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.
OBO-Edit 2.3.1
eco
rctauber
1.2
01:09:2018 10:49
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.
IAO
example of usage
IAO
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
IAO
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
IAO
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 biological process terms should be used in the GO with/from field
GO cellular component terms should be used in the GO with/from field
Chemical entity IDs should be used in the GO with/from field
Gene IDs should be used in the GO with/from field
GO molecular function terms should be used in the GO with/from field
Protein IDs should be used in the GO with/from field
Protein complex IDs should be used in the GO with/from field
Transcript IDs should be used in the GO with/from field
A legal document giving official permission to do something with the resource.
DC
license
subset_property
has_alternative_id
has_broad_synonym
database_cross_reference
has_exact_synonym
has_narrow_synonym
has_obo_format_version
has_obo_namespace
has_related_synonym
in_subset
shorthand
A core relation that holds between a whole and its part
has part
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
A type of information that is used to support an assertion.
eco
evidence code
evidence_code
ECO:0000000
evidence
A type of information that is used to support an assertion.
ECO:MCC
A type of curator inference where conclusions are drawn based on the background scientific knowledge of the curator.
eco
ECO:0000001
inference from background scientific knowledge
A type of curator inference where conclusions are drawn based on the background scientific knowledge of the curator.
ECO:SN
A type of experimental evidence resulting from the direct measurement of some aspect of a biological feature.
ECO:0005006
eco
ECO:0000002
direct assay evidence
A type of experimental evidence resulting from the direct measurement of some aspect of a biological feature.
ECO:SN
A type of direct assay evidence based on reconstructing a biological sample from its disassociated state to its original state.
eco
ECO:0000003
reconstitution assay evidence
A type of direct assay evidence based on reconstructing a biological sample from its disassociated state to its original state.
ECO:KAV
PMID:26029343
A type of fractionation evidence where sub-cellular components are separated based on their physical properties such as density in a sucrose density gradient.
eco
IDA: cell fractionation
ECO:0000004
If using this term for Gene Ontology annotation, it would be used most typically for annotations to the cellular component ontology.
cell fractionation evidence
A type of fractionation evidence where sub-cellular components are separated based on their physical properties such as density in a sucrose density gradient.
ECO:KIM
TAIR:TED
A type of protein assay evidence where the catalytic activity of an enzyme is determined.
ECO:0005001
MI:0415
eco
IDA: enzyme assays
ECO:0000005
enzyme assay evidence
A type of protein assay evidence where the catalytic activity of an enzyme is determined.
url:http://www.sciencedirect.com/science/article/pii/S2213020914000068
MI:0415
enzymatic study
A type of evidence resulting from manipulation of variables in order to discover cause and effect.
ECO:0005023
eco
ECO:0000006
experimental evidence
A type of evidence resulting from manipulation of variables in order to discover cause and effect.
url:http://holah.co.uk/page/experimental/
A type of protein detection assay evidence where a fluorescently labeled antibody is used to detect the presence or localization of a biomolecule within a cell.
eco
IDA: immunofluorescence
ECO:0000007
immunofluorescence evidence
A type of protein detection assay evidence where a fluorescently labeled antibody is used to detect the presence or localization of a biomolecule within a cell.
ECO:MCC
TAIR:TED
A type of experimental evidence that is based on characterization of gene expression.
eco
ECO:0000008
Use this evidence type when the annotation is inferred from the timing or location of expression of a gene. It may be difficult to determine whether the expression pattern truly indicates that a gene plays a role in a given process.
expression pattern evidence
A type of experimental evidence that is based on characterization of gene expression.
ECO:MCC
GO:IEP
A type of expression pattern evidence where abundance of a transcript is analyzed.
eco
ECO:0000009
transcript expression evidence
A type of expression pattern evidence where abundance of a transcript is analyzed.
ECO:RCT
A type of expression pattern evidence resulting from protein abundance quantification techniques.
eco
ECO:0000010
protein expression evidence
A type of expression pattern evidence resulting from protein abundance quantification techniques.
PMC:4029002
url:https://www.thermofisher.com/us/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/pierce-protein-methods/overview-protein-expression-systems.html
A type of experimental phenotypic evidence resulting from the effect that a given gene has on another gene or genes, and the products.
TAIR:TED
eco
ECO:0000011
genetic interaction evidence
A type of experimental phenotypic evidence resulting from the effect that a given gene has on another gene or genes, and the products.
ECO:RCT
PMID:11822023
A type of genetic interaction evidence where a wild-type copy of the gene in question is inserted into a mutant cell to see if it restores the wild-type phenotype in the mutant background.
eco
IGI: functional complementation
ECO:0000012
functional complementation evidence
A type of genetic interaction evidence where a wild-type copy of the gene in question is inserted into a mutant cell to see if it restores the wild-type phenotype in the mutant background.
PMID:27403640
A type of functional complementation evidence resulting from the introduction of a transgene to prevent, or "rescue" an organism from a condition.
eco
ECO:0000013
transgenic rescue experiment evidence
A type of functional complementation evidence resulting from the introduction of a transgene to prevent, or "rescue" an organism from a condition.
url:http://www.mdpi.com/1420-3049/19/9/13932/pdf
url:http://www.nature.com/gt/journal/v11/n15/full/3302282a.html
A type of experimental phenotypic evidence derived from the difference in two alleles of a corresponding gene that result from one or more changes in the genome.
eco
ECO:0000015
mutant phenotype evidence
A type of experimental phenotypic evidence derived from the difference in two alleles of a corresponding gene that result from one or more changes in the genome.
GO:IMP
A type of mutant phenotype evidence where a phenotype is associated with altered gene product which lacks the molecular function of the wild-type gene.
eco
ECO:0000016
loss-of-function mutant phenotype evidence
A type of mutant phenotype evidence where a phenotype is associated with altered gene product which lacks the molecular function of the wild-type gene.
SO:0002054
A type of experimental phenotypic evidence where a transgenic strain carrying the construct of a promoter cDNA fusion in which a gene of interest is driven by a defined promoter or enhancer is ectopically expressed in the defined pattern to characterize potential cellular properties and functions of a protein of interest.
eco
IMP: analysis of overexpression/ectopic expression phenotype
ECO:0000017
ectopic expression evidence
A type of experimental phenotypic evidence where a transgenic strain carrying the construct of a promoter cDNA fusion in which a gene of interest is driven by a defined promoter or enhancer is ectopically expressed in the defined pattern to characterize potential cellular properties and functions of a protein of interest.
PMID:10948520
PMID:19301619
A type of mutant phenotype evidence where a phenotype is observed while expressing an anti-sense version of a gene product in a wild-type (for that gene product) background.
eco
IMP: anti-sense experiments
ECO:0000018
anti-sense experiment evidence
A type of mutant phenotype evidence where a phenotype is observed while expressing an anti-sense version of a gene product in a wild-type (for that gene product) background.
ECO:SN
A type of mutant phenotype evidence where an RNA construct is introduced into a cell and the expression of the gene bearing its complementary sequence is suppressed.
eco
IMP: RNAi experiment
ECO:0000019
RNAi evidence
A type of mutant phenotype evidence where an RNA construct is introduced into a cell and the expression of the gene bearing its complementary sequence is suppressed.
ECO:MCC
A type of protein assay evidence based on the inhibition of the molecular function of a protein.
eco
ECO:0000020
specific protein inhibition evidence
A type of protein assay evidence based on the inhibition of the molecular function of a protein.
ECO:MCC
A type of experimental evidence that is based on characterization of an interaction between a gene product and another molecule.
ECO:0005025
MI:0045
eco
ECO:0000021
Molecules interacted with might include protein, nucleic acid, ion, or complex.
physical interaction evidence
A type of experimental evidence that is based on characterization of an interaction between a gene product and another molecule.
ECO:SN
MI:0045
experimental interaction detection
A type of physical interaction evidence where a cellular component subunit is isolated as part of purification of its larger complex.
MI:0025
eco
IPI: co-purification
ECO:0000022
co-purification evidence
A type of physical interaction evidence where a cellular component subunit is isolated as part of purification of its larger complex.
TAIR:TED
MI:0025
copurification
A type of physical interaction evidence that depends on the strength of the interaction between two entities.
MI:0400
ligand binding evidence
eco
ECO:0000023
affinity evidence
A type of physical interaction evidence that depends on the strength of the interaction between two entities.
ECO:MCC
PSI-MI:MI:0400
MI:0400
affinity technology
A type of affinity evidence resulting from the binding of a molecule to a protein or protein complex.
eco
ECO:0000024
protein binding evidence
A type of affinity evidence resulting from the binding of a molecule to a protein or protein complex.
GO:0005515
url:https://en.wikipedia.org/wiki/Mutation
A type of affinity evidence where proteins of interest (bait and prey) are covalently linked to incomplete fragments of a third protein (reporter) and expressed in vivo, at which time interaction between bait and prey proteins brings reporter fragments in close enough proximity to allow them to reform and become a functional reporter protein.
MI:0090
eco
ECO:0000025
Typically enzymes which confer resistance to antibiotics, such as Dihydrofolate reductase or Beta-lactamase, or proteins that give colorimetric or fluorescent signals are used. The Bait protein is generally the protein under study and the methods are readily adaptable to highthroughput mode.
hybrid interaction evidence
A type of affinity evidence where proteins of interest (bait and prey) are covalently linked to incomplete fragments of a third protein (reporter) and expressed in vivo, at which time interaction between bait and prey proteins brings reporter fragments in close enough proximity to allow them to reform and become a functional reporter protein.
ECO:MCC
PSI-MI:MI:0090
MI:0090
protein complementation assay
A type of experimental genomic evidence resulting from a process in which single stranded nucleic acids are allowed to interact so that complexes, or hybrids, are formed by molecules with sufficiently similar, complementary sequences.
eco
ECO:0000026
nucleic acid hybridization evidence
A type of experimental genomic evidence resulting from a process in which single stranded nucleic acids are allowed to interact so that complexes, or hybrids, are formed by molecules with sufficiently similar, complementary sequences.
OBI:0302903
A type of similarity evidence based on structural similarity of an annotated gene or gene product to another gene or group of genes.
eco
ECO:0000027
For GO annotation, in the case of a single gene, an accession for the related gene's sequence is entered in the evidence_with field.
structural similarity evidence
A type of similarity evidence based on structural similarity of an annotated gene or gene product to another gene or group of genes.
ECO:MCC
TAIR:TED
A type of match to sequence model evidence that is based on the presence of a recognized domain or motif in a gene product's (usually protein) primary sequence.
eco
ISS: recognized domains
ECO:0000028
motif similarity evidence
A type of match to sequence model evidence that is based on the presence of a recognized domain or motif in a gene product's (usually protein) primary sequence.
ECO:SN
A type of match to sequence model evidence resulting from a positive match of a protein, or set of proteins to a predictive model (signature) in the InterPro database.
eco
ECO:0000029
match to InterPro member signature evidence
A type of match to sequence model evidence resulting from a positive match of a protein, or set of proteins to a predictive model (signature) in the InterPro database.
PMC:2686546
url:http://www.ncbi.nlm.nih.gov/mesh?term=Nucleic+Acid+Hybridization
A type of BLAST evidence that is used in a manual assertion.
eco
curated BLAST analysis
ECO:0000030
BLAST evidence used in manual assertion
true
true
A type of BLAST evidence that is used in a manual assertion.
ECO:MCC
A type of protein BLAST evidence that is used in a manual assertion.
GO_REF:0000012
GO_REF:0000027
eco
curated protein BLAST analysis
ECO:0000031
protein BLAST evidence used in manual assertion
true
true
A type of protein BLAST evidence that is used in a manual assertion.
ECO:SN
GO_REF:0000012
Pairwise alignment (TIGR)
GO_REF:0000027
BLAST search criteria for ISS assignment in PAMGO_GAT
A type of nucleotide BLAST evidence that is used in a manual assertion.
eco
curated nucleic acid BLAST analysis
ECO:0000032
nucleotide BLAST evidence used in manual assertion
true
true
A type of nucleotide BLAST evidence that is used in a manual assertion.
ECO:SN
A type of author statement that is based on a cited reference.
eco
ECO:0000033
The traceable author statement (TAS) evidence code covers author statements that are attributed to a cited source. Typically this type of information comes from review articles. Material from the introductions and discussion sections of non-review papers may also be suitable if another reference is cited as the source of experimental work or analysis. When annotating with this code the curator should use caution and be aware that authors often cite papers dealing with experiments that were performed in organisms different from the one being discussed in the paper at hand. Thus a problem with the TAS code is that it may turn out from following up the references in the paper that no experiments were performed on the gene in the organism actually being characterized in the primary paper. For this reason we recommend (when time and resources allow) that curators track down the cited paper and annotate directly from the experimental paper using the appropriate experimental evidence code. When this is not possible and it is necessary to annotate from reviews, the TAS code is the appropriate code to use for statements that are associated with a cited reference. Once an annotation has been made to a given term using an experimental evidence code, we recommend removing any annotations made to the same term using the TAS evidence code.
traceable author statement
A type of author statement that is based on a cited reference.
ECO:MCC
GO:TAS
A type of author statement that is not associated with results presented or a cited reference.
eco
ECO:0000034
The non-traceable author statement evidence code should be used in all cases where the author makes a statement that a curator wants to capture but for which there are neither results presented nor a specific reference cited in the source used to make the annotation. The source of the information may be peer reviewed papers, textbooks, database records or vouchered specimens.
non-traceable author statement
A type of author statement that is not associated with results presented or a cited reference.
ECO:SN
A curator inference that results from research where no information about a biological feature was found in the scientific literature, at biological databases, or within other resources.
eco
ECO:0000035
An assertion of "no biological data found" carries the assumption that a more-or-less exhaustive search has been conducted.
no biological data found
A curator inference that results from research where no information about a biological feature was found in the scientific literature, at biological databases, or within other resources.
ECO:SN
An evidence that reflects an annotation was made before curators began tracking evidence types.
NR
not recorded
eco
ECO:0000037
The evidence not_recorded appears in some legacy annotations; it should not be used for new annotations.
not_recorded
true
An evidence that reflects an annotation was made before curators began tracking evidence types.
ECO:MCC
GO:NR
NR
GO:NR
not recorded
GO:NR
eco
ECO:0000038
transient rescue experiment evidence
A type of direct assay evidence resulting from determining the presence, abundance, structure, function, or activity of proteins.
ECO:0005022
eco
ECO:0000039
protein assay evidence
A type of direct assay evidence resulting from determining the presence, abundance, structure, function, or activity of proteins.
PMID:18429326
A type of affinity evidence resulting from quantitation of the analyte which depends on the reaction of an antigen (analyte) and an antibody.
ECO:0005018
eco
ECO:0000040
immunological assay evidence
A type of affinity evidence resulting from quantitation of the analyte which depends on the reaction of an antigen (analyte) and an antibody.
ERO:0001362
url:http://www.ncbi.nlm.nih.gov/books/NBK21589/,http://cores.ucsf.edu/protein-assay.html
A type of evidence resulting from comparing likeness of distinct biological entities.
IS
eco
inferred from similarity
ECO:0000041
similarity evidence
A type of evidence resulting from comparing likeness of distinct biological entities.
ECO:SN
A type of mutant phenotype evidence resulting from a phenotype that is associated with the altered gene product which possesses a new molecular function or a new pattern of gene expression.
eco
ECO:0000042
gain-of-function mutant phenotype evidence
A type of mutant phenotype evidence resulting from a phenotype that is associated with the altered gene product which possesses a new molecular function or a new pattern of gene expression.
SO:0002053
url:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3614608/
A type of similarity based on biomolecular sequence.
eco
ECO:0000044
A sequence similarity analysis may involve a gene or a gene product, and it could be based on similarity to a single other gene or to a group of other genes.
sequence similarity evidence
A type of similarity based on biomolecular sequence.
ECO:MCC
TAIR:TED
eco
ECO:0000045
spatial pattern of protein expression evidence
A type of protein expression evidence resulting from the quantification of protein production in a sample.
eco
ECO:0000046
protein expression level evidence
A type of protein expression evidence resulting from the quantification of protein production in a sample.
NBK:22011
url:http://www.informatics.jax.org/glossary/gain-of-function
eco
ECO:0000047
spatial pattern of transcript expression evidence
A type of transcript expression evidence resulting from quantifying transcript abundance.
eco
ECO:0000048
transcript expression level evidence
A type of transcript expression evidence resulting from quantifying transcript abundance.
ECO:RCT
A type of experimental phenotypic evidence that is based on the expression pattern of a reporter gene.
eco
IEP: expression of a reporter gene
ECO:0000049
reporter gene assay evidence
A type of experimental phenotypic evidence that is based on the expression pattern of a reporter gene.
TAIR:TED
A type of phenotypic evidence based on an author's phenotypic description of a species or higher level group explicitly referencing an observation of a voucher specimen, a specimen with a permanent museum catalog.
IVS
eco
ECO:0000050
voucher specimen analysis evidence
A type of phenotypic evidence based on an author's phenotypic description of a species or higher level group explicitly referencing an observation of a voucher specimen, a specimen with a permanent museum catalog.
TAIR:TED
A type of similarity based on genotype without respect to expression.
IGTS
eco
inferred from genetic similarity
ECO:0000051
A genetic similarity analysis might consider genetic markers, polymorphisms, alleles, or other characteristics sometimes considered as part of the field of traditional genetics. Although an attempt has been made to treat as distinct the concepts of "genetic", "genotypic", "genomic", and "sequence", there is considerable overlap in usage throughout the field of biology.
genetic similarity evidence
A type of similarity based on genotype without respect to expression.
ECO:MCC
PhenoScape:IGTS
A type of genetic interaction evidence resulting from a second mutation that either suppresses or enhances the phenotype expressed from an original mutation.
TAIR:TED
eco
IGI: 'traditional' genetic interactions (e.g. suppressors, synthetic lethals)
ECO:0000052
suppressor/enhancer interaction evidence
A type of genetic interaction evidence resulting from a second mutation that either suppresses or enhances the phenotype expressed from an original mutation.
url:http://biorxiv.org/content/early/2015/10/03/021592
url:http://www.wormbook.org/chapters/www:geneticsuppression/geneticsuppression.html
A type of combinatorial analysis where data are combined and evaluated by an algorithm.
TAIR:TED
eco
ECO:0000053
Combinatorial analyses could include experimental or computational results. Examples include: (i) large-scale experiment such as a genome-wide two-hybrid or genome-wide synthetic interactions; (ii) integration of large-scale data sets of various types; and (iii) text-based-computation, e.g. text-mining. For simple sequence comparisons, one should use the sequence similarity analysis evidence type. For microarray results alone, expression pattern analysis is appropriate; whereas, large-scale computational analysis should be used when microarray results are combined with the results of other types of large-scale experiments.
computational combinatorial evidence
A type of combinatorial analysis where data are combined and evaluated by an algorithm.
ECO:MCC
ECO:go
A type of genetic interaction evidence that is based on the phenotypic outcome of two mutations in unrelated genetic loci.
eco
IGI: double mutant analysis
ECO:0000054
double mutant phenotype evidence
A type of genetic interaction evidence that is based on the phenotypic outcome of two mutations in unrelated genetic loci.
ECO:RCT
A type of expression pattern evidence resulting from the hybridization of a target with a probe which is attached to the microarray surface.
eco
ECO:0000055
array experiment evidence
A type of expression pattern evidence resulting from the hybridization of a target with a probe which is attached to the microarray surface.
url:http://www.premierbiosoft.com/tech:notes/microarray.html
A type of genetic interaction evidence that is based on the suppression of one allelic effect by an allele at another genetic locus.
eco
IGI: epistatic interactions
ECO:0000056
Epistasis' can be used in different contexts in different areas of genetics. It is sometimes used to mean 'genetic interaction', whereas other times it may be specific to mutations that block the effects of other mutations.
epistatic interaction evidence
A type of genetic interaction evidence that is based on the suppression of one allelic effect by an allele at another genetic locus.
PMID:18852697
A type of similarity based on the expression of a genotype in an environment.
IPTS
phenotype similarity evidence
eco
inferred from phenotypic similarity
ECO:0000057
Phenotype is defined as the outcome of the expression of a genotype in a given environment. A comparison might involve whole organisms or sub-parts of organisms.
phenotypic similarity evidence
A type of similarity based on the expression of a genotype in an environment.
ECO:MCC
PhenoScape:IPTS
A type of array experiment 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
ECO:0000058
expression microarray evidence
A type of array experiment evidence resulting from simultaneous profiling of the expression levels of thousands of genes in a single experiment allowing analysis of genes and their networks.
url:http://www.illumina.com/techniques/microarrays/gene-expression-arrays.html
url:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2435252/
A type of experimental evidence that is based on the expression of a genotype in an environment.
ECO:0000014
ECO:0005017
eco
inferred from phenotype
ECO:0000059
experimental phenotypic evidence
A type of experimental evidence that is based on the expression of a genotype in an environment.
ECO:SN
A type of phenotypic similarity evidence based on the similarity of stucture locations or arrangements.
IPS
eco
ECO:0000060
positional similarity evidence
A type of phenotypic similarity evidence based on the similarity of stucture locations or arrangements.
TAIR:TED
A type of phenotypic evidence that is based on a gene product that is associated with a quantitative trait locus, but has not been cloned.
QTL analysis evidence
eco
IGI: quantitative trait analysis
ECO:0000061
quantitative trait analysis evidence
A type of phenotypic evidence that is based on a gene product that is associated with a quantitative trait locus, but has not been cloned.
TAIR:TED
eco
ECO:0000062
genomic microarray evidence
A type of phenotypic similarity evidence based on the similarity of the histological makeup of structures.
ICS
eco
ECO:0000063
compositional similarity evidence
A type of phenotypic similarity evidence based on the similarity of the histological makeup of structures.
TAIR:TED
A type of functional complementation evidence that is based on the insertion of a wild-type copy of a gene into a heterologous organism, with the mutation occurring in a homologous gene.
eco
IGI: functional complementation in heterologous system
ECO:0000064
functional complementation in heterologous system evidence
A type of functional complementation evidence that is based on the insertion of a wild-type copy of a gene into a heterologous organism, with the mutation occurring in a homologous gene.
TAIR:TED
A type of array experiment evidence resulting from the use of a CpG island (primarily unmethylated GC-rich, CpG-rich DNA sequences) microarray, that may be hybridized with methylated DNA fragments.
eco
ECO:0000065
CpG island microarray evidence
A type of array experiment evidence resulting from the use of a CpG island (primarily unmethylated GC-rich, CpG-rich DNA sequences) microarray, that may be hybridized with methylated DNA fragments.
PMID:21576262
url:http://www.atsjournals.org/doi/pdf/10.1165/ajrcmb.23.3.f196
A type of hybrid interaction evidence that is based on a protein-DNA complementation assay where a single promoter acts as bait and is screened against a library of prey transcription factors.
MI:0432
eco
IPI: yeast one-hybrid assay
ECO:0000066
The assay involves screening a library of candidate proteins for the ability bind to a target, cis-regulatory element or any other short, DNA binding sequence placed 5' to a yeast reporter gene (TAIR:TED).
yeast one-hybrid evidence
A type of hybrid interaction evidence that is based on a protein-DNA complementation assay where a single promoter acts as bait and is screened against a library of prey transcription factors.
ECO:MCC
PSI-MI:MI:0432
TAIR:TED
MI:0432
one hybrid
A type of phenotypic similarity evidence based on the similarity of embryological or post-embryonic orgin of structures.
IDS
eco
ECO:0000067
developmental similarity evidence
A type of phenotypic similarity evidence based on the similarity of embryological or post-embryonic orgin of structures.
TAIR:TED
A type of hybrid interaction evidence that is based on detection of protein-protein interaction by activation of a yeast reporter gene after a bait protein fused to a DNA-binding domain (which has been transfected into a yeast cell) is used to screen a cDNA library of clones fused to an activation domain.
eco
IPI: yeast two-hybrid assay
ECO:0000068
yeast 2-hybrid evidence
A type of hybrid interaction evidence that is based on detection of protein-protein interaction by activation of a yeast reporter gene after a bait protein fused to a DNA-binding domain (which has been transfected into a yeast cell) is used to screen a cDNA library of clones fused to an activation domain.
PMID:12734586
A type of nucleic acid hybridization evidence where methylation-sensitive restriction enzymes are utilized to analyze methylated DNA fragments by hybridizing them to a CpG island microarray.
eco
ECO:0000069
differential methylation hybridization evidence
A type of nucleic acid hybridization evidence where methylation-sensitive restriction enzymes are utilized to analyze methylated DNA fragments by hybridizing them to a CpG island microarray.
PMID:18987809
A type of immunoprecipitation evidence that involves precipitating two or more proteins via binding to an antibody specific to a single protein, followed by protein identification.
MI:0019
eco
IPI: co-immunoprecipitation
ECO:0000070
If performing GO annotation, the interacting protein is referenced in the evidence_with column.
co-immunoprecipitation evidence
A type of immunoprecipitation evidence that involves precipitating two or more proteins via binding to an antibody specific to a single protein, followed by protein identification.
ECO:MCC
MI:0019
coimmunoprecipitation
A type of phenotypic similarity evidence based on the similarity of shape, structure, or configuration in structures.
IMS
eco
ECO:0000071
morphological similarity evidence
A type of phenotypic similarity evidence based on the similarity of shape, structure, or configuration in structures.
TAIR:TED
A type of physical interaction evidence that is based on a genetic screening system that detects protein-protein interactions and is not based on a transcriptional readout.
eco
IPI: Sos-recruitment assay
ECO:0000072
Sos-recruitment assay evidence
true
A type of physical interaction evidence that is based on a genetic screening system that detects protein-protein interactions and is not based on a transcriptional readout.
TAIR:TED
A type of experimental evidence that is based on the characterization of an attribute of the genome underlying a gene product.
inferred from genomic analysis
eco
ECO:0000073
experimental genomic evidence
A type of experimental evidence that is based on the characterization of an attribute of the genome underlying a gene product.
ECO:MCC
A type of physical interaction evidence that is based on detection of protein-protein interaction between a bait and prey protein by in vivo reconstitution of split-ubiquitin (when bait and prey interact) and release of a reporter protein.
MI:0112
eco
IPI: split-ubiquitin assay
ECO:0000074
The bait protein is fused to the C-terminal ubiquitin (Cub) domain followed by a reporter protein, and the prey protein is fused to a mutated N terminal ubiquitin (NubG) domain. If bait and prey interact, their interaction brings the NubG and Cub domains close enough to reconstitute.TAIR:TED
split-ubiquitin assay evidence
A type of physical interaction evidence that is based on detection of protein-protein interaction between a bait and prey protein by in vivo reconstitution of split-ubiquitin (when bait and prey interact) and release of a reporter protein.
PMID:15064465
MI:0112
ubiquitin reconstruction
A type of phenotypic similarity evidence that is based on the categorization of genes by the similarity of expression profiles.
IGES
eco
ECO:0000075
gene expression similarity evidence
A type of phenotypic similarity evidence that is based on the categorization of genes by the similarity of expression profiles.
PMID:19958477
A type of physical interaction evidence that is based on detection of protein-protein interactions by separation of target proteins by SDS-PAGE which are blotted to a membrane, followed by denaturation and renaturation, probing with purified bait proteins, and detection of the target-bait complexes.
MI:0047
eco
IPI: far-Western analysis
ECO:0000076
The interacting protein is referenced in the evidence_with column.
far-Western blotting evidence
A type of physical interaction evidence that is based on detection of protein-protein interactions by separation of target proteins by SDS-PAGE which are blotted to a membrane, followed by denaturation and renaturation, probing with purified bait proteins, and detection of the target-bait complexes.
PMID:18079728
A type of polymerase chain reaction evidence resulting from initial modification of DNA by sodium bisulfite, converting all unmethylated cytosines to uracil, and subsequent amplification with primers specific for methylated versus unmethylated DNA.
methylation-specific PCR evidence
eco
ECO:0000077
methylation-specific polymerase chain reaction evidence
A type of polymerase chain reaction evidence resulting from initial modification of DNA by sodium bisulfite, converting all unmethylated cytosines to uracil, and subsequent amplification with primers specific for methylated versus unmethylated DNA.
PMC:38513
A type of DNA detection assay evidence that is based on detection of a specific DNA sequence by hybridization of labeled probes to any immobilized DNA fragment with sequence similarity.
Southern blot
eco
ISS: Southern blotting
ECO:0000078
The DNA fragments are prepared through gel electrophoresis then transferred to a filter membrane.
southern hybridization evidence
A type of DNA detection assay evidence that is based on detection of a specific DNA sequence by hybridization of labeled probes to any immobilized DNA fragment with sequence similarity.
PMID:18432697
A type of affinity evidence that results from separation of biochemical mixtures by selective binding of a compound to an immobilized compound on a polymeric matrix, subsequent removal of unattached components, and then displacement of the bond compound.
MI:0004
eco
IDA: affinity chromatography
ECO:0000079
"Used when an annotation is made based on affinity chromatography, which is a selective separation technique by which a compound (e.g., an antibody) is immobilized on a polymeric matrix and used to bind selectively other compounds. Following removal of the unattached components, the bound compound is displaced by changing the concentration of protons, salts, or cofactors in the eluent" (from original definition by TAIR:TED). Types of highly specific interaction might include those of antigen and antibody, enzyme and substrate, or receptor and ligand.
affinity chromatography evidence
A type of affinity evidence that results from separation of biochemical mixtures by selective binding of a compound to an immobilized compound on a polymeric matrix, subsequent removal of unattached components, and then displacement of the bond compound.
ECO:MCC
TAIR:TED
MI:0004
affinity chromatography technology
A type of similarity that indicates common ancestry.
IP
eco
ECO:0000080
phylogenetic evidence
A type of similarity that indicates common ancestry.
ECO:MCC
PhenoScape:IP
IP
PhenoScape:IP
A type of motif similarity evidence that is based on detection of a targeting sequence in the primary sequence of a protein through computational prediction and/or a manual examination of the sequence.
eco
ISS: targeting sequence prediction
ECO:0000081
targeting sequence prediction evidence
A type of motif similarity evidence that is based on detection of a targeting sequence in the primary sequence of a protein through computational prediction and/or a manual examination of the sequence.
ECO:RCT
TAIR:TED
A type of experimental genomic evidence where DNA polymerase is used to synthesize new strand of DNA complementary to the offered template strand.
PCR evidence
eco
ECO:0000082
polymerase chain reaction evidence
A type of experimental genomic evidence where DNA polymerase is used to synthesize new strand of DNA complementary to the offered template strand.
OBI:0000415
A type of motif similarity evidence that is based on detection of one, or more, transmembrane domains in the primary sequence of a protein through computational prediction and/or a manual examination of the sequence.
eco
ISS: transmembrane domain prediction
ECO:0000083
transmembrane domain prediction evidence
A type of motif similarity evidence that is based on detection of one, or more, transmembrane domains in the primary sequence of a protein through computational prediction and/or a manual examination of the sequence.
ECO:RCT
TAIR:TED
A type of genomic context evidence in which a gene product's identity is supported on the basis of the identity of neighboring genes.
mgiglio
2009-03-20T11:55:18Z
GO_REF:0000025
inferred from genome cluster
eco
ICL
ECO:0000084
Genomic cluster analyses include synteny and operon structure.
gene neighbors evidence
A type of genomic context evidence in which a gene product's identity is supported on the basis of the identity of neighboring genes.
ECO:MCC
GOC:MG
GO_REF:0000025
Operon structure as IGC evidence
A type of protein assay evidence that involves precipitation of a multivalent antigen by a bivalent antibody for protein isolation.
eco
IDA: immunoprecipitation
ECO:0000085
Transcription factors isolated in this way can be incubated with a radiolabeled probe to demonstrate binding.
immunoprecipitation evidence
A type of protein assay evidence that involves precipitation of a multivalent antigen by a bivalent antibody for protein isolation.
ECO:MCC
ECO:SW
TAIR:TED
A type of experimental genomic evidence resulting from a genome-wide estimate of DNA methylation by differential enzymatic digestion of genomic DNA with methylation-sensitive and methylation-insensitive isoschizomers followed by restrained PCR amplification of methylated sequences.
eco
ECO:0000086
intermethylated site amplification evidence
A type of experimental genomic evidence resulting from a genome-wide estimate of DNA methylation by differential enzymatic digestion of genomic DNA with methylation-sensitive and methylation-insensitive isoschizomers followed by restrained PCR amplification of methylated sequences.
PMID:18987810
url:https://www.ncbi.nlm.nih.gov/probe/docs/techpcr/
A type of microscopy evidence where antibodies are used to detect the location of molecules or other structures within cells or tissues.
eco
IDA: immunolocalization
ECO:0000087
immunolocalization evidence
A type of microscopy evidence where antibodies are used to detect the location of molecules or other structures within cells or tissues.
ECO:MCC
ECO:SN
A type of evidence that is based on a combination of experimental evidences or existing models of that system in a related species used for the reconstruction of a biological system.
mgiglio
2009-03-20T12:00:17Z
eco
ISR
inferred from system reconstruction
ECO:0000088
The biological system in question might be a multi-step process or pathway or a physical complex comprising several components. The components in the experimental evidence can come from the same species or a mix of species. The experimental evidences may be only partial or weak.
biological system reconstruction evidence
A type of evidence that is based on a combination of experimental evidences or existing models of that system in a related species used for the reconstruction of a biological system.
ECO:MCC
GOC:mg
A type of DNA detection assay evidence resulting from the use of restriction enzymes for direct end-labeling of DNA (creating landmarks), followed by high-resolution two-dimensional electrophoresis to visualize the landmarks.
SIB:PG
ECO:0001125
RLGS evidence
restriction landmark genome scanning evidence
eco
ECO:0000089
restriction landmark genomic scanning evidence
A type of DNA detection assay evidence resulting from the use of restriction enzymes for direct end-labeling of DNA (creating landmarks), followed by high-resolution two-dimensional electrophoresis to visualize the landmarks.
PMID:8388788
A type of immunolocalization evidence where the antibodies are labeled with colloidal gold particles whose location is then detected via microscopy.
eco
IDA: immunogold labelling
ECO:0000090
immunogold labelling evidence
A type of immunolocalization evidence where the antibodies are labeled with colloidal gold particles whose location is then detected via microscopy.
ECO:MCC
A type of immunolocalization evidence in which recombinant proteins fused with epitopes are recognized by antibodies.
eco
IDA: immunolocalization of epitope-tagged protein
ECO:0000092
epitope-tagged protein immunolocalization evidence
A type of immunolocalization evidence in which recombinant proteins fused with epitopes are recognized by antibodies.
TAIR:TED
A type of array experiment evidence resulting from the hybridization of a nucleic acid sample to a very large set of oligonucleotide probes, which have been attached individually in columns and rows to a solid support, to determine a base sequence, or to detect variations in a gene sequence, gene expression, or for gene mapping.
eco
ECO:0000093
oligonucleotide microarray evidence
A type of array experiment evidence resulting from the hybridization of a nucleic acid sample to a very large set of oligonucleotide probes, which have been attached individually in columns and rows to a solid support, to determine a base sequence, or to detect variations in a gene sequence, gene expression, or for gene mapping.
ECO:RCT
A type of direct assay evidence based on the effect of a substance, factor, or condition as measured in a living organism.
eco
IDA: bioassay
ECO:0000094
biological assay evidence
A type of direct assay evidence based on the effect of a substance, factor, or condition as measured in a living organism.
ECO:MCC
TAIR:TED
A type of in vivo assay evidence that measures one or more aspects of cell growth over a specified time period to indicate an induced or repressed regulatory effect.
mchibucos
2014-10-15T00:58:50Z
eco
growth curve analysis
ECO:0000095
Cell growth aspects can include growth rate and extent of growth. A cell growth curve acts as a natural reporter.
cell growth assay evidence
A type of in vivo assay evidence that measures one or more aspects of cell growth over a specified time period to indicate an induced or repressed regulatory effect.
ECO:SW
PomBase:MAH
A type of direct assay evidence based on an electrophoretic mobility shift of macromolecules, compounds, and proteins where solutions of protein and nucleic acid are combined and the resulting mixtures are electrophoresed under native conditions through polyacrylamide or agarose gel to detect protein-nucleic acid interactions.
MI:0413
EMSA: electrophoretic mobility shift assay
eco
Gel retardation assay
IDA: electrophoretic mobility shift assay
ECO:0000096
EMSA is often used for assessing TF-binding with fluorophore labelling. Protein-nucleic acid complexes generally migrate at a slower rate than the corresponding non-bonded nucleic acid.
electrophoretic mobility shift assay evidence
A type of direct assay evidence based on an electrophoretic mobility shift of macromolecules, compounds, and proteins where solutions of protein and nucleic acid are combined and the resulting mixtures are electrophoresed under native conditions through polyacrylamide or agarose gel to detect protein-nucleic acid interactions.
ECO:KIM
ECO:SW
PMID:17703195
TAIR:TED
MI:0413
electrophoretic mobility shift assay
Gel retardation assay
PMID:17703195
A type of array experiment evidence resulting from the use of a collection of cDNA molecules spotted in a 2D array onto a glass slide or other membrane for hybridization.
eco
ECO:0000097
cDNA microarray evidence
A type of array experiment evidence resulting from the use of a collection of cDNA molecules spotted in a 2D array onto a glass slide or other membrane for hybridization.
REO:0000924
url:https://www.ncbi.nlm.nih.gov/mesh?Db=mesh&term=Oligonucleotide+Array+Sequence+Analysis
A type of nucleic acid hybridization evidence based on localization of a specific segment of DNA or RNA by the application of a complementary strand of nucleic acid to which a reporter molecule is attached.
eco
IDA: in situ hybridization
ECO:0000098
in situ hybridization evidence
A type of nucleic acid hybridization evidence based on localization of a specific segment of DNA or RNA by the application of a complementary strand of nucleic acid to which a reporter molecule is attached.
url:https://www.ncbi.nlm.nih.gov/probe/docs/techish/
A type of direct assay evidence resulting from the separation of various cell components while preserving their individual functions.
eco
ECO:0000100
fractionation evidence
A type of direct assay evidence resulting from the separation of various cell components while preserving their individual functions.
NBK:26936
url:https://www.ncbi.nlm.nih.gov/books/NBK26936/
A type of array experiment evidence resulting from the use of a proprietary Affymetrix array which uses the proprietary GeneChip System for analyzing complex genetic information.
eco
ECO:0000101
Affymetrix array experiment evidence
A type of array experiment evidence resulting from the use of a proprietary Affymetrix array which uses the proprietary GeneChip System for analyzing complex genetic information.
ERO:0001265
A type of fractionation evidence resulting from a protein fractionated with other compounds, factors, or macromolecules.
eco
IDA: co-fractionation
ECO:0000102
co-fractionation evidence
A type of fractionation evidence resulting from a protein fractionated with other compounds, factors, or macromolecules.
TAIR:TED
A type of expression microarray evidence in which levels of RNA expression are determined by simultaneous measurement of tens of thousands of mRNA transcripts on a microarray.
REM evidence
eco
IEP: transcript levels (e.g. microarray data)
ECO:0000104
microarray RNA expression level evidence
A type of expression microarray evidence in which levels of RNA expression are determined by simultaneous measurement of tens of thousands of mRNA transcripts on a microarray.
PMID:20967621
A type of array experiment evidence resulting from the use of a proprietary NimbleGen array for measuring gene expression levels.
eco
ECO:0000105
Nimblegen array evidence
A type of array experiment evidence resulting from the use of a proprietary NimbleGen array for measuring gene expression levels.
PMID:15607417
url:https://roche-biochem.jp/pdf/products/microarray/user_guide/SeqCap/SeqCap_UserGuide_Delivery_ver3.0.pdf
A type of transcript expression level evidence based on electrophoresis and probing to determine levels of RNA expression using a complementary hybridization probe on the separated RNA samples.
Northern blot
eco
IEP: transcript levels (e.g. Northerns)
ECO:0000106
northern assay evidence
A type of transcript expression level evidence based on electrophoresis and probing to determine levels of RNA expression using a complementary hybridization probe on the separated RNA samples.
ECO:SW
TAIR:TED
A type of polymerase chain reaction evidence in which levels of RNA expression are determined through RT-PCR (quantitative or otherwise).
RT-PCR transcription evidence
eco
IEP: transcript levels (e.g. RT-PCR)
ECO:0000108
reverse transcription polymerase chain reaction transcription evidence
A type of polymerase chain reaction evidence in which levels of RNA expression are determined through RT-PCR (quantitative or otherwise).
TAIR:TED
A type of polymerase chain reaction evidence where RNA is reverse transcribed into cDNA and amplified for product measurement in real time for transcription analysis i.e. qPCR.
RT-PCR evidence
qRT-PCR
eco
ECO:0000109
The starting product for PCR, and therefore amplification volume, is directly correlated to the transcription rate.
reverse transcription polymerase chain reaction evidence
A type of polymerase chain reaction evidence where RNA is reverse transcribed into cDNA and amplified for product measurement in real time for transcription analysis i.e. qPCR.
ECO:SW
PMID:11013345
PMID:12901609
qRT-PCR
PMID:12901609
A type of nuclease protection assay evidence where mRNA is hybridized with radiolabeled RNA probes after which RNAse is added to digest the unbound, nonresistant single-stranded overhang regions, later the remaining probe target hybrids are purified and resolved on denaturing polyacrylamide gel, and quantified by autoradiography.
ribonuclease protection assay
RPA
eco
IEP: RNA protection assay
RNAse protection assay
ECO:0000110
RNA protection assay evidence
A type of nuclease protection assay evidence where mRNA is hybridized with radiolabeled RNA probes after which RNAse is added to digest the unbound, nonresistant single-stranded overhang regions, later the remaining probe target hybrids are purified and resolved on denaturing polyacrylamide gel, and quantified by autoradiography.
ECO:SW
PMID:23457339
TAIR:TED
A type of gel electrophoresis evidence where proteins are separated using gel electrophoresis and then they are blotted on a nitrocellulose or polyvinylidene difluoride (PVDF) membrane, later an antibody with a dye or an enzyme is added to the solution which is able to bind to its specific protein and this product is detected either by chemiluminescent detection technique or fluorescence imaging technique.
eco
IEP: protein levels (e.g. Western blots)
Western blot expression analysis
protein immunoblot
ECO:0000112
Western blot is used for protein detection and analysis. A mixed protein sample is separated through polyacrylamide gel electrophoresis then transferred to a membrane, such as polyvinylidene fluoride (PVDF), and labeled with protein-specific antibodies.
western blot evidence
A type of gel electrophoresis evidence where proteins are separated using gel electrophoresis and then they are blotted on a nitrocellulose or polyvinylidene difluoride (PVDF) membrane, later an antibody with a dye or an enzyme is added to the solution which is able to bind to its specific protein and this product is detected either by chemiluminescent detection technique or fluorescence imaging technique.
ECO:SW
PMID:23050259
TAIR:TED
A type of protein expression evidence where a protein of interest is isolated on the basis of its hybridization to an antibody raised to a homologous protein.
eco
IEP: expression library screening
ECO:0000114
expression library screen evidence
A type of protein expression evidence where a protein of interest is isolated on the basis of its hybridization to an antibody raised to a homologous protein.
ECO:MCC
TAIR:TED
A type of nucleic acid hybridization evidence in which preferential or exclusive expression of genes in one cell type or tissue is compared to another cell type or tissue when mRNA from each sample is reverse transcribed, labeled, and hybridized to a cDNA library to compare hybridization patterns.
eco
IEP: differential hybridization
ECO:0000116
Differential hybridization identifies differentially expressed cloned genes. Two different mRNA-derived probes are used to demonstrate RNA expression under a specific condition.
differential hybridization evidence
A type of nucleic acid hybridization evidence in which preferential or exclusive expression of genes in one cell type or tissue is compared to another cell type or tissue when mRNA from each sample is reverse transcribed, labeled, and hybridized to a cDNA library to compare hybridization patterns.
PMID:14668817
A type of nucleic acid hybridization evidence in which preferential or exclusive expression of genes in one cell type or tissue are compared to another cell type or tissue when denatured ds-cDNA from the two samples are hybridized, and the common sequences are 'subtracted'.
eco
IEP: subtractive hybridization
ECO:0000118
Subtractive hybridization is used for isolation and identification of transcripts involving the removal of any sequences present in the control from the test probe to detect only transcripts present in the sample. The method is PCR-based for the comparison of two cDNA libraries.
subtractive hybridization evidence
A type of nucleic acid hybridization evidence in which preferential or exclusive expression of genes in one cell type or tissue are compared to another cell type or tissue when denatured ds-cDNA from the two samples are hybridized, and the common sequences are 'subtracted'.
