay result that is derived from a parallelized sequencing technique. ECO:MCC Illumina sequencing evidence 2010-11-15T02:38:03Z A high throughput nucleotide sequencing result derived by Illumina (Solexa) sequencing technology. 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. Solexa sequencing result eco mchibucos OBI:0000724 Solexa sequencing result A high throughput nucleotide sequencing result derived by Illumina (Solexa) sequencing technology. ECO:MCC 454 pyrosequencing evidence 2010-11-15T03:50:14Z 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. A high throughput nucleotide sequencing result derived by 454 pyrosequencing technology. ECO:0000223 eco mchibucos pyrosequencing OBI:0000730 pyrosequencing A high throughput nucleotide sequencing result derived by 454 pyrosequencing technology. ECO:MCC SOLiD sequencing evidence 2010-11-15T04:17:41Z A high throughput nucleotide sequencing result derived by SOLiD sequencing technology. 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. eco mchibucos A high throughput nucleotide sequencing result derived by SOLiD sequencing technology. ECO:MCC OBI:0000706 chain termination sequencing evidence 2010-11-15T04:46:31Z A nucleotide sequencing assay result derived by the chain termination sequencing method. 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. ECO:0000225 Sanger sequencing dye terminator sequencing eco mchibucos A nucleotide sequencing assay result derived by the chain termination sequencing method. ECO:MCC OBI:0000695 chromatin immunoprecipitation evidence 2010-11-16T01:29:08Z A type of immunoprecipitation evidence that is used to identify a protein binding site on a genomic DNA sequence. ChIP evidence 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). ECO:0000226 PSI-MI:MI:0402 eco mchibucos chromatin immunoprecipitation assay PSI-MI:MI:0402 A type of immunoprecipitation evidence that is used to identify a protein binding site on a genomic DNA sequence. ECO:MCC chromatin immunoprecipitation-PCR evidence 2010-11-16T05:02:00Z 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. ChIP-PCR evidence ChIP-PCR is often used to validate ChIP-chip results and less frequently,ChIP-Seq results. ECO:0000227 eco mchibucos 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 chromatin immunoprecipitation-qPCR evidence 2010-11-16T05:26:47Z A chromatin immunoprecipitation (ChIP) evidence that uses quantitative polymerase chain reaction (qPCR) for DNA detection. ChIP-qPCR evidence ECO:0000228 eco mchibucos A chromatin immunoprecipitation (ChIP) evidence that uses quantitative polymerase chain reaction (qPCR) for DNA detection. ECO:MCC chromatin immunoprecipitation-seq evidence 2010-11-16T05:30:41Z 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. ChIP-SEQ evidence 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. ChIP-seq evidence ECO:0000229 eco mchibucos ChIP-seq evidence PMID:22955991 ChIP-SEQ evidence OBI:0000716 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 chromatin immunoprecipitation-chip evidence 2010-11-16T05:43:55Z 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. 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. ChIP-chip evidence ChIP-on-chip evidence ECO:0000230 PSI-MI:MI:0225 eco mchibucos 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 chromatin immunoprecipitation array PSI-MI:MI:0225 quantitative polymerase chain reaction evidence 2010-11-16T05:57:20Z 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:0000231 Q-PCR evidence 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). eco mchibucos qRT-PCR evidence quantitative PCR evidence real-time PCR evidence real-time 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 chromosome conformation capture-based evidence 2010-11-17T12:27:14Z 3C 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. 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. ECO:0000232 chromosome conformation capture eco mchibucos 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 chromosome conformation capture evidence 2010-11-17T12:46:15Z 3C 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. 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:0000233 eco mchibucos 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 circularized chromosome conformation capture evidence 2010-11-19T01:20:28Z 4C 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. 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:0000234 chromosome conformation capture on chip circularized 3C eco mchibucos 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 carbon-copy chromosome conformation capture evidence 2010-11-19T01:22:20Z 5C 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. A type of chromosome conformation capture-based evidence that is derived by performing ligation-mediated amplification (LMA) prior to product quantitation. ECO:0000235 carbon-copy 3C eco mchibucos A type of chromosome conformation capture-based evidence that is derived by performing ligation-mediated amplification (LMA) prior to product quantitation. ECO:MCC chromosome conformation capture-PCR evidence 2010-11-19T03:00:47Z 3C 3C-PCR A type of chromosome conformation capture evidence that is derived by performing polymerase chain reaction (PCR) in the quantitation step. ECO:0000236 eco mchibucos A type of chromosome conformation capture evidence that is derived by performing polymerase chain reaction (PCR) in the quantitation step. ECO:MCC chromosome conformation capture-qPCR evidence 2010-11-19T03:06:47Z 3C-qPCR 3C-quantitative PCR 3C-real-time PCR A type of chromosome conformation capture evidence that is derived by performing quantitative polymerase chain reaction (qPCR) in the quantitation step. ECO:0000237 eco mchibucos A type of chromosome conformation capture evidence that is derived by performing quantitative polymerase chain reaction (qPCR) in the quantitation step. ECO:MCC Hi-C evidence 2010-11-19T04:24:03Z A type of chromosome conformation capture-based evidence that is derived by performing immunoprecipitation enrichment of ligated fragments events prior to product quantitation. 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. eco mchibucos 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 chromosome conformation capture sequencing evidence 2010-11-30T03:22:25Z 3C sequencing 3C-seq 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. 4C sequencing 4C-seq 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:0000239 circularized 3C sequencing circularized 3C-seq eco mchibucos 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 anatomical perturbation evidence 2010-12-06T12:24:16Z ECO:0000240 Experimental phenotypic evidence where a structural feature of an organism is disrupted. eco mchibucos ECO:MCC Experimental phenotypic evidence where a structural feature of an organism is disrupted. environmental perturbation evidence 2010-12-06T12:33:58Z ECO:0000241 Experimental phenotypic evidence where the extra-organismal context of an organism is modified. Many environmental factors are subject to modification, such as temperature, pressure, humidity, radiation, and so forth. eco mchibucos mechanical constraint evidence ECO:MCC Experimental phenotypic evidence where the extra-organismal context of an organism is modified. tissue ablation evidence 2010-12-06T12:33:58Z 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. A type of anatomical perturbation that is based on disruption of tissue. ECO:0000242 ablated tissue evidence eco mchibucos A type of anatomical perturbation that is based on disruption of tissue. ECO:MCC tissue grafting evidence 2010-12-06T12:33:58Z A type of anatomical perturbation that is based on adding tissue to an organism through a graft procedure. ECO:0000243 eco mchibucos A type of anatomical perturbation that is based on adding tissue to an organism through a graft procedure. ECO:MCC combinatorial evidence used in manual assertion 2010-12-09T02:02:12Z A type of combinatorial analysis that is used in a manual assertion. 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. ECO:0000244 eco mchibucos A type of combinatorial analysis that is used in a manual assertion. ECO:MCC true true computational combinatorial evidence used in manual assertion 2010-12-09T02:37:54Z A type of computational combinatorial analysis that is used in a manual assertion. ECO:0000245 GOECO:RCA RCA eco inferred from reviewed computational analysis mchibucos GOECO:RCA inferred from reviewed computational analysis GOECO:RCA RCA true inferred from reviewed computational analysis GOECO:RCA true A type of computational combinatorial analysis that is used in a manual assertion. ECO:MCC computational combinatorial evidence used in automatic assertion 2010-12-09T02:37:54Z A type of computational combinatorial analysis that is used in an automatic assertion. ECO:0000246 eco mchibucos A type of computational combinatorial analysis that is used in an automatic assertion. ECO:MCC true true sequence alignment evidence used in manual assertion 2010-12-09T05:12:27Z ECO:0000247 GOECO:ISA ISA Sequence alignment evidence that is used in a manual assertion. eco inferred from sequence alignment mchibucos inferred from sequence alignment GOECO:ISA true GOECO:ISA inferred from sequence alignment GOECO:ISA ISA true ECO:MCC Sequence alignment evidence that is used in a manual assertion. sequence alignment evidence used in automatic assertion 2010-12-09T05:12:27Z ECO:0000248 Sequence alignment evidence that is used in an automatic assertion. eco mchibucos true true ECO:MCC Sequence alignment evidence that is used in an automatic assertion. sequence similarity evidence used in automatic assertion 2010-12-09T05:22:30Z ECO:0000249 Sequence similarity evidence that is used in an automatic assertion. eco mchibucos true true ECO:MCC Sequence similarity evidence that is used in an automatic assertion. sequence similarity evidence used in manual assertion 2010-12-09T05:22:30Z A type of sequence similarity evidence that is used in a manual assertion. ECO:0000250 GOECO:ISS ISS eco inferred from sequence or structural similarity mchibucos true true GOECO:ISS inferred from sequence or structural similarity GOECO:ISS ISS inferred from sequence or structural similarity GOECO:ISS A type of sequence similarity evidence that is used in a manual assertion. ECO:MCC similarity evidence used in automatic assertion 2010-12-09T05:28:12Z ECO:0000251 Similarity evidence that is used in an automatic assertion. eco mchibucos true true ECO:MCC Similarity evidence that is used in an automatic assertion. similarity evidence used in manual assertion 2010-12-09T05:28:12Z ECO:0000252 Similarity evidence that is used in a manual assertion. eco mchibucos true true ECO:MCC Similarity evidence that is used in a manual assertion. genetic similarity evidence used in manual assertion 2010-12-10T01:42:44Z ECO:0000253 Genetic similarity evidence that is used in a manual assertion. eco mchibucos ECO:MCC Genetic similarity evidence that is used in a manual assertion. true true genetic similarity evidence used in automatic assertion 2010-12-10T01:42:44Z ECO:0000254 Genetic similarity evidence that is used in an automatic assertion. eco mchibucos true true ECO:MCC Genetic similarity evidence that is used in an automatic assertion. match to sequence model evidence used in manual assertion 2010-12-10T02:26:35Z A match to sequence model evidence that is employed in a manual assertion. ECO:0000255 GOECO:ISM GO_REF:0000011 ISM eco inferred from sequence model mchibucos true A match to sequence model evidence that is employed in a manual assertion. ECO:MCC true GOECO:ISM ISM GOECO:ISM inferred from sequence model Hidden Markov Models (TIGR) GO_REF:0000011 inferred from sequence model GOECO:ISM match to sequence model evidence used in automatic assertion 2010-12-10T02:26:35Z A match to sequence model evidence that is employed in an automatic assertion. ECO:0000256 GO_REF:0000002 GO_REF:0000107 eco mchibucos true true A match to sequence model evidence that is employed in an automatic assertion. ECO:MCC Gene Ontology annotation through association of InterPro records with GO terms. GO_REF:0000002 Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl GO_REF:0000107 motif similarity evidence used in manual assertion 2010-12-10T02:44:34Z ECO:0000257 Motif similarity evidence that is employed in a manual assertion. eco mchibucos true ECO:MCC Motif similarity evidence that is employed in a manual assertion. true motif similarity evidence used in automatic assertion 2010-12-10T02:44:34Z ECO:0000258 Motif similarity evidence that is employed in an automatic assertion. eco mchibucos ECO:MCC Motif similarity evidence that is employed in an automatic assertion. true true match to InterPro member signature evidence used in automatic assertion 2010-12-10T02:54:51Z A match to InterPro member signature evidence that is employed in an automatic assertion. ECO:0000259 eco mchibucos true A match to InterPro member signature evidence that is employed in an automatic assertion. ECO:MCC true match to InterPro member signature evidence used in manual assertion 2010-12-10T02:54:51Z A match to InterPro member signature evidence that is employed in a manual assertion. ECO:0000260 eco mchibucos true A match to InterPro member signature evidence that is employed in a manual assertion. ECO:MCC true targeting sequence prediction evidence used in automatic assertion 2010-12-10T03:02:49Z A targeting sequence prediction that is employed in an automatic assertion. ECO:0000261 eco mchibucos A targeting sequence prediction that is employed in an automatic assertion. ECO:MCC true true targeting sequence prediction evidence used in manual assertion 2010-12-10T03:02:49Z A targeting sequence prediction that is employed in a manual assertion. ECO:0000262 eco mchibucos A targeting sequence prediction that is employed in a manual assertion. ECO:MCC true true transmembrane domain prediction evidence used in automatic assertion 2010-12-10T03:28:35Z ECO:0000263 Transmembrane domain prediction that is employed in an automatic assertion. eco mchibucos true true ECO:MCC Transmembrane domain prediction that is employed in an automatic assertion. transmembrane domain prediction evidence used in manual assertion 2010-12-10T03:28:35Z ECO:0000264 Transmembrane domain prediction that is employed in a manual assertion. eco mchibucos true true ECO:MCC Transmembrane domain prediction that is employed in a manual assertion. sequence orthology evidence used in automatic assertion 2010-12-10T03:39:41Z ECO:0000265 GO_REF:0000019 GO_REF:0000020 GO_REF:0000035 GO_REF:0000049 Ortholog evidence Sequence orthology evidence that is employed in an automatic assertion. eco mchibucos Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins. GO_REF:0000020 Automatic transfer of experimentally verified manual GO annotation data to fungal orthologs using Ensembl Compara GO_REF:0000049 Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara GO_REF:0000019 Automatic transfer of experimentally verified manual GO annotation data to plant orthologs using Ensembl Compara GO_REF:0000035 true ECO:MCC Sequence orthology evidence that is employed in an automatic assertion. true sequence orthology evidence used in manual assertion 2010-12-10T03:39:41Z A type of sequence orthology evidence that is used in a manual assertion. ECO:0000266 GOECO:ISO ISO Ortholog evidence eco inferred from sequence orthology mchibucos GOECO:ISO inferred from sequence orthology GOECO:ISO ISO A type of sequence orthology evidence that is used in a manual assertion. ECO:MCC true inferred from sequence orthology GOECO:ISO true enzyme-linked immunoabsorbent assay evidence 2010-12-14T01:57:13Z 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:0000267 ELISA evidence ELISA is sometimes used in the study of transcriptional regulation to identify a produced protein, especially secreted protein. PSI-MI:MI:0411 eco enzyme-linked immunosorbent assay mchibucos enzyme linked immunosorbent assay PSI-MI:MI:0411 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 flow cytometry evidence 2010-12-14T02:07:08Z A direct assay that passes a stream of cells or particles past a light source, followed by using a detector to monitor light scatter or fluorochrome excitation to characterize the cells or particles. ECO:0000268 FCM eco mchibucos A direct assay that passes a stream of cells or particles past a light source, followed by using a detector to monitor light scatter or fluorochrome excitation to characterize the cells or particles. ECO:MCC experimental evidence used in manual assertion 2010-12-20T05:36:49Z A type of experimental evidence that is used in a manual assertion. ECO:0000269 EXP GOECO:EXP eco inferred from experiment mchibucos true A type of experimental evidence that is used in a manual assertion. ECO:MCC true inferred from experiment GOECO:EXP GOECO:EXP inferred from experiment EXP GOECO:EXP expression evidence used in manual assertion 2010-12-20T05:46:39Z A type of expression pattern evidence that is used in a manual assertion. ECO:0000270 GOECO:IEP IEP eco inferred from expression pattern mchibucos GOECO:IEP IEP inferred from expression pattern GOECO:IEP true GOECO:IEP inferred from expression pattern A type of expression pattern evidence that is used in a manual assertion. ECO:MCC true array experiment evidence used in manual assertion 2010-12-20T05:51:58Z A type of array experiment evidence that is used in a manual assertion. ECO:0000271 eco mchibucos true true A type of array experiment evidence that is used in a manual assertion. ECO:MCC Affymetrix array experiment evidence used in manual assertion 2010-12-20T05:53:36Z A type of Affymetrix array experiment evidence that is used in a manual assertion. ECO:0000272 eco mchibucos true A type of Affymetrix array experiment evidence that is used in a manual assertion. ECO:MCC true cDNA microarray evidence used in manual assertion 2010-12-20T05:55:49Z A type of evidence arising from a cDNA microarray experiment that is used in a manual assertion. ECO:0000273 eco mchibucos true A type of evidence arising from a cDNA microarray experiment that is used in a manual assertion. ECO:MCC true CpG island microarray evidence used in manual assertion 2010-12-20T05:58:44Z A type of evidence arising from a CpG island microarray experiment that is used in a manual assertion. ECO:0000274 eco mchibucos A type of evidence arising from a CpG island microarray experiment that is used in a manual assertion. ECO:MCC true true expression microarray evidence used in manual assertion 2010-12-20T06:01:26Z A type of expression microarray evidence that is used in a manual assertion. ECO:0000275 eco mchibucos true A type of expression microarray evidence that is used in a manual assertion. ECO:MCC true genomic microarray evidence used in manual assertion 2010-12-20T06:03:28Z A type of evidence arising from a genomic microarray experiment that is used in a manual assertion. ECO:0000276 eco mchibucos true true A type of evidence arising from a genomic microarray experiment that is used in a manual assertion. ECO:MCC Nimblegen array evidence used in manual assertion 2010-12-20T06:05:20Z A type of evidence arising from a Nimblegen array experiment that is used in a manual assertion. ECO:0000277 eco mchibucos A type of evidence arising from a Nimblegen array experiment that is used in a manual assertion. ECO:MCC true true oligonucleotide microarray evidence used in manual assertion 2010-12-20T06:09:45Z A type of evidence arising from an oligonucleotide microarray experiment that is used in a manual assertion. ECO:0000278 eco mchibucos true A type of evidence arising from an oligonucleotide microarray experiment that is used in a manual assertion. ECO:MCC true western blot evidence used in manual assertion 2010-12-20T06:20:01Z A type of Western blot assay that is used in a manual assertion. ECO:0000279 eco mchibucos true true A type of Western blot assay that is used in a manual assertion. ECO:MCC protein expression level evidence used in manual assertion 2010-12-20T06:21:54Z A type of protein expression level analysis that is used in a manual assertion. ECO:0000280 eco mchibucos true A type of protein expression level analysis that is used in a manual assertion. ECO:MCC true expression library screen evidence used in manual assertion 2010-12-20T06:24:05Z A type of expression library screen evidence that is used in a manual assertion. ECO:0000281 eco mchibucos A type of expression library screen evidence that is used in a manual assertion. ECO:MCC true true heterologous protein expression evidence used in manual assertion 2010-12-20T06:27:04Z A type of heterologous protein expression analysis that is used in a manual assertion. ECO:0000282 eco mchibucos true true A type of heterologous protein expression analysis that is used in a manual assertion. ECO:MCC spatial pattern of protein expression evidence used in manual assertion 2010-12-20T06:31:44Z A type of protein expression spatial pattern analysis that is used in a manual assertion. ECO:0000283 eco mchibucos true true A type of protein expression spatial pattern analysis that is used in a manual assertion. ECO:MCC protein expression evidence used in manual assertion 2010-12-20T06:33:46Z A type of protein expression analysis that is used in a manual assertion. ECO:0000284 eco mchibucos A type of protein expression analysis that is used in a manual assertion. ECO:MCC true true true microarray RNA expression level evidence used in manual assertion 2010-12-20T06:41:33Z A type of microarray RNA expression level data that is used in manual assertion. ECO:0000285 eco mchibucos true A type of microarray RNA expression level data that is used in manual assertion. ECO:MCC true true transcript expression level evidence used in manual assertion 2010-12-20T06:52:03Z A type of transcript expression level data that is used in manual assertion. ECO:0000286 eco mchibucos true A type of transcript expression level data that is used in manual assertion. ECO:MCC true differential hybridization evidence used in manual assertion 2010-12-20T06:55:14Z A type of differential hybridization experiment that is used in a manual assertion. ECO:0000287 eco mchibucos A type of differential hybridization experiment that is used in a manual assertion. ECO:MCC true true RNA protection assay evidence used in manual assertion 2010-12-20T06:57:33Z A type of RNA protection assay that is used in a manual assertion. ECO:0000288 eco mchibucos true true A type of RNA protection assay that is used in a manual assertion. ECO:MCC spatial pattern of transcript expression evidence used in manual assertion 2010-12-20T06:59:18Z A type of spatial pattern of transcript expression analysis that is used in a manual assertion. ECO:0000289 eco mchibucos true A type of spatial pattern of transcript expression analysis that is used in a manual assertion. ECO:MCC true subtractive hybridization evidence used in manual assertion 2010-12-20T07:00:48Z A type of subtractive hybridization experiment that is used in a manual assertion. ECO:0000290 eco mchibucos A type of subtractive hybridization experiment that is used in a manual assertion. ECO:MCC true true transcript expression evidence used in manual assertion 2010-12-20T07:02:08Z A type of transcript expression evidence that is used in a manual assertion. ECO:0000291 eco mchibucos true A type of transcript expression evidence that is used in a manual assertion. ECO:MCC true morpholino experiment evidence 2011-01-10T03:36:25Z A type of experimental phenotypic evidence that uses anti-sense by introducing morpholino oligonucleotides into the cytosol of a cell. 