1.2
24:11:2015 11:44
For more details, see https://github.com/evidenceontology/evidenceontology
OBO-Edit 2.3.1
eco
snadendla
definition
GO biological process terms should be used in the GO with/from field
GO cellular component terms should be used in the GO with/from field
Chemical entity IDs should be used in the GO with/from field
Gene IDs should be used in the GO with/from field
GO molecular function terms should be used in the GO with/from field
Protein IDs should be used in the GO with/from field
Protein complex IDs should be used in the GO with/from field
Transcript IDs should be used in the GO with/from field
subset_property
has_alternative_id
has_broad_synonym
database_cross_reference
has_exact_synonym
has_narrow_synonym
has_obo_format_version
has_obo_namespace
has_related_synonym
in_subset
shorthand
used_in
2010-12-09T05:00:20Z
A relation connecting a piece of evidence to an assertion method, where that assertion method is supported by the evidence.
ECO:9000000
In the future we may use a more generic relation with weaker domain and range constraints taken from IAO, RO or OBI.
eco
mchibucos
used_in
used_in
A relation connecting a piece of evidence to an assertion method, where that assertion method is supported by the evidence.
GOC:cjm
uses
ECO:9000001
eco
uses
uses
evidence
A type of information that is used to support an assertion.
ECO:0000000
eco
evidence code
evidence_code
A type of information that is used to support an assertion.
ECO:MCC
inference from background scientific knowledge
A curator inference that links the current annotation to a different evidence-based annotation via background knowledge of the curator.
ECO:0000001
IC
eco
inferred by curator
A curator inference that links the current annotation to a different evidence-based annotation via background knowledge of the curator.
ECO:MCC
ECO:go
GO:IC
inferred by curator
GO:IC
IC
direct assay evidence
ECO:0000002
Experimental evidence that is based on direct measurement of some aspect of a biological feature.
eco
ECO:MCC
Experimental evidence that is based on direct measurement of some aspect of a biological feature.
GO:IDA
reconstitution assay evidence
A type of direct assay evidence based on reconstructing a biological sample from its disassociated state to its original state.
ECO:0000003
eco
A type of direct assay evidence based on reconstructing a biological sample from its disassociated state to its original state.
ECO:KAV
PMID:26029343
cell fractionation evidence
A type of fractionation evidence where sub-cellular components are separated based on their physical properties such as density in a sucrose density gradient.
ECO:0000004
IDA: cell fractionation
If using this term for Gene Ontology annotation, it would be used most typically for annotations to the cellular component ontology.
eco
A type of fractionation evidence where sub-cellular components are separated based on their physical properties such as density in a sucrose density gradient.
ECO:KIM
TAIR:TED
enzyme assay evidence
ECO:0000005
IDA: enzyme assays
PSI-MI:MI:0415
Used when an annotation is made based on assays that determine the catalytic activity of enzymes.
eco
TAIR:TED
Used when an annotation is made based on assays that determine the catalytic activity of enzymes.
enzymatic study
PSI-MI:MI:0415
experimental evidence
An evidence type that is based on the results of a laboratory assay.
ECO:0000006
EXP
eco
inferred from experiment
An evidence type that is based on the results of a laboratory assay.
ECO:MCC
GOC:ecd
GO:EXP
inferred from experiment
EXP
GO:EXP
immunofluorescence evidence
A type of protein detection assay evidence where a fluorescently labeled antibody is used to detect the presence or localization of a biomolecule within a cell.
ECO:0000007
IDA: immunofluorescence
eco
A type of protein detection assay evidence where a fluorescently labeled antibody is used to detect the presence or localization of a biomolecule within a cell.
ECO:MCC
TAIR:TED
expression pattern evidence
ECO:0000008
Experimental evidence that is based on characterization of gene expression.
IEP
Use this evidence type when the annotation is inferred from the timing or location of expression of a gene. It may be difficult to determine whether the expression pattern truly indicates that a gene plays a role in a given process.
eco
inferred from expression pattern
ECO:MCC
Experimental evidence that is based on characterization of gene expression.
GO:IEP
GO:IEP
IEP
GO:IEP
inferred from expression pattern
transcript expression evidence
ECO:0000009
eco
protein expression evidence
ECO:0000010
eco
genetic interaction evidence
ECO:0000011
TAIR:TED:0000006
eco
functional complementation evidence
ECO:0000012
IGI: functional complementation
Used when an annotation is made based on a functional complementation assay in which a wild-type copy of the gene in question is inserted into a mutant background in the organism of the gene's origin or a heterologous organism with a mutation in the homologous gene.
eco
TAIR:TED
Used when an annotation is made based on a functional complementation assay in which a wild-type copy of the gene in question is inserted into a mutant background in the organism of the gene's origin or a heterologous organism with a mutation in the homologous gene.
transgenic rescue experiment evidence
ECO:0000013
eco
mutant phenotype evidence
ECO:0000015
The IMP evidence code covers those cases when the function, process or cellular localization of a gene product is inferred based on differences in the function, process, or cellular localization between two different alleles of the corresponding gene. The IMP code is used for cases where one allele may be designated 'wild-type' and another as 'mutant'. It is also used in cases where allelic variation occurs naturally and no specific allele is designated as wild-type or mutant. Caution should be used when making annotations from gain-of-function mutations as it may be difficult to infer a gene's normal function from a gain of function mutation, although it is sometimes possible.
eco
GO:IMP
The IMP evidence code covers those cases when the function, process or cellular localization of a gene product is inferred based on differences in the function, process, or cellular localization between two different alleles of the corresponding gene. The IMP code is used for cases where one allele may be designated 'wild-type' and another as 'mutant'. It is also used in cases where allelic variation occurs naturally and no specific allele is designated as wild-type or mutant. Caution should be used when making annotations from gain-of-function mutations as it may be difficult to infer a gene's normal function from a gain of function mutation, although it is sometimes possible.
loss-of-function mutant phenotype evidence
ECO:0000016
eco
ectopic expression evidence
ECO:0000017
IMP: analysis of overexpression/ectopic expression phenotype
Used when an annotation is made based on the analysis of the phenotype of a wild-type or mutant transgenic organism that has been engineered to overexpress or ectopically express the gene product in question.
eco
TAIR:TED
Used when an annotation is made based on the analysis of the phenotype of a wild-type or mutant transgenic organism that has been engineered to overexpress or ectopically express the gene product in question.
anti-sense experiment evidence
ECO:0000018
IMP: anti-sense experiments
Used when an annotation is based on a phenotype observed when expressing an anti-sense version of a gene product in a wild-type (for that gene product) background.
eco
TAIR:TED
Used when an annotation is based on a phenotype observed when expressing an anti-sense version of a gene product in a wild-type (for that gene product) background.
RNAi evidence
ECO:0000019
IMP: RNAi experiment
Inference based on a phenotype observed when expressing an RNAi construct that includes a fragment of the gene product in a wild-type (for that gene product) background. A double-stranded RNA specifically suppresses the expression of the gene bearing its complementary sequence.
eco
Inference based on a phenotype observed when expressing an RNAi construct that includes a fragment of the gene product in a wild-type (for that gene product) background. A double-stranded RNA specifically suppresses the expression of the gene bearing its complementary sequence.
TAIR:TED
specific protein inhibition evidence
A type of protein assay evidence based on the inhibition of the molecular function of a protein.
ECO:0000020
eco
A type of protein assay evidence based on the inhibition of the molecular function of a protein.
ECO:MCC
physical interaction evidence
ECO:0000021
Experimental evidence that is based on characterization of an interaction between a gene product and another molecule.
Molecules interacted with might include protein, nucleic acid, ion, or complex.
PSI-MI:MI:0045
eco
experimental interaction detection
PSI-MI:MI:0045
ECO:MCC
Experimental evidence that is based on characterization of an interaction between a gene product and another molecule.
co-purification evidence
A type of physical interaction evidence where a cellular component subunit is isolated as part of purification of its larger complex.
ECO:0000022
IPI: co-purification
PSI-MI:MI:0025
eco
copurification
PSI-MI:MI:0025
A type of physical interaction evidence where a cellular component subunit is isolated as part of purification of its larger complex.
TAIR:TED
affinity evidence
A type of physical interaction evidence that depends on the strength of the interaction between two entities.
ECO:0000023
PSI-MI:MI:0400
eco
ligand binding evidence
A type of physical interaction evidence that depends on the strength of the interaction between two entities.
ECO:MCC
PSI-MI:MI:0400
affinity technology
PSI-MI:MI:0400
protein binding evidence
ECO:0000024
eco
hybrid interaction evidence
A type of affinity evidence where proteins of interest (bait and prey) are covalently linked to incomplete fragments of a third protein (reporter) and expressed in vivo, at which time interaction between bait and prey proteins brings reporter fragments in close enough proximity to allow them to reform and become a functional reporter protein.
ECO:0000025
PSI-MI:MI:0090
Typically enzymes which confer resistance to antibiotics, such as Dihydrofolate reductase or Beta-lactamase, or proteins that give colorimetric or fluorescent signals are used. The Bait protein is generally the protein under study and the methods are readily adaptable to highthroughput mode.
eco
protein complementation assay
PSI-MI:MI:0090
A type of affinity evidence where proteins of interest (bait and prey) are covalently linked to incomplete fragments of a third protein (reporter) and expressed in vivo, at which time interaction between bait and prey proteins brings reporter fragments in close enough proximity to allow them to reform and become a functional reporter protein.