PMID:11298187
A type of experimental phenotypic evidence in which a gene and/or gene product is investigated in a transgenic organism that has been engineered to overexpress that gene product.
eco
IMP: analysis of overexpression/ectopic expression phenotype
ECO:0000120
over expression analysis evidence
A type of experimental phenotypic evidence in which a gene and/or gene product is investigated in a transgenic organism that has been engineered to overexpress that gene product.
PMID:22419077
A type of protein assay evidence where sub-cellular localization of a protein within a cell is determined.
eco
ECO:0000122
protein localization evidence
A type of protein assay evidence where sub-cellular localization of a protein within a cell is determined.
GO:0008104
url:http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019937
A type of protein localization evidence resulting from the fusion of a protein of interest to a labeling protein which has enzymatic activity or fluorescence properties.
eco
ECO:0000124
fusion protein localization evidence
A type of protein localization evidence resulting from the fusion of a protein of interest to a labeling protein which has enzymatic activity or fluorescence properties.
MI:0240
A type of fusion protein localization evidence resulting from the labeling of a protein of interest with green fluorescent protein (GFP) from the jellyfish Aequorea victoria.
GFP fusion protein localization evidence
eco
IDA: localization of GFP/YFP fusion protein
ECO:0000126
green fluorescent protein fusion protein localization evidence
A type of fusion protein localization evidence resulting from the labeling of a protein of interest with green fluorescent protein (GFP) from the jellyfish Aequorea victoria.
PMID:9759496
A type of fusion protein localization evidence resulting from the labeling of a protein of interest with yellow fluorescent protein (YFP), which was created by mutating green fluorescent protein (GFP) of the Aequorea victoria.
YFP fusion protein localization evidence
eco
IDA: localization of GFP/YFP fusion protein
ECO:0000128
yellow fluorescent protein fusion protein localization evidence
A type of fusion protein localization evidence resulting from the labeling of a protein of interest with yellow fluorescent protein (YFP), which was created by mutating green fluorescent protein (GFP) of the Aequorea victoria.
MI:0368
url:http://www.jbc.org/content/276/31/29188.long
A type of fusion protein localization evidence resulting from the targeted insertion of the beta-glucuronidase (GUS) coding gene as a reporter gene for the localization of a particular gene product.
GUS fusion protein localization evidence
GUS staining evidence
eco
IDA: localization of GUS fusion protein
ECO:0000130
beta-glucuronidase fusion protein localization evidence
A type of fusion protein localization evidence resulting from the targeted insertion of the beta-glucuronidase (GUS) coding gene as a reporter gene for the localization of a particular gene product.
ECO:RCT
A type of fusion protein localization evidence resulting from the targeted insertion of the beta-galactosidase coding gene (lacZ) into a specific gene to create a beta-galactosidase-tagged fusion protein.
LacZ fusion protein localization evidence
eco
ECO:0000132
beta-galactosidase fusion protein localization evidence
A type of fusion protein localization evidence resulting from the targeted insertion of the beta-galactosidase coding gene (lacZ) into a specific gene to create a beta-galactosidase-tagged fusion protein.
PMID:23681629
A type of direct assay evidence resulting from the activity assessment of transport proteins.
eco
IDA: transport assay
ECO:0000134
transport assay evidence
A type of direct assay evidence resulting from the activity assessment of transport proteins.
PMID:18401524
A type of affinity evidence resulting from the binding of a molecule to a nucleic acid.
eco
ECO:0000136
nucleic acid binding evidence
A type of affinity evidence resulting from the binding of a molecule to a nucleic acid.
GO:0003676
A type of nucleic acid binding evidence resulting from an enzyme displaying binding activity to specific ribohomopolymer.
eco
IDA: ribohomopolymer binding assay
ECO:0000138
ribohomopolymer binding assay evidence
A type of nucleic acid binding evidence resulting from an enzyme displaying binding activity to specific ribohomopolymer.
PMC:102612
A type of chromatography evidence that uses a thin layer of adsorbent (such as silica gel, alumina, or cellulose) on a flat, inert substrate.
TLC evidence
eco
IDA: thin layer chromatography
ECO:0000140
thin layer chromatography evidence
A type of chromatography evidence that uses a thin layer of adsorbent (such as silica gel, alumina, or cellulose) on a flat, inert substrate.
ECO:MCC
A type of protein binding evidence resulting from a metal ion binding to a protein at a specific binding site.
eco
ECO:0000142
protein:ion binding evidence
A type of protein binding evidence resulting from a metal ion binding to a protein at a specific binding site.
PMID:2377604
A type of nucleic acid binding evidence in which DNA-protein binding is detected using labeled DNA as probes, hybridized to electrophoretically separated proteins.
eco
IDA: Southwestern analysis
ECO:0000144
Southwestern blot evidence
A type of nucleic acid binding evidence in which DNA-protein binding is detected using labeled DNA as probes, hybridized to electrophoretically separated proteins.
ECO:RCT
TAIR:TED
A type of nucleic acid binding evidence in which RNA-protein binding is detected using labeled RNA as probes, hybridized to electrophoretically separated proteins.
eco
IDA: Northwestern analysis
ECO:0000146
Northwestern blot evidence
A type of nucleic acid binding evidence in which RNA-protein binding is detected using labeled RNA as probes, hybridized to electrophoretically separated proteins.
ECO:RCT
TAIR:TED
eco
IDA: in vitro binding assay
ECO:0000148
in vitro binding evidence
true
A type of reconstitution assay evidence resulting from the use of reconstituted polymerase transcription systems to investigate RNA synthesis.
eco
IDA: in vitro reconstitution assay with recombinant protein
ECO:0000150
in vitro transcription reconstitution assay evidence
A type of reconstitution assay evidence resulting from the use of reconstituted polymerase transcription systems to investigate RNA synthesis.
PMID:9237163
A type of in vitro transcription reconstitution assay evidence resulting from the use of recombinant proteins in preparation of a fully-defined transcription system.
eco
IDA: in vitro reconstitution assay with recombinant protein
ECO:0000152
in vitro recombinant protein transcription reconstitution assay evidence
A type of in vitro transcription reconstitution assay evidence resulting from the use of recombinant proteins in preparation of a fully-defined transcription system.
PMID:9237165
A type of protein expression evidence where a gene from one cell is inserted into a cell that does not typically contain that gene and heterologous protein expression is assessed.
eco
IDA: protein expression in heterologous system
ECO:0000154
heterologous protein expression evidence
A type of protein expression evidence where a gene from one cell is inserted into a cell that does not typically contain that gene and heterologous protein expression is assessed.
ECO:KAV
A type of fractionation evidence resulting from the isolation of a single type of protein from a complex mixture.
eco
ECO:0000156
protein separation evidence
A type of fractionation evidence resulting from the isolation of a single type of protein from a complex mixture.
ERO:0000526
eco
IDA: protein separation and direct sequencing
ECO:0000158
protein separation followed by direct sequencing evidence
eco
IDA: protein separation and fragment identification
ECO:0000160
protein separation followed by fragment identification evidence
A type of transport assay evidence in which the uptake mechanism of a transporter is investigated in a cell that does not normally express that protein.
eco
IDA: uptake assay in heterologous system
ECO:0000162
The transporter is a recombinant protein.
heterologous system uptake evidence
A type of transport assay evidence in which the uptake mechanism of a transporter is investigated in a cell that does not normally express that protein.
ECO:RCT
doi:10.1146/annurev.pp.46.060195.002223
A type of direct assay evidence where electrical properties of cells or tissues are studied.
eco
ECO:0000164
The scale of electrophysiology assays can range from small, e.g. a single ion channel, to large, e.g. an entire organ such as a heart.
electrophysiology assay evidence
A type of direct assay evidence where electrical properties of cells or tissues are studied.
ECO:KAV
A type of voltage clamp recording evidence which involves using two electrodes inserted into a large cell (often a xenopus oocyte) where one electrode is used to measure the internal potential (voltage) of the cell and the other electrode is used to clamp the current.
eco
IDA: two-electrode voltage clamp technique
ECO:0000166
two-electrode voltage clamp recording evidence
A type of voltage clamp recording evidence which involves using two electrodes inserted into a large cell (often a xenopus oocyte) where one electrode is used to measure the internal potential (voltage) of the cell and the other electrode is used to clamp the current.
ECO:SN
PMID:23529422
A type of direct assay evidence resulting from the detection and quantification of transcribed RNA.
eco
ECO:0000168
transcription assay evidence
A type of direct assay evidence resulting from the detection and quantification of transcribed RNA.
MeSH:D014158
url:https://bmcmolbiol.biomedcentral.com/articles/10.1186/1471-2199-15-7
A type of transcription assay evidence in which sequence-specific binding proteins that increase transcription of a specific target gene or genes are identified, quantified, and/or analyzed.
eco
IDA: transcriptional activation assay
ECO:0000170
transcriptional activation assay
A type of transcription assay evidence in which sequence-specific binding proteins that increase transcription of a specific target gene or genes are identified, quantified, and/or analyzed.
url:http://smcg.ccg.unam.mx/enp-unam/05-TranscripYRegulacion/transcription.pdf
A type of experimental phenotypic evidence in which the biochemical aspect of a mutation is analyzed.
eco
IMP: analysis of biochemical trait
ECO:0000172
For example, the accumulation of a biosynthetic intermediate.
biochemical trait analysis evidence
A type of experimental phenotypic evidence in which the biochemical aspect of a mutation is analyzed.
ECO:RCT
A type of mutant phenotype evidence in which the physiological response of a mutant when presented with an external stimulus is determined.
eco
IMP: analysis of physiological response
ECO:0000174
Examples include: abnormal growth of the root in response to gravity, delay in flowering in response to varying light conditions.
mutant physiological response evidence
A type of mutant phenotype evidence in which the physiological response of a mutant when presented with an external stimulus is determined.
ECO:RCT
A type of mutant phenotype evidence in which traits arising from a mutation are visually examined.
eco
IMP: analysis of visible trait
ECO:0000176
mutant visible phenotype evidence
A type of mutant phenotype evidence in which traits arising from a mutation are visually examined.
ECO:RCT
A type of evidence in which the location of the gene within the genome provides insight into its function, or provides evolutionary insight.
eco
ECO:0000177
This type of evidence might include identity of neighboring genes, operon structure, synteny, phylogenetic analysis, or other whole-genome analysis.
genomic context evidence
A type of evidence in which the location of the gene within the genome provides insight into its function, or provides evolutionary insight.
PMID:21609955
A type of biological assay evidence resulting from an assay performed on or in an organism.
eco
ECO:0000178
in vivo assay evidence
A type of biological assay evidence resulting from an assay performed on or in an organism.
ECO:RCT
url:https://www.cancer.gov/publications/dictionaries/cancer-terms?cdrid=46352
A type of experimental evidence arising from the investigation of an animal model system.
eco
ECO:0000179
animal model system study evidence
A type of experimental evidence arising from the investigation of an animal model system.
ECO:MCC
A type of experimental evidence arising from a controlled investigation that uses human subjects.
eco
ECO:0000180
clinical study evidence
A type of experimental evidence arising from a controlled investigation that uses human subjects.
ECO:MCC
A type of biological assay evidence resulting from an assay performed outside the living organism, in an artificial setting.
ECO:0005013
eco
ECO:0000181
in vitro assay evidence
A type of biological assay evidence resulting from an assay performed outside the living organism, in an artificial setting.
ECO:RCT
url:https://www.cancer.gov/publications/dictionaries/cancer-terms?cdrid=45733
A type of biological assay evidence resulting from a sample of microorganisms or living tissue grown in a medium.
eco
ECO:0000182
in vitro culture assay evidence
A type of biological assay evidence resulting from a sample of microorganisms or living tissue grown in a medium.
ECO:RCT
A type of in vitro assay evidence resulting from studies in which the components are derived from resting, nonstimulated cells, therefore all reactions occur in vitro.
in vitro assay
eco
ECO:0000183
cell-free assay evidence
A type of in vitro assay evidence resulting from studies in which the components are derived from resting, nonstimulated cells, therefore all reactions occur in vitro.
PMID:18453125
A type of specific protein inhibition evidence where the protein under study is an enzyme.
eco
ECO:0000184
enzyme inhibition evidence
A type of specific protein inhibition evidence where the protein under study is an enzyme.
ECO:MCC
A type of sequence similarity evidence in which an annotation is made based on a manually-reviewed or published sequence alignment
mchibucos
2010-03-18T12:21:31Z
ECO:00000057
eco
ECO:0000200
Such alignments may be pairwise alignments or multiple alignments.
sequence alignment evidence
A type of sequence similarity evidence in which an annotation is made based on a manually-reviewed or published sequence alignment
url:http://www.geneontology.org/GO.evidence.shtml
A type of sequence similarity evidence in which orthology is established by multiple criteria, including amino acid and/or nucleotide sequence comparisons and one or more of the following: phylogenetic analysis, coincident expression, conserved map location, functional complementation, immunological cross-reaction, similarity in subcellular localization, subunit structure, substrate specificity, and response to specific inhibitors.
mchibucos
2010-03-18T12:30:06Z
ECO:00000060
eco
ortholog evidence
ECO:0000201
Orthology is a relationship between genes in different species indicating that the genes derive from a common ancestor.
sequence orthology evidence
A type of sequence similarity evidence in which orthology is established by multiple criteria, including amino acid and/or nucleotide sequence comparisons and one or more of the following: phylogenetic analysis, coincident expression, conserved map location, functional complementation, immunological cross-reaction, similarity in subcellular localization, subunit structure, substrate specificity, and response to specific inhibitors.
url:http://www.geneontology.org/GO.evidence.shtml
A type of sequence similarity evidence in which the function of a gene product is predicted based on a sequence-based statistical model.
mchibucos
2010-03-18T12:32:30Z
ECO:00000063
eco
ECO:0000202
Used when evidence from any kind of statistical model of a sequence or group of sequences is used to make a prediction about the function of a protein or RNA. Examples of relevant evidence are: Hidden Markov Models, PROSITE motifs, and tools such as tRNASCAN.
match to sequence model evidence
A type of sequence similarity evidence in which the function of a gene product is predicted based on a sequence-based statistical model.
ECO:MCC
url:http://www.geneontology.org/GO.evidence.shtml
An assertion method that does not involve human review.
mchibucos
2010-03-18T12:36:04Z
ECO:00000067
eco
ECO:0000203
An automatic assertion is based on computationally generated information that is not reviewed by a person prior to making the assertion. For example, one common type of automatic assertion involves creating an association of evidence with an entity based on commonness of attributes of that entity and another entity for which an assertion already exists. The commonness is determined algorithmically.
automatic assertion
An assertion method that does not involve human review.
ECO:MCC
An evidence type that is based on an assertion by the author of a paper, which is read by a curator.
mchibucos
2010-06-21T11:17:21Z
eco
ECO:0000204
author statement
An evidence type that is based on an assertion by the author of a paper, which is read by a curator.
ECO:MCC
A type of inferential evidence that is based on a conclusion drawn by a curator.
mchibucos
2010-08-18T05:55:12Z
eco
ECO:0000205
curator inference
A type of inferential evidence that is based on a conclusion drawn by a curator.
ECO:MCC
A type of pairwise sequence alignment evidence obtained with basic local alignment search tool (BLAST).
mchibucos
2010-08-06T04:48:24Z
eco
ECO:0000206
BLAST evidence
A type of pairwise sequence alignment evidence obtained with basic local alignment search tool (BLAST).
ECO:MCC
A type of BLAST evidence in which nucleotide sequences are aligned.
mchibucos
2010-08-06T04:49:58Z
eco
ECO:0000207
nucleotide BLAST evidence
A type of BLAST evidence in which nucleotide sequences are aligned.
ECO:MCC
A type of BLAST evidence in which amino acid or translated nucleotide sequences are aligned.
mchibucos
2010-08-06T04:50:45Z
eco
ECO:0000208
protein BLAST evidence
A type of BLAST evidence in which amino acid or translated nucleotide sequences are aligned.
ECO:MCC
A type of BLAST evidence that is used in an automatic assertion.
mchibucos
2010-08-06T04:55:21Z
eco
ECO:0000209
BLAST evidence used in automatic assertion
true
true
A type of BLAST evidence that is used in an automatic assertion.
ECO:MCC
A type of nucleotide BLAST evidence that is used in an automatic assertion.
mchibucos
2010-08-06T05:09:51Z
eco
ECO:0000210
nucleotide BLAST evidence used in automatic assertion
true
true
A type of nucleotide BLAST evidence that is used in an automatic assertion.
ECO:RCT
A type of protein BLAST evidence that is used in an automatic assertion.
mchibucos
2010-08-06T05:11:04Z
eco
ECO:0000211
protein BLAST evidence used in automatic assertion
true
true
A type of protein BLAST evidence that is used in an automatic assertion.
ECO:RCT
A type of evidence that arises out of the integration of more than one line of evidence.
mchibucos
2010-08-06T05:24:57Z
ECO:0000036
ECO:0000043
eco
inferred from in-silico analysis
ECO:0000212
A key aspect of this type of evidence is that two or more pieces of information are combined to generate an emergent type of evidence not possible with the constituent pieces of evidence alone. A combinatorial analysis typically involves incorporation of different types of evidence.
combinatorial evidence
A type of evidence that arises out of the integration of more than one line of evidence.
ECO:MCC
A type of combinatorial analysis that is used in an automatic assertion.
mchibucos
2010-08-06T05:28:33Z
eco
ECO:0000213
Combinatorial analyses could include experimental or computational results. Examples include: (i) large-scale experiment such as a genome-wide two-hybrid or genome-wide synthetic interactions; (ii) integration of large-scale data sets of various types; and (iii) text-based-computation, e.g. text-mining. For simple sequence comparisons, one should use the sequence similarity analysis evidence type. For microarray results alone, expression pattern analysis is appropriate; whereas, large-scale computational analysis should be used when microarray results are combined with the results of other types of large-scale experiments.
combinatorial evidence used in automatic assertion
true
true
A type of combinatorial analysis that is used in an automatic assertion.
ECO:MCC
A type of phylogenetic evidence whereby an aspect of an ancestral gene is inferred through the characterization of an aspect of a descendant gene.
mchibucos
2010-10-05T11:16:50Z
eco
ECO:0000214
This type of evidence can be used in support of both positive and "not" GO annotations. It should be used to annotate ancestral genes but not extant ones.
biological aspect of descendant evidence
A type of phylogenetic evidence whereby an aspect of an ancestral gene is inferred through the characterization of an aspect of a descendant gene.
ECO:MCC
A type of phylogenetic evidence characterized by long phylogenetic tree branch lengths following a duplication event.
mchibucos
2010-10-05T03:41:34Z
eco
ECO:0000215
Long branch lengths indicate that descendant sequences may have acquired different or additional functions than the ancestral sequence.
rapid divergence from ancestral sequence evidence
A type of phylogenetic evidence characterized by long phylogenetic tree branch lengths following a duplication event.
ECO:MCC
A type of phylogenetic evidence characterized by the absence of key sequence residues.
mchibucos
2010-10-05T03:43:17Z
eco
ECO:0000216
The loss of certain residues important for function can indicate that a sequence lacks a particular function.
phylogenetic determination of loss of key residues evidence
A type of phylogenetic evidence characterized by the absence of key sequence residues.
ECO:MCC
A means by which a statement is made about an entity.
mchibucos
2010-11-12T04:17:37Z
eco
ECO:0000217
assertion method
A means by which a statement is made about an entity.
ECO:MCC
An assertion method that involves human review.
mchibucos
2010-11-12T04:20:02Z
eco
ECO:0000218
A manual assertion could be based on evidence that is generated by and interpreted by a human or it could involve human review of computationally generated information.
manual assertion
An assertion method that involves human review.
ECO:MCC
A type of sequencing assay that determines the sequence of a biopolymer comprised of nucleotides.
mchibucos
2010-11-15T12:22:40Z
eco
DNA sequencing
ECO:0000219
nucleotide sequencing assay evidence
A type of sequencing assay that determines the sequence of a biopolymer comprised of nucleotides.
ECO:MCC
DNA sequencing
OBI:0000626
A type of experimental evidence where the order of molecules that constitute a biopolymer is determined.
mchibucos
2010-11-15T01:44:45Z
eco
ECO:0000220
sequencing assay evidence
A type of experimental evidence where the order of molecules that constitute a biopolymer is determined.
ECO:MCC
OBI:0600047
A type of nucleotide sequencing assay evidence in which a sequence is derived from a parallelized sequencing technique.
mchibucos
2010-11-15T02:19:34Z
eco
next generation sequencing evidence
ECO:0000221
Typically thousands to millions of reads are produced in parallel.
high throughput nucleotide sequencing assay evidence
A type of nucleotide sequencing assay evidence in which a sequence is derived from a parallelized sequencing technique.
ECO:MCC
A type of high throughput nucleotide sequencing evidence in which sequence is determined through hybridization of adaptor-ligated DNA to a glass slide on which each fragment is simultaneously clonally amplified, followed by progressive rounds of base incorporation with fluorescently-tagged nucleotides, washing, imaging, and cleavage.
mchibucos
2010-11-15T02:38:03Z
eco
Solexa sequencing result
ECO:0000222
In Illumina sequencing technology, adapters are ligated onto the ends of randomly fragmented DNA. After single-stranded fragments are bound to the inside surface of a flow cell channel, they undergo in-place bridge PCR amplification. To begin the sequencing cycle, labeled reversible terminators, primers and DNA polymerase are added, followed by laser excitation of the fluorescent label and high resolution scanning. After non-incorporated nucleotides are washed away and the dye is chemically removed, the next cycle repeats with four labeled reversible terminators, primers and DNA polymerase, again followed by imaging.
Illumina sequencing evidence
A type of high throughput nucleotide sequencing evidence in which sequence is determined through hybridization of adaptor-ligated DNA to a glass slide on which each fragment is simultaneously clonally amplified, followed by progressive rounds of base incorporation with fluorescently-tagged nucleotides, washing, imaging, and cleavage.
OBI:0000724
PMID:26000844
Solexa sequencing result
OBI:0000724
A type of high throughput nucleotide sequencing evidence in which the sequence for a ssDNA is determined by addition of primers and then nucleotides, one base pair at a time (which generate a specific fluorescence), to the target strand.
mchibucos
2010-11-15T03:50:14Z
pyrosequencing
eco
ECO:0000223
454 pyrosequencing technology amplifies individual DNA fragments inside water droplets within an oil solution (emulsion PCR). Within each droplet, a single DNA template is attached to a single primer-coated bead. Each bead is subsequently captured in a picolitre well within the sequencing machine. A luciferase-based readout system is used to identify individual nucleotides added to the nascent DNA.
The target strand is usually prepared by fragmentation, adaptor ligation, and amplification by emulsion PCR.
454 pyrosequencing evidence
A type of high throughput nucleotide sequencing evidence in which the sequence for a ssDNA is determined by addition of primers and then nucleotides, one base pair at a time (which generate a specific fluorescence), to the target strand.
EFO:0005016
pyrosequencing
OBI:0000730
A type of high throughput nucleotide sequencing evidence in which sequence is determined through rounds of ligation-based sequencing with fluorescently-labeled Di-base probes and cleavage, after which the template is reset, with a primer offset by one base, for subsequent rounds of ligation.
mchibucos
2010-11-15T04:17:41Z
eco
ECO:0000224
SOLiD sequencing technology is based on sequencing by ligation. After library preparation, emulsion PCR and bead enrichment are performed, including 3' modification of templates on selected beads to allow covalent bonding to a slide. 3' modified beads are attached to a glass slide and primers are added. Four fluorescently labeled di-base probes are added and multiple cycles of ligation, detection and cleavage are performed. The number of cycles determines read length. After a number of ligation cycles, the extension product is removed and another round of ligation cycles is performed with a new primer complimentary to the n-1 position of the template. Five rounds of primer reset are performed for each sequence tag.
Samples are prepared by fragmentation of a sample library, adaptor ligation, emulsion PCR, and attachment of resultant beads to glass slides.
SOLiD sequencing evidence
A type of high throughput nucleotide sequencing evidence in which sequence is determined through rounds of ligation-based sequencing with fluorescently-labeled Di-base probes and cleavage, after which the template is reset, with a primer offset by one base, for subsequent rounds of ligation.
OBI:0000706
A type of nucleotide sequencing assay in which DNA sequence is determined by addition of a primed DNA template to a reaction mixture, followed by addition of DNA polymerase, deoxynucleosidetriphosphates (dNTPs - one of which may be radiolabeled), and one of four di-deoxynucleotidetriphosphates (ddNTPs), after which DNA elongation is terminated and the DNA is separated by size and imaged.
mchibucos
2010-11-15T04:46:31Z
Sanger sequencing
dye terminator sequencing
eco
ECO:0000225
Chain termination sequencing, also called Sanger sequencing after its developer, uses dideoxynucleotide triphosphates (ddNTPs) as DNA chain terminators. Single-stranded DNA template, DNA primer, DNA polymerase, fluorescently or radioactively labeled nucleotides, and one of four ddNTPs are added together in each of four separate sequencing reactions. The synthesized and labeled DNA fragments from each of the four reactions are denatured, separated by size by gel electrophoresis, and visualized by autoradiography or UV light.
The ddNTPs lack an OH group so the next dNTP cannot be attached, causing chain termination.
chain termination sequencing evidence
A type of nucleotide sequencing assay in which DNA sequence is determined by addition of a primed DNA template to a reaction mixture, followed by addition of DNA polymerase, deoxynucleosidetriphosphates (dNTPs - one of which may be radiolabeled), and one of four di-deoxynucleotidetriphosphates (ddNTPs), after which DNA elongation is terminated and the DNA is separated by size and imaged.
OBI:0000695
A type of immunoprecipitation evidence that is used to identify a protein binding site on a genomic DNA sequence.
mchibucos
2010-11-16T01:29:08Z
MI:0402
ChIP evidence
eco
ECO:0000226
Chromatin immunoprecipitation (ChIP) is used to investigate protein-DNA interactions in vivo. DNA and proteins are chemically cross-linked in vivo to form chromatin complexes, followed by cell lysis and DNA shearing. Fragmented DNA-protein complexes are selectively enriched for a protein of interest using a specific antibody (immunoprecipitation). Protein digestion and DNA purification are performed prior to DNA detection via molecular cloning and sequencing, polymerase chain reaction (PCR), microarray analysis (ChIP-on-chip), or direct high-throughput sequencing (ChIP-seq).
chromatin immunoprecipitation evidence
A type of immunoprecipitation evidence that is used to identify a protein binding site on a genomic DNA sequence.
ECO:MCC
MI:0402
chromatin immunoprecipitation assay
A type of chromatin immunoprecipitation evidence that uses polymerase chain reaction (PCR) where specific primers are used on the pulled-down DNA for DNA detection.
mchibucos
2010-11-16T05:02:00Z
ChIP-PCR evidence
eco
ECO:0000227
ChIP-PCR is often used to validate ChIP-chip results and less frequently,ChIP-Seq results.
chromatin immunoprecipitation-PCR evidence
A type of chromatin immunoprecipitation evidence that uses polymerase chain reaction (PCR) where specific primers are used on the pulled-down DNA for DNA detection.
ECO:MCC
ECO:SW
PMID:18388953
A type of chromatin immunoprecipitation evidence in which protein-DNA interactions are investigated at known genomic binding sites through a process of ChIP, DNA purification, and finally quantitative polymerase chain reaction (qPCR) for DNA detection.
mchibucos
2010-11-16T05:26:47Z
ChIP-qPCR evidence
eco
ECO:0000228
chromatin immunoprecipitation-qPCR evidence
A type of chromatin immunoprecipitation evidence in which protein-DNA interactions are investigated at known genomic binding sites through a process of ChIP, DNA purification, and finally quantitative polymerase chain reaction (qPCR) for DNA detection.
url:https://www.diagenode.com/applications/chip-qpcr
A type of chromatin immunoprecipitation evidence that uses high-throughput sequencing where immunoprecipitated DNA fragments are funnelled into a massively parallel sequencer to produce multiple short reads for locating binding sites of DNA-associated proteins.
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.
mchibucos
2010-11-16T05:43:55Z
MI:0225
ChIP-chip evidence
ChIP-on-chip evidence
eco
ECO:0000230
A fixating agent such as formaldehyde is used to cross link proteins and DNA. Sonication is applied for DNA shearing. For transcription factor tagging, an antibody or epitope is employed. After cross-linking is reversed, the DNA is amplified and labeled with a flourophore for microarray which produces a resolution of aproximately 500 bp.
chromatin immunoprecipitation-chip evidence
A type of chromatin immunoprecipitation evidence that uses a tiling microarray for the detection of protein-bound DNA regions where chromatin is immunoprecipitated for protein tagging and DNA is sheared from the cross-linked protein-DNA complex to be arrayed revealing the protein-bound genomic regions.
ECO:MCC
ECO:SW
PMID:18388953
PMID:19381927
MI:0225
chromatin immunoprecipitation array
A type of polymerase chain reaction evidence where the reaction product is quantified in real-time across cycles by means of fluorescent dyes for detection and quantification of specific sequences in a DNA sample.
mchibucos
2010-11-16T05:57:20Z
Q-PCR evidence
quantitative PCR evidence
real-time PCR evidence
real-time polymerase chain reaction evidence
eco
qRT-PCR evidence
ECO:0000231
Quantitative PCR enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample. The dye is activated upon binding double-stranded DNA.
Although qRT-PCR is commonly found in literature synonymous to qPCR, it is preferable not to use this synonym as it is the accepted abbreviation for reverse transcription PCR. qPCR should be used instead (ISBN 978-0-470-68386-6 page 173).
quantitative polymerase chain reaction evidence
A type of polymerase chain reaction evidence where the reaction product is quantified in real-time across cycles by means of fluorescent dyes for detection and quantification of specific sequences in a DNA sample.
ECO:MCC
ECO:SW
A type of experimental evidence that is based on a five-step technique of cross-linking DNA in vivo, restriction digestion, intramolecular ligation, reversing DNA cross-links, and DNA processing and quantitation.
mchibucos
2010-11-17T12:27:14Z
3C
chromosome conformation capture
eco
ECO:0000232
Chromosome conformation capture technologies are used to study the structural properties and spatial organization of chromosomes inside cells. All types of chromosome conformation capture technology involve five primary steps: cross-linking of DNA in vivo, restriction digestion, intramolecular ligation, reversing cross-linkages, and DNA enrichment and quantitation. The last step is different for each type of chromosome conformation capture technology, and may include PCR (3C), inverse PCR (4C), or ligation-mediated amplification (5C). Methods for product quantitation can include agarose gel detection or real-time quantitative PCR in the case of 3C, or high-throughput sequencing or microarray analysis for 4C and 5C.
chromosome conformation capture-based evidence
A type of experimental evidence that is based on a five-step technique of cross-linking DNA in vivo, restriction digestion, intramolecular ligation, reversing DNA cross-links, and DNA processing and quantitation.
ECO:MCC
A type of chromosome conformation capture-based evidence that is derived by performing a type of polymerase chain reaction (PCR) in the final product quantitation step.
mchibucos
2010-11-17T12:46:15Z
3C
eco
ECO:0000233
3C is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 3C differs only in the fifth step, which involves performing either standard polymerase chain reaction (PCR) or quantitative PCR (qPCR) for product quantitation.
chromosome conformation capture evidence
A type of chromosome conformation capture-based evidence that is derived by performing a type of polymerase chain reaction (PCR) in the final product quantitation step.
ECO:MCC
A type of chromosome conformation capture-based evidence that is derived by inverse polymerase chain reaction (inverse PCR) on a prior circularized 3C library followed by product quantitation with a microarray.
mchibucos
2010-11-19T01:20:28Z
4C
chromosome conformation capture on chip
circularized 3C
eco
ECO:0000234
4C is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 4C differs only in the fifth step, which involves inverse polymerase chain reaction (inverse PCR) on a circularized 3C library prior to product quantitation.
circularized chromosome conformation capture evidence
A type of chromosome conformation capture-based evidence that is derived by inverse polymerase chain reaction (inverse PCR) on a prior circularized 3C library followed by product quantitation with a microarray.
ECO:MCC
A type of chromosome conformation capture-based evidence that is derived by performing ligation-mediated amplification (LMA) prior to product quantitation.
mchibucos
2010-11-19T01:22:20Z
5C
carbon-copy 3C
eco
ECO:0000235
5C is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 5C differs only in the fifth step, which involves ligation-mediated amplification (LMA) followed by product quantitation.
carbon-copy chromosome conformation capture evidence
A type of chromosome conformation capture-based evidence that is derived by performing ligation-mediated amplification (LMA) prior to product quantitation.
ECO:MCC
A type of chromosome conformation capture evidence that is derived by performing polymerase chain reaction (PCR) in the quantitation step.
mchibucos
2010-11-19T03:00:47Z
3C
3C-PCR
eco
ECO:0000236
chromosome conformation capture-PCR evidence
A type of chromosome conformation capture evidence that is derived by performing polymerase chain reaction (PCR) in the quantitation step.
ECO:MCC
A type of chromosome conformation capture evidence that is derived by performing quantitative polymerase chain reaction (qPCR) in the quantitation step.
mchibucos
2010-11-19T03:06:47Z
3C-qPCR
3C-quantitative PCR
3C-real-time PCR
eco
ECO:0000237
chromosome conformation capture-qPCR evidence
A type of chromosome conformation capture evidence that is derived by performing quantitative polymerase chain reaction (qPCR) in the quantitation step.
ECO:MCC
A type of chromosome conformation capture-based evidence that is derived by performing immunoprecipitation enrichment of ligated fragments events prior to product quantitation.
mchibucos
2010-11-19T04:24:03Z
eco
ECO:0000238
Hi-C is used to study the structural properties and spatial organization of chromosomes inside cells. Hi-C is similar to other types of chromosome conformation capture technology, but involves the addition of biotinylated nucleotides during the second or fourth step and enrichment for ligated fragments using immunoprecipitation after the fourth step.
Hi-C evidence
A type of chromosome conformation capture-based evidence that is derived by performing immunoprecipitation enrichment of ligated fragments events prior to product quantitation.
ECO:MCC
A type of chromosome conformation capture-based evidence that is derived by inverse polymerase chain reaction (inverse PCR) on a circularized 3C library prior to product quantitation with high-throughput (HT) sequencing.
mchibucos
2010-11-30T03:22:25Z
3C sequencing
3C-seq
4C sequencing
4C-seq
circularized 3C sequencing
circularized 3C-seq
eco
ECO:0000239
3C-seq is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 3C-seq differs only in the fifth step, which involves inverse polymerase chain reaction (PCR) on a circularized 3C library prior to product quantitation.
chromosome conformation capture sequencing evidence
A type of chromosome conformation capture-based evidence that is derived by inverse polymerase chain reaction (inverse PCR) on a circularized 3C library prior to product quantitation with high-throughput (HT) sequencing.
ECO:MCC
A type of experimental phenotypic evidence in which the phenotype of an organism is observed after the disruption of a structural feature.
mchibucos
2010-12-06T12:24:16Z
eco
ECO:0000240
anatomical perturbation evidence
A type of experimental phenotypic evidence in which the phenotype of an organism is observed after the disruption of a structural feature.
ECO:MCC
A type of experimental phenotypic evidence in which the phenotype of an organism is observed after modification of the extra-organismal context.
mchibucos
2010-12-06T12:33:58Z
eco
mechanical constraint evidence
ECO:0000241
Many environmental factors are subject to modification, such as temperature, pressure, humidity, radiation, and so forth.
environmental perturbation evidence
A type of experimental phenotypic evidence in which the phenotype of an organism is observed after modification of the extra-organismal context.
ECO:MCC
A type of anatomical perturbation that is based on disruption of tissue.
mchibucos
2010-12-06T12:33:58Z
ablated tissue evidence
eco
ECO:0000242
A tissue ablation experiment involves observing the phenotype of an entity whose tissues have been disrupted through genetic or biochemical manipulation, physical destruction, or some other means.
tissue ablation evidence
A type of anatomical perturbation that is based on disruption of tissue.
ECO:MCC
A type of anatomical perturbation that is based on adding tissue to an organism through a graft procedure.
mchibucos
2010-12-06T12:33:58Z
eco
ECO:0000243
tissue grafting evidence
A type of anatomical perturbation that is based on adding tissue to an organism through a graft procedure.
ECO:MCC
A type of combinatorial analysis that is used in a manual assertion.
mchibucos
2010-12-09T02:02:12Z
eco
ECO:0000244
Combinatorial analyses could include experimental or computational results. Examples include: (i) large-scale experiment such as a genome-wide two-hybrid or genome-wide synthetic interactions; (ii) integration of large-scale data sets of various types; and (iii) text-based-computation, e.g. text-mining. For simple sequence comparisons, one should use the sequence similarity analysis evidence type. For microarray results alone, expression pattern analysis is appropriate; whereas, large-scale computational analysis should be used when microarray results are combined with the results of other types of large-scale experiments.
combinatorial evidence used in manual assertion
true
true
A type of combinatorial analysis that is used in a manual assertion.
ECO:MCC
A type of computational combinatorial analysis that is used in a manual assertion.
mchibucos
2010-12-09T02:37:54Z
GOECO:RCA
RCA
inferred from reviewed computational analysis
eco
ECO:0000245
computational combinatorial evidence used in manual assertion
http://geneontology.org/page/rca-inferred-reviewed-computational-analysis
true
true
A type of computational combinatorial analysis that is used in a manual assertion.
ECO:MCC
GOECO:RCA
inferred from reviewed computational analysis
RCA
GOECO:RCA
inferred from reviewed computational analysis
GOECO:RCA
A type of computational combinatorial analysis that is used in an automatic assertion.
mchibucos
2010-12-09T02:37:54Z
eco
ECO:0000246
computational combinatorial evidence used in automatic assertion
true
true
A type of computational combinatorial analysis that is used in an automatic assertion.
ECO:MCC
A type of sequence alignment evidence that is used in a manual assertion.
mchibucos
2010-12-09T05:12:27Z
GOECO:ISA
ISA
inferred from sequence alignment
eco
ECO:0000247
sequence alignment evidence used in manual assertion
http://geneontology.org/page/isa-inferred-sequence-alignment
true
true
A type of sequence alignment evidence that is used in a manual assertion.
ECO:RCT
GOECO:ISA
inferred from sequence alignment
ISA
GOECO:ISA
inferred from sequence alignment
GOECO:ISA
A type of sequence alignment evidence that is used in an automatic assertion.
mchibucos
2010-12-09T05:12:27Z
eco
ECO:0000248
sequence alignment evidence used in automatic assertion
true
true
A type of sequence alignment evidence that is used in an automatic assertion.
ECO:RCT
A type of sequence similarity evidence that is used in an automatic assertion.
mchibucos
2010-12-09T05:22:30Z
eco
ECO:0000249
sequence similarity evidence used in automatic assertion
true
true
A type of sequence similarity evidence that is used in an automatic assertion.
ECO:RCT
A type of sequence similarity evidence that is used in a manual assertion.
mchibucos
2010-12-09T05:22:30Z
GOECO:ISS
ISS
inferred from sequence or structural similarity
eco
ECO:0000250
sequence similarity evidence used in manual assertion
http://geneontology.org/page/iss-inferred-sequence-or-structural-similarity
true
true
A type of sequence similarity evidence that is used in a manual assertion.
ECO:MCC
GOECO:ISS
inferred from sequence or structural similarity
ISS
GOECO:ISS
inferred from sequence or structural similarity
GOECO:ISS
A type of similarity evidence that is used in an automatic assertion.
mchibucos
2010-12-09T05:28:12Z
eco
ECO:0000251
similarity evidence used in automatic assertion
true
true
A type of similarity evidence that is used in an automatic assertion.
ECO:RCT
A type of similarity evidence that is used in a manual assertion.
mchibucos
2010-12-09T05:28:12Z
eco
ECO:0000252
similarity evidence used in manual assertion
true
true
A type of similarity evidence that is used in a manual assertion.
ECO:RCT
A type of genetic similarity evidence that is used in a manual assertion.
mchibucos
2010-12-10T01:42:44Z
eco
ECO:0000253
genetic similarity evidence used in manual assertion
true
true
A type of genetic similarity evidence that is used in a manual assertion.
ECO:RCT
A type of genetic similarity evidence that is used in an automatic assertion.
mchibucos
2010-12-10T01:42:44Z
eco
ECO:0000254
genetic similarity evidence used in automatic assertion
true
true
A type of genetic similarity evidence that is used in an automatic assertion.
ECO:RCT
A type of match to sequence model evidence that is used in a manual assertion.
mchibucos
2010-12-10T02:26:35Z
GOECO:ISM
GO_REF:0000011
ISM
inferred from sequence model
eco
ECO:0000255
match to sequence model evidence used in manual assertion
http://geneontology.org/page/ism-inferred-sequence-model
true
true
A type of match to sequence model evidence that is used in a manual assertion.
ECO:RCT
GOECO:ISM
inferred from sequence model
GO_REF:0000011
Hidden Markov Models (TIGR)
ISM
GOECO:ISM
inferred from sequence model
GOECO:ISM
A type of match to sequence model evidence that is used in an automatic assertion.
mchibucos
2010-12-10T02:26:35Z
GO_REF:0000002
GO_REF:0000107
eco
ECO:0000256
match to sequence model evidence used in automatic assertion
true
true
A type of match to sequence model evidence that is used in an automatic assertion.
ECO:RCT
GO_REF:0000002
Gene Ontology annotation through association of InterPro records with GO terms.
GO_REF:0000107
Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl
A type of motif similarity evidence that is used in a manual assertion.
mchibucos
2010-12-10T02:44:34Z
eco
ECO:0000257
motif similarity evidence used in manual assertion
true
true
A type of motif similarity evidence that is used in a manual assertion.
ECO:RCT
A type of motif similarity evidence that is used in an automatic assertion.
mchibucos
2010-12-10T02:44:34Z
eco
ECO:0000258
motif similarity evidence used in automatic assertion
true
true
A type of motif similarity evidence that is used in an automatic assertion.
ECO:RCT
A type of match to InterPro member signature evidence that is used in an automatic assertion.
mchibucos
2010-12-10T02:54:51Z
eco
ECO:0000259
match to InterPro member signature evidence used in automatic assertion
true
true
A type of match to InterPro member signature evidence that is used in an automatic assertion.
ECO:RCT
A type of match to InterPro member signature evidence that is used in a manual assertion.
mchibucos
2010-12-10T02:54:51Z
eco
ECO:0000260
match to InterPro member signature evidence used in manual assertion
true
true
A type of match to InterPro member signature evidence that is used in a manual assertion.
ECO:RCT
A type of targeting sequence prediction that is used in an automatic assertion.
mchibucos
2010-12-10T03:02:49Z
eco
ECO:0000261
targeting sequence prediction evidence used in automatic assertion
true
true
A type of targeting sequence prediction that is used in an automatic assertion.
ECO:RCT
A type of targeting sequence prediction that is used in a manual assertion.
mchibucos
2010-12-10T03:02:49Z
eco
ECO:0000262
targeting sequence prediction evidence used in manual assertion
true
true
A type of targeting sequence prediction that is used in a manual assertion.
ECO:RCT
A type of transmembrane domain prediction that is used in an automatic assertion.
mchibucos
2010-12-10T03:28:35Z
eco
ECO:0000263
transmembrane domain prediction evidence used in automatic assertion
true
true
A type of transmembrane domain prediction that is used in an automatic assertion.
ECO:RCT
A type of transmembrane domain prediction that is used in a manual assertion.
mchibucos
2010-12-10T03:28:35Z
eco
ECO:0000264
transmembrane domain prediction evidence used in manual assertion
true
true
A type of transmembrane domain prediction that is used in a manual assertion.
ECO:RCT
A type of sequence orthology evidence that is used in an automatic assertion.
mchibucos
2010-12-10T03:39:41Z
GO_REF:0000019
GO_REF:0000020
GO_REF:0000035
GO_REF:0000049
eco
Ortholog evidence
ECO:0000265
sequence orthology evidence used in automatic assertion
true
true
A type of sequence orthology evidence that is used in an automatic assertion.
