The Evidence & Conclusion Ontology (ECO) describes types of scientific evidence within the biological research domain that arise from laboratory experiments, computational methods, literature curation, or other means.
Evidence & Conclusion Ontology (ECO)
10:10:2022 16:21
eco
ECO (https://github.com/evidenceontology/evidenceontology) is released into the public domain under CC0 1.0 Universal (CC0 1.0). Anyone is free to copy, modify, or distribute the work, even for commercial purposes, without asking permission. Please see the Public Domain Dedication (https://creativecommons.org/publicdomain/zero/1.0/) for an easy-to-read description of CC0 1.0 or the full legal code (https://creativecommons.org/publicdomain/zero/1.0/legalcode) for more detailed information. To get a sense of why ECO is CC0 as opposed to licensed under CC-BY, please read this thoughtful discussion (https://github.com/OBOFoundry/OBOFoundry.github.io/issues/285) on the OBO Foundry GitHub site.
has GO evidence code
A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
example of usage
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
definition
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
term editor
formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
definition source
The 'term requester' can credit the person, organization or project who request the ontology term.,The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
IAO
ontology term requester
Grouping classes used by GO
go_groupings
GO biological process terms should be used in the GO with/from field
valid_with_biological_process
GO cellular component terms should be used in the GO with/from field
valid_with_cellular_component
Chemical entity IDs should be used in the GO with/from field
valid_with_chemical_entity
Gene IDs should be used in the GO with/from field
valid_with_gene
GO molecular function terms should be used in the GO with/from field
valid_with_molecular_function
Protein IDs should be used in the GO with/from field
valid_with_protein
Protein complex IDs should be used in the GO with/from field
valid_with_protein_complex
Transcript IDs should be used in the GO with/from field
valid_with_transcript
description
title
license
subset_property
auto-generated-by
created_by
creation_date
date
default-namespace
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
id
in_subset
is_inferred
saved-by
shorthand
a core relation that holds between a part and its whole
part_of
part of
part of
a core relation that holds between a whole and its part
has_part
has part
has part
realized in
realizes
preceded by
precedes
A relation connecting a piece of evidence to an assertion method, where that assertion method is supported by the evidence.
mchibucos
2010-12-09T05:00:20Z
ECO:9000000
eco
used_in
used_in
In the future we may use a more generic relation with weaker domain and range constraints taken from IAO, RO or OBI.
used_in
A relation connecting a piece of evidence to an assertion method, where that assertion method is supported by the evidence.
GOC:cjm
ECO:9000001
eco
uses
uses
uses
has measurement unit label
A (currently) primitive relation that relates an information artifact to an entity.
is about
m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q
is quality measurement of
inverse of the relation of is quality measurement of
is quality measured as
The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process
is_supported_by_data
The inverse property of is_specified_input_of
has_specified_input
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
is_specified_input_of
The inverse property of is_specified_output_of
has_specified_output
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
is_specified_output_of
This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
achieves_planned_objective
the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car.
has grain
This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
objective_achieved_by
A relation between an information content entity and a value specification that specifies its value.
has value specification
is a relationship between a process and a preceding occurrent that directly caused the later one to occur
process is result of
A relationship between two material entities that form a complex based on a selective, non-covalent interaction.
bound_to
a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
inheres in
a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
bearer of
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates in
a relation between a process and a continuant, in which the continuant is somehow involved in the process
has participant
A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.
is concretized as
A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.
concretizes
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
function of
a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
quality of
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
role of
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
has function
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
has quality
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
has role
a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
derives from
a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
derives into
a relation between two independent continuants, the location and the target, in which the target is entirely within the location
location of
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
located in
immediately preceded by
immediately precedes
regulates
regulates
negatively_regulates
negatively regulates
positively_regulates
positively regulates
temporal relation
is member of is a mereological relation between a item and a collection.
member of
has member is a mereological relation between a collection and an item.
has member
has measurement value
A relation between a value specification and a number that quantifies it.
has specified numeric value
A relation between a value specification and a literal.
has specified value
entity
An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
continuant
An entity that has temporal parts and that happens, unfolds or develops through time.
occurrent
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
independent continuant
spatial region
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
process
disposition
A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
realizable entity
quality
A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
specifically dependent continuant
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
role
site
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
generically dependent continuant
function
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
material entity
continuant fiat boundary
immaterial entity
An adenosine 5'-phosphate in which the 5'-phosphate is a triphosphate group. It is involved in the transportation of chemical energy during metabolic pathways.
ATP
Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc.
peptide
High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
deoxyribonucleic acid
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
molecular entity
cytochalasin
A member of the class of acrylamides that results from the formal condensation of acrylic acid with ammonia.
acrylamide
A chemical entity constituting the smallest component of an element having the chemical properties of the element.
atom
A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
nucleic acid
High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
ribonucleic acid
A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
macromolecule
double-stranded DNA
A pyrimidine 2'-deoxyribonucleoside compound having 5-bromouracil as the nucleobase.
5-bromo-2'-deoxyuridine
A synthetic radioactive isotope of chromium having a half-life of 27.7 days and decaying by electron capture with emission of gamma rays (0.32 MeV); it is used to label red blood cells for measurement of mass or volume, survival time, and sequestration studies, for the diagnosis of gastrointestinal bleeding, and to label platelets to study their survival.
chromium-51
Thymidine linked to the radioisotope tritium. Used to label DNA in the study of cellular and viral DNA synthesis.
tritiated thymidine
Any type of light microscopy assay where the specimen can be made to fluoresce (emit energy as visible light) by illuminating it with light of specific wavelengths. These specimens are called fluorophores.
fluorescence microscopy assay
Microscopy where the specimen is illuminated with visible light and a system of lenses is used to produce an image.
light microscopy assay
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
cell
cell
A cell in vitro that is or has been maintained or propagated as part of a cell culture.
cultured cell
A lymphocyte of B lineage that is capable of B cell mediated immunity.
A lymphocyte of B lineage with the phenotype CD19-positive, CD20-positive, and capable of B cell mediated immunity.
B cell
The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
neuron
neuron
A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin.
lymphocyte
A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.
experimentally modified cell in vitro
A leukocyte with a single non-segmented nucleus in the mature form.
mononuclear cell
A cell that is part of the nervous system.
neural cell
A complex of two or more molecular entities that are not covalently bound.
complex of molecular entities
A type of information that is used to support an assertion.
eco
evidence code
evidence_code
ECO:0000000
evidence
A type of information that is used to support an assertion.
ECO:MCC
A type of curator inference where conclusions are drawn based on the background scientific knowledge of the curator.
eco
ECO:0000001
inference from background scientific knowledge
A type of curator inference where conclusions are drawn based on the background scientific knowledge of the curator.
ECO:SN
A type of experimental evidence resulting from the direct measurement of some aspect of a biological feature.
ECO:0005006
eco
ECO:0000002
direct assay evidence
A type of experimental evidence resulting from the direct measurement of some aspect of a biological feature.
ECO:SN
A type of direct assay evidence based on reconstructing a biological sample from its disassociated state to its original state.
eco
ECO:0000003
reconstitution assay evidence
A type of direct assay evidence based on reconstructing a biological sample from its disassociated state to its original state.
ECO:KAV
PMID:26029343
A type of fractionation evidence where sub-cellular components are separated based on their physical properties such as density in a sucrose density gradient.
eco
cell fractionation
ECO:0000004
If using this term for Gene Ontology annotation, it would be used most typically for annotations to the cellular component ontology.
cell fractionation evidence
A type of fractionation evidence where sub-cellular components are separated based on their physical properties such as density in a sucrose density gradient.
ECO:KIM
TAIR:TED
A type of protein assay evidence where the catalytic activity of an enzyme is determined.
ECO:0005001
MI:0415
enzyme assay evidence
eco
enzyme assays
ECO:0000005
enzymatic activity assay evidence
A type of protein assay evidence where the catalytic activity of an enzyme is determined.
url:http://www.sciencedirect.com/science/article/pii/S2213020914000068
MI:0415
enzymatic study
A type of evidence that is the output of a scientific procedure performed to make a discovery, test a hypothesis, or demonstrate a known fact.
ECO:0005023
eco
ECO:0000006
experimental evidence
true
A type of evidence that is the output of a scientific procedure performed to make a discovery, test a hypothesis, or demonstrate a known fact.
OED:experiment
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
immunofluorescence
ECO:0000007
immunofluorescence evidence
A type of protein detection assay evidence where a fluorescently labeled antibody is used to detect the presence or localization of a biomolecule within a cell.
ECO:MCC
TAIR:TED
The 10 previously identified GlnR-regulated genes were all confirmed to be under GlnR control during nitrogen stress (i.e. differential expression in the wild type compared to the DeltaglnR mutant), but in addition a total of 392 genes were significantly up-regulated and 291 significantly down regulated (Additional file 1: Table S1). This indicates that GlnR mediates (directly or indirectly) the expression of over 680 genes.
A type of experimental evidence that is based on characterization of gene expression.
eco
ECO:0000008
Use this evidence type when the annotation is inferred from the timing or location of expression of a gene. It may be difficult to determine whether the expression pattern truly indicates that a gene plays a role in a given process.
expression pattern evidence
The 10 previously identified GlnR-regulated genes were all confirmed to be under GlnR control during nitrogen stress (i.e. differential expression in the wild type compared to the DeltaglnR mutant), but in addition a total of 392 genes were significantly up-regulated and 291 significantly down regulated (Additional file 1: Table S1). This indicates that GlnR mediates (directly or indirectly) the expression of over 680 genes.
PMID:23642041
A type of experimental evidence that is based on characterization of gene expression.
ECO:MCC
GO:IEP
A type of expression pattern evidence where abundance of a transcript is analyzed.
ECO:0000048
transcript expression level evidence
transcriptomics evidence
eco
ECO:0000009
transcript expression evidence
A type of expression pattern evidence where abundance of a transcript is analyzed.
ECO:RCT
In the BL21(DE3)(pJS429) cells, the levels of ClpP2s and VapC10 remained unchanged over a 2-hour period of translation arrest, but the VapB10 level showed to be decreased with a half-life (Figure 7C) similar to that observed in the strain BL21(DE3)(pJS883) (Figure 7B). These indicate that ClpXP2s could degrade VapB10 regardless of the presence or absence of VapC10.
A type of expression pattern evidence resulting from protein abundance quantification techniques.
ECO:0000046
protein expression level evidence
eco
ECO:0000010
protein expression evidence
In the BL21(DE3)(pJS429) cells, the levels of ClpP2s and VapC10 remained unchanged over a 2-hour period of translation arrest, but the VapB10 level showed to be decreased with a half-life (Figure 7C) similar to that observed in the strain BL21(DE3)(pJS883) (Figure 7B). These indicate that ClpXP2s could degrade VapB10 regardless of the presence or absence of VapC10.
PMID:24260461
A type of expression pattern evidence resulting from protein abundance quantification techniques.
NBK:22011
PMC:PMC4029002
url:http://www.informatics.jax.org/glossary/gain-of-function
url:https://www.thermofisher.com/us/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/pierce-protein-methods/overview-protein-expression-systems.html
A type of experimental phenotypic evidence resulting from the effect that a given gene has on another gene or genes, and the products.
TAIR:TED
eco
ECO:0000011
genetic interaction evidence
A type of experimental phenotypic evidence resulting from the effect that a given gene has on another gene or genes, and the products.
ECO:RCT
PMID:11822023
In addition, complementation of the ompR mutation in strain AR6 with plasmid pBR3 resulted in an increase in beta-galactosidase activity (1303 +- 80 Miller units), indicating that the His-tagged OmpR protein, expressed from the gene introduced in trans, was able to positively regulate flhDC expression.
Trans-complementation of fimR on pDL276 (pHR6) in strain DeltafimR harboring pfim(445 b)-cat restored wild-type pfim expression (Figure S1). Taken together, pfim is negatively regulated by FimR.
A type of genetic interaction evidence where a wild-type copy of the gene in question is inserted into a mutant cell to see if it restores the wild-type phenotype in the mutant background.
eco
functional complementation
ECO:0000012
functional complementation evidence
In addition, complementation of the ompR mutation in strain AR6 with plasmid pBR3 resulted in an increase in beta-galactosidase activity (1303 +- 80 Miller units), indicating that the His-tagged OmpR protein, expressed from the gene introduced in trans, was able to positively regulate flhDC expression.
PMID:20830609
Trans-complementation of fimR on pDL276 (pHR6) in strain DeltafimR harboring pfim(445 b)-cat restored wild-type pfim expression (Figure S1). Taken together, pfim is negatively regulated by FimR.
PMID:23823757
A type of genetic interaction evidence where a wild-type copy of the gene in question is inserted into a mutant cell to see if it restores the wild-type phenotype in the mutant background.
PMID:27403640
A type of functional complementation evidence resulting from the introduction of a transgene to prevent, or "rescue" an organism from a condition.
eco
ECO:0000013
transgenic rescue experiment evidence
A type of functional complementation evidence resulting from the introduction of a transgene to prevent, or "rescue" an organism from a condition.
url:http://www.mdpi.com/1420-3049/19/9/13932/pdf
url:http://www.nature.com/gt/journal/v11/n15/full/3302282a.html
Indeed, the GroEL protein appears to be more abundant in the LM3 wild type strain compared to the LM3-2 mutant strain, suggesting the involvement of the CcpA protein in the positive regulation of its expression.
A type of experimental phenotypic evidence in which an observable phenotypic difference results from a change or mutation in DNA.
eco
ECO:0000015
Note that mutations need not be negative. Changes to DNA sequence (mutations) may be detrimental, have no impact, or be beneficial.
The allele that encodes the phenotype most common in a particular natural population is referred to as the wild type allele, while any other form of that allele is known as the mutant form.
mutant phenotype evidence
Indeed, the GroEL protein appears to be more abundant in the LM3 wild type strain compared to the LM3-2 mutant strain, suggesting the involvement of the CcpA protein in the positive regulation of its expression.
PMID:17129387
A type of experimental phenotypic evidence in which an observable phenotypic difference results from a change or mutation in DNA.
GO:IMP
A type of mutant phenotype evidence where a phenotype is associated with altered gene product which lacks the molecular function of the wild-type gene.
eco
ECO:0000016
loss-of-function mutant phenotype evidence
A type of mutant phenotype evidence where a phenotype is associated with altered gene product which lacks the molecular function of the wild-type gene.
SO:0002054
A type of experimental phenotypic evidence where a transgenic strain carrying the construct of a promoter cDNA fusion in which a gene of interest is driven by a defined promoter or enhancer is ectopically expressed in the defined pattern to characterize potential cellular properties and functions of a protein of interest.
eco
analysis of overexpression/ectopic expression phenotype
ECO:0000017
ectopic expression evidence
A type of experimental phenotypic evidence where a transgenic strain carrying the construct of a promoter cDNA fusion in which a gene of interest is driven by a defined promoter or enhancer is ectopically expressed in the defined pattern to characterize potential cellular properties and functions of a protein of interest.
PMID:10948520
PMID:19301619
A type of mutant phenotype evidence where a phenotype is observed while expressing an anti-sense version of a gene product in a wild-type (for that gene product) background.
eco
anti-sense experiments
ECO:0000018
anti-sense experiment evidence
A type of mutant phenotype evidence where a phenotype is observed while expressing an anti-sense version of a gene product in a wild-type (for that gene product) background.
ECO:SN
A type of mutant phenotype evidence where an RNA construct is introduced into a cell and the expression of the gene bearing its complementary sequence is suppressed.
eco
RNAi experiment
ECO:0000019
RNAi evidence
A type of mutant phenotype evidence where an RNA construct is introduced into a cell and the expression of the gene bearing its complementary sequence is suppressed.
ECO:MCC
A type of direct assay evidence based on the inhibition of the molecular function of a protein.
specific protein inhibition evidence
eco
ECO:0000020
protein inhibition evidence
A type of direct assay evidence based on the inhibition of the molecular function of a protein.
ECO:MCC
A type of experimental evidence that is based on characterization of an interaction between a gene product and another molecule.
ECO:0005025
MI:0045
eco
ECO:0000021
Molecules interacted with might include protein, nucleic acid, ion, or complex.
physical interaction evidence
A type of experimental evidence that is based on characterization of an interaction between a gene product and another molecule.
ECO:SN
MI:0045
experimental interaction detection
A type of physical interaction evidence where a cellular component subunit is isolated as part of purification of its larger complex.
MI:0025
eco
co-purification
ECO:0000022
co-purification evidence
A type of physical interaction evidence where a cellular component subunit is isolated as part of purification of its larger complex.
TAIR:TED
MI:0025
copurification
A type of physical interaction evidence that depends on the strength of the interaction between two entities.
MI:0400
ligand binding evidence
eco
ECO:0000023
affinity evidence
A type of physical interaction evidence that depends on the strength of the interaction between two entities.
ECO:MCC
MI:0400
MI:0400
affinity technology
A type of affinity evidence resulting from the binding of a molecule to a protein or protein complex.
eco
ECO:0000024
protein binding evidence
A type of affinity evidence resulting from the binding of a molecule to a protein or protein complex.
GO:0005515
url:https://en.wikipedia.org/wiki/Mutation
A type of protein binding 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.
DisProt:FedericaQuaglia
MI:0090
bait-prey protein pull-down evidence
eco
ECO:0000025
Typically enzymes which confer resistance to antibiotics, such as Dihydrofolate reductase or Beta-lactamase, or proteins that give colorimetric or fluorescent signals are used. The Bait protein is generally the protein under study and the methods are readily adaptable to highthroughput mode.
bait-prey hybrid interaction evidence
A type of protein binding 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
MI:0090
MI:0090
protein complementation assay
A type of experimental genomic evidence resulting from a process in which single stranded nucleic acids are allowed to interact so that complexes, or hybrids, are formed by molecules with sufficiently similar, complementary sequences.
eco
ECO:0000026
This term has been made obsolete with the clean up of experimental genomic evidence branch.
nucleic acid hybridization evidence
true
A type of experimental genomic evidence resulting from a process in which single stranded nucleic acids are allowed to interact so that complexes, or hybrids, are formed by molecules with sufficiently similar, complementary sequences.
OBI:0302903
The secondary structure of VapC10 (Figure S2), predicted with the 3DJIGSAW prediction tool [36] and the DALI server [37], exhibited homology with several well studied VapC toxins, such as the first PIN domain structure for the protein PAE2754 from the archae bacterium Pyrobaculum aerophilum (30).
A type of similarity evidence based on structural similarity of an annotated gene or gene product to another gene or group of genes.
eco
ECO:0000027
For GO annotation, in the case of a single gene, an accession for the related gene's sequence is entered in the evidence_with field.
structural similarity evidence
The secondary structure of VapC10 (Figure S2), predicted with the 3DJIGSAW prediction tool [36] and the DALI server [37], exhibited homology with several well studied VapC toxins, such as the first PIN domain structure for the protein PAE2754 from the archae bacterium Pyrobaculum aerophilum (30).
PMID:24260461
A type of similarity evidence based on structural similarity of an annotated gene or gene product to another gene or group of genes.
ECO:MCC
TAIR:TED
A CRP box-like sequence was found in the promoter-proximate region of sycO-ypkA-yopJ [4], indicating the direct association of CRP with the sycO-ypkA-yopJ promoter region.
To identify further CopR target genes, the binding motif TGAAGATTTnnTGAAGATTT was used to search for similar sequences in the whole C. glutamicum genome using the ERGO (TM) bioinformatics suite (Integrated Genomics, Illinois, USA) allowing four mutations, no deletions and no insertions. 46 hits were found, but only in six cases the putative CopR binding site was located in intergenic regions up to 200 bp upstream of the start codon of the neighbouring gene (cg1336, cg2976, cg3187, cg3337, cg3357 and cg0414).
A type of match to sequence model evidence that is based on the presence of a recognized domain or motif in a gene product's (usually protein) primary sequence.
eco
recognized domains
ECO:0000028
motif similarity evidence
A CRP box-like sequence was found in the promoter-proximate region of sycO-ypkA-yopJ [4], indicating the direct association of CRP with the sycO-ypkA-yopJ promoter region.
PMID:19703315
To identify further CopR target genes, the binding motif TGAAGATTTnnTGAAGATTT was used to search for similar sequences in the whole C. glutamicum genome using the ERGO (TM) bioinformatics suite (Integrated Genomics, Illinois, USA) allowing four mutations, no deletions and no insertions. 46 hits were found, but only in six cases the putative CopR binding site was located in intergenic regions up to 200 bp upstream of the start codon of the neighbouring gene (cg1336, cg2976, cg3187, cg3337, cg3357 and cg0414).
PMID:21799779
A type of match to sequence model evidence that is based on the presence of a recognized domain or motif in a gene product's (usually protein) primary sequence.
ECO:SN
A type of match to sequence model evidence resulting from a positive match of a protein, or set of proteins to a predictive model (signature) in the InterPro database.
eco
ECO:0000029
match to InterPro member signature evidence
A type of match to sequence model evidence resulting from a positive match of a protein, or set of proteins to a predictive model (signature) in the InterPro database.
PMC:PMC2686546
url:http://www.ncbi.nlm.nih.gov/mesh?term=Nucleic+Acid+Hybridization
ISA
A type of BLAST evidence that is used in a manual assertion.
eco
curated BLAST analysis
ECO:0000030
BLAST evidence used in manual assertion
true
A type of BLAST evidence that is used in a manual assertion.
ECO:MCC
ISA
A type of protein BLAST evidence that is used in a manual assertion.
GO_REF:0000012
GO_REF:0000027
eco
curated protein BLAST analysis
ECO:0000031
protein BLAST evidence used in manual assertion
true
A type of protein BLAST evidence that is used in a manual assertion.