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. anti-sense eco mchibucos A type of experimental phenotypic evidence that uses anti-sense by introducing morpholino oligonucleotides into the cytosol of a cell. ECO:MCC systematic evolution of ligands by exponential amplification evidence 2011-01-10T04:23:50Z 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:0000293 PSI-MI:MI:0657 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. SELEX evidence eco in vitro evolution evidence in vitro selection evidence mchibucos systematic evolution of ligands by exponential enrichment PSI-MI:MI:0657 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 bacterial one-hybrid evidence 2011-01-10T06:16:20Z 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). B1H evidence 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. ECO:0000294 eco mchibucos 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 RNA-seq evidence 2011-01-11T12:54:50Z A type of transcript expression evidence based on high-throughput (HT) sequencing of fragmented cDNA molecules. ECO:0000295 RNA sequencing 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. WTSS eco mchibucos whole transcriptome shotgun sequencing A type of transcript expression evidence based on high-throughput (HT) sequencing of fragmented cDNA molecules. ECO:MCC PMID:18611170 whole transcriptome shotgun sequencing green fluorescent protein transcript localization evidence 2011-01-11T02:31:19Z A transcriptional activation assay that uses a green fluorescent protein (GFP) reporter gene. ECO:0000296 This term describes transcriptional activation; to describe immunolocalization of the protein, use the term "immunolocalization of green fluorescent protein". eco localization of GFP transcript mchibucos A transcriptional activation assay that uses a green fluorescent protein (GFP) reporter gene. ECO:MCC LacZ transcript localization evidence 2011-01-11T02:53:19Z A transcriptional activation assay that uses a LacZ reporter gene. ECO:0000297 This term describes transcriptional activation; to describe immunolocalization of the protein, use the term "immunolocalization of LacZ protein". eco mchibucos A transcriptional activation assay that uses a LacZ reporter gene. ECO:MCC cleavage arrested development evidence 2011-01-11T03:28:49Z A type of experimental phenotypic evidence where embryonic development proceeds although cytokinesis is blocked. 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. eco mchibucos A type of experimental phenotypic evidence where embryonic development proceeds although cytokinesis is blocked. ECO:MCC cytochalasin experiment evidence 2011-01-11T03:30:29Z A type of cleavage arrested development that arises after treatment with cytochalasin. Cytochalasin inhibits cytokinesis by blocking the formation of contractile microfilaments. ECO:0000299 eco mchibucos A type of cleavage arrested development that arises after treatment with cytochalasin. ECO:MCC green fluorescent protein immunolocalization evidence 2011-01-11T03:48:50Z A type of immunolocalization evidence data that was generated using green fluorescent protein (GFP) as a marker. ECO:0000300 GFP immunolocalization evidence This term describes immunolocalization of the protein; to describe transcriptional activation, use the term "localization of green fluorescent protein transcript". eco mchibucos A type of immunolocalization evidence data that was generated using green fluorescent protein (GFP) as a marker. ECO:MCC beta-galactosidase protein immunolocalization evidence 2011-01-11T04:06:40Z A type of immunolocalization evidence that was generated using LacZ protein as a marker. ECO:0000301 LacZ protein immunolocalization evidence This term describes immunolocalization of the protein; to describe transcriptional activation, use the term "localization of LacZ transcript". eco mchibucos A type of immunolocalization evidence that was generated using LacZ protein as a marker. ECO:MCC author statement used in manual assertion 2011-01-20T02:26:47Z A type of author statement that is used in a manual assertion. ECO:0000302 eco mchibucos A type of author statement that is used in a manual assertion. ECO:MCC true true non-traceable author statement used in manual assertion 2011-01-20T02:29:50Z A type of non-traceable author statement that is used in a manual assertion. ECO:0000303 GOECO:NAS NAS eco mchibucos non-traceable author statement true GOECO:NAS non-traceable author statement non-traceable author statement GOECO:NAS A type of non-traceable author statement that is used in a manual assertion. ECO:MCC GOECO:NAS NAS true traceable author statement used in manual assertion 2011-01-20T02:31:03Z A type of traceable author statement that is used in a manual assertion. ECO:0000304 GOECO:TAS TAS eco mchibucos traceable author statement A type of traceable author statement that is used in a manual assertion. ECO:MCC true true GOECO:TAS TAS traceable author statement GOECO:TAS GOECO:TAS traceable author statement curator inference used in manual assertion 2011-01-20T02:33:32Z A type of curator inference that is used in a manual assertion. ECO:0000305 GOECO:IC IC eco inferred by curator mchibucos true inferred by curator GOECO:IC true GOECO:IC IC A type of curator inference that is used in a manual assertion. ECO:MCC GOECO:IC inferred by curator inference from background scientific knowledge used in manual assertion 2011-01-20T02:35:11Z A type of inference from background scientific knowledge that is used in a manual assertion. ECO:0000306 eco mchibucos true A type of inference from background scientific knowledge that is used in a manual assertion. ECO:MCC true no biological data found used in manual assertion 2011-01-20T02:43:18Z A type of no biological data found that is used in a manual assertion. ECO:0000307 GOECO:ND ND eco mchibucos no biological data available GOECO:ND ND true true no biological data available GOECO:ND A type of no biological data found that is used in a manual assertion. ECO:MCC GOECO:ND no biological data available biological aspect of ancestor evidence 2011-02-04T05:41:26Z 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: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. eco mchibucos 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 cap analysis of gene expression evidence 2011-02-17T01:33:09Z 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. CAGE 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. ECO:0000309 eco mchibucos 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 a cap-trapper system. ECO:MCC nano-cap analysis of gene expression evidence 2011-02-17T01:33:34Z 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: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. eco mchibucos nanoCAGE PMID:20543846 nanoCAGE 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 imported information 2011-03-02T05:24:13Z An evidence type that is based on work performed by a person or group prior to a use by different person or group. ECO:0000311 eco mchibucos An evidence type that is based on work performed by a person or group prior to a use by different person or group. ECO:MCC imported information used in manual assertion 2011-03-02T05:29:44Z A type of imported information that is used in a manual assertion. ECO:0000312 eco mchibucos true A type of imported information that is used in a manual assertion. ECO:MCC true imported information used in automatic assertion 2011-03-02T05:33:43Z A type of imported information that is used in an automatic assertion. ECO:0000313 eco mchibucos true A type of imported information that is used in an automatic assertion. ECO:MCC true direct assay evidence used in manual assertion 2011-10-28T04:59:31Z A type of direct assay evidence that is used in a manual assertion. ECO:0000314 GOECO:IDA IDA eco inferred from direct assay mchibucos GOECO:IDA IDA GOECO:IDA inferred from direct assay true inferred from direct assay GOECO:IDA true A type of direct assay evidence that is used in a manual assertion. ECO:MCC mutant phenotype evidence used in manual assertion 2011-10-28T05:12:49Z A type of mutant phenotype evidence that is used in a manual assertion. ECO:0000315 GOECO:IMP IMP eco inferred from mutant phenotype mchibucos GOECO:IMP IMP A type of mutant phenotype evidence that is used in a manual assertion. ECO:MCC true true GOECO:IMP inferred from mutant phenotype inferred from mutant phenotype GOECO:IMP genetic interaction evidence used in manual assertion 2011-10-28T05:14:42Z A type of genetic interaction experiment evidence that is used in a manual assertion. ECO:0000316 GOECO:IGI IGI eco inferred from genetic interaction mchibucos true GOECO:IGI IGI A type of genetic interaction experiment evidence that is used in a manual assertion. ECO:MCC GOECO:IGI inferred from genetic interaction true inferred from genetic interaction GOECO:IGI genomic context evidence used in manual assertion 2011-10-28T05:22:53Z A type of genomic context evidence that is used in a manual assertion. ECO:0000317 GOECO:IGC IGC eco inferred from genomic context mchibucos true true GOECO:IGC IGC A type of genomic context evidence that is used in a manual assertion. ECO:MCC GOECO:IGC inferred from genomic context inferred from genomic context GOECO:IGC biological aspect of ancestor evidence used in manual assertion 2011-10-28T05:23:51Z A type of biological aspect of ancestor evidence that is used in a manual assertion. ECO:0000318 GOECO:IBA IBA eco inferred from biological aspect of ancestor mchibucos true inferred from biological aspect of ancestor GOECO:IBA true GOECO:IBA inferred from biological aspect of ancestor GOECO:IBA IBA A type of biological aspect of ancestor evidence that is used in a manual assertion. ECO:MCC biological aspect of descendant evidence used in manual assertion 2011-10-28T05:25:09Z A type of biological aspect of descendant evidence that is used in a manual assertion. ECO:0000319 GOECO:IBD IBD eco inferred from biological aspect of descendant mchibucos GOECO:IBD IBD inferred from biological aspect of descendant GOECO:IBD true GOECO:IBD inferred from biological aspect of descendant A type of biological aspect of descendant evidence that is used in a manual assertion. ECO:MCC true phylogenetic determination of loss of key residues evidence used in manual assertion 2011-10-28T05:25:48Z A type of phylogenetic determination of loss of key residues evidence that is used in a manual assertion. ECO:0000320 GOECO:IKR GOECO:IMR IKR IMR eco inferred from key residues inferred from missing residues mchibucos GOECO:IKR IMR inferred from key residues GOECO:IKR A type of phylogenetic determination of loss of key residues evidence that is used in a manual assertion. ECO:MCC GOECO:IKR inferred from missing residues true true GOECO:IKR inferred from key residues inferred from missing residues GOECO:IMR GOECO:IKR IKR rapid divergence from ancestral sequence evidence used in manual assertion 2011-10-28T05:26:42Z A type of rapid divergence from ancestral sequence evidence that is used in a manual assertion. ECO:0000321 GOECO:IRD IRD eco inferred from rapid divergence mchibucos GOECO:IRD IRD true true inferred from rapid divergence GOECO:IRD GOECO:IRD inferred from rapid divergence A type of rapid divergence from ancestral sequence evidence that is used in a manual assertion. ECO:MCC imported manually asserted information used in automatic assertion 2011-12-13T12:04:48Z ECO:0000322 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. GO_REF:0000037 GO_REF:0000039 GO_REF:0000041 eco mchibucos Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries. GO_REF:0000037 IEA (UniProt UniPathway) GO_REF:0000041 Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries. GO_REF:0000039 ECO:MCC 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. imported automatically asserted information used in automatic assertion 2011-12-13T02:06:25Z 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:0000323 GO_REF:0000038 GO_REF:0000040 eco mchibucos Gene Ontology annotation based on the automatic assignment of UniProtKB Subcellular Location terms in UniProtKB/TrEMBL entries. GO_REF:0000040 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 Gene Ontology annotation based on automatic assignment of UniProtKB keywords in UniProtKB/TrEMBL entries. GO_REF:0000038 imaging assay evidence 2012-02-23T12:01:43Z Direct assay evidence derived from analysis of an image. ECO:0000324 ECO:0001122 eco mchibucos radiologic test evidence Direct assay evidence derived from analysis of an image. ECO:MCC chromatography evidence 2012-05-16T11:46:27Z 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:0000325 chromatographic evidence eco mchibucos 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 transcript splice pattern evidence 2012-06-08T11:03:59Z 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:0000326 eco mchibucos 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 whole transcript splice pattern evidence 2012-06-08T11:11:24Z A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features. 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. eco mchibucos 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 coding sequence splice pattern evidence 2012-06-08T11:21:57Z 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: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. eco mchibucos 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 whole transcript splice pattern evidence used in manual assertion 2012-06-08T11:40:03Z 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: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. eco mchibucos 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 true coding sequence splice pattern evidence used in manual assertion 2012-06-08T11:43:47Z 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: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. eco mchibucos 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 true true coding sequence splice pattern evidence used in automatic assertion 2012-06-08T11:48:09Z 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: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. eco mchibucos 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 true whole transcript splice pattern evidence used in automatic assertion 2012-06-08T11:49:17Z 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: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. eco mchibucos 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 sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence 2012-07-31T02:56:43Z A type of gel electrophoresis evidence where proteins are separated according to their electrophoretic mobility. 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. SDS-PAGE evidence eco mchibucos 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 particle size and count assay evidence 2012-07-31T03:19:32Z A type of direct assay evidence resulting from an assay where both the size of and number of particles in a sample are determined. An example of an instrument used to analyze particle sizes and counts is the Beckman Coulter® Z Series system. ECO:0000334 eco mchibucos 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 substance quantification evidence 2012-07-31T03:52:46Z A type of direct assay evidence where the quantity of a substance used as part of an assay is measured. 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. eco mchibucos A type of direct assay evidence where the quantity of a substance used as part of an assay is measured. ECO:MCC competitive growth assay evidence 2012-08-24T12:03:58Z 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. ECO:0000336 eco fitness profiling mchibucos GOC:MAH PMID:20537132 fitness profiling 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 gel electrophoresis evidence 2012-08-24T12:11:51Z 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:0000337 Molecules typically separated include DNA, RNA, or protein. The gel is typically made of agarose, polyacrylamide, or starch. eco mchibucos 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 pulsed-field gel electrophoresis evidence 2012-08-24T12:34:01Z ECO:0000338 Gel electrophoresis evidence that employs alternately pulsed, perpendicularly oriented electrical fields, at least one of which is inhomogeneous, to separate large DNA molecules on an agarose gel. PFGE eco mchibucos Gel electrophoresis evidence that employs alternately pulsed, perpendicularly oriented electrical fields, at least one of which is inhomogeneous, to separate large DNA molecules on an agarose gel. PMID:6373014 two-dimensional agarose gel electrophoresis evidence 2-D agarose gel electrophoresis 2012-08-24T12:42:37Z 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. 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. eco mchibucos 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 plasmid maintenance assay evidence 2012-08-24T01:27:58Z ECO:0000340 Experimental evidence from an assay in which a mitotically stable plasmid (or minichromosome) is introduced into cells, cells are grown without selection for several generations, the proportion of cells that retain the plasmid is then determined (by comparing colony numbers on selective versus non-selective media), and the loss per generation calculated. eco mchibucos minichromosome maintenance assay evidence PMID:6323245 minichromosome maintenance assay evidence ECO:MCC Experimental evidence from an assay in which a mitotically stable plasmid (or minichromosome) is introduced into cells, cells are grown without selection for several generations, the proportion of cells that retain the plasmid is then determined (by comparing colony numbers on selective versus non-selective media), and the loss per generation calculated. PMID:6323245 specific protein inhibition by antibody evidence 2012-08-24T01:48:24Z A type of specific protein inhibition evidence where the molecular function of a protein is inhibited by an antibody. ECO:0000341 eco mchibucos A type of specific protein inhibition evidence where the molecular function of a protein is inhibited by an antibody. ECO:MCC Support of intron position by RNA-seq alignment evidence 2013-04-03T04:22:05Z A type of transcript splice pattern evidence where intron locations in predicted transcripts are compared to intron locations supported by RNA-seq evidence. 