ECO:RCT
GO_REF:0000019
Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara
GO_REF:0000020
Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins.
GO_REF:0000035
Automatic transfer of experimentally verified manual GO annotation data to plant orthologs using Ensembl Compara
GO_REF:0000049
Automatic transfer of experimentally verified manual GO annotation data to fungal orthologs using Ensembl Compara
A type of sequence orthology evidence that is used in a manual assertion.
mchibucos
2010-12-10T03:39:41Z
GOECO:ISO
ISO
inferred from sequence orthology
eco
Ortholog evidence
ECO:0000266
sequence orthology evidence used in manual assertion
http://geneontology.org/page/iso-inferred-sequence-orthology
true
true
A type of sequence orthology evidence that is used in a manual assertion.
ECO:MCC
GOECO:ISO
inferred from sequence orthology
ISO
GOECO:ISO
inferred from sequence orthology
GOECO:ISO
A type of protein detection assay evidence where an antigen is bound to a substrate, and an antibody directly or indirectly linked to an enzyme is utilized to determine the amount of bound antigen which is visualized with a color change in the substrate.
mchibucos
2010-12-14T01:57:13Z
MI:0411
ELISA evidence
enzyme-linked immunosorbent assay
eco
ECO:0000267
ELISA is sometimes used in the study of transcriptional regulation to identify a produced protein, especially secreted protein.
enzyme-linked immunoabsorbent assay evidence
A type of protein detection assay evidence where an antigen is bound to a substrate, and an antibody directly or indirectly linked to an enzyme is utilized to determine the amount of bound antigen which is visualized with a color change in the substrate.
ECO:MCC
ECO:SW
PMID:23949770
MI:0411
enzyme linked immunosorbent assay
A type of direct assay evidence in which cells or particles are characterized by passing them through a light source and monitoring the resultant light scatter or fluorochrome excitation.
mchibucos
2010-12-14T02:07:08Z
FCM
eco
ECO:0000268
flow cytometry evidence
A type of direct assay evidence in which cells or particles are characterized by passing them through a light source and monitoring the resultant light scatter or fluorochrome excitation.
ECO:MCC
A type of experimental evidence that is used in a manual assertion.
mchibucos
2010-12-20T05:36:49Z
GOECO:EXP
EXP
inferred from experiment
eco
ECO:0000269
experimental evidence used in manual assertion
http://geneontology.org/page/exp-inferred-experiment
true
true
A type of experimental evidence that is used in a manual assertion.
ECO:MCC
GOECO:EXP
inferred from experiment
EXP
GOECO:EXP
inferred from experiment
GOECO:EXP
A type of expression pattern evidence that is used in a manual assertion.
mchibucos
2010-12-20T05:46:39Z
GOECO:IEP
IEP
inferred from expression pattern
eco
ECO:0000270
expression evidence used in manual assertion
http://geneontology.org/page/iep-inferred-expression-pattern
true
true
A type of expression pattern evidence that is used in a manual assertion.
ECO:MCC
GOECO:IEP
inferred from expression pattern
IEP
GOECO:IEP
inferred from expression pattern
GOECO:IEP
A type of array experiment evidence that is used in a manual assertion.
mchibucos
2010-12-20T05:51:58Z
eco
ECO:0000271
array experiment evidence used in manual assertion
true
true
A type of array experiment evidence that is used in a manual assertion.
ECO:MCC
A type of Affymetrix array experiment evidence that is used in a manual assertion.
mchibucos
2010-12-20T05:53:36Z
eco
ECO:0000272
Affymetrix array experiment evidence used in manual assertion
true
true
A type of Affymetrix array experiment evidence that is used in a manual assertion.
ECO:MCC
A type of evidence arising from a cDNA microarray experiment that is used in a manual assertion.
mchibucos
2010-12-20T05:55:49Z
eco
ECO:0000273
cDNA microarray evidence used in manual assertion
true
true
A type of evidence arising from a cDNA microarray experiment that is used in a manual assertion.
ECO:MCC
A type of evidence arising from a CpG island microarray experiment that is used in a manual assertion.
mchibucos
2010-12-20T05:58:44Z
eco
ECO:0000274
CpG island microarray evidence used in manual assertion
true
true
A type of evidence arising from a CpG island microarray experiment that is used in a manual assertion.
ECO:MCC
A type of expression microarray evidence that is used in a manual assertion.
mchibucos
2010-12-20T06:01:26Z
eco
ECO:0000275
expression microarray evidence used in manual assertion
true
true
A type of expression microarray evidence that is used in a manual assertion.
ECO:MCC
A type of evidence arising from a genomic microarray experiment that is used in a manual assertion.
mchibucos
2010-12-20T06:03:28Z
eco
ECO:0000276
genomic microarray evidence used in manual assertion
true
true
A type of evidence arising from a genomic microarray experiment that is used in a manual assertion.
ECO:MCC
A type of evidence arising from a Nimblegen array experiment that is used in a manual assertion.
mchibucos
2010-12-20T06:05:20Z
eco
ECO:0000277
Nimblegen array evidence used in manual assertion
true
true
A type of evidence arising from a Nimblegen array experiment that is used in a manual assertion.
ECO:MCC
A type of evidence arising from an oligonucleotide microarray experiment that is used in a manual assertion.
mchibucos
2010-12-20T06:09:45Z
eco
ECO:0000278
oligonucleotide microarray evidence used in manual assertion
true
true
A type of evidence arising from an oligonucleotide microarray experiment that is used in a manual assertion.
ECO:MCC
A type of Western blot assay that is used in a manual assertion.
mchibucos
2010-12-20T06:20:01Z
eco
ECO:0000279
western blot evidence used in manual assertion
true
true
A type of Western blot assay that is used in a manual assertion.
ECO:MCC
A type of protein expression level analysis that is used in a manual assertion.
mchibucos
2010-12-20T06:21:54Z
eco
ECO:0000280
protein expression level evidence used in manual assertion
true
true
A type of protein expression level analysis that is used in a manual assertion.
ECO:MCC
A type of expression library screen evidence that is used in a manual assertion.
mchibucos
2010-12-20T06:24:05Z
eco
ECO:0000281
expression library screen evidence used in manual assertion
true
true
A type of expression library screen evidence that is used in a manual assertion.
ECO:MCC
A type of heterologous protein expression analysis that is used in a manual assertion.
mchibucos
2010-12-20T06:27:04Z
eco
ECO:0000282
heterologous protein expression evidence used in manual assertion
true
true
A type of heterologous protein expression analysis that is used in a manual assertion.
ECO:MCC
A type of protein expression spatial pattern analysis that is used in a manual assertion.
mchibucos
2010-12-20T06:31:44Z
eco
ECO:0000283
spatial pattern of protein expression evidence used in manual assertion
true
true
A type of protein expression spatial pattern analysis that is used in a manual assertion.
ECO:MCC
A type of protein expression analysis that is used in a manual assertion.
mchibucos
2010-12-20T06:33:46Z
eco
ECO:0000284
protein expression evidence used in manual assertion
true
true
true
A type of protein expression analysis that is used in a manual assertion.
ECO:MCC
A type of microarray RNA expression level data that is used in manual assertion.
mchibucos
2010-12-20T06:41:33Z
eco
ECO:0000285
microarray RNA expression level evidence used in manual assertion
true
true
true
A type of microarray RNA expression level data that is used in manual assertion.
ECO:MCC
A type of transcript expression level data that is used in manual assertion.
mchibucos
2010-12-20T06:52:03Z
eco
ECO:0000286
transcript expression level evidence used in manual assertion
true
true
A type of transcript expression level data that is used in manual assertion.
ECO:MCC
A type of differential hybridization experiment that is used in a manual assertion.
mchibucos
2010-12-20T06:55:14Z
eco
ECO:0000287
differential hybridization evidence used in manual assertion
true
true
A type of differential hybridization experiment that is used in a manual assertion.
ECO:MCC
A type of RNA protection assay that is used in a manual assertion.
mchibucos
2010-12-20T06:57:33Z
eco
ECO:0000288
RNA protection assay evidence used in manual assertion
true
true
A type of RNA protection assay that is used in a manual assertion.
ECO:MCC
A type of spatial pattern of transcript expression analysis that is used in a manual assertion.
mchibucos
2010-12-20T06:59:18Z
eco
ECO:0000289
spatial pattern of transcript expression evidence used in manual assertion
true
true
A type of spatial pattern of transcript expression analysis that is used in a manual assertion.
ECO:MCC
A type of subtractive hybridization experiment that is used in a manual assertion.
mchibucos
2010-12-20T07:00:48Z
eco
ECO:0000290
subtractive hybridization evidence used in manual assertion
true
true
A type of subtractive hybridization experiment that is used in a manual assertion.
ECO:MCC
A type of transcript expression evidence that is used in a manual assertion.
mchibucos
2010-12-20T07:02:08Z
eco
ECO:0000291
transcript expression evidence used in manual assertion
true
true
A type of transcript expression evidence that is used in a manual assertion.
ECO:MCC
A type of mutant phenotype evidence that uses anti-sense by introducing morpholino oligonucleotides into the cytosol of a cell.
mchibucos
2011-01-10T03:36:25Z
anti-sense
eco
ECO:0000292
Morpholino oligonucleotides modify gene expression by blocking access of other molecules to specific, approximately 25-base-long regions of the base-pairing surfaces of ribonucleic acid (RNA). To achieve this anti-sense knockdown technique, delivery of the morpholino can be achieved via microinjection, electroporation, or another method.
morpholino experiment evidence
A type of mutant phenotype evidence that uses anti-sense by introducing morpholino oligonucleotides into the cytosol of a cell.
ECO:MCC
A type of evidence arising from a physical interaction analysis where a combinatorial chemistry technique is used to identify oligonucleotides that bind to a target ligand.
mchibucos
2011-01-10T04:23:50Z
MI:0657
SELEX evidence
in vitro selection evidence
eco
in vitro evolution evidence
ECO:0000293
SELEX begins with the synthesis of a large oligonucleotide library, either single-stranded DNA or RNA, which consists of random fixed-length sequences flanked by constant 5' and 3' ends that serve as primers. The library is exposed to a target ligand, typically a protein or small organic compound. Unbound sequences are removed, typically with affinity chromatography. Bound sequences are eluted and the nucleic acid is extracted, followed by PCR amplification (RNA is first reverse transcribed). PCR product is converted to single stranded (DNA) or transcribed (RNA). Oligonucleotides are bound to the ligand again and the process is repeated with increasing elution stringency. After several rounds of the process, recovered oligonucleotides are sequenced and analyzed to reveal the binding specificity of the protein.
systematic evolution of ligands by exponential amplification evidence
A type of evidence arising from a physical interaction analysis where a combinatorial chemistry technique is used to identify oligonucleotides that bind to a target ligand.
ECO:MCC
url:http://en.wikipedia.org/wiki/Systematic_Evolution_of_Ligands_by_Exponential_Enrichment
MI:0657
systematic evolution of ligands by exponential enrichment
A type of hybrid interaction evidence that uses bacterial transformation with two plasmids to assess in vivo binding of a DNA-binding domain (bait) and DNA target site (prey).
mchibucos
2011-01-10T06:16:20Z
B1H evidence
eco
ECO:0000294
Bacterial one-hybrid assay is a method for screening a library of candidate proteins (prey plasmid) for the ability to bind to a target, cis-regulatory element or any other short, DNA binding sequence placed 5' to reporter genes (bait plasmid). Transformation of a bacterial host with two different plasmids is required: One is designed to express the "bait". The other plasmid contains a "prey" which, if bound to by the chimeric fusion product, drives expression of downstream reporter genes.
bacterial one-hybrid evidence
A type of hybrid interaction evidence that uses bacterial transformation with two plasmids to assess in vivo binding of a DNA-binding domain (bait) and DNA target site (prey).
ECO:MCC
A type of transcript evidence based on high-throughput (HT) sequencing of fragmented cDNA molecules.
mchibucos
2011-01-11T12:54:50Z
WTSS
whole transcriptome shotgun sequencing
eco
RNA sequencing
ECO:0000295
Total RNA is isolated from cells and mRNA is purified by targeting the 3' polyadenylated (poly(A)) tail with poly(T) oligos covalently attached to a substrate. Next, cDNA fragments are generated either by hydrolysis of RNA into 200-300 base oligonucleotides, preceded by reverse transcription, or by reverse transcription initiated by random primers. The cDNA second strand is synthesized, fragments are adapter ligated and high-throughput sequencing is performed by Roche 454, Illumina, ABI-SOLiD, or another HT sequencing technology. Resulting sort reads are aligned against a reference genome, and downstream analysis is performed.
RNA-seq evidence
A type of transcript evidence based on high-throughput (HT) sequencing of fragmented cDNA molecules.
ECO:MCC
whole transcriptome shotgun sequencing
PMID:18611170
A type of transcriptional activation assay evidence that is based on transcriptional activation of a green fluorescent protein (GFP) reporter gene.
mchibucos
2011-01-11T02:31:19Z
localization of GFP transcript
eco
ECO:0000296
This term describes transcriptional activation; to describe immunolocalization of the protein, use the term "immunolocalization of green fluorescent protein".
green fluorescent protein transcript localization evidence
A type of transcriptional activation assay evidence that is based on transcriptional activation of a green fluorescent protein (GFP) reporter gene.
ECO:MCC
ECO:RCT
A type of transcriptional activation assay evidence that is based on transcriptional activation of a LacZ reporter gene.
mchibucos
2011-01-11T02:53:19Z
eco
ECO:0000297
This term describes transcriptional activation; to describe immunolocalization of the protein, use the term "immunolocalization of LacZ protein".
LacZ transcript localization evidence
A type of transcriptional activation assay evidence that is based on transcriptional activation of a LacZ reporter gene.
ECO:MCC
A type of experimental phenotypic evidence where embryonic development proceeds although cytokinesis is blocked.
mchibucos
2011-01-11T03:28:49Z
eco
ECO:0000298
In the embryos of some organisms, inhibition of cytokinesis blocks neither the cell cycle nor the unfolding of the developmental program. As such, embryonic morphology can be frozen, allowing analysis of the developmental fate of each cell present at the time of cleavage arrest.
cleavage arrested development evidence
A type of experimental phenotypic evidence where embryonic development proceeds although cytokinesis is blocked.
ECO:MCC
A type of cleavage arrested development that arises after treatment with cytochalasin.
mchibucos
2011-01-11T03:30:29Z
eco
ECO:0000299
Cytochalasin inhibits cytokinesis by blocking the formation of contractile microfilaments.
cytochalasin experiment evidence
A type of cleavage arrested development that arises after treatment with cytochalasin.
ECO:MCC
A type of immunolocalization evidence data that was generated using green fluorescent protein (GFP) as a marker.
mchibucos
2011-01-11T03:48:50Z
GFP immunolocalization evidence
eco
ECO:0000300
This term describes immunolocalization of the protein; to describe transcriptional activation, use the term "localization of green fluorescent protein transcript".
green fluorescent protein immunolocalization evidence
A type of immunolocalization evidence data that was generated using green fluorescent protein (GFP) as a marker.
ECO:MCC
A type of immunolocalization evidence that was generated using LacZ protein as a marker.
mchibucos
2011-01-11T04:06:40Z
LacZ protein immunolocalization evidence
eco
ECO:0000301
This term describes immunolocalization of the protein; to describe transcriptional activation, use the term "localization of LacZ transcript".
beta-galactosidase protein immunolocalization evidence
A type of immunolocalization evidence that was generated using LacZ protein as a marker.
ECO:MCC
A type of author statement that is used in a manual assertion.
mchibucos
2011-01-20T02:26:47Z
eco
ECO:0000302
author statement used in manual assertion
true
true
A type of author statement that is used in a manual assertion.
ECO:MCC
A type of non-traceable author statement that is used in a manual assertion.
mchibucos
2011-01-20T02:29:50Z
GOECO:NAS
NAS
non-traceable author statement
eco
ECO:0000303
non-traceable author statement used in manual assertion
http://geneontology.org/page/nas-non-traceable-author-statement
true
true
A type of non-traceable author statement that is used in a manual assertion.
ECO:MCC
GOECO:NAS
non-traceable author statement
NAS
GOECO:NAS
non-traceable author statement
GOECO:NAS
A type of traceable author statement that is used in a manual assertion.
mchibucos
2011-01-20T02:31:03Z
GOECO:TAS
TAS
traceable author statement
eco
ECO:0000304
traceable author statement used in manual assertion
http://geneontology.org/page/tas-traceable-author-statement
true
true
A type of traceable author statement that is used in a manual assertion.
ECO:MCC
GOECO:TAS
traceable author statement
TAS
GOECO:TAS
traceable author statement
GOECO:TAS
A type of curator inference that is used in a manual assertion.
mchibucos
2011-01-20T02:33:32Z
GOECO:IC
IC
inferred by curator
eco
ECO:0000305
curator inference used in manual assertion
http://geneontology.org/page/ic-inferred-curator
true
true
A type of curator inference that is used in a manual assertion.
ECO:MCC
GOECO:IC
inferred by curator
IC
GOECO:IC
inferred by curator
GOECO:IC
A type of inference from background scientific knowledge that is used in a manual assertion.
mchibucos
2011-01-20T02:35:11Z
eco
ECO:0000306
inference from background scientific knowledge used in manual assertion
true
true
A type of inference from background scientific knowledge that is used in a manual assertion.
ECO:MCC
A type of no biological data found that is used in a manual assertion.
mchibucos
2011-01-20T02:43:18Z
GOECO:ND
ND
no biological data available
eco
ECO:0000307
no biological data found used in manual assertion
http://geneontology.org/page/nd-no-biological-data-available
true
true
A type of no biological data found that is used in a manual assertion.
ECO:MCC
GOECO:ND
no biological data available
ND
GOECO:ND
no biological data available
GOECO:ND
A type of phylogenetic evidence whereby an aspect of a descendant gene is inferred through the characterization of an aspect of an ancestral gene.
mchibucos
2011-02-04T05:41:26Z
eco
ECO:0000308
First, a characteristic of the most recent common ancestor (MRCA) is inferred from experimental evidence in descendants; this is followed by inferring a characteristic of a descendant of the MRCA. This type of evidence can be used in support of both positive and "not" GO annotations.
biological aspect of ancestor evidence
A type of phylogenetic evidence whereby an aspect of a descendant gene is inferred through the characterization of an aspect of an ancestral gene.
ECO:MCC
A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by a cap-trapper system.
mchibucos
2011-02-17T01:33:09Z
CAGE
eco
ECO:0000309
Complementary DNA (cDNA) is synthesized from microgram quantities of mRNA using first-strand cDNA primer (oligo dT12-18) and reverse transcriptase in the presence of trehalose and sorbitol, followed by selection of full-length cDNA with biotinylated cap-trapper. Linkers are attached to the 5' ends of full-length enriched cDNAs to introduce a recognition site for the restriction endonuclease MmeI, which creates a two base overhang. After amplification, sequencing tags are concatenated for high-throughput sequencing. Resulting sort reads are aligned against a reference genome, and downstream analysis is performed.
cap analysis of gene expression evidence
A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by a cap-trapper system.
ECO:MCC
CAGE
PMID:16489339
A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by reverse transcriptase template switching.
mchibucos
2011-02-17T01:33:34Z
eco
nanoCAGE
ECO:0000310
NanoCAGE captures the 5' ends of molecules by template switching. When polymerizing the cDNA of a capped mRNA, the reverse transcriptase adds extra cytosines that are complementary to the cap. Each 5' full length cDNAs is extended upon hybridization of the riboguanosine-tailed template switching oligonucleotides to these extra cytosines. In semisuppressive PCR, the short templates fold intramolecularly and prevent the binding of primers, which precludes amplification; longer molecules are less likely to fold and are thus amplified. Templates derived from reaction artifacts form stable homoduplexes, also precluding amplification. After template switching, semisuppressive PCR, and EcoP151 cleavage, 25-bp tags are ligated to bar code-containing oligonucleotide adaptors. After PCR amplification, the nanoCAGE tags are sequenced by synthesis. NanoCAGE requires as little as 10 nanograms of total RNA.
nano-cap analysis of gene expression evidence
A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by reverse transcriptase template switching.
ECO:MCC
nanoCAGE
PMID:20543846
A type of evidence that is based on work performed by a person or group prior to a use by a different person or group.
mchibucos
2011-03-02T05:24:13Z
eco
ECO:0000311
imported information
A type of evidence that is based on work performed by a person or group prior to a use by a different person or group.
ECO:MCC
A type of imported information that is used in a manual assertion.
mchibucos
2011-03-02T05:29:44Z
eco
ECO:0000312
imported information used in manual assertion
true
true
A type of imported information that is used in a manual assertion.
ECO:MCC
A type of imported information that is used in an automatic assertion.
mchibucos
2011-03-02T05:33:43Z
eco
ECO:0000313
imported information used in automatic assertion
true
true
A type of imported information that is used in an automatic assertion.
ECO:MCC
A type of direct assay evidence that is used in a manual assertion.
mchibucos
2011-10-28T04:59:31Z
GOECO:IDA
inferred from direct assay
eco
IDA
ECO:0000314
direct assay evidence used in manual assertion
http://geneontology.org/page/ida-inferred-direct-assay
true
true
A type of direct assay evidence that is used in a manual assertion.
ECO:MCC
GOECO:IDA
inferred from direct assay
inferred from direct assay
GOECO:IDA
IDA
GOECO:IDA
A type of mutant phenotype evidence that is used in a manual assertion.
mchibucos
2011-10-28T05:12:49Z
GOECO:IMP
eco
IMP
inferred from mutant phenotype
ECO:0000315
mutant phenotype evidence used in manual assertion
http://geneontology.org/page/imp-inferred-mutant-phenotype
true
true
A type of mutant phenotype evidence that is used in a manual assertion.
ECO:MCC
GOECO:IMP
inferred from mutant phenotype
IMP
GOECO:IMP
inferred from mutant phenotype
GOECO:IMP
A type of genetic interaction experiment evidence that is used in a manual assertion.
mchibucos
2011-10-28T05:14:42Z
GOECO:IGI
IGI
inferred from genetic interaction
eco
ECO:0000316
genetic interaction evidence used in manual assertion
http://geneontology.org/page/igi-inferred-genetic-interaction
true
true
A type of genetic interaction experiment evidence that is used in a manual assertion.
ECO:MCC
GOECO:IGI
inferred from genetic interaction
IGI
GOECO:IGI
inferred from genetic interaction
GOECO:IGI
A type of genomic context evidence that is used in a manual assertion.
mchibucos
2011-10-28T05:22:53Z
GOECO:IGC
IGC
inferred from genomic context
eco
ECO:0000317
genomic context evidence used in manual assertion
http://geneontology.org/page/igc-inferred-genomic-context
true
true
A type of genomic context evidence that is used in a manual assertion.
ECO:MCC
GOECO:IGC
inferred from genomic context
IGC
GOECO:IGC
inferred from genomic context
GOECO:IGC
A type of biological aspect of ancestor evidence that is used in a manual assertion.
mchibucos
2011-10-28T05:23:51Z
GOECO:IBA
IBA
inferred from biological aspect of ancestor
eco
ECO:0000318
biological aspect of ancestor evidence used in manual assertion
http://geneontology.org/page/iba-inferred-biological-aspect-ancestor
true
true
A type of biological aspect of ancestor evidence that is used in a manual assertion.
ECO:MCC
GOECO:IBA
inferred from biological aspect of ancestor
IBA
GOECO:IBA
inferred from biological aspect of ancestor
GOECO:IBA
A type of biological aspect of descendant evidence that is used in a manual assertion.
mchibucos
2011-10-28T05:25:09Z
GOECO:IBD
IBD
inferred from biological aspect of descendant
eco
ECO:0000319
biological aspect of descendant evidence used in manual assertion
http://geneontology.org/page/ibd-inferred-biological-aspect-descendent
true
true
A type of biological aspect of descendant evidence that is used in a manual assertion.
ECO:MCC
GOECO:IBD
inferred from biological aspect of descendant
IBD
GOECO:IBD
inferred from biological aspect of descendant
GOECO:IBD
A type of phylogenetic determination of loss of key residues evidence that is used in a manual assertion.
mchibucos
2011-10-28T05:25:48Z
GOECO:IKR
GOECO:IMR
IKR
IMR
inferred from key residues
inferred from missing residues
eco
ECO:0000320
phylogenetic determination of loss of key residues evidence used in manual assertion
http://geneontology.org/page/ikr-inferred-key-residues
true
true
A type of phylogenetic determination of loss of key residues evidence that is used in a manual assertion.
ECO:MCC
GOECO:IKR
inferred from key residues
GOECO:IMR
inferred from missing residues
IKR
GOECO:IKR
IMR
GOECO:IKR
inferred from key residues
GOECO:IKR
inferred from missing residues
GOECO:IKR
A type of rapid divergence from ancestral sequence evidence that is used in a manual assertion.
mchibucos
2011-10-28T05:26:42Z
GOECO:IRD
IRD
inferred from rapid divergence
eco
ECO:0000321
rapid divergence from ancestral sequence evidence used in manual assertion
http://geneontology.org/page/ird-inferred-rapid-divergence
true
true
A type of rapid divergence from ancestral sequence evidence that is used in a manual assertion.
ECO:MCC
GOECO:IRD
inferred from rapid divergence
IRD
GOECO:IRD
inferred from rapid divergence
GOECO:IRD
Evidence that was initially used in manual assertion by one person or group, which is imported by a second person or group and used in automatic assertion.
mchibucos
2011-12-13T12:04:48Z
GO_REF:0000037
GO_REF:0000039
GO_REF:0000041
eco
ECO:0000322
imported manually asserted information used in automatic assertion
Evidence that was initially used in manual assertion by one person or group, which is imported by a second person or group and used in automatic assertion.
ECO:MCC
GO_REF:0000037
Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.
GO_REF:0000039
Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries.
GO_REF:0000041
IEA (UniProt UniPathway)
A type of imported information used in automatic assertion that was initially used in automatic assertion by one person or group, which is imported by a second person or group and used in automatic assertion.
mchibucos
2011-12-13T02:06:25Z
GO_REF:0000038
GO_REF:0000040
eco
ECO:0000323
imported automatically asserted information used in automatic assertion
A type of imported information used in automatic assertion that was initially used in automatic assertion by one person or group, which is imported by a second person or group and used in automatic assertion.
ECO:MCC
GO_REF:0000038
Gene Ontology annotation based on automatic assignment of UniProtKB keywords in UniProtKB/TrEMBL entries.
GO_REF:0000040
Gene Ontology annotation based on the automatic assignment of UniProtKB Subcellular Location terms in UniProtKB/TrEMBL entries.
A type of direct assay evidence in which an image is created and analyzed.
mchibucos
2012-02-23T12:01:43Z
ECO:0001122
ECO:0005024
ECO:MCC
radiologic test evidence
eco
ECO:0000324
imaging assay evidence
A type of experimental evidence that is based on separation of constituent parts of a mixture (the mobile phase) as they pass differentially through a stationary phase due to differences in partition coefficient and retention on the stationary phase.
mchibucos
2012-05-16T11:46:27Z
chromatographic evidence
eco
ECO:0000325
chromatography evidence
A type of experimental evidence that is based on separation of constituent parts of a mixture (the mobile phase) as they pass differentially through a stationary phase due to differences in partition coefficient and retention on the stationary phase.
ECO:MCC
A type of sequence alignment evidence that is based on comparing the position of exon junctions, relative to a reference genome, for a transcript annotation and a supporting transcript.
mchibucos
2012-06-08T11:03:59Z
eco
ECO:0000326
transcript splice pattern evidence
A type of sequence alignment evidence that is based on comparing the position of exon junctions, relative to a reference genome, for a transcript annotation and a supporting transcript.
ECO:MCC
A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features.
mchibucos
2012-06-08T11:11:24Z
eco
ECO:0000327
This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that have the same splice pattern as a RefSeq transcript. If such full transcript information is not available, RefSeq reports sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, supported by the evidence term ECO:0000328 or a child.
whole transcript splice pattern evidence
A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features.
ECO:MCC
A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript.
mchibucos
2012-06-08T11:21:57Z
eco
ECO:0000328
This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, but for which full transcript information is unavailable. For sequences that have the same splice pattern as a whole RefSeq transcript, use the evidence term ECO:0000327 or a child.
coding sequence splice pattern evidence
A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript.
ECO:MCC
A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features, and is used in manual assertion.
mchibucos
2012-06-08T11:40:03Z
eco
ECO:0000329
This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that have the same splice pattern as a RefSeq transcript. If such full transcript information is not available, RefSeq reports sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, supported by the evidence term ECO:0000328 or a child.
whole transcript splice pattern evidence used in manual assertion
true
true
A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features, and is used in manual assertion.
ECO:MCC
A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript, and is used in manual assertion.
mchibucos
2012-06-08T11:43:47Z
eco
ECO:0000330
This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, but for which full transcript information is unavailable. For sequences that have the same splice pattern as a whole RefSeq transcript, use the evidence term ECO:0000327 or a child.
coding sequence splice pattern evidence used in manual assertion
true
true
A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript, and is used in manual assertion.
ECO:MCC
A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript, and is used in automatic assertion.
mchibucos
2012-06-08T11:48:09Z
eco
ECO:0000331
This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, but for which full transcript information is unavailable. For sequences that have the same splice pattern as a whole RefSeq transcript, use the evidence term ECO:0000327 or a child.
coding sequence splice pattern evidence used in automatic assertion
true
true
A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript, and is used in automatic assertion.
ECO:MCC
A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features, and is used in automatic assertion.
mchibucos
2012-06-08T11:49:17Z
eco
ECO:0000332
This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that have the same splice pattern as a RefSeq transcript. If such full transcript information is not available, RefSeq reports sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, supported by the evidence term ECO:0000328 or a child.
whole transcript splice pattern evidence used in automatic assertion
true
true
A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features, and is used in automatic assertion.
ECO:MCC
A type of gel electrophoresis evidence where proteins are separated according to their electrophoretic mobility.
mchibucos
2012-07-31T02:56:43Z
SDS-PAGE evidence
eco
ECO:0000333
Electrophoretic mobility is a function of both the length and charge of a protein. The protein sample is linearized with sodium dodecyl sulfate (SDS), an anionic detergent. Typically, polypeptides bound with SDS possess an even distribution of charge per unit mass, and subsequent fractionation is by size.
sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence
A type of gel electrophoresis evidence where proteins are separated according to their electrophoretic mobility.
ECO:MCC
PubMed:4861258
url:http://www.nature.com/nmeth/journal/v2/n1/full/nmeth0105-83.html
url:http://www.ncbi.nlm.nih.gov/Class/NAWBIS/Modules/Protein/protein18.html
A type of direct assay evidence resulting from an assay where both the size of and number of particles in a sample are determined.
mchibucos
2012-07-31T03:19:32Z
eco
ECO:0000334
An example of an instrument used to analyze particle sizes and counts is the Beckman Coulter® Z Series system.
particle size and count assay evidence
A type of direct assay evidence resulting from an assay where both the size of and number of particles in a sample are determined.
ECO:MCC
A type of direct assay evidence where the quantity of a substance used as part of an assay is measured.
mchibucos
2012-07-31T03:52:46Z
eco
ECO:0000335
Two examples of substance quantification assay are (i) measuring how much of a radiolabelled compound is taken up by a cell and (ii) measuring how much of a substrate is turned over by a given enzyme.
substance quantification evidence
A type of direct assay evidence where the quantity of a substance used as part of an assay is measured.
ECO:MCC
A type of biological assay evidence in which a mutated strain of a microorganism, such as a yeast or bacterium, is grown competitively with wild-type cells and the relative fitness of the strains is assessed.
mchibucos
2012-08-24T12:03:58Z
fitness profiling
eco
ECO:0000336
competitive growth assay evidence
A type of biological assay evidence in which a mutated strain of a microorganism, such as a yeast or bacterium, is grown competitively with wild-type cells and the relative fitness of the strains is assessed.
GOC:MAH
PMID:14718172
PMID:20537132
fitness profiling
GOC:MAH
PMID:20537132
A type of direct assay evidence where molecules have been sorted according to their size and charge by moving through a gel in the presence of an electric field.
mchibucos
2012-08-24T12:11:51Z
ECO:0005026
eco
ECO:0000337
Molecules typically separated include DNA, RNA, or protein. The gel is typically made of agarose, polyacrylamide, or starch.
gel electrophoresis evidence
A type of direct assay evidence where molecules have been sorted according to their size and charge by moving through a gel in the presence of an electric field.
ECO:MCC
wikipedia:Gel_electrophoresis
A type of gel electrophoresis evidence in which large DNA molecules are separated on agarose gel by alternately pulsed, perpendicularly oriented electrical fields, at least one of which is inhomogeneous.
mchibucos
2012-08-24T12:34:01Z
PFGE
eco
ECO:0000338
pulsed-field gel electrophoresis evidence
A type of gel electrophoresis evidence in which large DNA molecules are separated on agarose gel by alternately pulsed, perpendicularly oriented electrical fields, at least one of which is inhomogeneous.
PMID:6373014
A type of gel electrophoresis evidence where DNA molecules are electrophoresed on a low percentage agarose gel followed by high voltage electrophoresis on a higher percentage agarose gel in the presence of ethidium bromide.
mchibucos
2012-08-24T12:42:37Z
2-D agarose gel electrophoresis
eco
ECO:0000339
The first dimension gel is intentionally run at low voltage in low percentage agarose to separate DNA molecules in proportion to their mass. The second dimension is run at high voltage in a gel of higher agarose concentration in the presence of ethidium bromide so that the mobility of a non-linear molecule is drastically influenced by its shape.
two-dimensional agarose gel electrophoresis evidence
A type of gel electrophoresis evidence where DNA molecules are electrophoresed on a low percentage agarose gel followed by high voltage electrophoresis on a higher percentage agarose gel in the presence of ethidium bromide.
PMID:16118435
PMID:8594382
A type of experimental evidence in which retention of an introduced plasmid is determined when a mitotically stable plasmid (or minichromosome) is introduced into cells, which are grown without selection for several generations.
mchibucos
2012-08-24T01:27:58Z
minichromosome maintenance assay evidence
eco
ECO:0000340
Loss per generation is determined by comparing colony numbers on selective and non-selective media.
plasmid maintenance assay evidence
A type of experimental evidence in which retention of an introduced plasmid is determined when a mitotically stable plasmid (or minichromosome) is introduced into cells, which are grown without selection for several generations.
ECO:MCC
PMID:6323245
minichromosome maintenance assay evidence
PMID:6323245
A type of specific protein inhibition evidence where the molecular function of a protein is inhibited by an antibody.
mchibucos
2012-08-24T01:48:24Z
eco
ECO:0000341
specific protein inhibition by antibody evidence
A type of specific protein inhibition evidence where the molecular function of a protein is inhibited by an antibody.
ECO:MCC
A type of RNA-seq evidence where intron locations in predicted transcripts are compared to intron locations supported by RNA-seq evidence.
mchibucos
2013-04-03T04:22:05Z
eco
ECO:0000342
RNA-seq alignment intron location evidence is used by NCBI RefSeq (http://www.ncbi.nlm.nih.gov/refseq). Exon-exon boundaries (or intron locations) of a RefSeq transcript, as determined by aligning the transcript to a reference chromosome, are compared to intron locations supported by RNAseq data.
Support of intron position by RNA-seq alignment evidence
A type of RNA-seq evidence where intron locations in predicted transcripts are compared to intron locations supported by RNA-seq evidence.
ECO:MCC
A type of support of intron position by RNA-seq alignment evidence where RNA-seq alignment from a single sample supports all of the intron positions (exon pairs) predicted for a transcript.
mchibucos
2013-04-03T04:41:48Z
eco
ECO:0000343
Full support entails that all exon pairs represented in the transcript are supported. For example, for a transcript containing five exons, if liver RNA-seq reads support all four introns but brain RNA-seq supports only three introns, then the liver data fully support the transcript exons whereas the brain data do not.
Full support of intron position by RNA-seq alignment evidence
A type of support of intron position by RNA-seq alignment evidence where RNA-seq alignment from a single sample supports all of the intron positions (exon pairs) predicted for a transcript.
ECO:MCC
A type of support of intron position by RNA-seq alignment evidence where RNA-seq alignment to a genome supports only some of the intron positions (exon pairs) predicted for a transcript.
mchibucos
2013-04-03T04:50:46Z
eco
ECO:0000344
Partial support can occur in two ways. First, one or more exon-exon pair (intron) is not supported by any RNA-seq sample included in the analysis. Second, no single RNA-seq sample provides support for all exon-exon pairs (introns) represented in a transcript, but all represented exons are supported by at least one sample.
Partial support of intron position by RNA-seq alignment evidence
A type of support of intron position by RNA-seq alignment evidence where RNA-seq alignment to a genome supports only some of the intron positions (exon pairs) predicted for a transcript.
ECO:MCC
mchibucos
2013-04-03T05:10:34Z
eco
ECO:0000345
single exon transcript confirmation via alignment evidence
A type of support of intron position by RNA-seq alignment evidence that is used in a manual assertion.
mchibucos
2013-04-04T04:37:35Z
eco
ECO:0000346
Support of intron position by RNA-seq alignment evidence used in manual assertion
true
true
A type of support of intron position by RNA-seq alignment evidence that is used in a manual assertion.
ECO:MCC
A type of support of intron position by RNA-seq alignment evidence that is used in an automatic assertion.
mchibucos
2013-04-04T04:38:45Z
eco
ECO:0000347
Support of intron position by RNA-seq alignment evidence used in automatic assertion
true
true
A type of support of intron position by RNA-seq alignment evidence that is used in an automatic assertion.
ECO:MCC
A type of full support of intron position by RNA-seq alignment evidence that is used in an automatic assertion.
mchibucos
2013-04-04T04:40:19Z
eco
ECO:0000348
Full support of intron position by RNA-seq alignment evidence used in automatic assertion
true
true
A type of full support of intron position by RNA-seq alignment evidence that is used in an automatic assertion.
ECO:MCC
A type of full support of intron position by RNA-seq alignment evidence that is used in a manual assertion.
mchibucos
2013-04-04T04:41:34Z
eco
ECO:0000349
Full support of intron position by RNA-seq alignment evidence used in manual assertion
true
true
A type of full support of intron position by RNA-seq alignment evidence that is used in a manual assertion.
ECO:MCC
A type of partial support of intron position by RNA-seq alignment evidence that is used in an automatic assertion.
mchibucos
2013-04-04T04:42:53Z
eco
ECO:0000350
Partial support of intron position by RNA-seq alignment evidence used in automatic assertion
true
true
A type of partial support of intron position by RNA-seq alignment evidence that is used in an automatic assertion.
ECO:MCC
A type of partial support of intron position by RNA-seq alignment evidence that is used in a manual assertion.
mchibucos
2013-04-04T04:43:56Z
eco
ECO:0000351
Partial support of intron position by RNA-seq alignment evidence used in manual assertion
true
true
A type of partial support of intron position by RNA-seq alignment evidence that is used in a manual assertion.
ECO:MCC
A type of evidence that is used in an manual assertion.
mchibucos
eco
ECO:0000352
evidence used in manual assertion
true
true
A type of evidence that is used in an manual assertion.
ECO:MCC
A type of physical interaction evidence that is used in a manual assertion.
mchibucos
2013-10-31T21:01:27Z
GOECO:IPI
IPI
inferred from physical interaction
eco
ECO:0000353
physical interaction evidence used in manual assertion
http://geneontology.org/page/ipi-inferred-physical-interaction
true
true
A type of physical interaction evidence that is used in a manual assertion.
ECO:MCC
GOECO:IPI
inferred from physical interaction
IPI
GOECO:IPI
inferred from physical interaction
GOECO:IPI
A type of gene neighbors evidence that is used in a manual assertion.
mchibucos
2013-11-19T13:37:24Z
GO_REF:0000025
eco
ECO:0000354
gene neighbors evidence used in manual assertion
true
true
A type of gene neighbors evidence that is used in a manual assertion.
ECO:MCC
GO_REF:0000025
operon structure as IGC evidence
A type of phylogenetic evidence characterized by the mapping of the character states of living organisms onto phylogenies using the method of maximum parsimony.
mchibucos
2014-04-22T17:02:31Z
eco
ECO:0000355
Example of use: "The presence of paired evaginated hemispheres and olfactory bulbs in both agnathan and gnathostome radiations suggests that such hemispheres were also present in the common ancestor." PMID: 7013637. Northcutt RG. (1981) Evolution of the telencephalon in nonmammals. Ann. Rev. Neurosci.
phylogenetic distribution evidence
A type of phylogenetic evidence characterized by the mapping of the character states of living organisms onto phylogenies using the method of maximum parsimony.
ECO:MCC
PMID:21238344
A type of transcript expression evidence resulting from the assessment of microarray data to detect differential gene expression.
mchibucos
2014-09-26T16:21:45Z
eco
ECO:0000356
differential gene expression evidence from microarray experiment
A type of transcript expression evidence resulting from the assessment of microarray data to detect differential gene expression.
PMC:2762517
A type of transcript expression evidence resulting from the detection and analysis of differential gene expression in an RNA-seq dataset.
mchibucos
2014-09-26T16:22:57Z
eco
ECO:0000357
differential gene expression evidence from RNA-seq experiment
A type of transcript expression evidence resulting from the detection and analysis of differential gene expression in an RNA-seq dataset.
PMID:24020486
A type of transcript expression evidence resulting from a microarray analysis with the use of the Gene Set Enrichment Analysis (GSEA) method or the Fisher's-Exact (FE) method to assess the differential expression.
mchibucos
2014-09-26T16:25:47Z
eco
ECO:0000358
differential geneset expression evidence from microarray experiment (GSEA, Fisher-exact)
A type of transcript expression evidence resulting from a microarray analysis with the use of the Gene Set Enrichment Analysis (GSEA) method or the Fisher's-Exact (FE) method to assess the differential expression.
PMID:19725948
A type of transcript expression evidence resulting from the use of the Gene Set Enrichment Analysis (GSEA) method or Fisher's-Exact (FE) method to assess an RNA-seq dataset for differential gene expression.
mchibucos
2014-09-26T16:26:48Z
eco
ECO:0000359
differential geneset expression evidence from RNA-seq experiment (GSEA, Fisher-exact)
A type of transcript expression evidence resulting from the use of the Gene Set Enrichment Analysis (GSEA) method or Fisher's-Exact (FE) method to assess an RNA-seq dataset for differential gene expression.
PMC:2881125
mchibucos
2014-09-26T16:39:11Z
eco
ECO:0000360
biological target-disease association via drug
A type of evidence where an assertion is derived from another assertion via logical inference or some non-logical but rational means.
mchibucos
2015-07-14T11:19:37Z
eco
ECO:0000361
Inference is the process of deriving logical conclusions from premises known or assumed to be true, or alternatively, arriving at conclusions via some non-logical means of observation of patterns of facts, which can result in identifying new meanings and contexts for understanding. Given the evidence provided by a set of premises, deductive reasoning involves drawing conclusions that necessarily follow, i.e. are certain, whereas inductive reasoning generates conclusions that are likely to be, but are not necessarily, true.
inferential evidence
A type of evidence where an assertion is derived from another assertion via logical inference or some non-logical but rational means.
ECO:MCC
A type of inferential evidence based on a computationally derived unary inference or an inference chain in which at least one step is
computationally derived.
mchibucos
2015-07-14T11:24:27Z
eco
ECO:0000362
evidence based on computational logical inference
A type of inferential evidence based on a computationally derived unary inference or an inference chain in which at least one step is
computationally derived.
ECO:MCC
GOC:MC
A type of evidence based on computational logical inference that is used in automatic assertion.
mchibucos
2015-07-14T11:35:08Z
GO_REF:0000108
eco
ECO:0000363
evidence based on computational logical inference used in automatic assertion
true
true
A type of evidence based on computational logical inference that is used in automatic assertion.
ECO:MCC
GO_REF:0000108
Automatic assignment of GO terms using logical inference, based on on inter-ontology links
A type of evidence based on logical inference from a manually curated annotation that is used in an automatic assertion.
mchibucos
2015-07-14T11:44:19Z
eco
ECO:0000364
evidence based on logical inference from manual annotation used in automatic assertion
A type of evidence based on logical inference from a manually curated annotation that is used in an automatic assertion.