ECO:SN
GO_REF:0000012
Pairwise alignment (TIGR)
GO_REF:0000027
BLAST search criteria for ISS assignment in PAMGO_GAT
ISA
A type of nucleotide BLAST evidence that is used in a manual assertion.
eco
curated nucleic acid BLAST analysis
ECO:0000032
nucleotide BLAST evidence used in manual assertion
true
A type of nucleotide BLAST evidence that is used in a manual assertion.
ECO:SN
A type of author statement in which the author makes a statement that is not supported by information in that particular publication, but rather can be traced to a reference cited by that publication.
eco
traceable author statement
ECO:0000033
author statement supported by traceable reference
A type of author statement in which the author makes a statement that is not supported by information in that particular publication, but rather can be traced to a reference cited by that publication.
ECO:RCT
GO:TAS
A type of author statement that is not associated with results presented or a cited reference.
eco
non-traceable author statement
ECO:0000034
author statement without traceable support
A type of author statement that is not associated with results presented or a cited reference.
ECO:SN
A type of curator inference that results when research finds no evidence information in the scientific literature, at reference databases, or from other resources.
eco
ECO:0000035
An assertion of "no evidence data found" carries the assumption that a more-or-less exhaustive search has been conducted.
no evidence data found
A type of curator inference that results when research finds no evidence information in the scientific literature, at reference databases, or from other resources.
ECO:SN
eco
ECO:0000037
The evidence not_recorded appears in some legacy annotations; it should not be used for new annotations.
not_recorded
true
A type of functional complementation evidence resulting from the introduction of nucleic acids, which are not permanently incorporated into the genome, to temporarily prevent, or "rescue" an organism from a condition.
eco
ECO:0000038
transient rescue experiment evidence
A type of direct assay evidence resulting from determining the presence, abundance, structure, function, or activity of proteins.
ECO:0005022
eco
ECO:0000039
protein assay evidence
true
A type of direct assay evidence resulting from determining the presence, abundance, structure, function, or activity of proteins.
PMID:18429326
A type of affinity evidence resulting from quantitation of the analyte which depends on the reaction of an antigen (analyte) and an antibody.
ECO:0005018
eco
ECO:0000040
immunological assay evidence
A type of affinity evidence resulting from quantitation of the analyte which depends on the reaction of an antigen (analyte) and an antibody.
ERO:0001362
url:http://www.ncbi.nlm.nih.gov/books/NBK21589/,http://cores.ucsf.edu/protein-assay.html
A type of evidence resulting from comparing likeness of distinct biological entities.
IS
eco
inferred from similarity
ECO:0000041
similarity evidence
A type of evidence resulting from comparing likeness of distinct biological entities.
ECO:SN
A type of mutant phenotype evidence resulting from an altered gene product which possesses a new molecular function or a new pattern of gene expression.
gain-of-function mutant phenotype evidence
eco
ECO:0000042
gain-of-function mutant phenotypic evidence
A type of mutant phenotype evidence resulting from an altered gene product which possesses a new molecular function or a new pattern of gene expression.
SO:0002053
url:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3614608/
A type of similarity based on biomolecular sequence.
eco
ECO:0000044
A sequence similarity analysis may involve a gene or a gene product, and it could be based on similarity to a single other gene or to a group of other genes.
sequence similarity evidence
A type of similarity based on biomolecular sequence.
ECO:MCC
TAIR:TED
A type of protein expression evidence that accounts for the position of RNA translation to a protein product ranging in scale from differing tissues to regions of an anatomical structure.
eco
ECO:0000045
spatial pattern of protein expression evidence
A type of transcript expression evidence that accounts for the position of transcription ranging in scale from the position of genes on the chromosome to differing tissues to regions of an anatomical structure.
eco
ECO:0000047
spatial pattern of transcript expression evidence
A type of expression pattern evidence that is based on the expression pattern of a reporter gene.
eco
expression of a reporter gene
ECO:0000049
reporter gene assay evidence
A type of expression pattern evidence that is based on the expression pattern of a reporter gene.
TAIR:TED
A type of experimental phenotypic evidence based on an authors phenotypic description of a species (or higher-level group), which explicitly references an observation made of a voucher specimen (a specimen with a permanent museum catalog).
IVS
voucher specimen analysis evidence
eco
ECO:0000050
voucher specimen phenotypic analysis evidence
A type of experimental phenotypic evidence based on an authors phenotypic description of a species (or higher-level group), which explicitly references an observation made of a voucher specimen (a specimen with a permanent museum catalog).
TAIR:TED
A type of similarity based on genotype without respect to expression.
IGTS
eco
inferred from genetic similarity
ECO:0000051
A genetic similarity analysis might consider genetic markers, polymorphisms, alleles, or other characteristics sometimes considered as part of the field of traditional genetics. Although an attempt has been made to treat as distinct the concepts of "genetic", "genotypic", "genomic", and "sequence", there is considerable overlap in usage throughout the field of biology.
genetic similarity evidence
A type of similarity based on genotype without respect to expression.
ECO:MCC
PhenoScape:IGTS
A type of genetic interaction evidence resulting from a second mutation that either suppresses or enhances the phenotype expressed from an original mutation.
TAIR:TED
suppressor/enhancer interaction evidence
eco
'traditional' genetic interactions (e.g. suppressors, synthetic lethals)
ECO:0000052
suppressor/enhancer interaction phenotypic evidence
A type of genetic interaction evidence resulting from a second mutation that either suppresses or enhances the phenotype expressed from an original mutation.
url:http://biorxiv.org/content/early/2015/10/03/021592
url:http://www.wormbook.org/chapters/www:geneticsuppression/geneticsuppression.html
IEA
A type of automatically integrated combinatorial evidence that is used in an automatic assertion.
ECO:0000246
TAIR:TED
eco
ECO:0000053
Combinatorial analyses could include experimental or computational results. Examples include: (i) large-scale experiment such as a genome-wide two-hybrid or genome-wide synthetic interactions; (ii) integration of large-scale data sets of various types; and (iii) text-based-computation, e.g. text-mining. For simple sequence comparisons, one should use the sequence similarity analysis evidence type. For microarray results alone, expression pattern analysis is appropriate; whereas, large-scale computational analysis should be used when microarray results are combined with the results of other types of large-scale experiments.
automatically integrated combinatorial evidence used in automatic assertion
true
true
A type of automatically integrated combinatorial evidence that is used in an automatic assertion.
ECO:MCC
ECO:RCT
In the hns slyA double mutant, hlyE expression was twofold greater than in the parent, and slightly higher than the hns single mutant, suggesting that slyA has a small negative effect on hlyE expressionin the absence of H-NS.
A type of mutant phenotype evidence resulting from an experiment typically constructed to determine if two different genes have an observable genetic interaction (functional connection) as the result of a mutation occurring in the alleles of the two genes of interest.
double mutant phenotype evidence
eco
double mutant analysis
ECO:0000054
double mutant phenotypic evidence
In the hns slyA double mutant, hlyE expression was twofold greater than in the parent, and slightly higher than the hns single mutant, suggesting that slyA has a small negative effect on hlyE expressionin the absence of H-NS.
PMID:17892462
A type of mutant phenotype evidence resulting from an experiment typically constructed to determine if two different genes have an observable genetic interaction (functional connection) as the result of a mutation occurring in the alleles of the two genes of interest.
ECO:RCT
PMID:18305163
eco
ECO:0000055
This general 'array experiment' term should not be used - replace with the specific type of array (e.g. ECO:0000097, ECO:0000062, ECO:0000104, etc.)
array experiment evidence
true
A type of genetic interaction evidence resulting from the suppression of one allelic effect by an allele at another genetic locus.
epistatic interaction evidence
eco
epistatic interactions
ECO:0000056
Epistasis' can be used in different contexts in different areas of genetics. It is sometimes used to mean 'genetic interaction', whereas other times it may be specific to mutations that block the effects of other mutations.
epistatic interaction phenotypic evidence
A type of genetic interaction evidence resulting from the suppression of one allelic effect by an allele at another genetic locus.
PMID:18852697
A type of similarity based on the expression of a genotype in an environment.
IPTS
phenotype similarity evidence
eco
inferred from phenotypic similarity
ECO:0000057
Phenotype is defined as the outcome of the expression of a genotype in a given environment. A comparison might involve whole organisms or sub-parts of organisms.
phenotypic similarity evidence
A type of similarity based on the expression of a genotype in an environment.
ECO:MCC
PhenoScape:IPTS
S. lividans AdpA directly regulates at least the six AdpA-dependent genes listed above and identified by microarrays and qRT-PCR analysis.
To identify the regulon of the response regulator CopR, the transcriptome of the DeltacopRS deletion mutant was compared to that of the wild type using DNA microarrays. For cells grown in standard CGXII medium (1.25 microM CuSO4), no significant gene expression differences were observed, indicating that the CopRS two-component system is not active under this condition (data not shown).
A type of transcript expression evidence resulting from simultaneous profiling of the expression levels of thousands of genes in a single experiment allowing analysis of genes and their networks.
ECO:0000356
differential gene expression evidence from microarray experiment
eco
ECO:0000058
expression microarray evidence
S. lividans AdpA directly regulates at least the six AdpA-dependent genes listed above and identified by microarrays and qRT-PCR analysis.
PMID:24694298
To identify the regulon of the response regulator CopR, the transcriptome of the DeltacopRS deletion mutant was compared to that of the wild type using DNA microarrays. For cells grown in standard CGXII medium (1.25 microM CuSO4), no significant gene expression differences were observed, indicating that the CopRS two-component system is not active under this condition (data not shown).
PMID:21799779
A type of transcript expression evidence resulting from simultaneous profiling of the expression levels of thousands of genes in a single experiment allowing analysis of genes and their networks.
url:http://www.illumina.com/techniques/microarrays/gene-expression-arrays.html
url:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2435252/
A type of experimental evidence that is based on an observable characteristic trait, which is the result of the expression of an organisms genotype in an environment.
ECO:0000014
ECO:0005017
eco
inferred from phenotype
ECO:0000059
Observable characteristic traits can be morphology, development, behavior, biochemical or physiological properties, etc.
experimental phenotypic evidence
A type of experimental evidence that is based on an observable characteristic trait, which is the result of the expression of an organisms genotype in an environment.
ECO:SN
A type of phenotypic similarity evidence based on the similarity of stucture locations or arrangements.
IPS
eco
ECO:0000060
positional similarity evidence
A type of phenotypic similarity evidence based on the similarity of stucture locations or arrangements.
TAIR:TED
A type of phenotypic evidence that is based on a gene product that is associated with a quantitative trait locus, but has not been cloned.
QTL analysis evidence
eco
quantitative trait analysis
ECO:0000061
quantitative trait analysis evidence
A type of phenotypic evidence that is based on a gene product that is associated with a quantitative trait locus, but has not been cloned.
TAIR:TED
A type of expression microarray evidence where expression level is quantified by sample biotin-labeled cRNA (transcribed from an unknown RNA sample) hybridized to DNA oligonuclotides immoblized on a solid surface.
genomic microarray evidence
eco
ECO:0000062
cRNA to DNA expression microarray evidence
A type of expression microarray evidence where expression level is quantified by sample biotin-labeled cRNA (transcribed from an unknown RNA sample) hybridized to DNA oligonuclotides immoblized on a solid surface.
url:https://link.springer.com/chapter/10.1007/978-94-017-9716-0_30
A type of phenotypic similarity evidence based on the similarity of the histological makeup of structures.
ICS
eco
ECO:0000063
compositional similarity evidence
A type of phenotypic similarity evidence based on the similarity of the histological makeup of structures.
TAIR:TED
A type of functional complementation evidence that is based on the insertion of a wild-type copy of a gene into a heterologous organism, with the mutation occurring in a homologous gene.
eco
functional complementation in heterologous system
ECO:0000064
functional complementation in heterologous system evidence
A type of functional complementation evidence that is based on the insertion of a wild-type copy of a gene into a heterologous organism, with the mutation occurring in a homologous gene.
TAIR:TED
A type of bait-prey hybrid interaction evidence that is based on a protein-DNA complementation assay where a single promoter acts as bait and is screened against a library of prey transcription factors.
MI:0432
eco
yeast one-hybrid assay
ECO:0000066
The assay involves screening a library of candidate proteins for the ability bind to a target, cis-regulatory element or any other short, DNA binding sequence placed 5' to a yeast reporter gene (TAIR:TED).
yeast one-hybrid evidence
A type of bait-prey 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
MI:0432
TAIR:TED
MI:0432
one hybrid
A type of phenotypic similarity evidence based on the similarity of embryological or post-embryonic orgin of structures.
IDS
eco
ECO:0000067
developmental similarity evidence
A type of phenotypic similarity evidence based on the similarity of embryological or post-embryonic orgin of structures.
TAIR:TED
A type of bait-prey hybrid interaction evidence that is based on detection of protein-protein interaction by activation of a yeast reporter gene after a bait protein fused to a DNA-binding domain (which has been transfected into a yeast cell) is used to screen a cDNA library of clones fused to an activation domain.
eco
yeast two-hybrid assay
ECO:0000068
yeast 2-hybrid evidence
A type of bait-prey hybrid interaction evidence that is based on detection of protein-protein interaction by activation of a yeast reporter gene after a bait protein fused to a DNA-binding domain (which has been transfected into a yeast cell) is used to screen a cDNA library of clones fused to an activation domain.
PMID:12734586
A type of in vitro methylation assay evidence where methylation-sensitive restriction enzymes are utilized to compare differential methylation between two samples by first shearing DNA, followed by end-blunting, ligation of linkers, methylation sensitive restriction, PCR using linker primers, dye labeling and relative quantification of methylated DNA fragments by two-colored array hybridization to a CpG island microarray for visual assessment.
ECO:0000065
CpG island microarray evidence
eco
ECO:0000069
Color is indicative of methylation status - be it hypo- (pseudo-green), hyper- (pseudo-red), or equal methylation (pseudo-yellow).
differential methylation hybridization evidence
A type of in vitro methylation assay evidence where methylation-sensitive restriction enzymes are utilized to compare differential methylation between two samples by first shearing DNA, followed by end-blunting, ligation of linkers, methylation sensitive restriction, PCR using linker primers, dye labeling and relative quantification of methylated DNA fragments by two-colored array hybridization to a CpG island microarray for visual assessment.
PMID:18987809
A type of immunoprecipitation evidence that involves precipitating two or more proteins via binding to an antibody specific to a single protein, followed by protein identification.
MI:0019
eco
co-immunoprecipitation
ECO:0000070
If performing GO annotation, the interacting protein is referenced in the evidence_with column.
co-immunoprecipitation evidence
A type of immunoprecipitation evidence that involves precipitating two or more proteins via binding to an antibody specific to a single protein, followed by protein identification.
ECO:MCC
MI:0019
coimmunoprecipitation
A type of phenotypic similarity evidence based on the similarity of shape, structure, or configuration in structures.
IMS
eco
ECO:0000071
morphological similarity evidence
A type of phenotypic similarity evidence based on the similarity of shape, structure, or configuration in structures.
TAIR:TED
eco
ECO:0000072
Sos-recruitment assay evidence
true
A type of experimental evidence that is based on the characterization of an attribute of the genome underlying a gene product.
inferred from genomic analysis
eco
ECO:0000073
This term has been made obsolete with the clean up of experimental genomic evidence branch.
experimental genomic evidence
true
A type of experimental evidence that is based on the characterization of an attribute of the genome underlying a gene product.
ECO:MCC
A type of protein fragment functional complementation evidence that is based on detection of protein-protein interaction between a bait and prey protein by in vivo reconstitution of split-ubiquitin (when bait and prey interact) and release of a reporter protein.
MI:0112
eco
split-ubiquitin assay
ECO:0000074
The bait protein is fused to the C-terminal ubiquitin (Cub) domain followed by a reporter protein, and the prey protein is fused to a mutated N terminal ubiquitin (NubG) domain. If bait and prey interact, their interaction brings the NubG and Cub domains close enough to reconstitute.TAIR:TED
split-ubiquitin functional complementation evidence
A type of protein fragment functional complementation evidence that is based on detection of protein-protein interaction between a bait and prey protein by in vivo reconstitution of split-ubiquitin (when bait and prey interact) and release of a reporter protein.
PMID:15064465
MI:0112
ubiquitin reconstruction
A type of phenotypic similarity evidence that is based on the categorization of genes by the similarity of expression profiles.
IGES
eco
ECO:0000075
gene expression similarity evidence
A type of phenotypic similarity evidence that is based on the categorization of genes by the similarity of expression profiles.
PMID:19958477
A type of physical interaction evidence that is based on detection of protein-protein interactions by separation of target proteins by SDS-PAGE which are blotted to a membrane, followed by denaturation and renaturation, probing with purified bait proteins, and detection of the target-bait complexes.
MI:0047
eco
far-Western analysis
ECO:0000076
The interacting protein is referenced in the evidence_with column.
far-Western blotting evidence
A type of physical interaction evidence that is based on detection of protein-protein interactions by separation of target proteins by SDS-PAGE which are blotted to a membrane, followed by denaturation and renaturation, probing with purified bait proteins, and detection of the target-bait complexes.
PMID:18079728
A type of in vitro methylation assay evidence resulting from initial modification of DNA by sodium bisulfite, converting all unmethylated cytosines to uracil, and subsequent amplification with primers specific for methylated versus unmethylated DNA.
MS-PCR
MSP
methylation-specific PCR evidence
eco
ECO:0000077
The product is the amplification of existing sequences - i.e. more DNA that can be further processed e.g. sequenced, DNA fingerprinting.
methylation-specific polymerase chain reaction evidence
A type of in vitro methylation assay evidence resulting from initial modification of DNA by sodium bisulfite, converting all unmethylated cytosines to uracil, and subsequent amplification with primers specific for methylated versus unmethylated DNA.
PMC:PMC38513
PMID:8790415
A type of DNA detection assay evidence that is based on detection of a specific DNA sequence by hybridization of labeled probes to any immobilized DNA fragment with sequence similarity.
Southern blot
eco
Southern blotting
ECO:0000078
The DNA fragments are prepared through gel electrophoresis then transferred to a filter membrane.
southern hybridization evidence
A type of DNA detection assay evidence that is based on detection of a specific DNA sequence by hybridization of labeled probes to any immobilized DNA fragment with sequence similarity.
PMID:18432697
A type of affinity evidence that results from separation of biochemical mixtures by selective binding of a compound to an immobilized compound on a polymeric matrix, subsequent removal of unattached components, and then displacement of the bound compound.
MI:0004
eco
affinity chromatography
ECO:0000079
"Used when an annotation is made based on affinity chromatography, which is a selective separation technique by which a compound (e.g., an antibody) is immobilized on a polymeric matrix and used to bind selectively other compounds. Following removal of the unattached components, the bound compound is displaced by changing the concentration of protons, salts, or cofactors in the eluent" (from original definition by TAIR:TED). Types of highly specific interaction might include those of antigen and antibody, enzyme and substrate, or receptor and ligand.
affinity chromatography evidence
A type of affinity evidence that results from separation of biochemical mixtures by selective binding of a compound to an immobilized compound on a polymeric matrix, subsequent removal of unattached components, and then displacement of the bound compound.
ECO:MCC
TAIR:TED
MI:0004
affinity chromatography technology
Comparative phylogenomics along with MLST (multilocus sequence typing) and whole genome sequecing has shown that ribotype 078 lineage is different than other C. difficile lineages [22].
A type of similarity that indicates common ancestry.
IP
eco
ECO:0000080
phylogenetic evidence
Comparative phylogenomics along with MLST (multilocus sequence typing) and whole genome sequecing has shown that ribotype 078 lineage is different than other C. difficile lineages [22].
PMID:24713082
A type of similarity that indicates common ancestry.
ECO:MCC
PhenoScape:IP
IP
PhenoScape:IP
A type of motif similarity evidence that is based on detection of a targeting sequence in the primary sequence of a protein through computational prediction and/or a manual examination of the sequence.
eco
targeting sequence prediction
ECO:0000081
targeting sequence prediction evidence
A type of motif similarity evidence that is based on detection of a targeting sequence in the primary sequence of a protein through computational prediction and/or a manual examination of the sequence.
ECO:RCT
TAIR:TED
A type of experimental genomic evidence where DNA polymerase is used to synthesize new strand of DNA complementary to the offered template strand.
PCR evidence
eco
ECO:0000082
This term has been made obsolete because PCR is not evidence. The children have been appropriately placed under other parents.
polymerase chain reaction evidence
true
A type of experimental genomic evidence where DNA polymerase is used to synthesize new strand of DNA complementary to the offered template strand.
OBI:0000415
A type of motif similarity evidence that is based on detection of one, or more, transmembrane domains in the primary sequence of a protein through computational prediction and/or a manual examination of the sequence.
eco
transmembrane domain prediction
ECO:0000083
transmembrane domain prediction evidence
A type of motif similarity evidence that is based on detection of one, or more, transmembrane domains in the primary sequence of a protein through computational prediction and/or a manual examination of the sequence.
ECO:RCT
TAIR:TED
A type of genomic context evidence in which a gene product's identity is supported on the basis of the identity of neighboring genes.
mgiglio
2009-03-20T11:55:18Z
GO_REF:0000025
inferred from genome cluster
eco
ICL
ECO:0000084
Genomic cluster analyses include synteny and operon structure.
gene neighbors evidence
A type of genomic context evidence in which a gene product's identity is supported on the basis of the identity of neighboring genes.
ECO:MCC
GOC:MG
GO_REF:0000025
Operon structure as IGC evidence
A type of protein binding evidence that involves precipitation of a multivalent antigen by a bivalent antibody for protein isolation.