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. eco mchibucos A type of transcript splice pattern evidence where intron locations in predicted transcripts are compared to intron locations supported by RNA-seq evidence. ECO:MCC Full support of intron position by RNA-seq alignment evidence 2013-04-03T04:41:48Z 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: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. eco mchibucos 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 Partial support of intron position by RNA-seq alignment evidence 2013-04-03T04:50:46Z 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: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. eco mchibucos 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 single exon transcript confirmation via alignment evidence 2013-04-03T05:10:34Z ECO:0000345 eco mchibucos Support of intron position by RNA-seq alignment evidence used in manual assertion 2013-04-04T04:37:35Z A type of support of intron position by RNA-seq alignment evidence that is used in a manual assertion. ECO:0000346 eco mchibucos A type of support of intron position by RNA-seq alignment evidence that is used in a manual assertion. ECO:MCC true true Support of intron position by RNA-seq alignment evidence used in automatic assertion 2013-04-04T04:38:45Z A type of support of intron position by RNA-seq alignment evidence that is used in an automatic assertion. ECO:0000347 eco mchibucos A type of support of intron position by RNA-seq alignment evidence that is used in an automatic assertion. ECO:MCC true true Full support of intron position by RNA-seq alignment evidence used in automatic assertion 2013-04-04T04:40:19Z A type of full support of intron position by RNA-seq alignment evidence that is used in an automatic assertion. ECO:0000348 eco mchibucos true true A type of full support of intron position by RNA-seq alignment evidence that is used in an automatic assertion. ECO:MCC Full support of intron position by RNA-seq alignment evidence used in manual assertion 2013-04-04T04:41:34Z A type of full support of intron position by RNA-seq alignment evidence that is used in a manual assertion. ECO:0000349 eco mchibucos true A type of full support of intron position by RNA-seq alignment evidence that is used in a manual assertion. ECO:MCC true Partial support of intron position by RNA-seq alignment evidence used in automatic assertion 2013-04-04T04:42:53Z A type of partial support of intron position by RNA-seq alignment evidence that is used in an automatic assertion. ECO:0000350 eco mchibucos true A type of partial support of intron position by RNA-seq alignment evidence that is used in an automatic assertion. ECO:MCC true Partial support of intron position by RNA-seq alignment evidence used in manual assertion 2013-04-04T04:43:56Z A type of partial support of intron position by RNA-seq alignment evidence that is used in a manual assertion. ECO:0000351 eco mchibucos true true A type of partial support of intron position by RNA-seq alignment evidence that is used in a manual assertion. ECO:MCC evidence used in manual assertion A type of evidence that is used in an manual assertion. ECO:0000352 eco mchibucos A type of evidence that is used in an manual assertion. ECO:MCC true true physical interaction evidence used in manual assertion 2013-10-31T21:01:27Z A type of physical interaction evidence that is used in a manual assertion. ECO:0000353 GOECO:IPI IPI eco inferred from physical interaction mchibucos GOECO:IPI IPI true GOECO:IPI inferred from physical interaction A type of physical interaction evidence that is used in a manual assertion. ECO:MCC inferred from physical interaction GOECO:IPI true gene neighbors evidence used in manual assertion 2013-11-19T13:37:24Z A type of gene neighbors evidence that is used in a manual assertion. ECO:0000354 GO_REF:0000025 eco mchibucos A type of gene neighbors evidence that is used in a manual assertion. ECO:MCC operon structure as IGC evidence GO_REF:0000025 true phylogenetic distribution evidence 2014-04-22T17:02:31Z 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: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. eco mchibucos 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 differential gene expression evidence from microarray experiment 2014-09-26T16:21:45Z ECO:0000356 eco mchibucos differential gene expression evidence from RNA-seq experiment 2014-09-26T16:22:57Z ECO:0000357 eco mchibucos differential geneset expression evidence from microarray experiment (GSEA, Fisher-exact) 2014-09-26T16:25:47Z ECO:0000358 eco mchibucos differential geneset expression evidence from RNA-seq experiment (GSEA, Fisher-exact) 2014-09-26T16:26:48Z ECO:0000359 eco mchibucos biological target-disease association via drug 2014-09-26T16:39:11Z ECO:0000360 eco mchibucos inferential evidence 2015-07-14T11:19:37Z A type of evidence where an assertion is derived from another assertion via logical inference or some non-logical but rational means. 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. eco mchibucos A type of evidence where an assertion is derived from another assertion via logical inference or some non-logical but rational means. ECO:MCC evidence based on computational logical inference 2015-07-14T11:24:27Z 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:0000362 eco mchibucos 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 evidence based on computational logical inference used in automatic assertion 2015-07-14T11:35:08Z A type of evidence based on computational logical inference that is used in automatic assertion. ECO:0000363 GO_REF:0000108 eco mchibucos true Automatic assignment of GO terms using logical inference, based on on inter-ontology links GO_REF:0000108 A type of evidence based on computational logical inference that is used in automatic assertion. ECO:MCC true evidence based on logical inference from manual annotation used in automatic assertion 2015-07-14T11:44:19Z A type of evidence based on logical inference from a manually curated annotation that is used in an automatic assertion. ECO:0000364 eco mchibucos A type of evidence based on logical inference from a manually curated annotation that is used in an automatic assertion. ECO:MCC evidence based on logical inference from automatic annotation used in automatic assertion 2015-07-14T11:45:25Z A type of evidence based on logical inference from an automatically curated annotation that is used in an automatic assertion. ECO:0000366 eco mchibucos A type of evidence based on logical inference from an automatically curated annotation that is used in an automatic assertion. ECO:MCC evidence used in automatic assertion A type of evidence that is used in an automatic assertion. ECO:0000501 GOECO:IEA GO_REF:0000003 GO_REF:0000004 GO_REF:0000023 IEA cjm eco inferred from electronic annotation true true Gene Ontology annotation based on Swiss-Prot Subcellular Location vocabulary mapping. GO_REF:0000023 Gene Ontology annotation based on Enzyme Commission mapping. GO_REF:0000003 A type of evidence that is used in an automatic assertion. ECO:cjm inferred from electronic annotation GOECO:IEA Gene Ontology annotation based on Swiss-Prot keyword mapping. GO_REF:0000004 GOECO:IEA inferred from electronic annotation GOECO:IEA IEA 3D cell culture evidence 2014-03-16T11:30:54Z ECO:0001001 eco mchibucos [3H]arachidonic acid release assay evidence 2014-03-16T11:30:54Z ECO:0001002 eco mchibucos [3H]-thymidine incorporation assay evidence 2014-03-16T11:30:54Z ECO:0001003 eco mchibucos 51Cr release assay evidence 2014-03-16T11:30:54Z ECO:0001004 eco mchibucos 7-aminoactinomycin staining evidence 2014-03-16T11:30:54Z 7-AAD staining evidence 7-amino-actinomycin D staining evidence ECO:0001005 eco mchibucos adhesion assay evidence 2014-03-16T11:30:54Z ECO:0001006 eco mchibucos adoptive cell transfer evidence 2014-03-16T11:30:54Z 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. Adoptive immunotherapy ECO:0001007 eco mchibucos passive immunization 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 Alamar blue assay evidence 2014-03-16T11:30:54Z ECO:0001008 eco mchibucos allograft transplantation experiment evidence 2014-03-16T11:30:54Z 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. Allotransplantation ECO:0001009 allografting eco mchibucos tissue grafting 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/ anion-exchange chromatography evidence 2014-03-16T11:30:54Z 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:0001010 eco mchibucos 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 annexin-V staining evidence 2014-03-16T11:30:54Z ECO:0001011 eco mchibucos behavioral assay evidence 2014-03-16T11:30:54Z ECO:0001012 eco mchibucos blocking monoclonal antibody evidence 2014-03-16T11:30:54Z ECO:0001013 eco mchibucos blocking peptide evidence 2014-03-16T11:30:54Z ECO:0001014 eco mchibucos blocking polyclonal antibody evidence 2014-03-16T11:30:54Z ECO:0001015 eco mchibucos blood test evidence 2014-03-16T11:30:54Z A type of direct assay evidence where a blood sample is extracted from an organism to analyze different blood components. ECO:0001016 eco mchibucos 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 Boyden chamber assay evidence 2014-03-16T11:30:54Z ECO:0001017 eco mchibucos bromodeoxyuridine incorporation assay evidence 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:0001018 eco mchibucos caspase assay evidence 2014-03-16T11:30:54Z ECO:0001019 eco mchibucos cell counting evidence 2014-03-16T11:30:54Z ECO:0001020 eco mchibucos cell permeability assay evidence 2014-03-16T11:30:54Z ECO:0001021 eco mchibucos carboxyfluorescein diacetate succinimidyl ester staining evidence 2014-03-16T11:30:54Z CFDA-SE staining evidence CFSE-staining evidence ECO:0001022 eco mchibucos chemiluminescence-linked immunoassay evidence 2014-03-16T11:30:54Z CLIA evidence ECO:0001023 eco mchibucos chimeric protein evidence 2014-03-16T11:30:54Z ECO:0001024 eco mchibucos co-electrophoresis evidence 2014-03-16T11:30:54Z ECO:0001025 eco mchibucos co-localization evidence 2014-03-16T11:30:54Z ECO:0001026 eco mchibucos colony counting evidence 2014-03-16T11:30:54Z ECO:0001027 eco mchibucos co-sedimentation assay evidence 2014-03-16T11:30:54Z ECO:0001028 eco mchibucos comet assay evidence 2014-03-16T11:30:54Z ECO:0001029 eco mchibucos conditional knockout evidence 2014-03-16T11:30:54Z ECO:0001030 eco mchibucos conditional knockin evidence 2014-03-16T11:30:54Z ECO:0001031 eco mchibucos constitutively active mutant evidence 2014-03-16T11:30:54Z ECO:0001032 eco mchibucos cross-linking evidence 2014-03-16T11:30:54Z ECO:0001033 eco mchibucos crystallography evidence 2014-03-16T11:30:54Z ECO:0001034 eco mchibucos cytochemistry evidence 2014-03-16T11:30:54Z ECO:0001035 eco mchibucos cytochrome C release assay evidence 2014-03-16T11:30:54Z ECO:0001036 eco mchibucos 4',6-diamidino-2-phenylindole staining evidence 2014-03-16T11:30:54Z DAPI staining evidence ECO:0001037 eco mchibucos deletion evidence 2014-03-16T11:30:54Z ECO:0001038 eco mchibucos DNA laddering assay evidence 2014-03-16T11:30:54Z ECO:0001039 eco mchibucos RNA dot blot assay evidence 2014-03-16T11:30:54Z 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:0001040 RNA dot blot eco mchibucos 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 RNA microarray evidence 2014-03-16T11:30:54Z ECO:0001041 eco mchibucos dominant-negative mutant evidence 2014-03-16T11:30:54Z ECO:0001042 eco mchibucos Edman degradation evidence used in manual assertion 2014-03-17T16:59:00Z A type of Edman degradation evidence that is used in a manual assertion. ECO:0001043 eco mchibucos A type of Edman degradation evidence that is used in a manual assertion. ECO:MCC true true Edman degradation evidence 2014-03-16T11:30:54Z ECO:0001044 eco mchibucos eTag assay evidence 2014-03-16T11:30:54Z ECO:0001045 eco mchibucos filter binding assay evidence 2014-03-16T11:30:54Z ECO:0001046 eco mchibucos fluorescence in situ hybridization evidence 2014-03-16T11:30:54Z ECO:0001047 eco mchibucos fluorescence resonance energy transfer evidence 2014-03-16T11:30:54Z ECO:0001048 FRET eco mchibucos gel-filtration evidence 2014-03-16T11:30:54Z ECO:0001049 eco mchibucos histochemistry evidence 2014-03-16T11:30:54Z ECO:0001050 eco mchibucos histology evidence 2014-03-16T11:30:54Z ECO:0001051 eco mchibucos high-performance liquid chromatography evidence 2014-03-16T11:30:54Z ECO:0001052 HPLC evidence eco mchibucos immunocytochemistry evidence 2014-03-16T11:30:54Z ECO:0001053 eco mchibucos immunodepletion evidence 2014-03-16T11:30:54Z ECO:0001054 eco mchibucos immunohistochemistry evidence 2014-03-16T11:30:54Z ECO:0001055 eco mchibucos induced mutation evidence 2014-03-16T11:30:54Z ECO:0001056 eco mchibucos in vitro acetylation assay evidence 2014-03-16T11:30:54Z 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:0001057 eco mchibucos 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 in vitro cleavage assay evidence 2014-03-16T11:30:54Z A type of in vitro assay evidence where the cleavage of a protein by a protease is detected in an in vitro experiment. The cleavage gives rise to protein fragments. ECO:0001058 eco mchibucos A type of in vitro assay evidence where the cleavage of a protein by a protease is detected in an in vitro experiment. The cleavage gives rise to protein fragments. ECO:SN PMID:21121091 SIB:PG in vitro deubiquitination assay evidence 2014-03-16T11:30:54Z A type of in vitro assay evidence where the removal of ubiquitin groups on a protein is detected in vitro. ECO:0001059 eco mchibucos 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 in vitro deacetylation assay evidence 2014-03-16T11:30:54Z A type of in vitro assay evidence where the removal of acetyl groups from a compound is detected in an in vitro experiment. ECO:0001060 eco mchibucos 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 in vitro defarnesylation assay evidence 2014-03-16T11:30:54Z A type of in vitro assay evidence where the removal of farnesyl groups from a protein is detected in an in vitro experiment. ECO:0001061 eco mchibucos 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 in vitro demethylation assay evidence 2014-03-16T11:30:54Z A type of in vitro assay evidence where the removal of methyl groups from a compound is detected in an in vitro experiment. ECO:0001062 eco mchibucos 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 in vitro desumoylation assay evidence 2014-03-16T11:30:54Z A type of in vitro assay evidence where the removal of sumo groups is detected on a protein in vitro. ECO:0001063 eco mchibucos 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/ in vitro farnesylation assay evidence 2014-03-16T11:30:54Z A type of in vitro assay evidence where farnesylated residues in proteins are detected in an in vitro experiment. ECO:0001064 eco mchibucos 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 in vitro methylation assay evidence 2014-03-16T11:30:54Z 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:0001065 eco mchibucos 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 in vitro palmitoylation assay evidence 2014-03-16T11:30:54Z A type of in vitro assay evidence where palmitoylated residues in proteins are detected in an in vitro experiment. ECO:0001066 eco mchibucos 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 in vitro phosphatase assay evidence 2014-03-16T11:30:54Z A type of in vitro assay evidence where the removal of phosphatase groups on a protein is detected in an in vitro experiment. ECO:0001067 eco mchibucos 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 in vitro protein kinase assay evidence 2014-03-16T11:30:54Z A type of in vitro assay evidence where phosphorylated residues in a protein are detected in an in vitro experiment. ECO:0001068 eco mchibucos 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 in vitro polyADP-ribosylation assay evidence 2014-03-16T11:30:54Z A type of in vitro assay evidence where ADP-ribosylated residues in proteins are detected in an in vitro experiment. ECO:0001069 eco mchibucos 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 in vitro sumoylation assay evidence 2014-03-16T11:30:54Z A type of in vitro assay evidence where sumoylated residues are detected on a protein in an in vitro experiment. ECO:0001070 eco mchibucos 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/ in vitro transcription assay evidence 2014-03-16T11:30:54Z 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:0001071 eco mchibucos 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 in vitro translation assay evidence 2014-03-16T11:30:54Z A type of in vitro assay evidence where de novo protein synthesis is detected in an in vitro experiment. ECO:0001072 eco mchibucos 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 in vitro ubiquitination assay evidence 2014-03-16T11:30:54Z A type of in vitro assay evidence where ubiquitinated residues are detected on a protein in an in vitro experiment. ECO:0001073 eco mchibucos 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 in vivo acetylation assay evidence 2014-03-16T11:30:54Z 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:0001074 eco mchibucos 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 in vivo cleavage assay evidence 2014-03-16T11:30:54Z A type of in vivo assay evidence where the cleavage of a protein by a protease is detected in cells in vivo. The cleavage gives rise to protein fragments. ECO:0001075 eco mchibucos A type of in vivo assay evidence where the cleavage of a protein by a protease is detected in cells in vivo. The cleavage gives rise to protein fragments. ECO:SN PMID:22154596 SIB:PG in vivo deacetylation assay evidence 2014-03-16T11:30:54Z A type of in vivo assay evidence where the removal of acetyl groups from a compound is detected in cells in vivo. ECO:0001076 eco mchibucos 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 in vivo defarnesylation assay evidence 2014-03-16T11:30:54Z A type of in vivo assay evidence where removal of farnesyl groups from a protein is detected in cells in vivo. ECO:0001077 eco mchibucos 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 in vivo demethylation assay evidence 2014-03-16T11:30:54Z A type of in vivo assay evidence where the removal of methyl groups from a compound is detected in cells in vivo. ECO:0001078 eco mchibucos 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 in vivo deubiquitination assay evidence 2014-03-16T11:30:54Z A type of in vivo assay evidence where the removal of ubiquitin groups on a protein is detected in cells in vivo. ECO:0001079 eco mchibucos 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 in vivo desumoylation assay evidence 2014-03-16T11:30:54Z A type of in vivo assay evidence where the removal of sumo groups on a protein is detected in cells in vivo. ECO:0001080 eco mchibucos 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/ in vivo farnesylation assay evidence 2014-03-16T11:30:54Z A type of in vivo assay evidence where farnesylated residues in proteins are detected in cells in vivo. ECO:0001081 eco mchibucos A type of in vivo assay evidence where farnesylated residues in proteins are detected in cells in vivo. ECO:SN PMID:9030603 SIB:PG in vivo methylation assay evidence 2014-03-16T11:30:54Z 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:0001082 eco mchibucos 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 in vivo palmitoylation assay evidence 2014-03-16T11:30:54Z A type of in vivo assay evidence where palmitoylated residues in proteins are detected in cells in vivo. ECO:0001083 eco mchibucos A type of in vivo assay evidence where palmitoylated residues in proteins are detected in cells in vivo. ECO:SN PMID:10329400 SIB:PG in vivo phosphatase assay evidence 2014-03-16T11:30:54Z A type of in vivo assay evidence where the removal of phosphate groups on a protein is detected in cells in vivo. ECO:0001084 eco mchibucos 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 