ECO:MCC
A type of evidence based on logical inference from an automatically curated annotation that is used in an automatic assertion.
mchibucos
2015-07-14T11:45:25Z
eco
ECO:0000366
evidence based on logical inference from automatic annotation used in automatic assertion
A type of evidence based on logical inference from an automatically curated annotation that is used in an automatic assertion.
ECO:MCC
A type of evidence that is used in an automatic assertion.
cjm
GOECO:IEA
GO_REF:0000003
GO_REF:0000004
GO_REF:0000023
IEA
inferred from electronic annotation
eco
ECO:0000501
evidence used in automatic assertion
http://geneontology.org/page/automatically-assigned-evidence-codes
true
true
A type of evidence that is used in an automatic assertion.
ECO:cjm
GOECO:IEA
inferred from electronic annotation
GO_REF:0000003
Gene Ontology annotation based on Enzyme Commission mapping.
GO_REF:0000004
Gene Ontology annotation based on Swiss-Prot keyword mapping.
GO_REF:0000023
Gene Ontology annotation based on Swiss-Prot Subcellular Location vocabulary mapping.
IEA
GOECO:IEA
inferred from electronic annotation
GOECO:IEA
A type of in vitro cell based assay evidence resulting from the growth of cells in a micro-environment that mimics real tissue and establishes physiological cell-cell and cell-substrate interactions that regulate proliferation and differentiation.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001001
3D cell culture evidence
A type of in vitro cell based assay evidence resulting from the growth of cells in a micro-environment that mimics real tissue and establishes physiological cell-cell and cell-substrate interactions that regulate proliferation and differentiation.
PMID:21042962
url:http://volttecnologia.com.br/wp-content/uploads/2016/03/Drug-discovery.pdf
A type of in vitro cell based assay evidence resulting from labeling cells with [3H]arachidonic acid and subsequently determining the release of the arachidonic acid by the cells.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001002
[3H]arachidonic acid release assay evidence
A type of in vitro cell based assay evidence resulting from labeling cells with [3H]arachidonic acid and subsequently determining the release of the arachidonic acid by the cells.
ISBN:0323152295
PMID:20693009
A type of DNA synthesis cell proliferation assay evidence resulting from the measurement of cell proliferation rate by determining the incorporation of [3H]-thymidine into cellular nucleic acids.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001003
[3H]-thymidine incorporation assay evidence
A type of DNA synthesis cell proliferation assay evidence resulting from the measurement of cell proliferation rate by determining the incorporation of [3H]-thymidine into cellular nucleic acids.
OBI:0000669
url:http://www.scientistsolutions.com/forum/cell-culture-and-tissue-culture-proliferationapoptosis/3h-thymidine-incorporation-assay-rat-1a
A type of cytotoxicity assay evidence resulting from the measurement of the amount of radioactive 51Cr released in the supernatant of a sample of 51Cr pre-labeled cells via cytolysis by effector cells (cytotoxic T-cells).
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001004
51Cr release assay evidence
A type of cytotoxicity assay evidence resulting from the measurement of the amount of radioactive 51Cr released in the supernatant of a sample of 51Cr pre-labeled cells via cytolysis by effector cells (cytotoxic T-cells).
PMC:3929704
url:http://www4.mpbio.com/ecom/docs/proddata.nsf/5f64ffd4f38c2fda8525645d00769d68/53d2a75653615bab852568cb00572ff3?OpenDocument
A type of apoptotic assay evidence resulting from the use of 7-aminoactinomycin D (7-AAD) to distinguish viable, apoptotic, and dead cells, using the fact that permeability of the cell membrane, and fluorescence intensity, is low in early apoptotic cells and high in late apoptotic and dead cells.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
7-AAD staining evidence
7-amino-actinomycin D staining evidence
eco
ECO:0001005
7-aminoactinomycin staining evidence
A type of apoptotic assay evidence resulting from the use of 7-aminoactinomycin D (7-AAD) to distinguish viable, apoptotic, and dead cells, using the fact that permeability of the cell membrane, and fluorescence intensity, is low in early apoptotic cells and high in late apoptotic and dead cells.
ECO:RCT
A type of in vitro cell based assay evidence resulting from the analysis of cell binding either to extracellular matrix proteins or other cells.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001006
adhesion assay evidence
A type of in vitro cell based assay evidence resulting from the analysis of cell binding either to extracellular matrix proteins or other cells.
PMID:15576904
PMID:21909903
A type of ex vivo assay evidence derived by ex vivo selection of tumor-reactive lymphocytes, and their activation and numerical expansion before re-infusion to the autologous tumor-bearing host.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
Adoptive immunotherapy
passive immunization
eco
ECO:0001007
adoptive cell transfer evidence
A type of ex vivo assay evidence derived by ex vivo selection of tumor-reactive lymphocytes, and their activation and numerical expansion before re-infusion to the autologous tumor-bearing host.
ECO:SN
url:http://jco.ascopubs.org/content/23/10/2346.full.pdf+html
url:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2305722/pdf/nihms42807.pdf
A type of cell viability assay evidence resulting from the continuous measurement of fluorescence intensity from the viable cells, where cell permeable compound, resazurin in Alamar blue is reduced to fluorescent resorufin.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001008
Alamar blue assay evidence
A type of cell viability assay evidence resulting from the continuous measurement of fluorescence intensity from the viable cells, where cell permeable compound, resazurin in Alamar blue is reduced to fluorescent resorufin.
PMC:3478843
url:https://www.thermofisher.com/us/en/home/references/protocols/cell-and-tissue-analysis/cell-profilteration-assay-protocols/cell-viability-with-alamarblue.html
A type of anatomical perturbation evidence where an organ or tissue is transplanted from one individual to another of the same species with a different genotype.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
Allotransplantation
allografting
tissue grafting
eco
ECO:0001009
allograft transplantation experiment evidence
A type of anatomical perturbation evidence where an organ or tissue is transplanted from one individual to another of the same species with a different genotype.
ECO:SN
url:http://www.nature.com/subjects/allograft
url:http://www.organdonor.gov/about/terms_and_topics/
A type of chromatography evidence where a positively charged ion exchange resin with an affinity for molecules having net negative surface charges is used to separate the molecules.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001010
anion-exchange chromatography evidence
A type of chromatography evidence where a positively charged ion exchange resin with an affinity for molecules having net negative surface charges is used to separate the molecules.
ECO:SN
PMID:20978968
url:http://www.bio-rad.com/en-us/applications-technologies/anion-exchange-chromatography
url:http://www.uta.edu/faculty/sawasthi/Enzymology-4351-5324/Class%20Syllabus%20Enzymology/Ion%20Exchange%20Chromatography-1.pdf
A type of apoptotic assay evidence resulting from the addition and subsequent binding of Annexin V to phosphatidylserine in cells to detect if they are viable, apoptotic, or necrotic.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001011
annexin-V staining evidence
A type of apoptotic assay evidence resulting from the addition and subsequent binding of Annexin V to phosphatidylserine in cells to detect if they are viable, apoptotic, or necrotic.
PMC:3169266
A type of experimental phenotypic evidence resulting from behavioral phenotyping and analysis to assess cognitive functioning.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001012
behavioral assay evidence
A type of experimental phenotypic evidence resulting from behavioral phenotyping and analysis to assess cognitive functioning.
PMID:24462904
A type of immunological assay evidence resulting from inhibitory effect of monoclonal antibody combining with an antigen over other antibodies.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001013
blocking monoclonal antibody evidence
A type of immunological assay evidence resulting from inhibitory effect of monoclonal antibody combining with an antigen over other antibodies.
PMID:11292349
url:http://www.sciencedirect.com/science/article/pii/S0140673600034966
A type of immunological assay evidence resulting from the use of peptides to block antibodies from binding to their targets.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001014
blocking peptide evidence
A type of immunological assay evidence resulting from the use of peptides to block antibodies from binding to their targets.
ECO:RCT
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001015
blocking polyclonal antibody evidence
A type of direct assay evidence where a blood sample is extracted from an organism to analyze different blood components.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001016
blood test evidence
A type of direct assay evidence where a blood sample is extracted from an organism to analyze different blood components.
ECO:SN
url:https://www.nhlbi.nih.gov/health/health-topics/topics/bdt
A type of chemotaxis assay evidence resulting from the analysis of the number of cells that migrate from the upper compartment of a chamber (separated by a micro-porous membrane) to the lower compartment, in which chemotactic agents are present.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001017
Boyden chamber assay evidence
A type of chemotaxis assay evidence resulting from the analysis of the number of cells that migrate from the upper compartment of a chamber (separated by a micro-porous membrane) to the lower compartment, in which chemotactic agents are present.
PMID:13872176
PMID:15576901
A type of nucleotide analog incorporation evidence resulting from the incorporation of bromodeoxyuridine (BrdU) as a thymidine analog into nuclear DNA, resulting in a label that can be tracked using antibody probes.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
5-bromo-2'-deoxyuridine incorporation assay evidence
BUdR incorporation assay evidence
BrdU incorporation assay evidence
BrdUrd incorporation assay evidence
eco
ECO:0001018
bromodeoxyuridine incorporation assay evidence
A type of nucleotide analog incorporation evidence resulting from the incorporation of bromodeoxyuridine (BrdU) as a thymidine analog into nuclear DNA, resulting in a label that can be tracked using antibody probes.
PMID:23690005
A type of apoptotic assay evidence resulting from the detection of caspase activation, which results in the cleaving of intracellular substrates during apoptosis.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001019
caspase assay evidence
A type of apoptotic assay evidence resulting from the detection of caspase activation, which results in the cleaving of intracellular substrates during apoptosis.
PMID:18314058
PMID:25086023
A type of in vitro cell based assay evidence resulting from the quantification of a sample of cells.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001020
cell counting evidence
A type of in vitro cell based assay evidence resulting from the quantification of a sample of cells.
ECO:RCT
A type of in vitro cell based assay evidence resulting from the quantification of cell permeability.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001021
cell permeability assay evidence
A type of in vitro cell based assay evidence resulting from the quantification of cell permeability.
PMID:16962665
A type of staining evidence resulting from monitoring division by the use of carboxyfluorescein diacetate succinimidyl ester (CFSE) to label intracellular molecules with carboxyfluorescein; when a labeled cell divides, the number of carboxyfluorescein-tagged molecules is split.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
CFDA-SE staining evidence
CFSE-staining evidence
eco
ECO:0001022
carboxyfluorescein diacetate succinimidyl ester staining evidence
A type of staining evidence resulting from monitoring division by the use of carboxyfluorescein diacetate succinimidyl ester (CFSE) to label intracellular molecules with carboxyfluorescein; when a labeled cell divides, the number of carboxyfluorescein-tagged molecules is split.
PMC:3185625
A type of protein detection assay evidence resulting from a complex (a chemiluminescent compound, protein and a steroidal hapten) utilized as a labeled antigen, which emits light when treated with hydrogen peroxide and copper acetate at a high pH.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
CLIA evidence
eco
ECO:0001023
chemiluminescence-linked immunoassay evidence
A type of protein detection assay evidence resulting from a complex (a chemiluminescent compound, protein and a steroidal hapten) utilized as a labeled antigen, which emits light when treated with hydrogen peroxide and copper acetate at a high pH.
PMID:659901
A type of mutant phenotype evidence resulting from the fusion of two or more different genes to create one protein product.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001024
chimeric protein evidence
A type of mutant phenotype evidence resulting from the fusion of two or more different genes to create one protein product.
PMID:22588898
PMID:25832756
A type of gel electrophoresis evidence resulting from the electrophoresis of two substances together, allowing for the characterization of ligand/nucleic acid binding interactions.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001025
co-electrophoresis evidence
A type of gel electrophoresis evidence resulting from the electrophoresis of two substances together, allowing for the characterization of ligand/nucleic acid binding interactions.
PMID:7668395
A type of imaging assay evidence resulting from the limited observation of the co-occurrence of molecules in a subcellular location.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001026
co-localization evidence
A type of imaging assay evidence resulting from the limited observation of the co-occurrence of molecules in a subcellular location.
PMC:3074624
A type of direct assay evidence resulting from the counting of microbial colonies that arise from viable cells grown on a plate or dish.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001027
colony counting evidence
A type of direct assay evidence resulting from the counting of microbial colonies that arise from viable cells grown on a plate or dish.
PMID:16558698
PMID:23457446
A type of physical interaction evidence resulting from the separation of a mixture of molecules under the influence of a force such as artificial gravity, where molecules sedimenting together are assumed to interact.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001028
co-sedimentation assay evidence
A type of physical interaction evidence resulting from the separation of a mixture of molecules under the influence of a force such as artificial gravity, where molecules sedimenting together are assumed to interact.
MI:0027
A type of gel electrophoresis evidence resulting in the assessment of DNA breakage in a cell, based on size and shape of DNA migration.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001029
comet assay evidence
A type of gel electrophoresis evidence resulting in the assessment of DNA breakage in a cell, based on size and shape of DNA migration.
OBI:0302736
PMID:10737956
A type of knockout evidence resulting from a temporally-restricted and/or tissue-specific targeted gene removal.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001030
conditional knockout evidence
A type of knockout evidence resulting from a temporally-restricted and/or tissue-specific targeted gene removal.
PMC:3572410
A type of knockin evidence resulting from the targeted introduction of a temporally-restricted and/or tissue-specific mutation.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001031
conditional knockin evidence
A type of knockin evidence resulting from the targeted introduction of a temporally-restricted and/or tissue-specific mutation.
PMID:16832820
A type of experimental phenotypic evidence resulting from a constitutively active mutant (CAM), resulting in mutant proteins that remain active in the absence of upstream signals.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001032
constitutively active mutant evidence
A type of experimental phenotypic evidence resulting from a constitutively active mutant (CAM), resulting in mutant proteins that remain active in the absence of upstream signals.
PMID:12217490
A type of protein binding evidence resulting from the identification of two interacting proteins (that exist in close proximity) by linking through covalent bonds followed by identification
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001033
cross-linking evidence
A type of protein binding evidence resulting from the identification of two interacting proteins (that exist in close proximity) by linking through covalent bonds followed by identification
PMID:15530987
PMID:19241040
A type of structure determination evidence resulting from the use of a narrow beam of x-rays to identify molecular structures by creating a diffraction pattern.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001034
crystallography evidence
A type of structure determination evidence resulting from the use of a narrow beam of x-rays to identify molecular structures by creating a diffraction pattern.
MI:0114
A type of expression pattern evidence resulting from localizing chemical components of cells and organelles on histological sections.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001035
cytochemistry evidence
A type of expression pattern evidence resulting from localizing chemical components of cells and organelles on histological sections.
PMID:11597006
A type of apoptotic assay evidence resulting from the identification of an accumulation of Cytochrome c in the cytoplasm after its release from the mitochondria, an early event in apoptosis.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001036
cytochrome C release assay evidence
A type of apoptotic assay evidence resulting from the identification of an accumulation of Cytochrome c in the cytoplasm after its release from the mitochondria, an early event in apoptosis.
PMID:10914021
PMID:12815469
A type of staining evidence resulting from 4',6-diamidino-2-phenylindole (DAPI) binding to AT regions of DNA and emitting a blue fluorescence.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
DAPI staining evidence
eco
ECO:0001037
4',6-diamidino-2-phenylindole staining evidence
A type of staining evidence resulting from 4',6-diamidino-2-phenylindole (DAPI) binding to AT regions of DNA and emitting a blue fluorescence.
PMID:8580206
url:https://www.thermofisher.com/us/en/home/references/protocols/cell-and-tissue-analysis/protocols/dapi-imaging-protocol.html
A type of experimental phenotypic evidence resulting from a mutation in which there is a removal of one or more contiguous nucleotides.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
ECO:0005510
eco
ECO:0001038
deletion mutation evidence
A type of experimental phenotypic evidence resulting from a mutation in which there is a removal of one or more contiguous nucleotides.
SO:0000159
A type of apoptotic assay evidence resulting from the visualization of the DNA ladder (apoptotic DNA fragmentation) in gel electrophoresis.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001039
DNA laddering assay evidence
A type of apoptotic assay evidence resulting from the visualization of the DNA ladder (apoptotic DNA fragmentation) in gel electrophoresis.
PMC:4401164
A type of RNA detection assay evidence based on the direct application of a RNA mixture in a circular motion on a matrix for hybridization with labeled DNA fragments.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
RNA dot blot
ECO:0001040
RNA dot blot assay evidence
A type of RNA detection assay evidence based on the direct application of a RNA mixture in a circular motion on a matrix for hybridization with labeled DNA fragments.
ECO:SW
PMID:21424648
A type of RNA detection assay evidence resulting from sample mRNAs (to be compared) that are reverse transcribed, labeled with fluorescent markers, and hybridized to a microarray for analysis of the intensity of each fluorophore at each array location with a laser scanner.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001041
RNA microarray evidence
A type of RNA detection assay evidence resulting from sample mRNAs (to be compared) that are reverse transcribed, labeled with fluorescent markers, and hybridized to a microarray for analysis of the intensity of each fluorophore at each array location with a laser scanner.
PMID:20967621
A type of experimental phenotypic evidence resulting from the analysis of a mutated gene producing mutant polypeptides that disrupt the activity of the wild-type genes.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001042
dominant-negative mutant evidence
A type of experimental phenotypic evidence resulting from the analysis of a mutated gene producing mutant polypeptides that disrupt the activity of the wild-type genes.
PMC:2217636
PMID:8018332
A type of Edman degradation evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:59:00Z
eco
ECO:0001043
Edman degradation evidence used in manual assertion
true
true
A type of Edman degradation evidence that is used in a manual assertion.
ECO:MCC
A type of protein detection assay evidence resulting from labeling a termonal amino acid residue and cleaving it from a peptide by sequentially removing one residue at a time from the amino end of the peptide, without disrupting the bonds.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001044
Edman degradation evidence
A type of protein detection assay evidence resulting from labeling a termonal amino acid residue and cleaving it from a peptide by sequentially removing one residue at a time from the amino end of the peptide, without disrupting the bonds.
OBI:0000705
doi:10.3891/acta.chem.scand.04-0283
A type of affinity evidence resulting from the quantitative analysis of gene and protein expression monitored by proprietary eTag reporters.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001045
eTag assay evidence
A type of affinity evidence resulting from the quantitative analysis of gene and protein expression monitored by proprietary eTag reporters.
PMID:15137949
A type of physical interaction evidence resulting from a mixture of two molecules passed through a nitrocellulose filter, where one may be immobilized on the filter, and if the immobilized molecule is capable of binding to the other, it will be retained on the filter as well.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001046
filter binding assay evidence
A type of physical interaction evidence resulting from a mixture of two molecules passed through a nitrocellulose filter, where one may be immobilized on the filter, and if the immobilized molecule is capable of binding to the other, it will be retained on the filter as well.
PMID:23028069
A type of expression pattern evidence and in situ hybridization evidence resulting from the use of fluorescent probes to detect complementary sequences of nucleic acids.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001047
fluorescence in situ hybridization evidence
A type of expression pattern evidence and in situ hybridization evidence resulting from the use of fluorescent probes to detect complementary sequences of nucleic acids.
PMC:346675
PMID:6812046
A type of physical interaction evidence resulting from the measurement of the proximity of two fluorophores, where the energy from an excited molecular fluorophore to another fluorophore can only occur within ~10nm.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
FRET
eco
ECO:0001048
fluorescence resonance energy transfer evidence
A type of physical interaction evidence resulting from the measurement of the proximity of two fluorophores, where the energy from an excited molecular fluorophore to another fluorophore can only occur within ~10nm.
PMID:11516318
PMID:15696158
A type of chromatography evidence resulting from the exclusion of proteins based on molecular size by filtration through a porous matrix (swollen gel), from which larger molecules are excluded.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001049
gel-filtration evidence
A type of chromatography evidence resulting from the exclusion of proteins based on molecular size by filtration through a porous matrix (swollen gel), from which larger molecules are excluded.
CHMO:0001011
doi:10.1038/nmeth0506-410
A type of expression pattern evidence resulting from the identification of chemical components in cells and tissues.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001050
histochemistry evidence
A type of expression pattern evidence resulting from the identification of chemical components in cells and tissues.
MMO:0000497
A type of imaging assay evidence resulting from the qualitative microscopic examination of cells or tissues.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001051
histology evidence
A type of imaging assay evidence resulting from the qualitative microscopic examination of cells or tissues.
OBI:0600020
A type of chromatography evidence resulting from the separation of molecules in a solute by forcing the solvent containing the sample through a column packed with nonporous particles at high pressure.
mchibucos
2014-03-16T11:30:54Z
HPLC evidence
eco
ECO:0001052
high-performance liquid chromatography evidence
A type of chromatography evidence resulting from the separation of molecules in a solute by forcing the solvent containing the sample through a column packed with nonporous particles at high pressure.
PMID:16376355
A type of protein detection assay evidence resulting from the use of antibodies linked to coloring agents to localize structures in cell cultures to identify proteins.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001053
immunocytochemistry evidence
A type of protein detection assay evidence resulting from the use of antibodies linked to coloring agents to localize structures in cell cultures to identify proteins.
MI:1200
OBI:0001986
A type of immunological assay evidence resulting from the use of antibodies to remove specific proteins from a sample.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001054
immunodepletion evidence
A type of immunological assay evidence resulting from the use of antibodies to remove specific proteins from a sample.
BAO:0002505
A type of protein detection assay evidence resulting from the use of antibodies to detect proteins in localized cells of tissue sections.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001055
immunohistochemistry evidence
A type of protein detection assay evidence resulting from the use of antibodies to detect proteins in localized cells of tissue sections.
OBI:0001986
A type of genetic transformation evidence resulting from a mutation induced by a mutagenic compounds or irradiation.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001056
induced mutation evidence
A type of genetic transformation evidence resulting from a mutation induced by a mutagenic compounds or irradiation.
OBI:0001154
A type of in vitro assay evidence where acetylated residues are detected in a compound (such as a protein or a nucleic acid) in an in vitro experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001057
in vitro acetylation assay evidence
A type of in vitro assay evidence where acetylated residues are detected in a compound (such as a protein or a nucleic acid) in an in vitro experiment.
ECO:SN
SIB:PG
url:http://www.perkinelmer.com/resources/technicalresources/applicationsupportknowledgebase/radiometric/acetylation.xhtml
A type of in vitro assay evidence that is based on the detection protein fragements from the cleavage of a protein by a protease in vitro.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001058
in vitro cleavage assay evidence
A type of in vitro assay evidence that is based on the detection protein fragements from the cleavage of a protein by a protease in vitro.
PMID:21121091
A type of in vitro assay evidence where the removal of ubiquitin groups on a protein is detected in vitro.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001059
in vitro deubiquitination assay evidence
A type of in vitro assay evidence where the removal of ubiquitin groups on a protein is detected in vitro.
ECO:SN
PMID:19692941
SIB:PG
A type of in vitro assay evidence where the removal of acetyl groups from a compound is detected in an in vitro experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001060
in vitro deacetylation assay evidence
A type of in vitro assay evidence where the removal of acetyl groups from a compound is detected in an in vitro experiment.
ECO:SN
SIB:PG
url:http://www.perkinelmer.com/resources/technicalresources/applicationsupportknowledgebase/radiometric/acetylation.xhtml
A type of in vitro assay evidence where the removal of farnesyl groups from a protein is detected in an in vitro experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001061
in vitro defarnesylation assay evidence
A type of in vitro assay evidence where the removal of farnesyl groups from a protein is detected in an in vitro experiment.
ECO:SN
PMID:16126733
SIB:PG
A type of in vitro assay evidence where the removal of methyl groups from a compound is detected in an in vitro experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001062
in vitro demethylation assay evidence
A type of in vitro assay evidence where the removal of methyl groups from a compound is detected in an in vitro experiment.
ECO:SN
SIB:PG
url:http://en.wikipedia.org/wiki/Demethylation
A type of in vitro assay evidence where the removal of sumo groups is detected on a protein in vitro.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001063
in vitro desumoylation assay evidence
A type of in vitro assay evidence where the removal of sumo groups is detected on a protein in vitro.
ECO:SN
SIB:PG
url:http://www.enzolifesciences.com/BML-UW8955/sumoylation-kit/
A type of in vitro assay evidence where farnesylated residues in proteins are detected in an in vitro experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001064
in vitro farnesylation assay evidence
A type of in vitro assay evidence where farnesylated residues in proteins are detected in an in vitro experiment.
ECO:SN
SIB:PG
url:http://en.wikipedia.org/wiki/Farnesyltransferase
A type of in vitro assay evidence where methylated residues are detected in a compound (such as a protein or a nucleic acid) in an in vitro experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001065
in vitro methylation assay evidence
A type of in vitro assay evidence where methylated residues are detected in a compound (such as a protein or a nucleic acid) in an in vitro experiment.
ECO:SN
SIB:PG
url:http://en.wikipedia.org/wiki/Methylation
A type of in vitro assay evidence where palmitoylated residues in proteins are detected in an in vitro experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001066
in vitro palmitoylation assay evidence
A type of in vitro assay evidence where palmitoylated residues in proteins are detected in an in vitro experiment.
ECO:SN
PMID:17077383
SIB:PG
A type of in vitro assay evidence where the removal of phosphatase groups on a protein is detected in an in vitro experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001067
in vitro phosphatase assay evidence
A type of in vitro assay evidence where the removal of phosphatase groups on a protein is detected in an in vitro experiment.
ECO:SN
SIB:PG
url:http://en.wikipedia.org/wiki/Phosphatase
A type of in vitro assay evidence where phosphorylated residues in a protein are detected in an in vitro experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001068
in vitro protein kinase assay evidence
A type of in vitro assay evidence where phosphorylated residues in a protein are detected in an in vitro experiment.
ECO:SN
SIB:PG
url:http://en.wikipedia.org/wiki/Protein_kinase
url:http://en.wikipedia.org/wiki/Protein_phosphorylation
A type of in vitro assay evidence where ADP-ribosylated residues in proteins are detected in an in vitro experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001069
in vitro polyADP-ribosylation assay evidence
A type of in vitro assay evidence where ADP-ribosylated residues in proteins are detected in an in vitro experiment.
ECO:SN
PMID:21870253
SIB:PG
A type of in vitro assay evidence where sumoylated residues are detected on a protein in an in vitro experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001070
in vitro sumoylation assay evidence
A type of in vitro assay evidence where sumoylated residues are detected on a protein in an in vitro experiment.
ECO:SN
SIB:PG
url:http://www.enzolifesciences.com/BML-UW8955/sumoylation-kit/
A type of in vitro assay evidence where transcription is detected in vitro to validate the activation or repression ablity of a transcription factor in the absence of other proteins present in in vivo conditions.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001071
in vitro transcription assay evidence
A type of in vitro assay evidence where transcription is detected in vitro to validate the activation or repression ablity of a transcription factor in the absence of other proteins present in in vivo conditions.
ECO:SN
ECO:SW
PMID:21125481
SIB:PG
A type of in vitro assay evidence where de novo protein synthesis is detected in an in vitro experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001072
in vitro translation assay evidence
A type of in vitro assay evidence where de novo protein synthesis is detected in an in vitro experiment.
ECO:SN
PMID:18230759
SIB:PG
A type of in vitro assay evidence where ubiquitinated residues are detected on a protein in an in vitro experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001073
in vitro ubiquitination assay evidence
A type of in vitro assay evidence where ubiquitinated residues are detected on a protein in an in vitro experiment.
ECO:SN
PMID:19692941
SIB:PG
A type of in vivo assay evidence where acetylated residues are detected in a compound (such as a protein or a nucleic acid) in cells in vivo.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001074
in vivo acetylation assay evidence
A type of in vivo assay evidence where acetylated residues are detected in a compound (such as a protein or a nucleic acid) in cells in vivo.
ECO:SN
SIB:PG
url:http://www.perkinelmer.com/resources/technicalresources/applicationsupportknowledgebase/radiometric/acetylation.xhtml
A type of in vivo assay evidence that is based on the detection of protein fragments from the cleavage of a protein by a protease in vivo.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001075
in vivo cleavage assay evidence
A type of in vivo assay evidence that is based on the detection of protein fragments from the cleavage of a protein by a protease in vivo.
ECO:SN
PMID:22154596
A type of in vivo assay evidence where the removal of acetyl groups from a compound is detected in cells in vivo.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001076
in vivo deacetylation assay evidence
A type of in vivo assay evidence where the removal of acetyl groups from a compound is detected in cells in vivo.
ECO:SN
SIB:PG
url:http://www.perkinelmer.com/resources/technicalresources/applicationsupportknowledgebase/radiometric/acetylation.xhtml
A type of in vivo assay evidence where removal of farnesyl groups from a protein is detected in cells in vivo.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001077
in vivo defarnesylation assay evidence
A type of in vivo assay evidence where removal of farnesyl groups from a protein is detected in cells in vivo.
ECO:SN
PMID:15556768
PMID:16507103
SIB:PG
A type of in vivo assay evidence where the removal of methyl groups from a compound is detected in cells in vivo.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001078
in vivo demethylation assay evidence
A type of in vivo assay evidence where the removal of methyl groups from a compound is detected in cells in vivo.
ECO:SN
SIB:PG
url:http://en.wikipedia.org/wiki/Demethylation
A type of in vivo assay evidence where the removal of ubiquitin groups on a protein is detected in cells in vivo.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001079
in vivo deubiquitination assay evidence
A type of in vivo assay evidence where the removal of ubiquitin groups on a protein is detected in cells in vivo.
ECO:SN
PMID:19692941
SIB:PG
A type of in vivo assay evidence where the removal of sumo groups on a protein is detected in cells in vivo.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001080
in vivo desumoylation assay evidence
A type of in vivo assay evidence where the removal of sumo groups on a protein is detected in cells in vivo.
ECO:SN
SIB:PG
url:http://www.enzolifesciences.com/BML-UW8955/sumoylation-kit/
A type of in vivo assay evidence where farnesylated residues in proteins are detected in cells in vivo.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001081
in vivo farnesylation assay evidence
A type of in vivo assay evidence where farnesylated residues in proteins are detected in cells in vivo.
ECO:SN
PMID:9030603
SIB:PG
A type of in vivo assay evidence where methylated residues are detected in a compound (such as a protein or a nucleic acid) in vivo.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001082
in vivo methylation assay evidence
A type of in vivo assay evidence where methylated residues are detected in a compound (such as a protein or a nucleic acid) in vivo.
ECO:SN
SIB:PG
url:http://en.wikipedia.org/wiki/Methylation
A type of in vivo assay evidence where palmitoylated residues in proteins are detected in cells in vivo.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001083
in vivo palmitoylation assay evidence
A type of in vivo assay evidence where palmitoylated residues in proteins are detected in cells in vivo.
ECO:SN
PMID:10329400
SIB:PG
A type of in vivo assay evidence where the removal of phosphate groups on a protein is detected in cells in vivo.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001084
in vivo phosphatase assay evidence
A type of in vivo assay evidence where the removal of phosphate groups on a protein is detected in cells in vivo.
ECO:SN
SIB:PG
url:http://en.wikipedia.org/wiki/Phosphatase
A type of in vivo assay evidence where phosphorylated residues in a protein are detected in cells in vivo.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001085
in vivo protein kinase assay evidence
A type of in vivo assay evidence where phosphorylated residues in a protein are detected in cells in vivo.
ECO:SN
SIB:PG
url:http://en.wikipedia.org/wiki/Protein_kinase
url:http://en.wikipedia.org/wiki/Protein_phosphorylation
A type of in vivo assay evidence where sumoylated residues are detected on a protein in cells in vivo.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001086
in vivo sumoylation assay evidence
A type of in vivo assay evidence where sumoylated residues are detected on a protein in cells in vivo.
ECO:SN
SIB:PG
url:http://www.enzolifesciences.com/BML-UW8955/sumoylation-kit/
A type of in vivo assay evidence where transcription is detected in cells in vivo.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001087
in vivo transcription assay evidence
A type of in vivo assay evidence where transcription is detected in cells in vivo.
ECO:SN
PMID:12181418
SIB:PG
A type of in vivo assay evidence where de novo protein synthesis is detected in cells in vivo.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001088
in vivo translation assay evidence
A type of in vivo assay evidence where de novo protein synthesis is detected in cells in vivo.
ECO:SN
PMID:24901308
SIB:PG
A type of in vivo assay evidence where ubiquitinated residues on a protein are detected in cells in vivo.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001089
in vivo ubiquitination assay evidence
A type of in vivo assay evidence where ubiquitinated residues on a protein are detected in cells in vivo.
ECO:SN
PMID:19692941
SIB:PG
A type of genetic transformation evidence resulting from the targetted replacement of a wild-type DNA sequence with a different sequence.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001090
knockin evidence
A type of genetic transformation evidence resulting from the targetted replacement of a wild-type DNA sequence with a different sequence.
PMID:18077807
PMID:21800101
A type of genetic transformation evidence resulting from the removal of a particular gene (or genes), disrupting the function and allowing for functional analysis.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001091
knockout evidence
A type of genetic transformation evidence resulting from the removal of a particular gene (or genes), disrupting the function and allowing for functional analysis.
PMC:2782548
A type of physical interaction evidence resulting from the qualitative and quantitative analysis of the affinity with which a protein binds to a lipid.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001092
lipid binding assay evidence
A type of physical interaction evidence resulting from the qualitative and quantitative analysis of the affinity with which a protein binds to a lipid.
PMID:22848065
PMID:23681540
A type of physical interaction evidence resulting from the analysis of protein-protein interactions by use of a luciferase enzyme fused to a particular protein (or proteins), which are coexpressed with epitope-tagged partners in mammalian cells.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
LUMIER assay
eco
ECO:0001093
luminescence-based mammalian interactome mapping assay evidence
A type of physical interaction evidence resulting from the analysis of protein-protein interactions by use of a luciferase enzyme fused to a particular protein (or proteins), which are coexpressed with epitope-tagged partners in mammalian cells.
MI:0729
PMID:15761153
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001094
macroscopy evidence
A type of hybrid interaction evidence resulting from the analysis of proteins of interest attached to two portions of the transcriptional activator, and in interaction bring the two portions together to increase expression of the reporter gene.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001095
mammalian 2-hybrid assay evidence
A type of hybrid interaction evidence resulting from the analysis of proteins of interest attached to two portions of the transcriptional activator, and in interaction bring the two portions together to increase expression of the reporter gene.
ECO:RCT
PMID:9043710
A type of spectrometry evidence resulting from identifying the amount and type of material entities present in a sample by fragmenting it and measuring the mass-to-charge ratio of the resulting particles.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001096
mass spectrometry evidence
A type of spectrometry evidence resulting from identifying the amount and type of material entities present in a sample by fragmenting it and measuring the mass-to-charge ratio of the resulting particles.
OBI:0000470
A type of imaging assay evidence resulting from the use of technology to visualize and provide information about the body to diagnose, treat, or monitor medical conditions.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001097
medical imaging evidence
A type of imaging assay evidence resulting from the use of technology to visualize and provide information about the body to diagnose, treat, or monitor medical conditions.
url:http://www.fda.gov/Radiation-EmittingProducts/RadiationEmittingProductsandProcedures/MedicalImaging/ucm2005914.htm
A type of direct assay evidence where a microscope was used to view a sample.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001098
microscopy evidence
A type of direct assay evidence where a microscope was used to view a sample.
ECO:MCC
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001099
motility wound healing assay evidence
A type of metabolic cell proliferation assay evidence resulting from 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) in combination with phenazine methyl sulfate (PMS) as an intermediate electron acceptor reagent to produce a soluble formazan dye in viable cells.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium
eco
ECO:0001100
MTS assay evidence
A type of metabolic cell proliferation assay evidence resulting from 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) in combination with phenazine methyl sulfate (PMS) as an intermediate electron acceptor reagent to produce a soluble formazan dye in viable cells.
NBK:144065
PMID:1867954
A type of metabolic cell proliferation assay evidence resulting from the reduction of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) to its insoluble purple formazan dye in viable cells.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide
eco
ECO:0001101
MTT assay evidence
A type of metabolic cell proliferation assay evidence resulting from the reduction of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) to its insoluble purple formazan dye in viable cells.
NBK:144065
PMID:6606682
A type of protein detection assay evidence resulting from determination of analyte concentration by fluorescent bead sets attached to an antibody (to a specific analyte) with a fluorescent reporter dye label attached to a second antibody (to a specific analyte).
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001102
multiplex bead-based immunoassay evidence
A type of protein detection assay evidence resulting from determination of analyte concentration by fluorescent bead sets attached to an antibody (to a specific analyte) with a fluorescent reporter dye label attached to a second antibody (to a specific analyte).
PMC:1534009
A type of experimental phenotypic evidence resulting from the observation of the impact of a natural mutation on the expressed traits.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001103
natural variation mutant evidence
A type of experimental phenotypic evidence resulting from the observation of the impact of a natural mutation on the expressed traits.
ECO:RCT
A type of apoptotic assay evidence resulting from the nuclei fragmenting into smaller pieces during programmed cell death.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001104
nuclear fragmentation evidence
A type of apoptotic assay evidence resulting from the nuclei fragmenting into smaller pieces during programmed cell death.
PMID:16738861
A type of structure determination evidence resulting from the use of an MRI to provide chemical information about tissue metabolites.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
NMR spectroscopy
eco
ECO:0001105
nuclear magnetic resonance spectroscopy evidence
A type of structure determination evidence resulting from the use of an MRI to provide chemical information about tissue metabolites.
PMID:16428685
A type of RNA detection assay evidence resulting from the detection and quantitation of specific RNAs (from a sample of total cellular RNA) that are bound by antisense RNA or DNA probes and therefore protected from nucleases.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001106
nuclease protection assay evidence
A type of RNA detection assay evidence resulting from the detection and quantitation of specific RNAs (from a sample of total cellular RNA) that are bound by antisense RNA or DNA probes and therefore protected from nucleases.
PMID:17486122
PMID:18428580
A type of DNA synthesis cell proliferation assay evidence resulting from the analysis and measurement of the incorporation of nucleotide analog(s) into the DNA.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001107
nucleotide analog incorporation evidence
A type of DNA synthesis cell proliferation assay evidence resulting from the analysis and measurement of the incorporation of nucleotide analog(s) into the DNA.
PMC:3149870
A type of protein binding evidence resulting from the panning of a phage library where the individual phage displayed a different peptide or protein by fusion to coat proteins on the capsid.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001108
phage display evidence
A type of protein binding evidence resulting from the panning of a phage library where the individual phage displayed a different peptide or protein by fusion to coat proteins on the capsid.
MI:0084
PMID:11680867
A type of protein assay evidence resulting from the identification of the phosphorylated residue in a protein by amino acid analysis.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001109
phosphoamino acid analysis evidence
A type of protein assay evidence resulting from the identification of the phosphorylated residue in a protein by amino acid analysis.
PMID:11680867
PMID:18429115
SIB:PG
mchibucos
2014-03-16T11:30:54Z
phosphopeptide affinity enrichment evidence
eco
ECO:0001110
peptide affinity enrichment evidence
A type of direct assay evidence resulting from the physical examination and measurement of the feature of a subject or sample.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001111
physical examination evidence
A type of direct assay evidence resulting from the physical examination and measurement of the feature of a subject or sample.
ECO:RCT
A type of protein assay evidence resulting from protein-bound peptides detected from a collection of peptides arranged as an array and incubated with the partner protein in order to map protein-protein interaction sites.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
phosphopeptide array evidence
eco
ECO:0001112
peptide array evidence
A type of protein assay evidence resulting from protein-bound peptides detected from a collection of peptides arranged as an array and incubated with the partner protein in order to map protein-protein interaction sites.
PMID:21243154
A type of experimental phenotypic evidence resulting from the change in a single nucleotide.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001113
point mutation evidence
A type of experimental phenotypic evidence resulting from the change in a single nucleotide.
SO:1000008
A type of staining evidence resulting from the binding and labeling of DNA (during apoptosis, when there is a loss of nuclear DNA content) with propidium iodide (PI) to identify the cells from which it originated.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001114
propidium iodide staining evidence
A type of staining evidence resulting from the binding and labeling of DNA (during apoptosis, when there is a loss of nuclear DNA content) with propidium iodide (PI) to identify the cells from which it originated.
PMID:17406435
A type of direct assay evidence resulting from the analysis of a molecule by its intrinsic fluorescence, or by attaching it with a fluorophore.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001115
fluorescence evidence
A type of direct assay evidence resulting from the analysis of a molecule by its intrinsic fluorescence, or by attaching it with a fluorophore.
url:http://www.nature.com/subjects/biological-fluorescence
A type of protein detection assay evidence resulting from protein samples immobilized on a membrane, then subsequently incubated and imaged.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001116
protein dot blot assay evidence
A type of protein detection assay evidence resulting from protein samples immobilized on a membrane, then subsequently incubated and imaged.
doi:10.1007/978-94-009-0951-9_24
A type of protein detection assay evidence resulting from proteins immobilized to prepare protein chips, or microwells, that can be utilized to determine presence of proteins, monitor differential expression profiles, and/or study protein interactions.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001117
protein microarray evidence
A type of protein detection assay evidence resulting from proteins immobilized to prepare protein chips, or microwells, that can be utilized to determine presence of proteins, monitor differential expression profiles, and/or study protein interactions.
PMC:1828913
A type of sequencing assay evidence resulting from determining the sequence of amino acids in a protein.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001118
protein sequencing assay evidence
A type of sequencing assay evidence resulting from determining the sequence of amino acids in a protein.
ERO:0001287
A type of mass spectrometry evidence resulting from quantitative analysis of peptides, proteins, and proteomes.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001119
quantitative mass spectrometry evidence
A type of mass spectrometry evidence resulting from quantitative analysis of peptides, proteins, and proteomes.
PMID:22665296
A type of direct assay evidence resulting from the assessment of biological reactions by use of a radioactive isotope to label the reactant.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
radioassay
radioisotopic assay
eco
ECO:0001120
radioisotope assay evidence
A type of direct assay evidence resulting from the assessment of biological reactions by use of a radioactive isotope to label the reactant.
ISBN:978-3-642-50036-7
A type of protein detection assay evidence resulting from the use of a radioligand to measure the binding of a substance to a specific antibody or other receptor system.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001121
radioimmunoassay evidence
A type of protein detection assay evidence resulting from the use of a radioligand to measure the binding of a substance to a specific antibody or other receptor system.
MeSH:D011863
A type of direct assay evidence from the analysis of the real-time interaction between an analyte in solution and its interactant linked to the surface of the resonant mirror.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001123
resonant mirror biosensor evidence
A type of direct assay evidence from the analysis of the real-time interaction between an analyte in solution and its interactant linked to the surface of the resonant mirror.
PMID:19151938
A type of DNA detection assay evidence resulting from homologous DNA fragments digested by restriction enzymes, and the resulting restriction fragments are sorted by length to illustrate differences.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001124
restriction fragment detection evidence
A type of DNA detection assay evidence resulting from homologous DNA fragments digested by restriction enzymes, and the resulting restriction fragments are sorted by length to illustrate differences.
doi:10.1007/978-94-009-0951-9_24
url:http://www.ncbi.nlm.nih.gov/probe/docs/techrflp/
A type of spectrometry evidence resulting from the evaluation of a molecule in a fluid by its ability to alter the transmission of light at specific wavelengths.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001126
spectrophotometry evidence
A type of spectrometry evidence resulting from the evaluation of a molecule in a fluid by its ability to alter the transmission of light at specific wavelengths.
MMO:0000173
A type of physical interaction evidence based on real-time, rapid plasmon generation on the interface between a planar surface and vacuum that measures changes in refractive index close to the sensor surface when an analyte and its immobilized ligand bind to observe and characterize molecular interaction.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
SPR evidence
eco
ECO:0001127
Plasmons are generated by an incident light beam.
surface plasmon resonance evidence
A type of physical interaction evidence based on real-time, rapid plasmon generation on the interface between a planar surface and vacuum that measures changes in refractive index close to the sensor surface when an analyte and its immobilized ligand bind to observe and characterize molecular interaction.
ECO:SW
PMID:11578932
PMID:19151937
PMID:8574707
SPR evidence
PMID:11578932
A type of experimental phenotypic evidence resulting from a transplantation in which the transplanted material (stem cells) is from an individual's identical twin.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001128
syngeneic transplantation experiment evidence
A type of experimental phenotypic evidence resulting from a transplantation in which the transplanted material (stem cells) is from an individual's identical twin.