CollecTF
eco
immunoprecipitation
ECO:0000085
Transcription factors isolated in this way can be incubated with a radiolabeled probe to demonstrate binding.
immunoprecipitation evidence
A type of protein binding evidence that involves precipitation of a multivalent antigen by a bivalent antibody for protein isolation.
ECO:MCC
ECO:SW
TAIR:TED
A type of in vitro methylation assay evidence resulting from a genome-wide estimate of DNA methylation by differential enzymatic digestion of genomic DNA with methylation-sensitive and methylation-insensitive isoschizomers, followed by restrained PCR amplification of sequences methylated at both ends and resolving the PCR products in a denaturing polyacrylamide-sequencing gel to generate fingerprints that consist of multiple anonymous bands that represent the DNA methylome of the cell.
AIMS
eco
ECO:0000086
The bands can be individually isolated and characterized which leads to the identification of hypo- and hypermethylation events.
amplification of intermethylated sites evidence
A type of in vitro methylation assay evidence resulting from a genome-wide estimate of DNA methylation by differential enzymatic digestion of genomic DNA with methylation-sensitive and methylation-insensitive isoschizomers, followed by restrained PCR amplification of sequences methylated at both ends and resolving the PCR products in a denaturing polyacrylamide-sequencing gel to generate fingerprints that consist of multiple anonymous bands that represent the DNA methylome of the cell.
PMID:18987810
url:https://www.ncbi.nlm.nih.gov/probe/docs/techpcr/
A type of microscopy evidence where antibodies are used to detect the location of molecules or other structures within cells or tissues.
eco
immunolocalization
ECO:0000087
immunolocalization evidence
A type of microscopy evidence where antibodies are used to detect the location of molecules or other structures within cells or tissues.
ECO:MCC
ECO:SN
A type of curator inference that is based on a combination of experimental evidences or existing models of that system in a related species used for the reconstruction of a biological system.
mgiglio
2009-03-20T12:00:17Z
eco
ISR
inferred from system reconstruction
ECO:0000088
The biological system in question might be a multi-step process or pathway or a physical complex comprising several components. The components in the experimental evidence can come from the same species or a mix of species. The experimental evidences may be only partial or weak.
biological system reconstruction evidence
A type of curator inference that is based on a combination of experimental evidences or existing models of that system in a related species used for the reconstruction of a biological system.
ECO:MCC
GOC:mg
A type of DNA detection assay evidence resulting from the use of restriction enzymes for direct end-labeling of DNA (creating landmarks), followed by high-resolution two-dimensional electrophoresis to visualize the landmarks.
SIB:PG
ECO:0001125
RLGS evidence
restriction landmark genome scanning evidence
eco
ECO:0000089
restriction landmark genomic scanning evidence
A type of DNA detection assay evidence resulting from the use of restriction enzymes for direct end-labeling of DNA (creating landmarks), followed by high-resolution two-dimensional electrophoresis to visualize the landmarks.
PMID:8388788
A type of immunolocalization evidence where the antibodies are labeled with colloidal gold particles whose location is then detected via microscopy.
eco
immunogold labelling
ECO:0000090
immunogold labelling evidence
A type of immunolocalization evidence where the antibodies are labeled with colloidal gold particles whose location is then detected via microscopy.
ECO:MCC
A type of immunolocalization evidence in which recombinant proteins fused with epitopes are recognized by antibodies.
eco
immunolocalization of epitope-tagged protein
ECO:0000092
epitope-tagged protein immunolocalization evidence
A type of immunolocalization evidence in which recombinant proteins fused with epitopes are recognized by antibodies.
TAIR:TED
A type of DNA detection assay evidence evidence where gene sequence or variation is determined or detected by fluorescently-labeled DNA fragments hybridized to sequence-specific oligonucleotides immobilized on an array.
DNA microarray
oligonucleotide microarray evidence
SNP array evidence
single nucleotide polymorphism array evidence
eco
ECO:0000093
array-based sequence capture evidence
A type of DNA detection assay evidence evidence where gene sequence or variation is determined or detected by fluorescently-labeled DNA fragments hybridized to sequence-specific oligonucleotides immobilized on an array.
PMID:21049075
eco
ECO:0000094
The children of 'biological assay evidence' have been moved under 'direct assay evidence', and this term has been deprecated with no children left.
biological assay evidence
true
A type of cell growth assay evidence that measures one or more aspects of cell growth over a specified time period to indicate an induced or repressed regulatory effect.
mchibucos
2014-10-15T00:58:50Z
eco
growth curve analysis
ECO:0000095
Cell growth aspects can include growth rate and extent of growth. A cell growth curve acts as a natural reporter.
cell growth regulation assay evidence
A type of cell growth 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
Each of the promoter-proximal regions of qrr2 - 4 was subjected to EMSA with the purified His-OpaR protein (Fig. 6b). The results showed that His-OpaR was able to bind to each of the three DNA fragments tested in a dose-dependent manner in vitro.
A type of affinity evidence based on an electrophoretic mobility shift of macromolecules, where proteins, nucleic acids, or both, are combined and the resulting mixtures are electrophoresed under native conditions through polyacrylamide or agarose gel to detect interactions/complexes between proteins and/or nucleic acid.
CollecTF
MI:0413
EMSA: electrophoretic mobility shift assay
eco
Gel retardation assay
electrophoretic mobility shift assay
ECO:0000096
EMSA is often used for assessing TF-binding with fluorophore labelling. Protein-nucleic acid complexes generally migrate at a slower rate than the corresponding non-bonded nucleic acid.
electrophoretic mobility shift assay evidence
Each of the promoter-proximal regions of qrr2 - 4 was subjected to EMSA with the purified His-OpaR protein (Fig. 6b). The results showed that His-OpaR was able to bind to each of the three DNA fragments tested in a dose-dependent manner in vitro.
PMID:22506036
A type of affinity evidence based on an electrophoretic mobility shift of macromolecules, where proteins, nucleic acids, or both, are combined and the resulting mixtures are electrophoresed under native conditions through polyacrylamide or agarose gel to detect interactions/complexes between proteins and/or nucleic acid.
ECO:KIM
ECO:SW
PMID:17703195
TAIR:TED
MI:0413
electrophoretic mobility shift assay
Gel retardation assay
PMID:17703195
A type of expression microarray evidence where expression level is quantified by fluroescently-labeled cDNA (reverse transcribed from an unknown RNA sample) hybridized to DNA immobilized on a solid surface.
CollecTF
ECO:0001041
ECO:0005524
eco
DNA microarray
RNA microarray
ECO:0000097
cDNA to DNA expression microarray evidence
A type of expression microarray evidence where expression level is quantified by fluroescently-labeled cDNA (reverse transcribed from an unknown RNA sample) hybridized to DNA immobilized on a solid surface.
ECO:RCT
A type of nucleic acid hybridization evidence based on localization of a specific segment of DNA or RNA by the application of a complementary strand of nucleic acid to which a reporter molecule is attached.
eco
in situ hybridization
ECO:0000098
This term has been made obsolete with the clean up of experimental genomic evidence branch.
obsolete in situ hybridization evidence
true
A type of nucleic acid hybridization evidence based on localization of a specific segment of DNA or RNA by the application of a complementary strand of nucleic acid to which a reporter molecule is attached.
url:https://www.ncbi.nlm.nih.gov/probe/docs/techish/
A type of direct assay evidence resulting from the separation of various cell components while preserving their individual functions.
eco
ECO:0000100
fractionation evidence
A type of direct assay evidence resulting from the separation of various cell components while preserving their individual functions.
NBK:26936
url:https://www.ncbi.nlm.nih.gov/books/NBK26936/
A type of cRNA to DNA expression microarray evidence resulting from the use of a proprietary Affymetrix GeneChip System for analyzing complex genetic information.
Affymetrix array experiment evidence
eco
ECO:0000101
Affymetrix GeneChip evidence
A type of cRNA to DNA expression microarray evidence resulting from the use of a proprietary Affymetrix GeneChip System for analyzing complex genetic information.
ERO:0001265
A type of fractionation evidence resulting from a protein fractionated with other compounds, factors, or macromolecules.
eco
co-fractionation
ECO:0000102
co-fractionation evidence
A type of fractionation evidence resulting from a protein fractionated with other compounds, factors, or macromolecules.
TAIR:TED
A type of expression microarray evidence where expression levels are quantified by hybridization of fluorescently-labeled DNA to cDNA (reverse transcribed from an unknown RNA sample) immobilized on a solid surface.
REM evidence
RNA expression microarray evidence
microarray RNA expression level evidence
eco
transcript levels (e.g. microarray data)
ECO:0000104
REM is a 'reverse-format' microarray, where the unknown sample is immoblized to a surface and known DNA is hybridized to that.
DNA to cDNA expression microarray evidence
A type of expression microarray evidence where expression levels are quantified by hybridization of fluorescently-labeled DNA to cDNA (reverse transcribed from an unknown RNA sample) immobilized on a solid surface.
ECO:RCT
PMID:15329382
REM is a 'reverse-format' microarray, where the unknown sample is immoblized to a surface and known DNA is hybridized to that.
PMID:15329382
A type of cDNA to DNA expression microarray evidence resulting from the use of a proprietary NimbleGen array to measure expression levels.
eco
ECO:0000105
Nimblegen array evidence
A type of cDNA to DNA expression microarray evidence resulting from the use of a proprietary NimbleGen array to measure expression levels.
PMID:15607417
url:https://roche-biochem.jp/pdf/products/microarray/user_guide/SeqCap/SeqCap_UserGuide_Delivery_ver3.0.pdf
Northern blot analysis indicated that there was one major band of 1.5-kb (which was used for the stability determination) and two other minor bands of approximately 3.0- and 6.0-kb, which constituted less than 5% of the total signal (Fig. 1C), suggesting that other genes may be cotranscribed along with SMU.1882.
A type of transcript expression evidence based on electrophoresis and probing to determine levels of RNA expression using a complementary hybridization probe on the separated RNA samples.
CollecTF
RNA blot evidence
northern assay evidence
eco
transcript levels (e.g. Northerns)
ECO:0000106
northern blot evidence
Northern blot analysis indicated that there was one major band of 1.5-kb (which was used for the stability determination) and two other minor bands of approximately 3.0- and 6.0-kb, which constituted less than 5% of the total signal (Fig. 1C), suggesting that other genes may be cotranscribed along with SMU.1882.
PMID:21124877
A type of transcript expression evidence based on electrophoresis and probing to determine levels of RNA expression using a complementary hybridization probe on the separated RNA samples.
ECO:SW
TAIR:TED
Taken together, the results of the RT-PCR analyses and the reporter fusion assays indicate that expression of SMU.1882 is up regulated in the presence of CovR.
The RT-PCR assay indicated that the sycO, ypkA and yopJ genes (designated as pCD12, pCD13 and pCD14 in Y. pestis 91001 [19], respectively) were transcribed as a single primary RNA (Fig. 1), and thereby these three genes constituted a single operon in Y. pestis Microtus strain 201.
Using reverse transcription-PCR, we found that primers designed to span the intergenic regions between zur and the znuC homolog, as well as znuC and znuB homolog each generated a PCR product (Figure 2A). This indicated that these genes were transcribed on the same mRNA.
A type of RNA detection assay evidence where an RNA transcript is reverse transcribed into cDNA and amplified to qualitatively detect gene expression.
CollecTF
ECO:0000108
reverse transcription polymerase chain reaction transcription evidence
RT-PCR
eco
transcript levels (e.g. RT-PCR)
ECO:0000109
The starting product for PCR, and therefore amplification volume, is directly correlated to the transcription rate.
reverse transcription polymerase chain reaction evidence
Taken together, the results of the RT-PCR analyses and the reporter fusion assays indicate that expression of SMU.1882 is up regulated in the presence of CovR.
PMID:21124877
The RT-PCR assay indicated that the sycO, ypkA and yopJ genes (designated as pCD12, pCD13 and pCD14 in Y. pestis 91001 [19], respectively) were transcribed as a single primary RNA (Fig. 1), and thereby these three genes constituted a single operon in Y. pestis Microtus strain 201.
PMID:19703315
Using reverse transcription-PCR, we found that primers designed to span the intergenic regions between zur and the znuC homolog, as well as znuC and znuB homolog each generated a PCR product (Figure 2A). This indicated that these genes were transcribed on the same mRNA.
PMID:24086521
A type of RNA detection assay evidence where an RNA transcript is reverse transcribed into cDNA and amplified to qualitatively detect gene expression.
ECO:SW
PMID:11013345
PMID:12901609
fur RPAs were performed on RNA isolated from each strain, and an increase in fur expression was seen for G27, 26695, and the Fur swap strain under iron-depletion shock conditions while little to no increase was seen under iron-limited growth conditions (Fig. 4D and data not shown). This data shows that Fur autoregulation is consistent in each strain and further supports the notion that the AA difference in Fur is not responsible for the difference in sodB regulation between G27 and 26695.
A type of nuclease protection assay evidence where mRNA is hybridized with radiolabeled RNA probes after which RNAse is added to digest the unbound, nonresistant single-stranded overhang regions, later the remaining probe target hybrids are purified and resolved on denaturing polyacrylamide gel, and quantified by autoradiography.
CollecTF
ribonuclease protection assay
RPA
eco
RNA protection assay
RNAse protection assay
ECO:0000110
RNA protection assay evidence
fur RPAs were performed on RNA isolated from each strain, and an increase in fur expression was seen for G27, 26695, and the Fur swap strain under iron-depletion shock conditions while little to no increase was seen under iron-limited growth conditions (Fig. 4D and data not shown). This data shows that Fur autoregulation is consistent in each strain and further supports the notion that the AA difference in Fur is not responsible for the difference in sodB regulation between G27 and 26695.
PMID:19399190
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
When we determined the proteolysis role of Lons in VapBC10 proteins by Western blot analysis using the strains BL21(DE3)(pJS882) and BL21(DE3)(pJS427), the levels of VapB10 and VapC10 remained stable over the course of translation inhibition (Figure 7D and E). Thus, Lon could not degrade VapBC10 proteins, consistent with our drop growth evidence (Figure 6B).
A type of protein expression evidence where proteins are separated using gel electrophoresis, blotted onto a membrane, and probed with an antibody that can be detected via light or radioactive emission.
CollecTF
ECO:0005602
protein expression level evidence based on western blot
eco
Western blot expression analysis
protein immunoblot
protein levels (e.g. Western blots)
ECO:0000112
Western blot is used for protein detection and analysis. A mixed protein sample is separated through polyacrylamide gel electrophoresis then transferred to a membrane, such as polyvinylidene fluoride (PVDF), and labeled with protein-specific antibodies.
qualitative western immunoblotting evidence
When we determined the proteolysis role of Lons in VapBC10 proteins by Western blot analysis using the strains BL21(DE3)(pJS882) and BL21(DE3)(pJS427), the levels of VapB10 and VapC10 remained stable over the course of translation inhibition (Figure 7D and E). Thus, Lon could not degrade VapBC10 proteins, consistent with our drop growth evidence (Figure 6B).
PMID:24260461
A type of protein expression evidence where proteins are separated using gel electrophoresis, blotted onto a membrane, and probed with an antibody that can be detected via light or radioactive emission.
ECO:SW
PMID:23050259
TAIR:TED
A type of protein expression evidence where a protein of interest is isolated on the basis of its hybridization to an antibody raised to a homologous protein.
eco
expression library screening
ECO:0000114
expression library screen evidence
A type of protein expression evidence where a protein of interest is isolated on the basis of its hybridization to an antibody raised to a homologous protein.
ECO:MCC
TAIR:TED
A type of nucleic acid hybridization evidence in which preferential or exclusive expression of genes in one cell type or tissue is compared to another cell type or tissue when mRNA from each sample is reverse transcribed, labeled, and hybridized to a cDNA library to compare hybridization patterns.
eco
differential hybridization
ECO:0000116
Differential hybridization identifies differentially expressed cloned genes. Two different mRNA-derived probes are used to demonstrate RNA expression under a specific condition.
differential hybridization evidence
A type of nucleic acid hybridization evidence in which preferential or exclusive expression of genes in one cell type or tissue is compared to another cell type or tissue when mRNA from each sample is reverse transcribed, labeled, and hybridized to a cDNA library to compare hybridization patterns.
PMID:14668817
A type of nucleic acid hybridization evidence in which preferential or exclusive expression of genes in one cell type or tissue are compared to another cell type or tissue when denatured ds-cDNA from the two samples are hybridized, and the common sequences are 'subtracted'.
eco
subtractive hybridization
ECO:0000118
Subtractive hybridization is used for isolation and identification of transcripts involving the removal of any sequences present in the control from the test probe to detect only transcripts present in the sample. The method is PCR-based for the comparison of two cDNA libraries.
subtractive hybridization evidence
A type of nucleic acid hybridization evidence in which preferential or exclusive expression of genes in one cell type or tissue are compared to another cell type or tissue when denatured ds-cDNA from the two samples are hybridized, and the common sequences are 'subtracted'.
PMID:11298187
In contrast, when RpoQ was overexpressed in either the wild type or the DeltalitR mutant, both were essentially nonmotile (Fig. 7), suggesting that quorum signaling regulates motility, at least in part, through an RpoQ mechanism downstream of LitR.
A type of experimental phenotypic evidence in which a gene and/or gene product is investigated in a transgenic organism that has been engineered to overexpress that gene product.
eco
analysis of overexpression/ectopic expression phenotype
ECO:0000120
over expression analysis evidence
In contrast, when RpoQ was overexpressed in either the wild type or the DeltalitR mutant, both were essentially nonmotile (Fig. 7), suggesting that quorum signaling regulates motility, at least in part, through an RpoQ mechanism downstream of LitR.
PMID:22233679
A type of experimental phenotypic evidence in which a gene and/or gene product is investigated in a transgenic organism that has been engineered to overexpress that gene product.
PMID:22419077
A type of localization evidence where sub-cellular localization of a protein is determined.
eco
ECO:0000122
protein localization evidence
A type of localization evidence where sub-cellular localization of a protein is determined.
GO:0008104
url:http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019937
A type of protein localization evidence resulting from the fusion of a protein of interest to a labeling protein which has enzymatic activity or fluorescence properties.
eco
ECO:0000124
fusion protein localization evidence
A type of protein localization evidence resulting from the fusion of a protein of interest to a labeling protein which has enzymatic activity or fluorescence properties.
MI:0240
A type of fusion protein localization evidence resulting from the labeling of a protein of interest with green fluorescent protein (GFP) from the jellyfish Aequorea victoria.
GFP fusion protein localization evidence
eco
localization of GFP/YFP fusion protein
ECO:0000126
green fluorescent protein fusion protein localization evidence
A type of fusion protein localization evidence resulting from the labeling of a protein of interest with green fluorescent protein (GFP) from the jellyfish Aequorea victoria.
PMID:9759496
A type of fusion protein localization evidence resulting from the labeling of a protein of interest with yellow fluorescent protein (YFP), which was created by mutating green fluorescent protein (GFP) of the Aequorea victoria.
YFP fusion protein localization evidence
eco
localization of GFP/YFP fusion protein
ECO:0000128
yellow fluorescent protein fusion protein localization evidence
A type of fusion protein localization evidence resulting from the labeling of a protein of interest with yellow fluorescent protein (YFP), which was created by mutating green fluorescent protein (GFP) of the Aequorea victoria.
MI:0368
url:http://www.jbc.org/content/276/31/29188.long
A type of fusion protein localization evidence resulting from the targeted insertion of the beta-glucuronidase (GUS) coding gene as a reporter gene for the localization of a particular gene product.
GUS fusion protein localization evidence
GUS staining evidence
eco
localization of GUS fusion protein
ECO:0000130
beta-glucuronidase fusion protein localization evidence
A type of fusion protein localization evidence resulting from the targeted insertion of the beta-glucuronidase (GUS) coding gene as a reporter gene for the localization of a particular gene product.
ECO:RCT
A type of fusion protein localization evidence resulting from the targeted insertion of the beta-galactosidase coding gene (lacZ) into a specific gene to create a beta-galactosidase-tagged fusion protein.
LacZ fusion protein localization evidence
eco
ECO:0000132
beta-galactosidase fusion protein localization evidence
A type of fusion protein localization evidence resulting from the targeted insertion of the beta-galactosidase coding gene (lacZ) into a specific gene to create a beta-galactosidase-tagged fusion protein.
PMID:23681629
A type of direct assay evidence resulting from the activity assessment of transport proteins.
eco
transport assay
ECO:0000134
transport assay evidence
A type of direct assay evidence resulting from the activity assessment of transport proteins.
PMID:18401524
A type of affinity evidence resulting from the binding of a molecule to a nucleic acid.
eco
ECO:0000136
nucleic acid binding evidence
A type of affinity evidence resulting from the binding of a molecule to a nucleic acid.
GO:0003676
A type of nucleic acid binding evidence resulting from an enzyme displaying binding activity to specific ribohomopolymer.
eco
ribohomopolymer binding assay
ECO:0000138
ribohomopolymer binding assay evidence
A type of nucleic acid binding evidence resulting from an enzyme displaying binding activity to specific ribohomopolymer.
PMC:PMC102612
A type of chromatography evidence that uses a thin layer of adsorbent (such as silica gel, alumina, or cellulose) on a flat, inert substrate.
TLC evidence
eco
thin layer chromatography
ECO:0000140
thin layer chromatography evidence
A type of chromatography evidence that uses a thin layer of adsorbent (such as silica gel, alumina, or cellulose) on a flat, inert substrate.
ECO:MCC
A type of protein binding evidence resulting from a metal ion binding to a protein at a specific binding site.
eco
ECO:0000142
protein:ion binding evidence
A type of protein binding evidence resulting from a metal ion binding to a protein at a specific binding site.