in vivo protein kinase assay evidence 2014-03-16T11:30:54Z A type of in vivo assay evidence where phosphorylated residues in a protein are detected in cells in vivo. ECO:0001085 eco mchibucos 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 in vivo sumoylation assay evidence 2014-03-16T11:30:54Z A type of in vivo assay evidence where sumoylated residues are detected on a protein in cells in vivo. ECO:0001086 eco mchibucos 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/ in vivo transcription assay evidence 2014-03-16T11:30:54Z A type of in vivo assay evidence where transcription is detected in cells in vivo. ECO:0001087 eco mchibucos A type of in vivo assay evidence where transcription is detected in cells in vivo. ECO:SN PMID:12181418 SIB:PG in vivo translation assay evidence 2014-03-16T11:30:54Z A type of in vivo assay evidence where de novo protein synthesis is detected in cells in vivo. ECO:0001088 eco mchibucos A type of in vivo assay evidence where de novo protein synthesis is detected in cells in vivo. ECO:SN PMID:24901308 SIB:PG in vivo ubiquitination assay evidence 2014-03-16T11:30:54Z A type of in vivo assay evidence where ubiquitinated residues on a protein are detected in cells in vivo. ECO:0001089 eco mchibucos 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 knockin evidence 2014-03-16T11:30:54Z ECO:0001090 eco mchibucos knockout evidence 2014-03-16T11:30:54Z ECO:0001091 eco mchibucos lipid binding assay evidence 2014-03-16T11:30:54Z ECO:0001092 eco mchibucos luminescence-based mammalian interactome mapping assay evidence 2014-03-16T11:30:54Z ECO:0001093 LUMIER assay eco mchibucos macroscopy evidence 2014-03-16T11:30:54Z ECO:0001094 eco mchibucos mammalian 2-hybrid assay evidence 2014-03-16T11:30:54Z ECO:0001095 eco mchibucos mass spectrometry evidence 2014-03-16T11:30:54Z ECO:0001096 eco mchibucos medical imaging evidence 2014-03-16T11:30:54Z ECO:0001097 eco mchibucos microscopy evidence 2014-03-16T11:30:54Z A type of direct assay evidence where a microscope was used to view a sample. ECO:0001098 eco mchibucos A type of direct assay evidence where a microscope was used to view a sample. ECO:MCC motility wound healing assay evidence 2014-03-16T11:30:54Z ECO:0001099 eco mchibucos MTS assay evidence 2014-03-16T11:30:54Z 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium ECO:0001100 eco mchibucos MTT assay evidence 2014-03-16T11:30:54Z 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide ECO:0001101 eco mchibucos multiplex bead-based immunoassay evidence 2014-03-16T11:30:54Z ECO:0001102 eco mchibucos natural variation mutant evidence 2014-03-16T11:30:54Z ECO:0001103 eco mchibucos nuclear fragmentation evidence 2014-03-16T11:30:54Z ECO:0001104 eco mchibucos nuclear magnetic resonance spectroscopy evidence 2014-03-16T11:30:54Z ECO:0001105 NMR spectroscopy eco mchibucos nuclease protection assay evidence 2014-03-16T11:30:54Z ECO:0001106 eco mchibucos nucleotide analog incorporation evidence 2014-03-16T11:30:54Z ECO:0001107 eco mchibucos phage display evidence 2014-03-16T11:30:54Z ECO:0001108 eco mchibucos phosphoamino acid analysis evidence 2014-03-16T11:30:54Z ECO:0001109 eco mchibucos peptide affinity enrichment evidence 2014-03-16T11:30:54Z ECO:0001110 eco mchibucos phosphopeptide affinity enrichment evidence physical examination evidence 2014-03-16T11:30:54Z ECO:0001111 eco mchibucos peptide array evidence 2014-03-16T11:30:54Z ECO:0001112 eco mchibucos phosphopeptide array evidence point mutation evidence 2014-03-16T11:30:54Z ECO:0001113 eco mchibucos propidium iodide staining evidence 2014-03-16T11:30:54Z ECO:0001114 eco mchibucos fluorescence evidence 2014-03-16T11:30:54Z ECO:0001115 eco mchibucos protein dot blot assay evidence 2014-03-16T11:30:54Z ECO:0001116 eco mchibucos protein microarray evidence 2014-03-16T11:30:54Z ECO:0001117 eco mchibucos protein sequencing assay evidence 2014-03-16T11:30:54Z ECO:0001118 eco mchibucos quantitative mass spectrometry evidence 2014-03-16T11:30:54Z ECO:0001119 eco mchibucos radioisotope assay evidence 2014-03-16T11:30:54Z ECO:0001120 eco mchibucos radioassay radioisotopic assay radioimmunoassay evidence 2014-03-16T11:30:54Z ECO:0001121 eco mchibucos resonant mirror biosensor evidence 2014-03-16T11:30:54Z ECO:0001123 eco mchibucos restriction fragment detection evidence 2014-03-16T11:30:54Z ECO:0001124 eco mchibucos spectrophotometry evidence 2014-03-16T11:30:54Z ECO:0001126 eco mchibucos surface plasmon resonance evidence 2014-03-16T11:30:54Z 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:0001127 Plasmons are generated by an incident light beam. SPR evidence eco mchibucos PMID:11578932 SPR 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 syngeneic transplantation experiment evidence 2014-03-16T11:30:54Z ECO:0001128 eco mchibucos TACE activity assay evidence 2014-03-16T11:30:54Z ECO:0001129 Tumor necrosis factor - alpha converting enzyme activity assay eco mchibucos tissue microarray evidence 2014-03-16T11:30:54Z ECO:0001130 eco mchibucos transgenic organism evidence 2014-03-16T11:30:54Z ECO:0001131 eco mchibucos tryptic phosphopeptide mapping assay evidence 2014-03-16T11:30:54Z ECO:0001132 eco mchibucos terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence 2014-03-16T11:30:54Z ECO:0001133 TUNEL assay evidence TdT-mediated dUTP-biotin nick end labeling assay eco mchibucos terminal deoxynucleotidyl transferase-dUTP nick end labeling assay evidence urine test evidence 2014-03-16T11:30:54Z ECO:0001134 eco mchibucos wound healing assay evidence 2014-03-16T11:30:54Z ECO:0001135 eco mchibucos WST-1 assay evidence 2014-03-16T11:30:54Z ECO:0001136 eco mchibucos xenotransplantation experiment evidence 2014-03-16T11:30:54Z 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:0001137 Xenograft transplantation Xenografting Xenotransplantation eco mchibucos tissue grafting 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/ 3D cell culture evidence used in manual assertion 2014-03-17T15:18:35Z A type of 3D cell culture evidence that is used in a manual assertion. ECO:0001138 eco mchibucos true true A type of 3D cell culture evidence that is used in a manual assertion. ECO:MCC 51Cr release assay evidence used in manual assertion 2014-03-17T15:20:55Z A type of 51Cr release assay evidence that is used in a manual assertion. ECO:0001139 eco mchibucos A type of 51Cr release assay evidence that is used in a manual assertion. ECO:MCC true true 7-aminoactinomycin staining evidence used in manual assertion 2014-03-17T15:22:01Z A type of 7-aminoactinomycin staining evidence that is used in a manual assertion. ECO:0001140 eco mchibucos A type of 7-aminoactinomycin staining evidence that is used in a manual assertion. ECO:MCC true true [3H]-thymidine incorporation assay evidence used in manual assertion 2014-03-17T15:31:52Z A type of [3H]-thymidine incorporation assay evidence that is used in a manual assertion. ECO:0001141 eco mchibucos true true A type of [3H]-thymidine incorporation assay evidence that is used in a manual assertion. ECO:MCC [3H]arachidonic acid release assay evidence used in manual assertion 2014-03-17T15:32:44Z A type of [3H]arachidonic acid release assay evidence that is used in a manual assertion. ECO:0001142 eco mchibucos A type of [3H]arachidonic acid release assay evidence that is used in a manual assertion. ECO:MCC true true adhesion assay evidence used in manual assertion 2014-03-17T15:33:38Z A type of adhesion assay evidence that is used in a manual assertion. ECO:0001143 eco mchibucos true A type of adhesion assay evidence that is used in a manual assertion. ECO:MCC true adoptive cell transfer evidence used in manual assertion 2014-03-17T15:36:19Z A type of adoptive cell transfer evidence that is used in a manual assertion. ECO:0001144 eco mchibucos A type of adoptive cell transfer evidence that is used in a manual assertion. ECO:MCC true true Alamar blue assay evidence used in manual assertion 2014-03-17T15:37:21Z A type of Alamar blue assay evidence that is used in a manual assertion. ECO:0001145 eco mchibucos A type of Alamar blue assay evidence that is used in a manual assertion. ECO:MCC true true allograft transplantation experiment evidence used in manual assertion 2014-03-17T15:38:22Z A type of allograft transplantation experiment evidence that is used in a manual assertion. ECO:0001146 eco mchibucos true A type of allograft transplantation experiment evidence that is used in a manual assertion. ECO:MCC true anion-exchange chromatography evidence used in manual assertion 2014-03-17T15:44:30Z A type of anion-exchange chromatography evidence that is used in a manual assertion. ECO:0001147 eco mchibucos A type of anion-exchange chromatography evidence that is used in a manual assertion. ECO:MCC true true annexin-V staining evidence used in manual assertion 2014-03-17T15:52:01Z A type of annexin-V staining evidence that is used in a manual assertion. ECO:0001148 eco mchibucos true true A type of annexin-V staining evidence that is used in a manual assertion. ECO:MCC behavioral assay evidence used in manual assertion 2014-03-17T15:53:38Z A type of behavioral assay evidence used that is used in a manual assertion. ECO:0001149 eco mchibucos true true A type of behavioral assay evidence used that is used in a manual assertion. ECO:MCC blocking monoclonal antibody evidence used in manual assertion 2014-03-17T15:54:44Z A type of blocking monoclonal antibody evidence that is used in a manual assertion. ECO:0001150 eco mchibucos true true A type of blocking monoclonal antibody evidence that is used in a manual assertion. ECO:MCC blocking peptide evidence used in manual assertion 2014-03-17T15:55:33Z A type of blocking peptide evidence that is used in a manual assertion. ECO:0001151 eco mchibucos true A type of blocking peptide evidence that is used in a manual assertion. ECO:MCC true blocking polyclonal antibody evidence used in manual assertion 2014-03-17T16:01:39Z A type of blocking polyclonal antibody evidence tthat is used in a manual assertion. ECO:0001152 eco mchibucos A type of blocking polyclonal antibody evidence tthat is used in a manual assertion. ECO:MCC true true blood test evidence used in manual assertion 2014-03-17T16:02:47Z A type of blood test evidence that is used in a manual assertion. ECO:0001153 eco mchibucos A type of blood test evidence that is used in a manual assertion. ECO:MCC true true Boyden chamber assay evidence used in manual assertion 2014-03-17T16:03:53Z A type of Boyden chamber assay evidence that is used in a manual assertion. ECO:0001154 eco mchibucos A type of Boyden chamber assay evidence that is used in a manual assertion. ECO:MCC true true bromodeoxyuridine incorporation assay evidence used in manual assertion 2014-03-17T16:04:49Z A type of BrdU incorporation assay evidence that is used in a manual assertion. ECO:0001155 eco mchibucos A type of BrdU incorporation assay evidence that is used in a manual assertion. ECO:MCC true true caspase assay evidence used in manual assertion 2014-03-17T16:06:06Z A type of caspase assay evidence that is used in a manual assertion. ECO:0001156 eco mchibucos true true A type of caspase assay evidence that is used in a manual assertion. ECO:MCC cell counting evidence used in manual assertion 2014-03-17T16:07:13Z A type of cell counting evidence that is used in a manual assertion. ECO:0001157 eco mchibucos true A type of cell counting evidence that is used in a manual assertion. ECO:MCC true cell permeability assay evidence used in manual assertion 2014-03-17T16:07:58Z A type of cell permeability assay evidence that is used in a manual assertion. ECO:0001158 eco mchibucos true true A type of cell permeability assay evidence that is used in a manual assertion. ECO:MCC carboxyfluorescein diacetate succinimidyl ester staining evidence used in manual assertion 2014-03-17T16:08:54Z A type of carboxyfluorescein diacetate succinimidyl ester staining evidence that is used in a manual assertion. ECO:0001159 eco mchibucos true true A type of carboxyfluorescein diacetate succinimidyl ester staining evidence that is used in a manual assertion. ECO:MCC chemiluminescence-linked immunoassay evidence used in manual assertion 2014-03-17T16:09:55Z A type of chemiluminescence-linked immunoassay evidence that is used in a manual assertion. ECO:0001160 eco mchibucos A type of chemiluminescence-linked immunoassay evidence that is used in a manual assertion. ECO:MCC true true chimeric protein evidence used in manual assertion 2014-03-17T16:10:40Z A type of chimeric protein evidence that is used in a manual assertion. ECO:0001161 eco mchibucos A type of chimeric protein evidence that is used in a manual assertion. ECO:MCC true true co-electrophoresis evidence used in manual assertion 2014-03-17T16:11:22Z A type of co-electrophoresis evidence that is used in a manual assertion. ECO:0001162 eco mchibucos true true A type of co-electrophoresis evidence that is used in a manual assertion. ECO:MCC co-localization evidence used in manual assertion 2014-03-17T16:12:04Z A type of co-localization evidence that is used in a manual assertion. ECO:0001163 eco mchibucos A type of co-localization evidence that is used in a manual assertion. ECO:MCC true true co-sedimentation assay evidence used in manual assertion 2014-03-17T16:12:55Z A type of co-sedimentation assay evidence that is used in a manual assertion. ECO:0001164 eco mchibucos A type of co-sedimentation assay evidence that is used in a manual assertion. ECO:MCC true true colony counting evidence used in manual assertion 2014-03-17T16:14:57Z A type of colony counting evidence that is used in a manual assertion. ECO:0001165 eco mchibucos true true A type of colony counting evidence that is used in a manual assertion. ECO:MCC comet assay evidence used in manual assertion 2014-03-17T16:16:01Z A type of comet assay evidence that is used in a manual assertion. ECO:0001166 eco mchibucos true A type of comet assay evidence that is used in a manual assertion. ECO:MCC true conditional knockin evidence used in manual assertion 2014-03-17T16:17:22Z A type of conditional knockin evidence that is used in a manual assertion. ECO:0001167 eco mchibucos A type of conditional knockin evidence that is used in a manual assertion. ECO:MCC true true conditional knockout evidence used in manual assertion 2014-03-17T16:17:58Z A type of conditional knockout evidence that is used in a manual assertion. ECO:0001168 eco mchibucos A type of conditional knockout evidence that is used in a manual assertion. ECO:MCC true true constitutively active mutant evidence used in manual assertion 2014-03-17T16:20:23Z A type of constitutively active mutant evidence that is used a in manual assertion. ECO:0001169 eco mchibucos true A type of constitutively active mutant evidence that is used a in manual assertion. ECO:MCC true cross-linking evidence used in manual assertion 2014-03-17T16:21:29Z A type of cross-linking evidence that is used in a manual assertion. ECO:0001170 eco mchibucos true true true A type of cross-linking evidence that is used in a manual assertion. ECO:MCC crystallography evidence used in manual assertion 2014-03-17T16:22:20Z A type of crystallography evidence that is used in a manual assertion. ECO:0001171 eco mchibucos true true A type of crystallography evidence that is used in a manual assertion. ECO:MCC cytochemistry evidence used in manual assertion 2014-03-17T16:23:10Z A type of cytochemistry evidence that is used in a manual assertion. ECO:0001172 eco mchibucos true true A type of cytochemistry evidence that is used in a manual assertion. ECO:MCC cytochrome C release assay evidence used in manual assertion 2014-03-17T16:23:53Z A type of cytochrome C release assay evidence that is used in a manual assertion. ECO:0001173 eco mchibucos A type of cytochrome C release assay evidence that is used in a manual assertion. ECO:MCC true true 4',6-diamidino-2-phenylindole staining evidence used in manual assertion 2014-03-17T16:25:03Z A type of 4',6-diamidino-2-phenylindole staining evidence that is used in a manual assertion. ECO:0001174 eco mchibucos true A type of 4',6-diamidino-2-phenylindole staining evidence that is used in a manual assertion. ECO:MCC true deletion evidence used in manual assertion 2014-03-17T16:25:54Z A type of deletion evidence that is used in a manual assertion. ECO:0001175 eco mchibucos A type of deletion evidence that is used in a manual assertion. ECO:MCC true true DNA laddering assay evidence used in manual assertion 2014-03-17T16:26:46Z A type of DNA laddering assay evidence that is used in a manual assertion. ECO:0001176 eco mchibucos true A type of DNA laddering assay evidence that is used in a manual assertion. ECO:MCC true RNA dot blot assay evidence used in manual assertion 2014-03-17T16:45:52Z A type of RNA dot blot assay evidence that is used in a manual assertion. ECO:0001177 eco mchibucos true true A type of RNA dot blot assay evidence that is used in a manual assertion. ECO:MCC RNA microarray evidence used in manual assertion 2014-03-17T16:46:50Z A type of RNA microarray evidence that is used in a manual assertion. ECO:0001178 eco mchibucos true true A type of RNA microarray evidence that is used in a manual assertion. ECO:MCC dominant-negative mutant evidence used in manual assertion 2014-03-17T16:47:44Z A type of dominant-negative mutant evidence that is used in a manual assertion. ECO:0001179 eco mchibucos true A type of dominant-negative mutant evidence that is used in a manual assertion. ECO:MCC true eTag assay evidence used in manual assertion 2014-03-17T16:59:39Z A type of eTag assay evidence that is used in a manual assertion. ECO:0001180 eco mchibucos A type of eTag assay evidence that is used in a manual assertion. ECO:MCC true true filter binding assay evidence used in manual assertion 2014-03-17T17:03:28Z A type of filter binding assay evidence that is used in a manual assertion. ECO:0001181 eco mchibucos A type of filter binding assay evidence that is used in a manual assertion. ECO:MCC true true fluorescence in situ hybridization evidence used in manual assertion 2014-03-17T17:04:20Z A type of fluorescence in situ hybridization evidence that is used in a manual assertion. ECO:0001182 eco mchibucos true A type of fluorescence in situ hybridization evidence that is used in a manual assertion. ECO:MCC true fluorescence resonance energy transfer evidence used in manual assertion 2014-03-17T17:05:22Z A type of fluorescence resonance energy transfer evidence that is used in a manual assertion. ECO:0001183 eco mchibucos true true A type of fluorescence resonance energy transfer evidence that is used in a manual assertion. ECO:MCC gel-filtration evidence used in manual assertion 2014-03-17T17:06:14Z A type of gel-filtration evidence that is used in a manual assertion. ECO:0001184 eco mchibucos A type of gel-filtration evidence that is used in a manual assertion. ECO:MCC true true histochemistry evidence used in manual assertion 2014-03-17T17:07:19Z A type of histochemistry evidence that is used in a manual assertion. ECO:0001185 eco mchibucos true true A type of histochemistry evidence that is used in a manual assertion. ECO:MCC immunocytochemistry evidence used in manual assertion 2014-03-17T17:12:39Z A type of immunocytochemistry evidence that is used in a manual assertion. ECO:0001186 eco mchibucos true A type of immunocytochemistry evidence that is used in a manual assertion. ECO:MCC true histology evidence used in manual assertion 2014-03-17T17:09:50Z A type of histology evidence that is used in a manual assertion. ECO:0001187 eco mchibucos A type of histology evidence that is used in a manual assertion. ECO:MCC true true immunodepletion evidence used in manual assertion 2014-03-17T17:16:19Z A type of immunodepletion evidence that is used in a manual assertion. ECO:0001188 eco mchibucos true true A type of immunodepletion evidence that is used in a manual assertion. ECO:MCC immunohistochemistry evidence used in manual assertion 2014-03-17T17:17:22Z A type of immunohistochemistry evidence that is used in a manual assertion. ECO:0001189 eco mchibucos true A type of immunohistochemistry evidence that is used in a manual assertion. ECO:MCC true in vitro acetylation assay evidence used in manual assertion 2014-03-17T17:19:24Z A type of in vitro acetylation assay evidence that is used in a manual assertion. ECO:0001190 eco mchibucos true true A type of in vitro acetylation assay evidence that is used in a manual assertion. ECO:MCC in vitro cleavage assay evidence used in manual assertion 2014-03-17T17:21:22Z A type of in vitro cleavage assay evidence that is used in a manual