ECO:MCC
PSI-MI:MI:0090
nucleic acid hybridization evidence
ECO:0000026
eco
structural similarity evidence
A type of similarity evidence based on structural similarity of an annotated gene or gene product to another gene or group of genes.
ECO:0000027
For GO annotation, in the case of a single gene, an accession for the related gene's sequence is entered in the evidence_with field.
eco
A type of similarity evidence based on structural similarity of an annotated gene or gene product to another gene or group of genes.
ECO:MCC
TAIR:TED
motif similarity evidence
ECO:0000028
ISS: recognized domains
Used when an annotation is made based on the presence of a recognized domain or motif in a gene product's (usually protein) primary sequence.
eco
TAIR:TED
Used when an annotation is made based on the presence of a recognized domain or motif in a gene product's (usually protein) primary sequence.
match to InterPro signature evidence
ECO:0000029
eco
BLAST evidence used in manual assertion
A type of BLAST evidence that is used in a manual assertion.
ECO:0000030
curated BLAST analysis
eco
A type of BLAST evidence that is used in a manual assertion.
ECO:MCC
true
true
protein BLAST evidence used in manual assertion
ECO:0000031
GO_REF:0000012
GO_REF:0000027
Protein BLAST evidence that is used in a manual assertion.
curated protein BLAST analysis
eco
true
Pairwise alignment (TIGR)
GO_REF:0000012
true
BLAST search criteria for ISS assignment in PAMGO_GAT
GO_REF:0000027
ECO:MCC
Protein BLAST evidence that is used in a manual assertion.
nucleotide BLAST evidence used in manual assertion
ECO:0000032
Nucleotide BLAST evidence that is used in a manual assertion.
curated nucleic acid BLAST analysis
eco
ECO:MCC
Nucleotide BLAST evidence that is used in a manual assertion.
true
true
traceable author statement
An author statement that is based on a cited reference.
ECO:0000033
The traceable author statement (TAS) evidence code covers author statements that are attributed to a cited source. Typically this type of information comes from review articles. Material from the introductions and discussion sections of non-review papers may also be suitable if another reference is cited as the source of experimental work or analysis. When annotating with this code the curator should use caution and be aware that authors often cite papers dealing with experiments that were performed in organisms different from the one being discussed in the paper at hand. Thus a problem with the TAS code is that it may turn out from following up the references in the paper that no experiments were performed on the gene in the organism actually being characterized in the primary paper. For this reason we recommend (when time and resources allow) that curators track down the cited paper and annotate directly from the experimental paper using the appropriate experimental evidence code. When this is not possible and it is necessary to annotate from reviews, the TAS code is the appropriate code to use for statements that are associated with a cited reference. Once an annotation has been made to a given term using an experimental evidence code, we recommend removing any annotations made to the same term using the TAS evidence code.
eco
An author statement that is based on a cited reference.
ECO:MCC
GO:TAS
non-traceable author statement
An author statement that is not associated with results presented or a cited reference.
ECO:0000034
The non-traceable author statement evidence code should be used in all cases where the author makes a statement that a curator wants to capture but for which there are neither results presented nor a specific reference cited in the source used to make the annotation. The source of the information may be peer reviewed papers, textbooks, database records or vouchered specimens.
eco
An author statement that is not associated with results presented or a cited reference.
ECO:MCC
no biological data found
A curator inference that results from research where no information about a biological feature was found in the scientific literature, at biological databases, or within other resources.
An assertion of "no biological data found" carries the assumption that a more-or-less exhaustive search has been conducted.
ECO:0000035
ND
eco
no biological data available
GO:ND
no biological data available
GO:ND
ND
A curator inference that results from research where no information about a biological feature was found in the scientific literature, at biological databases, or within other resources.
ECO:MCC
GO:ND
not_recorded
An evidence that reflects an annotation was made before curators began tracking evidence types.
ECO:0000037
NR
The evidence not_recorded appears in some legacy annotations; it should not be used for new annotations.
eco
not recorded
true
An evidence that reflects an annotation was made before curators began tracking evidence types.
ECO:MCC
GO:NR
GO:NR
NR
GO:NR
not recorded
transient rescue experiment evidence
ECO:0000038
eco
protein assay evidence
ECO:0000039
eco
immunological assay evidence
ECO:0000040
eco
similarity evidence
An evidence type that is based on comparing likeness of distinct biological entities.
ECO:0000041
IS
eco
inferred from similarity
An evidence type that is based on comparing likeness of distinct biological entities.
ECO:MCC
PhenoScape:IS
gain-of-function mutant phenotype evidence
ECO:0000042
eco
sequence similarity evidence
A sequence similarity analysis may involve a gene or a gene product, and it could be based on similarity to a single other gene or to a group of other genes.
A type of similarity based on biomolecular sequence.
ECO:0000044
ISS
eco
inferred from sequence or structural similarity
inferred from sequence similarity
GO:ISS
ISS
A type of similarity based on biomolecular sequence.
ECO:MCC
TAIR:TED
GO:ISS
inferred from sequence or structural similarity
spatial pattern of protein expression evidence
ECO:0000045
eco
protein expression level evidence
ECO:0000046
eco
spatial pattern of transcript expression evidence
ECO:0000047
eco
transcript expression level evidence
ECO:0000048
eco
reporter gene assay evidence
ECO:0000049
IEP: expression of a reporter gene
Used when an annotation is made on the basis of the expression pattern of a reporter gene. The reporter gene may consist of the native promoter of the gene in question that drives the expression of a readily assayable gene product such as GUS or GFP. The reporter gene may also be a marker of a particular type of physiological response.
eco
TAIR:TED
Used when an annotation is made on the basis of the expression pattern of a reporter gene. The reporter gene may consist of the native promoter of the gene in question that drives the expression of a readily assayable gene product such as GUS or GFP. The reporter gene may also be a marker of a particular type of physiological response.
voucher specimen analysis evidence
ECO:0000050
IVS
Used when an annotation is made on the basis of for a phenotype description for a species or higher level group that given by an author who explicitly references an observation of a voucher specimen(s). Voucher specimens are defined as those specimens with permanent museum catalog numbers. Thus it would be possible for a person to examine this particular specimen and observe the annotated phenotype.
eco
PhenoScape:DOA
Used when an annotation is made on the basis of for a phenotype description for a species or higher level group that given by an author who explicitly references an observation of a voucher specimen(s). Voucher specimens are defined as those specimens with permanent museum catalog numbers. Thus it would be possible for a person to examine this particular specimen and observe the annotated phenotype.
genetic similarity evidence
A genetic similarity analysis might consider genetic markers, polymorphisms, alleles, or other characteristics sometimes considered as part of the field of traditional genetics. Although an attempt has been made to treat as distinct the concepts of "genetic", "genotypic", "genomic", and "sequence", there is considerable overlap in usage throughout the field of biology.
A type of similarity based on genotype without respect to expression.
ECO:0000051
IGTS
eco
inferred from genetic similarity
A type of similarity based on genotype without respect to expression.
ECO:MCC
PhenoScape:IGTS
suppressor/enhancer interaction evidence
ECO:0000052
IGI: 'traditional' genetic interactions (e.g. suppressors, synthetic lethals)
TAIR:TED:0000063
eco
computational combinatorial evidence
A type of combinatorial analysis where data are combined and evaluated by an algorithm.
Combinatorial analyses could include experimental or computational results. Examples include: (i) large-scale experiment such as a genome-wide two-hybrid or genome-wide synthetic interactions; (ii) integration of large-scale data sets of various types; and (iii) text-based-computation, e.g. text-mining. For simple sequence comparisons, one should use the sequence similarity analysis evidence type. For microarray results alone, expression pattern analysis is appropriate; whereas, large-scale computational analysis should be used when microarray results are combined with the results of other types of large-scale experiments.
ECO:0000053
TAIR:TED:0000004
eco
A type of combinatorial analysis where data are combined and evaluated by an algorithm.
ECO:MCC
ECO:go
double mutant phenotype evidence
ECO:0000054
IGI: double mutant analysis
Used when an annotation is made based on the phenotype of double mutant organism that contains a mutation in the gene product of interest in addition to a second mutation at an unrelated locus.
eco
TAIT:TED
Used when an annotation is made based on the phenotype of double mutant organism that contains a mutation in the gene product of interest in addition to a second mutation at an unrelated locus.
array experiment evidence
ECO:0000055
eco
epistatic interaction evidence
ECO:0000056
IGI: epistatic interactions
Used when an annotation is based on results of epistatis analysis of an allele of the gene in question and a mutant allele at another locus.
eco
TAIR:TED
Used when an annotation is based on results of epistatis analysis of an allele of the gene in question and a mutant allele at another locus.
phenotypic similarity evidence
A type of similarity based on the expression of a genotype in an environment.
ECO:0000057
IPTS
Phenotype is defined as the outcome of the expression of a genotype in a given environment. A comparison might involve whole organisms or sub-parts of organisms.
eco
inferred from phenotypic similarity
A type of similarity based on the expression of a genotype in an environment.
ECO:MCC
PhenoScape:IPTS
expression microarray evidence
ECO:0000058
eco
experimental phenotypic evidence
ECO:0000014
ECO:0000059
Experimental evidence that is based on the expression of a genotype in an environment.
eco
inferred from phenotype
ECO:MCC
Experimental evidence that is based on the expression of a genotype in an environment.
positional similarity evidence
ECO:0000060
IPS
Used when an annotation is made based on the similarity of the location and or arrangement of structures.
eco
PhenoScape:IPS
Used when an annotation is made based on the similarity of the location and or arrangement of structures.
quantitative trait analysis evidence
A type of experimental phenotypic evidence where an annotation is made for a gene product that has not been cloned but is associated with a quantitative trait locus.