PMID:2377604
A type of nucleic acid binding evidence in which DNA-protein binding is detected using labeled DNA as probes, hybridized to electrophoretically separated proteins.
eco
Southwestern analysis
ECO:0000144
Southwestern blot evidence
A type of nucleic acid binding evidence in which DNA-protein binding is detected using labeled DNA as probes, hybridized to electrophoretically separated proteins.
ECO:RCT
TAIR:TED
A type of nucleic acid binding evidence in which RNA-protein binding is detected using labeled RNA as probes, hybridized to electrophoretically separated proteins.
eco
Northwestern analysis
ECO:0000146
Northwestern blot evidence
A type of nucleic acid binding evidence in which RNA-protein binding is detected using labeled RNA as probes, hybridized to electrophoretically separated proteins.
ECO:RCT
TAIR:TED
eco
ECO:0000148
in vitro binding evidence
true
As shown in Fig. 5, addition of reconstituted RNA polymerase holoenzyme, but not the core enzyme, generated expected size bands of 193-nt and 158-nt when P1882 and Pami, respectively, were used as template (lanes 2 and 7). However, the addition of CovR did not lead to any observable increase in transcription from P1882.
A type of reconstitution assay evidence resulting from the use of reconstituted polymerase transcription systems to investigate RNA synthesis.
eco
in vitro reconstitution assay with recombinant protein
ECO:0000150
in vitro transcription reconstitution assay evidence
As shown in Fig. 5, addition of reconstituted RNA polymerase holoenzyme, but not the core enzyme, generated expected size bands of 193-nt and 158-nt when P1882 and Pami, respectively, were used as template (lanes 2 and 7). However, the addition of CovR did not lead to any observable increase in transcription from P1882.
PMID:21124877
A type of reconstitution assay evidence resulting from the use of reconstituted polymerase transcription systems to investigate RNA synthesis.
PMID:9237163
A type of in vitro transcription reconstitution assay evidence resulting from the use of recombinant proteins in preparation of a fully-defined transcription system.
eco
in vitro reconstitution assay with recombinant protein
ECO:0000152
in vitro recombinant protein transcription reconstitution assay evidence
A type of in vitro transcription reconstitution assay evidence resulting from the use of recombinant proteins in preparation of a fully-defined transcription system.
PMID:9237165
A type of protein expression evidence where a gene from one cell is inserted into a cell that does not typically contain that gene and heterologous protein expression is assessed.
eco
protein expression in heterologous system
ECO:0000154
heterologous protein expression evidence
A type of protein expression evidence where a gene from one cell is inserted into a cell that does not typically contain that gene and heterologous protein expression is assessed.
ECO:KAV
A type of fractionation evidence resulting from the isolation of a single type of protein from a complex mixture.
eco
ECO:0000156
protein separation evidence
A type of fractionation evidence resulting from the isolation of a single type of protein from a complex mixture.
ERO:0000526
A type of protein separation evidence that is followed by direct protein sequencing whereby a protein's amino acid sequence is determined experimentally by Edman degradation or by mass spectrometry.
eco
protein separation and direct sequencing
ECO:0000158
protein separation followed by direct sequencing evidence
A type of protein separation evidence which then utilizes the screening and identification of small-molecules that bind to proteins.
eco
protein separation and fragment identification
ECO:0000160
protein separation followed by fragment identification evidence
A type of protein separation evidence which then utilizes the screening and identification of small-molecules that bind to proteins.
https://pubs.acs.org/doi/10.1021/bi3005126
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5632530/
A type of transport assay evidence in which the uptake mechanism of a transporter is investigated in a cell that does not normally express that protein.
eco
uptake assay in heterologous system
ECO:0000162
The transporter is a recombinant protein.
heterologous system uptake evidence
A type of transport assay evidence in which the uptake mechanism of a transporter is investigated in a cell that does not normally express that protein.
ECO:RCT
doi:10.1146/annurev.pp.46.060195.002223
A type of direct assay evidence where electrical properties of cells or tissues are studied.
eco
ECO:0000164
The scale of electrophysiology assays can range from small, e.g. a single ion channel, to large, e.g. an entire organ such as a heart.
electrophysiology assay evidence
A type of direct assay evidence where electrical properties of cells or tissues are studied.
ECO:KAV
A type of voltage clamp recording evidence which involves using two electrodes inserted into a large cell (often a xenopus oocyte) where one electrode is used to measure the internal potential (voltage) of the cell and the other electrode is used to clamp the current.
eco
two-electrode voltage clamp technique
ECO:0000166
two-electrode voltage clamp recording evidence
A type of voltage clamp recording evidence which involves using two electrodes inserted into a large cell (often a xenopus oocyte) where one electrode is used to measure the internal potential (voltage) of the cell and the other electrode is used to clamp the current.
ECO:SN
PMID:23529422
A type of direct assay evidence resulting from the detection and quantification of transcribed RNA.
eco
ECO:0000168
transcription assay evidence
A type of direct assay evidence resulting from the detection and quantification of transcribed RNA.
MeSH:D014158
url:https://bmcmolbiol.biomedcentral.com/articles/10.1186/1471-2199-15-7
A type of transcription assay evidence in which sequence-specific binding proteins that increase transcription of a specific target gene or genes are identified, quantified, and/or analyzed.
eco
transcriptional activation assay
ECO:0000170
transcriptional activation assay evidence
A type of transcription assay evidence in which sequence-specific binding proteins that increase transcription of a specific target gene or genes are identified, quantified, and/or analyzed.
url:http://smcg.ccg.unam.mx/enp-unam/05-TranscripYRegulacion/transcription.pdf
A type of experimental phenotypic evidence in which the biochemical aspect of a mutation is analyzed.
eco
analysis of biochemical trait
ECO:0000172
For example, the accumulation of a biosynthetic intermediate.
biochemical trait analysis evidence
A type of experimental phenotypic evidence in which the biochemical aspect of a mutation is analyzed.
ECO:RCT
A type of mutant phenotype evidence in which the physiological response of a mutant when presented with an external stimulus is determined.
eco
analysis of physiological response
ECO:0000174
Examples include: abnormal growth of the root in response to gravity, delay in flowering in response to varying light conditions.
mutant physiological response evidence
A type of mutant phenotype evidence in which the physiological response of a mutant when presented with an external stimulus is determined.
ECO:RCT
A type of mutant phenotype evidence in which traits arising from a mutation are visually examined.
eco
analysis of visible trait
ECO:0000176
mutant visible phenotype evidence
A type of mutant phenotype evidence in which traits arising from a mutation are visually examined.
ECO:RCT
A type of similarity evidence in which the location of the gene within the genome provides insight into the gene's function or evolutionary insight.
eco
ECO:0000177
This type of evidence might include identity of neighboring genes, operon structure, synteny, phylogenetic analysis, or other whole-genome analysis.
genomic context evidence
A type of similarity evidence in which the location of the gene within the genome provides insight into the gene's function or evolutionary insight.
PMID:10958625
PMID:21609955
A type of direct assay evidence resulting from a sample of microorganisms or living tissue grown in a medium.
eco
ECO:0000178
in vivo assay evidence
A type of direct assay evidence resulting from a sample of microorganisms or living tissue grown in a medium.
ECO:RCT
url:https://www.cancer.gov/publications/dictionaries/cancer-terms?cdrid=46352
A type of experimental evidence arising from the investigation of an animal model system.
eco
ECO:0000179
animal model system study evidence
A type of experimental evidence arising from the investigation of an animal model system.
ECO:MCC
A type of experimental evidence arising from a controlled investigation that uses human subjects.
eco
ECO:0000180
clinical study evidence
A type of experimental evidence arising from a controlled investigation that uses human subjects.
ECO:MCC
A type of direct assay evidence resulting from a process performed outside the living organism, where the components of an organism have been isolated from their usual biological context, to permit a more detailed or more convenient analysis in an artificial setting.
ECO:0005013
eco
ECO:0000181
in vitro assay evidence
A type of direct assay evidence resulting from a process performed outside the living organism, where the components of an organism have been isolated from their usual biological context, to permit a more detailed or more convenient analysis in an artificial setting.
ECO:RCT
url:https://www.cancer.gov/publications/dictionaries/cancer-terms?cdrid=45733
eco
ECO:0000182
Use ECO:0001563 (cell growth assay evidence) in place of this term.
in vitro culture assay evidence
true
A type of direct assay evidence resulting from studies in which cytoplasmic and/or nuclear cellular components from resting, nonstimulated cells, are isolated by ultracentrifugation to provide molecular machinery that can be used in reactions in the absence of many of the other cellular components for the purpose of in vitro protein synthesis, transcription, DNA replication, etc.
in vitro assay
eco
ECO:0000183
cell-free assay evidence
A type of direct assay evidence resulting from studies in which cytoplasmic and/or nuclear cellular components from resting, nonstimulated cells, are isolated by ultracentrifugation to provide molecular machinery that can be used in reactions in the absence of many of the other cellular components for the purpose of in vitro protein synthesis, transcription, DNA replication, etc.
PMID:18453125
A type of protein inhibition evidence and enzymatic acitivty evidence where the protein under study is an enzyme.
eco
ECO:0000184
enzyme inhibition evidence
A type of protein inhibition evidence and enzymatic acitivty evidence where the protein under study is an enzyme.
ECO:MCC
A type of sequence similarity evidence in which an annotation is made based on a manually-reviewed or published sequence alignment
mchibucos
2010-03-18T12:21:31Z
ECO:00000057
eco
ECO:0000200
Such alignments may be pairwise alignments or multiple alignments.
sequence alignment evidence
A type of sequence similarity evidence in which an annotation is made based on a manually-reviewed or published sequence alignment
url:http://www.geneontology.org/GO.evidence.shtml
A type of sequence similarity evidence in which orthology is established by multiple criteria, including amino acid and/or nucleotide sequence comparisons and one or more of the following: phylogenetic analysis, coincident expression, conserved map location, functional complementation, immunological cross-reaction, similarity in subcellular localization, subunit structure, substrate specificity, and response to specific inhibitors.
mchibucos
2010-03-18T12:30:06Z
ECO:00000060
eco
ortholog evidence
ECO:0000201
Orthology is a relationship between genes in different species indicating that the genes derive from a common ancestor.
sequence orthology evidence
A type of sequence similarity evidence in which orthology is established by multiple criteria, including amino acid and/or nucleotide sequence comparisons and one or more of the following: phylogenetic analysis, coincident expression, conserved map location, functional complementation, immunological cross-reaction, similarity in subcellular localization, subunit structure, substrate specificity, and response to specific inhibitors.
url:http://www.geneontology.org/GO.evidence.shtml
A putative rho-independent terminator sequence (GCCTGACTACATAGATGTCAGGC) was identified at position 402-bp downstream of SMU.1882 by TransTerm (transterm.dev.java.net) program.
A type of sequence similarity evidence in which the function of a gene product is predicted based on a sequence-based statistical model.
mchibucos
2010-03-18T12:32:30Z
ECO:00000063
eco
ECO:0000202
Used when evidence from any kind of statistical model of a sequence or group of sequences is used to make a prediction about the function of a protein or RNA. Examples of relevant evidence are: Hidden Markov Models, PROSITE motifs, and tools such as tRNASCAN.
match to sequence model evidence
A putative rho-independent terminator sequence (GCCTGACTACATAGATGTCAGGC) was identified at position 402-bp downstream of SMU.1882 by TransTerm (transterm.dev.java.net) program.
PMID:21124877
A type of sequence similarity evidence in which the function of a gene product is predicted based on a sequence-based statistical model.
ECO:MCC
url:http://www.geneontology.org/GO.evidence.shtml
An assertion method that does not involve human review.
mchibucos
2010-03-18T12:36:04Z
ECO:00000067
eco
ECO:0000203
An automatic assertion is based on computationally generated information that is not reviewed by a person prior to making the assertion. For example, one common type of automatic assertion involves creating an association of evidence with an entity based on commonness of attributes of that entity and another entity for which an assertion already exists. The commonness is determined algorithmically.
automatic assertion
An assertion method that does not involve human review.
ECO:MCC
A type of documented statement evidence that is based on an assertion by the author of a paper, which is read by a curator.
mchibucos
2010-06-21T11:17:21Z
ECO:0007010
eco
ECO:0000204
author statement
A type of documented statement evidence that is based on an assertion by the author of a paper, which is read by a curator.
ECO:MCC
A type of inferential evidence that is based on a conclusion drawn by a curator.
mchibucos
2010-08-18T05:55:12Z
eco
ECO:0000205
curator inference
A type of inferential evidence that is based on a conclusion drawn by a curator.
ECO:MCC
A type of pairwise sequence alignment evidence obtained with basic local alignment search tool (BLAST).
mchibucos
2010-08-06T04:48:24Z
eco
ECO:0000206
BLAST evidence
A type of pairwise sequence alignment evidence obtained with basic local alignment search tool (BLAST).
ECO:MCC
A type of BLAST evidence in which nucleotide sequences are aligned.
mchibucos
2010-08-06T04:49:58Z
eco
ECO:0000207
nucleotide BLAST evidence
A type of BLAST evidence in which nucleotide sequences are aligned.
ECO:MCC
Blast search of S. meliloti genome for homologues of X. campestris Ohr protein revealed two paralogues, SMa2389 and SMc00040, showing 52 and 57% identity respectively with Ohr of X. campestris.
A type of BLAST evidence in which amino acid or translated nucleotide sequences are aligned.
mchibucos
2010-08-06T04:50:45Z
eco
ECO:0000208
protein BLAST evidence
Blast search of S. meliloti genome for homologues of X. campestris Ohr protein revealed two paralogues, SMa2389 and SMc00040, showing 52 and 57% identity respectively with Ohr of X. campestris.
PMID:21569462
A type of BLAST evidence in which amino acid or translated nucleotide sequences are aligned.
ECO:MCC
IEA
A type of BLAST evidence that is used in an automatic assertion.
mchibucos
2010-08-06T04:55:21Z
eco
ECO:0000209
BLAST evidence used in automatic assertion
true
A type of BLAST evidence that is used in an automatic assertion.
ECO:MCC
IEA
A type of nucleotide BLAST evidence that is used in an automatic assertion.
mchibucos
2010-08-06T05:09:51Z
eco
ECO:0000210
nucleotide BLAST evidence used in automatic assertion
true
A type of nucleotide BLAST evidence that is used in an automatic assertion.
ECO:RCT
IEA
A type of protein BLAST evidence that is used in an automatic assertion.
mchibucos
2010-08-06T05:11:04Z
eco
ECO:0000211
protein BLAST evidence used in automatic assertion
true
A type of protein BLAST evidence that is used in an automatic assertion.
ECO:RCT
A type of evidence in which at least two distinct types of evidence have been integrated.
mchibucos
2010-08-06T05:24:57Z
ECO:0000036
ECO:0000043
eco
inferred from in-silico analysis
ECO:0000212
A key aspect of this type of evidence is that two or more pieces of information are combined to generate an emergent type of evidence not possible with the constituent pieces of evidence alone. A combinatorial analysis typically involves incorporation of different types of evidence.
combinatorial evidence
A type of evidence in which at least two distinct types of evidence have been integrated.
ECO:MCC
ECO:RCT
IEA
A type of combinatorial analysis that is used in an automatic assertion.
mchibucos
2010-08-06T05:28:33Z
eco
inferred from in-silico analysis
ECO:0000213
Combinatorial analyses could include experimental or computational results. Examples include: (i) large-scale experiment such as a genome-wide two-hybrid or genome-wide synthetic interactions; (ii) integration of large-scale data sets of various types; and (iii) text-based-computation, e.g. text-mining. For simple sequence comparisons, one should use the sequence similarity analysis evidence type. For microarray results alone, expression pattern analysis is appropriate; whereas, large-scale computational analysis should be used when microarray results are combined with the results of other types of large-scale experiments.
combinatorial evidence used in automatic assertion
true
A type of combinatorial analysis that is used in an automatic assertion.
ECO:MCC
A type of phylogenetic evidence whereby an aspect of an ancestral gene is inferred through the characterization of an aspect of a descendant gene.
mchibucos
2010-10-05T11:16:50Z
eco
ECO:0000214
This type of evidence can be used in support of both positive and "not" GO annotations. It should be used to annotate ancestral genes but not extant ones.
biological aspect of descendant evidence
A type of phylogenetic evidence whereby an aspect of an ancestral gene is inferred through the characterization of an aspect of a descendant gene.
ECO:MCC
A type of phylogenetic evidence characterized by long phylogenetic tree branch lengths following a duplication event.
mchibucos
2010-10-05T03:41:34Z
eco
ECO:0000215
Long branch lengths indicate that descendant sequences may have acquired different or additional functions than the ancestral sequence.
rapid divergence from ancestral sequence evidence
A type of phylogenetic evidence characterized by long phylogenetic tree branch lengths following a duplication event.
ECO:MCC
A type of phylogenetic evidence characterized by the absence of key sequence residues.
mchibucos
2010-10-05T03:43:17Z
eco
ECO:0000216
The loss of certain residues important for function can indicate that a sequence lacks a particular function.
phylogenetic determination of loss of key residues evidence
A type of phylogenetic evidence characterized by the absence of key sequence residues.
ECO:MCC
A means by which a statement is made about an entity.
mchibucos
2010-11-12T04:17:37Z
eco
ECO:0000217
assertion method
A means by which a statement is made about an entity.
ECO:MCC
An assertion method that involves human review.
mchibucos
2010-11-12T04:20:02Z
eco
ECO:0000218
A manual assertion could be based on evidence that is generated by and interpreted by a human or it could involve human review of computationally generated information.
manual assertion
An assertion method that involves human review.
ECO:MCC
A type of sequencing assay that determines the sequence of a biopolymer comprised of nucleotides.
mchibucos
2010-11-15T12:22:40Z
eco
DNA sequencing
ECO:0000219
nucleotide sequencing assay evidence
A type of sequencing assay that determines the sequence of a biopolymer comprised of nucleotides.
ECO:MCC
DNA sequencing
OBI:0000626
A type of experimental evidence where the order of molecules that constitute a biopolymer is determined.
mchibucos
2010-11-15T01:44:45Z
eco
ECO:0000220
sequencing assay evidence
A type of experimental evidence where the order of molecules that constitute a biopolymer is determined.
ECO:MCC
OBI:0600047
A type of nucleotide sequencing assay evidence in which a sequence is derived from a parallelized sequencing technique.
mchibucos
2010-11-15T02:19:34Z
eco
next generation sequencing evidence
ECO:0000221
Typically thousands to millions of reads are produced in parallel.
high throughput nucleotide sequencing assay evidence
A type of nucleotide sequencing assay evidence in which a sequence is derived from a parallelized sequencing technique.
ECO:MCC
A type of high throughput nucleotide sequencing evidence in which sequence is determined through hybridization of adaptor-ligated DNA to a glass slide on which each fragment is simultaneously clonally amplified, followed by progressive rounds of base incorporation with fluorescently-tagged nucleotides, washing, imaging, and cleavage.
mchibucos
2010-11-15T02:38:03Z
eco
Solexa sequencing result
ECO:0000222
In Illumina sequencing technology, adapters are ligated onto the ends of randomly fragmented DNA. After single-stranded fragments are bound to the inside surface of a flow cell channel, they undergo in-place bridge PCR amplification. To begin the sequencing cycle, labeled reversible terminators, primers and DNA polymerase are added, followed by laser excitation of the fluorescent label and high resolution scanning. After non-incorporated nucleotides are washed away and the dye is chemically removed, the next cycle repeats with four labeled reversible terminators, primers and DNA polymerase, again followed by imaging.
Illumina sequencing evidence
A type of high throughput nucleotide sequencing evidence in which sequence is determined through hybridization of adaptor-ligated DNA to a glass slide on which each fragment is simultaneously clonally amplified, followed by progressive rounds of base incorporation with fluorescently-tagged nucleotides, washing, imaging, and cleavage.
OBI:0000724
PMID:26000844
Solexa sequencing result
OBI:0000724
A type of high throughput nucleotide sequencing evidence in which the sequence for a ssDNA is determined by addition of primers and then nucleotides, one base pair at a time (which generate a specific fluorescence), to the target strand.
mchibucos
2010-11-15T03:50:14Z
pyrosequencing
eco
ECO:0000223
454 pyrosequencing technology amplifies individual DNA fragments inside water droplets within an oil solution (emulsion PCR). Within each droplet, a single DNA template is attached to a single primer-coated bead. Each bead is subsequently captured in a picolitre well within the sequencing machine. A luciferase-based readout system is used to identify individual nucleotides added to the nascent DNA.
The target strand is usually prepared by fragmentation, adaptor ligation, and amplification by emulsion PCR.
454 pyrosequencing evidence
A type of high throughput nucleotide sequencing evidence in which the sequence for a ssDNA is determined by addition of primers and then nucleotides, one base pair at a time (which generate a specific fluorescence), to the target strand.
EFO:0005016
pyrosequencing
OBI:0000730
A type of high throughput nucleotide sequencing evidence in which sequence is determined through rounds of ligation-based sequencing with fluorescently-labeled Di-base probes and cleavage, after which the template is reset, with a primer offset by one base, for subsequent rounds of ligation.
mchibucos
2010-11-15T04:17:41Z
eco
ECO:0000224
SOLiD sequencing technology is based on sequencing by ligation. After library preparation, emulsion PCR and bead enrichment are performed, including 3' modification of templates on selected beads to allow covalent bonding to a slide. 3' modified beads are attached to a glass slide and primers are added. Four fluorescently labeled di-base probes are added and multiple cycles of ligation, detection and cleavage are performed. The number of cycles determines read length. After a number of ligation cycles, the extension product is removed and another round of ligation cycles is performed with a new primer complimentary to the n-1 position of the template. Five rounds of primer reset are performed for each sequence tag.