assertion. ECO:0001191 eco mchibucos true A type of in vitro cleavage assay evidence that is used in a manual assertion. ECO:MCC true in vitro deacetylation assay evidence used in manual assertion 2014-03-17T17:23:42Z A type of in vitro deacetylation assay evidence that is used in a manual assertion. ECO:0001192 eco mchibucos A type of in vitro deacetylation assay evidence that is used in a manual assertion. ECO:MCC true true in vitro defarnesylation assay evidence used in manual assertion 2014-03-17T17:25:45Z A type of in vitro defarnesylation assay evidence that is used in a manual assertion. ECO:0001193 eco mchibucos true true A type of in vitro defarnesylation assay evidence that is used in a manual assertion. ECO:MCC in vitro demethylation assay evidence used in manual assertion 2014-03-17T17:27:00Z A type of in vitro demethylation assay evidence that is used in a manual assertion. ECO:0001194 eco mchibucos A type of in vitro demethylation assay evidence that is used in a manual assertion. ECO:MCC true true in vitro desumoylation assay evidence used in manual assertion 2014-03-17T17:29:01Z A type of in vitro desumoylation assay evidence that is used in a manual assertion. ECO:0001195 eco mchibucos A type of in vitro desumoylation assay evidence that is used in a manual assertion. ECO:MCC true true in vitro deubiquitination assay evidence used in manual assertion 2014-03-17T17:29:48Z A type of in vitro deubiquitination assay evidence that is used in a manual assertion. ECO:0001196 eco mchibucos A type of in vitro deubiquitination assay evidence that is used in a manual assertion. ECO:MCC true true in vitro farnesylation assay evidence used in manual assertion 2014-03-17T17:30:50Z A type of in vitro farnesylation assay evidence that is used in a manual assertion. ECO:0001197 eco mchibucos A type of in vitro farnesylation assay evidence that is used in a manual assertion. ECO:MCC true true in vitro methylation assay evidence used in manual assertion 2014-03-17T17:31:54Z A type of in vitro methylation assay evidence that is used in a manual assertion. ECO:0001198 eco mchibucos true A type of in vitro methylation assay evidence that is used in a manual assertion. ECO:MCC true in vitro palmitoylation assay evidence used in manual assertion 2014-03-17T17:32:57Z A type of in vitro palmitoylation assay evidence that is used in a manual assertion. ECO:0001199 eco mchibucos true true A type of in vitro palmitoylation assay evidence that is used in a manual assertion. ECO:MCC in vitro phosphatase assay evidence used in manual assertion 2014-03-17T17:34:16Z A type of in vitro phosphatase assay evidence that is used in a manual assertion. ECO:0001200 eco mchibucos true A type of in vitro phosphatase assay evidence that is used in a manual assertion. ECO:MCC true in vitro polyADP-ribosylation assay evidence used in manual assertion 2014-03-17T17:34:57Z A type of in vitro polyADP-ribosylation assay evidence that is used in a manual assertion. ECO:0001201 eco mchibucos true true A type of in vitro polyADP-ribosylation assay evidence that is used in a manual assertion. ECO:MCC in vitro protein kinase assay evidence used in manual assertion 2014-03-17T17:39:57Z A type of in vitro protein kinase assay evidence that is used in a manual assertion. ECO:0001202 eco mchibucos true true A type of in vitro protein kinase assay evidence that is used in a manual assertion. ECO:MCC in vitro sumoylation assay evidence used in manual assertion 2014-03-17T17:41:25Z A type of in vitro sumoylation assay evidence that is used in a manual assertion. ECO:0001203 eco mchibucos true A type of in vitro sumoylation assay evidence that is used in a manual assertion. ECO:MCC true in vitro transcription assay evidence used in manual assertion 2014-03-17T17:44:40Z A type of in vitro transcription assay evidence that is used in a manual assertion. ECO:0001204 eco mchibucos A type of in vitro transcription assay evidence that is used in a manual assertion. ECO:MCC true true in vitro translation assay evidence used in manual assertion 2014-03-17T17:46:30Z A type of in vitro translation assay evidence that is used in a manual assertion. ECO:0001205 eco mchibucos true A type of in vitro translation assay evidence that is used in a manual assertion. ECO:MCC true in vitro ubiquitination assay evidence used in manual assertion 2014-03-17T17:47:18Z A type of in vitro ubiquitination assay evidence that is used in a manual assertion. ECO:0001206 eco mchibucos true true A type of in vitro ubiquitination assay evidence that is used in a manual assertion. ECO:MCC in vivo acetylation assay evidence used in manual assertion 2014-03-17T17:48:56Z A type of in vivo acetylation assay evidence that is used in manual assertion. ECO:0001207 eco mchibucos true true A type of in vivo acetylation assay evidence that is used in manual assertion. ECO:MCC in vivo cleavage assay evidence used in manual assertion 2014-03-17T17:49:43Z A type of in vivo cleavage assay evidence that is used in a manual assertion. ECO:0001208 eco mchibucos A type of in vivo cleavage assay evidence that is used in a manual assertion. ECO:MCC true true in vivo deacetylation assay evidence used in manual assertion 2014-03-17T17:50:47Z A type of in vivo deacetylation assay evidence that is used in a manual assertion. ECO:0001209 eco mchibucos true true A type of in vivo deacetylation assay evidence that is used in a manual assertion. ECO:MCC in vivo defarnesylation assay evidence used in manual assertion 2014-03-17T17:52:41Z A type of in vivo defarnesylation assay evidence that is used in a manual assertion. ECO:0001210 eco mchibucos true A type of in vivo defarnesylation assay evidence that is used in a manual assertion. ECO:MCC true in vivo demethylation assay evidence used in manual assertion 2014-03-17T17:53:40Z A type of in vivo demethylation assay evidence that is used in a manual assertion. ECO:0001211 eco mchibucos A type of in vivo demethylation assay evidence that is used in a manual assertion. ECO:MCC true true in vivo desumoylation assay evidence used in manual assertion 2014-03-17T17:54:36Z A type of in vivo desumoylation assay evidence that is used in a manual assertion. ECO:0001212 eco mchibucos true A type of in vivo desumoylation assay evidence that is used in a manual assertion. ECO:MCC true in vivo deubiquitination assay evidence used in manual assertion 2014-03-17T17:56:28Z A type of in vivo deubiquitination assay evidence that is used in a manual assertion. ECO:0001213 eco mchibucos A type of in vivo deubiquitination assay evidence that is used in a manual assertion. ECO:MCC true true in vivo farnesylation assay evidence used in manual assertion 2014-03-17T17:57:18Z A type of in vivo farnesylation assay evidence that is used in a manual assertion. ECO:0001214 eco mchibucos true true A type of in vivo farnesylation assay evidence that is used in a manual assertion. ECO:MCC in vivo methylation assay evidence used in manual assertion 2014-03-17T18:03:16Z A type of in vivo methylation assay evidence that is used in a manual assertion. ECO:0001215 eco mchibucos A type of in vivo methylation assay evidence that is used in a manual assertion. ECO:MCC true true in vivo palmitoylation assay evidence used in manual assertion 2014-03-17T18:04:07Z A type of in vivo palmitoylation assay evidence that is used in a manual assertion. ECO:0001216 eco mchibucos true true A type of in vivo palmitoylation assay evidence that is used in a manual assertion. ECO:MCC in vivo phosphatase assay evidence used in manual assertion 2014-03-17T18:06:08Z A type of in vivo phosphatase assay evidence that is used in a manual assertion. ECO:0001217 eco mchibucos true true A type of in vivo phosphatase assay evidence that is used in a manual assertion. ECO:MCC in vivo protein kinase assay evidence used in manual assertion 2014-03-17T18:07:58Z A type of in vivo protein kinase assay evidence that is used in a manual assertion. ECO:0001218 eco mchibucos A type of in vivo protein kinase assay evidence that is used in a manual assertion. ECO:MCC true true in vivo sumoylation assay evidence used in manual assertion 2014-03-17T18:09:49Z A type of in vivo sumoylation assay evidence that is used in a manual assertion. ECO:0001219 eco mchibucos A type of in vivo sumoylation assay evidence that is used in a manual assertion. ECO:MCC true true in vivo transcription assay evidence used in manual assertion 2014-03-17T18:11:20Z A type of in vivo transcription assay evidence that is used in a manual assertion. ECO:0001220 eco mchibucos true A type of in vivo transcription assay evidence that is used in a manual assertion. ECO:MCC true in vivo translation assay evidence used in manual assertion 2014-03-17T18:42:50Z A type of in vivo translation assay evidence that is used in a manual assertion. ECO:0001221 eco mchibucos true true A type of in vivo translation assay evidence that is used in a manual assertion. ECO:MCC in vivo ubiquitination assay evidence used in manual assertion 2014-03-17T18:44:11Z A type of in vivo ubiquitination assay evidence that is used in a manual assertion. ECO:0001222 eco mchibucos A type of in vivo ubiquitination assay evidence that is used in a manual assertion. ECO:MCC true true induced mutation evidence used in manual assertion 2014-03-17T18:45:56Z A type of induced mutation evidence that is used in a manual assertion. ECO:0001223 eco mchibucos true true A type of induced mutation evidence that is used in a manual assertion. ECO:MCC knockin evidence used in manual assertion 2014-03-17T18:49:35Z A type of knockin evidence that is used in a manual assertion. ECO:0001224 eco mchibucos true A type of knockin evidence that is used in a manual assertion. ECO:MCC true knockout evidence used in manual assertion 2014-03-17T18:51:31Z A type of knockout evidence that is used in a manual assertion. ECO:0001225 eco mchibucos A type of knockout evidence that is used in a manual assertion. ECO:MCC true true lipid binding assay evidence used in manual assertion 2014-03-17T18:52:19Z A type of lipid binding assay evidence that is used in a manual assertion. ECO:0001226 eco mchibucos true true A type of lipid binding assay evidence that is used in a manual assertion. ECO:MCC luminescence-based mammalian interactome mapping assay evidence used in manual assertion 2014-03-17T18:55:16Z A type of LUMIER assay evidence that is used in a manual assertion. ECO:0001227 eco mchibucos true true A type of LUMIER assay evidence that is used in a manual assertion. ECO:MCC macroscopy evidence used in manual assertion 2014-03-17T18:56:21Z A type of macroscopy evidence that is used in a manual assertion. ECO:0001228 eco mchibucos A type of macroscopy evidence that is used in a manual assertion. ECO:MCC true true mammalian 2-hybrid assay evidence used in manual assertion 2014-03-17T18:57:25Z A type of mammalian 2-hybrid assay evidence that is used in a manual assertion. ECO:0001229 eco mchibucos true true A type of mammalian 2-hybrid assay evidence that is used in a manual assertion. ECO:MCC mass spectrometry evidence used in manual assertion 2014-03-17T18:59:50Z A type of mass spectrometry evidence that is used in a manual assertion. ECO:0001230 eco mchibucos true true A type of mass spectrometry evidence that is used in a manual assertion. ECO:MCC medical imaging evidence used in manual assertion 2014-03-17T19:04:43Z A type of medical imaging evidence that is used in a manual assertion. ECO:0001231 eco mchibucos true A type of medical imaging evidence that is used in a manual assertion. ECO:MCC true microscopy evidence used in manual assertion 2014-03-17T19:05:37Z A type of microscopy evidence that is used in a manual assertion. ECO:0001232 eco mchibucos true A type of microscopy evidence that is used in a manual assertion. ECO:MCC true motility wound healing assay evidence used in manual assertion 2014-03-17T19:08:13Z A type of motility wound healing assay evidence that is used in a manual assertion. ECO:0001233 eco mchibucos true A type of motility wound healing assay evidence that is used in a manual assertion. ECO:MCC true MTS assay evidence used in manual assertion 2014-03-17T19:08:51Z A type of MTS assay evidence that is used in a manual assertion. ECO:0001234 eco mchibucos A type of MTS assay evidence that is used in a manual assertion. ECO:MCC true true MTT assay evidence used in manual assertion 2014-03-17T19:13:17Z A type of MTT assay evidence that is used in a manual assertion. ECO:0001235 eco mchibucos true true A type of MTT assay evidence that is used in a manual assertion. ECO:MCC multiplex bead-based immunoassay evidence used in manual assertion 2014-03-17T19:14:03Z A type of multiplex bead-based immunoassay evidence that is used in a manual assertion. ECO:0001236 eco mchibucos true A type of multiplex bead-based immunoassay evidence that is used in a manual assertion. ECO:MCC true natural variation mutant evidence used in manual assertion 2014-03-17T19:15:48Z A type of natural variation mutant evidence that is used in a manual assertion. ECO:0001237 eco mchibucos true A type of natural variation mutant evidence that is used in a manual assertion. ECO:MCC true nuclear magnetic resonance spectroscopy evidence used in manual assertion 2014-03-17T19:18:50Z A type of nuclear magnetic resonance spectroscopy evidence that is used in a manual assertion. ECO:0001238 eco mchibucos true true A type of nuclear magnetic resonance spectroscopy evidence that is used in a manual assertion. ECO:MCC nuclear fragmentation evidence used in manual assertion 2014-03-17T19:19:55Z A type of nuclear fragmentation evidence that is used in a manual assertion. ECO:0001239 eco mchibucos A type of nuclear fragmentation evidence that is used in a manual assertion. ECO:MCC true true nuclease protection assay evidence used in manual assertion 2014-03-17T19:23:41Z A type of nuclease protection assay evidence that is used in a manual assertion. ECO:0001240 eco mchibucos A type of nuclease protection assay evidence that is used in a manual assertion. ECO:MCC true true nucleotide analog incorporation evidence used in manual assertion 2014-03-17T19:25:17Z A type of nucleotide analog incorporation evidence that is used in a manual assertion. ECO:0001241 eco mchibucos true A type of nucleotide analog incorporation evidence that is used in a manual assertion. ECO:MCC true phage display evidence used in manual assertion 2014-03-17T19:27:17Z A type of phage display evidence that is used in a manual assertion. ECO:0001242 eco mchibucos true true true A type of phage display evidence that is used in a manual assertion. ECO:MCC phosphoamino acid analysis evidence used in manual assertion 2014-03-17T19:28:59Z A type of phosphoamino acid analysis evidence that is used in a manual assertion. ECO:0001243 eco mchibucos true A type of phosphoamino acid analysis evidence that is used in a manual assertion. ECO:MCC true peptide affinity enrichment evidence used in manual assertion 2014-03-17T19:30:13Z A type of peptide affinity enrichment evidence that is used in a manual assertion. ECO:0001244 eco mchibucos true A type of peptide affinity enrichment evidence that is used in a manual assertion. ECO:MCC true peptide array evidence used in manual assertion 2014-03-17T20:16:45Z A type of peptide array evidence that is used in a manual assertion. ECO:0001245 eco mchibucos true A type of peptide array evidence that is used in a manual assertion. ECO:MCC true physical examination evidence used in manual assertion 2014-03-17T20:17:27Z A type of physical examination evidence that is used in a manual assertion. ECO:0001246 eco mchibucos true A type of physical examination evidence that is used in a manual assertion. ECO:MCC true point mutation evidence used in manual assertion 2014-03-17T20:18:10Z A type of point mutation evidence that is used in a manual assertion. ECO:0001247 eco mchibucos A type of point mutation evidence that is used in a manual assertion. ECO:MCC true true propidium iodide staining evidence used in manual assertion 2014-03-17T20:18:58Z A type of propidium iodide staining evidence that is used in a manual assertion. ECO:0001248 eco mchibucos true A type of propidium iodide staining evidence that is used in a manual assertion. ECO:MCC true fluorescence evidence used in manual assertion 2014-03-17T20:19:35Z A type of protein detection by fluorescence evidence that is used in a manual assertion. ECO:0001249 eco mchibucos true A type of protein detection by fluorescence evidence that is used in a manual assertion. ECO:MCC true protein dot blot assay evidence used in manual assertion 2014-03-17T20:20:30Z A type of protein dot blot assay evidence that is used in a manual assertion. ECO:0001250 eco mchibucos true true A type of protein dot blot assay evidence that is used in a manual assertion. ECO:MCC protein microarray evidence used in manual assertion 2014-03-17T20:21:11Z A type of protein microarray evidence that is used in a manual assertion. ECO:0001251 eco mchibucos true A type of protein microarray evidence that is used in a manual assertion. ECO:MCC true protein sequencing assay evidence used in manual assertion 2014-03-17T20:22:08Z A type of protein sequencing assay evidence that is used in a manual assertion. ECO:0001252 eco mchibucos true true A type of protein sequencing assay evidence that is used in a manual assertion. ECO:MCC quantitative mass spectrometry evidence used in manual assertion 2014-03-17T20:23:15Z A type of quantitative mass spectrometry evidence that is used in a manual assertion. ECO:0001253 eco mchibucos true A type of quantitative mass spectrometry evidence that is used in a manual assertion. ECO:MCC true radioisotope assay evidence used in manual assertion 2014-03-17T20:27:05Z A type of radioisotope assay evidence that is used in a manual assertion. ECO:0001254 eco mchibucos A type of radioisotope assay evidence that is used in a manual assertion. ECO:MCC true true radioimmunoassay evidence used in manual assertion 2014-03-17T20:28:04Z A type of radioimmunoassay evidence that is used in a manual assertion. ECO:0001255 eco mchibucos true true A type of radioimmunoassay evidence that is used in a manual assertion. ECO:MCC imaging assay evidence used in manual assertion 2014-03-17T20:29:00Z A type of imaging assay evidence that is used in a manual assertion. ECO:0001256 eco mchibucos true A type of imaging assay evidence that is used in a manual assertion. ECO:MCC true restriction fragment detection evidence used in manual assertion 2014-03-17T20:29:05Z A type of restriction fragment detection evidence that is used in a manual assertion. ECO:0001257 eco mchibucos true true A type of restriction fragment detection evidence that is used in a manual assertion. ECO:MCC spectrophotometry evidence used in manual assertion 2014-03-17T20:29:09Z A type of spectrophotometry evidence that is used in a manual assertion. ECO:0001258 eco mchibucos true A type of spectrophotometry evidence that is used in a manual assertion. ECO:MCC true syngeneic transplantation experiment evidence used in manual assertion 2014-03-17T20:29:13Z A type of syngeneic transplantation experiment evidence that is used in a manual assertion. ECO:0001259 eco mchibucos true true A type of syngeneic transplantation experiment evidence that is used in a manual assertion. ECO:MCC xenotransplantation experiment evidence used in manual assertion 2014-03-17T20:29:18Z A type of xenotransplantation experiment evidence that is used in a manual assertion. ECO:0001260 eco mchibucos true A type of xenotransplantation experiment evidence that is used in a manual assertion. ECO:MCC true WST-1 assay evidence used in manual assertion 2014-03-17T20:29:22Z A type of WST-1 assay evidence that is used in a manual assertion. ECO:0001261 eco mchibucos true true A type of WST-1 assay evidence that is used in a manual assertion. ECO:MCC wound healing assay evidence used in manual assertion 2014-03-17T20:29:26Z A type of wound healing assay evidence that is used in a manual assertion. ECO:0001262 eco mchibucos A type of wound healing assay evidence that is used in a manual assertion. ECO:MCC true true urine test evidence used in manual assertion 2014-03-17T20:29:30Z A type of urine test evidence that is used in a manual assertion. ECO:0001263 eco mchibucos true true A type of urine test evidence that is used in a manual assertion. ECO:MCC terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence used in manual assertion 2014-03-17T20:29:34Z A type of TUNEL assay evidence that is used in a manual assertion. ECO:0001264 eco mchibucos true A type of TUNEL assay evidence that is used in a manual assertion. ECO:MCC