ECO:0000061
IGI: quantitative trait analysis
eco
A type of experimental phenotypic evidence where an annotation is made for a gene product that has not been cloned but is associated with a quantitative trait locus.
TAIR:tn
genomic microarray evidence
ECO:0000062
eco
compositional similarity evidence
ECO:0000063
ICS
Used when an annotation is made based on the similarity of the histological makeup of structures.
eco
PhenoScape:ICS
Used when an annotation is made based on the similarity of the histological makeup of structures.
functional complementation in heterologous system evidence
ECO:0000064
IGI: functional complementation in heterologous system
Used when an annotation is made based on a functional complementation assay in which a wild-type copy of the gene in question is inserted into a heterologous organism with a mutation in the homologous gene.
eco
TAIR:TED
Used when an annotation is made based on a functional complementation assay in which a wild-type copy of the gene in question is inserted into a heterologous organism with a mutation in the homologous gene.
CpG island microarray evidence
ECO:0000065
eco
yeast one-hybrid evidence
A type of hybrid interaction evidence that is based on a protein-DNA complementation assay where a single promoter acts as bait and is screened against a library of prey transcription factors.
ECO:0000066
IPI: yeast one-hybrid assay
PSI-MI:MI:0432
The assay involves screening a library of candidate proteins for the ability bind to a target, cis-regulatory element or any other short, DNA binding sequence placed 5' to a yeast reporter gene (TAIR:TED).
eco
A type of hybrid interaction evidence that is based on a protein-DNA complementation assay where a single promoter acts as bait and is screened against a library of prey transcription factors.
ECO:MCC
PSI-MI:MI:0432
TAIR:TED
one hybrid
PSI-MI:MI:0432
developmental similarity evidence
ECO:0000067
IDS
Used when an annotation is made based on the similarity of embryological and/or post-embryonic origin of structures.
eco
PhenoScape:IDS
Used when an annotation is made based on the similarity of embryological and/or post-embryonic origin of structures.
yeast 2-hybrid evidence
ECO:0000068
IPI: yeast two-hybrid assay
Used when an annotation is based on the interaction between two proteins in a yeast two-hybrid assay. The assay involves screening a trap-tagged library with a bait-tagged vector. The library is tagged with a DNA-binding domain (trap) and the bait is tagged with a transcriptional activation domain. Interaction between a library-trap protein and the bait results in activation of a yeast reporter gene whose transcription can be experimentally assayed.
eco
TAIR:TED
Used when an annotation is based on the interaction between two proteins in a yeast two-hybrid assay. The assay involves screening a trap-tagged library with a bait-tagged vector. The library is tagged with a DNA-binding domain (trap) and the bait is tagged with a transcriptional activation domain. Interaction between a library-trap protein and the bait results in activation of a yeast reporter gene whose transcription can be experimentally assayed.
differential methylation hybridization evidence
ECO:0000069
eco
co-immunoprecipitation evidence
A type of immunoprecipitation evidence that involves precipitating two or more proteins via binding to an antibody specific to a single protein, followed by protein identification.
ECO:0000070
IPI: co-immunoprecipitation
If performing GO annotation, the interacting protein is referenced in the evidence_with column.
PSI-MI:MI:0019
eco
coimmunoprecipitation
PSI-MI:MI:0019
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
morphological similarity evidence
ECO:0000071
IMS
Used when an annotation is made based on the similarity of the shape, structure or overall configuration of structures.
eco
PhenoScape:IMS
Used when an annotation is made based on the similarity of the shape, structure or overall configuration of structures.
Sos-recruitment assay evidence
A type of physical interaction evidence that is based on a genetic screening system that detects protein-protein interactions and is not based on a transcriptional readout.
ECO:0000072
IPI: Sos-recruitment assay
eco
true
A type of physical interaction evidence that is based on a genetic screening system that detects protein-protein interactions and is not based on a transcriptional readout.
TAIR:TED
experimental genomic evidence
ECO:0000073
Experimental evidence that characterizes an attribute of the genome underlying a gene product.
eco
inferred from genomic analysis
ECO:MCC
Experimental evidence that characterizes an attribute of the genome underlying a gene product.
split-ubiquitin assay evidence
ECO:0000074
IPI: split-ubiquitin assay
PSI-MI:MI:0112
Used when an annotation is based on the interaction of two proteins in a split-ubiquitin assay. The bait protein is fused to the C-terminal ubiquitin (Cub) domain followed by a reporter protein, and the prey protein is fused to a mutated N terminal ubiquiting (NubG) domain. If bait and prey interact, their interaction brings the NubG and Cub domains close enough together to reconstitute split-ubiquitin, resulting in the release of the reporter protein by the action of the UBPs.
eco
TAIR:TED
Used when an annotation is based on the interaction of two proteins in a split-ubiquitin assay. The bait protein is fused to the C-terminal ubiquitin (Cub) domain followed by a reporter protein, and the prey protein is fused to a mutated N terminal ubiquiting (NubG) domain. If bait and prey interact, their interaction brings the NubG and Cub domains close enough together to reconstitute split-ubiquitin, resulting in the release of the reporter protein by the action of the UBPs.
ubiquitin reconstruction
PSI-MI:MI:0112
gene expression similarity evidence
ECO:0000075
IGES
Used when an annotation is made based on the similarity of expression of genes in structures.
eco
PhenoScape:IGES
Used when an annotation is made based on the similarity of expression of genes in structures.
far-Western blotting evidence
ECO:0000076
IPI: far-Western analysis
PSI-MI:MI:0047
Used when an annotation is based on the interaction of protein with another in a far-Western assay. The assay involves separating target proteins on an SDS-PAGE gel, blotting to a membrane, hybridization with a protein probe and visualization using a probe-directed antibody. The interacting protein is referenced in the evidence_with column.
eco
TAIR:TED
Used when an annotation is based on the interaction of protein with another in a far-Western assay. The assay involves separating target proteins on an SDS-PAGE gel, blotting to a membrane, hybridization with a protein probe and visualization using a probe-directed antibody. The interacting protein is referenced in the evidence_with column.
methylation-specific polymerase chain reaction evidence
ECO:0000077
eco
methylation-specific PCR evidence
southern hybridization evidence
ECO:0000078
ISS: Southern blotting
Southern blot
Used when an annotation is based on the hybridization of a probe derived from the gene in question with a gene of known function/process/component. Can also be used when a probe derived from a gene of known function/process/component hybridizes with the gene in question.
eco
TAIR:TED
Used when an annotation is based on the hybridization of a probe derived from the gene in question with a gene of known function/process/component. Can also be used when a probe derived from a gene of known function/process/component hybridizes with the gene in question.
affinity chromatography evidence
"Used when an annotation is made based on affinity chromatography, which is a selective separation technique by which a compound (e.g., an antibody) is immobilized on a polymeric matrix and used to bind selectively other compounds. Following removal of the unattached components, the bound compound is displaced by changing the concentration of protons, salts, or cofactors in the eluent" (from original definition by TAIR:TED). Types of highly specific interaction might include those of antigen and antibody, enzyme and substrate, or receptor and ligand.
A type of affinity evidence that results from separation of biochemical mixtures by selective binding of a compound to an immobilized compound on a polymeric matrix, subsequent removal of unattached components, and then displacement of the bond compound.
ECO:0000079
IDA: affinity chromatography
PSI-MI:MI:0004
eco
affinity chromatography technology
PSI-MI:MI:0004
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
phylogenetic evidence
A type of similarity that indicates common ancestry.
ECO:0000080
IP
eco
IP
PhenoScape:IP
A type of similarity that indicates common ancestry.
ECO:MCC
PhenoScape:IP
targeting sequence prediction evidence
ECO:0000081
ISS: targeting sequence prediction
Used when a component annotation is made based on the presence of a targeting sequence in a protein's primary sequence. The presence of the targeting sequence may be detected by computational prediction and/or the author's manual examination of the sequence.
eco
TAIR:TED
Used when a component annotation is made based on the presence of a targeting sequence in a protein's primary sequence. The presence of the targeting sequence may be detected by computational prediction and/or the author's manual examination of the sequence.
polymerase chain reaction evidence
ECO:0000082
PCR evidence
eco
transmembrane domain prediction evidence
ECO:0000083
ISS: transmembrane domain prediction
Used when a component annotation is made based on the presence of one or more transmembrane domains in a protein's primary sequence. The presence of the transmembrane domains may be detected by computational prediction and/or the author's manual examination of the sequence.
eco
TAIR:TED
Used when a component annotation is made based on the presence of one or more transmembrane domains in a protein's primary sequence. The presence of the transmembrane domains may be detected by computational prediction and/or the author's manual examination of the sequence.
gene neighbors evidence
2009-03-20T11:55:18Z
ECO:0000084
Evidence that supports the identity of a gene product on the basis of the identity of neighboring genes.
GO_REF:0000025
Genomic cluster analyses include synteny and operon structure.
ICL
eco
inferred from genome cluster
mgiglio
Operon structure as IGC evidence
GO_REF:0000025
ECO:MCC
Evidence that supports the identity of a gene product on the basis of the identity of neighboring genes.
GOC:mg
immunoprecipitation evidence
A type of protein assay evidence that involves precipitation of a multivalent antigen by a bivalent antibody for protein isolation.