Samples are prepared by fragmentation of a sample library, adaptor ligation, emulsion PCR, and attachment of resultant beads to glass slides.
SOLiD sequencing evidence
A type of high throughput nucleotide sequencing evidence in which sequence is determined through rounds of ligation-based sequencing with fluorescently-labeled Di-base probes and cleavage, after which the template is reset, with a primer offset by one base, for subsequent rounds of ligation.
OBI:0000706
A type of nucleotide sequencing assay in which DNA sequence is determined by addition of a primed DNA template to a reaction mixture, followed by addition of DNA polymerase, deoxynucleosidetriphosphates (dNTPs - one of which may be radiolabeled), and one of four di-deoxynucleotidetriphosphates (ddNTPs), after which DNA elongation is terminated and the DNA is separated by size and imaged.
mchibucos
2010-11-15T04:46:31Z
Sanger sequencing
dye terminator sequencing
eco
ECO:0000225
Chain termination sequencing, also called Sanger sequencing after its developer, uses dideoxynucleotide triphosphates (ddNTPs) as DNA chain terminators. Single-stranded DNA template, DNA primer, DNA polymerase, fluorescently or radioactively labeled nucleotides, and one of four ddNTPs are added together in each of four separate sequencing reactions. The synthesized and labeled DNA fragments from each of the four reactions are denatured, separated by size by gel electrophoresis, and visualized by autoradiography or UV light.
The ddNTPs lack an OH group so the next dNTP cannot be attached, causing chain termination.
chain termination sequencing evidence
A type of nucleotide sequencing assay in which DNA sequence is determined by addition of a primed DNA template to a reaction mixture, followed by addition of DNA polymerase, deoxynucleosidetriphosphates (dNTPs - one of which may be radiolabeled), and one of four di-deoxynucleotidetriphosphates (ddNTPs), after which DNA elongation is terminated and the DNA is separated by size and imaged.
OBI:0000695
A type of immunoprecipitation evidence that is used to identify a protein binding site on a genomic DNA sequence.
mchibucos
2010-11-16T01:29:08Z
MI:0402
ChIP evidence
eco
ECO:0000226
Chromatin immunoprecipitation (ChIP) is used to investigate protein-DNA interactions in vivo. DNA and proteins are chemically cross-linked in vivo to form chromatin complexes, followed by cell lysis and DNA shearing. Fragmented DNA-protein complexes are selectively enriched for a protein of interest using a specific antibody (immunoprecipitation). Protein digestion and DNA purification are performed prior to DNA detection via molecular cloning and sequencing, polymerase chain reaction (PCR), microarray analysis (ChIP-on-chip), or direct high-throughput sequencing (ChIP-seq).
chromatin immunoprecipitation evidence
A type of immunoprecipitation evidence that is used to identify a protein binding site on a genomic DNA sequence.
ECO:MCC
MI:0402
chromatin immunoprecipitation assay
A type of chromatin immunoprecipitation evidence that uses polymerase chain reaction (PCR) where specific primers are used on the pulled-down DNA for DNA detection.
CollecTF
mchibucos
2010-11-16T05:02:00Z
ChIP-PCR evidence
eco
ECO:0000227
ChIP-PCR is often used to validate ChIP-chip results and less frequently,ChIP-Seq results.
chromatin immunoprecipitation-PCR evidence
A type of chromatin immunoprecipitation evidence that uses polymerase chain reaction (PCR) where specific primers are used on the pulled-down DNA for DNA detection.
ECO:MCC
ECO:SW
PMID:18388953
To confirm the in vivo binding of FimR to pfim, and to determine the impact of Mn2+ and Fe2+ on the binding activity of FimR, chromatin immunoprecipitation (ChIP) assay-quantitative real time PCR (qPCR) with anti-FimR antibody was employed as detailed in the materials and methods. The strongest binding of FimR to pfim was detected in cells grown in the presence of 50 microM MnCl2 and 50 microM FeSO4 (Figure 5, lane IV), whereas minimal amounts of MnCl2 (0.01 microM) and FeSO4 (0.1 microM) led to the weakest binding (Figure 5, lane I).
A type of chromatin immunoprecipitation evidence in which protein-DNA interactions are investigated at known genomic binding sites through a process of ChIP, DNA purification, and finally quantitative polymerase chain reaction (qPCR) for DNA detection.
mchibucos
2010-11-16T05:26:47Z
ChIP-qPCR evidence
eco
ECO:0000228
chromatin immunoprecipitation-qPCR evidence
To confirm the in vivo binding of FimR to pfim, and to determine the impact of Mn2+ and Fe2+ on the binding activity of FimR, chromatin immunoprecipitation (ChIP) assay-quantitative real time PCR (qPCR) with anti-FimR antibody was employed as detailed in the materials and methods. The strongest binding of FimR to pfim was detected in cells grown in the presence of 50 microM MnCl2 and 50 microM FeSO4 (Figure 5, lane IV), whereas minimal amounts of MnCl2 (0.01 microM) and FeSO4 (0.1 microM) led to the weakest binding (Figure 5, lane I).
PMID:23823757
A type of chromatin immunoprecipitation evidence in which protein-DNA interactions are investigated at known genomic binding sites through a process of ChIP, DNA purification, and finally quantitative polymerase chain reaction (qPCR) for DNA detection.
url:https://www.diagenode.com/applications/chip-qpcr
A type of chromatin immunoprecipitation evidence that uses high-throughput sequencing where immunoprecipitated DNA fragments are funnelled into a massively parallel sequencer to produce multiple short reads for locating binding sites of DNA-associated proteins.
CollecTF
mchibucos
2010-11-16T05:30:41Z
ChIP-SEQ evidence
ChIP-seq evidence
eco
ECO:0000229
ChIP-Seq experiments often use the input as a control to eliminate biases. To obtain similar results, ChIP-chip with high-density tiling arrays can be used.
chromatin immunoprecipitation-seq evidence
A type of chromatin immunoprecipitation evidence that uses high-throughput sequencing where immunoprecipitated DNA fragments are funnelled into a massively parallel sequencer to produce multiple short reads for locating binding sites of DNA-associated proteins.
ECO:MCC
ECO:SW
OBI:0000716
PMID:22955991
ChIP-SEQ evidence
OBI:0000716
ChIP-seq evidence
PMID:22955991
A type of chromatin immunoprecipitation evidence that uses a tiling microarray for the detection of protein-bound DNA regions where chromatin is immunoprecipitated for protein tagging and DNA is sheared from the cross-linked protein-DNA complex to be arrayed revealing the protein-bound genomic regions.
CollecTF
mchibucos
2010-11-16T05:43:55Z
MI:0225
ChIP-chip evidence
ChIP-on-chip evidence
eco
ECO:0000230
A fixating agent such as formaldehyde is used to cross link proteins and DNA. Sonication is applied for DNA shearing. For transcription factor tagging, an antibody or epitope is employed. After cross-linking is reversed, the DNA is amplified and labeled with a flourophore for microarray which produces a resolution of aproximately 500 bp.
chromatin immunoprecipitation-chip evidence
A type of chromatin immunoprecipitation evidence that uses a tiling microarray for the detection of protein-bound DNA regions where chromatin is immunoprecipitated for protein tagging and DNA is sheared from the cross-linked protein-DNA complex to be arrayed revealing the protein-bound genomic regions.
ECO:MCC
ECO:SW
PMID:18388953
PMID:19381927
MI:0225
chromatin immunoprecipitation array
A type of DNA detection assay evidence where the reaction product is quantified in real-time across cycles by means of fluorescent dyes or fluorescent probes for detection and quantification of specific sequences in a DNA sample.
CollecTF
mchibucos
2010-11-16T05:57:20Z
Q-PCR evidence
qPCR evidence
quantitative PCR evidence
quantitative real-time PCR evidence
real time polymerase chain reaction evidence
real-time PCR evidence
real-time quantitative PCR
eco
qRT-PCR evidence
ECO:0000231
Quantitative PCR enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample. The dye is activated upon binding double-stranded DNA.
Although qRT-PCR is commonly found in literature synonymous to qPCR, it is preferable not to use this synonym as it is the accepted abbreviation for reverse transcription PCR. qPCR should be used instead (ISBN 978-0-470-68386-6 page 173).
qPCR can be used to quantitatively determine levels of gene expression.
quantitative polymerase chain reaction evidence
A type of DNA detection assay evidence where the reaction product is quantified in real-time across cycles by means of fluorescent dyes or fluorescent probes for detection and quantification of specific sequences in a DNA sample.
ECO:MCC
ECO:SW
A type of experimental evidence that is based on a five-step technique of cross-linking DNA in vivo, restriction digestion, intramolecular ligation, reversing DNA cross-links, DNA processing, and quantitation that serves to analyze the spatial organization of chromatin in a cell and quantify the number of interactions between genomic loci that are nearby in 3-D space.
mchibucos
2010-11-17T12:27:14Z
chromosome conformation capture-based evidence
3C
chromosome conformation capture
eco
ECO:0000232
Chromosome conformation capture technologies are used to study the structural properties and spatial organization of chromosomes inside cells. All types of chromosome conformation capture technology involve five primary steps: cross-linking of DNA in vivo, restriction digestion, intramolecular ligation, reversing cross-linkages, and DNA enrichment and quantitation. The last step is different for each type of chromosome conformation capture technology, and may include PCR (3C), inverse PCR (4C), or ligation-mediated amplification (5C). Methods for product quantitation can include agarose gel detection or real-time quantitative PCR in the case of 3C, or high-throughput sequencing or microarray analysis for 4C and 5C.
chromosome conformation-based evidence
A type of experimental evidence that is based on a five-step technique of cross-linking DNA in vivo, restriction digestion, intramolecular ligation, reversing DNA cross-links, DNA processing, and quantitation that serves to analyze the spatial organization of chromatin in a cell and quantify the number of interactions between genomic loci that are nearby in 3-D space.
ECO:MCC
A type of chromosome conformation-based evidence that is derived by 1) quantifying interactions between a single pair of genomic loci and not multiple interactions and 2) performing polymerase chain reaction (PCR) in the final product quantitation step.
mchibucos
2010-11-17T12:46:15Z
3C
chromosome conformation capture evidence
chromosome conformation capture-PCR evidence
eco
ECO:0000233
3C is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 3C differs only in the fifth step, which involves performing either standard polymerase chain reaction (PCR) or quantitative PCR (qPCR) for product quantitation.
3C evidence
A type of chromosome conformation-based evidence that is derived by 1) quantifying interactions between a single pair of genomic loci and not multiple interactions and 2) performing polymerase chain reaction (PCR) in the final product quantitation step.
ECO:MCC
A type of chromosome conformation-based evidence that is derived by inverse polymerase chain reaction (inverse PCR) on a prior circularized 3C library followed by product quantitation with a microarray.
mchibucos
2010-11-19T01:20:28Z
chromosome conformation capture on chip
circularized 3C
circularized chromosome conformation capture evidence
eco
ECO:0000234
4C is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 4C differs only in the fifth step, which involves inverse polymerase chain reaction (inverse PCR) on a circularized 3C library prior to product quantitation.
4C evidence
A type of chromosome conformation-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
PMID:17033624
A type of chromosome conformation-based evidence that is derived by performing ligation-mediated amplification (LMA) prior to product quantitation.
mchibucos
2010-11-19T01:22:20Z
5C
carbon-copy 3C
carbon-copy chromosome conformation capture evidence
eco
ECO:0000235
5C is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 5C differs only in the fifth step, which involves ligation-mediated amplification (LMA) followed by product quantitation.
5C evidence
A type of chromosome conformation-based evidence that is derived by performing ligation-mediated amplification (LMA) prior to product quantitation.
ECO:MCC
A type of chromosome conformation capture evidence that is derived by performing polymerase chain reaction (PCR) in the quantitation step.
mchibucos
2010-11-19T03:00:47Z
3C
3C-PCR
eco
ECO:0000236
See 3C evidence. 3C evidence was initially developed using PCR.
chromosome conformation capture-PCR evidence
true
A type of chromosome conformation capture evidence that is derived by performing polymerase chain reaction (PCR) in the quantitation step.
ECO:MCC
A type of 3C evidence evidence that 1) quantifies interactions between a single pair of genomic loci (not multiple interactions) and 2) performs quantitative polymerase chain reaction (qPCR) in the quantitation step.
mchibucos
2010-11-19T03:06:47Z
3C-quantitative PCR
3C-real-time PCR
chromosome conformation capture-qPCR evidence
eco
ECO:0000237
3C-qPCR evidence
A type of 3C evidence evidence that 1) quantifies interactions between a single pair of genomic loci (not multiple interactions) and 2) performs quantitative polymerase chain reaction (qPCR) in the quantitation step.
ECO:MCC
PMID:17641637
PMID:26025624
A type of chromosome conformation-based evidence that is derived by performing immunoprecipitation enrichment of the biotin labelled ligated fragments events prior to sequencing of the library and mapping it to the genome.
mchibucos
2010-11-19T04:24:03Z
eco
ECO:0000238
Hi-C is used to study the structural properties and spatial organization of chromosomes inside cells. Hi-C is similar to other types of chromosome conformation capture technology, but involves the addition of biotinylated nucleotides during the second or fourth step and enrichment for ligated fragments using immunoprecipitation after the fourth step.
Hi-C evidence
A type of chromosome conformation-based evidence that is derived by performing immunoprecipitation enrichment of the biotin labelled ligated fragments events prior to sequencing of the library and mapping it to the genome.
ECO:MCC
A type of chromosome conformation-based evidence that is derived by inverse polymerase chain reaction (inverse PCR) on a circularized 3C library prior to product quantitation with multiplexed high-throughput (HT) sequencing.
mchibucos
2010-11-30T03:22:25Z
3C sequencing
circularized 3C sequencing
circularized 3C-seq
eco
chromosome conformation capture sequencing evidence
ECO:0000239
3C-seq is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 3C-seq differs only in the fifth step, which involves inverse polymerase chain reaction (PCR) on a circularized 3C library prior to product quantitation.
3C-seq evidence
A type of chromosome conformation-based evidence that is derived by inverse polymerase chain reaction (inverse PCR) on a circularized 3C library prior to product quantitation with multiplexed high-throughput (HT) sequencing.
ECO:MCC
PMID:23411633
A type of experimental phenotypic evidence resulting from the disruption of a structural feature.
mchibucos
2010-12-06T12:24:16Z
anatomical perturbation evidence
eco
ECO:0000240
anatomical perturbation phenotypic evidence
A type of experimental phenotypic evidence resulting from the disruption of a structural feature.
ECO:MCC
A type of experimental phenotypic evidence resulting from modification to the surroundings or conditions in which an organism lives or operates.
mchibucos
2010-12-06T12:33:58Z
environmental perturbation evidence
eco
mechanical constraint evidence
ECO:0000241
Many environmental factors are subject to modification, such as temperature, pressure, humidity, radiation, and so forth.
environmental perturbation phenotypic evidence
A type of experimental phenotypic evidence resulting from modification to the surroundings or conditions in which an organism lives or operates.
ECO:MCC
A type of anatomical perturbation phenotypic evidence resulting from the surgical removal of tissue or subcellular components.
mchibucos
2010-12-06T12:33:58Z
ablated tissue evidence
tissue ablation evidence
eco
ECO:0000242
tissue ablation phenotypic evidence
A type of anatomical perturbation phenotypic evidence resulting from the surgical removal of tissue or subcellular components.
ECO:MCC
A type of anatomical perturbation phenotypic evidence resulting from the addition of tissue to an organism through a graft procedure.
mchibucos
2010-12-06T12:33:58Z
tissue grafting evidence
eco
ECO:0000243
tissue grafting phenotypic evidence
A type of anatomical perturbation phenotypic evidence resulting from the addition of tissue to an organism through a graft procedure.
ECO:MCC
A type of combinatorial analysis that is used in a manual assertion.
mchibucos
2010-12-09T02:02:12Z
eco
inferred from in-silico analysis
ECO:0000244
Combinatorial analyses could include experimental or computational results. Examples include: (i) large-scale experiment such as a genome-wide two-hybrid or genome-wide synthetic interactions; (ii) integration of large-scale data sets of various types; and (iii) text-based-computation, e.g. text-mining. For simple sequence comparisons, one should use the sequence similarity analysis evidence type. For microarray results alone, expression pattern analysis is appropriate; whereas, large-scale computational analysis should be used when microarray results are combined with the results of other types of large-scale experiments.
combinatorial evidence used in manual assertion
true
A type of combinatorial analysis that is used in a manual assertion.
ECO:MCC
RCA
A type of automatically integrated combinatorial evidence that is used in a manual assertion.
mchibucos
2010-12-09T02:37:54Z
GOECO:RCA
RCA
inferred from reviewed computational analysis
eco
computational combinatorial evidence used in manual assertion
ECO:0000245
automatically integrated combinatorial evidence used in manual assertion
http://geneontology.org/page/rca-inferred-reviewed-computational-analysis
true
true
RCA
Default
A type of automatically integrated combinatorial evidence that is used in a manual assertion.
ECO:RCT
GOECO:RCA
inferred from reviewed computational analysis
RCA
GOECO:RCA
inferred from reviewed computational analysis
GOECO:RCA
A type of computational combinatorial analysis that is used in an automatic assertion.
mchibucos
2010-12-09T02:37:54Z
eco
ECO:0000246
Merged with ECO:0000053.
computational combinatorial evidence used in automatic assertion
true
A type of computational combinatorial analysis that is used in an automatic assertion.
ECO:MCC
ISA
A type of sequence alignment evidence that is used in a manual assertion.
mchibucos
2010-12-09T05:12:27Z
GOECO:ISA
ISA
inferred from sequence alignment
eco
ECO:0000247
sequence alignment evidence used in manual assertion
http://geneontology.org/page/isa-inferred-sequence-alignment
true
ISA
Default
A type of sequence alignment evidence that is used in a manual assertion.
ECO:RCT
GOECO:ISA
inferred from sequence alignment
ISA
GOECO:ISA
inferred from sequence alignment
GOECO:ISA
IEA
A type of sequence alignment evidence that is used in an automatic assertion.
mchibucos
2010-12-09T05:12:27Z
eco
ECO:0000248
sequence alignment evidence used in automatic assertion
true
A type of sequence alignment evidence that is used in an automatic assertion.
ECO:RCT
IEA
A type of sequence similarity evidence that is used in an automatic assertion.
mchibucos
2010-12-09T05:22:30Z
GO_REF:0000107
eco
ECO:0000249
sequence similarity evidence used in automatic assertion
true
true
A type of sequence similarity evidence that is used in an automatic assertion.
ECO:RCT
GO_REF:0000107
Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl
ISS
A type of sequence similarity evidence that is used in a manual assertion.
mchibucos
2010-12-09T05:22:30Z
GOECO:ISS
ISS
inferred from sequence or structural similarity
eco
ECO:0000250
sequence similarity evidence used in manual assertion
http://geneontology.org/page/iss-inferred-sequence-or-structural-similarity
true
true
ISS
Default
A type of sequence similarity evidence that is used in a manual assertion.
ECO:MCC
GOECO:ISS
inferred from sequence or structural similarity
ISS
GOECO:ISS
inferred from sequence or structural similarity
GOECO:ISS
IEA
A type of similarity evidence that is used in an automatic assertion.
mchibucos
2010-12-09T05:28:12Z
IS
eco
inferred from similarity
ECO:0000251
similarity evidence used in automatic assertion
true
A type of similarity evidence that is used in an automatic assertion.
ECO:RCT
A type of similarity evidence that is used in a manual assertion.
mchibucos
2010-12-09T05:28:12Z
IS
eco
inferred from similarity
ECO:0000252
similarity evidence used in manual assertion
true
A type of similarity evidence that is used in a manual assertion.
ECO:RCT
A type of genetic similarity evidence that is used in a manual assertion.
mchibucos
2010-12-10T01:42:44Z
IGTS
eco
inferred from genetic similarity
ECO:0000253
genetic similarity evidence used in manual assertion
true
A type of genetic similarity evidence that is used in a manual assertion.
ECO:RCT
IEA
A type of genetic similarity evidence that is used in an automatic assertion.
mchibucos
2010-12-10T01:42:44Z
IGTS
eco
inferred from genetic similarity
ECO:0000254
genetic similarity evidence used in automatic assertion
true
A type of genetic similarity evidence that is used in an automatic assertion.
ECO:RCT
ISM
A type of match to sequence model evidence that is used in a manual assertion.
mchibucos
2010-12-10T02:26:35Z
GOECO:ISM
GO_REF:0000011
ISM
inferred from sequence model
eco
ECO:0000255
match to sequence model evidence used in manual assertion
http://geneontology.org/page/ism-inferred-sequence-model
true
ISM
Default
A type of match to sequence model evidence that is used in a manual assertion.
ECO:RCT
GOECO:ISM
inferred from sequence model
GO_REF:0000011
Hidden Markov Models (TIGR)
ISM
GOECO:ISM
inferred from sequence model
GOECO:ISM
IEA
A type of match to sequence model evidence that is used in an automatic assertion.
mchibucos
2010-12-10T02:26:35Z
GO_REF:0000002
eco
ECO:0000256
match to sequence model evidence used in automatic assertion
true
A type of match to sequence model evidence that is used in an automatic assertion.
ECO:RCT
GO_REF:0000002
Gene Ontology annotation through association of InterPro records with GO terms.
ISM
A type of motif similarity evidence that is used in a manual assertion.
mchibucos
2010-12-10T02:44:34Z
eco
recognized domains
ECO:0000257
motif similarity evidence used in manual assertion
true
A type of motif similarity evidence that is used in a manual assertion.