true tryptic phosphopeptide mapping assay evidence used in manual assertion 2014-03-17T20:29:38Z A type of tryptic phosphopeptide mapping assay evidence that is used in a manual assertion. ECO:0001265 eco mchibucos true true A type of tryptic phosphopeptide mapping assay evidence that is used in a manual assertion. ECO:MCC transgenic organism evidence used in manual assertion 2014-03-17T20:29:41Z A type of transgenic organism evidence that is used in a manual assertion. ECO:0001266 eco mchibucos true A type of transgenic organism evidence that is used in a manual assertion. ECO:MCC true tissue microarray evidence used in manual assertion 2014-03-17T20:29:45Z A type of tissue microarray evidence that is used in a manual assertion. ECO:0001267 eco mchibucos true true A type of tissue microarray evidence that is used in a manual assertion. ECO:MCC TACE activity assay evidence used in manual assertion 2014-03-17T20:29:49Z A type of TACE activity assay evidence that is used in a manual assertion. ECO:0001268 eco mchibucos true A type of TACE activity assay evidence that is used in a manual assertion. ECO:MCC true surface plasmon resonance evidence used in manual assertion 2014-03-17T20:29:54Z A type of surface plasmon resonance evidence that is used in a manual assertion. ECO:0001269 eco mchibucos true true A type of surface plasmon resonance evidence that is used in a manual assertion. ECO:MCC restriction landmark genomic scanning evidence used in manual assertion 2014-03-17T20:29:58Z A type of restriction landmark genome scanning evidence that is used in a manual assertion. ECO:0001270 eco mchibucos true true A type of restriction landmark genome scanning evidence that is used in a manual assertion. ECO:MCC resonant mirror biosensor evidence used in manual assertion 2014-03-17T20:30:02Z A type of resonant mirror biosensor evidence that is used in a manual assertion. ECO:0001271 eco mchibucos true true A type of resonant mirror biosensor evidence that is used in a manual assertion. ECO:MCC high-performance liquid chromatography evidence used in manual assertion 2014-03-16T20:49:54Z A type of high-performance liquid chromatography evidence that is used in a manual assertion. ECO:0001272 eco mchibucos true A type of high-performance liquid chromatography evidence that is used in a manual assertion. ECO:MCC true ectopic expression evidence used in manual assertion 2014-03-17T22:34:56Z A type of ectopic expression evidence that is used in a manual assertion. ECO:0001273 eco mchibucos true true A type of ectopic expression evidence that is used in a manual assertion. ECO:MCC protein-binding microarray evidence 2015-06-05T14:36:00Z A type of oligonucleotide microarray evidence that detects binding of a tagged protein to an array of oligonucleotide probes representing potential binding sites. ECO:0001601 PBM evidence eco swolfish A type of oligonucleotide microarray evidence that detects binding of a tagged protein to an array of oligonucleotide probes representing potential binding sites. PMID:22146299 in vivo cell staining evidence 2015-06-08T11:51:37Z 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. ECO:0001603 eco swolfish vital staining evidence GOC:MAH vital 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 alkaline phosphatase reporter gene assay evidence 2015-10-29T15:53:45Z 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. Alkaline phosphatase reporter assay produces a hybrid protein with alkaline phosphatase activity following transportation across the cellular membrane. ECO:0001801 SEAP reporter assay Secreted Embryonic Alkaline Phosphatase reporter assay eco swolfish 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 beta-galactosidase reporter gene assay evidence 2015-10-29T15:57:10Z 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:0001802 The assay is often performed using a plasmid borne construction on a lacZ strain. beta-gal reporter gene assay eco lacZ reporter gene assay swolfish 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 chloramphenicol acetyltransferase reporter gene assay evidence 2015-10-29T16:06:42Z 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. CAT reporter gene assay ECO:0001803 The amount of acetylated chloramphenicol is directly proportional to the amount of CAT enzyme present. eco swolfish CAT reporter gene assay PMID:1630936 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 beta-glucuronidase reporter gene assay evidence 2015-10-29T16:11:02Z 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:0001804 GUS reporter gene assay eco swolfish 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 luciferase reporter gene assay evidence 2015-10-29T16:15:39Z 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:0001805 eco swolfish 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 chromatin immunoprecipitation- exonuclease evidence 2015-10-29T16:37:36Z 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. ChIP-exo ECO:0001806 eco swolfish 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 electrophoretic mobility shift assay evidence used in manual assertion 2015-11-03T12:13:17Z A type of electrophoretic mobility shift that is used in a manual assertion. ECO:0001807 eco swolfish A type of electrophoretic mobility shift that is used in a manual assertion. ECO:SW true true reverse transcription polymerase chain reaction evidence used in manual assertion 2015-11-03T12:22:46Z A type of reverse transcription polymerase chain reaction evidence that is used in a manual assertion. ECO:0001808 eco swolfish true A type of reverse transcription polymerase chain reaction evidence that is used in a manual assertion. ECO:SW true DNA affinity chromatography evidence 2015-11-03T13:48:49Z 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. 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 purification ECO:0001809 eco swolfish 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 DNAse footprinting evidence 2015-11-03T13:55:15Z 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. 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. eco swolfish 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 fluorescence anisotropy evidence 2015-11-03T14:01:36Z 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:0001811 FA FP Fluorescence polarization 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. eco swolfish FP PMCID:3277431 PMID:20232898 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 Fluorescence polarization PMCID:3277431 PMID:20232898 genomic systematic evolution of ligands by exponential amplification evidence 2015-11-03T14:05:37Z 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:0001812 The reported sequences should always be verified for presence in the genome sequence. eco genomic SELEX swolfish PMID:20541015 genomic SELEX 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 heteronuclear single quantum coherence spectroscopy evidence 2015-11-03T14:11:06Z 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. 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. ECO:0001813 HSQC eco swolfish 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 methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence 2015-11-03T14:24:04Z 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:0001814 MPE Fe(II) footprinting MPE-EDTA Fe(II) footprinting Methidiumpropyl-EDTA Fe(II) footprinting eco swolfish MPE Fe(II) footprinting PMID:6225070 Methidiumpropyl-EDTA Fe(II) footprinting PMID:6225070 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-EDTA Fe(II) footprinting PMID:6225070 copper-phenanthroline footprinting evidence 1,10-Phenanthroline-copper footprinting 2015-11-04T08:37:51Z 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:0001815 OP-Cu Complex eco swolfish OP-Cu Complex PMID:1384472 1,10-Phenanthroline-copper footprinting PMID:1384472 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 green fluorescent protein reporter gene assay evidence 2015-11-04T08:58:42Z 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:0001816 GFP promoter fusion GFP reporter gene assay eco green fluorescent protein promoter fusion swolfish 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 glutathione S-transferase pull-down assay evidence 2015-11-04T09:05:56Z 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:0001817 GST pull-down assay The recombinant protein can also be eluted following the pull-down and analyzed further with qPCR or sequencing. eco swolfish GST pull-down assay PMID:26096507 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 hydroxyl-radical footprinting evidence 2015-11-04T09:20:26Z 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:0001818 eco swolfish 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 primer extension assay evidence 2015-11-04T09:33:18Z A type of transcript expression level 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:0001819 The most commonly used radiolabel is 32P. eco swolfish A type of transcript expression level 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 rapid amplification of cDNA ends polymerase chain reaction evidence 2015-11-04T09:48:38Z 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:0001820 RACE PCR RACE PCR is frequently used to verify transcription start sites relevant to the function of transcription factor binding sites such as repression. eco swolfish 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 PMI:17498297 RACE PCR RNA sequencing assay evidence 2015-11-04T10:15:57Z 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:0001821 RNA-Seq WTTS Whole Transcriptome Shotgun Sequencing eco swolfish PMID:23851085 Whole Transcriptome Shotgun Sequencing PMID:23851085 RNA-Seq 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 survival rate analysis evidence 2015-11-04T10:48:59Z 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:0001822 eco swolfish 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 x-ray crystallography evidence 2015-11-04T10:56:22Z 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: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. eco swolfish 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 DNA adenine methyltransferase identification evidence 2015-11-05T15:56:13Z 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. DamID ECO:0001824 The methylation tag is detected with methylation-sensitive restriction enzymes, DpnI and DpnII. eco swolfish 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 isothermal titration calorimetry evidence 2015-11-05T16:06:20Z 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:0001825 ITC 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)). eco swolfish 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 ultraviolet light footprinting evidence 2015-11-05T16:13:36Z 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:0001826 UV footprinting eco swolfish ultraviolet footprinting 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 premethylation interference footprinting evidence 2015-11-05T16:16:27Z 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:0001827 eco methylation interference footprinting swolfish 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 visual sequence inspection evidence 2015-11-10T14:40:16Z 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:0001828 eco swolfish 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 ferric uptake regulator titration assay evidence 2015-11-10T14:55:36Z 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:0001829 FURTA Fluorescence polarization eco swolfish Fluorescence polarization PMID:15689115 FURTA PMID:10713425 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 cell viability assay evidence 2015-02-13T12:08:01Z ECO:0005004 eco snadendla cell proliferation assay evidence 2015-02-11T16:27:13Z ECO:0005007 eco snadendla DNA synthesis cell proliferation assay evidence 2015-02-11T16:30:10Z ECO:0005008 eco snadendla metabolic cell proliferation assay evidence 2015-02-11T16:36:33Z ECO:0005009 eco snadendla cell proliferation marker detection assay evidence 2015-02-11T16:37:23Z ECO:0005010 eco snadendla ATP bioluminescence assay evidence 2015-02-11T16:47:30Z ECO:0005011 eco snadendla cytotoxicity assay evidence 2015-02-12T11:39:35Z ECO:0005012 eco snadendla in vitro cell based assay evidence 2015-02-12T13:26:55Z ECO:0005014 eco snadendla staining evidence 2015-02-19T11:48:57Z ECO:0005019 eco snadendla chemotaxis assay evidence 2015-02-19T13:10:20Z ECO:0005021 eco snadendla genetic transformation evidence 2015-03-16T15:33:50Z ECO:0005027 eco snadendla structure determination evidence 2015-03-20T12:16:17Z ECO:0005031 eco snadendla electron microscopy evidence 2015-03-20T12:21:48Z ECO:0005033 eco snadendla apoptotic assay evidence 2015-04-07T21:58:24Z ECO:0005034 eco snadendla in vivo polyADP-ribosylation assay evidence 2015-06-15T15:35:05Z A type of in vivo assay evidence where ADP-ribosylated residues in proteins are detected in cells in vivo. ECO:0005500 eco snadendla 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 in vivo polyADP-ribosylation assay evidence used in manual assertion 2015-06-15T15:37:23Z A type of in vivo polyADP-ribosylation assay evidence that is used in a manual assertion. ECO:0005501 eco snadendla true A type of in vivo polyADP-ribosylation assay evidence that is used in a manual assertion. ECO:SN true ex vivo assay evidence 2015-06-26T11:46:15Z 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:0005502 eco snadendla 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 two-dimensional polyacrylamide gel electrophoresis evidence 2015-10-01T16:23:20Z 2D PAGE 2D-PAGE 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:0005503 Two-dimensional polyacrylamide gel electrophoresis is commonly employed to establish a proteome for an organism and demonstrate expression changes. eco snadendla 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 spectrometry evidence 2015-08-14T15:48:08Z ECO:0005504 eco snadendla regular expression motif search evidence 2015-10-09T13:51:52Z 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: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). eco snadendla 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 missense mutation evidence 2015-09-18T16:52:34Z ECO:0005506 eco snadendla nonsense mutation evidence 2015-09-18T16:55:32Z ECO:0005507 eco snadendla silent mutation evidence 2015-09-18T17:01:12Z ECO:0005508 eco snadendla insertion mutation evidence 2015-09-18T17:02:03Z ECO:0005509 eco snadendla deletion mutation evidence 2015-09-18T17:02:45Z ECO:0005510 eco snadendla duplication mutation evidence 2015-09-18T17:03:25Z ECO:0005511 eco snadendla frameshift mutation evidence 2015-09-18T17:05:49Z ECO:0005512 eco snadendla repeat expansion mutation evidence 2015-09-18T17:06:34Z ECO:0005513 eco snadendla splice site mutation evidence 2015-09-18T17:07:29Z ECO:0005514 eco snadendla translocation mutation evidence 2015-09-18T17:08:01Z ECO:0005515 eco snadendla molecule detection assay evidence 2015-09-24T15:54:21Z ECO:0005516 eco snadendla protein detection assay evidence 2015-09-25T14:27:40Z ECO:0005517 eco snadendla RNA detection assay evidence 2015-09-25T14:43:53Z ECO:0005518 eco snadendla DNA detection assay evidence 2015-09-25T19:33:25Z ECO:0005519 eco snadendla interferometric reflectance imaging sensor evidence 2015-09-28T16:01:01Z 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. 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. ECO:0005520 IRIS SRIB Spectral Reflectance Imaging Biosensor eco snadendla 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 S1 nuclease protection assay evidence 2015-09-28T17:16:56Z 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:0005521 eco snadendla 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 DNA dot blot assay evidence 2015-09-30T10:03:03Z ECO:0005522 eco snadendla DNA dot blot assay evidence used in manual assertion 2015-09-30T10:04:00Z A type of DNA dot blot assay evidence that is used in a manual assertion. ECO:0005523 eco snadendla true A type of DNA dot blot assay evidence that is used in a manual assertion. ECO:SN ECO:SW true DNA microarray evidence 2015-09-30T10:12:48Z A type of DNA detection assay evidence where complimentary ssDNA is attached to a solid glass, silicon, or plastic surface and is hybridized with a labeled sample of extracted mRNA or amplified cDNA and stimulated with a laser for fluorescence detected with a scanner. DNA chip DNA-array expression analysis ECO:0005524 The mRNA extraction is performed in induced and non-induced cells and reverse transcribed with different fluorophore labeling for controls and experiment. Fluorescence is measured at two different wavelengths and the ratio between the two fluorescence intensities corresponds to the induction level. eco snadendla DNA chip PMID:10398077 A type of DNA detection assay evidence where complimentary ssDNA is attached to a solid glass, silicon, or plastic surface and is hybridized with a labeled sample of extracted mRNA or amplified cDNA and stimulated with a laser for fluorescence detected with a scanner. ECO:SW PMID:17660860 DNA microarray evidence used in manual assertion 2015-09-30T10:13:09Z A type of DNA microarray evidence that is used in a manual assertion. ECO:0005525 eco snadendla A type of DNA microarray evidence that is used in a manual assertion. ECO:SN ECO:SW true true matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence 2015-09-30T10:51:56Z 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: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. MALDI-TOF Mass Spectrometry MALDI-TOF-MS eco snadendla 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 matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence used in manual assertion 2015-09-30T10:58:51Z A type of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence that is used in a manual assertion. ECO:0005527 eco snadendla 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 true true site-directed mutagenesis evidence 2015-09-30T11:34:41Z 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: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. eco site directed mutagenesis snadendla 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 random mutagenesis evidence 2015-09-30T11:55:03Z 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: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. eco snadendla 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 random mutagenesis evidence used in manual assertion 2015-09-30T11:57:00Z A type of random mutagenesis evidence that is used in a manual assertion. ECO:0005530 eco snadendla true true motif discovery evidence 2015-09-30T15:04:45Z 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: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 (PMID: 19892760), from peaks in ChIP-seq experiments with the TF (PMID: 16264194), or from the comparative genomics analysis of the promoter regions of orthologs (PMID: 23032607). eco snadendla 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 consensus search evidence 2015-10-09T14:12:54Z 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: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. eco snadendla 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 phylogenetic footprinting evidence 2015-09-30T16:23:02Z 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: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). eco snadendla 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 comparative genomics motif search evidence 2015-10-09T14:30:38Z 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: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. eco snadendla 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 machine learning prediction of motif instance evidence 2015-10-01T11:58:36Z 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: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). eco snadendla 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 position-specific scoring matrix motif search evidence 2015-10-09T15:04:35Z 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:0005536 PSSM PSSM motif search This technique is used to predict transcription factor binding sites in gene promoter regions by using a position weight matrix approach. (PMID: 15604457). eco snadendla 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 xylE reporter gene assay evidence 2015-10-28T15:31:28Z 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:0005537 eco snadendla 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 computationally derived logical inference 2015-11-17T15:15:50Z ECO:0005538 eco snadendla true computationally derived logical inference used in automatic assertion 2015-11-17T15:17:47Z ECO:0005539 eco snadendla true computationally derived logical inference from automatic assertion used in automatic assertion 2015-11-17T15:24:42Z ECO:0005540 eco snadendla true computationally derived logical inference from manual assertion used in automatic assertion 2015-11-17T15:32:03Z ECO:0005541 eco snadendla true biological system reconstruction evidence by experimental evidence from single species used in manual assertion 2015-12-16T15:32:41Z A type of biological system reconstruction evidence by experimental evidence from single species that is used in a manual assertion. 