ECO:0000085
IDA: immunoprecipitation
Transcription factors isolated in this way can be incubated with a radiolabeled probe to demonstrate binding.
eco
A type of protein assay evidence that involves precipitation of a multivalent antigen by a bivalent antibody for protein isolation.
ECO:MCC
ECO:SW
TAIR:TED
intermethylated site amplification evidence
ECO:0000086
eco
immunolocalization evidence
A type of protein assay evidence that involves the use of antibodies to detect biomolecules.
ECO:0000087
IDA: immunolocalization
eco
A type of protein assay evidence that involves the use of antibodies to detect biomolecules.
ECO:MCC
biological system reconstruction
2009-03-20T12:00:17Z
ECO:0000088
Evidence based on reconstruction of a biological system that is based on an existing experimentally supported model of that biological system.
ISR
The biological system in question might be a multi-step process or a physical complex comprising several components. A common basis for system reconstruction is orthology, where all of the components of an experimentally characterized complex exist in one organism; if a second organism contains orthologs of all components, then the existence of the complex is inferred. In the case of a genome-wide analysis, a gene product is said to fulfill a necessary function for a pathway or complex when, with all of the other necessary functions or components also present, the pathway or complex is reconstructed.
eco
inferred from system reconstruction
mgiglio
ECO:MCC
Evidence based on reconstruction of a biological system that is based on an existing experimentally supported model of that biological system.
GOC:mg
restriction landmark genomic scanning evidence
ECO:0000089
ECO:0001125
RLGS evidence
eco
restriction landmark genome scanning evidence
immunogold labelling evidence
A type of protein assay evidence that involves attaching colloidal gold particles to a secondary antibody, which is attached to a primary antibody that binds a specific protein or cell part, followed by visualization with electron microscopy.
ECO:0000090
IDA: immunogold labelling
eco
A type of protein assay evidence that involves attaching colloidal gold particles to a secondary antibody, which is attached to a primary antibody that binds a specific protein or cell part, followed by visualization with electron microscopy.
ECO:MCC
epitope-tagged protein immunolocalization evidence
ECO:0000092
IDA: immunolocalization of epitope-tagged protein
Used when an annotation is made based on immunolocalization of recombinant proteins fused with epitopes that are recognized by antibodies.
eco
TAIR:TED
Used when an annotation is made based on immunolocalization of recombinant proteins fused with epitopes that are recognized by antibodies.
oligonucleotide microarray evidence
ECO:0000093
eco
biological assay evidence
Direct assay evidence that is derived by using a living organism to measure the effect of a substance, factor, or condition.
ECO:0000094
IDA: bioassay
eco
Direct assay evidence that is derived by using a living organism to measure the effect of a substance, factor, or condition.
ECO:MCC
TAIR:TED
cell growth assay evidence
2014-10-15T00:58:50Z
A type of in vivo assay evidence that measures one or more aspects of cell growth over a specified time period to indicate an induced or repressed regulatory effect.
Cell growth aspects can include growth rate and extent of growth. A cell growth curve acts as a natural reporter.
ECO:0000095
eco
growth curve analysis
mchibucos
A type of in vivo assay evidence that measures one or more aspects of cell growth over a specified time period to indicate an induced or repressed regulatory effect.
ECO:SW
PomBase:MAH
electrophoretic mobility shift assay evidence
A type of direct assay evidence based on an electrophoretic mobility shift of macromolecules, compounds, and proteins where solutions of protein and nucleic acid are combined and the resulting mixtures are electrophoresed under native conditions through polyacrylamide or agarose gel to detect protein-nucleic acid interactions.
ECO:0000096
EMSA is often used for assessing TF-binding with fluorophore labelling. Protein-nucleic acid complexes generally migrate at a slower rate than the corresponding non-bonded nucleic acid.
EMSA: electrophoretic mobility shift assay
Gel retardation assay
IDA: electrophoretic mobility shift assay
PSI-MI:MI:0413
eco
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
electrophoretic mobility shift assay
PSI-MI:MI:0413
Gel retardation assay
PMID:17703195
cDNA microarray evidence
ECO:0000097
eco
in situ hybridization evidence
ECO:0000098
IDA: in situ hybridization
Used when an annotation is made based on a method that hybridizes a labeled nucleic acid probe to a tissue or cell specimen in which the cellular structures are still intact. Depending on the label and protocol used, the probe may detect complementary DNA or RNA by hybridizing specifically to that gene or sequence.
eco
TAIR:TED
Used when an annotation is made based on a method that hybridizes a labeled nucleic acid probe to a tissue or cell specimen in which the cellular structures are still intact. Depending on the label and protocol used, the probe may detect complementary DNA or RNA by hybridizing specifically to that gene or sequence.
fractionation evidence
ECO:0000100
eco
Affymetrix array experiment evidence
ECO:0000101
eco
co-fractionation evidence
ECO:0000102
IDA: co-fractionation
Used when an annotation is made based on fractionation of a protein with other compounds, factors, or macromolecules.
eco
TAIR:TED
Used when an annotation is made based on fractionation of a protein with other compounds, factors, or macromolecules.
microarray RNA expression level evidence
ECO:0000104
IEP: transcript levels (e.g. microarray data)
Used when an annotation is made based on levels of RNA expression determined by microarray experiment.
eco
TAIR:TED
Used when an annotation is made based on levels of RNA expression determined by microarray experiment.
Nimblegen array evidence
ECO:0000105
eco
Northern assay evidence
A type of transcript expression level evidence based on electrophoresis and probing to determine levels of RNA expression using a complementary hybridization probe on the separated RNA samples.
ECO:0000106
IEP: transcript levels (e.g. Northerns)
Northern blot
eco
A type of transcript expression level evidence based on electrophoresis and probing to determine levels of RNA expression using a complementary hybridization probe on the separated RNA samples.
ECO:SW
TAIR:TED
reverse transcription polymerase chain reaction transcription evidence
ECO:0000108
IEP: transcript levels (e.g. RT-PCR)
RT-PCR transcription evidence
Used when an annotation is made based on levels of RNA expression determined by an RT-PCR experiment (quantitative or otherwise).
eco
TAIR:TED
Used when an annotation is made based on levels of RNA expression determined by an RT-PCR experiment (quantitative or otherwise).
reverse transcription polymerase chain reaction evidence
A type of polymerase chain reaction evidence where RNA is reverse transcribed into cDNA and amplified for product measurement in real time for transcription analysis i.e. qPCR.
ECO:0000109
RT-PCR evidence
The starting product for PCR, and therefore amplification volume, is directly correlated to the transcription rate.
eco
qRT-PCR
PMID:12901609
qRT-PCR
A type of polymerase chain reaction evidence where RNA is reverse transcribed into cDNA and amplified for product measurement in real time for transcription analysis i.e. qPCR.
ECO:SW
PMID:11013345
PMID:12901609
RNA protection assay evidence
A type of nuclease protection assay evidence used for transcription start-site localization where mRNA is hybridize with radiolabeled RNA probes after which RNAse is added to digest the unbound, nonresistant single-stranded overhang regions and the resistant fragment size and identity is determined with gel electrophoresis.
ECO:0000110
IEP: RNA protection assay
RNAse protection assay
RPA
eco
ribonuclease protection assay
A type of nuclease protection assay evidence used for transcription start-site localization where mRNA is hybridize with radiolabeled RNA probes after which RNAse is added to digest the unbound, nonresistant single-stranded overhang regions and the resistant fragment size and identity is determined with gel electrophoresis.
ECO:SW
PMID:23457339
TAIR:TED
western blot evidence
A type of protein expression level evidence where specific proteins from a mixed sample are detected and their expression levels are quantified using Western blotting technique.
ECO:0000112
IEP: protein levels (e.g. Western blots)
Western blot expression analysis
Western blot is used for protein detection and analysis. A mixed protein sample is separated through polyacrylamide gel electrophoresis then transferred to a membrane, such as polyvinylidene fluoride (PVDF), and labeled with protein-specific antibodies.
eco
protein immunoblot
A type of protein expression level evidence where specific proteins from a mixed sample are detected and their expression levels are quantified using Western blotting technique.
ECO:SW
PMID:23050259
TAIR:TED
expression library screen evidence
A type of protein expression evidence where a protein of interest is isolated on the basis of its hybridization to an antibody raised to a homologous protein.
ECO:0000114
IEP: expression library screening
eco
A type of protein expression evidence where a protein of interest is isolated on the basis of its hybridization to an antibody raised to a homologous protein.