ECO:RCT
IEA
A type of motif similarity evidence that is used in an automatic assertion.
mchibucos
2010-12-10T02:44:34Z
eco
recognized domains
ECO:0000258
motif similarity evidence used in automatic assertion
true
A type of motif similarity evidence that is used in an automatic assertion.
ECO:RCT
IEA
A type of match to InterPro member signature evidence that is used in an automatic assertion.
mchibucos
2010-12-10T02:54:51Z
eco
ECO:0000259
match to InterPro member signature evidence used in automatic assertion
true
A type of match to InterPro member signature evidence that is used in an automatic assertion.
ECO:RCT
ISM
A type of match to InterPro member signature evidence that is used in a manual assertion.
mchibucos
2010-12-10T02:54:51Z
eco
ECO:0000260
match to InterPro member signature evidence used in manual assertion
true
A type of match to InterPro member signature evidence that is used in a manual assertion.
ECO:RCT
IEA
A type of targeting sequence prediction that is used in an automatic assertion.
mchibucos
2010-12-10T03:02:49Z
eco
targeting sequence prediction
ECO:0000261
targeting sequence prediction evidence used in automatic assertion
true
A type of targeting sequence prediction that is used in an automatic assertion.
ECO:RCT
ISM
A type of targeting sequence prediction that is used in a manual assertion.
mchibucos
2010-12-10T03:02:49Z
eco
targeting sequence prediction
ECO:0000262
targeting sequence prediction evidence used in manual assertion
true
A type of targeting sequence prediction that is used in a manual assertion.
ECO:RCT
IEA
A type of transmembrane domain prediction that is used in an automatic assertion.
mchibucos
2010-12-10T03:28:35Z
eco
transmembrane domain prediction
ECO:0000263
transmembrane domain prediction evidence used in automatic assertion
true
A type of transmembrane domain prediction that is used in an automatic assertion.
ECO:RCT
ISM
A type of transmembrane domain prediction that is used in a manual assertion.
mchibucos
2010-12-10T03:28:35Z
eco
transmembrane domain prediction
ECO:0000264
transmembrane domain prediction evidence used in manual assertion
true
A type of transmembrane domain prediction that is used in a manual assertion.
ECO:RCT
IEA
A type of sequence orthology evidence that is used in an automatic assertion.
mchibucos
2010-12-10T03:39:41Z
GO_REF:0000035
eco
Ortholog evidence
ortholog evidence
ECO:0000265
sequence orthology evidence used in automatic assertion
true
A type of sequence orthology evidence that is used in an automatic assertion.
ECO:RCT
GO_REF:0000035
Automatic transfer of experimentally verified manual GO annotation data to plant orthologs using Ensembl Compara
ISO
A type of sequence orthology evidence that is used in a manual assertion.
mchibucos
2010-12-10T03:39:41Z
GOECO:ISO
ISO
inferred from sequence orthology
eco
Ortholog evidence
ortholog evidence
ECO:0000266
sequence orthology evidence used in manual assertion
http://geneontology.org/page/iso-inferred-sequence-orthology
true
ISO
Default
A type of sequence orthology evidence that is used in a manual assertion.
ECO:MCC
GOECO:ISO
inferred from sequence orthology
ISO
GOECO:ISO
inferred from sequence orthology
GOECO:ISO
A type of protein detection assay evidence where an antigen is bound to a substrate, and an antibody directly or indirectly linked to an enzyme is utilized to determine the amount of bound antigen which is visualized with a color change in the substrate.
CollecTF
mchibucos
2010-12-14T01:57:13Z
MI:0411
ELISA evidence
enzyme-linked immunosorbent assay
eco
ECO:0000267
ELISA is sometimes used in the study of transcriptional regulation to identify a produced protein, especially secreted protein.
enzyme-linked immunoabsorbent assay evidence
A type of protein detection assay evidence where an antigen is bound to a substrate, and an antibody directly or indirectly linked to an enzyme is utilized to determine the amount of bound antigen which is visualized with a color change in the substrate.
ECO:MCC
ECO:SW
PMID:23949770
MI:0411
enzyme linked immunosorbent assay
A type of direct assay evidence in which cells or particles are characterized by passing them through a light source and monitoring the resultant light scatter or fluorochrome excitation.
mchibucos
2010-12-14T02:07:08Z
FCM
eco
ECO:0000268
flow cytometry evidence
A type of direct assay evidence in which cells or particles are characterized by passing them through a light source and monitoring the resultant light scatter or fluorochrome excitation.
ECO:MCC
EXP
A type of experimental evidence that is used in a manual assertion.
mchibucos
2010-12-20T05:36:49Z
GOECO:EXP
EXP
inferred from experiment
eco
ECO:0000269
experimental evidence used in manual assertion
http://geneontology.org/page/exp-inferred-experiment
true
EXP
Default
A type of experimental evidence that is used in a manual assertion.
ECO:MCC
GOECO:EXP
inferred from experiment
EXP
GOECO:EXP
inferred from experiment
GOECO:EXP
IEP
A type of expression pattern evidence that is used in a manual assertion.
mchibucos
2010-12-20T05:46:39Z
GOECO:IEP
IEP
inferred from expression pattern
eco
ECO:0000270
expression pattern evidence used in manual assertion
http://geneontology.org/page/iep-inferred-expression-pattern
true
IEP
Default
A type of expression pattern evidence that is used in a manual assertion.
ECO:MCC
GOECO:IEP
inferred from expression pattern
IEP
GOECO:IEP
inferred from expression pattern
GOECO:IEP
mchibucos
2010-12-20T05:51:58Z
eco
ECO:0000271
This general 'array experiment' term should not be used - replace with the specific type of array (e.g. ECO:0000273, ECO:0000276, ECO:0000285, etc.)
array experiment evidence used in manual assertion
true
IEP
A type of Affymetrix GeneChip evidence that is used in a manual assertion.
mchibucos
2010-12-20T05:53:36Z
Affymetrix array experiment evidence
eco
ECO:0000272
Affymetrix GeneChip evidence used in manual assertion
true
A type of Affymetrix GeneChip evidence that is used in a manual assertion.
ECO:MCC
IEP
A type of cDNA to DNA expression microarray evidence that is used in a manual assertion.
mchibucos
2010-12-20T05:55:49Z
ECO:0001178
ECO:0005525
eco
DNA microarray|RNA microarray
ECO:0000273
cDNA to DNA expression microarray evidence used in manual assertion
true
A type of cDNA to DNA expression microarray evidence that is used in a manual assertion.
ECO:MCC
IDA
A type of differential methylation hybridization evidence that is used in a manual assertion.
mchibucos
2010-12-20T05:58:44Z
CpG island microarray evidence
CpG island microarray evidence used in manual assertion
eco
ECO:0000274
differential methylation hybridization evidence used in manual assertion
true
A type of differential methylation hybridization evidence that is used in a manual assertion.
ECO:RCT
IEP
A type of expression microarray evidence that is used in a manual assertion.
mchibucos
2010-12-20T06:01:26Z
eco
differential gene expression evidence from microarray experiment
ECO:0000275
expression microarray evidence used in manual assertion
true
A type of expression microarray evidence that is used in a manual assertion.
ECO:MCC
IEP
A type of cRNA to DNA expression microarray evidence that is used in a manual assertion.
mchibucos
2010-12-20T06:03:28Z
genomic microarray evidence
genomic microarray evidence used in manual assertion
eco
ECO:0000276
cRNA to DNA expression microarray evidence used in manual assertion
true
A type of cRNA to DNA expression microarray evidence that is used in a manual assertion.
ECO:RCT
IEP
A type of evidence arising from a Nimblegen array experiment that is used in a manual assertion.
mchibucos
2010-12-20T06:05:20Z
eco
ECO:0000277
Nimblegen array evidence used in manual assertion
true
A type of evidence arising from a Nimblegen array experiment that is used in a manual assertion.
ECO:MCC
EXP
A type of array-based sequence capture evidence that is used in a manual assertion.
mchibucos
2010-12-20T06:09:45Z
DNA microarray
oligonucleotide microarray evidence
oligonucleotide microarray evidence used in manual assertion
eco
SNP array evidence
single nucleotide polymorphism array evidence
ECO:0000278
array-based sequence capture evidence used in manual assertion
true
A type of array-based sequence capture evidence that is used in a manual assertion.
ECO:MCC
IEP
A type of qualitative western immunoblotting evidence that is used in a manual assertion.
mchibucos
2010-12-20T06:20:01Z
ECO:0007183
protein expression level evidence based on western blot used in manual assertion
eco
Western blot expression analysis
protein immunoblot
protein levels (e.g. Western blots)
ECO:0000279
qualitative western immunoblotting evidence used in manual assertion
true
true
A type of qualitative western immunoblotting evidence that is used in a manual assertion.
ECO:MCC
IEP
A type of expression library screen evidence that is used in a manual assertion.
mchibucos
2010-12-20T06:24:05Z
eco
expression library screening
ECO:0000281
expression library screen evidence used in manual assertion
true
A type of expression library screen evidence that is used in a manual assertion.
ECO:MCC
IEP
A type of heterologous protein expression analysis that is used in a manual assertion.
mchibucos
2010-12-20T06:27:04Z
eco
protein expression in heterologous system
ECO:0000282
heterologous protein expression evidence used in manual assertion
true
A type of heterologous protein expression analysis that is used in a manual assertion.
ECO:MCC
IEP
A type of protein expression spatial pattern analysis that is used in a manual assertion.
mchibucos
2010-12-20T06:31:44Z
eco
ECO:0000283
spatial pattern of protein expression evidence used in manual assertion
true
A type of protein expression spatial pattern analysis that is used in a manual assertion.
ECO:MCC
IEP
A type of protein expression analysis that is used in a manual assertion.
mchibucos
2010-12-20T06:33:46Z
ECO:0000280
protein expression level evidence used in manual assertion
eco
ECO:0000284
protein expression evidence used in manual assertion
true
A type of protein expression analysis that is used in a manual assertion.
ECO:MCC
IEP
A type of DNA to cDNA expression microarray evidence that is used in a manual assertion.
mchibucos
2010-12-20T06:41:33Z
REM evidence
RNA expression microarray evidence
microarray RNA expression level evidence
eco
transcript levels (e.g. microarray data)
ECO:0000285
DNA to cDNA expression microarray evidence used in manual assertion
A type of DNA to cDNA expression microarray evidence that is used in a manual assertion.
ECO:MCC
true
IEP
A type of differential hybridization experiment that is used in a manual assertion.
mchibucos
2010-12-20T06:55:14Z
eco
differential hybridization
ECO:0000287
differential hybridization evidence used in manual assertion
true
A type of differential hybridization experiment that is used in a manual assertion.
ECO:MCC
EXP
A type of RNA protection assay that is used in a manual assertion.
mchibucos
2010-12-20T06:57:33Z
ribonuclease protection assay
eco
RNA protection assay|RPA
RNAse protection assay
ECO:0000288
RNA protection assay evidence used in manual assertion
true
A type of RNA protection assay that is used in a manual assertion.
ECO:MCC
IEP
A type of spatial pattern of transcript expression analysis that is used in a manual assertion.
mchibucos
2010-12-20T06:59:18Z
eco
ECO:0000289
spatial pattern of transcript expression evidence used in manual assertion
true
A type of spatial pattern of transcript expression analysis that is used in a manual assertion.
ECO:MCC
IEP
A type of subtractive hybridization experiment that is used in a manual assertion.
mchibucos
2010-12-20T07:00:48Z
eco
subtractive hybridization
ECO:0000290
subtractive hybridization evidence used in manual assertion
true
A type of subtractive hybridization experiment that is used in a manual assertion.
ECO:MCC
IEP
A type of transcript expression evidence that is used in a manual assertion.
mchibucos
2010-12-20T07:02:08Z
ECO:0000286
transcript expression level evidence
transcriptomics evidence used in manual assertion
eco
ECO:0000291
transcript expression evidence used in manual assertion
true
A type of transcript expression evidence that is used in a manual assertion.
ECO:MCC
A type of mutant phenotype evidence that uses anti-sense by introducing morpholino oligonucleotides into the cytosol of a cell.
mchibucos
2011-01-10T03:36:25Z
anti-sense
eco
ECO:0000292
Morpholino oligonucleotides modify gene expression by blocking access of other molecules to specific, approximately 25-base-long regions of the base-pairing surfaces of ribonucleic acid (RNA). To achieve this anti-sense knockdown technique, delivery of the morpholino can be achieved via microinjection, electroporation, or another method.
morpholino experiment evidence
A type of mutant phenotype evidence that uses anti-sense by introducing morpholino oligonucleotides into the cytosol of a cell.
ECO:MCC
A total of 160 SELEX fragments were cloned and sequenced, which were classified into 29 CRP-binding sequences, including 13 previously identified loci and 16 newly identified sites (Table S2). When the CRP-binding sequences are located upstream or near promoters of the flanking genes, these genes are predicted to be under the control of CRP.
A type of evidence arising from a physical interaction analysis where a combinatorial chemistry technique is used to identify oligonucleotides that bind to a target ligand.
mchibucos
2011-01-10T04:23:50Z
MI:0657
SELEX evidence
in vitro selection evidence
eco
in vitro evolution evidence
ECO:0000293
SELEX begins with the synthesis of a large oligonucleotide library, either single-stranded DNA or RNA, which consists of random fixed-length sequences flanked by constant 5' and 3' ends that serve as primers. The library is exposed to a target ligand, typically a protein or small organic compound. Unbound sequences are removed, typically with affinity chromatography. Bound sequences are eluted and the nucleic acid is extracted, followed by PCR amplification (RNA is first reverse transcribed). PCR product is converted to single stranded (DNA) or transcribed (RNA). Oligonucleotides are bound to the ligand again and the process is repeated with increasing elution stringency. After several rounds of the process, recovered oligonucleotides are sequenced and analyzed to reveal the binding specificity of the protein.
systematic evolution of ligands by exponential amplification evidence
A total of 160 SELEX fragments were cloned and sequenced, which were classified into 29 CRP-binding sequences, including 13 previously identified loci and 16 newly identified sites (Table S2). When the CRP-binding sequences are located upstream or near promoters of the flanking genes, these genes are predicted to be under the control of CRP.
PMID:21673794
A type of evidence arising from a physical interaction analysis where a combinatorial chemistry technique is used to identify oligonucleotides that bind to a target ligand.
ECO:MCC
url:http://en.wikipedia.org/wiki/Systematic_Evolution_of_Ligands_by_Exponential_Enrichment
MI:0657
systematic evolution of ligands by exponential enrichment
Bacterial one-hybrid assays confirmed the interaction between MtrA and the regulatory sequence of the dnaA initiator gene.
A type of bait-prey hybrid interaction evidence that uses bacterial transformation with two plasmids to assess in vivo binding of a DNA-binding domain (bait) and DNA target site (prey).
mchibucos
2011-01-10T06:16:20Z
B1H evidence
eco
ECO:0000294
Bacterial one-hybrid assay is a method for screening a library of candidate proteins (prey plasmid) for the ability to bind to a target, cis-regulatory element or any other short, DNA binding sequence placed 5' to reporter genes (bait plasmid). Transformation of a bacterial host with two different plasmids is required: One is designed to express the "bait". The other plasmid contains a "prey" which, if bound to by the chimeric fusion product, drives expression of downstream reporter genes.
bacterial one-hybrid evidence
Bacterial one-hybrid assays confirmed the interaction between MtrA and the regulatory sequence of the dnaA initiator gene.
PMID:20843371
A type of bait-prey hybrid interaction evidence that uses bacterial transformation with two plasmids to assess in vivo binding of a DNA-binding domain (bait) and DNA target site (prey).
ECO:MCC
A type of transcript evidence based on high-throughput (HT) sequencing of fragmented cDNA molecules.
mchibucos
2011-01-11T12:54:50Z
ECO:0000357
ECO:0001821
RNA sequencing assay evidence
RNA-seq evidence
RNAseq evidence
WTSS
whole transcriptome shotgun sequencing
differential gene expression evidence from RNA-seq experiment
eco
RNA sequencing
ECO:0000295
Total RNA is isolated from cells and mRNA is purified by targeting the 3' polyadenylated (poly(A)) tail with poly(T) oligos covalently attached to a substrate. Next, cDNA fragments are generated either by hydrolysis of RNA into 200-300 base oligonucleotides, preceded by reverse transcription, or by reverse transcription initiated by random primers. The cDNA second strand is synthesized, fragments are adapter ligated and high-throughput sequencing is performed by Roche 454, Illumina, ABI-SOLiD, or another HT sequencing technology. Resulting sort reads are aligned against a reference genome, and downstream analysis is performed.
RNA-sequencing evidence
A type of transcript evidence based on high-throughput (HT) sequencing of fragmented cDNA molecules.
ECO:MCC
whole transcriptome shotgun sequencing
PMID:18611170
A type of experimental phenotypic evidence where embryonic development proceeds although cytokinesis is blocked.
mchibucos
2011-01-11T03:28:49Z
eco
ECO:0000298
In the embryos of some organisms, inhibition of cytokinesis blocks neither the cell cycle nor the unfolding of the developmental program. As such, embryonic morphology can be frozen, allowing analysis of the developmental fate of each cell present at the time of cleavage arrest.
cleavage arrested development evidence
A type of experimental phenotypic evidence where embryonic development proceeds although cytokinesis is blocked.
ECO:MCC
A type of cleavage arrested development that arises after treatment with cytochalasin.
mchibucos
2011-01-11T03:30:29Z
eco
ECO:0000299
Cytochalasin inhibits cytokinesis by blocking the formation of contractile microfilaments.
cytochalasin experiment evidence
A type of cleavage arrested development that arises after treatment with cytochalasin.
ECO:MCC
A type of immunolocalization evidence data that was generated using green fluorescent protein (GFP) as a marker.
mchibucos
2011-01-11T03:48:50Z
GFP immunolocalization evidence
eco
ECO:0000300
This term describes immunolocalization of the protein; to describe transcriptional activation, use the term "localization of green fluorescent protein transcript".
green fluorescent protein immunolocalization evidence
A type of immunolocalization evidence data that was generated using green fluorescent protein (GFP) as a marker.
ECO:MCC
A type of immunolocalization evidence that was generated using LacZ protein as a marker.
mchibucos
2011-01-11T04:06:40Z
LacZ protein immunolocalization evidence
eco
ECO:0000301
This term describes immunolocalization of the protein; to describe transcriptional activation, use the term "localization of LacZ transcript".
beta-galactosidase protein immunolocalization evidence
A type of immunolocalization evidence that was generated using LacZ protein as a marker.
ECO:MCC
A type of author statement that is used in a manual assertion.
mchibucos
2011-01-20T02:26:47Z
ECO:0007764
author inference used in manual assertion
eco
ECO:0000302
author statement used in manual assertion
true
A type of author statement that is used in a manual assertion.
ECO:MCC
NAS
A type of author statement without traceable support that is used in a manual assertion.
mchibucos
2011-01-20T02:29:50Z
GOECO:NAS
NAS
eco
non-traceable author statement
ECO:0000303
author statement without traceable support used in manual assertion
http://geneontology.org/page/nas-non-traceable-author-statement
true
NAS
Default
A type of author statement without traceable support that is used in a manual assertion.
ECO:MCC
GOECO:NAS
non-traceable author statement
NAS
GOECO:NAS
non-traceable author statement
GOECO:NAS
TAS
A type of author statement supported by traceable reference that is used in a manual assertion.
mchibucos
2011-01-20T02:31:03Z
GOECO:TAS
TAS
eco
traceable author statement
ECO:0000304
author statement supported by traceable reference used in manual assertion
http://geneontology.org/page/tas-traceable-author-statement
true
TAS
Default
A type of author statement supported by traceable reference that is used in a manual assertion.
ECO:MCC
GOECO:TAS
traceable author statement
TAS
GOECO:TAS
traceable author statement
GOECO:TAS
IC
A type of curator inference that is used in a manual assertion.
mchibucos
2011-01-20T02:33:32Z
GOECO:IC
IC
inferred by curator
eco
ECO:0000305
curator inference used in manual assertion
http://geneontology.org/page/ic-inferred-curator
true
IC
Default
A type of curator inference that is used in a manual assertion.
ECO:MCC
GOECO:IC
inferred by curator
IC
GOECO:IC
inferred by curator
GOECO:IC
IC
A type of inference from background scientific knowledge that is used in a manual assertion.
mchibucos
2011-01-20T02:35:11Z
eco
ECO:0000306
inference from background scientific knowledge used in manual assertion
true
A type of inference from background scientific knowledge that is used in a manual assertion.
ECO:MCC
ND
An inference that results when research finds no evidence information in the scientific literature, at reference databases, or from other resources that is used in an manual assertion.
mchibucos
2011-01-20T02:43:18Z
GOECO:ND
ND
no biological data available
eco
ECO:0000307
no evidence data found used in manual assertion
http://geneontology.org/page/nd-no-biological-data-available
true
ND
Default
An inference that results when research finds no evidence information in the scientific literature, at reference databases, or from other resources that is used in an manual assertion.
ECO:MCC
GOECO:ND
no biological data available
ND
GOECO:ND
no biological data available
GOECO:ND
A type of phylogenetic evidence whereby an aspect of a descendant gene is inferred through the characterization of an aspect of an ancestral gene.
mchibucos
2011-02-04T05:41:26Z
eco
ECO:0000308
First, a characteristic of the most recent common ancestor (MRCA) is inferred from experimental evidence in descendants; this is followed by inferring a characteristic of a descendant of the MRCA. This type of evidence can be used in support of both positive and "not" GO annotations.
biological aspect of ancestor evidence
A type of phylogenetic evidence whereby an aspect of a descendant gene is inferred through the characterization of an aspect of an ancestral gene.