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. eco snadendla 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 biological system reconstruction evidence by experimental evidence from mixed species used in manual assertion 2015-12-16T15:45:01Z A type of biological system reconstruction evidence by experimental evidence from mixed species that is used in a manual assertion. 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. eco snadendla 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 biological system reconstruction evidence based on orthology evidence used in manual assertion 2015-12-18T16:20:49Z A type of biological system reconstruction evidence based on orthology evidence that is used in a manual assertion. 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. eco snadendla true A type of biological system reconstruction evidence based on orthology evidence that is used in a manual assertion. ECO:SN biological system reconstruction evidence based on orthology evidence 2015-12-16T15:57:37Z 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: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. eco snadendla 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 biological system reconstruction evidence based on paralogy evidence used in manual assertion 2015-12-16T16:05:15Z A type of biological system reconstruction evidence based on paralogy evidence that is used in a manual assertion. 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. eco snadendla true A type of biological system reconstruction evidence based on paralogy evidence that is used in a manual assertion. ECO:SN PMID:15660128 biological system reconstruction evidence based on inference from background scientific knowledge used in manual assertion 2015-12-16T16:07:42Z A type of biological system reconstruction evidence based on inference from background scientific knowledge that is used in a manual assertion. 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. eco snadendla 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 true true biological system reconstruction evidence based on inference from background scientific knowledge 2015-12-18T15:32:15Z A type of biological system reconstruction based solely on background scientific knowledge of that biological system. 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. eco snadendla A type of biological system reconstruction based solely on background scientific knowledge of that biological system. ECO:SN PMID:17876790 biological system reconstruction evidence based on homology evidence 2015-12-18T15:49:46Z 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: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. eco snadendla 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 biological system reconstruction evidence based on paralogy evidence 2015-12-18T16:24:08Z 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: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. eco snadendla 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 biological system reconstruction evidence by experimental evidence 2015-12-18T16:34:13Z A type of biological system reconstruction evidence that uses experimental evidence as support. ECO:0005551 eco snadendla A type of biological system reconstruction evidence that uses experimental evidence as support. ECO:SN PMID:19450514 PMID:22232657 biological system reconstruction evidence by experimental evidence from mixed species 2015-12-18T16:35:13Z 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: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. eco snadendla 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 biological system reconstruction evidence by experimental evidence from single species 2015-12-18T16:36:44Z A type of biological system reconstruction where the experimental evidence is derived by using multiple experiments in a single species. 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. eco snadendla A type of biological system reconstruction where the experimental evidence is derived by using multiple experiments in a single species. ECO:SN pairwise sequence alignment evidence 2016-02-08T14:30:46Z 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:0005554 eco snadendla 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/ multiple sequence alignment evidence 2016-02-08T14:31:24Z 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:0005555 eco snadendla 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/ multiple sequence alignment evidence used in manual assertion 2016-02-08T14:59:18Z A type of multiple sequence alignment evidence that is used in a manual assertion. ECO:0005556 eco snadendla A type of multiple sequence alignment evidence that is used in a manual assertion. ECO:SN true true multiple sequence alignment evidence used in automatic assertion 2016-02-08T15:00:50Z A type of multiple sequence alignment evidence that is used in an automatic assertion. ECO:0005557 eco snadendla true true A type of multiple sequence alignment evidence that is used in an automatic assertion. ECO:SN motif discovery evidence used in manual assertion 2016-02-08T15:07:47Z A type of motif discovery evidence that is used in a manual assertion. ECO:0005558 eco snadendla true true A type of motif discovery evidence that is used in a manual assertion. ECO:SN motif discovery evidence used in automatic assertion 2016-02-08T15:08:19Z A type of motif discovery evidence that is used in an automatic assertion. ECO:0005559 eco snadendla true true A type of motif discovery evidence that is used in an automatic assertion. ECO:SN pairwise sequence alignment evidence used in manual assertion 2016-02-08T15:17:05Z A type of pairwise sequence alignment evidence that is used in a manual assertion. ECO:0005560 eco snadendla true A type of pairwise sequence alignment evidence that is used in a manual assertion. ECO:SN true pairwise sequence alignment evidence used in automatic assertion 2016-02-08T15:17:52Z A type of pairwise sequence alignment evidence that is used in an automatic evidence. ECO:0005561 eco snadendla true A type of pairwise sequence alignment evidence that is used in an automatic evidence. ECO:SN true in gel protein kinase assay evidence 2016-02-09T12:05:29Z ECO:0005562 eco snadendla macroscopic current trace evidence 2016-02-09T12:40:03Z A type of electrophysiology assay evidence that involves recording trace of the current (pA) going through the analyzed ion channels determined from voltage clamp current recording. ECO:0005563 eco snadendla A type of electrophysiology assay 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 current density evidence 2016-02-09T12:43:07Z A type of electrophysiology assay evidence that involves measuring the amount of current (pA) going through the ion channels per unit of membrane. ECO:0005564 eco snadendla 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 single channel conductance evidence 2016-02-09T12:45:42Z ECO:0005565 eco snadendla true sustained current evidence 2016-02-09T12:46:54Z 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:0005566 eco snadendla 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 steady state activation curve evidence 2016-02-09T12:48:17Z ECO:0005567 eco snadendla true steady state inactivation curve evidence 2016-02-09T12:50:45Z ECO:0005568 eco snadendla true window current trace evidence 2016-02-09T12:57:16Z ECO:0005569 eco snadendla true use dependence of inactivation evidence 2016-02-09T12:58:18Z 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:0005570 eco snadendla 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 current clamp voltage recording evidence 2016-02-12T13:58:32Z A type of electrophysiology assay evidence that involves recording the change in membrane potential caused by applying specific current to the cell. ECO:0005571 birnlex:2278 eco snadendla 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 current clamp voltage recording protocol birnlex:2278 whole-cell voltage clamp recording evidence 2016-02-12T14:06:40Z A type of electrophysiology assay evidence that involves direct measurement of ionic current across a membrane while controlling the membrane potential by maintaining the voltage. ECO:0005572 birnlex:2281 eco snadendla A type of electrophysiology assay 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 whole-cell voltage clamp recording protocol birnlex:2281 cell-attached single-channel recording evidence 2016-02-12T14:07:39Z A type of electrophysiology assay 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:0005573 birnlex:2283 eco snadendla A type of electrophysiology assay 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 cell-attached single-channel recording protocol birnlex:2283 cell-detached inside-out single-channel recording evidence 2016-02-12T14:16:53Z A type of electrophysiology assay 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:0005574 birnlex:2286 eco snadendla cell-detached inside-out single-channel recording protocol birnlex:2286 A type of electrophysiology assay 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 reconstituted bilayer single-channel patch recording evidence 2016-02-12T14:17:46Z A type of electrophysiology assay 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:0005575 birnlex:2287 eco snadendla reconstituted bilayer single-channel patch recording protocol birnlex:2287 A type of electrophysiology assay 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 voltage clamp current recording evidence 2016-02-12T14:18:36Z 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:0005576 birnlex:2279 eco snadendla 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 voltage clamp current recording protocol birnlex:2279 electroencephalography recording evidence 2016-02-12T14:19:21Z 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:0005577 birnlex:2293 eco snadendla electroencephalography recording protocol birnlex:2293 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 super-resolution microscopy evidence 2016-02-12T15:20:47Z 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:0005578 eco snadendla 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 immunogold labelling evidence used in manual assertion 2016-02-12T15:38:03Z A type of immunogold labelling evidence that is used in a manual assertion. ECO:0005579 eco snadendla true A type of immunogold labelling evidence that is used in a manual assertion. ECO:SN true flow cytometry evidence used in manual assertion 2016-02-12T16:04:23Z A type of flow cytometry evidence that is used in a manual assertion. ECO:0005580 eco snadendla A type of flow cytometry evidence that is used in a manual assertion. ECO:SN true true enzyme-linked immunoabsorbent assay evidence used in manual assertion 2016-02-12T16:23:38Z A type of enzyme-linked immunoabsorbent assay evidence that is used in a manual assertion. ECO:0005581 eco snadendla true true A type of enzyme-linked immunoabsorbent assay evidence that is used in a manual assertion. ECO:SN cell-detached outside-out single-channel recording evidence 2016-03-02T10:47:25Z A type of electrophysiology assay 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:0005582 eco snadendla A type of electrophysiology assay 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 cut-open oocyte voltage clamp recording evidence 2016-03-02T11:29:32Z A type of electrophysiology assay 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:0005583 eco snadendla A type of electrophysiology assay 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 macropatch voltage clamp recording evidence 2016-03-02T11:33:48Z A type of electrophysiology assay 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:0005584 eco snadendla A type of electrophysiology assay 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 high throughput mass spectrometry evidence 2016-03-02T12:33:07Z 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: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. eco snadendla 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 high throughput mass spectrometry evidence used in manual assertion 2016-03-02T12:50:02Z A type of high throughput mass spectrometry evidence that is used in a manual assertion. ECO:0005586 eco snadendla A type of high throughput mass spectrometry evidence that is used in a manual assertion. ECO:SN confocal microscopy evidence 2016-03-17T12:29:45Z 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:0005587 eco snadendla 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 wide-field microscopy evidence 2016-03-17T12:30:27Z 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:0005588 eco snadendla 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 confocal microscopy evidence used in manual assertion 2016-03-17T12:32:24Z A type confocal microscopy evidence that is used in a manual assertion. ECO:0005589 eco snadendla A type confocal microscopy evidence that is used in a manual assertion. ECO:SN true true wide-field microscopy evidence used in manual assertion 2016-03-17T12:34:42Z A type of wide-field microscopy evidence that is used in a manual assertion. ECO:0005590 eco snadendla A type of wide-field microscopy evidence that is used in a manual assertion. ECO:SN true true immunogold labelling electron microscopy assay evidence 2016-03-17T15:43:00Z 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:0005591 eco snadendla 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 immunogold labelling electron microscopy assay evidence used in manual assertion 2016-03-17T16:39:37Z A type of immunogold labelling electron microscopy assay evidence that is used in a manual assertion. ECO:0005592 eco snadendla true A type of immunogold labelling electron microscopy assay evidence that is used in a manual assertion. ECO:SN true immunodetection assay evidence 2016-03-17T17:07:33Z A type of direct assay evidence that involves the use of antibodies to detect biomolecules. ECO:0005593 eco snadendla A type of direct assay evidence that involves the use of antibodies to detect biomolecules. ECO:SN immunoperoxidase immunolocalization evidence 2016-03-17T17:11:34Z A type of immunolocalization evidence involving enzymatic detection of a peroxidase tagged antibody. ECO:0005594 eco snadendla A type of immunolocalization evidence involving enzymatic detection of a peroxidase tagged antibody. ECO:SN immunoperoxidase immunolocalization evidence used in manual assertion 2016-03-17T17:14:05Z A type of immunoperoxidase immunolocalization evidence that is used in a manual assertion. ECO:0005595 eco snadendla true true A type of immunoperoxidase immunolocalization evidence that is used in a manual assertion. ECO:SN immunoperoxidase immunolocalization electron microscopy evidence 2016-03-17T17:16:38Z A type of immunoperoxidase immunolocalization evidence where electron microscopy technique is used for enzymatic detection of a peroxidase tagged antibody. ECO:0005596 Immunoperoxidase labelling electron microscopy eco snadendla A type of immunoperoxidase immunolocalization evidence where electron microscopy technique is used for enzymatic detection of a peroxidase tagged antibody. ECO:SN immunoperoxidase immunolocalization electron microscopy evidence used in manual assertion 2016-03-17T17:23:56Z A type of immunoperoxidase immunolocalization electron microscopy evidence that is used in a manual assertion. ECO:0005597 eco snadendla A type of immunoperoxidase immunolocalization electron microscopy evidence that is used in a manual assertion. ECO:SN true true wide-field fluorescence microscopy evidence 2016-03-18T11:53:56Z 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: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. eco snadendla 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 immunofluorescence wide-field microscopy evidence 2016-03-18T11:55:40Z A type of wide-field fluorescence microscopy evidence where fluorescently tagged antibodies are imaged that are used to bind to their antigens. ECO:0005599 eco snadendla wide-field epifluorescence microscopy 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 immunofluorescence confocal microscopy evidence 2016-03-18T12:48:42Z 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:0005600 This allows visualization of sub cellular distribution of biomolecules of interest. eco snadendla 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 immunofluorescence confocal microscopy evidence used in manual assertion 2016-03-18T12:52:04Z A type of immunofluorescence confocal microscopy evidence that is used in a manual assertion. ECO:0005601 eco snadendla true true true A type of immunofluorescence confocal microscopy evidence that is used in a manual assertion. ECO:SN protein expression level evidence based on western blot 2016-03-18T13:02:29Z 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:0005602 eco snadendla 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 protein mass spectrometry evidence 2016-03-18T13:11:37Z A type of mass spectrometry evidence where one or more protein analyses are performed. ECO:0005603 eco snadendla A type of mass spectrometry evidence where one or more protein analyses are performed. ECO:SN cross-streak test evidence 2016-03-29T15:40:54Z 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:0005604 eco snadendla 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 disk diffusion test evidence 2016-03-29T16:02:22Z 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:0005605 eco snadendla zone of inhibition 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 cell transfection experiment evidence 2016-03-29T16:59:17Z 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:0005606 eco snadendla 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/ tethered cell assay evidence 2016-03-31T15:51:10Z 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:0005607 eco snadendla 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 tumble frequency assay evidence 2016-03-31T16:42:35Z 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:0005608 Temporal assay eco snadendla 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 capillary assay evidence 2016-03-31T16:45:29Z 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: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. eco snadendla 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 biological system reconstruction evidence based on homology evidence used in manual assertion 2016-03-31T17:00:03Z A type of biological system reconstruction evidence based on homology evidence that is used in a manual assertion. 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. eco snadendla true A type of biological system reconstruction evidence based on homology evidence that is used in a manual assertion. ECO:SN true inference from experimental data evidence 2016-04-12T16:55:16Z 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:0005611 IED eco inferred from experimental data snadendla 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 inference from phenotype manipulation evidence 2016-04-12T17:09:43Z 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. 