ECO:MCC
TAIR:TED
differential hybridization evidence
ECO:0000116
IEP: differential hybridization
Used when an annotation is made based on results of a differential hybridization experiment that demonstrates expression of an RNA under one condition and not another.
eco
TAIR:TED
Used when an annotation is made based on results of a differential hybridization experiment that demonstrates expression of an RNA under one condition and not another.
subtractive hybridization evidence
ECO:0000118
IEP: subtractive hybridization
Used when an annotation is made based on results of a subtractive hybridization experiment that demonstrates expression of an RNA under one condition and not another.
eco
TAIR:TED
Used when an annotation is made based on results of a subtractive hybridization experiment that demonstrates expression of an RNA under one condition and not another.
over expression analysis evidence
ECO:0000120
IMP: analysis of overexpression/ectopic expression phenotype
Used when an annotation is made based on the analysis of the phenotype of a wild-type or mutant transgenic organism that has been engineered to overexpress the gene product in question.
eco
TAIR:TED
Used when an annotation is made based on the analysis of the phenotype of a wild-type or mutant transgenic organism that has been engineered to overexpress the gene product in question.
protein localization evidence
ECO:0000122
eco
fusion protein localization evidence
ECO:0000124
eco
green fluorescent protein fusion protein localization evidence
ECO:0000126
GFP fusion protein localization evidence
IDA: localization of GFP/YFP fusion protein
eco
yellow fluorescent protein fusion protein localization evidence
ECO:0000128
IDA: localization of GFP/YFP fusion protein
YFP fusion protein localization evidence
eco
beta-glucuronidase fusion protein localization evidence
ECO:0000130
GUS fusion protein localization evidence
GUS staining evidence
IDA: localization of GUS fusion protein
eco
beta-galactosidase fusion protein localization evidence
ECO:0000132
LacZ fusion protein localization evidence
eco
transport assay evidence
ECO:0000134
IDA: transport assay
eco
nucleic acid binding evidence
ECO:0000136
eco
ribohomopolymer binding assay evidence
ECO:0000138
IDA: ribohomopolymer binding assay
eco
thin layer chromatography evidence
A type of chromatography evidence that uses a thin layer of adsorbent (such as silica gel, alumina, or cellulose) on a flat, inert substrate.
ECO:0000140
IDA: thin layer chromatography
TLC evidence
eco
A type of chromatography evidence that uses a thin layer of adsorbent (such as silica gel, alumina, or cellulose) on a flat, inert substrate.
ECO:MCC
protein:ion binding evidence
ECO:0000142
eco
Southwestern blot evidence
ECO:0000144
IDA: Southwestern analysis
Used when an annotation is made based on a Southwestern blot analysis, which detects DNA binding of proteins using labeled DNA as probe hybridizing to electrophoretically separated proteins.
eco
TAIR:TED
Used when an annotation is made based on a Southwestern blot analysis, which detects DNA binding of proteins using labeled DNA as probe hybridizing to electrophoretically separated proteins.
Northwestern blot evidence
ECO:0000146
IDA: Northwestern analysis
Used when an annotation is made based on a Northwestern blot analysis, which detects RNA binding of proteins using labeled RNA as probe hybridizing to electrophoretically separated proteins.
eco
TAIR:TED
Used when an annotation is made based on a Northwestern blot analysis, which detects RNA binding of proteins using labeled RNA as probe hybridizing to electrophoretically separated proteins.
in vitro binding evidence
ECO:0000148
IDA: in vitro binding assay
eco
true
in vitro transcription reconstitution assay evidence
ECO:0000150
IDA: in vitro reconstitution assay with recombinant protein
eco
in vitro recombinant protein transcription reconstitution assay evidence
ECO:0000152
IDA: in vitro reconstitution assay with recombinant protein
eco
heterologous protein expression evidence
A type of protein expression evidence where a gene from one cell is inserted into a cell that does not typically contain that gene and heterologous protein expression is assessed.
ECO:0000154
IDA: protein expression in heterologous system
eco
A type of protein expression evidence where a gene from one cell is inserted into a cell that does not typically contain that gene and heterologous protein expression is assessed.
ECO:KAV
protein separation evidence
ECO:0000156
eco
protein separation followed by direct sequencing evidence
ECO:0000158
IDA: protein separation and direct sequencing
eco
protein separation followed by fragment identification evidence
ECO:0000160
IDA: protein separation and fragment identification
eco
heterologous system uptake evidence
ECO:0000162
IDA: uptake assay in heterologous system
Used when an annotation is made based on small molecule update assays carried out in a heterologous system that contains a recombinant protein.
eco
TAIR:TED
Used when an annotation is made based on small molecule update assays carried out in a heterologous system that contains a recombinant protein.
electrophysiology assay evidence
A type of direct assay evidence where electrical properties of cells or tissues are studied.
ECO:0000164
The scale of electrophysiology assays can range from small, e.g. a single ion channel, to large, e.g. an entire organ such as a heart.
eco
A type of direct assay evidence where electrical properties of cells or tissues are studied.
ECO:KAV
two-electrode voltage clamp experiment evidence
ECO:0000166
IDA: two-electrode voltage clamp technique
eco
transcription assay
ECO:0000168
eco
transcriptional activation assay
ECO:0000170
IDA: transcriptional activation assay
Used when an annotation is made based on assays that show transcriptional activation of a specific target reporter gene.
eco
TAIR:TED
Used when an annotation is made based on assays that show transcriptional activation of a specific target reporter gene.
biochemical trait analysis evidence
ECO:0000172
IMP: analysis of biochemical trait
Used when an annotation is made based on the analysis of a biochemical aspect of a mutant phenotype; for example, the accumulation of a biosynthetic intermediate.
eco
TAIR:TED
Used when an annotation is made based on the analysis of a biochemical aspect of a mutant phenotype; for example, the accumulation of a biosynthetic intermediate.
mutant physiological response evidence
ECO:0000174
IMP: analysis of physiological response
Used when an annotation is made based on the physiological response of a mutant to an external stimulus; for example, abnormal growth of the root in response to gravity, delay in flowering in response to varying light conditions.
eco
TAIR:TED
Used when an annotation is made based on the physiological response of a mutant to an external stimulus; for example, abnormal growth of the root in response to gravity, delay in flowering in response to varying light conditions.
mutant visible phenotype evidence
ECO:0000176
IMP: analysis of visible trait
Used when an annotation is made based on the visual examination of a mutant phenotype; for example, abnormalities in organism morphology.
eco
TAIR:TED
Used when an annotation is made based on the visual examination of a mutant phenotype; for example, abnormalities in organism morphology.
genomic context evidence
An evidence type that is based on the location of a gene, which gives rise to a gene product, within the genome.
ECO:0000177
This type of evidence might include identity of neighboring genes, operon structure, synteny, phylogenetic analysis, or other whole-genome analysis.
eco
An evidence type that is based on the location of a gene, which gives rise to a gene product, within the genome.
ECO:MCC
ECO:go
in vivo assay evidence
ECO:0000178
eco
animal model system study evidence
A type of experimental evidence arising from the investigation of an animal model system.
ECO:0000179
eco
A type of experimental evidence arising from the investigation of an animal model system.
ECO:MCC
clinical study evidence
A type of experimental evidence arising from a controlled investigation that uses human subjects.
ECO:0000180
eco
A type of experimental evidence arising from a controlled investigation that uses human subjects.
ECO:MCC
in vitro assay evidence
ECO:0000181
eco
in vitro culture assay evidence
ECO:0000182
eco
cell-free assay evidence
ECO:0000183
eco
in vitro assay
enzyme inhibition evidence
A type of specific protein inhibition evidence where the protein under study is an enzyme.
ECO:0000184
eco
A type of specific protein inhibition evidence where the protein under study is an enzyme.
ECO:MCC
sequence alignment evidence
2010-03-18T12:21:31Z
ECO:00000057
ECO:0000200
ISA
Used when a sequence alignment is the basis for making an annotation, but only when the alignment has been manually reviewed; or if the information is in a published paper, the authors have manually reviewed the evidence. Such alignments may be pairwise alignments or multiple alignments. BLAST produces pairwise alignments and any annotations based solely on the evaluation of BLAST results should use this code.
eco
inferred from sequence alignment
mchibucos
GO:ISA
ISA
GO:ISA
inferred from sequence alignment
Used when a sequence alignment is the basis for making an annotation, but only when the alignment has been manually reviewed; or if the information is in a published paper, the authors have manually reviewed the evidence. Such alignments may be pairwise alignments or multiple alignments. BLAST produces pairwise alignments and any annotations based solely on the evaluation of BLAST results should use this code.
url:http://www.geneontology.org/GO.evidence.shtml
sequence orthology evidence
2010-03-18T12:30:06Z
ECO:00000060
ECO:0000201
ISO
Orthology is a relationship between genes in different species indicating that the genes derive from a common ancestor. Orthology is established by multiple criteria generally including amino acid and/or nucleotide sequence comparisons and one or more of the following: phylogenetic analysis, coincident expression, conserved map location, functional complementation, immunological cross-reaction, similarity in subcellular localization, subunit structure, substrate specificity, and response to specific inhibitors.
eco
inferred from sequence orthology
mchibucos
ortholog evidence
GO:ISO
ISO
Orthology is a relationship between genes in different species indicating that the genes derive from a common ancestor. Orthology is established by multiple criteria generally including amino acid and/or nucleotide sequence comparisons and one or more of the following: phylogenetic analysis, coincident expression, conserved map location, functional complementation, immunological cross-reaction, similarity in subcellular localization, subunit structure, substrate specificity, and response to specific inhibitors.
url:http://www.geneontology.org/GO.evidence.shtml
GO:ISO
inferred from sequence orthology
match to sequence model evidence
2010-03-18T12:32:30Z
ECO:00000063
ECO:0000202
ISM
Sequence similarity evidence that is based on a sequence-based statistical model that predicts the function of a gene product.
Used when evidence from any kind of statistical model of a sequence or group of sequences is used to make a prediction about the function of a protein or RNA. Examples of relevant evidence are: Hidden Markov Models, PROSITE motifs, and tools such as tRNASCAN.
eco
inferred from sequence model
mchibucos
GO:ISM
ISM
ECO:MCC
Sequence similarity evidence that is based on a sequence-based statistical model that predicts the function of a gene product.
url:http://www.geneontology.org/GO.evidence.shtml
GO:ISM
inferred from sequence model
automatic assertion
2010-03-18T12:36:04Z
An assertion method that does not involve human review.