ECO:MCC
A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by a cap-trapper system.
mchibucos
2011-02-17T01:33:09Z
CAGE
eco
ECO:0000309
Complementary DNA (cDNA) is synthesized from microgram quantities of mRNA using first-strand cDNA primer (oligo dT12-18) and reverse transcriptase in the presence of trehalose and sorbitol, followed by selection of full-length cDNA with biotinylated cap-trapper. Linkers are attached to the 5' ends of full-length enriched cDNAs to introduce a recognition site for the restriction endonuclease MmeI, which creates a two base overhang. After amplification, sequencing tags are concatenated for high-throughput sequencing. Resulting sort reads are aligned against a reference genome, and downstream analysis is performed.
cap analysis of gene expression evidence
A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by a cap-trapper system.
ECO:MCC
CAGE
PMID:16489339
A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by reverse transcriptase template switching.
mchibucos
2011-02-17T01:33:34Z
eco
nanoCAGE
ECO:0000310
NanoCAGE captures the 5' ends of molecules by template switching. When polymerizing the cDNA of a capped mRNA, the reverse transcriptase adds extra cytosines that are complementary to the cap. Each 5' full length cDNAs is extended upon hybridization of the riboguanosine-tailed template switching oligonucleotides to these extra cytosines. In semisuppressive PCR, the short templates fold intramolecularly and prevent the binding of primers, which precludes amplification; longer molecules are less likely to fold and are thus amplified. Templates derived from reaction artifacts form stable homoduplexes, also precluding amplification. After template switching, semisuppressive PCR, and EcoP151 cleavage, 25-bp tags are ligated to bar code-containing oligonucleotide adaptors. After PCR amplification, the nanoCAGE tags are sequenced by synthesis. NanoCAGE requires as little as 10 nanograms of total RNA.
nano-cap analysis of gene expression evidence
A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by reverse transcriptase template switching.
ECO:MCC
nanoCAGE
PMID:20543846
A type of documented statement evidence that is based on work performed by a person or group prior to a use by a different person or group.
mchibucos
2011-03-02T05:24:13Z
eco
ECO:0000311
imported information
A type of documented statement evidence that is based on work performed by a person or group prior to a use by a different person or group.
ECO:MCC
A type of imported information that is used in a manual assertion.
mchibucos
2011-03-02T05:29:44Z
eco
ECO:0000312
imported information used in manual assertion
true
A type of imported information that is used in a manual assertion.
ECO:MCC
IEA
A type of imported information that is used in an automatic assertion.
mchibucos
2011-03-02T05:33:43Z
eco
ECO:0000313
imported information used in automatic assertion
true
A type of imported information that is used in an automatic assertion.
ECO:MCC
IDA
A type of direct assay evidence that is used in a manual assertion.
mchibucos
2011-10-28T04:59:31Z
GOECO:IDA
IDA
inferred from direct assay
eco
ECO:0000314
direct assay evidence used in manual assertion
http://geneontology.org/page/ida-inferred-direct-assay
true
IDA
Default
A type of direct assay evidence that is used in a manual assertion.
ECO:MCC
GOECO:IDA
inferred from direct assay
IDA
GOECO:IDA
inferred from direct assay
GOECO:IDA
IMP
A type of mutant phenotype evidence that is used in a manual assertion.
mchibucos
2011-10-28T05:12:49Z
GOECO:IMP
IMP
inferred from mutant phenotype
eco
ECO:0000315
mutant phenotype evidence used in manual assertion
http://geneontology.org/page/imp-inferred-mutant-phenotype
true
IMP
Default
A type of mutant phenotype evidence that is used in a manual assertion.
ECO:MCC
GOECO:IMP
inferred from mutant phenotype
IMP
GOECO:IMP
inferred from mutant phenotype
GOECO:IMP
IGI
A type of genetic interaction experiment evidence that is used in a manual assertion.
mchibucos
2011-10-28T05:14:42Z
GOECO:IGI
IGI
inferred from genetic interaction
eco
ECO:0000316
genetic interaction evidence used in manual assertion
http://geneontology.org/page/igi-inferred-genetic-interaction
true
IGI
Default
A type of genetic interaction experiment evidence that is used in a manual assertion.
ECO:MCC
GOECO:IGI
inferred from genetic interaction
IGI
GOECO:IGI
inferred from genetic interaction
GOECO:IGI
IGC
A type of genomic context evidence that is used in a manual assertion.
mchibucos
2011-10-28T05:22:53Z
GOECO:IGC
IGC
inferred from genomic context
eco
ECO:0000317
genomic context evidence used in manual assertion
http://geneontology.org/page/igc-inferred-genomic-context
true
IGC
Default
A type of genomic context evidence that is used in a manual assertion.
ECO:MCC
GOECO:IGC
inferred from genomic context
IGC
GOECO:IGC
inferred from genomic context
GOECO:IGC
IBA
A type of biological aspect of ancestor evidence that is used in a manual assertion.
mchibucos
2011-10-28T05:23:51Z
GOECO:IBA
IBA
inferred from biological aspect of ancestor
eco
ECO:0000318
biological aspect of ancestor evidence used in manual assertion
http://geneontology.org/page/iba-inferred-biological-aspect-ancestor
true
IBA
Default
A type of biological aspect of ancestor evidence that is used in a manual assertion.
ECO:MCC
GOECO:IBA
inferred from biological aspect of ancestor
IBA
GOECO:IBA
inferred from biological aspect of ancestor
GOECO:IBA
IBD
A type of biological aspect of descendant evidence that is used in a manual assertion.
mchibucos
2011-10-28T05:25:09Z
GOECO:IBD
IBD
inferred from biological aspect of descendant
eco
ECO:0000319
biological aspect of descendant evidence used in manual assertion
http://geneontology.org/page/ibd-inferred-biological-aspect-descendent
true
IBD
Default
A type of biological aspect of descendant evidence that is used in a manual assertion.
ECO:MCC
GOECO:IBD
inferred from biological aspect of descendant
IBD
GOECO:IBD
inferred from biological aspect of descendant
GOECO:IBD
IKR
A type of phylogenetic determination of loss of key residues evidence that is used in a manual assertion.
mchibucos
2011-10-28T05:25:48Z
GOECO:IKR
GOECO:IMR
IKR
IMR
inferred from key residues
inferred from missing residues
eco
ECO:0000320
phylogenetic determination of loss of key residues evidence used in manual assertion
http://geneontology.org/page/ikr-inferred-key-residues
true
IKR
Default
A type of phylogenetic determination of loss of key residues evidence that is used in a manual assertion.
ECO:MCC
GOECO:IKR
inferred from key residues
GOECO:IMR
inferred from missing residues
IKR
GOECO:IKR
IMR
GOECO:IKR
inferred from key residues
GOECO:IKR
inferred from missing residues
GOECO:IKR
IRD
A type of rapid divergence from ancestral sequence evidence that is used in a manual assertion.
mchibucos
2011-10-28T05:26:42Z
GOECO:IRD
IRD
inferred from rapid divergence
eco
ECO:0000321
rapid divergence from ancestral sequence evidence used in manual assertion
http://geneontology.org/page/ird-inferred-rapid-divergence
true
IRD
Default
A type of rapid divergence from ancestral sequence evidence that is used in a manual assertion.
ECO:MCC
GOECO:IRD
inferred from rapid divergence
IRD
GOECO:IRD
inferred from rapid divergence
GOECO:IRD
IEA
Evidence that was initially used in manual assertion by one person or group, which is imported by a second person or group and used in automatic assertion.
mchibucos
2011-12-13T12:04:48Z
eco
ECO:0000322
imported manually asserted information used in automatic assertion
Evidence that was initially used in manual assertion by one person or group, which is imported by a second person or group and used in automatic assertion.
ECO:MCC
IEA
A type of imported information used in automatic assertion that was initially used in automatic assertion by one person or group, which is imported by a second person or group and used in automatic assertion.
mchibucos
2011-12-13T02:06:25Z
eco
ECO:0000323
imported automatically asserted information used in automatic assertion
A type of imported information used in automatic assertion that was initially used in automatic assertion by one person or group, which is imported by a second person or group and used in automatic assertion.
ECO:MCC
In the images shown in Figure 9, the MelR focus is 15 x 33 nm across the shortest and longest axes of the oval in the complex with the shortened arm (right hand panel), compared to 9 x 12 nm in the other complex (centre panel). The simplest explanation for these observations, that is consistent with the location of sites in the DNA fragment (Figure 9), is that one type of complex contains 3 MelR molecules bound at sites 2, 1 and 1' (centre panel), whilst the other contains 4 MelR molecules bound at sites 2, 1, 1' and R (right panel).
A type of direct assay evidence in which an image is created and analyzed.
mchibucos
2012-02-23T12:01:43Z
ECO:0001122
ECO:0005024
ECO:MCC
radiologic test evidence
eco
ECO:0000324
imaging assay evidence
In the images shown in Figure 9, the MelR focus is 15 x 33 nm across the shortest and longest axes of the oval in the complex with the shortened arm (right hand panel), compared to 9 x 12 nm in the other complex (centre panel). The simplest explanation for these observations, that is consistent with the location of sites in the DNA fragment (Figure 9), is that one type of complex contains 3 MelR molecules bound at sites 2, 1 and 1' (centre panel), whilst the other contains 4 MelR molecules bound at sites 2, 1, 1' and R (right panel).
PMID:18346968
A type of experimental evidence that is based on separation of constituent parts of a mixture (the mobile phase) as they pass differentially through a stationary phase due to differences in partition coefficient and retention on the stationary phase.
mchibucos
2012-05-16T11:46:27Z
chromatographic evidence
eco
ECO:0000325
chromatography evidence
A type of experimental evidence that is based on separation of constituent parts of a mixture (the mobile phase) as they pass differentially through a stationary phase due to differences in partition coefficient and retention on the stationary phase.
ECO:MCC
A type of sequence alignment evidence that is based on comparing the position of exon junctions, relative to a reference genome, for a transcript annotation and a supporting transcript.
mchibucos
2012-06-08T11:03:59Z
eco
ECO:0000326
transcript splice pattern evidence
A type of sequence alignment evidence that is based on comparing the position of exon junctions, relative to a reference genome, for a transcript annotation and a supporting transcript.
ECO:MCC
A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features.
mchibucos
2012-06-08T11:11:24Z
eco
ECO:0000327
This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that have the same splice pattern as a RefSeq transcript. If such full transcript information is not available, RefSeq reports sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, supported by the evidence term ECO:0000328 or a child.
whole transcript splice pattern evidence
A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features.
ECO:MCC
A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript.
mchibucos
2012-06-08T11:21:57Z
eco
ECO:0000328
This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, but for which full transcript information is unavailable. For sequences that have the same splice pattern as a whole RefSeq transcript, use the evidence term ECO:0000327 or a child.
coding sequence splice pattern evidence
A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript.
ECO:MCC
ISA
A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features, and is used in manual assertion.
mchibucos
2012-06-08T11:40:03Z
eco
ECO:0000329
This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that have the same splice pattern as a RefSeq transcript. If such full transcript information is not available, RefSeq reports sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, supported by the evidence term ECO:0000328 or a child.
whole transcript splice pattern evidence used in manual assertion
true
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
ISA
A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript, and is used in manual assertion.
mchibucos
2012-06-08T11:43:47Z
eco
ECO:0000330
This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, but for which full transcript information is unavailable. For sequences that have the same splice pattern as a whole RefSeq transcript, use the evidence term ECO:0000327 or a child.
coding sequence splice pattern evidence used in manual assertion
true
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
IEA
A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript, and is used in automatic assertion.
mchibucos
2012-06-08T11:48:09Z
eco
ECO:0000331
This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, but for which full transcript information is unavailable. For sequences that have the same splice pattern as a whole RefSeq transcript, use the evidence term ECO:0000327 or a child.
coding sequence splice pattern evidence used in automatic assertion
true
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
IEA
A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features, and is used in automatic assertion.
mchibucos
2012-06-08T11:49:17Z
eco
ECO:0000332
This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that have the same splice pattern as a RefSeq transcript. If such full transcript information is not available, RefSeq reports sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, supported by the evidence term ECO:0000328 or a child.
whole transcript splice pattern evidence used in automatic assertion
true
A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features, and is used in automatic assertion.
ECO:MCC
A type of gel electrophoresis evidence where proteins are separated according to their electrophoretic mobility.
mchibucos
2012-07-31T02:56:43Z
SDS-PAGE evidence
eco
ECO:0000333
Electrophoretic mobility is a function of both the length and charge of a protein. The protein sample is linearized with sodium dodecyl sulfate (SDS), an anionic detergent. Typically, polypeptides bound with SDS possess an even distribution of charge per unit mass, and subsequent fractionation is by size.
sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence
A type of gel electrophoresis evidence where proteins are separated according to their electrophoretic mobility.
ECO:MCC
PubMed:4861258
url:http://www.nature.com/nmeth/journal/v2/n1/full/nmeth0105-83.html
url:http://www.ncbi.nlm.nih.gov/Class/NAWBIS/Modules/Protein/protein18.html
A type of direct assay evidence resulting from an assay where both the size of and number of particles in a sample are determined.
mchibucos
2012-07-31T03:19:32Z
eco
ECO:0000334
An example of an instrument used to analyze particle sizes and counts is the Beckman Coulter® Z Series system.
particle size and count assay evidence
A type of direct assay evidence resulting from an assay where both the size of and number of particles in a sample are determined.
ECO:MCC
A type of direct assay evidence where the quantity of a substance used as part of an assay is measured.
mchibucos
2012-07-31T03:52:46Z
eco
ECO:0000335
Two examples of substance quantification assay are (i) measuring how much of a radiolabelled compound is taken up by a cell and (ii) measuring how much of a substrate is turned over by a given enzyme.
substance quantification evidence
A type of direct assay evidence where the quantity of a substance used as part of an assay is measured.
ECO:MCC
A type of cell proliferation 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 usually by means of a fluorescent marker and flow cytometric analysis.
mchibucos
2012-08-24T12:03:58Z
fitness profiling
eco
ECO:0000336
competitive growth assay evidence
A type of cell proliferation 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 usually by means of a fluorescent marker and flow cytometric analysis.
GOC:MAH
PMID:14718172
PMID:20537132
fitness profiling
GOC:MAH
PMID:20537132
We analyzed the electrophoretic pattern of cytosolic proteins extracted from LM3 and LM3-2 cells, grown under standard conditions up to mid-exponential phase (Fig. 1). The presence of differentially expressed proteins in the two strains, together with results of previous studies [28,29] demonstrated the role of CcpA as global regulator in L. plantarum.
A type of direct assay evidence where molecules have been sorted according to their size and charge by moving through a gel in the presence of an electric field.
mchibucos
2012-08-24T12:11:51Z
ECO:0005026
eco
ECO:0000337
Molecules typically separated include DNA, RNA, or protein. The gel is typically made of agarose, polyacrylamide, or starch.
gel electrophoresis evidence
We analyzed the electrophoretic pattern of cytosolic proteins extracted from LM3 and LM3-2 cells, grown under standard conditions up to mid-exponential phase (Fig. 1). The presence of differentially expressed proteins in the two strains, together with results of previous studies [28,29] demonstrated the role of CcpA as global regulator in L. plantarum.
PMID:17129387
A type of direct assay evidence where molecules have been sorted according to their size and charge by moving through a gel in the presence of an electric field.
ECO:MCC
wikipedia:Gel_electrophoresis
A type of gel electrophoresis evidence in which large DNA molecules are separated on agarose gel by alternately pulsed, perpendicularly oriented electrical fields, at least one of which is inhomogeneous.
mchibucos
2012-08-24T12:34:01Z
PFGE
eco
ECO:0000338
pulsed-field gel electrophoresis evidence
A type of gel electrophoresis evidence in which large DNA molecules are separated on agarose gel by alternately pulsed, perpendicularly oriented electrical fields, at least one of which is inhomogeneous.
PMID:6373014
A type of gel electrophoresis evidence where DNA molecules are electrophoresed on a low percentage agarose gel followed by high voltage electrophoresis on a higher percentage agarose gel in the presence of ethidium bromide.
mchibucos
2012-08-24T12:42:37Z
2-D agarose gel electrophoresis
eco
ECO:0000339
The first dimension gel is intentionally run at low voltage in low percentage agarose to separate DNA molecules in proportion to their mass. The second dimension is run at high voltage in a gel of higher agarose concentration in the presence of ethidium bromide so that the mobility of a non-linear molecule is drastically influenced by its shape.
two-dimensional agarose gel electrophoresis evidence
A type of gel electrophoresis evidence where DNA molecules are electrophoresed on a low percentage agarose gel followed by high voltage electrophoresis on a higher percentage agarose gel in the presence of ethidium bromide.
PMID:16118435
PMID:8594382
A type of experimental evidence in which a plasmid that is capable of being replicated is introduced into cells, cells are grown without selection for several generations, and retention of the plasmid is determined.
mchibucos
2012-08-24T01:27:58Z
minichromosome maintenance assay evidence
eco
ECO:0000340
Loss per generation is determined by comparing colony numbers on selective and non-selective media.
plasmid maintenance assay evidence
A type of experimental evidence in which a plasmid that is capable of being replicated is introduced into cells, cells are grown without selection for several generations, and retention of the plasmid is determined.
ECO:MCC
PMID:6323245
minichromosome maintenance assay evidence
PMID:6323245
A type of specific protein inhibition evidence where the molecular function of a protein is inhibited by an antibody.
mchibucos
2012-08-24T01:48:24Z
eco
ECO:0000341
specific protein inhibition by antibody evidence
A type of specific protein inhibition evidence where the molecular function of a protein is inhibited by an antibody.
ECO:MCC
A type of RNA-seq evidence where intron locations in predicted transcripts are compared to intron locations supported by RNA-seq evidence.
mchibucos
2013-04-03T04:22:05Z
Support of intron positions by RNA-seq alignment evidence
eco
ECO:0000342
RNA-seq alignment intron location evidence is used by NCBI RefSeq (http://www.ncbi.nlm.nih.gov/refseq). Exon-exon boundaries (or intron locations) of a RefSeq transcript, as determined by aligning the transcript to a reference chromosome, are compared to intron locations supported by RNAseq data.
support of intron positions by RNA-sequencing alignment evidence
A type of RNA-seq evidence where intron locations in predicted transcripts are compared to intron locations supported by RNA-seq evidence.
ECO:MCC
A type of support of intron positions by RNA-sequencing alignment evidence where RNA-seq alignment from a single sample supports all of the intron positions (exon pairs) predicted for a transcript.
mchibucos
2013-04-03T04:41:48Z
Full support of intron positions by RNA-seq alignment evidence
eco
ECO:0000343
Full support entails that all exon pairs represented in the transcript are supported. For example, for a transcript containing five exons, if liver RNA-seq reads support all four introns but brain RNA-seq supports only three introns, then the liver data fully support the transcript exons whereas the brain data do not.
full support of intron positions by RNA-sequencing alignment evidence
A type of support of intron positions by RNA-sequencing alignment evidence where RNA-seq alignment from a single sample supports all of the intron positions (exon pairs) predicted for a transcript.
ECO:MCC
A type of support of intron positions by RNA-sequencing alignment evidence where RNA-seq alignment to a genome supports only some of the intron positions (exon pairs) predicted for a transcript.
mchibucos
2013-04-03T04:50:46Z
Partial support of intron positions by RNA-seq alignment evidence
eco
ECO:0000344
Partial support can occur in two ways. First, one or more exon-exon pair (intron) is not supported by any RNA-seq sample included in the analysis. Second, no single RNA-seq sample provides support for all exon-exon pairs (introns) represented in a transcript, but all represented exons are supported by at least one sample.
partial support of intron positions by RNA-sequencing alignment evidence
A type of support of intron positions by RNA-sequencing alignment evidence where RNA-seq alignment to a genome supports only some of the intron positions (exon pairs) predicted for a transcript.
ECO:MCC
A type of sequence alignment evidence resulting from the comparison of a single exon transcript to a collection / database of known single exon genes.
mchibucos
2013-04-03T05:10:34Z
eco
ECO:0000345
single exon transcript confirmation via alignment evidence
A type of sequence alignment evidence resulting from the comparison of a single exon transcript to a collection / database of known single exon genes.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4897596/
IEP
A type of support of intron positions by RNA-sequencing alignment evidence that is used in a manual assertion.
mchibucos
2013-04-04T04:37:35Z
Support of intron positions by RNA-seq alignment evidence used in manual assertion
eco
ECO:0000346
support of intron positions by RNA-sequencing alignment evidence used in manual assertion
true
A type of support of intron positions by RNA-sequencing alignment evidence that is used in a manual assertion.
ECO:MCC
IEA
A type of support of intron positions by RNA-sequencing alignment evidence that is used in an automatic assertion.
mchibucos
2013-04-04T04:38:45Z
Support of intron positions by RNA-seq alignment evidence used in automatic assertion
eco
ECO:0000347
support of intron positions by RNA-sequencing alignment evidence used in automatic assertion
true
A type of support of intron positions by RNA-sequencing alignment evidence that is used in an automatic assertion.
ECO:MCC
IEA
A type of full support of intron positions by RNA-sequencing alignment evidence that is used in an automatic assertion.
mchibucos
2013-04-04T04:40:19Z
Full support of intron positions by RNA-seq alignment evidence used in automatic assertion
eco
ECO:0000348
full support of intron positions by RNA-sequencing alignment evidence used in automatic assertion
true
A type of full support of intron positions by RNA-sequencing alignment evidence that is used in an automatic assertion.