PMID:18469352
A type of enzyme assay evidence resulting from the analysis of tumor necrosis factor (TNF)-a converting enzyme (TACE), which releases a soluble TNF-a from the membrane-bound precursor protein.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
Tumor necrosis factor - alpha converting enzyme activity assay
eco
ECO:0001129
TACE activity assay evidence
A type of enzyme assay evidence resulting from the analysis of tumor necrosis factor (TNF)-a converting enzyme (TACE), which releases a soluble TNF-a from the membrane-bound precursor protein.
PMC:1808921
A type of array experiment evidence resulting from the analysis of section(s) of a paraffin block containing embedded tissues cores arranged in an array pattern.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001130
tissue microarray evidence
A type of array experiment evidence resulting from the analysis of section(s) of a paraffin block containing embedded tissues cores arranged in an array pattern.
PMID:11770905
A type of genetic transformation evidence resulting from an organism that has had its expressed phenotype altered by modification.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001131
transgenic organism evidence
A type of genetic transformation evidence resulting from an organism that has had its expressed phenotype altered by modification.
OBI:1000048
A type of mass spectrometry evidence resulting from the analysis of prepared phosphopeptides separated in two dimensions on a TLC plate.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001132
tryptic phosphopeptide mapping assay evidence
A type of mass spectrometry evidence resulting from the analysis of prepared phosphopeptides separated in two dimensions on a TLC plate.
PMID:18429120
A type of apoptotic assay evidence resulting from the visualization of DNA fragmentation by detection of exposed 3'-OH ends, localized by terminal deoxynucleotidyl transferase (TdT) which then catalyzes the addition of labeled dUTPs.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
TUNEL assay evidence
TdT-mediated dUTP-biotin nick end labeling assay
terminal deoxynucleotidyl transferase-dUTP nick end labeling assay evidence
eco
ECO:0001133
terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence
A type of apoptotic assay evidence resulting from the visualization of DNA fragmentation by detection of exposed 3'-OH ends, localized by terminal deoxynucleotidyl transferase (TdT) which then catalyzes the addition of labeled dUTPs.
PMID:22566045
A type of direct assay evidence resulting from the analysis of a urine sample.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001134
urine test evidence
A type of direct assay evidence resulting from the analysis of a urine sample.
ECO:RCT
A type of in vitro assay evidence resulting from the creation of a wound in a cell monolayer, then capturing images at regular intervals to observe directional cell migration during the closure of the wound.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001135
wound healing assay evidence
A type of in vitro assay evidence resulting from the creation of a wound in a cell monolayer, then capturing images at regular intervals to observe directional cell migration during the closure of the wound.
PMID:15576902
A type of metabolic cell proliferation assay evidence resulting from the assessment of metabolic activity from a water-soluble tetrazolium salt WST-1 being reduced outside the cell (by reacting with mitochondrial succinate-tetrazolium reductase) to form a formazan dye.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001136
WST-1 assay evidence
A type of metabolic cell proliferation assay evidence resulting from the assessment of metabolic activity from a water-soluble tetrazolium salt WST-1 being reduced outside the cell (by reacting with mitochondrial succinate-tetrazolium reductase) to form a formazan dye.
PMID:18417231
A type of anatomical perturbation evidence where live cells, tissues, or organs from a non-human animal source are transplanted, implanted or infused into a human recipient.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
Xenograft transplantation
Xenografting
Xenotransplantation
tissue grafting
eco
ECO:0001137
xenotransplantation experiment evidence
A type of anatomical perturbation evidence where live cells, tissues, or organs from a non-human animal source are transplanted, implanted or infused into a human recipient.
ECO:SN
url:http://ilarjournal.oxfordjournals.org/content/37/1/16.full.pdf+html
url:http://www.fda.gov/BiologicsBloodVaccines/Xenotransplantation/
A type of 3D cell culture evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T15:18:35Z
eco
ECO:0001138
3D cell culture evidence used in manual assertion
true
true
A type of 3D cell culture evidence that is used in a manual assertion.
ECO:MCC
A type of 51Cr release assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T15:20:55Z
eco
ECO:0001139
51Cr release assay evidence used in manual assertion
true
true
A type of 51Cr release assay evidence that is used in a manual assertion.
ECO:MCC
A type of 7-aminoactinomycin staining evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T15:22:01Z
eco
ECO:0001140
7-aminoactinomycin staining evidence used in manual assertion
true
true
A type of 7-aminoactinomycin staining evidence that is used in a manual assertion.
ECO:MCC
A type of [3H]-thymidine incorporation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T15:31:52Z
eco
ECO:0001141
[3H]-thymidine incorporation assay evidence used in manual assertion
true
true
A type of [3H]-thymidine incorporation assay evidence that is used in a manual assertion.
ECO:MCC
A type of [3H]arachidonic acid release assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T15:32:44Z
eco
ECO:0001142
[3H]arachidonic acid release assay evidence used in manual assertion
true
true
A type of [3H]arachidonic acid release assay evidence that is used in a manual assertion.
ECO:MCC
A type of adhesion assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T15:33:38Z
eco
ECO:0001143
adhesion assay evidence used in manual assertion
true
true
A type of adhesion assay evidence that is used in a manual assertion.
ECO:MCC
A type of adoptive cell transfer evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T15:36:19Z
eco
ECO:0001144
adoptive cell transfer evidence used in manual assertion
true
true
A type of adoptive cell transfer evidence that is used in a manual assertion.
ECO:MCC
A type of Alamar blue assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T15:37:21Z
eco
ECO:0001145
Alamar blue assay evidence used in manual assertion
true
true
A type of Alamar blue assay evidence that is used in a manual assertion.
ECO:MCC
A type of allograft transplantation experiment evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T15:38:22Z
eco
ECO:0001146
allograft transplantation experiment evidence used in manual assertion
true
true
A type of allograft transplantation experiment evidence that is used in a manual assertion.
ECO:MCC
A type of anion-exchange chromatography evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T15:44:30Z
eco
ECO:0001147
anion-exchange chromatography evidence used in manual assertion
true
true
A type of anion-exchange chromatography evidence that is used in a manual assertion.
ECO:MCC
A type of annexin-V staining evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T15:52:01Z
eco
ECO:0001148
annexin-V staining evidence used in manual assertion
true
true
A type of annexin-V staining evidence that is used in a manual assertion.
ECO:MCC
A type of behavioral assay evidence used that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T15:53:38Z
eco
ECO:0001149
behavioral assay evidence used in manual assertion
true
true
A type of behavioral assay evidence used that is used in a manual assertion.
ECO:MCC
A type of blocking monoclonal antibody evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T15:54:44Z
eco
ECO:0001150
blocking monoclonal antibody evidence used in manual assertion
true
true
A type of blocking monoclonal antibody evidence that is used in a manual assertion.
ECO:MCC
A type of blocking peptide evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T15:55:33Z
eco
ECO:0001151
blocking peptide evidence used in manual assertion
true
true
A type of blocking peptide evidence that is used in a manual assertion.
ECO:MCC
A type of blocking polyclonal antibody evidence tthat is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:01:39Z
eco
ECO:0001152
blocking polyclonal antibody evidence used in manual assertion
true
true
A type of blocking polyclonal antibody evidence tthat is used in a manual assertion.
ECO:MCC
A type of blood test evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:02:47Z
eco
ECO:0001153
blood test evidence used in manual assertion
true
true
A type of blood test evidence that is used in a manual assertion.
ECO:MCC
A type of Boyden chamber assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:03:53Z
eco
ECO:0001154
Boyden chamber assay evidence used in manual assertion
true
true
A type of Boyden chamber assay evidence that is used in a manual assertion.
ECO:MCC
A type of BrdU incorporation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:04:49Z
eco
ECO:0001155
bromodeoxyuridine incorporation assay evidence used in manual assertion
true
true
A type of BrdU incorporation assay evidence that is used in a manual assertion.
ECO:MCC
A type of caspase assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:06:06Z
eco
ECO:0001156
caspase assay evidence used in manual assertion
true
true
A type of caspase assay evidence that is used in a manual assertion.
ECO:MCC
A type of cell counting evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:07:13Z
eco
ECO:0001157
cell counting evidence used in manual assertion
true
true
A type of cell counting evidence that is used in a manual assertion.
ECO:MCC
A type of cell permeability assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:07:58Z
eco
ECO:0001158
cell permeability assay evidence used in manual assertion
true
true
A type of cell permeability assay evidence that is used in a manual assertion.
ECO:MCC
A type of carboxyfluorescein diacetate succinimidyl ester staining evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:08:54Z
eco
ECO:0001159
carboxyfluorescein diacetate succinimidyl ester staining evidence used in manual assertion
true
true
A type of carboxyfluorescein diacetate succinimidyl ester staining evidence that is used in a manual assertion.
ECO:MCC
A type of chemiluminescence-linked immunoassay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:09:55Z
eco
ECO:0001160
chemiluminescence-linked immunoassay evidence used in manual assertion
true
true
A type of chemiluminescence-linked immunoassay evidence that is used in a manual assertion.
ECO:MCC
A type of chimeric protein evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:10:40Z
eco
ECO:0001161
chimeric protein evidence used in manual assertion
true
true
A type of chimeric protein evidence that is used in a manual assertion.
ECO:MCC
A type of co-electrophoresis evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:11:22Z
eco
ECO:0001162
co-electrophoresis evidence used in manual assertion
true
true
A type of co-electrophoresis evidence that is used in a manual assertion.
ECO:MCC
A type of co-localization evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:12:04Z
eco
ECO:0001163
co-localization evidence used in manual assertion
true
true
A type of co-localization evidence that is used in a manual assertion.
ECO:MCC
A type of co-sedimentation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:12:55Z
eco
ECO:0001164
co-sedimentation assay evidence used in manual assertion
true
true
A type of co-sedimentation assay evidence that is used in a manual assertion.
ECO:MCC
A type of colony counting evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:14:57Z
eco
ECO:0001165
colony counting evidence used in manual assertion
true
true
A type of colony counting evidence that is used in a manual assertion.
ECO:MCC
A type of comet assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:16:01Z
eco
ECO:0001166
comet assay evidence used in manual assertion
true
true
A type of comet assay evidence that is used in a manual assertion.
ECO:MCC
A type of conditional knockin evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:17:22Z
eco
ECO:0001167
conditional knockin evidence used in manual assertion
true
true
A type of conditional knockin evidence that is used in a manual assertion.
ECO:MCC
A type of conditional knockout evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:17:58Z
eco
ECO:0001168
conditional knockout evidence used in manual assertion
true
true
A type of conditional knockout evidence that is used in a manual assertion.
ECO:MCC
A type of constitutively active mutant evidence that is used a in manual assertion.
SIB:PG
mchibucos
2014-03-17T16:20:23Z
eco
ECO:0001169
constitutively active mutant evidence used in manual assertion
true
true
A type of constitutively active mutant evidence that is used a in manual assertion.
ECO:MCC
A type of cross-linking evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:21:29Z
eco
ECO:0001170
cross-linking evidence used in manual assertion
true
true
A type of cross-linking evidence that is used in a manual assertion.
ECO:MCC
A type of crystallography evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:22:20Z
eco
ECO:0001171
crystallography evidence used in manual assertion
true
true
A type of crystallography evidence that is used in a manual assertion.
ECO:MCC
A type of cytochemistry evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:23:10Z
eco
ECO:0001172
cytochemistry evidence used in manual assertion
true
true
A type of cytochemistry evidence that is used in a manual assertion.
ECO:MCC
A type of cytochrome C release assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:23:53Z
eco
ECO:0001173
cytochrome C release assay evidence used in manual assertion
true
true
A type of cytochrome C release assay evidence that is used in a manual assertion.
ECO:MCC
A type of 4',6-diamidino-2-phenylindole staining evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:25:03Z
eco
ECO:0001174
4',6-diamidino-2-phenylindole staining evidence used in manual assertion
true
true
A type of 4',6-diamidino-2-phenylindole staining evidence that is used in a manual assertion.
ECO:MCC
A type of deletion evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:25:54Z
eco
ECO:0001175
deletion mutation evidence used in manual assertion
true
true
A type of deletion evidence that is used in a manual assertion.
ECO:MCC
A type of DNA laddering assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:26:46Z
eco
ECO:0001176
DNA laddering assay evidence used in manual assertion
true
true
A type of DNA laddering assay evidence that is used in a manual assertion.
ECO:MCC
A type of RNA dot blot assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:45:52Z
eco
ECO:0001177
RNA dot blot assay evidence used in manual assertion
true
true
A type of RNA dot blot assay evidence that is used in a manual assertion.
ECO:MCC
A type of RNA microarray evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:46:50Z
eco
ECO:0001178
RNA microarray evidence used in manual assertion
true
true
A type of RNA microarray evidence that is used in a manual assertion.
ECO:MCC
A type of dominant-negative mutant evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:47:44Z
eco
ECO:0001179
dominant-negative mutant evidence used in manual assertion
true
true
A type of dominant-negative mutant evidence that is used in a manual assertion.
ECO:MCC
A type of eTag assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:59:39Z
eco
ECO:0001180
eTag assay evidence used in manual assertion
true
true
A type of eTag assay evidence that is used in a manual assertion.
ECO:MCC
A type of filter binding assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:03:28Z
eco
ECO:0001181
filter binding assay evidence used in manual assertion
true
true
A type of filter binding assay evidence that is used in a manual assertion.
ECO:MCC
A type of fluorescence in situ hybridization evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:04:20Z
eco
ECO:0001182
fluorescence in situ hybridization evidence used in manual assertion
true
true
A type of fluorescence in situ hybridization evidence that is used in a manual assertion.
ECO:MCC
A type of fluorescence resonance energy transfer evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:05:22Z
eco
ECO:0001183
fluorescence resonance energy transfer evidence used in manual assertion
true
true
A type of fluorescence resonance energy transfer evidence that is used in a manual assertion.
ECO:MCC
A type of gel-filtration evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:06:14Z
eco
ECO:0001184
gel-filtration evidence used in manual assertion
true
true
A type of gel-filtration evidence that is used in a manual assertion.
ECO:MCC
A type of histochemistry evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:07:19Z
eco
ECO:0001185
histochemistry evidence used in manual assertion
true
true
A type of histochemistry evidence that is used in a manual assertion.
ECO:MCC
A type of immunocytochemistry evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:12:39Z
eco
ECO:0001186
immunocytochemistry evidence used in manual assertion
true
true
A type of immunocytochemistry evidence that is used in a manual assertion.
ECO:MCC
A type of histology evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:09:50Z
eco
ECO:0001187
histology evidence used in manual assertion
true
true
A type of histology evidence that is used in a manual assertion.
ECO:MCC
A type of immunodepletion evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:16:19Z
eco
ECO:0001188
immunodepletion evidence used in manual assertion
true
true
A type of immunodepletion evidence that is used in a manual assertion.
ECO:MCC
A type of immunohistochemistry evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:17:22Z
eco
ECO:0001189
immunohistochemistry evidence used in manual assertion
true
true
A type of immunohistochemistry evidence that is used in a manual assertion.
ECO:MCC
A type of in vitro acetylation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:19:24Z
eco
ECO:0001190
in vitro acetylation assay evidence used in manual assertion
true
true
A type of in vitro acetylation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vitro cleavage assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:21:22Z
eco
ECO:0001191
in vitro cleavage assay evidence used in manual assertion
true
true
A type of in vitro cleavage assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vitro deacetylation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:23:42Z
eco
ECO:0001192
in vitro deacetylation assay evidence used in manual assertion
true
true
A type of in vitro deacetylation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vitro defarnesylation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:25:45Z
eco
ECO:0001193
in vitro defarnesylation assay evidence used in manual assertion
true
true
A type of in vitro defarnesylation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vitro demethylation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:27:00Z
eco
ECO:0001194
in vitro demethylation assay evidence used in manual assertion
true
true
A type of in vitro demethylation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vitro desumoylation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:29:01Z
eco
ECO:0001195
in vitro desumoylation assay evidence used in manual assertion
true
true
A type of in vitro desumoylation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vitro deubiquitination assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:29:48Z
eco
ECO:0001196
in vitro deubiquitination assay evidence used in manual assertion
true
true
A type of in vitro deubiquitination assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vitro farnesylation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:30:50Z
eco
ECO:0001197
in vitro farnesylation assay evidence used in manual assertion
true
true
A type of in vitro farnesylation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vitro methylation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:31:54Z
eco
ECO:0001198
in vitro methylation assay evidence used in manual assertion
true
true
A type of in vitro methylation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vitro palmitoylation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:32:57Z
eco
ECO:0001199
in vitro palmitoylation assay evidence used in manual assertion
true
true
A type of in vitro palmitoylation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vitro phosphatase assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:34:16Z
eco
ECO:0001200
in vitro phosphatase assay evidence used in manual assertion
true
true
A type of in vitro phosphatase assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vitro polyADP-ribosylation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:34:57Z
eco
ECO:0001201
in vitro polyADP-ribosylation assay evidence used in manual assertion
true
true
A type of in vitro polyADP-ribosylation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vitro protein kinase assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:39:57Z
eco
ECO:0001202
in vitro protein kinase assay evidence used in manual assertion
true
true
A type of in vitro protein kinase assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vitro sumoylation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:41:25Z
eco
ECO:0001203
in vitro sumoylation assay evidence used in manual assertion
true
true
A type of in vitro sumoylation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vitro transcription assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:44:40Z
eco
ECO:0001204
in vitro transcription assay evidence used in manual assertion
true
true
A type of in vitro transcription assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vitro translation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:46:30Z
eco
ECO:0001205
in vitro translation assay evidence used in manual assertion
true
true
A type of in vitro translation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vitro ubiquitination assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:47:18Z
eco
ECO:0001206
in vitro ubiquitination assay evidence used in manual assertion
true
true
A type of in vitro ubiquitination assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vivo acetylation assay evidence that is used in manual assertion.
SIB:PG
mchibucos
2014-03-17T17:48:56Z
eco
ECO:0001207
in vivo acetylation assay evidence used in manual assertion
true
true
A type of in vivo acetylation assay evidence that is used in manual assertion.
ECO:MCC
A type of in vivo cleavage assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:49:43Z
eco
ECO:0001208
in vivo cleavage assay evidence used in manual assertion
true
true
A type of in vivo cleavage assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vivo deacetylation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:50:47Z
eco
ECO:0001209
in vivo deacetylation assay evidence used in manual assertion
true
true
A type of in vivo deacetylation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vivo defarnesylation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:52:41Z
eco
ECO:0001210
in vivo defarnesylation assay evidence used in manual assertion
true
true
A type of in vivo defarnesylation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vivo demethylation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:53:40Z
eco
ECO:0001211
in vivo demethylation assay evidence used in manual assertion
true
true
A type of in vivo demethylation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vivo desumoylation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:54:36Z
eco
ECO:0001212
in vivo desumoylation assay evidence used in manual assertion
true
true
A type of in vivo desumoylation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vivo deubiquitination assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:56:28Z
eco
ECO:0001213
in vivo deubiquitination assay evidence used in manual assertion
true
true
A type of in vivo deubiquitination assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vivo farnesylation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:57:18Z
eco
ECO:0001214
in vivo farnesylation assay evidence used in manual assertion
true
true
A type of in vivo farnesylation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vivo methylation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T18:03:16Z
eco
ECO:0001215
in vivo methylation assay evidence used in manual assertion
true
true
A type of in vivo methylation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vivo palmitoylation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T18:04:07Z
eco
ECO:0001216
in vivo palmitoylation assay evidence used in manual assertion
true
true
A type of in vivo palmitoylation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vivo phosphatase assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T18:06:08Z
eco
ECO:0001217
in vivo phosphatase assay evidence used in manual assertion
true
true
A type of in vivo phosphatase assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vivo protein kinase assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T18:07:58Z
eco
ECO:0001218
in vivo protein kinase assay evidence used in manual assertion
true
true
A type of in vivo protein kinase assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vivo sumoylation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T18:09:49Z
eco
ECO:0001219
in vivo sumoylation assay evidence used in manual assertion
true
true
A type of in vivo sumoylation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vivo transcription assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T18:11:20Z
eco
ECO:0001220
in vivo transcription assay evidence used in manual assertion
true
true
A type of in vivo transcription assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vivo translation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T18:42:50Z
eco
ECO:0001221
in vivo translation assay evidence used in manual assertion
true
true
A type of in vivo translation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vivo ubiquitination assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T18:44:11Z
eco
ECO:0001222
in vivo ubiquitination assay evidence used in manual assertion
true
true
A type of in vivo ubiquitination assay evidence that is used in a manual assertion.
ECO:MCC
A type of induced mutation evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T18:45:56Z
eco
ECO:0001223
induced mutation evidence used in manual assertion
true
true
A type of induced mutation evidence that is used in a manual assertion.
ECO:MCC
A type of knockin evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T18:49:35Z
eco
ECO:0001224
knockin evidence used in manual assertion
true
true
A type of knockin evidence that is used in a manual assertion.
ECO:MCC
A type of knockout evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T18:51:31Z
eco
ECO:0001225
knockout evidence used in manual assertion
true
true
A type of knockout evidence that is used in a manual assertion.
ECO:MCC
A type of lipid binding assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T18:52:19Z
eco
ECO:0001226
lipid binding assay evidence used in manual assertion
true
true
A type of lipid binding assay evidence that is used in a manual assertion.
ECO:MCC
A type of LUMIER assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T18:55:16Z
eco
ECO:0001227
luminescence-based mammalian interactome mapping assay evidence used in manual assertion
true
true
A type of LUMIER assay evidence that is used in a manual assertion.
ECO:MCC
A type of macroscopy evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T18:56:21Z
eco
ECO:0001228
macroscopy evidence used in manual assertion
true
true
A type of macroscopy evidence that is used in a manual assertion.
ECO:MCC
A type of mammalian 2-hybrid assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T18:57:25Z
eco
ECO:0001229
mammalian 2-hybrid assay evidence used in manual assertion
true
true
A type of mammalian 2-hybrid assay evidence that is used in a manual assertion.
ECO:MCC
A type of mass spectrometry evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T18:59:50Z
eco
ECO:0001230
mass spectrometry evidence used in manual assertion
true
true
A type of mass spectrometry evidence that is used in a manual assertion.
ECO:MCC
A type of medical imaging evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T19:04:43Z
eco
ECO:0001231
medical imaging evidence used in manual assertion
true
true
A type of medical imaging evidence that is used in a manual assertion.
ECO:MCC
A type of microscopy evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T19:05:37Z
eco
ECO:0001232
microscopy evidence used in manual assertion
true
true
A type of microscopy evidence that is used in a manual assertion.
ECO:MCC
A type of motility wound healing assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T19:08:13Z
eco
ECO:0001233
motility wound healing assay evidence used in manual assertion
true
true
A type of motility wound healing assay evidence that is used in a manual assertion.
ECO:MCC
A type of MTS assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T19:08:51Z
eco
ECO:0001234
MTS assay evidence used in manual assertion
true
true
A type of MTS assay evidence that is used in a manual assertion.
ECO:MCC
A type of MTT assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T19:13:17Z
eco
ECO:0001235
MTT assay evidence used in manual assertion
true
true
A type of MTT assay evidence that is used in a manual assertion.
ECO:MCC
A type of multiplex bead-based immunoassay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T19:14:03Z
eco
ECO:0001236
multiplex bead-based immunoassay evidence used in manual assertion
true
true
A type of multiplex bead-based immunoassay evidence that is used in a manual assertion.
ECO:MCC
A type of natural variation mutant evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T19:15:48Z
eco
ECO:0001237
natural variation mutant evidence used in manual assertion
true
true
A type of natural variation mutant evidence that is used in a manual assertion.
ECO:MCC
A type of nuclear magnetic resonance spectroscopy evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T19:18:50Z
eco
ECO:0001238
nuclear magnetic resonance spectroscopy evidence used in manual assertion
true
true
A type of nuclear magnetic resonance spectroscopy evidence that is used in a manual assertion.
ECO:MCC
A type of nuclear fragmentation evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T19:19:55Z
eco
ECO:0001239
nuclear fragmentation evidence used in manual assertion
true
true
A type of nuclear fragmentation evidence that is used in a manual assertion.
ECO:MCC
A type of nuclease protection assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T19:23:41Z
eco
ECO:0001240
nuclease protection assay evidence used in manual assertion
true
true
A type of nuclease protection assay evidence that is used in a manual assertion.
ECO:MCC
A type of nucleotide analog incorporation evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T19:25:17Z
eco
ECO:0001241
nucleotide analog incorporation evidence used in manual assertion
true
true
A type of nucleotide analog incorporation evidence that is used in a manual assertion.
ECO:MCC
A type of phage display evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T19:27:17Z
eco
ECO:0001242
phage display evidence used in manual assertion
true
true
A type of phage display evidence that is used in a manual assertion.
ECO:MCC
A type of phosphoamino acid analysis evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T19:28:59Z
eco
ECO:0001243
phosphoamino acid analysis evidence used in manual assertion
true
true
A type of phosphoamino acid analysis evidence that is used in a manual assertion.
ECO:MCC
A type of peptide affinity enrichment evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T19:30:13Z
eco
ECO:0001244
peptide affinity enrichment evidence used in manual assertion
true
true
A type of peptide affinity enrichment evidence that is used in a manual assertion.
ECO:MCC
A type of peptide array evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:16:45Z
eco
ECO:0001245
peptide array evidence used in manual assertion
true
true
A type of peptide array evidence that is used in a manual assertion.
ECO:MCC
A type of physical examination evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:17:27Z
eco
ECO:0001246
physical examination evidence used in manual assertion
true
true
A type of physical examination evidence that is used in a manual assertion.
ECO:MCC
A type of point mutation evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:18:10Z
eco
ECO:0001247
point mutation evidence used in manual assertion
true
true
A type of point mutation evidence that is used in a manual assertion.
ECO:MCC
A type of propidium iodide staining evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:18:58Z
eco
ECO:0001248
propidium iodide staining evidence used in manual assertion
true
true
A type of propidium iodide staining evidence that is used in a manual assertion.
ECO:MCC
A type of protein detection by fluorescence evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:19:35Z
eco
ECO:0001249
fluorescence evidence used in manual assertion
true
true
A type of protein detection by fluorescence evidence that is used in a manual assertion.
ECO:MCC
A type of protein dot blot assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:20:30Z
eco
ECO:0001250
protein dot blot assay evidence used in manual assertion
true
true
A type of protein dot blot assay evidence that is used in a manual assertion.
ECO:MCC
A type of protein microarray evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:21:11Z
eco
ECO:0001251
protein microarray evidence used in manual assertion
true
true
A type of protein microarray evidence that is used in a manual assertion.
ECO:MCC
A type of protein sequencing assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:22:08Z
eco
ECO:0001252
protein sequencing assay evidence used in manual assertion
true
true
A type of protein sequencing assay evidence that is used in a manual assertion.
ECO:MCC
A type of quantitative mass spectrometry evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:23:15Z
eco
ECO:0001253
quantitative mass spectrometry evidence used in manual assertion
true
true
A type of quantitative mass spectrometry evidence that is used in a manual assertion.
ECO:MCC
A type of radioisotope assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:27:05Z
eco
ECO:0001254
radioisotope assay evidence used in manual assertion
true
true
A type of radioisotope assay evidence that is used in a manual assertion.
ECO:MCC
A type of radioimmunoassay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:28:04Z
eco
ECO:0001255
radioimmunoassay evidence used in manual assertion
true
true
A type of radioimmunoassay evidence that is used in a manual assertion.
ECO:MCC
A type of imaging assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:29:00Z
eco
ECO:0001256
imaging assay evidence used in manual assertion
true
true
A type of imaging assay evidence that is used in a manual assertion.
ECO:MCC
A type of restriction fragment detection evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:29:05Z
eco
ECO:0001257
restriction fragment detection evidence used in manual assertion
true
true
A type of restriction fragment detection evidence that is used in a manual assertion.
ECO:MCC
A type of spectrophotometry evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:29:09Z
eco
ECO:0001258
spectrophotometry evidence used in manual assertion
true
true
A type of spectrophotometry evidence that is used in a manual assertion.
ECO:MCC
A type of syngeneic transplantation experiment evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:29:13Z
eco
ECO:0001259
syngeneic transplantation experiment evidence used in manual assertion
true
true
A type of syngeneic transplantation experiment evidence that is used in a manual assertion.
ECO:MCC
A type of xenotransplantation experiment evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:29:18Z
eco
ECO:0001260
xenotransplantation experiment evidence used in manual assertion
true
true
A type of xenotransplantation experiment evidence that is used in a manual assertion.
ECO:MCC
A type of WST-1 assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:29:22Z
eco
ECO:0001261
WST-1 assay evidence used in manual assertion
true
true
A type of WST-1 assay evidence that is used in a manual assertion.
ECO:MCC
A type of wound healing assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:29:26Z
eco
ECO:0001262
wound healing assay evidence used in manual assertion
true
true
A type of wound healing assay evidence that is used in a manual assertion.
ECO:MCC
A type of urine test evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:29:30Z
eco
ECO:0001263
urine test evidence used in manual assertion
true
true
A type of urine test evidence that is used in a manual assertion.
ECO:MCC
A type of TUNEL assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:29:34Z
eco
ECO:0001264
terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence used in manual assertion
true
true
A type of TUNEL assay evidence that is used in a manual assertion.
ECO:MCC
A type of tryptic phosphopeptide mapping assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:29:38Z
eco
ECO:0001265
tryptic phosphopeptide mapping assay evidence used in manual assertion
true
true
A type of tryptic phosphopeptide mapping assay evidence that is used in a manual assertion.
ECO:MCC
A type of transgenic organism evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:29:41Z
eco
ECO:0001266
transgenic organism evidence used in manual assertion
true
true
A type of transgenic organism evidence that is used in a manual assertion.
ECO:MCC
A type of tissue microarray evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:29:45Z
eco
ECO:0001267
tissue microarray evidence used in manual assertion
true
true
A type of tissue microarray evidence that is used in a manual assertion.
ECO:MCC
A type of TACE activity assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:29:49Z
eco
ECO:0001268
TACE activity assay evidence used in manual assertion
true
true
A type of TACE activity assay evidence that is used in a manual assertion.
ECO:MCC
A type of surface plasmon resonance evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:29:54Z
eco
ECO:0001269
surface plasmon resonance evidence used in manual assertion
true
true
A type of surface plasmon resonance evidence that is used in a manual assertion.
ECO:MCC
A type of restriction landmark genome scanning evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:29:58Z
eco
ECO:0001270
restriction landmark genomic scanning evidence used in manual assertion
true
true
A type of restriction landmark genome scanning evidence that is used in a manual assertion.
ECO:MCC
A type of resonant mirror biosensor evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:30:02Z
eco
ECO:0001271
resonant mirror biosensor evidence used in manual assertion
true
true
A type of resonant mirror biosensor evidence that is used in a manual assertion.
ECO:MCC
A type of high-performance liquid chromatography evidence that is used in a manual assertion.
mchibucos
2014-03-16T20:49:54Z
eco
ECO:0001272
high-performance liquid chromatography evidence used in manual assertion
true
true
A type of high-performance liquid chromatography evidence that is used in a manual assertion.
ECO:MCC
A type of ectopic expression evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T22:34:56Z
eco
ECO:0001273
ectopic expression evidence used in manual assertion
true
true
A type of ectopic expression evidence that is used in a manual assertion.
ECO:MCC
A type of oligonucleotide microarray evidence that detects binding of a tagged protein to an array of oligonucleotide probes representing potential binding sites.
swolfish
2015-06-05T14:36:00Z
PBM evidence
eco
ECO:0001601
protein-binding microarray evidence
A type of oligonucleotide microarray evidence that detects binding of a tagged protein to an array of oligonucleotide probes representing potential binding sites.
PMID:22146299
A type of in vivo assay evidence in which living cells are stained with a vital stain, i.e. dye that can be used on living cells without causing cell death.
swolfish
2015-06-08T11:51:37Z
eco
vital staining evidence
ECO:0001603
in vivo cell staining evidence
A type of in vivo assay evidence in which living cells are stained with a vital stain, i.e. dye that can be used on living cells without causing cell death.
GOC:MAH
vital staining evidence
GOC:MAH
A type of reporter gene assay evidence based on the fusion of selected genes with the phoA gene to express alkaline phosphatase in periplasmic space for protein tracing.
swolfish
2015-10-29T15:53:45Z
eco
SEAP reporter assay
Secreted Embryonic Alkaline Phosphatase reporter assay
ECO:0001801
Alkaline phosphatase reporter assay produces a hybrid protein with alkaline phosphatase activity following transportation across the cellular membrane.
alkaline phosphatase reporter gene assay evidence
A type of reporter gene assay evidence based on the fusion of selected genes with the phoA gene to express alkaline phosphatase in periplasmic space for protein tracing.
ECO:SW
PMID:11823238
A type of reporter gene assay evidence based on the fusion of the lacZ gene to a specific promoter for the expression of beta-galactosidase which will appear blue when grown on a X-gal medium.
swolfish
2015-10-29T15:57:10Z
beta-gal reporter gene assay
eco
lacZ reporter gene assay
ECO:0001802
The assay is often performed using a plasmid borne construction on a lacZ strain.
beta-galactosidase reporter gene assay evidence
A type of reporter gene assay evidence based on the fusion of the lacZ gene to a specific promoter for the expression of beta-galactosidase which will appear blue when grown on a X-gal medium.
ECO:SW
PMID:20439410
A type of reporter gene assay evidence based on the fusion of the CAT gene to a specific promoter for the expression of chloramphenicol acetyltransferase which confers resistance to the chloramphenicol antibiotic.
swolfish
2015-10-29T16:06:42Z
CAT reporter gene assay
eco
ECO:0001803
The amount of acetylated chloramphenicol is directly proportional to the amount of CAT enzyme present.
chloramphenicol acetyltransferase reporter gene assay evidence
A type of reporter gene assay evidence based on the fusion of the CAT gene to a specific promoter for the expression of chloramphenicol acetyltransferase which confers resistance to the chloramphenicol antibiotic.
ECO:SW
PMID:1630936
CAT reporter gene assay
PMID:1630936
A type of reporter gene assay evidence where the beta-glucuronidase enzyme from Escherichia coli is used as the reporter to transform non-fluorescent substrates into fluorescents for detection.
swolfish
2015-10-29T16:11:02Z
GUS reporter gene assay
eco
ECO:0001804
beta-glucuronidase reporter gene assay evidence
A type of reporter gene assay evidence where the beta-glucuronidase enzyme from Escherichia coli is used as the reporter to transform non-fluorescent substrates into fluorescents for detection.
ECO:SW
A type of reporter gene assay evidence where luciferase, an oxidative enzyme, is used as the reporter to detect a gene product with bioluminescence.
swolfish
2015-10-29T16:15:39Z
eco
ECO:0001805
luciferase reporter gene assay evidence
A type of reporter gene assay evidence where luciferase, an oxidative enzyme, is used as the reporter to detect a gene product with bioluminescence.
ECO:SW
PMID:17623934
A type of chromatin immunoprecipitation evidence that uses gama-exonuclease to digest TF-unbound DNA after ChIP for the identification of transcription factor binding site locations with high-resolution data.
swolfish
2015-10-29T16:37:36Z
ChIP-exo
eco
ECO:0001806
chromatin immunoprecipitation- exonuclease evidence
A type of chromatin immunoprecipitation evidence that uses gama-exonuclease to digest TF-unbound DNA after ChIP for the identification of transcription factor binding site locations with high-resolution data.
ECO:SW
PMID:25249628
ChIP-exo
PMID:25249628
A type of electrophoretic mobility shift that is used in a manual assertion.
swolfish
2015-11-03T12:13:17Z
eco
ECO:0001807
electrophoretic mobility shift assay evidence used in manual assertion
true
true
A type of electrophoretic mobility shift that is used in a manual assertion.
ECO:SW
A type of reverse transcription polymerase chain reaction evidence that is used in a manual assertion.
swolfish
2015-11-03T12:22:46Z
eco
ECO:0001808
reverse transcription polymerase chain reaction evidence used in manual assertion
true
true
A type of reverse transcription polymerase chain reaction evidence that is used in a manual assertion.
ECO:SW
A type of chromatography evidence where immobilized promoter DNA is labeled and bound to a matrix through which a protein mixture is poured and then eluted to purify specific DNA binding proteins.
swolfish
2015-11-03T13:48:49Z
eco
DNA affinity purification
ECO:0001809
Biotinylation is commonly used for labeling and beads are commonly used as the matrix. Bound protein will remain attached to the beads. Results can be detected through gel electrophoresis and then sequenced by mass-spectrometry. This technique can be used to demonstrate binding of a purified protein, or to purify the binding protein from crude extract or protein mixture.
DNA affinity chromatography evidence
A type of chromatography evidence where immobilized promoter DNA is labeled and bound to a matrix through which a protein mixture is poured and then eluted to purify specific DNA binding proteins.
ECO:SW
PMID:11694305
PMID:11725488
A type of nucleic acid binding evidence where proteins that have been bound to DNA protect a binding site from enzymatic cleavage with DNAse, thereby detecting protein-DNA interactions.
swolfish
2015-11-03T13:55:15Z
eco
DNase protection
ECO:0001810
In DNAse footingprinting amplified DNA combined with TF and DNAse is electrophoresed for fragment comparison with a non-TF control sample. TF-bound fragments do not appear in the gel. Such fragments can be isolated, purified, and sequenced. This technique is often used to identify the binding motif of a TF resolving the protected region to 50-100 bp which can be further examined for TF-binding sites.
DNAse footprinting evidence
A type of nucleic acid binding evidence where proteins that have been bound to DNA protect a binding site from enzymatic cleavage with DNAse, thereby detecting protein-DNA interactions.
ECO:SW
PMID:212715
PMID:22194258
A type of fluorescence evidence based on rapid and quantitative analysis of diverse molecular interactions, enzyme activities, and nucleic acid hybridization which uses a fluorophore to measure the binding constants and kinetics of reactions that cause a change in the rotational time of the molecules.
swolfish
2015-11-03T14:01:36Z
FA
eco
FP
Fluorescence polarization
ECO:0001811
The degree of polarization of a fluorophore is inversely related to its molecular rotation. When the fluorophore is bound to a small molecule, the rate at which it tumbles can decrease significantly from when it is bound tightly to a large protein. If the fluorophore is attached to the larger protein in a binding pair, the difference in polarization between bound and unbound states will be smaller and less accurate. The degree of binding is calculated by using the difference in anisotropy of the partially bound, free, and fully bound states measured by titrating the two binding partners. Fluorescence polarixation assays are homogeneous.
fluorescence anisotropy evidence
A type of fluorescence evidence based on rapid and quantitative analysis of diverse molecular interactions, enzyme activities, and nucleic acid hybridization which uses a fluorophore to measure the binding constants and kinetics of reactions that cause a change in the rotational time of the molecules.
ECO:SW
PMID:20232898
FP
PMCID:3277431
PMID:20232898
Fluorescence polarization
PMCID:3277431
PMID:20232898
A type of systematic evolution of ligands by exponential amplification evidence based on a restricted genomic DNA library to identify naturally occurring genomic aptamers and RNA-protein interaction networks with RNA-binding protein as bait and high-throughput sequencing.
swolfish
2015-11-03T14:05:37Z
genomic SELEX
eco
ECO:0001812
The reported sequences should always be verified for presence in the genome sequence.
genomic systematic evolution of ligands by exponential amplification evidence
A type of systematic evolution of ligands by exponential amplification evidence based on a restricted genomic DNA library to identify naturally occurring genomic aptamers and RNA-protein interaction networks with RNA-binding protein as bait and high-throughput sequencing.
ECO:SW
PMID:20541015
PMID:21720957
genomic SELEX
PMID:20541015
A type of nuclear magnetic resonance spectroscopy evidence based on two-dimensional NMR for elucidation of the chemical structure of an isolated or synthesized chemical compound where the characteristic transfer magnetization of a proton to a nitrogen or carbon isotope is monitored by NMR, generating a specific peak in the spectrum.
swolfish
2015-11-03T14:11:06Z
HSQC
eco
ECO:0001813
Chemical shifts in the spectrum indicating binding can be detected from analysis of a protein spectrum in the presence or absence of its cognate DNA binding site.
heteronuclear single quantum coherence spectroscopy evidence
A type of nuclear magnetic resonance spectroscopy evidence based on two-dimensional NMR for elucidation of the chemical structure of an isolated or synthesized chemical compound where the characteristic transfer magnetization of a proton to a nitrogen or carbon isotope is monitored by NMR, generating a specific peak in the spectrum.
ECO:SW
PMID:19856946
HSQC
PMID:19856946
A type of nucleic acid binding evidence where the synthetic molecule methidiumpropyl-EDTA (MPE) is used to cleave ligand-protected DNA, followed by analysis of the restriction fragments to generate a footprint (i.e. size and location) of small molecule binding sites on the DNA.
swolfish
2015-11-03T14:24:04Z
eco
MPE Fe(II) footprinting
MPE-EDTA Fe(II) footprinting
Methidiumpropyl-EDTA Fe(II) footprinting
ECO:0001814
methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence
A type of nucleic acid binding evidence where the synthetic molecule methidiumpropyl-EDTA (MPE) is used to cleave ligand-protected DNA, followed by analysis of the restriction fragments to generate a footprint (i.e. size and location) of small molecule binding sites on the DNA.
ECO:SW
PMID:6225070
MPE Fe(II) footprinting
PMID:6225070
MPE-EDTA Fe(II) footprinting
PMID:6225070
Methidiumpropyl-EDTA Fe(II) footprinting
PMID:6225070
A type of nucleic acid binding evidence where nucleic acid that has been bound to protein is cleaved with 1,10-phenanthroline-copper complex resulting in a high-resolution footprint of sequence-specific protein-DNA contacts.
swolfish
2015-11-04T08:37:51Z
1,10-Phenanthroline-copper footprinting
eco
OP-Cu Complex
ECO:0001815
copper-phenanthroline footprinting evidence
A type of nucleic acid binding evidence where nucleic acid that has been bound to protein is cleaved with 1,10-phenanthroline-copper complex resulting in a high-resolution footprint of sequence-specific protein-DNA contacts.
ECO:SW
PMID:11691942
1,10-Phenanthroline-copper footprinting
PMID:1384472
OP-Cu Complex
PMID:1384472
A type of reporter gene assay evidence based on the fusion of select genes with the green fluorescent protein (GFP) gene for detection with bioluminescence of the gene product when exposed to blue ultraviolet light.
swolfish
2015-11-04T08:58:42Z
GFP reporter gene assay
eco
GFP promoter fusion
green fluorescent protein promoter fusion
ECO:0001816
green fluorescent protein reporter gene assay evidence
A type of reporter gene assay evidence based on the fusion of select genes with the green fluorescent protein (GFP) gene for detection with bioluminescence of the gene product when exposed to blue ultraviolet light.
ECO:SW
PMID:11989662
GFP reporter gene assay
PMID:11989662
A type of protein binding evidence where a gene is fused with the GST gene and the resulting recombinant bait protein is captured on an immobilized Glutathione affinity ligand and incubated with prey protein to identify and characterize protein-protein interactions.
swolfish
2015-11-04T09:05:56Z
GST pull-down assay
eco
ECO:0001817
The recombinant protein can also be eluted following the pull-down and analyzed further with qPCR or sequencing.
glutathione S-transferase pull-down assay evidence
A type of protein binding evidence where a gene is fused with the GST gene and the resulting recombinant bait protein is captured on an immobilized Glutathione affinity ligand and incubated with prey protein to identify and characterize protein-protein interactions.
ECO:SW
PMID:26096507
GST pull-down assay
PMID:26096507
A type of nucleic acid binding evidence used to identify protein-binding sites on the DNA molecule where DNA that has been bound to protein is digested with hydroxyl radical produced by reduction of hydrogen peroxide with iron (II), followed by separating the cleavage products on a denaturing electrophoresis gel.
swolfish
2015-11-04T09:20:26Z
eco
ECO:0001818
hydroxyl-radical footprinting evidence
A type of nucleic acid binding evidence used to identify protein-binding sites on the DNA molecule where DNA that has been bound to protein is digested with hydroxyl radical produced by reduction of hydrogen peroxide with iron (II), followed by separating the cleavage products on a denaturing electrophoresis gel.