An automatic assertion is based on computationally generated information that is not reviewed by a person prior to making the assertion. For example, one common type of automatic assertion involves creating an association of evidence with an entity based on commonness of attributes of that entity and another entity for which an assertion already exists. The commonness is determined algorithmically.
ECO:00000067
ECO:0000203
eco
mchibucos
An assertion method that does not involve human review.
ECO:MCC
author statement
2010-06-21T11:17:21Z
An evidence type that is based on an assertion by the author of a paper, which is read by a curator.
ECO:0000204
eco
mchibucos
An evidence type that is based on an assertion by the author of a paper, which is read by a curator.
ECO:MCC
curator inference
2010-08-18T05:55:12Z
A type of inferential evidence that is based on a conclusion drawn by a curator.
ECO:0000205
eco
mchibucos
A type of inferential evidence that is based on a conclusion drawn by a curator.
ECO:MCC
BLAST evidence
2010-08-06T04:48:24Z
A type of sequence alignment evidence obtained with basic local alignment search tool (BLAST).
ECO:0000206
eco
mchibucos
A type of sequence alignment evidence obtained with basic local alignment search tool (BLAST).
ECO:MCC
nucleotide BLAST evidence
2010-08-06T04:49:58Z
BLAST evidence from aligning nucleotide sequence with nucleotide sequence.
ECO:0000207
eco
mchibucos
BLAST evidence from aligning nucleotide sequence with nucleotide sequence.
ECO:MCC
protein BLAST evidence
2010-08-06T04:50:45Z
BLAST evidence from aligning amino acid or translated nucleotide sequence with amino acid or translated nucleotide sequence.
ECO:0000208
eco
mchibucos
BLAST evidence from aligning amino acid or translated nucleotide sequence with amino acid or translated nucleotide sequence.
ECO:MCC
BLAST evidence used in automatic assertion
2010-08-06T04:55:21Z
A type of BLAST evidence that is used in an automatic assertion.
ECO:0000209
eco
mchibucos
true
A type of BLAST evidence that is used in an automatic assertion.
ECO:MCC
true
nucleotide BLAST evidence used in automatic assertion
2010-08-06T05:09:51Z
ECO:0000210
Nucleotide BLAST evidence that is used in an automatic assertion.
eco
mchibucos
ECO:MCC
Nucleotide BLAST evidence that is used in an automatic assertion.
true
true
protein BLAST evidence used in automatic assertion
2010-08-06T05:11:04Z
ECO:0000211
Protein BLAST evidence that is used in an automatic assertion.
eco
mchibucos
true
true
ECO:MCC
Protein BLAST evidence that is used in an automatic assertion.
combinatorial evidence
2010-08-06T05:24:57Z
A key aspect of this type of evidence is that two or more pieces of information are combined to generate an emergent type of evidence not possible with the constituent pieces of evidence alone. A combinatorial analysis typically involves incorporation of different types of evidence.
A type of evidence that arises out of the integration of more than one line of evidence.
ECO:0000036
ECO:0000043
ECO:0000212
eco
inferred from in-silico analysis
mchibucos
A type of evidence that arises out of the integration of more than one line of evidence.
ECO:MCC
combinatorial evidence used in automatic assertion
2010-08-06T05:28:33Z
A type of combinatorial analysis that is used in an automatic assertion.
Combinatorial analyses could include experimental or computational results. Examples include: (i) large-scale experiment such as a genome-wide two-hybrid or genome-wide synthetic interactions; (ii) integration of large-scale data sets of various types; and (iii) text-based-computation, e.g. text-mining. For simple sequence comparisons, one should use the sequence similarity analysis evidence type. For microarray results alone, expression pattern analysis is appropriate; whereas, large-scale computational analysis should be used when microarray results are combined with the results of other types of large-scale experiments.
ECO:0000213
eco
mchibucos
A type of combinatorial analysis that is used in an automatic assertion.
ECO:MCC
true
true
biological aspect of descendant evidence
2010-10-05T11:16:50Z
A type of phylogenetic evidence whereby an aspect of an ancestral gene is inferred through the characterization of an aspect of a descendant gene.
ECO:0000214
This type of evidence can be used in support of both positive and "not" GO annotations. It should be used to annotate ancestral genes but not extant ones.
eco
mchibucos
A type of phylogenetic evidence whereby an aspect of an ancestral gene is inferred through the characterization of an aspect of a descendant gene.
ECO:MCC
rapid divergence from ancestral sequence evidence
2010-10-05T03:41:34Z
A type of phylogenetic evidence characterized by long phylogenetic tree branch lengths following a duplication event.
ECO:0000215
Long branch lengths indicate that descendant sequences may have acquired different or additional functions than the ancestral sequence.
eco
mchibucos
A type of phylogenetic evidence characterized by long phylogenetic tree branch lengths following a duplication event.
ECO:MCC
phylogenetic determination of loss of key residues evidence
2010-10-05T03:43:17Z
A type of phylogenetic evidence characterized by the absence of key sequence residues.
ECO:0000216
The loss of certain residues important for function can indicate that a sequence lacks a particular function.
eco
mchibucos
A type of phylogenetic evidence characterized by the absence of key sequence residues.
ECO:MCC
assertion method
2010-11-12T04:17:37Z
A means by which a statement is made about an entity.
ECO:0000217
eco
mchibucos
A means by which a statement is made about an entity.
ECO:MCC
manual assertion
2010-11-12T04:20:02Z
A manual assertion could be based on evidence that is generated by and interpreted by a human or it could involve human review of computationally generated information.
An assertion method that involves human review.
ECO:0000218
eco
mchibucos
An assertion method that involves human review.
ECO:MCC
nucleotide sequencing assay evidence
2010-11-15T12:22:40Z
A sequencing assay result for a biopolymer that comprises nucleotides.
DNA sequencing
ECO:0000219
eco
mchibucos
DNA sequencing
OBI:0000626
A sequencing assay result for a biopolymer that comprises nucleotides.
ECO:MCC
sequencing assay evidence
2010-11-15T01:44:45Z
A type of experimental evidence where the order of molecules that constitute a biopolymer is determined.
ECO:0000220
eco
mchibucos
A type of experimental evidence where the order of molecules that constitute a biopolymer is determined.
ECO:MCC
OBI:0600047
high throughput nucleotide sequencing assay evidence
2010-11-15T02:19:34Z
A nucleotide sequencing assay result that is derived from a parallelized sequencing technique.
ECO:0000221
Typically thousands to millions of reads are produced in parallel.
eco
mchibucos
A nucleotide sequencing assay result that is derived from a parallelized sequencing technique.
ECO:MCC
Illumina sequencing evidence
2010-11-15T02:38:03Z
A high throughput nucleotide sequencing result derived by Illumina (Solexa) sequencing technology.
ECO:0000222
In Illumina sequencing technology, adapters are ligated onto the ends of randomly fragmented DNA. After single-stranded fragments are bound to the inside surface of a flow cell channel, they undergo in-place bridge PCR amplification. To begin the sequencing cycle, labeled reversible terminators, primers and DNA polymerase are added, followed by laser excitation of the fluorescent label and high resolution scanning. After non-incorporated nucleotides are washed away and the dye is chemically removed, the next cycle repeats with four labeled reversible terminators, primers and DNA polymerase, again followed by imaging.
Solexa sequencing result
eco
mchibucos
A high throughput nucleotide sequencing result derived by Illumina (Solexa) sequencing technology.
ECO:MCC
OBI:0000724
Solexa sequencing result
454 pyrosequencing evidence
2010-11-15T03:50:14Z
454 pyrosequencing technology amplifies individual DNA fragments inside water droplets within an oil solution (emulsion PCR). Within each droplet, a single DNA template is attached to a single primer-coated bead. Each bead is subsequently captured in a picolitre well within the sequencing machine. A luciferase-based readout system is used to identify individual nucleotides added to the nascent DNA.
A high throughput nucleotide sequencing result derived by 454 pyrosequencing technology.
ECO:0000223
eco
mchibucos
pyrosequencing
OBI:0000730
pyrosequencing
A high throughput nucleotide sequencing result derived by 454 pyrosequencing technology.
ECO:MCC
SOLiD sequencing evidence
2010-11-15T04:17:41Z
A high throughput nucleotide sequencing result derived by SOLiD sequencing technology.
ECO:0000224
SOLiD sequencing technology is based on sequencing by ligation. After library preparation, emulsion PCR and bead enrichment are performed, including 3' modification of templates on selected beads to allow covalent bonding to a slide. 3' modified beads are attached to a glass slide and primers are added. Four fluorescently labeled di-base probes are added and multiple cycles of ligation, detection and cleavage are performed. The number of cycles determines read length. After a number of ligation cycles, the extension product is removed and another round of ligation cycles is performed with a new primer complimentary to the n-1 position of the template. Five rounds of primer reset are performed for each sequence tag.
eco
mchibucos
A high throughput nucleotide sequencing result derived by SOLiD sequencing technology.
ECO:MCC
OBI:0000706
chain termination sequencing evidence
2010-11-15T04:46:31Z
A nucleotide sequencing assay result derived by the chain termination sequencing method.
Chain termination sequencing, also called Sanger sequencing after its developer, uses dideoxynucleotide triphosphates (ddNTPs) as DNA chain terminators. Single-stranded DNA template, DNA primer, DNA polymerase, fluorescently or radioactively labeled nucleotides, and one of four ddNTPs are added together in each of four separate sequencing reactions. The synthesized and labeled DNA fragments from each of the four reactions are denatured, separated by size by gel electrophoresis, and visualized by autoradiography or UV light.