ECO:MCC
IEP
A type of full support of intron positions by RNA-sequencing alignment evidence that is used in a manual assertion.
mchibucos
2013-04-04T04:41:34Z
Full support of intron positions by RNA-seq alignment evidence used in manual assertion
eco
ECO:0000349
full support of intron positions by RNA-sequencing alignment evidence used in manual assertion
true
A type of full support of intron positions by RNA-sequencing alignment evidence that is used in a manual assertion.
ECO:MCC
IEA
A type of partial support of intron positions by RNA-sequencing alignment evidence that is used in an automatic assertion.
mchibucos
2013-04-04T04:42:53Z
Partial support of intron positions by RNA-seq alignment evidence used in automatic assertion
eco
ECO:0000350
partial support of intron positions by RNA-sequencing alignment evidence used in automatic assertion
true
A type of partial support of intron positions by RNA-sequencing alignment evidence that is used in an automatic assertion.
ECO:MCC
IEP
A type of partial support of intron positions by RNA-sequencing alignment evidence that is used in a manual assertion.
mchibucos
2013-04-04T04:43:56Z
Partial support of intron positions by RNA-seq alignment evidence used in manual assertion
eco
ECO:0000351
partial support of intron positions by RNA-sequencing alignment evidence used in manual assertion
true
A type of partial support of intron positions by RNA-sequencing alignment evidence that is used in a manual assertion.
ECO:MCC
A type of evidence that is used in an manual assertion.
mchibucos
eco
ECO:0000352
evidence used in manual assertion
true
true
A type of evidence that is used in an manual assertion.
ECO:MCC
IPI
A type of physical interaction evidence that is used in a manual assertion.
mchibucos
2013-10-31T21:01:27Z
GOECO:IPI
IPI
inferred from physical interaction
eco
ECO:0000353
physical interaction evidence used in manual assertion
http://geneontology.org/page/ipi-inferred-physical-interaction
true
IPI
Default
A type of physical interaction evidence that is used in a manual assertion.
ECO:MCC
GOECO:IPI
inferred from physical interaction
IPI
GOECO:IPI
inferred from physical interaction
GOECO:IPI
IGC
A type of gene neighbors evidence that is used in a manual assertion.
mchibucos
2013-11-19T13:37:24Z
inferred from genome cluster
GO_REF:0000025
eco
ICL
ECO:0000354
gene neighbors evidence used in manual assertion
true
A type of gene neighbors evidence that is used in a manual assertion.
ECO:MCC
GO_REF:0000025
operon structure as IGC evidence
A type of phylogenetic evidence characterized by the mapping of the character states of living organisms onto phylogenies using the method of maximum parsimony.
mchibucos
2014-04-22T17:02:31Z
eco
ECO:0000355
Example of use: "The presence of paired evaginated hemispheres and olfactory bulbs in both agnathan and gnathostome radiations suggests that such hemispheres were also present in the common ancestor." PMID:7013637. Northcutt RG. (1981) Evolution of the telencephalon in nonmammals. Ann. Rev. Neurosci.
phylogenetic distribution evidence
A type of phylogenetic evidence characterized by the mapping of the character states of living organisms onto phylogenies using the method of maximum parsimony.
ECO:MCC
PMID:21238344
A type of transcript expression evidence resulting from a microarray analysis with the use of the Gene Set Enrichment Analysis (GSEA) method or the Fisher's-Exact (FE) method to assess the differential expression.
mchibucos
2014-09-26T16:25:47Z
eco
ECO:0000358
differential geneset expression evidence from microarray experiment (GSEA, Fisher-exact)
A type of transcript expression evidence resulting from a microarray analysis with the use of the Gene Set Enrichment Analysis (GSEA) method or the Fisher's-Exact (FE) method to assess the differential expression.
PMID:19725948
A type of transcript expression evidence resulting from the use of the Gene Set Enrichment Analysis (GSEA) method or Fisher's-Exact (FE) method to assess an RNA-seq dataset for differential gene expression.
mchibucos
2014-09-26T16:26:48Z
eco
ECO:0000359
differential geneset expression evidence from RNA-seq experiment (GSEA, Fisher-exact)
A type of transcript expression evidence resulting from the use of the Gene Set Enrichment Analysis (GSEA) method or Fisher's-Exact (FE) method to assess an RNA-seq dataset for differential gene expression.
PMC:PMC2881125
A type of experimental evidence resulting from the prediction of drug-target interactions by computational means.
mchibucos
2014-09-26T16:39:11Z
eco
ECO:0000360
biological target-disease association via drug evidence
A type of experimental evidence resulting from the prediction of drug-target interactions by computational means.
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2199-x
A type of evidence where an assertion is derived from another assertion via logical inference or some non-logical but rational means.
mchibucos
2015-07-14T11:19:37Z
eco
ECO:0000361
Inference is the process of deriving logical conclusions from premises known or assumed to be true, or alternatively, arriving at conclusions via some non-logical means of observation of patterns of facts, which can result in identifying new meanings and contexts for understanding. Given the evidence provided by a set of premises, deductive reasoning involves drawing conclusions that necessarily follow, i.e. are certain, whereas inductive reasoning generates conclusions that are likely to be, but are not necessarily, true.
inferential evidence
A type of evidence where an assertion is derived from another assertion via logical inference or some non-logical but rational means.
ECO:MCC
A type of inferential evidence based on a computationally derived unary inference or an inference chain in which at least one step is
computationally derived.
mchibucos
2015-07-14T11:24:27Z
evidence based on computational logical inference
eco
ECO:0000362
computational inference
A type of inferential evidence based on a computationally derived unary inference or an inference chain in which at least one step is
computationally derived.
ECO:MCC
GOC:MC
IEA
A type of evidence based on computational logical inference that is used in automatic assertion.
mchibucos
2015-07-14T11:35:08Z
GO_REF:0000108
evidence based on computational logical inference used in automatic assertion
eco
ECO:0000363
computational inference used in automatic assertion
true
true
A type of evidence based on computational logical inference that is used in automatic assertion.
ECO:MCC
GO_REF:0000108
Automatic assignment of GO terms using logical inference, based on on inter-ontology links
IEA
A type of evidence based on logical inference from a manually curated annotation that is used in an automatic assertion.
mchibucos
2015-07-14T11:44:19Z
eco
ECO:0000364
evidence based on logical inference from manual annotation used in automatic assertion
A type of evidence based on logical inference from a manually curated annotation that is used in an automatic assertion.
ECO:MCC
IEA
A type of evidence based on logical inference from an automatically curated annotation that is used in an automatic assertion.
mchibucos
2015-07-14T11:45:25Z
eco
ECO:0000366
evidence based on logical inference from automatic annotation used in automatic assertion
A type of evidence based on logical inference from an automatically curated annotation that is used in an automatic assertion.
ECO:MCC
IEA
A type of evidence that is used in an automatic assertion.
cjm
GOECO:IEA
GO_REF:0000003
GO_REF:0000004
GO_REF:0000020
GO_REF:0000041
GO_REF:0000043
GO_REF:0000044
GO_REF:0000116
IEA
inferred from electronic annotation
eco
ECO:0000501
evidence used in automatic assertion
http://geneontology.org/page/automatically-assigned-evidence-codes
true
true
IEA
Default
A type of evidence that is used in an automatic assertion.
ECO:cjm
GOECO:IEA
inferred from electronic annotation
GO_REF:0000003
Gene Ontology annotation based on Enzyme Commission mapping.
GO_REF:0000004
Gene Ontology annotation based on Swiss-Prot keyword mapping.
GO_REF:0000020
Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins.
GO_REF:0000041
IEA (UniProt UniPathway)
GO_REF:0000043
Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping.
GO_REF:0000044
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt.
GO_REF:0000116
Automatic Gene Ontology annotation based on Rhea mapping.
IEA
GOECO:IEA
inferred from electronic annotation
GOECO:IEA
A type of cell proliferation assay evidence resulting from the growth of cells in a micro-environment that mimics real tissue and establishes physiological cell-cell and cell-substrate interactions that regulate proliferation and differentiation.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001001
3D cell culture evidence
A type of cell proliferation assay evidence resulting from the growth of cells in a micro-environment that mimics real tissue and establishes physiological cell-cell and cell-substrate interactions that regulate proliferation and differentiation.
PMID:21042962
url:http://volttecnologia.com.br/wp-content/uploads/2016/03/Drug-discovery.pdf
A type of cell-based assay evidence resulting from labeling cells with [3H]arachidonic acid and subsequently determining the release of the arachidonic acid by the cells.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001002
[3H]arachidonic acid release assay evidence
A type of cell-based assay evidence resulting from labeling cells with [3H]arachidonic acid and subsequently determining the release of the arachidonic acid by the cells.
ISBN:0323152295
PMID:20693009
A type of DNA synthesis cell proliferation assay evidence resulting from the measurement of cell proliferation rate by determining the incorporation of [3H]-thymidine into cellular nucleic acids.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001003
[3H]-thymidine incorporation assay evidence
A type of DNA synthesis cell proliferation assay evidence resulting from the measurement of cell proliferation rate by determining the incorporation of [3H]-thymidine into cellular nucleic acids.
OBI:0000669
url:http://www.scientistsolutions.com/forum/cell-culture-and-tissue-culture-proliferationapoptosis/3h-thymidine-incorporation-assay-rat-1a
A type of cytotoxicity assay evidence resulting from the measurement of the amount of radioactive 51Cr released in the supernatant of a sample of 51Cr pre-labeled cells via cytolysis by effector cells (cytotoxic T-cells).
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001004
51Cr release assay evidence
A type of cytotoxicity assay evidence resulting from the measurement of the amount of radioactive 51Cr released in the supernatant of a sample of 51Cr pre-labeled cells via cytolysis by effector cells (cytotoxic T-cells).
PMC:PMC3929704
url:http://www4.mpbio.com/ecom/docs/proddata.nsf/5f64ffd4f38c2fda8525645d00769d68/53d2a75653615bab852568cb00572ff3?OpenDocument
A type of apoptotic assay evidence resulting from the use of 7-aminoactinomycin D (7-AAD) to distinguish viable, apoptotic, and dead cells, using the fact that permeability of the cell membrane, and fluorescence intensity, is low in early apoptotic cells and high in late apoptotic and dead cells.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
7-AAD staining evidence
7-amino-actinomycin D staining evidence
eco
ECO:0001005
7-aminoactinomycin staining evidence
A type of apoptotic assay evidence resulting from the use of 7-aminoactinomycin D (7-AAD) to distinguish viable, apoptotic, and dead cells, using the fact that permeability of the cell membrane, and fluorescence intensity, is low in early apoptotic cells and high in late apoptotic and dead cells.
ECO:RCT
A type of cell-based assay evidence resulting from the analysis of cell binding either to extracellular matrix proteins or other cells.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001006
adhesion assay evidence
A type of cell-based assay evidence resulting from the analysis of cell binding either to extracellular matrix proteins or other cells.
PMID:15576904
PMID:21909903
A type of ex vivo assay evidence derived by ex vivo selection of tumor-reactive lymphocytes, and their activation and numerical expansion before re-infusion to the autologous tumor-bearing host.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
Adoptive immunotherapy
passive immunization
eco
ECO:0001007
adoptive cell transfer evidence
A type of ex vivo assay evidence derived by ex vivo selection of tumor-reactive lymphocytes, and their activation and numerical expansion before re-infusion to the autologous tumor-bearing host.
ECO:SN
url:http://jco.ascopubs.org/content/23/10/2346.full.pdf+html
url:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2305722/pdf/nihms42807.pdf
A type of cell viability assay evidence resulting from the continuous measurement of fluorescence intensity from the viable cells, where a cell permeable compound, resazurin (the active ingredient of alamarBlue), is reduced to fluorescent resorufin.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001008
alamarBlue assay evidence
A type of cell viability assay evidence resulting from the continuous measurement of fluorescence intensity from the viable cells, where a cell permeable compound, resazurin (the active ingredient of alamarBlue), is reduced to fluorescent resorufin.
PMC:PMC3478843
url:https://www.thermofisher.com/us/en/home/references/protocols/cell-and-tissue-analysis/cell-profilteration-assay-protocols/cell-viability-with-alamarblue.html
A type of anatomical perturbation phenotypic evidence resulting from the transplantation of an organ or tissue from one individual of the same species with a different genotype.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
Allotransplantation
allograft transplantation experiment evidence
allografting
tissue grafting
eco
ECO:0001009
allograft transplantation phenotypic evidence
A type of anatomical perturbation phenotypic evidence resulting from the transplantation of an organ or tissue from one individual of the same species with a different genotype.
ECO:SN
url:http://www.nature.com/subjects/allograft
url:http://www.organdonor.gov/about/terms_and_topics/
A type of chromatography evidence where a positively charged ion exchange resin with an affinity for molecules having net negative surface charges is used to separate the molecules.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001010
anion-exchange chromatography evidence
A type of chromatography evidence where a positively charged ion exchange resin with an affinity for molecules having net negative surface charges is used to separate the molecules.
ECO:SN
PMID:20978968
url:http://www.bio-rad.com/en-us/applications-technologies/anion-exchange-chromatography
url:http://www.uta.edu/faculty/sawasthi/Enzymology-4351-5324/Class%20Syllabus%20Enzymology/Ion%20Exchange%20Chromatography-1.pdf
A type of apoptotic assay evidence resulting from the addition and subsequent binding of Annexin V to phosphatidylserine in cells to detect if they are viable, apoptotic, or necrotic.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001011
annexin-V staining evidence
A type of apoptotic assay evidence resulting from the addition and subsequent binding of Annexin V to phosphatidylserine in cells to detect if they are viable, apoptotic, or necrotic.
PMC:PMC3169266
A type of experimental phenotypic evidence resulting from behavioral phenotyping and analysis to assess cognitive functioning.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
behavioral assay evidence
eco
ECO:0001012
cognitive assay phenotypic evidence
A type of experimental phenotypic evidence resulting from behavioral phenotyping and analysis to assess cognitive functioning.
PMID:24462904
A type of immunological assay evidence resulting from inhibitory effect of monoclonal antibody combining with an antigen over other antibodies.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001013
blocking monoclonal antibody evidence
A type of immunological assay evidence resulting from inhibitory effect of monoclonal antibody combining with an antigen over other antibodies.
PMID:11292349
url:http://www.sciencedirect.com/science/article/pii/S0140673600034966
A type of immunological assay evidence resulting from the use of peptides to block antibodies from binding to their targets.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001014
blocking peptide evidence
A type of immunological assay evidence resulting from the use of peptides to block antibodies from binding to their targets.
ECO:RCT
A type of immunological assay evidence resulting from the inhibitory effect of polyclonal antibodies (antibodies secreted by different B cell lineages), which while not reacting with a specific antigen, serve to prevent other antibodies from doing so.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001015
blocking polyclonal antibody evidence
A type of direct assay evidence where a blood sample is extracted from an organism to analyze different blood components.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001016
blood test evidence
A type of direct assay evidence where a blood sample is extracted from an organism to analyze different blood components.
ECO:SN
url:https://www.nhlbi.nih.gov/health/health-topics/topics/bdt
A type of chemotaxis assay evidence where the presence or absence of positive or negative chemotaxis is determined by measuring the number of cells that migrate from the upper compartment of a chamber (separated by a micro-porous membrane) to the lower compartment, in which chemotactic agents are present.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001017
Boyden chamber assay evidence
A type of chemotaxis assay evidence where the presence or absence of positive or negative chemotaxis is determined by measuring the number of cells that migrate from the upper compartment of a chamber (separated by a micro-porous membrane) to the lower compartment, in which chemotactic agents are present.
PMID:13872176
PMID:15576901
A type of nucleotide analog incorporation evidence resulting from the incorporation of bromodeoxyuridine (BrdU) as a thymidine analog into nuclear DNA, resulting in a label that can be tracked using antibody probes.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
ECO:0005010
cell proliferation marker detection assay evidence
5-bromo-2'-deoxyuridine incorporation assay evidence
BUdR incorporation assay evidence
BrdU incorporation assay evidence
BrdUrd incorporation assay evidence
eco
ECO:0001018
bromodeoxyuridine incorporation assay evidence
A type of nucleotide analog incorporation evidence resulting from the incorporation of bromodeoxyuridine (BrdU) as a thymidine analog into nuclear DNA, resulting in a label that can be tracked using antibody probes.
PMID:23690005
A type of apoptotic assay evidence resulting from the detection of caspase activation, which results in the cleaving of intracellular substrates during apoptosis.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001019
caspase assay evidence
A type of apoptotic assay evidence resulting from the detection of caspase activation, which results in the cleaving of intracellular substrates during apoptosis.
PMID:18314058
PMID:25086023
A type of cell-based assay evidence resulting from the quantification of a sample of cells.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001020
cell counting evidence
A type of cell-based assay evidence resulting from the quantification of a sample of cells.
ECO:RCT
A type of cell-based assay evidence resulting from the quantification of cell permeability.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001021
cell permeability assay evidence
A type of cell-based assay evidence resulting from the quantification of cell permeability.
PMID:16962665
A type of staining evidence resulting from monitoring division by the use of carboxyfluorescein diacetate succinimidyl ester (CFSE) to label intracellular molecules with carboxyfluorescein; when a labeled cell divides, the number of carboxyfluorescein-tagged molecules is split.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
CFDA-SE staining evidence
CFSE-staining evidence
eco
ECO:0001022
carboxyfluorescein diacetate succinimidyl ester staining evidence
A type of staining evidence resulting from monitoring division by the use of carboxyfluorescein diacetate succinimidyl ester (CFSE) to label intracellular molecules with carboxyfluorescein; when a labeled cell divides, the number of carboxyfluorescein-tagged molecules is split.
PMC:PMC3185625
A type of protein detection assay evidence resulting from a complex (a chemiluminescent compound, protein and a steroidal hapten) utilized as a labeled antigen, which emits light when treated with hydrogen peroxide and copper acetate at a high pH.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
CLIA evidence
eco
ECO:0001023
chemiluminescence-linked immunoassay evidence
A type of protein detection assay evidence resulting from a complex (a chemiluminescent compound, protein and a steroidal hapten) utilized as a labeled antigen, which emits light when treated with hydrogen peroxide and copper acetate at a high pH.
PMID:659901
A type of mutant phenotype evidence resulting from the fusion of two or more different genes to create one protein product.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
chimeric protein evidence
eco
ECO:0001024
chimeric protein phenotypic evidence
A type of mutant phenotype evidence resulting from the fusion of two or more different genes to create one protein product.
PMID:22588898
PMID:25832756
A type of gel electrophoresis evidence resulting from the electrophoresis of two substances together, allowing for the characterization of ligand/nucleic acid binding interactions.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001025
co-electrophoresis evidence
A type of gel electrophoresis evidence resulting from the electrophoresis of two substances together, allowing for the characterization of ligand/nucleic acid binding interactions.
PMID:7668395
A type of imaging assay evidence resulting from the limited observation of the co-occurrence of molecules in a subcellular location.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001026
co-localization evidence
A type of imaging assay evidence resulting from the limited observation of the co-occurrence of molecules in a subcellular location.
PMC:PMC3074624
A type of direct assay evidence resulting from the counting of microbial colonies that arise from viable cells grown on a plate or dish.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001027
colony counting evidence
A type of direct assay evidence resulting from the counting of microbial colonies that arise from viable cells grown on a plate or dish.
PMID:16558698
PMID:23457446
A type of physical interaction evidence resulting from the separation of a mixture of molecules under the influence of a force such as artificial gravity, where molecules sedimenting together are assumed to interact.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001028
co-sedimentation assay evidence
A type of physical interaction evidence resulting from the separation of a mixture of molecules under the influence of a force such as artificial gravity, where molecules sedimenting together are assumed to interact.
MI:0027
A type of gel electrophoresis evidence resulting in the assessment of DNA breakage in a cell, based on size and shape of DNA migration.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001029
comet assay evidence
A type of gel electrophoresis evidence resulting in the assessment of DNA breakage in a cell, based on size and shape of DNA migration.
OBI:0302736
PMID:10737956
A type of knockout evidence resulting from a temporally-restricted and/or tissue-specific targeted gene removal.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001030
conditional knockout evidence
A type of knockout evidence resulting from a temporally-restricted and/or tissue-specific targeted gene removal.
PMC:PMC3572410
A type of knockin evidence resulting from the targeted introduction of a temporally-restricted and/or tissue-specific mutation.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001031
conditional knockin evidence
A type of knockin evidence resulting from the targeted introduction of a temporally-restricted and/or tissue-specific mutation.
PMID:16832820
A type of experimental phenotypic evidence resulting from a constitutively active mutant (CAM), resulting in mutant proteins that remain active in the absence of upstream signals.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001032
constitutively active mutant evidence
A type of experimental phenotypic evidence resulting from a constitutively active mutant (CAM), resulting in mutant proteins that remain active in the absence of upstream signals.
PMID:12217490
To confirm this intriguing observation, we cross-linked AdpA and DNA in the presence of increasing amounts of ATP (figure 2b(iii)). In this assay, ATP prevented the formation of AdpA - DNA complexes in a concentration-dependent manner, an outcome consistent with the results obtained by SPR analysis.
A type of protein binding evidence resulting from the identification of two interacting proteins (that exist in close proximity) by linking through covalent bonds followed by identification
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001033
cross-linking evidence
To confirm this intriguing observation, we cross-linked AdpA and DNA in the presence of increasing amounts of ATP (figure 2b(iii)). In this assay, ATP prevented the formation of AdpA - DNA complexes in a concentration-dependent manner, an outcome consistent with the results obtained by SPR analysis.
PMID:22870392
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