ECO:SW
PMID:18546600
PMID:19378159
PMID:3090544
A type of transcript expression level evidence used to determine expression levels of mRNA where a radiolabeled synthetic oligonucleotide primer is annealed to mRNA at the transcription start site of a gene and the mRNA is extended with reverse transcriptase producing cDNA which is electrophoresed on a polyacrylamide gel and autoradiographed, and the band size is proportional to the initial RNA.
swolfish
2015-11-04T09:33:18Z
eco
ECO:0001819
The most commonly used radiolabel is 32P.
primer extension assay evidence
A type of transcript expression level evidence used to determine expression levels of mRNA where a radiolabeled synthetic oligonucleotide primer is annealed to mRNA at the transcription start site of a gene and the mRNA is extended with reverse transcriptase producing cDNA which is electrophoresed on a polyacrylamide gel and autoradiographed, and the band size is proportional to the initial RNA.
ECO:SW
PMID:23378648
A type of polymerase chain reaction evidence where a mRNA primer is used for RT-PCR and terminal deoxynucleotidyl transferase (TdT) is used to add identical nucleotides to the 3' end of the cDNA after which PCR with a different primer and TdT-oligomer are performed in the other sense to obtain the full length sequence of a RNA transcript.
swolfish
2015-11-04T09:48:38Z
RACE PCR
eco
ECO:0001820
RACE PCR is frequently used to verify transcription start sites relevant to the function of transcription factor binding sites such as repression.
rapid amplification of cDNA ends polymerase chain reaction evidence
A type of polymerase chain reaction evidence where a mRNA primer is used for RT-PCR and terminal deoxynucleotidyl transferase (TdT) is used to add identical nucleotides to the 3' end of the cDNA after which PCR with a different primer and TdT-oligomer are performed in the other sense to obtain the full length sequence of a RNA transcript.
ECO:SW
PMID:17498297
RACE PCR
PMI:17498297
A type of nucleotide sequencing assay evidence where RNA is extracted from a cell, reverse transcribed to cDNA for a snapshot of an organism's transcriptome with precise measurement of transcript levels and their isoforms.
swolfish
2015-11-04T10:15:57Z
RNA-Seq
WTTS
Whole Transcriptome Shotgun Sequencing
eco
ECO:0001821
Use ECO:0000295 (RNA-seq evidence) in place of this term.
RNA sequencing assay evidence
true
A type of nucleotide sequencing assay evidence where RNA is extracted from a cell, reverse transcribed to cDNA for a snapshot of an organism's transcriptome with precise measurement of transcript levels and their isoforms.
ECO:SW
PMID:19015660
RNA-Seq
PMID:23851085
Whole Transcriptome Shotgun Sequencing
PMID:23851085
A type of knockout evidence based on the survival of an organism in a particular environment where a gene for an enzyme or regulator is knocked out and results are used as a natural reporter.
swolfish
2015-11-04T10:48:59Z
eco
ECO:0001822
survival rate analysis evidence
A type of knockout evidence based on the survival of an organism in a particular environment where a gene for an enzyme or regulator is knocked out and results are used as a natural reporter.
ECO:SW
A type of crystallography evidence where a purified sample at high concentration is crystallised and the crystals are exposed to an x ray beam to obtain three dimensional molecular structure of proteins and biological macromolecules.
swolfish
2015-11-04T10:56:22Z
eco
ECO:0001823
X-ray crystallography can be used for a crystal used to probe at the tridimensional structure of proteins. In some cases, it is possible to co-crystallize the protein bound to its DNA binding site, providing detail on the particular arrangement of the two components.
x-ray crystallography evidence
A type of crystallography evidence where a purified sample at high concentration is crystallised and the crystals are exposed to an x ray beam to obtain three dimensional molecular structure of proteins and biological macromolecules.
ECO:SW
PMID:23135450
PMID:24648090
A type of affinity evidence used to identify DNA binding sites in eukaryotes where Escherichia coli DNA adenine methyltransferase (Dam) is fused to a transcription factor, co-factor, chromatin-associated protein, or nuclear-associated protein, followed by a methyl-dependent PCR to localize methyltransferase in the region of the binding site.
swolfish
2015-11-05T15:56:13Z
DamID
eco
ECO:0001824
The methylation tag is detected with methylation-sensitive restriction enzymes, DpnI and DpnII.
DNA adenine methyltransferase identification evidence
A type of affinity evidence used to identify DNA binding sites in eukaryotes where Escherichia coli DNA adenine methyltransferase (Dam) is fused to a transcription factor, co-factor, chromatin-associated protein, or nuclear-associated protein, followed by a methyl-dependent PCR to localize methyltransferase in the region of the binding site.
ECO:SW
PMID:16938559
PMID:17545983
PMID:19588092
DamID
PMID:19588092
A type of affinity evidence where the absorbed or released heat of a biomolecular binding event is directly measured in a reference cell and sample cell after the addition of a ligand using a microcalorimeter for a complete thermodynamic profile of the molecular interaction.
swolfish
2015-11-05T16:06:20Z
ITC
eco
ECO:0001825
When ITC is used to study TF, the temperature of two identical cells containing a known concentration of TF is monitored. After the ligand is added to the cells in precisely measured aliquots, the temperature difference in each cell is observed to determine target binding. This value can be used to compute the energetics of the reaction and hence, binding affinity of the TF for the DNA fragment. The thermodynamic profile that is measured includes the values of binding constant (K(a)), stoichiometry (n), and the enthalpy of binding (DeltaH(b)).
isothermal titration calorimetry evidence
A type of affinity evidence where the absorbed or released heat of a biomolecular binding event is directly measured in a reference cell and sample cell after the addition of a ligand using a microcalorimeter for a complete thermodynamic profile of the molecular interaction.
ECO:SW
PMID:10527727
ITC
PMID:10527727
A type of nucleic acid binding evidence where DNA is non-specifically fragmented with ultraviolet light while protein-bound regions are protected from UV damage and strand breakage patterns are analyzed by PAGE and sequenced to detect protein-DNA contacts.
swolfish
2015-11-05T16:13:36Z
eco
UV footprinting
ultraviolet footprinting
ECO:0001826
ultraviolet light footprinting evidence
A type of nucleic acid binding evidence where DNA is non-specifically fragmented with ultraviolet light while protein-bound regions are protected from UV damage and strand breakage patterns are analyzed by PAGE and sequenced to detect protein-DNA contacts.
ECO:SW
PMID:2842760
PMID:7602584
A type of nucleic acid binding evidence used to identify protein binding sites on the DNA molecule where multiple copies of a DNA fragment containing a putative TF-binding site are randomly methylated with dimethyl sulfate (DMS) and cleaved at the methyl group, followed by separating the cleavage products on a denaturing electrophoresis gel.
swolfish
2015-11-05T16:16:27Z
eco
methylation interference footprinting
ECO:0001827
premethylation interference footprinting evidence
A type of nucleic acid binding evidence used to identify protein binding sites on the DNA molecule where multiple copies of a DNA fragment containing a putative TF-binding site are randomly methylated with dimethyl sulfate (DMS) and cleaved at the methyl group, followed by separating the cleavage products on a denaturing electrophoresis gel.
ECO:SW
PMID:1583685
A type of inference from background scientific knowledge used in manual assertion where a visual inspection of promoter region is made to identify putative binding sites.
swolfish
2015-11-10T14:40:16Z
eco
ECO:0001828
visual sequence inspection evidence
A type of inference from background scientific knowledge used in manual assertion where a visual inspection of promoter region is made to identify putative binding sites.
ECO:SW
A type of reporter gene assay evidence used to locate and isolate Fur sites where a plasmid library is created and cloned into a cell line with a ferric uptake regulator (Fur)-repressed reporter and the Fur protein is titrated away from its binding site on the reporter, after which the cell is isolated and plasmid extracted for further sequence analysis.
swolfish
2015-11-10T14:55:36Z
FURTA
eco
Fluorescence polarization
ECO:0001829
ferric uptake regulator titration assay evidence
A type of reporter gene assay evidence used to locate and isolate Fur sites where a plasmid library is created and cloned into a cell line with a ferric uptake regulator (Fur)-repressed reporter and the Fur protein is titrated away from its binding site on the reporter, after which the cell is isolated and plasmid extracted for further sequence analysis.
ECO:SW
PMID:10713425
PMID:7642488
PMID:8107138
FURTA
PMID:10713425
Fluorescence polarization
PMID:15689115
A type of in vitro cell based assay evidence resulting from analyzing the difference between the number (estimation) of cells at the start and the remaining viable cells at the end of the assay.
snadendla
2015-02-13T12:08:01Z
eco
ECO:0005004
cell viability assay evidence
A type of in vitro cell based assay evidence resulting from analyzing the difference between the number (estimation) of cells at the start and the remaining viable cells at the end of the assay.
NBK:144065
A type of in vitro cell based assay evidence resulting from the measurement of cell proliferation.
snadendla
2015-02-11T16:27:13Z
eco
ECO:0005007
cell proliferation assay evidence
A type of in vitro cell based assay evidence resulting from the measurement of cell proliferation.
ECO:RCT
A type of cell proliferation assay evidence resulting from the measure of proliferation by estimation of DNA synthesis.
snadendla
2015-02-11T16:30:10Z
eco
ECO:0005008
DNA synthesis cell proliferation assay evidence
A type of cell proliferation assay evidence resulting from the measure of proliferation by estimation of DNA synthesis.
PMC:3908118
A type of cell proliferation assay resulting from the assessment of metabolic activity.
snadendla
2015-02-11T16:36:33Z
eco
ECO:0005009
metabolic cell proliferation assay evidence
A type of cell proliferation assay resulting from the assessment of metabolic activity.
ECO:RCT
snadendla
2015-02-11T16:37:23Z
eco
ECO:0005010
cell proliferation marker detection assay evidence
A type of cell proliferation assay evidence resulting from the analysis of ATP concentration (light intensity) when luciferase catalyzes the oxidation of luciferin in the presence of ATP, magnesium ions and molecular oxygen.
snadendla
2015-02-11T16:47:30Z
eco
ECO:0005011
ATP bioluminescence assay evidence
A type of cell proliferation assay evidence resulting from the analysis of ATP concentration (light intensity) when luciferase catalyzes the oxidation of luciferin in the presence of ATP, magnesium ions and molecular oxygen.
PMID:15344559
snadendla
2015-02-12T11:39:35Z
eco
ECO:0005012
cytotoxicity assay evidence
A type of in vitro assay evidence resulting from the use of live cells.
snadendla
2015-02-12T13:26:55Z
eco
ECO:0005014
in vitro cell based assay evidence
A type of in vitro assay evidence resulting from the use of live cells.
ECO:RCT
A type of direct assay evidence resulting from the use of stains or dyes to aid in analysis of a microscopic image.
snadendla
2015-02-19T11:48:57Z
eco
ECO:0005019
staining evidence
A type of direct assay evidence resulting from the use of stains or dyes to aid in analysis of a microscopic image.
ECO:RCT
A type of in vitro cell based assay evidence resulting from a given chemical substance causing a movement response, or not, in the sample cells or organisms.
snadendla
2015-02-19T13:10:20Z
eco
ECO:0005021
chemotaxis assay evidence
A type of in vitro cell based assay evidence resulting from a given chemical substance causing a movement response, or not, in the sample cells or organisms.
PMC:3667641
A type of mutant phenotype evidence resulting from the conversion of one genotype into another by the introduction of exogenous DNA.
snadendla
2015-03-16T15:33:50Z
eco
ECO:0005027
genetic transformation evidence
A type of mutant phenotype evidence resulting from the conversion of one genotype into another by the introduction of exogenous DNA.
ECO:RCT
A type of experimental evidence resulting from the visualization and examination of chemical and/or molecular structures.
snadendla
2015-03-20T12:16:17Z
eco
ECO:0005031
structure determination evidence
A type of experimental evidence resulting from the visualization and examination of chemical and/or molecular structures.
ECO:RCT
A type of microscopy evidence and structure determination evidence resulting from an electron beam utilized to create an image.
snadendla
2015-03-20T12:21:48Z
eco
ECO:0005033
electron microscopy evidence
A type of microscopy evidence and structure determination evidence resulting from an electron beam utilized to create an image.
ECO:RCT
A type of in vitro cell based assay evidence resulting from the occurrence, visualization, and/or analysis of apoptosis.
snadendla
2015-04-07T21:58:24Z
eco
ECO:0005034
apoptotic assay evidence
A type of in vitro cell based assay evidence resulting from the occurrence, visualization, and/or analysis of apoptosis.
ECO:RCT
A type of in vivo assay evidence where ADP-ribosylated residues in proteins are detected in cells in vivo.
snadendla
2015-06-15T15:35:05Z
eco
ECO:0005500
in vivo polyADP-ribosylation assay evidence
A type of in vivo assay evidence where ADP-ribosylated residues in proteins are detected in cells in vivo.
ECO:SN
PMID:2820766
SIB:PG
A type of in vivo polyADP-ribosylation assay evidence that is used in a manual assertion.
snadendla
2015-06-15T15:37:23Z
eco
ECO:0005501
in vivo polyADP-ribosylation assay evidence used in manual assertion
true
true
A type of in vivo polyADP-ribosylation assay evidence that is used in a manual assertion.
ECO:SN
A type of biological assay evidence derived by studying an organ, tissues, or cells taken from an organism in an external environment with the minimum alteration of natural conditions.
snadendla
2015-06-26T11:46:15Z
eco
ECO:0005502
ex vivo assay evidence
A type of biological assay evidence derived by studying an organ, tissues, or cells taken from an organism in an external environment with the minimum alteration of natural conditions.
ECO:SN
PMID:16305312
url:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2305722/pdf/nihms42807.pdf
A type of gel electrophoresis evidence that involves one dimension electrophoresis where biomolecules are electrophoresed on a low percentage polyacrylamide gel to be separated in proportion to their mass or isoelectric point, followed by high voltage electrophoresis on a higher percentage gel in the presence of ethidium bromide to alter non-linear molecular shape.
snadendla
2015-10-01T16:23:20Z
2D PAGE
2D-PAGE
eco
ECO:0005503
Two-dimensional polyacrylamide gel electrophoresis is commonly employed to establish a proteome for an organism and demonstrate expression changes.
two-dimensional polyacrylamide gel electrophoresis evidence
A type of gel electrophoresis evidence that involves one dimension electrophoresis where biomolecules are electrophoresed on a low percentage polyacrylamide gel to be separated in proportion to their mass or isoelectric point, followed by high voltage electrophoresis on a higher percentage gel in the presence of ethidium bromide to alter non-linear molecular shape.
ECO:SW
url:http://www.nature.com/nmeth/journal/v2/n1/full/nmeth0105-83.html
A type of experimental evidence resulting from the use of a spectrometer.
snadendla
2015-08-14T15:48:08Z
eco
ECO:0005504
spectrometry evidence
A type of experimental evidence resulting from the use of a spectrometer.
ECO:RCT
A type of motif similarity evidence where the motif, a local alignment of sequences, is represented by a regular expression, which captures the variability of nucleotides at each position in a discrete form and can then be used to search genetic sequences by identifying matches to the regular expression.
snadendla
2015-10-09T13:51:52Z
eco
ECO:0005505
Regular expression is a computational tool used for determining whether a given genome contains a DNA region resembling a transcription factor binding motif. For example A/T=W indicates A or T may be present in a column of the alignment. (PMID: 20708667).
regular expression motif search evidence
A type of motif similarity evidence where the motif, a local alignment of sequences, is represented by a regular expression, which captures the variability of nucleotides at each position in a discrete form and can then be used to search genetic sequences by identifying matches to the regular expression.
ECO:SW
PMID:17337630
A type of point mutation evidence resulting from a change in a base (or bases) causing the substitution of one amino acid for another.
snadendla
2015-09-18T16:52:34Z
eco
ECO:0005506
missense mutation evidence
A type of point mutation evidence resulting from a change in a base (or bases) causing the substitution of one amino acid for another.
SO:0001583
A type of point mutation evidence resulting in an incomplete and usually nonfunctional protein product because of a premature stop codon.
snadendla
2015-09-18T16:55:32Z
eco
ECO:0005507
nonsense mutation evidence
A type of point mutation evidence resulting in an incomplete and usually nonfunctional protein product because of a premature stop codon.
url:https://ghr.nlm.nih.gov/primer/mutationsanddisorders/possiblemutations
A type of point mutation evidence resulting from the change of a DNA nucleotide that does not cause any changes in the amino acid sequence.
snadendla
2015-09-18T17:01:12Z
eco
ECO:0005508
silent mutation evidence
A type of point mutation evidence resulting from the change of a DNA nucleotide that does not cause any changes in the amino acid sequence.
url:http://www.sciencemag.org/news/2006/12/sound-silent-mutation
A type of experimental phenotypic evidence resulting from a mutation in which there is an insertion of an additional nucleotide, or nucleotides.
snadendla
2015-09-18T17:02:03Z
eco
ECO:0005509
insertion mutation evidence
A type of experimental phenotypic evidence resulting from a mutation in which there is an insertion of an additional nucleotide, or nucleotides.
GO:0070705
A type of experimental phenotypic evidence resulting from a mutation in which inserted nucleotide(s) have a sequence identical to, or derived from, adjacent nucleotides.
snadendla
2015-09-18T17:03:25Z
eco
ECO:0005511
duplication mutation evidence
A type of experimental phenotypic evidence resulting from a mutation in which inserted nucleotide(s) have a sequence identical to, or derived from, adjacent nucleotides.
SO:1000035
A type of experimental phenotypic evidence resulting from any mutation that causes a shift in bases and therefore changes the code for the amino acids.
snadendla
2015-09-18T17:05:49Z
eco
ECO:0005512
frameshift mutation evidence
A type of experimental phenotypic evidence resulting from any mutation that causes a shift in bases and therefore changes the code for the amino acids.
url:https://ghr.nlm.nih.gov/primer/mutationsanddisorders/possiblemutations
A type of experimental phenotypic evidence resulting from a mutation that increases the number of times that a DNA sequence is repeated.
snadendla
2015-09-18T17:06:34Z
eco
ECO:0005513
repeat expansion mutation evidence
A type of experimental phenotypic evidence resulting from a mutation that increases the number of times that a DNA sequence is repeated.
PMID:9397685
url:https://ghr.nlm.nih.gov/primer/mutationsanddisorders/possiblemutations
A type of experimental phenotypic evidence resulting from a mutation in which there is a change in nucleotides at a splice site
snadendla
2015-09-18T17:07:29Z
eco
ECO:0005514
splice site mutation evidence
A type of experimental phenotypic evidence resulting from a mutation in which there is a change in nucleotides at a splice site
ECO:RCT
A type of experimental phenotypic evidence resulting from a mutation in which a region of a chromosome is transferred to a nonhomologous chromosome
snadendla
2015-09-18T17:08:01Z
eco
ECO:0005515
translocation mutation evidence
A type of experimental phenotypic evidence resulting from a mutation in which a region of a chromosome is transferred to a nonhomologous chromosome
ECO:RCT
A type of experimental evidence resulting from the detection and analysis of molecular markers.
snadendla
2015-09-24T15:54:21Z
eco
ECO:0005516
molecule detection assay evidence
A type of experimental evidence resulting from the detection and analysis of molecular markers.
ECO:RCT
A type of molecule detection assay evidence resulting from the detection and quantification of a protein, or multiple proteins.
snadendla
2015-09-25T14:27:40Z
eco
ECO:0005517
protein detection assay evidence
A type of molecule detection assay evidence resulting from the detection and quantification of a protein, or multiple proteins.
ECO:RCT
A type of molecule detection assay evidence resulting from the detection of specific RNAs.
snadendla
2015-09-25T14:43:53Z
eco
ECO:0005518
RNA detection assay evidence
A type of molecule detection assay evidence resulting from the detection of specific RNAs.
ECO:RCT
A type of molecule detection assay evidence resulting from the detection and visualization of a sequence of DNA.
snadendla
2015-09-25T19:33:25Z
eco
ECO:0005519
DNA detection assay evidence
A type of molecule detection assay evidence resulting from the detection and visualization of a sequence of DNA.
ECO:RCT
A type of molecule detection assay evidence based on changes in surface-reflected light due to ligand binding on the surface of a semi-transparent substrate to detect proteins, DNA, and other biological material in a multiplexed, high-throughput microarray format without labels.
snadendla
2015-09-28T16:01:01Z
IRIS
SRIB
Spectral Reflectance Imaging Biosensor
eco
ECO:0005520
Differences in the optical path lengths between a surface layer and a buried silica layer can be measured very precisely allowing optical height information to be converted to accumulated mass on the surface. For the purpose of TF-binding site identification, IRIS is coupled with DNA-arrays with immobilized potential binding regions exposed to the protein of interest and eluted. Protein-bound fragments exhibit changes in reflectance that can be used to gauge binding quantitatively.
interferometric reflectance imaging sensor evidence
A type of molecule detection assay evidence based on changes in surface-reflected light due to ligand binding on the surface of a semi-transparent substrate to detect proteins, DNA, and other biological material in a multiplexed, high-throughput microarray format without labels.
ECO:SW
PMID:21587155
PMID:24271115
A type of nuclease protection assay evidence where RNA is hybridized with complementary DNA probes and exposed to S1 nuclease for unbound RNA degradation after which the intact RNA is run on a gel for probe size determination and RNA identification to detect and map specific RNAs in a complex mixture of total cellular RNA.
snadendla
2015-09-28T17:16:56Z
eco
ECO:0005521
S1 nuclease protection assay evidence
A type of nuclease protection assay evidence where RNA is hybridized with complementary DNA probes and exposed to S1 nuclease for unbound RNA degradation after which the intact RNA is run on a gel for probe size determination and RNA identification to detect and map specific RNAs in a complex mixture of total cellular RNA.
ECO:SW
PMID:21390683
A type of DNA detection assay evidence resulting from evaluation of the relative abundance of target sequences hybridizing to DNA samples that are immobilized on a nitrocellulose or nylon membrane.
snadendla
2015-09-30T10:03:03Z
eco
ECO:0005522
DNA dot blot assay evidence
A type of DNA detection assay evidence resulting from evaluation of the relative abundance of target sequences hybridizing to DNA samples that are immobilized on a nitrocellulose or nylon membrane.
PMID:18265189
A type of DNA dot blot assay evidence that is used in a manual assertion.
snadendla
2015-09-30T10:04:00Z
eco
ECO:0005523
DNA dot blot assay evidence used in manual assertion
true
true
A type of DNA dot blot assay evidence that is used in a manual assertion.
ECO:SN
ECO:SW
A type of DNA detection assay evidence where complimentary ssDNA is attached to a solid glass, silicon, or plastic surface and is hybridized with a labeled sample of extracted mRNA or amplified cDNA and stimulated with a laser for fluorescence detected with a scanner.
snadendla
2015-09-30T10:12:48Z
eco
DNA chip
DNA-array expression analysis
ECO:0005524
The mRNA extraction is performed in induced and non-induced cells and reverse transcribed with different fluorophore labeling for controls and experiment. Fluorescence is measured at two different wavelengths and the ratio between the two fluorescence intensities corresponds to the induction level.
DNA microarray evidence
A type of DNA detection assay evidence where complimentary ssDNA is attached to a solid glass, silicon, or plastic surface and is hybridized with a labeled sample of extracted mRNA or amplified cDNA and stimulated with a laser for fluorescence detected with a scanner.
ECO:SW
PMID:17660860
DNA chip
PMID:10398077
A type of DNA microarray evidence that is used in a manual assertion.
snadendla
2015-09-30T10:13:09Z
eco
ECO:0005525
DNA microarray evidence used in manual assertion
true
true
A type of DNA microarray evidence that is used in a manual assertion.
ECO:SN
ECO:SW
A type of protein detection assay evidence where soft ionization is used for the analysis of biomolecules for mass determination in a three step process of plate preparation, radiation, and ionization with high throughput technology.
snadendla
2015-09-30T10:51:56Z
MALDI-TOF Mass Spectrometry
MALDI-TOF-MS
eco
ECO:0005526
MALDI-TOF MS is commonly used for protein identification in constructing a proteome where protein fingerprints obtained by microbial cells are compared with a database of reference spectra by means of various algorithms integrated in systems recently made commercially available.
matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence
A type of protein detection assay evidence where soft ionization is used for the analysis of biomolecules for mass determination in a three step process of plate preparation, radiation, and ionization with high throughput technology.
ECO:SW
PMID:21964792
PMID:25354905
A type of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence that is used in a manual assertion.
snadendla
2015-09-30T10:58:51Z
eco
ECO:0005527
matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence used in manual assertion
true
true
A type of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence that is used in a manual assertion.
ECO:SN
ECO:SW
A type of experimental phenotypic evidence based on target-specified mutagenesis for the characterization of various gene and protein interactions, structures, and functions where oligonucleotide primers are used to alter a nucleotide sequence.
snadendla
2015-09-30T11:34:41Z
site directed mutagenesis
eco
ECO:0005528
Site-directed mutagenesis is often performed in tandem with EMSA. It is often implemented only in conserved motif positions or serially through all positions of a site.
site-directed mutagenesis evidence
A type of experimental phenotypic evidence based on target-specified mutagenesis for the characterization of various gene and protein interactions, structures, and functions where oligonucleotide primers are used to alter a nucleotide sequence.
ECO:SW
PMID:21204030
PMID:24011050
PMID:3541892
A type of experimental phenotypic evidence where radiation or a DNA-damaging agent in vivo, or PCR with degenerate primers in vitro are used for non-targeted mutagenesis.
snadendla
2015-09-30T11:55:03Z
eco
ECO:0005529
Random mutagenesis is not often used in TF-binding site determination; however, it is sometimes used to investigate the effect of mutations in TF binding domains in conjunction with expression assays. Random mutations can also be introduced via chemicals, error-prone PCR (EP-PCR), degenerate oligonucleotides-Pfu(DOP), UV irradiation, mutator strains, nucleotide analogs, or DNA recombination.
random mutagenesis evidence
A type of experimental phenotypic evidence where radiation or a DNA-damaging agent in vivo, or PCR with degenerate primers in vitro are used for non-targeted mutagenesis.
ECO:SW
PMID:15153637
PMID:18265275
A type of random mutagenesis evidence that is used in a manual assertion.
snadendla
2015-09-30T11:57:00Z
eco
ECO:0005530
random mutagenesis evidence used in manual assertion
true
true
A type of multiple sequence alignment evidence based on a set of algorithms that infer over-represented motifs from a set of biological sequences returning one or more local multiple sequence alignment defining the inferred motifs.
snadendla
2015-09-30T15:04:45Z
eco
ECO:0005531
Relationship type between sequences (e.g. orthologs from multiple genomes or co-expressed genes in the same genome) is not necessarily assumed. The local multiple sequence alignment is typically ungapped. A common application of motif discovery is to infer the binding motif of a given transcription factor (TF). This can be based on the results of a whole-genome expression analysis, assuming that co-expressed genes are co-regulated by the same TF, from peaks in ChIP-seq experiments with the TF, or from the comparative genomics analysis of the promoter regions of orthologs.
motif discovery evidence
A type of multiple sequence alignment evidence based on a set of algorithms that infer over-represented motifs from a set of biological sequences returning one or more local multiple sequence alignment defining the inferred motifs.
ECO:SW
PMID:10812473
PMID:16845028
PMID:8211139
Relationship type between sequences (e.g. orthologs from multiple genomes or co-expressed genes in the same genome) is not necessarily assumed. The local multiple sequence alignment is typically ungapped. A common application of motif discovery is to infer the binding motif of a given transcription factor (TF). This can be based on the results of a whole-genome expression analysis, assuming that co-expressed genes are co-regulated by the same TF, from peaks in ChIP-seq experiments with the TF, or from the comparative genomics analysis of the promoter regions of orthologs.
PMID:19892760
PMID:23032607
A type of motif similarity evidence where the motif is represented by a consensus sequence which incorporates the most frequent nucleotide at each position acting as a generic representative for the sequences in the alignment, and is compared to the genetic sequence for a perfect or imperfect match.
snadendla
2015-10-09T14:12:54Z
eco
ECO:0005532
This technique is used to identify transcription factor binding sites by searching a bacterial genome for DNA regions resembling a given TF-binding motif. PMID: 17085555.
consensus search evidence
A type of motif similarity evidence where the motif is represented by a consensus sequence which incorporates the most frequent nucleotide at each position acting as a generic representative for the sequences in the alignment, and is compared to the genetic sequence for a perfect or imperfect match.
ECO:SW
PMID:15130839
A type of motif discovery evidence based on a set of algorithms that infer motifs in non-coding DNA sequences from the conservation of functional regulatory sites through evolution at a higher rate than their local surroundings for the identification of an evolutionary 'footprint'.
snadendla
2015-09-30T16:23:02Z
eco
ECO:0005533
The name derives to experimental footprinting techniques where transcription factor (TF)-binding sites are identified by sequencing the region of DNA protected from biochemical agents by the bound TF. This technique is used to identify or verify transcription factor-binding motifs, most commonly in the Eukaryota (PMID: 11997340).
phylogenetic footprinting evidence
A type of motif discovery evidence based on a set of algorithms that infer motifs in non-coding DNA sequences from the conservation of functional regulatory sites through evolution at a higher rate than their local surroundings for the identification of an evolutionary 'footprint'.
ECO:SW
PMID:16477324
PMID:3199442
A type of motif similarity evidence based on comparative genomics which uses a search method to scan a set of genomes for instances of a specific motif, and then applies a comparative criterion to analyze the collective strength of these predictions, based on the assumption that functional instances of the motif will be preserved by natural selection and their prediction will therefore be consistent across genomes.
snadendla
2015-10-09T14:30:38Z
eco
ECO:0005534
This technique is used to predict transcription factor binding sites in gene promoter regions by identifying conserved DNA regions across multiple genomes. PMID: 22305460. Orthology is a typical comparative criterion used.
comparative genomics motif search evidence
A type of motif similarity evidence based on comparative genomics which uses a search method to scan a set of genomes for instances of a specific motif, and then applies a comparative criterion to analyze the collective strength of these predictions, based on the assumption that functional instances of the motif will be preserved by natural selection and their prediction will therefore be consistent across genomes.
ECO:SW
PMID:10854408
A type of match to sequence model evidence which captures the application of a broad suite of supervised and unsupervised machine learning algorithms trained on known motif instances and applied to the prediction of novel putative instances of a motif in a set of biological sequences.
snadendla
2015-10-01T11:58:36Z
eco
ECO:0005535
Machine learning algorithms include, but are not limited to artificial neural networks, random-forest, k-means clustering, hidden Markov models. This suite of methods can be used to identify or verify transcription factor-binding sites in genomic sequences (PMID: 15703297).
machine learning prediction of motif instance evidence
A type of match to sequence model evidence which captures the application of a broad suite of supervised and unsupervised machine learning algorithms trained on known motif instances and applied to the prediction of novel putative instances of a motif in a set of biological sequences.
ECO:SW
PMID:17117497
PMID:2014171
A type of motif similarity evidence where the motif is represented by a position-specific frequency matrix (PSFM) that specifies the frequency of each base at each position of the motif, from which a position-specific scoring matrix (PSSM) can be derived under the framework of a log-likelihood ratio providing a scoring system based on the likelihood of a sequence given the motif, versus a genomic-frequency based null hypothesis.
snadendla
2015-10-09T15:04:35Z
PSSM motif search
PSSM
eco
ECO:0005536
This technique is used to predict transcription factor binding sites in gene promoter regions by using a position weight matrix approach. (PMID: 15604457).
position-specific scoring matrix motif search evidence
A type of motif similarity evidence where the motif is represented by a position-specific frequency matrix (PSFM) that specifies the frequency of each base at each position of the motif, from which a position-specific scoring matrix (PSSM) can be derived under the framework of a log-likelihood ratio providing a scoring system based on the likelihood of a sequence given the motif, versus a genomic-frequency based null hypothesis.
ECO:SW
PMID:10812473
A type of reporter gene assay evidence based on the fusion of the xylE gene to a specific promoter for the expression of catechol 2,3-dioxygenase that converts the colorless catechol substrate to yellow 2-hydroxymuconic semialdehyde for identification of the expression of a particular gene.
snadendla
2015-10-28T15:31:28Z
eco
ECO:0005537
xylE reporter gene assay evidence
A type of reporter gene assay evidence based on the fusion of the xylE gene to a specific promoter for the expression of catechol 2,3-dioxygenase that converts the colorless catechol substrate to yellow 2-hydroxymuconic semialdehyde for identification of the expression of a particular gene.
ECO:SW
PMID:2592344
snadendla
2015-11-17T15:15:50Z
eco
ECO:0005538
computationally derived logical inference
true
snadendla
2015-11-17T15:17:47Z
eco
ECO:0005539
computationally derived logical inference used in automatic assertion
true
snadendla
2015-11-17T15:24:42Z
eco
ECO:0005540
computationally derived logical inference from automatic assertion used in automatic assertion
true
snadendla
2015-11-17T15:32:03Z
eco
ECO:0005541
computationally derived logical inference from manual assertion used in automatic assertion
true
A type of biological system reconstruction evidence by experimental evidence from single species that is used in a manual assertion.
snadendla
2015-12-16T15:32:41Z
eco
ECO:0005542
Processes, pathways and complexes shown by a single experiment should not be annotated with this term but with ECO:0000353 or a child thereof.
biological system reconstruction evidence by experimental evidence from single species used in manual assertion
true
true
A type of biological system reconstruction evidence by experimental evidence from single species that is used in a manual assertion.
ECO:SN
PMID:19450514
A type of biological system reconstruction evidence by experimental evidence from mixed species that is used in a manual assertion.
snadendla
2015-12-16T15:45:01Z
eco
ECO:0005543
Inference is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. The evidence may originate from a combination of several experiments.
biological system reconstruction evidence by experimental evidence from mixed species used in manual assertion
true
true
A type of biological system reconstruction evidence by experimental evidence from mixed species that is used in a manual assertion.
ECO:SN
PMID:22232657
A type of biological system reconstruction evidence based on orthology evidence that is used in a manual assertion.
snadendla
2015-12-18T16:20:49Z
eco
ECO:0005544
Inference is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. Evidence may originate from a combination of several experiments.
biological system reconstruction evidence based on orthology evidence used in manual assertion
true
A type of biological system reconstruction evidence based on orthology evidence that is used in a manual assertion.
ECO:SN
A type of biological system reconstruction evidence based on homology evidence where the evidence is inferred by orthology from an existing experimentally supported model to a process, pathway or complex in another species.
snadendla
2015-12-16T15:57:37Z
eco
ECO:0005545
Inference is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. Evidence may originate from a combination of several experiments.
biological system reconstruction evidence based on orthology evidence
A type of biological system reconstruction evidence based on homology evidence where the evidence is inferred by orthology from an existing experimentally supported model to a process, pathway or complex in another species.
ECO:SN
PMID:15660128
A type of biological system reconstruction evidence based on paralogy evidence that is used in a manual assertion.
snadendla
2015-12-16T16:05:15Z
eco
ECO:0005546
Inference is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. Evidence may originate from a combination of several experiments.
biological system reconstruction evidence based on paralogy evidence used in manual assertion
true
A type of biological system reconstruction evidence based on paralogy evidence that is used in a manual assertion.
ECO:SN
PMID:15660128
A type of biological system reconstruction evidence based on inference from background scientific knowledge that is used in a manual assertion.
snadendla
2015-12-16T16:07:42Z
eco
ECO:0005547
Functional studies or ligand binding evidence are often used for the reconstruction of biological systems. It does not provide physical interaction evidence but uses proxies such a ligand binding evidences to infer the presence or absence of the complex components.
biological system reconstruction evidence based on inference from background scientific knowledge used in manual assertion
true
true
A type of biological system reconstruction evidence based on inference from background scientific knowledge that is used in a manual assertion.
ECO:SN
PMID:17876790
A type of biological system reconstruction based solely on background scientific knowledge of that biological system.
snadendla
2015-12-18T15:32:15Z
eco
ECO:0005548
The available knowledge is usually a combination of partial or weak experimental evidence where either some components are missing or no physical interaction evidence can be found but the system is inferred by similarity to related systems in taxonomically-disparate organisms with experimental evidence. Functional studies or ligand binding evidence are often used for the reconstruction of biological systems. It does not provide physical interaction evidence but uses proxies such a ligand binding evidences to infer the presence or absence of the complex components.
biological system reconstruction evidence based on inference from background scientific knowledge
A type of biological system reconstruction based solely on background scientific knowledge of that biological system.
ECO:SN
PMID:17876790
A type of biological system reconstruction where the evidence is inferred by homology based on conservation of sequence, function, and composition from an existing experimentally supported model to a process, pathway, or complex.
snadendla
2015-12-18T15:49:46Z
eco
ECO:0005549
Inference may be based on paralogy and/or orthology of the genome-encoded components and is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. Evidence may originate from a combination of several experiments in the same or another species.
biological system reconstruction evidence based on homology evidence
A type of biological system reconstruction where the evidence is inferred by homology based on conservation of sequence, function, and composition from an existing experimentally supported model to a process, pathway, or complex.
ECO:SN
PMID:15660128
A type of biological system reconstruction evidence based on homology evidence where the evidence is inferred by paralogy from an existing experimentally supported model to a process, pathway, or complex in the same species.
snadendla
2015-12-18T16:24:08Z
eco
ECO:0005550
Inference is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. Evidence may originate from a combination of several experiments.
biological system reconstruction evidence based on paralogy evidence
A type of biological system reconstruction evidence based on homology evidence where the evidence is inferred by paralogy from an existing experimentally supported model to a process, pathway, or complex in the same species.
ECO:SN
PMID:15660128
A type of biological system reconstruction evidence that uses experimental evidence as support.
snadendla
2015-12-18T16:34:13Z
eco
ECO:0005551
biological system reconstruction evidence by experimental evidence
A type of biological system reconstruction evidence that uses experimental evidence as support.
ECO:SN
PMID:19450514
PMID:22232657
A type of biological system reconstruction evidence where the experimental evidence is derived by using a mix of species used in the same experiment.
snadendla
2015-12-18T16:35:13Z
eco
ECO:0005552
Inference is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. The evidence may originate from a combination of several experiments.
biological system reconstruction evidence by experimental evidence from mixed species
A type of biological system reconstruction evidence where the experimental evidence is derived by using a mix of species used in the same experiment.
ECO:SN
PMID:22232657
A type of biological system reconstruction where the experimental evidence is derived by using multiple experiments in a single species.
snadendla
2015-12-18T16:36:44Z
eco
ECO:0005553
Processes, pathways and complexes shown by a single experiment should not be annotated with this term but with ECO:0000353 or a child thereof.
biological system reconstruction evidence by experimental evidence from single species
A type of biological system reconstruction where the experimental evidence is derived by using multiple experiments in a single species.
ECO:SN
A type of sequence alignment evidence where two sequences are aligned to identify regions of similarity that may indicate functional, structural and/or evolutionary relationships between two biological sequences (protein or nucleic acid).
snadendla
2016-02-08T14:30:46Z
eco
ECO:0005554
pairwise sequence alignment evidence
A type of sequence alignment evidence where two sequences are aligned to identify regions of similarity that may indicate functional, structural and/or evolutionary relationships between two biological sequences (protein or nucleic acid).
ECO:SN
url:http://www.ebi.ac.uk/Tools/psa/
A type of sequence alignment evidence where three or more biological sequences (protein or nucleic acid) of similar length are aligned to infer homology and the evolutionary relationships between the sequences studied.
snadendla
2016-02-08T14:31:24Z
eco
ECO:0005555
multiple sequence alignment evidence
A type of sequence alignment evidence where three or more biological sequences (protein or nucleic acid) of similar length are aligned to infer homology and the evolutionary relationships between the sequences studied.
ECO:SN
url:http://www.ebi.ac.uk/Tools/msa/
A type of multiple sequence alignment evidence that is used in a manual assertion.
snadendla
2016-02-08T14:59:18Z
eco
ECO:0005556
multiple sequence alignment evidence used in manual assertion
true
true
A type of multiple sequence alignment evidence that is used in a manual assertion.
ECO:SN
A type of multiple sequence alignment evidence that is used in an automatic assertion.
snadendla
2016-02-08T15:00:50Z
eco
ECO:0005557
multiple sequence alignment evidence used in automatic assertion
true
true
A type of multiple sequence alignment evidence that is used in an automatic assertion.
ECO:SN
A type of motif discovery evidence that is used in a manual assertion.
snadendla
2016-02-08T15:07:47Z
eco
ECO:0005558
motif discovery evidence used in manual assertion
true
true
A type of motif discovery evidence that is used in a manual assertion.
ECO:SN
A type of motif discovery evidence that is used in an automatic assertion.
snadendla
2016-02-08T15:08:19Z
eco
ECO:0005559
motif discovery evidence used in automatic assertion
true
true
A type of motif discovery evidence that is used in an automatic assertion.
ECO:SN
A type of pairwise sequence alignment evidence that is used in a manual assertion.
snadendla
2016-02-08T15:17:05Z
eco
ECO:0005560
pairwise sequence alignment evidence used in manual assertion
true
true
A type of pairwise sequence alignment evidence that is used in a manual assertion.
ECO:SN
A type of pairwise sequence alignment evidence that is used in an automatic evidence.
snadendla
2016-02-08T15:17:52Z
eco
ECO:0005561
pairwise sequence alignment evidence used in automatic assertion
true
true
A type of pairwise sequence alignment evidence that is used in an automatic evidence.
ECO:SN
A type of in vitro assay evidence resulting from the evaluation of the phosphorylation activity of kinase on a gel-incorporated substrate.
snadendla
2016-02-09T12:05:29Z
eco
ECO:0005562
in gel protein kinase assay evidence
A type of in vitro assay evidence resulting from the evaluation of the phosphorylation activity of kinase on a gel-incorporated substrate.
PMID:12372853
A type of voltage clamp recording evidence that involves recording trace of the current (pA) going through the analyzed ion channels determined from voltage clamp current recording.
snadendla
2016-02-09T12:40:03Z
eco
ECO:0005563
macroscopic current trace evidence
A type of voltage clamp recording evidence that involves recording trace of the current (pA) going through the analyzed ion channels determined from voltage clamp current recording.
ECO:SN
PMID:17938230
url:http://www.utdallas.edu/~tres/microelectrode/microelectrodes_ch03.pdf
A type of electrophysiology assay evidence that involves measuring the amount of current (pA) going through the ion channels per unit of membrane.
snadendla
2016-02-09T12:43:07Z
eco
ECO:0005564
current density evidence
A type of electrophysiology assay evidence that involves measuring the amount of current (pA) going through the ion channels per unit of membrane.
ECO:SN
url:http://circres.ahajournals.org/content/102/11/1298.full
url:http://www.bem.fi/book/04/04.htm
snadendla
2016-02-09T12:45:42Z
eco
ECO:0005565
single channel conductance evidence
true
A type of electrophysiology assay evidence that involves the measurement of the current that persists after the fast and slow inactivation of the analyzed channels.
snadendla
2016-02-09T12:46:54Z
eco
ECO:0005566
sustained current evidence
A type of electrophysiology assay evidence that involves the measurement of the current that persists after the fast and slow inactivation of the analyzed channels.
ECO:SN
url:http://www.nature.com/ncomms/journal/v3/n2/full/ncomms1717.html
snadendla
2016-02-09T12:48:17Z
eco
ECO:0005567
steady state activation curve evidence
true
snadendla
2016-02-09T12:50:45Z
eco
ECO:0005568
steady state inactivation curve evidence
true
snadendla
2016-02-09T12:57:16Z
eco
ECO:0005569
window current trace evidence
true
A type of electrophysiology assay evidence in which the amount of current remaining after a series of depolarization at different frequencies described as the normalized current related to the time course.
snadendla
2016-02-09T12:58:18Z
eco
ECO:0005570
use dependence of inactivation evidence
A type of electrophysiology assay evidence in which the amount of current remaining after a series of depolarization at different frequencies described as the normalized current related to the time course.