ECO:0000225
Sanger sequencing
dye terminator sequencing
eco
mchibucos
A nucleotide sequencing assay result derived by the chain termination sequencing method.
ECO:MCC
OBI:0000695
chromatin immunoprecipitation evidence
2010-11-16T01:29:08Z
A type of immunoprecipitation evidence that is used to identify a protein binding site on a genomic DNA sequence.
ChIP evidence
Chromatin immunoprecipitation (ChIP) is used to investigate protein-DNA interactions in vivo. DNA and proteins are chemically cross-linked in vivo to form chromatin complexes, followed by cell lysis and DNA shearing. Fragmented DNA-protein complexes are selectively enriched for a protein of interest using a specific antibody (immunoprecipitation). Protein digestion and DNA purification are performed prior to DNA detection via molecular cloning and sequencing, polymerase chain reaction (PCR), microarray analysis (ChIP-on-chip), or direct high-throughput sequencing (ChIP-seq).
ECO:0000226
PSI-MI:MI:0402
eco
mchibucos
A type of immunoprecipitation evidence that is used to identify a protein binding site on a genomic DNA sequence.
ECO:MCC
chromatin immunoprecipitation assay
PSI-MI:MI:0402
chromatin immunoprecipitation-PCR evidence
2010-11-16T05:02:00Z
A type of chromatin immunoprecipitation (ChIP) evidence that uses polymerase chain reaction (PCR) where specific primers are used on the pulled-down DNA for DNA detection.
ChIP-PCR evidence
ChIP-PCR is often used to validate ChIP-chip results and less frequently,ChIP-Seq results.
ECO:0000227
eco
mchibucos
A type of chromatin immunoprecipitation (ChIP) evidence that uses polymerase chain reaction (PCR) where specific primers are used on the pulled-down DNA for DNA detection.
ECO:MCC
ECO:SW
PMID:18388953
chromatin immunoprecipitation-qPCR evidence
2010-11-16T05:26:47Z
A chromatin immunoprecipitation (ChIP) evidence that uses quantitative polymerase chain reaction (qPCR) for DNA detection.
ChIP-qPCR evidence
ECO:0000228
eco
mchibucos
A chromatin immunoprecipitation (ChIP) evidence that uses quantitative polymerase chain reaction (qPCR) for DNA detection.
ECO:MCC
chromatin immunoprecipitation-seq evidence
2010-11-16T05:30:41Z
A chromatin immunoprecipitation (ChIP) evidence that uses high-throughput sequencing where immunoprecipitated DNA fragments are funneled into a massively parallel sequencer to produce multiple short reads for locating binding sites of DNA-associated proteins.
ChIP-SEQ evidence
ChIP-Seq experiments often use the input as a control to eliminate biases. To obtain similar results, ChIP-chip with high-density tiling arrays can be used.
ChIP-seq evidence
ECO:0000229
eco
mchibucos
ChIP-SEQ evidence
OBI:0000716
A chromatin immunoprecipitation (ChIP) evidence that uses high-throughput sequencing where immunoprecipitated DNA fragments are funneled 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
PMID:22955991
chromatin immunoprecipitation-chip evidence
2010-11-16T05:43:55Z
A fixating agent such as formaldehyde is used to cross link proteins and DNA. Sonication is applied for DNA shearing. For transcription factor tagging, an antibody or epitope is employed. After cross-linking is reversed, the DNA is amplified and labeled with a flourophore for microarray which produces a resolution of aproximately 500 bp.
A type of chromatin immunoprecipitation (ChIP) evidence that uses a tiling microarray for the detection of protein-bound DNA regions where chromatin is immunoprecipitated for protein tagging and DNA is sheared from the cross-linked protein-DNA complex to be arrayed revealing the protein-bound genomic regions.
ChIP-chip evidence
ChIP-on-chip evidence
ECO:0000230
PSI-MI:MI:0225
eco
mchibucos
chromatin immunoprecipitation array
PSI-MI:MI:0225
A type of chromatin immunoprecipitation (ChIP) 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
quantitative polymerase chain reaction evidence
2010-11-16T05:57:20Z
A type of polymerase chain reaction evidence where the reaction product is quantified in real-time across cycles by means of fluorescent dyes for detection and quantification of specific sequences in a DNA sample.
ECO:0000231
Q-PCR evidence
Quantitative PCR enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample. The dye is activated upon binding double-stranded DNA.
Although qRT-PCR is commonly found in literature synonymous to qPCR, it is preferable not to use this synonym as it is the accepted abbreviation for reverse transcription PCR. qPCR should be used instead (ISBN 978-0-470-68386-6 page 173).
eco
mchibucos
qRT-PCR evidence
quantitative PCR evidence
real-time PCR evidence
real-time polymerase chain reaction evidence
A type of polymerase chain reaction evidence where the reaction product is quantified in real-time across cycles by means of fluorescent dyes for detection and quantification of specific sequences in a DNA sample.
ECO:MCC
ECO:SW
chromosome conformation capture-based evidence
2010-11-17T12:27:14Z
3C
A type of experimental evidence that is based on a five-step technique of cross-linking DNA in vivo, restriction digestion, intramolecular ligation, reversing DNA cross-links, and DNA processing and quantitation.
Chromosome conformation capture technologies are used to study the structural properties and spatial organization of chromosomes inside cells. All types of chromosome conformation capture technology involve five primary steps: cross-linking of DNA in vivo, restriction digestion, intramolecular ligation, reversing cross-linkages, and DNA enrichment and quantitation. The last step is different for each type of chromosome conformation capture technology, and may include PCR (3C), inverse PCR (4C), or ligation-mediated amplification (5C). Methods for product quantitation can include agarose gel detection or real-time quantitative PCR in the case of 3C, or high-throughput sequencing or microarray analysis for 4C and 5C.
ECO:0000232
chromosome conformation capture
eco
mchibucos
A type of experimental evidence that is based on a five-step technique of cross-linking DNA in vivo, restriction digestion, intramolecular ligation, reversing DNA cross-links, and DNA processing and quantitation.
ECO:MCC
chromosome conformation capture evidence
2010-11-17T12:46:15Z
3C
3C is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 3C differs only in the fifth step, which involves performing either standard polymerase chain reaction (PCR) or quantitative PCR (qPCR) for product quantitation.
A type of chromosome conformation capture-based evidence that is derived by performing a type of polymerase chain reaction (PCR) in the final product quantitation step.
ECO:0000233
eco
mchibucos
A type of chromosome conformation capture-based evidence that is derived by performing a type of polymerase chain reaction (PCR) in the final product quantitation step.
ECO:MCC
circularized chromosome conformation capture evidence
2010-11-19T01:20:28Z
4C
4C is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 4C differs only in the fifth step, which involves inverse polymerase chain reaction (inverse PCR) on a circularized 3C library prior to product quantitation.
A type of chromosome conformation capture-based evidence that is derived by inverse polymerase chain reaction (inverse PCR) on a prior circularized 3C library followed by product quantitation with a microarray.
ECO:0000234
chromosome conformation capture on chip
circularized 3C
eco
mchibucos
A type of chromosome conformation capture-based evidence that is derived by inverse polymerase chain reaction (inverse PCR) on a prior circularized 3C library followed by product quantitation with a microarray.
ECO:MCC
carbon-copy chromosome conformation capture evidence
2010-11-19T01:22:20Z
5C
5C is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 5C differs only in the fifth step, which involves ligation-mediated amplification (LMA) followed by product quantitation.
A type of chromosome conformation capture-based evidence that is derived by performing ligation-mediated amplification (LMA) prior to product quantitation.
ECO:0000235
carbon-copy 3C
eco
mchibucos
A type of chromosome conformation capture-based evidence that is derived by performing ligation-mediated amplification (LMA) prior to product quantitation.
ECO:MCC
chromosome conformation capture-PCR evidence
2010-11-19T03:00:47Z
3C
3C-PCR
A type of chromosome conformation capture evidence that is derived by performing polymerase chain reaction (PCR) in the quantitation step.
ECO:0000236
eco
mchibucos
A type of chromosome conformation capture evidence that is derived by performing polymerase chain reaction (PCR) in the quantitation step.
ECO:MCC
chromosome conformation capture-qPCR evidence
2010-11-19T03:06:47Z
3C-qPCR
3C-quantitative PCR
3C-real-time PCR
A type of chromosome conformation capture evidence that is derived by performing quantitative polymerase chain reaction (qPCR) in the quantitation step.
ECO:0000237
eco
mchibucos
A type of chromosome conformation capture evidence that is derived by performing quantitative polymerase chain reaction (qPCR) in the quantitation step.
ECO:MCC
Hi-C evidence
2010-11-19T04:24:03Z
A type of chromosome conformation capture-based evidence that is derived by performing immunoprecipitation enrichment of ligated fragments events prior to product quantitation.
ECO:0000238
Hi-C is used to study the structural properties and spatial organization of chromosomes inside cells. Hi-C is similar to other types of chromosome conformation capture technology, but involves the addition of biotinylated nucleotides during the second or fourth step and enrichment for ligated fragments using immunoprecipitation after the fourth step.
eco
mchibucos
A type of chromosome conformation capture-based evidence that is derived by performing immunoprecipitation enrichment of ligated fragments events prior to product quantitation.
ECO:MCC
chromosome conformation capture sequencing evidence
2010-11-30T03:22:25Z
3C sequencing
3C-seq
3C-seq is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 3C-seq differs only in the fifth step, which involves inverse polymerase chain reaction (PCR) on a circularized 3C library prior to product quantitation.