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. ECO:0005612 IPM eco inferred from phenotype manipulation snadendla 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 inference by association of genotype from phenotype 2016-04-12T17:24:00Z 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:0005613 IAGP 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. eco inferred by association of genotype from phenotype snadendla 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 two-dimensional polyacrylamide gel electrophoresis evidence used in manual assertion 2016-05-06T11:03:08Z A type of two-dimensional polyacrylamide gel electrophoresis evidence that is used in a manual assertion. ECO:0005614 eco snadendla true true A type of two-dimensional polyacrylamide gel electrophoresis evidence that is used in a manual assertion. ECO:SN alkaline phosphatase reporter gene assay evidence used in manual assertion 2016-05-06T11:05:59Z A type of alkaline phosphatase reporter gene assay evidence that is used in a manual assertion. ECO:0005615 eco snadendla A type of alkaline phosphatase reporter gene assay evidence that is used in a manual assertion. ECO:SN true true beta-galactosidase reporter gene assay evidence used in manual assertion 2016-05-06T11:08:57Z A type of beta-galactosidase reporter gene assay evidence that is used in a manual assertion. ECO:0005616 eco snadendla true A type of beta-galactosidase reporter gene assay evidence that is used in a manual assertion. ECO:SN true chloramphenicol acetyltransferase reporter gene assay evidence used in manual assertion 2016-05-06T11:11:07Z A type of chloramphenicol acetyltransferase reporter gene assay evidence that is used in a manual assertion. ECO:0005617 eco snadendla A type of chloramphenicol acetyltransferase reporter gene assay evidence that is used in a manual assertion. ECO:SN true true chromatin immunoprecipitation-chip evidence used in automatic assertion 2016-05-06T11:17:04Z A type of chromatin immunoprecipitation-chip evidence that is used in an automatic assertion. ECO:0005618 eco snadendla true true A type of chromatin immunoprecipitation-chip evidence that is used in an automatic assertion. ECO:SN chromatin immunoprecipitation- exonuclease evidence used in automatic assertion 2016-05-06T11:22:25Z A type of chromatin immunoprecipitation- exonuclease evidence that is used in an automatic assertion. ECO:0005619 eco snadendla true A type of chromatin immunoprecipitation- exonuclease evidence that is used in an automatic assertion. ECO:SN true chromatin immunoprecipitation-PCR evidence used in manual assertion 2016-05-06T11:25:01Z A type of chromatin immunoprecipitation-PCR evidence that is used in a manual assertion. ECO:0005620 eco snadendla A type of chromatin immunoprecipitation-PCR evidence that is used in a manual assertion. ECO:SN true true chromatin immunoprecipitation-seq evidence used in automatic assertion 2016-05-06T11:29:13Z A type of chromatin immunoprecipitation-seq evidence that is used in an automatic assertion. ECO:0005621 eco snadendla true true A type of chromatin immunoprecipitation-seq evidence that is used in an automatic assertion. ECO:SN comparative genomics motif search evidence used in manual assertion 2016-05-06T14:49:36Z A type of comparative genomics motif search evidence that is used in a manual assertion. ECO:0005622 eco snadendla true true A type of comparative genomics motif search evidence that is used in a manual assertion. ECO:SN comparative genomics motif search evidence used in automatic assertion 2016-05-06T14:52:21Z A type of comparative genomics motif search evidence that is used in an automatic assertion. ECO:0005623 eco snadendla A type of comparative genomics motif search evidence that is used in an automatic assertion. ECO:SN true true consensus search evidence used in manual assertion 2016-05-06T14:54:53Z A type of consensus search evidence that is used in a manual assertion. ECO:0005624 eco snadendla true A type of consensus search evidence that is used in a manual assertion. ECO:SN true consensus search evidence used in automatic assertion 2016-05-06T14:58:22Z A type of consensus search evidence that is used in an automatic assertion. ECO:0005625 eco snadendla true A type of consensus search evidence that is used in an automatic assertion. ECO:SN true copper-phenanthroline footprinting evidence used in manual assertion 2016-05-06T15:01:25Z A type of copper-phenanthroline footprinting evidence that is used in a manual assertion. ECO:0005626 eco snadendla true true A type of copper-phenanthroline footprinting evidence that is used in a manual assertion. ECO:SN DNA adenine methyltransferase identification evidence used in manual assertion 2016-05-06T15:05:14Z A type of DNA adenine methyltransferase identification evidence that is used in a manual assertion. ECO:0005627 eco snadendla true A type of DNA adenine methyltransferase identification evidence that is used in a manual assertion. ECO:SN true DNA adenine methyltransferase identification evidence used in automatic assertion 2016-05-06T15:06:46Z A type of DNA adenine methyltransferase identification evidence that is used in an automatic assertion. ECO:0005628 eco snadendla A type of DNA adenine methyltransferase identification evidence that is used in an automatic assertion. ECO:SN true true DNA affinity chromatography evidence used in manual assertion 2016-05-06T15:08:40Z A type of DNA affinity chromatography evidence that is used in a manual assertion. ECO:0005629 eco snadendla true true A type of DNA affinity chromatography evidence that is used in a manual assertion. ECO:SN DNA microarray evidence used in automatic assertion 2016-05-06T15:31:51Z A type of DNA microarray evidence that is used in an automatic assertion. ECO:0005630 eco snadendla A type of DNA microarray evidence that is used in an automatic assertion. ECO:SN true true DNAse footprinting evidence used in manual assertion 2016-05-06T15:35:41Z A type of DNAse footprinting evidence that is used in a manual assertion. ECO:0005631 eco snadendla A type of DNAse footprinting evidence that is used in a manual assertion. ECO:SN true true fluorescence anisotropy evidence used in manual assertion 2016-05-06T15:45:40Z A type of fluorescence anisotropy evidence that is used in a manual assertion. ECO:0005632 eco snadendla true true A type of fluorescence anisotropy evidence that is used in a manual assertion. ECO:SN ferric uptake regulator titration assay evidence used in manual assertion 2016-05-06T15:49:18Z A type of ferric uptake regulator titration assay evidence that is used in a manual assertion. ECO:0005633 eco snadendla true A type of ferric uptake regulator titration assay evidence that is used in a manual assertion. ECO:SN true genomic systematic evolution of ligands by exponential amplification evidence used in manual assertion 2016-05-06T16:41:30Z A type of genomic systematic evolution of ligands by exponential amplification evidence that is used in a manual assertion. ECO:0005634 eco snadendla true true A type of genomic systematic evolution of ligands by exponential amplification evidence that is used in a manual assertion. ECO:SN genomic systematic evolution of ligands by exponential amplification evidence used in automatic assertion 2016-05-06T16:43:03Z A type of genomic systematic evolution of ligands by exponential amplification evidence that is used in an automatic assertion. ECO:0005635 eco snadendla true A type of genomic systematic evolution of ligands by exponential amplification evidence that is used in an automatic assertion. ECO:SN true green fluorescent protein reporter gene assay evidence used in manual assertion 2016-05-06T16:46:32Z A type of green fluorescent protein reporter gene assay evidence that is used in a manual assertion. ECO:0005636 eco snadendla true true A type of green fluorescent protein reporter gene assay evidence that is used in a manual assertion. ECO:SN green fluorescent protein reporter gene assay evidence used in automatic assertion 2016-05-06T16:48:29Z A type of green fluorescent protein reporter gene assay evidence that is used in an automatic assertion. ECO:0005637 eco snadendla A type of green fluorescent protein reporter gene assay evidence that is used in an automatic assertion. ECO:SN true true cell growth assay evidence used in manual assertion 2016-05-06T16:52:15Z A type of cell growth assay evidence that is used in a manual assertion. ECO:0005638 eco snadendla true true A type of cell growth assay evidence that is used in a manual assertion. ECO:SN cell growth assay evidence used in automatic assertion 2016-05-06T16:53:28Z A type of cell growth assay evidence that is used in an automatic assertion. ECO:0005639 eco snadendla true true A type of cell growth assay evidence that is used in an automatic assertion. ECO:SN glutathione S-transferase pull-down assay evidence used in manual assertion 2016-05-06T16:56:39Z A type of glutathione S-transferase pull-down assay evidence that is used in a manual assertion. ECO:0005640 eco snadendla true A type of glutathione S-transferase pull-down assay evidence that is used in a manual assertion. ECO:SN true true beta-glucuronidase reporter gene assay evidence used in manual assertion 2016-05-06T16:58:29Z A type of beta-glucuronidase reporter gene assay evidence that is used in a manual assertion. ECO:0005641 eco snadendla A type of beta-glucuronidase reporter gene assay evidence that is used in a manual assertion. ECO:SN true true heteronuclear single quantum coherence spectroscopy evidence used in manual assertion 2016-05-06T23:10:13Z A type of heteronuclear single quantum coherence spectroscopy evidence that is used in a manual assertion. ECO:0005642 eco snadendla A type of heteronuclear single quantum coherence spectroscopy evidence that is used in a manual assertion. ECO:SN true true hydroxyl-radical footprinting evidence used in manual assertion 2016-05-06T23:14:48Z A type of hydroxyl-radical footprinting evidence that is used in a manual assertion. ECO:0005643 eco snadendla true A type of hydroxyl-radical footprinting evidence that is used in a manual assertion. ECO:SN true immunoprecipitation evidence used in manual assertion 2016-05-06T23:20:49Z A type of immunoprecipitation evidence that is used in a manual assertion. ECO:0005644 eco snadendla A type of immunoprecipitation evidence that is used in a manual assertion. ECO:SN true true interferometric reflectance imaging sensor evidence used in manual assertion 2016-05-06T23:27:58Z A type of interferometric reflectance imaging sensor evidence that is used in a manual assertion. ECO:0005645 eco snadendla true true A type of interferometric reflectance imaging sensor evidence that is used in a manual assertion. ECO:SN interferometric reflectance imaging sensor evidence used in automatic assertion 2016-05-06T23:29:23Z A type of interferometric reflectance imaging sensor evidence that is used in an automatic assertion. ECO:0005646 eco snadendla A type of interferometric reflectance imaging sensor evidence that is used in an automatic assertion. ECO:SN true true isothermal titration calorimetry evidence used in manual assertion 2016-05-06T23:36:26Z A type of isothermal titration calorimetry evidence that is used in a manual assertion. ECO:0005647 eco snadendla true true A type of isothermal titration calorimetry evidence that is used in a manual assertion. ECO:SN luciferase reporter gene assay evidence used in manual assertion 2016-05-06T23:44:52Z A type of luciferase reporter gene assay evidence that is used in a manual assertion. ECO:0005648 eco snadendla true true A type of luciferase reporter gene assay evidence that is used in a manual assertion. ECO:SN machine learning prediction of motif instance evidence used in manual assertion 2016-05-06T23:51:30Z A type of machine learning prediction of motif instance evidence that is used in a manual assertion. ECO:0005649 eco snadendla true A type of machine learning prediction of motif instance evidence that is used in a manual assertion. ECO:SN true machine learning prediction of motif instance evidence used in automatic assertion 2016-05-06T23:54:00Z A type of machine learning prediction of motif instance evidence that is used in an automatic assertion. ECO:0005650 eco snadendla true A type of machine learning prediction of motif instance evidence that is used in an automatic assertion. ECO:SN true matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence used in automatic assertion 2016-05-06T23:57:30Z A type of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence that is used in an automatic assertion. ECO:0005651 eco snadendla 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 methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence used in manual assertion 2016-05-09T14:42:28Z A type of methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence that is used in a manual assertion. ECO:0005652 eco snadendla true A type of methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence that is used in a manual assertion. ECO:SN true northern assay evidence used in manual assertion 2016-05-09T14:48:03Z A type of northern assay evidence that is used in a manual assertion. ECO:0005653 eco snadendla A type of northern assay evidence that is used in a manual assertion. ECO:SN true true phylogenetic footprinting evidence used in manual assertion 2016-05-09T14:50:52Z A type of phylogenetic footprinting evidence that is used in a manual assertion. ECO:0005654 eco snadendla true A type of phylogenetic footprinting evidence that is used in a manual assertion. ECO:SN true phylogenetic footprinting evidence used in automatic assertion 2016-05-09T14:51:55Z A type of phylogenetic footprinting evidence that is used in an automatic assertion. ECO:0005655 eco snadendla A type of phylogenetic footprinting evidence that is used in an automatic assertion. ECO:SN true true premethylation interference footprinting evidence used in manual assertion 2016-05-09T14:55:25Z A type of premethylation interference footprinting evidence that is used in a manual assertion. ECO:0005656 eco snadendla A type of premethylation interference footprinting evidence that is used in a manual assertion. ECO:SN true true primer extension assay evidence used in manual assertion 2016-05-09T14:58:38Z A type of primer extension assay evidence that is used in a manual assertion. ECO:0005657 eco snadendla true A type of primer extension assay evidence that is used in a manual assertion. ECO:SN true position-specific scoring matrix motif search evidence used in manual assertion 2016-05-09T15:01:31Z A type of position-specific scoring matrix motif search evidence that is used in a manual assertion. ECO:0005658 eco snadendla true A type of position-specific scoring matrix motif search evidence that is used in a manual assertion. ECO:SN true position-specific scoring matrix motif search evidence used in automatic assertion 2016-05-09T15:02:31Z A type of position-specific scoring matrix motif search evidence that is used in an automatic assertion. ECO:0005659 eco snadendla A type of position-specific scoring matrix motif search evidence that is used in an automatic assertion. ECO:SN true true quantitative polymerase chain reaction evidence used in manual assertion 2016-05-09T15:09:01Z A type of quantitative polymerase chain reaction evidence that is used in a manual assertion. ECO:0005660 eco snadendla true true A type of quantitative polymerase chain reaction evidence that is used in a manual assertion. ECO:SN rapid amplification of cDNA ends polymerase chain reaction evidence used in manual assertion 2016-05-09T15:19:20Z A type of rapid amplification of cDNA ends polymerase chain reaction evidence that is used in a manual assertion. ECO:0005661 eco snadendla true A type of rapid amplification of cDNA ends polymerase chain reaction evidence that is used in a manual assertion. ECO:SN true regular expression motif search evidence used in manual assertion 2016-05-09T16:13:55Z A type of regular expression motif search evidence that is used in a manual assertion. ECO:0005662 eco snadendla A type of regular expression motif search evidence that is used in a manual assertion. ECO:SN true true regular expression motif search evidence used in automatic assertion 2016-05-09T16:15:03Z A type of regular expression motif search evidence that is used in an automatic assertion. ECO:0005663 eco snadendla true true A type of regular expression motif search evidence that is used in an automatic assertion. ECO:SN RNA sequencing assay evidence used in manual assertion 2016-05-09T16:18:35Z A type of RNA sequencing assay evidence that is used in a manual assertion. ECO:0005664 eco snadendla true A type of RNA sequencing assay evidence that is used in a manual assertion. ECO:SN true RNA sequencing assay evidence used in automatic assertion 2016-05-09T16:19:38Z A type of RNA sequencing assay evidence that is used in an automatic assertion. ECO:0005665 eco snadendla true true A type of RNA sequencing assay evidence that is used in an automatic assertion. ECO:SN S1 nuclease protection assay evidence used in manual assertion 2016-05-09T16:22:58Z A type of S1 nuclease protection assay evidence that is used in a manual assertion. ECO:0005666 eco snadendla true A type of S1 nuclease protection assay evidence that is used in a manual assertion. ECO:SN true site-directed mutagenesis evidence used in manual assertion 2016-05-09T16:29:13Z A type of site-directed mutagenesis evidence that is used in a manual assertion. ECO:0005667 eco snadendla true true A type of site-directed mutagenesis evidence that is used in a manual assertion. ECO:SN survival rate analysis evidence used in manual assertion 2016-05-09T16:31:08Z A type of survival rate analysis evidence that is used in a manual assertion. ECO:0005668 eco snadendla true A type of survival rate analysis evidence that is used in a manual assertion. ECO:SN true ultraviolet light footprinting evidence used in manual assertion 2016-05-09T16:33:44Z A type of ultraviolet light footprinting evidence that is used in a manual assertion. ECO:0005669 eco snadendla A type of ultraviolet light footprinting evidence that is used in a manual assertion. ECO:SN true true x-ray crystallography evidence used in manual assertion 2016-05-10T11:53:00Z A type of x-ray crystallography evidence that is used in a manual assertion. ECO:0005670 eco snadendla true A type of x-ray crystallography evidence that is used in a manual assertion. ECO:SN true x-ray crystallography evidence used in automatic assertion 2016-05-10T11:54:03Z A type of x-ray crystallography evidence that is used in an automatic assertion. ECO:0005671 eco snadendla A type of x-ray crystallography evidence that is used in an automatic assertion. ECO:SN true true xylE reporter gene assay evidence used in manual assertion 2016-05-10T11:57:15Z A type of xylE reporter gene assay evidence that is used in a manual assertion. ECO:0005672 eco snadendla true true A type of xylE reporter gene assay evidence that is used in a manual assertion. ECO:SN ad-hoc qualitative phenotype observation evidence 2016-05-10T12:57:41Z 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:0005673 eco snadendla 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 ad-hoc qualitative phenotype observation evidence used in manual assertion 2016-05-10T14:28:47Z A type of ad-hoc qualitative phenotype observation that is used in a manual assertion. ECO:0005674 eco snadendla true true A type of ad-hoc qualitative phenotype observation that is used in a manual assertion. ECO:SN ad-hoc quantitative phenotype observation evidence 2016-05-10T14:30:50Z 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:0005675 eco snadendla 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 ad-hoc quantitative phenotype observation evidence used in manual assertion 2016-05-10T14:34:50Z A type of ad-hoc quantitative phenotype observation evidence that is used in a manual assertion. ECO:0005676 eco snadendla true true A type of ad-hoc quantitative phenotype observation evidence that is used in a manual assertion. ECO:SN dilution assay evidence 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. spot assay critical dilution assay 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 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. enzyme assay evidence used in manual assertion A type of enzyme assay evidence that is used in a manual assertion. ECO:0005801 eco A type of enzyme assay evidence that is used in a manual assertion. ECO:SN true cell transfection experiment evidence used in manual assertion A type of cell transfection experiment evidence that is used in a manual assertion. ECO:0005802 eco true A type of cell transfection experiment evidence that is used in a manual assertion. ECO:SN motility assay evidence A type of direct assay evidence where the motility of a cell or cells is determined. ECO:0005803 eco A type of direct assay evidence where the motility of a cell or cells is determined. ECO:SN immunofluorescence evidence used in manual assertion A type of immunofluorescence evidence that is used in a manual assertion. ECO:0005804 eco A type of immunofluorescence evidence that is used in a manual assertion. ECO:SN yeast 2-hybrid evidence used in manual assertion A type of yeast 2-hybrid evidence that is used in a manual assertion. ECO:0005805 eco A type of yeast 2-hybrid evidence that is used in a manual assertion. ECO:SN