ECO:SN
url:http://circres.ahajournals.org/content/89/8/700.full
A type of electrophysiology assay evidence that involves recording the change in membrane potential caused by applying specific current to the cell.
snadendla
2016-02-12T13:58:32Z
birnlex:2278
current clamp voltage recording evidence
eco
ECO:0005571
current clamp recording evidence
A type of electrophysiology assay evidence that involves recording the change in membrane potential caused by applying specific current to the cell.
ECO:SN
url:http://www.nature.com/nprot/journal/v4/n8/full/nprot.2009.91.html
birnlex:2278
current clamp voltage recording protocol
A type of voltage clamp recording evidence that involves direct measurement of ionic current across a membrane while controlling the membrane potential by maintaining the voltage.
snadendla
2016-02-12T14:06:40Z
birnlex:2281
eco
ECO:0005572
whole-cell voltage clamp recording evidence
A type of voltage clamp recording evidence that involves direct measurement of ionic current across a membrane while controlling the membrane potential by maintaining the voltage.
ECO:SN
url:http://circres.ahajournals.org/content/72/1/91.full.pdf
birnlex:2281
whole-cell voltage clamp recording protocol
A type of patch-clamp recording evidence that involves isolation of a patch of membrane electrically from the external solution and to record current flowing into the patch and this is achieved by pressing a fire-polished glass pipette, which has been filled with a suitable electrolyte solution, against the surface of a cell and applying light suction.
snadendla
2016-02-12T14:07:39Z
birnlex:2283
cell-attached patch-clamp recording evidence
eco
ECO:0005573
cell-attached single-channel recording evidence
A type of patch-clamp recording evidence that involves isolation of a patch of membrane electrically from the external solution and to record current flowing into the patch and this is achieved by pressing a fire-polished glass pipette, which has been filled with a suitable electrolyte solution, against the surface of a cell and applying light suction.
ECO:SN
url:http://www.utdallas.edu/~tres/microelectrode/microelectrodes_ch04.pdf
birnlex:2283
cell-attached single-channel recording protocol
A type of patch-clamp recording evidence that involves study of individual ion channels by gently pulling the patch of membrane away from the cell, and the patch remains attached to the pipette with its cytoplasmic surface exposed to the bathing solution.
snadendla
2016-02-12T14:16:53Z
birnlex:2286
cell-detached inside-out patch-clamp recording evidence
eco
ECO:0005574
cell-detached inside-out single-channel recording evidence
A type of patch-clamp recording evidence that involves study of individual ion channels by gently pulling the patch of membrane away from the cell, and the patch remains attached to the pipette with its cytoplasmic surface exposed to the bathing solution.
ECO:SN
url:http://www.acnp.org/g4/GN401000005/CH005.html
birnlex:2286
cell-detached inside-out single-channel recording protocol
A type of patch-clamp reocrding evidence that involves ion channel analysis by incorporating the ion channels into liposomes suitable for patch-clamping which allows isolation and study of a specific population of channels into that bilayer membrane.
snadendla
2016-02-12T14:17:46Z
birnlex:2287
eco
ECO:0005575
reconstituted bilayer single-channel patch recording evidence
A type of patch-clamp reocrding evidence that involves ion channel analysis by incorporating the ion channels into liposomes suitable for patch-clamping which allows isolation and study of a specific population of channels into that bilayer membrane.
ECO:SN
url:http://nanion.de/images/stories/papers/Bilayers_lab-on-a-chip08.pdf
birnlex:2287
reconstituted bilayer single-channel patch recording protocol
A type of electrophysiology assay evidence that involves recording membrane potential by controlling the membrane voltage and measuring the transmembrane current required to maintain that voltage.
snadendla
2016-02-12T14:18:36Z
birnlex:2279
voltage clamp current recording evidence
eco
ECO:0005576
voltage clamp recording evidence
A type of electrophysiology assay evidence that involves recording membrane potential by controlling the membrane voltage and measuring the transmembrane current required to maintain that voltage.
ECO:SN
url:http://neurobio.drexelmed.edu/GaoWeb/Resources/Recording%20_Techniques.pdf
url:http://www.acnp.org/g4/GN401000005/CH005.html
birnlex:2279
voltage clamp current recording protocol
A type of electrophysiology assay evidence that involves recording the electrical activity of the brain by means of electrodes placed on the surface of the head.
snadendla
2016-02-12T14:19:21Z
birnlex:2293
eco
ECO:0005577
electroencephalography recording evidence
A type of electrophysiology assay evidence that involves recording the electrical activity of the brain by means of electrodes placed on the surface of the head.
ECO:SN
url:http://www.jove.com/science-education/5420/electro-encephalography-eeg
birnlex:2293
electroencephalography recording protocol
A type of microscopy evidence where the images are taken with a higher resolution than the diffraction limit that help in studying nanoscopic sub-cellular structures.
snadendla
2016-02-12T15:20:47Z
eco
ECO:0005578
super-resolution microscopy evidence
A type of microscopy evidence where the images are taken with a higher resolution than the diffraction limit that help in studying nanoscopic sub-cellular structures.
ECO:SN
url:http://journal.frontiersin.org/article/10.3389/fncel.2015.00007/full
A type of immunogold labelling evidence that is used in a manual assertion.
snadendla
2016-02-12T15:38:03Z
eco
ECO:0005579
immunogold labelling evidence used in manual assertion
true
true
A type of immunogold labelling evidence that is used in a manual assertion.
ECO:SN
A type of flow cytometry evidence that is used in a manual assertion.
snadendla
2016-02-12T16:04:23Z
eco
ECO:0005580
flow cytometry evidence used in manual assertion
true
true
A type of flow cytometry evidence that is used in a manual assertion.
ECO:SN
A type of enzyme-linked immunoabsorbent assay evidence that is used in a manual assertion.
snadendla
2016-02-12T16:23:38Z
eco
ECO:0005581
enzyme-linked immunoabsorbent assay evidence used in manual assertion
true
true
A type of enzyme-linked immunoabsorbent assay evidence that is used in a manual assertion.
ECO:SN
A type of patch-clamp recording evidence where a part of cellular membrane is detached from the cell and whose external face is exposed to the extracellular medium which allows isolating and studying a single or at least a small number of channels into that fragment (patch).
snadendla
2016-03-02T10:47:25Z
cell-detached outside-out patch-clamp evidence
eco
ECO:0005582
cell-detached outside-out single-channel recording evidence
A type of patch-clamp recording evidence where a part of cellular membrane is detached from the cell and whose external face is exposed to the extracellular medium which allows isolating and studying a single or at least a small number of channels into that fragment (patch).
ECO:SN
url:http://www.nature.com/nprot/journal/v2/n11/full/nprot.2007.403.html
A type of voltage clamp recording evidence that involves inserting the oocyte in a chamber that separates the surface into 3 regions where the top portion of the oocyte membrane is the region that is clamped from which currents are actually recorded while the bottom portion is the region of the oocyte that is cut-open, making it possible to inject current intracellularly through a low resistance pathway.
snadendla
2016-03-02T11:29:32Z
eco
ECO:0005583
cut-open oocyte voltage clamp recording evidence
A type of voltage clamp recording evidence that involves inserting the oocyte in a chamber that separates the surface into 3 regions where the top portion of the oocyte membrane is the region that is clamped from which currents are actually recorded while the bottom portion is the region of the oocyte that is cut-open, making it possible to inject current intracellularly through a low resistance pathway.
ECO:SN
PMID:9711615
A type of voltage clamp recording evidence where recording is done on a fragment of the cell membrane (attached to or detached from the cell) using a large tip diameter pipette that allows isolating and studying a small number of channels into that fragment (patch).
snadendla
2016-03-02T11:33:48Z
eco
ECO:0005584
macropatch voltage clamp recording evidence
A type of voltage clamp recording evidence where recording is done on a fragment of the cell membrane (attached to or detached from the cell) using a large tip diameter pipette that allows isolating and studying a small number of channels into that fragment (patch).
ECO:SN
url:http://jxb.oxfordjournals.org/content/50/Special_Issue/1037.full.pdf
A type of mass spectrometry evidence where mass-to-charge ratio (m/z) of gas-phase ions is measured which is used to identify and quantify molecules in complex solutions within the framework of high throughput studies.
snadendla
2016-03-02T12:33:07Z
eco
ECO:0005585
There are significant differences in data analysis and data evaluation if to compare a HTP mass-spec and a regular mass-spec. The regular mass spec method is quite a reliable technique for identifying a protein molecular weight and analysing its post-modifications, other mass-spec applications might require the additional quality controls and more stringent data evaluation. More complex sample mixture is processed, more quality questions should be addressed, such as a sample contamination and sensitivity of the mass spectrometer while using HTP mass-spec.
For HTP mass-spec, the analysis of the small data sets allows to manually assign the spectra to proteins or peptides, but for large data sets only the statistical tools can be used instead.
high throughput mass spectrometry evidence
A type of mass spectrometry evidence where mass-to-charge ratio (m/z) of gas-phase ions is measured which is used to identify and quantify molecules in complex solutions within the framework of high throughput studies.
ECO:SN
PMID:20805795
A type of high throughput mass spectrometry evidence that is used in a manual assertion.
snadendla
2016-03-02T12:50:02Z
eco
ECO:0005586
high throughput mass spectrometry evidence used in manual assertion
true
A type of high throughput mass spectrometry evidence that is used in a manual assertion.
ECO:SN
A type of microscopy evidence where sharp images are taken by excluding most of the light from the specimen that is not from the microscope's focal plane, thus allowing better contrast and less haze, which makes it possible to build three-dimensional reconstructions of a volume of the specimen by assembling a series of thin slices taken along the vertical axis.
snadendla
2016-03-17T12:29:45Z
eco
ECO:0005587
confocal microscopy evidence
A type of microscopy evidence where sharp images are taken by excluding most of the light from the specimen that is not from the microscope's focal plane, thus allowing better contrast and less haze, which makes it possible to build three-dimensional reconstructions of a volume of the specimen by assembling a series of thin slices taken along the vertical axis.
ECO:SN
url:http://www.physics.emory.edu/faculty/weeks//lab/papers/ebbe05.pdf
A type of microscopy evidence where imaging of a thin cell or a tissue specimen is performed by full aperture emission of light gathered by the microscope's objective, which maximizes the recorded signal and simultaneously minimizes the required exposure times.
snadendla
2016-03-17T12:30:27Z
eco
ECO:0005588
wide-field microscopy evidence
A type of microscopy evidence where imaging of a thin cell or a tissue specimen is performed by full aperture emission of light gathered by the microscope's objective, which maximizes the recorded signal and simultaneously minimizes the required exposure times.
ECO:SN
url:http://jcb.rupress.org/content/172/1/9.full
url:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3048960/
url:http://zeiss-campus.magnet.fsu.edu/articles/livecellimaging/techniques.html
A type confocal microscopy evidence that is used in a manual assertion.
snadendla
2016-03-17T12:32:24Z
eco
ECO:0005589
confocal microscopy evidence used in manual assertion
true
true
A type confocal microscopy evidence that is used in a manual assertion.
ECO:SN
A type of wide-field microscopy evidence that is used in a manual assertion.
snadendla
2016-03-17T12:34:42Z
eco
ECO:0005590
wide-field microscopy evidence used in manual assertion
true
true
A type of wide-field microscopy evidence that is used in a manual assertion.
ECO:SN
A type of immunogold labelling evidence where electron microscopy technique is used to detect the location of the antibodies labeled with colloidal gold particles.
snadendla
2016-03-17T15:43:00Z
eco
ECO:0005591
immunogold labelling electron microscopy assay evidence
A type of immunogold labelling evidence where electron microscopy technique is used to detect the location of the antibodies labeled with colloidal gold particles.
ECO:SN
PMID:4110101
A type of immunogold labelling electron microscopy assay evidence that is used in a manual assertion.
snadendla
2016-03-17T16:39:37Z
eco
ECO:0005592
immunogold labelling electron microscopy assay evidence used in manual assertion
true
true
true
A type of immunogold labelling electron microscopy assay evidence that is used in a manual assertion.
ECO:SN
A type of direct assay evidence that involves the use of antibodies to detect biomolecules.
snadendla
2016-03-17T17:07:33Z
eco
ECO:0005593
immunodetection assay evidence
A type of direct assay evidence that involves the use of antibodies to detect biomolecules.
ECO:SN
A type of immunolocalization evidence involving enzymatic detection of a peroxidase tagged antibody.
snadendla
2016-03-17T17:11:34Z
eco
ECO:0005594
immunoperoxidase immunolocalization evidence
A type of immunolocalization evidence involving enzymatic detection of a peroxidase tagged antibody.
ECO:SN
A type of immunoperoxidase immunolocalization evidence that is used in a manual assertion.
snadendla
2016-03-17T17:14:05Z
eco
ECO:0005595
immunoperoxidase immunolocalization evidence used in manual assertion
true
true
A type of immunoperoxidase immunolocalization evidence that is used in a manual assertion.
ECO:SN
A type of immunoperoxidase immunolocalization evidence where electron microscopy technique is used for enzymatic detection of a peroxidase tagged antibody.
snadendla
2016-03-17T17:16:38Z
Immunoperoxidase labelling electron microscopy
eco
ECO:0005596
immunoperoxidase immunolocalization electron microscopy evidence
A type of immunoperoxidase immunolocalization evidence where electron microscopy technique is used for enzymatic detection of a peroxidase tagged antibody.
ECO:SN
A type of immunoperoxidase immunolocalization electron microscopy evidence that is used in a manual assertion.
snadendla
2016-03-17T17:23:56Z
eco
ECO:0005597
immunoperoxidase immunolocalization electron microscopy evidence used in manual assertion
true
true
true
A type of immunoperoxidase immunolocalization electron microscopy evidence that is used in a manual assertion.
ECO:SN
A type of wide-field microscopy evidence where pure white and ultraviolet light are produced by a mercury lamp, passed through an optical filter (excitation filter), and directed to a sample via a dichroic mirror, followed by detection of the fluorescent light by a camera after it passes through an emission filter.
snadendla
2016-03-18T11:53:56Z
eco
ECO:0005598
The optical filter is used to select the wavelength of excitation light. The detection camera is typically a CCD camera. Both topographical and dynamic information of a sample are obtained.
wide-field fluorescence microscopy evidence
A type of wide-field microscopy evidence where pure white and ultraviolet light are produced by a mercury lamp, passed through an optical filter (excitation filter), and directed to a sample via a dichroic mirror, followed by detection of the fluorescent light by a camera after it passes through an emission filter.
ECO:SN
url:http://www.bristol.ac.uk/synaptic/research/techniques/widefield.html
A type of wide-field fluorescence microscopy evidence where fluorescently tagged antibodies are imaged that are used to bind to their antigens.
snadendla
2016-03-18T11:55:40Z
wide-field epifluorescence microscopy
eco
ECO:0005599
immunofluorescence wide-field microscopy evidence
A type of wide-field fluorescence microscopy evidence where fluorescently tagged antibodies are imaged that are used to bind to their antigens.
ECO:SN
url:http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0057135
A type of confocal microscopy evidence where light passes through immunofluorescent-stained tissue sections or cells and then the emitted light passes through the dichroic mirror and is focused onto the pinhole for subsequent detection.
snadendla
2016-03-18T12:48:42Z
eco
ECO:0005600
This allows visualization of sub cellular distribution of biomolecules of interest.
immunofluorescence confocal microscopy evidence
A type of confocal microscopy evidence where light passes through immunofluorescent-stained tissue sections or cells and then the emitted light passes through the dichroic mirror and is focused onto the pinhole for subsequent detection.
ECO:SN
url:http://www.physics.emory.edu/faculty/weeks/confocal/
url:https://www.hycultbiotech.com/media/wysiwyg/protocol_Immunofluorescence.pdf
A type of immunofluorescence confocal microscopy evidence that is used in a manual assertion.
snadendla
2016-03-18T12:52:04Z
eco
ECO:0005601
immunofluorescence confocal microscopy evidence used in manual assertion
true
true
true
A type of immunofluorescence confocal microscopy evidence that is used in a manual assertion.
ECO:SN
A type of protein expression level evidence where the level of expression of a protein is determined in a cell or tissue extract by western blot technique.
snadendla
2016-03-18T13:02:29Z
eco
ECO:0005602
protein expression level evidence based on western blot
A type of protein expression level evidence where the level of expression of a protein is determined in a cell or tissue extract by western blot technique.
ECO:SN
A type of mass spectrometry evidence where one or more protein analyses are performed.
snadendla
2016-03-18T13:11:37Z
eco
ECO:0005603
protein mass spectrometry evidence
A type of mass spectrometry evidence where one or more protein analyses are performed.
ECO:SN
A type of experimental evidence where the investigated organism or a potential antagonist is inoculated so as to grow along the diameter line of the agar medium in a Petri dish, then, potentially susceptible microbes (usually bacteria) are streaked perpendicularly to the growth line and inhibition of growth of a test microbe in the vicinity of that line suggests that the antagonist secretes one or more diffusible antibiotics.
snadendla
2016-03-29T15:40:54Z
eco
ECO:0005604
cross-streak test evidence
A type of experimental evidence where the investigated organism or a potential antagonist is inoculated so as to grow along the diameter line of the agar medium in a Petri dish, then, potentially susceptible microbes (usually bacteria) are streaked perpendicularly to the growth line and inhibition of growth of a test microbe in the vicinity of that line suggests that the antagonist secretes one or more diffusible antibiotics.
ECO:SN
url:www.jstor.org/stable/3792785
A type of experimental evidence where sensitivity/resistance to an antimicrobial agent is tested by impregnating small filter disks with a known concentration of antimicrobial agent which is then placed on a Mueller-Hinton agar plate inoculated with the test organism.
snadendla
2016-03-29T16:02:22Z
zone of inhibition evidence
eco
ECO:0005605
disk diffusion test evidence
A type of experimental evidence where sensitivity/resistance to an antimicrobial agent is tested by impregnating small filter disks with a known concentration of antimicrobial agent which is then placed on a Mueller-Hinton agar plate inoculated with the test organism.
ECO:SN
url:http://www.cdc.gov/nczved/resources/cholera/ch9.pdf
A type of experimental evidence where a foreign genetic material is introduced into the cell for study of gene function and regulation and protein function.
snadendla
2016-03-29T16:59:17Z
eco
ECO:0005606
cell transfection experiment evidence
A type of experimental evidence where a foreign genetic material is introduced into the cell for study of gene function and regulation and protein function.
ECO:SN
url:http://ch.promega.com/resources/product-guides-and-selectors/protocols-and-applications-guide/transfection/
url:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2911531/
A type of chemotaxis assay evidence where the presence or absence of positive or negative chemotaxis in swimming organisms is determined by observing the rotational behavior of the organism tethered to a coverslip by their flagella.
snadendla
2016-03-31T15:51:10Z
eco
ECO:0005607
tethered cell assay evidence
A type of chemotaxis assay evidence where the presence or absence of positive or negative chemotaxis in swimming organisms is determined by observing the rotational behavior of the organism tethered to a coverslip by their flagella.
ECO:SN
PMID:1103143
A type of chemotaxis assay evidence where the presence or absence of positive or negative chemotaxis in swimming organisms is determined by measuring chemotaxis in response to sudden concentration changes from one uniform spatial environment to another.
snadendla
2016-03-31T16:42:35Z
Temporal assay
eco
ECO:0005608
tumble frequency assay evidence
A type of chemotaxis assay evidence where the presence or absence of positive or negative chemotaxis in swimming organisms is determined by measuring chemotaxis in response to sudden concentration changes from one uniform spatial environment to another.
ECO:SN
PMID:4576832
A type of chemotaxis assay evidence where the presence or absence of positive or negative chemotaxis in swimming organisms is determined (typically bacteria or archaea) by measuring the rate of accumulation of the organism into a capillary.
snadendla
2016-03-31T16:45:29Z
eco
ECO:0005609
To determine the presence of positive chemotaxis, an attractant is placed in the capillary and the presence of positive chemotaxis is determined based on the amount of organism that accumulated in the capillary.
To determine the presence of negative chemotaxis, a repellent is added to the organismal suspension (but not in the capillary) and the organisms that fled into the capillary are measured.
capillary assay evidence
A type of chemotaxis assay evidence where the presence or absence of positive or negative chemotaxis in swimming organisms is determined (typically bacteria or archaea) by measuring the rate of accumulation of the organism into a capillary.
ECO:SN
PMID:4632978
A type of biological system reconstruction evidence based on homology evidence that is used in a manual assertion.
snadendla
2016-03-31T17:00:03Z
eco
ECO:0005610
Inference may be based on paralogy and/or orthology of the genome-encoded components and is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. Evidence may originate from a combination of several experiments in the same or another species.
biological system reconstruction evidence based on homology evidence used in manual assertion
true
true
A type of biological system reconstruction evidence based on homology evidence that is used in a manual assertion.
ECO:SN
A type of direct assay evidence used in manual assertion where phenotype or disease association is made with the gene because of involvement in the molecular mechanism of disease or involvement in a pathway known to contribute to a disease.
snadendla
2016-04-12T16:55:16Z
IED
inferred from experimental data
eco
ECO:0005611
inference from experimental data evidence
A type of direct assay evidence used in manual assertion where phenotype or disease association is made with the gene because of involvement in the molecular mechanism of disease or involvement in a pathway known to contribute to a disease.
ECO:SN
A type of mutant phenotype evidence used in manual assertion where variations or changes, such as mutations or abnormal levels of the product(s) of a single gene of interest, including non-mutational changes such as inhibition with antibodies or other inhibitors are determined.
snadendla
2016-04-12T17:09:43Z
IPM
inferred from phenotype manipulation
eco
ECO:0005612
Changes can include any gene mutation/knockout, over-expression or ectopic expression of wild-type or mutant genes, anti-sense experiments, RNAi experiments, specific protein inhibitors.
inference from phenotype manipulation evidence
A type of mutant phenotype evidence used in manual assertion where variations or changes, such as mutations or abnormal levels of the product(s) of a single gene of interest, including non-mutational changes such as inhibition with antibodies or other inhibitors are determined.
ECO:SN
A type of natural variation mutant evidence used in manual assertion where alleles are directly linked to phenotype and Mendelian diseases as a result of various experiments.
snadendla
2016-04-12T17:24:00Z
IAGP
inferred by association of genotype from phenotype
eco
ECO:0005613
Used for 1) polymorphism or segregation of genetic markers (SNPs, mutations, RFLPs, microsatellites); 2) polymorphism or segregation of physical markers (FISH, centromeric or heterochromatic regions, chromosomal banding patterns); 3) detection of polymorphisms in inbred stock.
inference by association of genotype from phenotype
A type of natural variation mutant evidence used in manual assertion where alleles are directly linked to phenotype and Mendelian diseases as a result of various experiments.
ECO:SN
A type of two-dimensional polyacrylamide gel electrophoresis evidence that is used in a manual assertion.
snadendla
2016-05-06T11:03:08Z
eco
ECO:0005614
two-dimensional polyacrylamide gel electrophoresis evidence used in manual assertion
true
true
A type of two-dimensional polyacrylamide gel electrophoresis evidence that is used in a manual assertion.
ECO:SN
A type of alkaline phosphatase reporter gene assay evidence that is used in a manual assertion.
snadendla
2016-05-06T11:05:59Z
eco
ECO:0005615
alkaline phosphatase reporter gene assay evidence used in manual assertion
true
true
A type of alkaline phosphatase reporter gene assay evidence that is used in a manual assertion.
ECO:SN
A type of beta-galactosidase reporter gene assay evidence that is used in a manual assertion.
snadendla
2016-05-06T11:08:57Z
eco
ECO:0005616
beta-galactosidase reporter gene assay evidence used in manual assertion
true
true
A type of beta-galactosidase reporter gene assay evidence that is used in a manual assertion.
ECO:SN
A type of chloramphenicol acetyltransferase reporter gene assay evidence that is used in a manual assertion.
snadendla
2016-05-06T11:11:07Z
eco
ECO:0005617
chloramphenicol acetyltransferase reporter gene assay evidence used in manual assertion
true
true
A type of chloramphenicol acetyltransferase reporter gene assay evidence that is used in a manual assertion.
ECO:SN
A type of chromatin immunoprecipitation-chip evidence that is used in an automatic assertion.
snadendla
2016-05-06T11:17:04Z
eco
ECO:0005618
chromatin immunoprecipitation-chip evidence used in automatic assertion
true
true
A type of chromatin immunoprecipitation-chip evidence that is used in an automatic assertion.
ECO:SN
A type of chromatin immunoprecipitation- exonuclease evidence that is used in an automatic assertion.
snadendla
2016-05-06T11:22:25Z
eco
ECO:0005619
chromatin immunoprecipitation- exonuclease evidence used in automatic assertion
true
true
A type of chromatin immunoprecipitation- exonuclease evidence that is used in an automatic assertion.
ECO:SN
A type of chromatin immunoprecipitation-PCR evidence that is used in a manual assertion.
snadendla
2016-05-06T11:25:01Z
eco
ECO:0005620
chromatin immunoprecipitation-PCR evidence used in manual assertion
true
true
A type of chromatin immunoprecipitation-PCR evidence that is used in a manual assertion.
ECO:SN
A type of chromatin immunoprecipitation-seq evidence that is used in an automatic assertion.
snadendla
2016-05-06T11:29:13Z
eco
ECO:0005621
chromatin immunoprecipitation-seq evidence used in automatic assertion
true
true
A type of chromatin immunoprecipitation-seq evidence that is used in an automatic assertion.
ECO:SN
A type of comparative genomics motif search evidence that is used in a manual assertion.
snadendla
2016-05-06T14:49:36Z
eco
ECO:0005622
comparative genomics motif search evidence used in manual assertion
true
true
A type of comparative genomics motif search evidence that is used in a manual assertion.
ECO:SN
A type of comparative genomics motif search evidence that is used in an automatic assertion.
snadendla
2016-05-06T14:52:21Z
eco
ECO:0005623
comparative genomics motif search evidence used in automatic assertion
true
true
A type of comparative genomics motif search evidence that is used in an automatic assertion.
ECO:SN
A type of consensus search evidence that is used in a manual assertion.
snadendla
2016-05-06T14:54:53Z
eco
ECO:0005624
consensus search evidence used in manual assertion
true
true
A type of consensus search evidence that is used in a manual assertion.
ECO:SN
A type of consensus search evidence that is used in an automatic assertion.
snadendla
2016-05-06T14:58:22Z
eco
ECO:0005625
consensus search evidence used in automatic assertion
true
true
A type of consensus search evidence that is used in an automatic assertion.
ECO:SN
A type of copper-phenanthroline footprinting evidence that is used in a manual assertion.
snadendla
2016-05-06T15:01:25Z
eco
ECO:0005626
copper-phenanthroline footprinting evidence used in manual assertion
true
true
A type of copper-phenanthroline footprinting evidence that is used in a manual assertion.
ECO:SN
A type of DNA adenine methyltransferase identification evidence that is used in a manual assertion.
snadendla
2016-05-06T15:05:14Z
eco
ECO:0005627
DNA adenine methyltransferase identification evidence used in manual assertion
true
true
A type of DNA adenine methyltransferase identification evidence that is used in a manual assertion.
ECO:SN
A type of DNA adenine methyltransferase identification evidence that is used in an automatic assertion.
snadendla
2016-05-06T15:06:46Z
eco
ECO:0005628
DNA adenine methyltransferase identification evidence used in automatic assertion
true
true
A type of DNA adenine methyltransferase identification evidence that is used in an automatic assertion.
ECO:SN
A type of DNA affinity chromatography evidence that is used in a manual assertion.
snadendla
2016-05-06T15:08:40Z
eco
ECO:0005629
DNA affinity chromatography evidence used in manual assertion
true
true
A type of DNA affinity chromatography evidence that is used in a manual assertion.
ECO:SN
A type of DNA microarray evidence that is used in an automatic assertion.
snadendla
2016-05-06T15:31:51Z
eco
ECO:0005630
DNA microarray evidence used in automatic assertion
true
true
A type of DNA microarray evidence that is used in an automatic assertion.
ECO:SN
A type of DNAse footprinting evidence that is used in a manual assertion.
snadendla
2016-05-06T15:35:41Z
eco
ECO:0005631
DNAse footprinting evidence used in manual assertion
true
true
A type of DNAse footprinting evidence that is used in a manual assertion.
ECO:SN
A type of fluorescence anisotropy evidence that is used in a manual assertion.
snadendla
2016-05-06T15:45:40Z
eco
ECO:0005632
fluorescence anisotropy evidence used in manual assertion
true
true
A type of fluorescence anisotropy evidence that is used in a manual assertion.
ECO:SN
A type of ferric uptake regulator titration assay evidence that is used in a manual assertion.
snadendla
2016-05-06T15:49:18Z
eco
ECO:0005633
ferric uptake regulator titration assay evidence used in manual assertion
true
true
A type of ferric uptake regulator titration assay evidence that is used in a manual assertion.
ECO:SN
A type of genomic systematic evolution of ligands by exponential amplification evidence that is used in a manual assertion.
snadendla
2016-05-06T16:41:30Z
eco
ECO:0005634
genomic systematic evolution of ligands by exponential amplification evidence used in manual assertion
true
true
A type of genomic systematic evolution of ligands by exponential amplification evidence that is used in a manual assertion.
ECO:SN
A type of genomic systematic evolution of ligands by exponential amplification evidence that is used in an automatic assertion.
snadendla
2016-05-06T16:43:03Z
eco
ECO:0005635
genomic systematic evolution of ligands by exponential amplification evidence used in automatic assertion
true
true
A type of genomic systematic evolution of ligands by exponential amplification evidence that is used in an automatic assertion.
ECO:SN
A type of green fluorescent protein reporter gene assay evidence that is used in a manual assertion.
snadendla
2016-05-06T16:46:32Z
eco
ECO:0005636
green fluorescent protein reporter gene assay evidence used in manual assertion
true
true
A type of green fluorescent protein reporter gene assay evidence that is used in a manual assertion.
ECO:SN
A type of green fluorescent protein reporter gene assay evidence that is used in an automatic assertion.
snadendla
2016-05-06T16:48:29Z
eco
ECO:0005637
green fluorescent protein reporter gene assay evidence used in automatic assertion
true
true
A type of green fluorescent protein reporter gene assay evidence that is used in an automatic assertion.
ECO:SN
A type of cell growth assay evidence that is used in a manual assertion.
snadendla
2016-05-06T16:52:15Z
eco
ECO:0005638
cell growth assay evidence used in manual assertion
true
true
A type of cell growth assay evidence that is used in a manual assertion.
ECO:SN
A type of cell growth assay evidence that is used in an automatic assertion.
snadendla
2016-05-06T16:53:28Z
eco
ECO:0005639
cell growth assay evidence used in automatic assertion
true
true
A type of cell growth assay evidence that is used in an automatic assertion.
ECO:SN
A type of glutathione S-transferase pull-down assay evidence that is used in a manual assertion.
snadendla
2016-05-06T16:56:39Z
eco
ECO:0005640
glutathione S-transferase pull-down assay evidence used in manual assertion
true
true
A type of glutathione S-transferase pull-down assay evidence that is used in a manual assertion.
ECO:SN
A type of beta-glucuronidase reporter gene assay evidence that is used in a manual assertion.
snadendla
2016-05-06T16:58:29Z
eco
ECO:0005641
beta-glucuronidase reporter gene assay evidence used in manual assertion
true
true
A type of beta-glucuronidase reporter gene assay evidence that is used in a manual assertion.
ECO:SN
A type of heteronuclear single quantum coherence spectroscopy evidence that is used in a manual assertion.
snadendla
2016-05-06T23:10:13Z
eco
ECO:0005642
heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
true
true
A type of heteronuclear single quantum coherence spectroscopy evidence that is used in a manual assertion.
ECO:SN
A type of hydroxyl-radical footprinting evidence that is used in a manual assertion.
snadendla
2016-05-06T23:14:48Z
eco
ECO:0005643
hydroxyl-radical footprinting evidence used in manual assertion
true
true
A type of hydroxyl-radical footprinting evidence that is used in a manual assertion.
ECO:SN
A type of immunoprecipitation evidence that is used in a manual assertion.
snadendla
2016-05-06T23:20:49Z
eco
ECO:0005644
immunoprecipitation evidence used in manual assertion
true
true
A type of immunoprecipitation evidence that is used in a manual assertion.
ECO:SN
A type of interferometric reflectance imaging sensor evidence that is used in a manual assertion.
snadendla
2016-05-06T23:27:58Z
eco
ECO:0005645
interferometric reflectance imaging sensor evidence used in manual assertion
true
true
A type of interferometric reflectance imaging sensor evidence that is used in a manual assertion.
ECO:SN
A type of interferometric reflectance imaging sensor evidence that is used in an automatic assertion.
snadendla
2016-05-06T23:29:23Z
eco
ECO:0005646
interferometric reflectance imaging sensor evidence used in automatic assertion
true
true
A type of interferometric reflectance imaging sensor evidence that is used in an automatic assertion.
ECO:SN
A type of isothermal titration calorimetry evidence that is used in a manual assertion.
snadendla
2016-05-06T23:36:26Z
eco
ECO:0005647
isothermal titration calorimetry evidence used in manual assertion
true
true
A type of isothermal titration calorimetry evidence that is used in a manual assertion.
ECO:SN
A type of luciferase reporter gene assay evidence that is used in a manual assertion.
snadendla
2016-05-06T23:44:52Z
eco
ECO:0005648
luciferase reporter gene assay evidence used in manual assertion
true
true
A type of luciferase reporter gene assay evidence that is used in a manual assertion.
ECO:SN
A type of machine learning prediction of motif instance evidence that is used in a manual assertion.
snadendla
2016-05-06T23:51:30Z
eco
ECO:0005649
machine learning prediction of motif instance evidence used in manual assertion
true
true
A type of machine learning prediction of motif instance evidence that is used in a manual assertion.
ECO:SN
A type of machine learning prediction of motif instance evidence that is used in an automatic assertion.
snadendla
2016-05-06T23:54:00Z
eco
ECO:0005650
machine learning prediction of motif instance evidence used in automatic assertion
true
true
A type of machine learning prediction of motif instance evidence that is used in an automatic assertion.
ECO:SN
A type of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence that is used in an automatic assertion.
snadendla
2016-05-06T23:57:30Z
eco
ECO:0005651
matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence used in automatic assertion
true
true
A type of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence that is used in an automatic assertion.
ECO:SN
A type of methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence that is used in a manual assertion.
snadendla
2016-05-09T14:42:28Z
eco
ECO:0005652
methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence used in manual assertion
true
true
A type of methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence that is used in a manual assertion.
ECO:SN
A type of northern assay evidence that is used in a manual assertion.
snadendla
2016-05-09T14:48:03Z
eco
ECO:0005653
northern assay evidence used in manual assertion
true
true
A type of northern assay evidence that is used in a manual assertion.
ECO:SN
A type of phylogenetic footprinting evidence that is used in a manual assertion.
snadendla
2016-05-09T14:50:52Z
eco
ECO:0005654
phylogenetic footprinting evidence used in manual assertion
true
true
A type of phylogenetic footprinting evidence that is used in a manual assertion.
ECO:SN
A type of phylogenetic footprinting evidence that is used in an automatic assertion.
snadendla
2016-05-09T14:51:55Z
eco
ECO:0005655
phylogenetic footprinting evidence used in automatic assertion
true
true
A type of phylogenetic footprinting evidence that is used in an automatic assertion.
ECO:SN
A type of premethylation interference footprinting evidence that is used in a manual assertion.
snadendla
2016-05-09T14:55:25Z
eco
ECO:0005656
premethylation interference footprinting evidence used in manual assertion
true
true
A type of premethylation interference footprinting evidence that is used in a manual assertion.
ECO:SN
A type of primer extension assay evidence that is used in a manual assertion.
snadendla
2016-05-09T14:58:38Z
eco
ECO:0005657
primer extension assay evidence used in manual assertion
true
true
A type of primer extension assay evidence that is used in a manual assertion.
ECO:SN
A type of position-specific scoring matrix motif search evidence that is used in a manual assertion.
snadendla
2016-05-09T15:01:31Z
eco
ECO:0005658
position-specific scoring matrix motif search evidence used in manual assertion
true
true
A type of position-specific scoring matrix motif search evidence that is used in a manual assertion.
ECO:SN
A type of position-specific scoring matrix motif search evidence that is used in an automatic assertion.
snadendla
2016-05-09T15:02:31Z
eco
ECO:0005659
position-specific scoring matrix motif search evidence used in automatic assertion
true
true
A type of position-specific scoring matrix motif search evidence that is used in an automatic assertion.
ECO:SN
A type of quantitative polymerase chain reaction evidence that is used in a manual assertion.
snadendla
2016-05-09T15:09:01Z
eco
ECO:0005660
quantitative polymerase chain reaction evidence used in manual assertion
true
true
A type of quantitative polymerase chain reaction evidence that is used in a manual assertion.
ECO:SN
A type of rapid amplification of cDNA ends polymerase chain reaction evidence that is used in a manual assertion.
snadendla
2016-05-09T15:19:20Z
eco
ECO:0005661
rapid amplification of cDNA ends polymerase chain reaction evidence used in manual assertion
true
true
A type of rapid amplification of cDNA ends polymerase chain reaction evidence that is used in a manual assertion.
ECO:SN
A type of regular expression motif search evidence that is used in a manual assertion.
snadendla
2016-05-09T16:13:55Z
eco
ECO:0005662
regular expression motif search evidence used in manual assertion
true
true
A type of regular expression motif search evidence that is used in a manual assertion.
ECO:SN
A type of regular expression motif search evidence that is used in an automatic assertion.
snadendla
2016-05-09T16:15:03Z
eco
ECO:0005663
regular expression motif search evidence used in automatic assertion
true
true
A type of regular expression motif search evidence that is used in an automatic assertion.
ECO:SN
A type of RNA sequencing assay evidence that is used in a manual assertion.
snadendla
2016-05-09T16:18:35Z
eco
ECO:0005664
Use ECO:0006068 (RNA-seq evidence used in manual assertion) in place of this term.
RNA sequencing assay evidence used in manual assertion
true
A type of RNA sequencing assay evidence that is used in a manual assertion.
ECO:SN
A type of RNA sequencing assay evidence that is used in an automatic assertion.
snadendla
2016-05-09T16:19:38Z
eco
ECO:0005665
Use ECO:0006069 (RNA-seq evidence used in automatic assertion) in place of this term.
RNA sequencing assay evidence used in automatic assertion
true
A type of RNA sequencing assay evidence that is used in an automatic assertion.
ECO:SN
A type of S1 nuclease protection assay evidence that is used in a manual assertion.
snadendla
2016-05-09T16:22:58Z
eco
ECO:0005666
S1 nuclease protection assay evidence used in manual assertion
true
true
A type of S1 nuclease protection assay evidence that is used in a manual assertion.
ECO:SN
A type of site-directed mutagenesis evidence that is used in a manual assertion.
snadendla
2016-05-09T16:29:13Z
eco
ECO:0005667
site-directed mutagenesis evidence used in manual assertion
true
true
A type of site-directed mutagenesis evidence that is used in a manual assertion.
ECO:SN
A type of survival rate analysis evidence that is used in a manual assertion.
snadendla
2016-05-09T16:31:08Z
eco
ECO:0005668
survival rate analysis evidence used in manual assertion
true
true
A type of survival rate analysis evidence that is used in a manual assertion.
ECO:SN
A type of ultraviolet light footprinting evidence that is used in a manual assertion.
snadendla
2016-05-09T16:33:44Z
eco
ECO:0005669
ultraviolet light footprinting evidence used in manual assertion
true
true
A type of ultraviolet light footprinting evidence that is used in a manual assertion.
ECO:SN
A type of x-ray crystallography evidence that is used in a manual assertion.
snadendla
2016-05-10T11:53:00Z
eco
ECO:0005670
x-ray crystallography evidence used in manual assertion
true
true
A type of x-ray crystallography evidence that is used in a manual assertion.
ECO:SN
A type of x-ray crystallography evidence that is used in an automatic assertion.
snadendla
2016-05-10T11:54:03Z
eco
ECO:0005671
x-ray crystallography evidence used in automatic assertion
true
true
A type of x-ray crystallography evidence that is used in an automatic assertion.
ECO:SN
A type of xylE reporter gene assay evidence that is used in a manual assertion.
snadendla
2016-05-10T11:57:15Z
eco
ECO:0005672
xylE reporter gene assay evidence used in manual assertion
true
true
A type of xylE reporter gene assay evidence that is used in a manual assertion.
ECO:SN
A type of experimental phenotypic evidence where a non-standard trait (e.g. natural competence) is assessed qualitatively (e.g. presence/absence) and used as a natural reporter to conclude that some genes or pathways are regulated by the transcription factor.
snadendla
2016-05-10T12:57:41Z
eco
ECO:0005673
ad-hoc qualitative phenotype observation evidence
A type of experimental phenotypic evidence where a non-standard trait (e.g. natural competence) is assessed qualitatively (e.g. presence/absence) and used as a natural reporter to conclude that some genes or pathways are regulated by the transcription factor.
ECO:SN
PMID:15150239
A type of ad-hoc qualitative phenotype observation that is used in a manual assertion.
snadendla
2016-05-10T14:28:47Z
eco
ECO:0005674
ad-hoc qualitative phenotype observation evidence used in manual assertion
true
true
A type of ad-hoc qualitative phenotype observation that is used in a manual assertion.
ECO:SN
A type of experimental phenotypic evidence where a quantifiable phenotypic trait (e.g. glucose intake) is assessed in a quantitative manner after induction of the regulatory mechanism and used as a natural reporter to conclude that some genes or pathways are regulated by the transcription factor.
snadendla
2016-05-10T14:30:50Z
eco
ECO:0005675
ad-hoc quantitative phenotype observation evidence
A type of experimental phenotypic evidence where a quantifiable phenotypic trait (e.g. glucose intake) is assessed in a quantitative manner after induction of the regulatory mechanism and used as a natural reporter to conclude that some genes or pathways are regulated by the transcription factor.
ECO:SN
PMID:15150239
A type of ad-hoc quantitative phenotype observation evidence that is used in a manual assertion.
snadendla
2016-05-10T14:34:50Z
eco
ECO:0005676
ad-hoc quantitative phenotype observation evidence used in manual assertion
true
true
A type of ad-hoc quantitative phenotype observation evidence that is used in a manual assertion.
ECO:SN
A direct assay evidence where the activity of a solution is determined by exposing an indicator culture or organism to a series of dilutions and determining the lowest concentration that elicits a biological response.
critical dilution assay
spot assay
For chemicals, bacteriocins, or phage, the indicator culture is typically present in a soft-agar layer on top of nutrient agar and a small quantity of each dilution is spotted onto the soft agar overlay.
dilution assay evidence
A direct assay evidence where the activity of a solution is determined by exposing an indicator culture or organism to a series of dilutions and determining the lowest concentration that elicits a biological response.
http://www.sciencedirect.com/science/article/pii/016770129400068I
A type of enzyme assay evidence that is used in a manual assertion.
eco
ECO:0005801
enzyme assay evidence used in manual assertion
true
A type of enzyme assay evidence that is used in a manual assertion.
ECO:SN
A type of cell transfection experiment evidence that is used in a manual assertion.
eco
ECO:0005802
cell transfection experiment evidence used in manual assertion
true
A type of cell transfection experiment evidence that is used in a manual assertion.
ECO:SN
A type of direct assay evidence where the motility of a cell or cells is determined.
eco
ECO:0005803
motility assay evidence
A type of direct assay evidence where the motility of a cell or cells is determined.
ECO:SN
A type of immunofluorescence evidence that is used in a manual assertion.
eco
ECO:0005804
immunofluorescence evidence used in manual assertion
true
A type of immunofluorescence evidence that is used in a manual assertion.
ECO:SN
A type of yeast 2-hybrid evidence that is used in a manual assertion.
eco
ECO:0005805
yeast 2-hybrid evidence used in manual assertion
true
A type of yeast 2-hybrid evidence that is used in a manual assertion.
ECO:SN
A type of evidence derived from exploiting the CyaA (calmodulin-activated adenylate cyclase toxin) secreted by Bordatella pertussis to synthesize cAMP and alter cellular physiology in a host cell for various biological applications.
rctauber
2016-06-15T08:42:16Z
eco
ECO:0006001
Cya fusion reporter assay evidence
A type of evidence derived from exploiting the CyaA (calmodulin-activated adenylate cyclase toxin) secreted by Bordatella pertussis to synthesize cAMP and alter cellular physiology in a host cell for various biological applications.
PMID:10217833
PMID:14702323
A type of Cya fusion reporter assay evidence that is used in a manual assertion.
rctauber
2010-06-15T08:44:10Z
eco
ECO:0006002
Cya fusion reporter assay evidence used in manual assertion
true
A type of Cya fusion reporter assay evidence that is used in a manual assertion.
ECO:RCT
A type of electron microscopy evidence that is used in a manual assertion.
rctauber
2016-10-12T12:32:29Z
eco
ECO:0006003
electron microscopy evidence used in manual assertion
true
A type of electron microscopy evidence that is used in a manual assertion.
ECO:RCT
A type of super-resolution microscopy evidence that is used in a manual assertion.
rctauber
2016-10-12T12:32:29Z
eco
ECO:0006004
super-resolution microscopy evidence used in manual assertion
true
A type of super-resolution microscopy evidence that is used in a manual assertion.
ECO:RCT
A type of fractionation evidence that is used in a manual assertion.
rctauber
2016-10-12T12:32:29Z
eco
ECO:0006005
fractionation evidence used in manual assertion
true
A type of fractionation evidence that is used in a manual assertion.
ECO:RCT
A type of electrophysiology assay evidence that is used in a manual assertion.
rctauber
2016-10-12T12:32:29Z
eco
ECO:0006006
electrophysiology assay evidence used in manual assertion
true
A type of electrophysiology assay evidence that is used in a manual assertion.
ECO:RCT
A type of chromatin immunoprecipitation-chip evidence that is used in a manual assertion.
rctauber
2016-10-21T11:55:53Z
eco
ECO:0006007
chromatin immunoprecipitation-chip evidence used in manual assertion
true
A type of chromatin immunoprecipitation-chip evidence that is used in a manual assertion.
ECO:RCT
A type of chromatin immunoprecipitation- exonuclease evidence that is used in a manual assertion.
rctauber
2016-10-21T11:55:53Z
eco
ECO:0006008
chromatin immunoprecipitation- exonuclease evidence used in manual assertion
true
A type of chromatin immunoprecipitation- exonuclease evidence that is used in a manual assertion.
ECO:RCT
A type of chromatin immunoprecipitation-seq evidence that is used in a manual assertion.
rctauber
2016-10-21T11:55:53Z
eco
ECO:0006009
chromatin immunoprecipitation-seq evidence used in manual assertion
true
A type of chromatin immunoprecipitation-seq evidence that is used in a manual assertion.
ECO:RCT
A type of nucleic acid binding evidence in which RNA-binding proteins are identified through cross-linking RNA and proteins by UV light, capturing RNA-protein complexes on oligo(dT) beads, and finally identifying by mass spectrometry.
rctauber
2016-10-21T12:28:17Z
ultraviolet light cross-linking RNA binding evidence
eco
ECO:0006010
mRNA interactome capture evidence
A type of nucleic acid binding evidence in which RNA-binding proteins are identified through cross-linking RNA and proteins by UV light, capturing RNA-protein complexes on oligo(dT) beads, and finally identifying by mass spectrometry.
PMID:27729395
A type of mRNA interactome capture evidence that is used in a manual assertion.
rctauber
2016-10-21T12:28:17Z
eco
ECO:0006011
mRNA interactome capture evidence used in manual assertion
true
A type of mRNA interactome capture evidence that is used in a manual assertion.
ECO:RCT
A type of electrophysiology assay evidence in which a glass micropipette is sealed to the surface of a cell membrane (patch) to study ion channels.
rctauber
2016-11-28T11:44:05Z
eco
ECO:0006012
patch-clamp recording evidence
A type of electrophysiology assay evidence in which a glass micropipette is sealed to the surface of a cell membrane (patch) to study ion channels.
ECO:RCT
A type of patch-clamp recording evidence that is used in a manual assertion.
rctauber
2016-11-28T11:44:05Z
eco
ECO:0006013
patch-clamp recording evidence used in manual assertion
A type of patch-clamp recording evidence that is used in a manual assertion.
ECO:RCT
A type of patch-clamp recording evidence in which a glass micropipette filled with a prepared solution is used to form a seal with the cell membrane followed by rupture of membrane to provide accurate and high resolution electrical property measurements of the whole cell.
rctauber
2016-11-28T11:44:05Z
eco
ECO:0006014
whole-cell patch-clamp recording evidence
A type of patch-clamp recording evidence in which a glass micropipette filled with a prepared solution is used to form a seal with the cell membrane followed by rupture of membrane to provide accurate and high resolution electrical property measurements of the whole cell.
PMID:27341060
A type of whole-cell patch-clamp recording evidence that is used in a manual assertion.
rctauber
2016-11-28T11:44:05Z
eco
ECO:0006015
whole-cell patch-clamp recording evidence used in manual assertion
A type of whole-cell patch-clamp recording evidence that is used in a manual assertion.
ECO:RCT
A type of traceable author statement that is based on a publication about a clinical study.
rctauber
2016-11-30T09:44:47Z
published clinical study evidence
eco
ECO:0006016
traceable author statement from published clinical study
A type of traceable author statement from published clinical study that is used in a manual assertion.
rctauber
2016-11-30T09:44:47Z
PCS
eco
ECO:0006017
Created and used by the Human Phenotype Ontology (HPO) Annotations group. Here it is used when evidence for an HPO annotation is information extracted from articles in the medical literature.
traceable author statement from published clinical study used in manual assertion
http://human-phenotype-ontology.github.io/documentation.html#annot
true
PCS
HPO:PCS
A type of curator inference that is based on the individual clinical experience of a clinician
rctauber
2016-11-30T09:44:47Z
individual clinical experience evidence
eco
ECO:0006018
inference based on individual clinical experience
A type of inference based on individual clinical experience that is used in a manual assertion.
rctauber
2016-11-30T09:44:47Z
ICE
eco
ECO:0006019
Created and used by the Human Phenotype Ontology (HPO) Annotations group. Here it is used for annotating disorders with a limited amount of published data, and is accompanied by a reference to the individual or center performing the annotation.
inference based on individual clinical experience used in manual assertion
http://human-phenotype-ontology.github.io/documentation.html#annot
true
ICE
HPO:ICE
A type of in vitro culture assay evidence in which biofilm growth is monitored and detected from attachment to development.
rctauber
2016-12-05T09:33:18Z
eco
ECO:0006020
biofilm formation assay evidence
A type of in vitro culture assay evidence in which biofilm growth is monitored and detected from attachment to development.
PMID:10547784
A type of biofilm formation assay evidence that is used in a manual assertion.
rctauber
2016-12-05T09:33:18Z
eco
ECO:0006021
biofilm formation assay evidence used in manual assertion
true
A type of biofilm formation assay evidence that is used in a manual assertion.
ECO:RCT
A type of biofilm formation assay evidence in which microtiter dishes or tubes are inoculated and incubated to promote biofilm formation, and then biofilms are detected by staining with crystal violet or safranin to observe phenotypes.
rctauber
2016-12-05T09:33:18Z
eco
ECO:0006022
microtiter plate biofilm assay evidence
A type of biofilm formation assay evidence in which microtiter dishes or tubes are inoculated and incubated to promote biofilm formation, and then biofilms are detected by staining with crystal violet or safranin to observe phenotypes.
PMID:10547784
A type of microtiter plate biofilm assay evidence that is used in a manual assertion.
rctauber
2016-12-05T09:33:18Z
eco
ECO:0006023
microtiter plate biofilm assay evidence used in manual assertion
true
A type of microtiter plate biofilm assay evidence that is used in a manual assertion.
ECO:RCT
A type of biofilm formation assay evidence in which biofilm formation is analyzed, without staining, over 4 to 48 hours by growth on a tilted multiwell plate.
rctauber
2016-12-05T09:33:18Z
ALI biofilm assay evidence
eco
ECO:0006024
Tilting of the plate positions the air-liquid interface on a clear portion to improve visability.
air-liquid interface assay evidence
A type of biofilm formation assay evidence in which biofilm formation is analyzed, without staining, over 4 to 48 hours by growth on a tilted multiwell plate.
PMID:18770545
A type of air-liquid interface assay evidence that is used in a manual assertion.
rctauber
2016-12-05T09:33:18Z
eco
ECO:0006025
air-liquid interface assay evidence used in manual assertion
true
A type of air-liquid interface assay evidence that is used in a manual assertion.
ECO:RCT
A type of biofilm formation assay evidence in which a colony is grown on a semipermeable membrane on an agar plate to continously supply nutrients by relocating to fresh plates.
rctauber
2016-12-05T09:33:18Z
eco
ECO:0006026
The plates commonly contain different carbon sources or antibiotic treatments to observe properties of the cells.
colony biofilm assay evidence
A type of biofilm formation assay evidence in which a colony is grown on a semipermeable membrane on an agar plate to continously supply nutrients by relocating to fresh plates.
PMID:18770545
A type of colony biofilm assay evidence that is used in a manual assertion.
rctauber
2016-12-05T09:33:18Z
eco
ECO:0006027
colony biofilm assay evidence used in manual assertion
true
A type of colony biofilm assay evidence that is used in a manual assertion.
ECO:RCT
A type of biofilm formation assay evidence in which mature bacterial biofilms are grown in a multiwell plate that has a growth medium continually pumped through the wells while waste is continually pumped out.
rctauber
2016-12-05T09:33:18Z
eco
ECO:0006028
Kadouri drip-fed biofilm assay evidence
A type of biofilm formation assay evidence in which mature bacterial biofilms are grown in a multiwell plate that has a growth medium continually pumped through the wells while waste is continually pumped out.
PMID:18770545
A type of Kadouri drip-fed biofilm assay evidence that is used in a manual assertion.
rctauber
2016-12-05T09:33:18Z
eco
ECO:0006029
Kadouri drip-fed biofilm assay evidence used in manual assertion
true
A type of Kadouri drip-fed biofilm assay evidence that is used in a manual assertion.
ECO:RCT
A type of co-immunoprecipitation evidence that is used in a manual assertion.
rctauber
2016-01-13T11:32:26Z
eco
ECO:0006030
co-immunoprecipitation evidence used in manual assertion
true
true
A type of co-immunoprecipitation evidence that is used in a manual assertion.
ECO:RCT
A type of immunolocalization evidence that is used in a manual assertion.
rctauber
2017-01-23T07:54:37Z
eco
ECO:0006031
immunolocalization evidence used in manual assertion
true
A type of immunolocalization evidence that is used in a manual assertion.
ECO:RCT
A type of experimental phenotypic evidence arising from experiment in which neuronal activity is manipulated using genetically encoded, optically activated neuronal actuators.
rctauber
2017-01-23T11:58:48Z
optogenetic actuator evidence
eco
ECO:0006032
optogenetic evidence
A type of experimental phenotypic evidence arising from experiment in which neuronal activity is manipulated using genetically encoded, optically activated neuronal actuators.
GOC:DOS
PMID:17035522
A type of optogenetic evidence that is used in a manual assertion.
rctauber
2017-01-23T11:58:48Z
eco
ECO:0006033
optogenetic evidence used in manual assertion
true
A type of optogenetic evidence that is used in a manual assertion.
ECO:RCT
A type of fluorescence evidence that is based on direct, quantitative measurement of some cellular property using a fluorescent sensor.
rctauber
2017-01-23T11:58:48Z
eco
ECO:0006034
Examples include sensors for ion concentration and potential difference across a membrane.
fluorescent sensor evidence
A type of fluorescence evidence that is based on direct, quantitative measurement of some cellular property using a fluorescent sensor.
GOC:DOS
A type of fluorescent sensor evidence that is used in a manual assertion.
rctauber
2017-01-23T11:58:48Z
eco
ECO:0006035
fluorescent sensor evidence used in manual assertion
true
A type of fluorescent sensor evidence that is used in a manual assertion.
ECO:RCT
A type of fluorescent sensor evidence that is based on direct, quantitative measurement of some cellular property using a genetically encoded fluorescent sensor.
rctauber
2017-01-23T11:58:48Z
optogenetic sensor evidence
eco
ECO:0006036
genetically encoded fluorescent sensor evidence
A type of fluorescent sensor evidence that is based on direct, quantitative measurement of some cellular property using a genetically encoded fluorescent sensor.
GOC:DOS
A type of genetically encoded fluorescent sensor evidence that is used in a manual assertion.
rctauber
2017-01-23T11:58:48Z
eco
ECO:0006037
genetically encoded fluorescent sensor evidence used in manual assertion
true
A type of genetically encoded fluorescent sensor evidence that is used in a manual assertion.
ECO:RCT
A type of fluorescent sensor evidence and electrophysiology assay evidence where the electrical properties of cells or tissues are studied using fluorescent sensors.
rctauber
2017-01-23T11:58:48Z
electrophysiology - optical assay evidence
eco
ECO:0006038
Examples include genetically encoded sensors that detect potential difference across plasma membrane.
genetically encoded fluorescent electrophysiology assay evidence
A type of fluorescent sensor evidence and electrophysiology assay evidence where the electrical properties of cells or tissues are studied using fluorescent sensors.
GOC:DOS
A type of genetically encoded fluorescent electrophysiology assay evidence that is used in a manual assertion.
rctauber
2017-01-23T11:58:48Z
eco
ECO:0006039
genetically encoded fluorescent electrophysiology assay evidence used in manual assertion
true
true
A type of genetically encoded fluorescent electrophysiology assay evidence that is used in a manual assertion.
ECO:RCT
A type of genetically encoded fluorescent electrophysiology assay evidence that is based on direct, quantitative measurement of ion concentration using a genetically encoded fluorescent sensor.
rctauber
2017-01-23T11:58:48Z
eco
ECO:0006040
Examples include the genetically encoded calcium indicator GCaMP.
genetically encoded fluorescent ion concentration sensor assay evidence
A type of genetically encoded fluorescent electrophysiology assay evidence that is based on direct, quantitative measurement of ion concentration using a genetically encoded fluorescent sensor.
GOC:DOS
A type of genetically encoded fluorescent ion concentration sensor assay evidence that is used in a manual assertion.
rctauber
2017-01-23T11:58:48Z
eco
ECO:0006041
genetically encoded fluorescent ion concentration sensor assay evidence used in manual assertion
true
A type of genetically encoded fluorescent ion concentration sensor assay evidence that is used in a manual assertion.
ECO:RCT
A type of cell fractionation evidence that is used in a manual assertion.
rctauber
2017-02-21T07:26:28Z
eco
ECO:0006042
cell fractionation evidence used in manual assertion
true
A type of cell fractionation evidence that is used in a manual assertion.
ECO:RCT
A type of electrophysiology assay evidence resulting from the use of electrodes to measure in vivo electrical activity coming from adjacent neurons.
rctauber
2017-02-21T07:26:28Z
eco
ECO:0006043
extracellular recording evidence
A type of electrophysiology assay evidence resulting from the use of electrodes to measure in vivo electrical activity coming from adjacent neurons.
url:http://www.nature.com/subjects/extracellular-recording
A type of extracellular recording evidence that is used in a manual assertion.
rctauber
2017-02-21T07:26:28Z
eco
ECO:0006044
extracellular recording evidence used in manual assertion
true
A type of extracellular recording evidence that is used in a manual assertion.
ECO:RCT
A type of extracellular recording evidence in which an extracellular microelectrode is used to measure the electrical activity of a single neuron.
rctauber
2017-02-21T07:26:28Z
eco
ECO:0006045
single-unit extracellular recording evidence
A type of extracellular recording evidence in which an extracellular microelectrode is used to measure the electrical activity of a single neuron.
doi:10.1385/0-89603-185-3:1
A type of single-unit extracellular recording evidence that is used in a manual assertion.
rctauber
2017-02-21T07:26:28Z
eco
ECO:0006046
single-unit extracellular recording evidence used in manual assertion
true
A type of single-unit extracellular recording evidence that is used in a manual assertion.
ECO:RCT
A type of extracellular recording evidence in which electrical activity is measured in either tissue or at a cellular level with microelectrodes.
rctauber
2017-02-21T07:26:28Z
local field potential recording evidence
eco
ECO:0006047
field potential recording evidence
A type of extracellular recording evidence in which electrical activity is measured in either tissue or at a cellular level with microelectrodes.
ECO:RCT
A type of field potential recording evidence that is used in a manual assertion.
rctauber
2017-02-21T07:26:28Z
eco
ECO:0006048
field potential recording evidence used in manual assertion
true
A type of field potential recording evidence that is used in a manual assertion.
ECO:RCT
A type of genetic transformation evidence that is used in a manual assertion
rctauber
02-21-2017T18:98:58Z
eco
ECO:0006049
genetic transformation evidence used in manual assertion
true
A type of genetic transformation evidence that is used in a manual assertion
ECO:RCT
A type of anti-sense experiment evidence that is used in a manual assertion.
rctauber
02-21-2017T18:98:58Z
eco
ECO:0006050
anti-sense experiment evidence used in manual assertion
true
A type of anti-sense experiment evidence that is used in a manual assertion.
ECO:RCT
A type of morpholino experiment evidence that is used in a manual assertion.
rctauber
02-21-2017T18:98:58Z
eco
ECO:0006051
morpholino experiment evidence used in manual assertion
true
A type of morpholino experiment evidence that is used in a manual assertion.
ECO:RCT
A type of RNAi evidence that is used in a manual assertion.
rctauber
02-21-2017T18:98:58Z
eco
ECO:0006052
RNAi evidence used in manual assertion
true
A type of RNAi evidence that is used in a manual assertion.
ECO:RCT
A type of experimental phenotypic evidence that arises from assaying the response of a cell, tissue, organ or organism following exposure to a receptor agonist or antagonist.
dosumis
2017-03-07T08:51:02Z
eco
ECO:0006053
pharmacological assay evidence
A type of experimental phenotypic evidence that arises from assaying the response of a cell, tissue, organ or organism following exposure to a receptor agonist or antagonist.
GOC:DOS
A type of experimental phenotypic evidence used in a manual assertion that arises from assaying the response of a cell, tissue, organ or organism following exposure to a receptor agonist or antagonist.
rctauber
2017-03-07T08:51:02Z
eco
ECO:0006054
pharmacological assay evidence used in manual assertion
true
A type of experimental phenotypic evidence used in a manual assertion that arises from assaying the response of a cell, tissue, organ or organism following exposure to a receptor agonist or antagonist.
GOC:DOS
A type of evidence where data generation is automated with equipment to allow for assaying samples or molecules in parallel.
mchibucos
2017-03-28T14:48:39Z
HT evidence
high-throughput evidence
high throughput cell biology evidence
high throughput screening evidence
eco
ECO:0006055
Some relevant articles include: PMID: 23340846, doi:10.1038/nmeth0607-523
high throughput evidence
A type of evidence where data generation is automated with equipment to allow for assaying samples or molecules in parallel.
ECO:MCC
A type of evidence that is used in a manual assertion where data generation is automated with equipment to allow for assaying large numbers of samples or molecules in parallel.
rctauber
2017-03-28T14:48:39Z
GOECO:HTP
HTP
inferred from high throughput experiment
eco
ECO:0006056
high throughput evidence used in manual assertion
true
A type of evidence that is used in a manual assertion where data generation is automated with equipment to allow for assaying large numbers of samples or molecules in parallel.
ECO:RCT
GOECO:HTP
inferred from high throughput experiment
HTP
GOECO:HTP
inferred from high throughput experiment
GOECO:HTP
A type of evidence that is used in an automatic assertion where data generation is automated with equipment to allow for assaying samples or molecules in parallel.
rctauber
2017-03-28T14:48:39Z
eco
ECO:0006057
high throughput evidence used in automatic assertion
true
A type of evidence that is used in an automatic assertion where data generation is automated with equipment to allow for assaying samples or molecules in parallel.
ECO:RCT
A type of high throughput evidence where a classical cell biology technique is automated with equipment to allow for assaying biomolecules in parallel.
mchibucos
2017-03-28T14:48:39Z
eco
omics experiment
ECO:0006058
HT methodologies may incorporate techniques from optics, chemistry, biology or image analysis (https://en.wikipedia.org/wiki/High_throughput_biology)
high throughput cell biology evidence
A type of high throughput evidence where a classical cell biology technique is automated with equipment to allow for assaying biomolecules in parallel.
ECO:MCC
A type of high throughput evidence used in a manual assertion where a classical cell biology technique is automated with equipment to allow for assaying biomolecules in parallel.
rctauber
2017-03-28T14:48:39Z
eco
ECO:0006059
high throughput cell biology evidence used in manual assertion
true
A type of high throughput evidence used in a manual assertion where a classical cell biology technique is automated with equipment to allow for assaying biomolecules in parallel.
ECO:RCT
A type of high throughput evidence used in an automatic assertion where a classical cell biology technique is automated with equipment to allow for assaying biomolecules in parallel.
rctauber
2017-03-28T14:48:39Z
eco
ECO:0006060
high throughput cell biology evidence used in automatic assertion
true
A type of high throughput evidence used in an automatic assertion where a classical cell biology technique is automated with equipment to allow for assaying biomolecules in parallel.
ECO:RCT
A type of wide-field fluorescence microscopy evidence used in a manual assertion where fluorescently tagged antibodies are imaged that are used to bind to their antigens.
rctauber
2017-05-15T08:57:07Z
eco
ECO:0006061
immunofluorescence wide-field microscopy evidence used in manual assertion
true
true
A type of wide-field fluorescence microscopy evidence used in a manual assertion where fluorescently tagged antibodies are imaged that are used to bind to their antigens.
ECO:SN
url:http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0057135
A type of wide-field microscopy evidence that is used in a manual assertion where pure white and ultraviolet light are produced by a mercury lamp, passed through an optical filter (excitation filter), and directed to a sample via a dichroic mirror, followed by detection of the fluorescent light by a camera after it passes through an emission filter.
rctauber
2017-05-15T09:01:19Z
eco
ECO:0006062
wide-field fluorescence microscopy evidence used in manual assertion
true
A type of wide-field microscopy evidence that is used in a manual assertion where pure white and ultraviolet light are produced by a mercury lamp, passed through an optical filter (excitation filter), and directed to a sample via a dichroic mirror, followed by detection of the fluorescent light by a camera after it passes through an emission filter.
ECO:SN
url:http://www.bristol.ac.uk/synaptic/research/techniques/widefield.html
A type of experimental phenotypic evidence that is used in a manual assertion where a gene and/or gene product is investigated in a transgenic organism that has been engineered to overexpress that gene product.
rctauber
2017-05-15T09:03:49Z
eco
ECO:0006063
over expression analysis evidence used in manual assertion
true
A type of experimental phenotypic evidence that is used in a manual assertion where a gene and/or gene product is investigated in a transgenic organism that has been engineered to overexpress that gene product.
PMID:22419077
A type of in vitro assay evidence that is used in a manual assertion where components are derived from resting, nonstimulated cells, therefore all reactions occur in vitro.
rctauber
2017-05-15T09:08:17Z
eco
ECO:0006064
cell-free assay evidence used in manual assertion
true
A type of in vitro assay evidence that is used in a manual assertion where components are derived from resting, nonstimulated cells, therefore all reactions occur in vitro.
PMID:18453125
A type of in vitro assay evidence that is used in a manual assertion where live cells are used.
rctauber
2017-05-15T09:11:13Z
eco
ECO:0006065
in vitro cell based assay evidence used in manual assertion
true
A type of in vitro assay evidence that is used in a manual assertion where live cells are used.
ECO:RCT
A type of fluorescence evidence where quantitative information on the diffusion properties of a sample is produced from the measurement of diffusion of fluorescent probes over time into an area that has been photobleached by a high-intensity laser pulse.
dosumis
rctauber
2017-05-16T10:55:40Z
FRAP evidence
eco
ECO:0006066
FRAP is a fluorescence microscopy-based technique.
fluorescence recovery after photobleaching evidence
A type of fluorescence evidence where quantitative information on the diffusion properties of a sample is produced from the measurement of diffusion of fluorescent probes over time into an area that has been photobleached by a high-intensity laser pulse.
PMID:26314367
FRAP is a fluorescence microscopy-based technique.
PMID:26314367
A type of fluorescence evidence that is used in a manual assertion where quantitative information on the diffusion properties of a sample is produced from the measurement of diffusion of fluorescent probes over time into an area that has been photobleached by a high-intensity laser pulse.
rctauber
2017-05-16T10:55:40Z
eco
ECO:0006067
fluorescence recovery after photobleaching evidence used in manual assertion
true
A type of high throughput nucleotide sequencing assay evidence used in a manual assertion based on high-throughput (HT) sequencing of fragmented cDNA molecules.
rctauber
2017-06-28T10:37:02Z
eco
ECO:0006068
RNA-seq evidence used in manual assertion
true
A type of high throughput nucleotide sequencing assay evidence used in a manual assertion based on high-throughput (HT) sequencing of fragmented cDNA molecules.
ECO:MCC
A type of high throughput nucleotide sequencing assay evidence used in an automatic assertion based on high-throughput (HT) sequencing of fragmented cDNA molecules.
rctauber
2017-06-28T10:37:02Z
eco
ECO:0006069
RNA-seq evidence used in automatic assertion
true
A type of high throughput nucleotide sequencing assay evidence used in an automatic assertion based on high-throughput (HT) sequencing of fragmented cDNA molecules.
ECO:MCC
A type of electron microscopy evidence resulting from the use of antibodies to identify the localization of antigens in cells and tissues.
dosumis
rctauber
2017-07-05T09:59:10Z
immunolabelling electron microscopy evidence
eco
ECO:0006070
immuno-labelling electron microscopy evidence
A type of electron microscopy evidence resulting from the use of antibodies to identify the localization of antigens in cells and tissues.
PMID:25151300
A type of electron microscopy evidence used in a manual assertion resulting from the use of antibodies to identify the localization of antigens in cells and tissues.
PMID:25151300
dosumis
rctauber
2017-07-05T09:59:10Z
eco
ECO:0006071
immuno-labelling electron microscopy evidence used in manual assertion
true
A type of electron microscopy evidence used in a manual assertion resulting from the use of antibodies to identify the localization of antigens in cells and tissues.
PMID:25151300
A type of super-resolution microscopy evidence resulting from the use of fluorescently-tagged antibodies to identify the localization of antigens in cells and tissue.
dosumis
rctauber
2017-07-05T09:59:10Z
eco
ECO:0006072
immunofluorescence super resolution microscopy evidence
A type of super-resolution microscopy evidence resulting from the use of fluorescently-tagged antibodies to identify the localization of antigens in cells and tissue.
PMID:19245833
A type of super-resolution microscopy evidence used in a manual assertion resulting from the use of fluorescently-tagged antibodies to identify the localization of antigens in cells and tissue.
dosumis
rctauber
2017-07-05T09:59:10Z
eco
ECO:0006073
immunofluorescence super resolution microscopy evidence used in manual assertion
true
A type of super-resolution microscopy evidence used in a manual assertion resulting from the use of fluorescently-tagged antibodies to identify the localization of antigens in cells and tissue.
PMID:19245833
A type of physical interaction evidence that is used in manual assertion where a cellular component subunit is isolated as part of purification of its larger complex.
rctauber
2017-09-14T09:19:19
eco
ECO:0006074
co-purification evidence used in manual assertion
true
A type of physical interaction evidence that is used in manual assertion where a cellular component subunit is isolated as part of purification of its larger complex.
TAIR:TED
A type of physical interaction evidence that is used in manual assertion that depends on the strength of the interaction between two entities.
rctauber
2017-09-14T09:19:20
eco
ECO:0006075
affinity evidence used in manual assertion
true
A type of physical interaction evidence that is used in manual assertion that depends on the strength of the interaction between two entities.
ECO:MCC
A type of affinity evidence that is used in manual assertion resulting from the binding of a molecule to a protein or protein complex.
rctauber
2017-09-14T09:19:21
eco
ECO:0006076
protein binding evidence used in manual assertion
true
true
A type of affinity evidence that is used in manual assertion resulting from the binding of a molecule to a protein or protein complex.
GO:0005515
A type of affinity evidence that is used in manual assertion where proteins of interest (bait and prey) are covalently linked to incomplete fragments of a third protein (reporter) and expressed in vivo, at which time interaction between bait and prey proteins brings reporter fragments in close enough proximity to allow them to reform and become a functional reporter protein.
rctauber
2017-09-14T09:19:22
eco
ECO:0006077
hybrid interaction evidence used in manual assertion
true
A type of affinity evidence that is used in manual assertion where proteins of interest (bait and prey) are covalently linked to incomplete fragments of a third protein (reporter) and expressed in vivo, at which time interaction between bait and prey proteins brings reporter fragments in close enough proximity to allow them to reform and become a functional reporter protein.
ECO:MCC
A type of affinity evidence that is used in manual assertion resulting from quantitation of the analyte which depends on the reaction of an antigen (analyte) and an antibody.
rctauber
2017-09-14T09:19:23
eco
ECO:0006078
immunological assay evidence used in manual assertion
true
A type of affinity evidence that is used in manual assertion resulting from quantitation of the analyte which depends on the reaction of an antigen (analyte) and an antibody.
ERO:0001362
A type of hybrid interaction evidence that is used in manual assertion that is based on a protein-DNA complementation assay where a single promoter acts as bait and is screened against a library of prey transcription factors.
rctauber
2017-09-14T09:19:24
eco
ECO:0006079
yeast one-hybrid evidence used in manual assertion
true
A type of hybrid interaction evidence that is used in manual assertion that is based on a protein-DNA complementation assay where a single promoter acts as bait and is screened against a library of prey transcription factors.
ECO:MCC
A type of physical interaction evidence that is used in a manual assertion that is based on detection of protein-protein interaction between a bait and prey protein by in vivo reconstitution of split-ubiquitin (when bait and prey interact) and release of a reporter protein.
rctauber
2017-09-14T09:19:25
eco
ECO:0006080
split-ubiquitin assay evidence used in manual assertion
true
A type of physical interaction evidence that is used in a manual assertion that is based on detection of protein-protein interaction between a bait and prey protein by in vivo reconstitution of split-ubiquitin (when bait and prey interact) and release of a reporter protein.
PMID:15064465
A type of physical interaction evidence that is used in a manual assertion that is based on detection of protein-protein interactions by separation of target proteins by SDS-PAGE which are blotted to a membrane, followed by denaturation and renaturation, probing with purified bait proteins, and detection of the target-bait complexes.
rctauber
2017-09-14T09:19:26
eco
ECO:0006081
far-Western blotting evidence used in manual assertion
true
A type of physical interaction evidence that is used in a manual assertion that is based on detection of protein-protein interactions by separation of target proteins by SDS-PAGE which are blotted to a membrane, followed by denaturation and renaturation, probing with purified bait proteins, and detection of the target-bait complexes.
PMID:18079728
A type of affinity evidence that is used in a manual assertion that results from separation of biochemical mixtures by selective binding of a compound to an immobilized compound on a polymeric matrix, subsequent removal of unattached components, and then displacement of the bond compound.
rctauber
2017-09-14T09:19:27
eco
ECO:0006082
affinity chromatography evidence used in manual assertion
true
A type of affinity evidence that is used in a manual assertion that results from separation of biochemical mixtures by selective binding of a compound to an immobilized compound on a polymeric matrix, subsequent removal of unattached components, and then displacement of the bond compound.
ECO:MCC
A type of affinity evidence that is used in a manual assertion resulting from the binding of a molecule to a nucleic acid.
rctauber
2017-09-14T09:19:28
eco
ECO:0006083
nucleic acid binding evidence used in manual assertion
true
A type of affinity evidence that is used in a manual assertion resulting from the binding of a molecule to a nucleic acid.
GO:0003676
A type of nucleic acid binding evidence that is used in a manual assertion resulting from an enzyme displaying binding activity to specific ribohomopolymer.
rctauber
2017-09-14T09:19:29
eco
ECO:0006084
ribohomopolymer binding assay evidence used in manual assertion
true
A type of nucleic acid binding evidence that is used in a manual assertion resulting from an enzyme displaying binding activity to specific ribohomopolymer.
PMC:102612
A type of protein binding evidence that is used in a manual assertion resulting from a metal ion binding to a protein at a specific binding site.
rctauber
2017-09-14T09:19:30
eco
ECO:0006085
protein:ion binding evidence used in manual assertion
true
A type of protein binding evidence that is used in a manual assertion resulting from a metal ion binding to a protein at a specific binding site.
PMID:2377604
A type of nucleic acid binding evidence that is used in a manual assertion in which DNA-protein binding is detected using labeled DNA as probes, hybridized to electrophoretically separated proteins.
rctauber
2017-09-14T09:19:31
eco
ECO:0006086
Southwestern blot evidence used in manual assertion
true
A type of nucleic acid binding evidence that is used in a manual assertion in which DNA-protein binding is detected using labeled DNA as probes, hybridized to electrophoretically separated proteins.
ECO:RCT
A type of nucleic acid binding evidence that is used in a manual assertion in which RNA-protein binding is detected using labeled RNA as probes, hybridized to electrophoretically separated proteins.
rctauber
2017-09-14T09:19:32
eco
ECO:0006087
Northwestern blot evidence used in manual assertion
true
A type of nucleic acid binding evidence that is used in a manual assertion in which RNA-protein binding is detected using labeled RNA as probes, hybridized to electrophoretically separated proteins.
ECO:RCT
A type of evidence that is used in a manual assertion arising from a physical interaction analysis where a combinatorial chemistry technique is used to identify oligonucleotides that bind to a target ligand.
rctauber
2017-09-14T09:19:33
eco
ECO:0006088
systematic evolution of ligands by exponential amplification evidence used in manual assertion
true
A type of evidence that is used in a manual assertion arising from a physical interaction analysis where a combinatorial chemistry technique is used to identify oligonucleotides that bind to a target ligand.
ECO:MCC
A type of hybrid interaction evidence that is used in a manual assertion that uses bacterial transformation with two plasmids to assess in vivo binding of a DNA-binding domain (bait) and DNA target site (prey).
rctauber
2017-09-14T09:19:34
eco
ECO:0006089
bacterial one-hybrid evidence used in manual assertion
true
A type of hybrid interaction evidence that is used in a manual assertion that uses bacterial transformation with two plasmids to assess in vivo binding of a DNA-binding domain (bait) and DNA target site (prey).
ECO:MCC
A type of oligonucleotide microarray evidence that is used in a manual assertion that detects binding of a tagged protein to an array of oligonucleotide probes representing potential binding sites.
rctauber
2017-09-14T09:19:35
eco
ECO:0006090
protein-binding microarray evidence used in manual assertion
true
true
A type of oligonucleotide microarray evidence that is used in a manual assertion that detects binding of a tagged protein to an array of oligonucleotide probes representing potential binding sites.
PMID:22146299
A type of genetic interaction evidence that is used in a manual assertion where a wild-type copy of the gene in question is inserted into a mutant cell to see if it restores the wild-type phenotype in the mutant background.
rctauber
2017-09-14T09:19:36
eco
ECO:0006091
functional complementation evidence used in manual assertion
true
A type of genetic interaction evidence that is used in a manual assertion where a wild-type copy of the gene in question is inserted into a mutant cell to see if it restores the wild-type phenotype in the mutant background.
PMID:27403640
A type of functional complementation evidence that is used in a manual assertion that is used in manual assertion resulting from the introduction of a transgene to prevent, or "rescue" an organism from a condition.
rctauber
2017-09-14T09:19:37
eco
ECO:0006092
transgenic rescue experiment evidence used in manual assertion
true
A type of functional complementation evidence that is used in a manual assertion that is used in manual assertion resulting from the introduction of a transgene to prevent, or "rescue" an organism from a condition.
url:http://www.nature.com/gt/journal/v11/n15/full/3302282a.html
A type of transient rescue experiment evidence that is used in a manual assertion.
rctauber
2017-09-14T09:19:38
eco
ECO:0006093
transient rescue experiment evidence used in manual assertion
true
A type of transient rescue experiment evidence that is used in a manual assertion.
ECO:RCT
A type of genetic interaction evidence that is used in a manual assertion resulting from a second mutation that either suppresses or enhances the phenotype expressed from an original mutation.
rctauber
2017-09-14T09:19:39
eco
ECO:0006094
suppressor/enhancer interaction evidence used in manual assertion
true
A type of genetic interaction evidence that is used in a manual assertion resulting from a second mutation that either suppresses or enhances the phenotype expressed from an original mutation.
url:http://www.wormbook.org/chapters/www:geneticsuppression/geneticsuppression.html
A type of genetic interaction evidence that is used in a manual assertion that is based on the phenotypic outcome of two mutations in unrelated genetic loci.
rctauber
2017-09-14T09:19:40
eco
ECO:0006095
double mutant phenotype evidence used in manual assertion
true
A type of genetic interaction evidence that is used in a manual assertion that is based on the phenotypic outcome of two mutations in unrelated genetic loci.
ECO:RCT
A type of genetic interaction evidence that is used in a manual assertion that is based on the suppression of one allelic effect by an allele at another genetic locus.
rctauber
2017-09-14T09:19:41
eco
ECO:0006096
epistatic interaction evidence used in manual assertion
true
A type of genetic interaction evidence that is used in a manual assertion that is based on the suppression of one allelic effect by an allele at another genetic locus.
PMID:18852697
A type of functional complementation evidence that is used in a manual assertion that is based on the insertion of a wild-type copy of a gene into a heterologous organism, with the mutation occurring in a homologous gene.
rctauber
2017-09-14T09:19:42
eco
ECO:0006097
functional complementation in heterologous system evidence used in manual assertion
true
A type of functional complementation evidence that is used in a manual assertion that is based on the insertion of a wild-type copy of a gene into a heterologous organism, with the mutation occurring in a homologous gene.
TAIR:TED
A type of mutant phenotype evidence based on the analysis of a mutation that allows normal function of the organism at low temperatures, but altered function at higher temperatures.
pgaudet
rctauber
2017-09-18T07:58:28
Ts mutation evidence
eco
ECO:0006098
temperature-sensitive mutant phenotype evidence
A type of mutant phenotype evidence based on the analysis of a mutation that allows normal function of the organism at low temperatures, but altered function at higher temperatures.
GOC:PG
PMID:19596904
A type of mutant phenotype evidence that is used in a manual assertion based on the analysis of a mutation that allows normal function of the organism at low temperatures, but altered function at higher temperatures.
pgaudet
rctauber
2017-09-18T07:58:28
eco
ECO:0006099
temperature-sensitive mutant phenotype evidence used in manual assertion
true
A type of mutant phenotype evidence that is used in a manual assertion based on the analysis of a mutation that allows normal function of the organism at low temperatures, but altered function at higher temperatures.
GOC:PG
PMID:19596904
A type of mutant phenotype evidence based on the analysis of a mutation which, in diploid organisms, must be present in both alleles for a phenotype to manifest itself.
pgaudet
rctauber
2017-09-18T07:58:28
eco
ECO:0006100
recessive mutant phenotype evidence
A type of mutant phenotype evidence based on the analysis of a mutation which, in diploid organisms, must be present in both alleles for a phenotype to manifest itself.
GOC:PG
NBK:21578
A type of mutant phenotype evidence that is used in a manual assertion based on the analysis of a mutation which, in diploid organisms, must be present in both alleles for a phenotype to manifest itself.
pgaudet
rctauber
2017-09-18T07:58:28
eco
ECO:0006101
recessive mutant phenotype evidence used in manual assertion
true
A type of mutant phenotype evidence that is used in a manual assertion based on the analysis of a mutation which, in diploid organisms, must be present in both alleles for a phenotype to manifest itself.
GOC:PG
NBK:21578
A type of high throughput evidence derived from high throughput analysis of differences in alleles of a corresponding gene.
GOC
rctauber
2017-10–05T07:39:47Z
eco
ECO:0007000
high throughput mutant phenotype evidence
A type of high throughput evidence derived from high throughput analysis of differences in alleles of a corresponding gene.
GO:IMP
A type of high throughput evidence that is used in a manual assertion derived from high throughput analysis of differences in alleles of a corresponding gene.
GOC
rctauber
2017-10–05T07:39:47Z
GOECO:HMP
HMP
inferred from high throughput mutant phenotype
eco
ECO:0007001
When using the HMP evidence code, the guidelines for IMP should be adhered to (http://geneontology.org/page/imp-inferred-mutant-phenotype)
high throughput mutant phenotype evidence used in manual assertion
true
true
A type of high throughput evidence that is used in a manual assertion derived from high throughput analysis of differences in alleles of a corresponding gene.
GO:IMP
GOECO:HMP
inferred from high throughput mutant phenotype
HMP
GOECO:HMP
inferred from high throughput mutant phenotype
GOECO:HMP
A type of high throughput evidence derived from the high throughput analysis of the effect that a given gene has on another gene or genes, and products.
GOC
rctauber
2017-10–05T07:39:47Z
eco
ECO:0007002
high throughput genetic interaction evidence
A type of high throughput evidence derived from the high throughput analysis of the effect that a given gene has on another gene or genes, and products.
PMID:11822023
A type of high throughput evidence that is used in a manual assertion derived from the high throughput analysis of the effect that a given gene has on another gene or genes, and products.
GOC
rctauber
2017-10–05T07:39:47Z
GOECO:HGI
HGI
inferred from high throughput genetic interaction
eco
ECO:0007003
When using the HGI evidence code, the guidelines for IGI should be adhered to (http://geneontology.org/page/igi-inferred-genetic-interaction)
high throughput genetic interaction evidence used in manual assertion
true
true
A type of high throughput evidence that is used in a manual assertion derived from the high throughput analysis of the effect that a given gene has on another gene or genes, and products.
PMID:11822023
GOECO:HGI
inferred from high throughput genetic interaction
HGI
GOECO:HGI
inferred from high throughput genetic interaction
GOECO:HGI
A type of high throughput evidence derived from the high throughput direct measurement of some aspect of a biological feature.
GOC
rctauber
2017-10–05T07:39:47Z
eco
ECO:0007004
high throughput direct assay evidence
A type of high throughput evidence derived from the high throughput direct measurement of some aspect of a biological feature.
ECO:MCC
A type of high throughput evidence that is used in a manual assertion derived from the high throughput direct measurement of some aspect of a biological feature.
GOC
rctauber
2017-10–05T07:39:47Z
GOECO:HDA
HDA
inferred from high throughput direct assay
eco
ECO:0007005
When using the HDA evidence code, the guidelines for IDA should be adhered to (http://geneontology.org/page/ida-inferred-direct-assay)
high throughput direct assay evidence used in manual assertion
true
true
A type of high throughput evidence that is used in a manual assertion derived from the high throughput direct measurement of some aspect of a biological feature.
ECO:MCC
GOECO:HDA
inferred from high throughput direct assay
HDA
GOECO:HDA
inferred from high throughput direct assay
GOECO:HDA
A type of high throughput evidence derived from the high throughput characterization of gene expression.
GOC
rctauber
2017-10–05T07:39:47Z
eco
ECO:0007006
high throughput expression pattern evidence
A type of high throughput evidence derived from the high throughput characterization of gene expression.
GO:IEP
A type of high throughput evidence that is used in a manual assertion derived from the high throughput characterization of gene expression.
GOC
rctauber
2017-10–05T07:39:47Z
GOECO:HEP
HEP
inferred from high throughput expression pattern
eco
ECO:0007007
When using the HEP evidence code, the guidelines for EXP should be adhered to (http://geneontology.org/page/iep-inferred-expression-pattern)
high throughput expression pattern evidence used in manual assertion
true
true
A type of high throughput evidence that is used in a manual assertion derived from the high throughput characterization of gene expression.
GO:IEP
GOECO:HEP
inferred from high throughput expression pattern
HEP
GOECO:HEP
inferred from high throughput expression pattern
GOECO:HEP
A type of protein binding evidence in which radioactive ligands are used to measure receptor-ligand interactions, such as in determining selectivity for a particular ligand.
fjungo
rctauber
2017-12-15T10:46:19Z
radioactive ligand binding assay evidence
radiometric ligand-binding assay evidence
competitive binding assay evidence
eco
ECO:0007008
radioligand binding assay evidence
A type of protein binding evidence in which radioactive ligands are used to measure receptor-ligand interactions, such as in determining selectivity for a particular ligand.
PMID:27471749
A type of radioligand binding assay evidence that is used in a manual assertion.
rctauber
2017-12-15T10:48:44Z
eco
ECO:0007009
radioligand binding assay evidence used in manual assertion
true
A type of radioligand binding assay evidence that is used in a manual assertion.
ECO:RCT