4C sequencing
4C-seq
A type of chromosome conformation capture-based evidence that is derived by inverse polymerase chain reaction (inverse PCR) on a circularized 3C library prior to product quantitation with high-throughput (HT) sequencing.
ECO:0000239
circularized 3C sequencing
circularized 3C-seq
eco
mchibucos
A type of chromosome conformation capture-based evidence that is derived by inverse polymerase chain reaction (inverse PCR) on a circularized 3C library prior to product quantitation with high-throughput (HT) sequencing.
ECO:MCC
anatomical perturbation evidence
2010-12-06T12:24:16Z
ECO:0000240
Experimental phenotypic evidence where a structural feature of an organism is disrupted.
eco
mchibucos
ECO:MCC
Experimental phenotypic evidence where a structural feature of an organism is disrupted.
environmental perturbation evidence
2010-12-06T12:33:58Z
ECO:0000241
Experimental phenotypic evidence where the extra-organismal context of an organism is modified.
Many environmental factors are subject to modification, such as temperature, pressure, humidity, radiation, and so forth.
eco
mchibucos
mechanical constraint evidence
ECO:MCC
Experimental phenotypic evidence where the extra-organismal context of an organism is modified.
tissue ablation evidence
2010-12-06T12:33:58Z
A tissue ablation experiment involves observing the phenotype of an entity whose tissues have been disrupted through genetic or biochemical manipulation, physical destruction, or some other means.
A type of anatomical perturbation that is based on disruption of tissue.
ECO:0000242
ablated tissue evidence
eco
mchibucos
A type of anatomical perturbation that is based on disruption of tissue.
ECO:MCC
tissue grafting evidence
2010-12-06T12:33:58Z
A type of anatomical perturbation that is based on adding tissue to an organism through a graft procedure.
ECO:0000243
eco
mchibucos
A type of anatomical perturbation that is based on adding tissue to an organism through a graft procedure.
ECO:MCC
combinatorial evidence used in manual assertion
2010-12-09T02:02:12Z
A type of combinatorial analysis that is used in a manual assertion.
Combinatorial analyses could include experimental or computational results. Examples include: (i) large-scale experiment such as a genome-wide two-hybrid or genome-wide synthetic interactions; (ii) integration of large-scale data sets of various types; and (iii) text-based-computation, e.g. text-mining. For simple sequence comparisons, one should use the sequence similarity analysis evidence type. For microarray results alone, expression pattern analysis is appropriate; whereas, large-scale computational analysis should be used when microarray results are combined with the results of other types of large-scale experiments.
ECO:0000244
eco
mchibucos
A type of combinatorial analysis that is used in a manual assertion.
ECO:MCC
true
true
computational combinatorial evidence used in manual assertion
2010-12-09T02:37:54Z
A type of computational combinatorial analysis that is used in a manual assertion.
ECO:0000245
GOECO:RCA
RCA
eco
inferred from reviewed computational analysis
mchibucos
GOECO:RCA
RCA
A type of computational combinatorial analysis that is used in a manual assertion.
ECO:MCC
GOECO:RCA
inferred from reviewed computational analysis
true
inferred from reviewed computational analysis
GOECO:RCA
true
computational combinatorial evidence used in automatic assertion
2010-12-09T02:37:54Z
A type of computational combinatorial analysis that is used in an automatic assertion.
ECO:0000246
eco
mchibucos
true
true
A type of computational combinatorial analysis that is used in an automatic assertion.
ECO:MCC
sequence alignment evidence used in manual assertion
2010-12-09T05:12:27Z
ECO:0000247
GOECO:ISA
ISA
Sequence alignment evidence that is used in a manual assertion.
eco
inferred from sequence alignment
mchibucos
ECO:MCC
Sequence alignment evidence that is used in a manual assertion.
GOECO:ISA
ISA
true
inferred from sequence alignment
GOECO:ISA
GOECO:ISA
inferred from sequence alignment
true
sequence alignment evidence used in automatic assertion
2010-12-09T05:12:27Z
ECO:0000248
Sequence alignment evidence that is used in an automatic assertion.
eco
mchibucos
true
true
ECO:MCC
Sequence alignment evidence that is used in an automatic assertion.
sequence similarity evidence used in automatic assertion
2010-12-09T05:22:30Z
ECO:0000249
Sequence similarity evidence that is used in an automatic assertion.
eco
mchibucos
true
true
ECO:MCC
Sequence similarity evidence that is used in an automatic assertion.
sequence similarity evidence used in manual assertion
2010-12-09T05:22:30Z
ECO:0000250
GOECO:ISS
Sequence similarity evidence that is used in a manual assertion.
eco
mchibucos
true
ECO:MCC
Sequence similarity evidence that is used in a manual assertion.
true
inferred from sequence or structural similarity
GOECO:ISS
similarity evidence used in automatic assertion
2010-12-09T05:28:12Z
ECO:0000251
Similarity evidence that is used in an automatic assertion.
eco
mchibucos
ECO:MCC
Similarity evidence that is used in an automatic assertion.
true
true
similarity evidence used in manual assertion
2010-12-09T05:28:12Z
ECO:0000252
Similarity evidence that is used in a manual assertion.
eco
mchibucos
true
ECO:MCC
Similarity evidence that is used in a manual assertion.
true
genetic similarity evidence used in manual assertion
2010-12-10T01:42:44Z
ECO:0000253
Genetic similarity evidence that is used in a manual assertion.
eco
mchibucos
ECO:MCC
Genetic similarity evidence that is used in a manual assertion.
true
true
genetic similarity evidence used in automatic assertion
2010-12-10T01:42:44Z
ECO:0000254
Genetic similarity evidence that is used in an automatic assertion.
eco
mchibucos
ECO:MCC
Genetic similarity evidence that is used in an automatic assertion.
true
true
match to sequence model evidence used in manual assertion
2010-12-10T02:26:35Z
A match to sequence model evidence that is employed in a manual assertion.
ECO:0000255
GOECO:ISM
GO_REF:0000011
eco
mchibucos
Hidden Markov Models (TIGR)
GO_REF:0000011
inferred from sequence model
GOECO:ISM
true
A match to sequence model evidence that is employed in a manual assertion.
ECO:MCC
true
match to sequence model evidence used in automatic assertion
2010-12-10T02:26:35Z
A match to sequence model evidence that is employed in an automatic assertion.
ECO:0000256
GO_REF:0000002
GO_REF:0000019
eco
mchibucos
Gene Ontology annotation through association of InterPro records with GO terms.
GO_REF:0000002
true
A match to sequence model evidence that is employed in an automatic assertion.
ECO:MCC
Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara
GO_REF:0000019
true
motif similarity evidence used in manual assertion
2010-12-10T02:44:34Z
ECO:0000257
Motif similarity evidence that is employed in a manual assertion.
eco
mchibucos
true
ECO:MCC
Motif similarity evidence that is employed in a manual assertion.
true
motif similarity evidence used in automatic assertion
2010-12-10T02:44:34Z
ECO:0000258
Motif similarity evidence that is employed in an automatic assertion.
eco
mchibucos
true
true
ECO:MCC
Motif similarity evidence that is employed in an automatic assertion.
match to InterPro signature evidence used in automatic assertion
2010-12-10T02:54:51Z
A match to InterPro signature evidence that is employed in an automatic assertion.
ECO:0000259
eco
mchibucos
true
true
A match to InterPro signature evidence that is employed in an automatic assertion.
ECO:MCC
match to InterPro signature evidence used in manual assertion
2010-12-10T02:54:51Z
A match to InterPro signature evidence that is employed in a manual assertion.
ECO:0000260
eco
mchibucos
true
true
A match to InterPro signature evidence that is employed in a manual assertion.
ECO:MCC
targeting sequence prediction evidence used in automatic assertion
2010-12-10T03:02:49Z
A targeting sequence prediction that is employed in an automatic assertion.
ECO:0000261
eco
mchibucos
true
true
A targeting sequence prediction that is employed in an automatic assertion.
ECO:MCC
targeting sequence prediction evidence used in manual assertion
2010-12-10T03:02:49Z
A targeting sequence prediction that is employed in a manual assertion.
ECO:0000262
eco
mchibucos
A targeting sequence prediction that is employed in a manual assertion.
ECO:MCC
true
true
transmembrane domain prediction evidence used in automatic assertion
2010-12-10T03:28:35Z
ECO:0000263
Transmembrane domain prediction that is employed in an automatic assertion.
eco
mchibucos
true
ECO:MCC
Transmembrane domain prediction that is employed in an automatic assertion.
true
transmembrane domain prediction evidence used in manual assertion
2010-12-10T03:28:35Z
ECO:0000264
Transmembrane domain prediction that is employed in a manual assertion.
eco
mchibucos
true
ECO:MCC
Transmembrane domain prediction that is employed in a manual assertion.
true
sequence orthology evidence used in automatic assertion
2010-12-10T03:39:41Z
ECO:0000265
GO_REF:0000003
GO_REF:0000019
GO_REF:0000035
Ortholog evidence
Sequence orthology evidence that is employed in an automatic assertion.
eco
mchibucos
Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara
GO_REF:0000019
ECO:MCC
Sequence orthology evidence that is employed in an automatic assertion.
Gene Ontology annotation based on Enzyme Commission mapping.
GO_REF:0000003
true
true
Automatic transfer of experimentally verified manual GO annotation data to plant orthologs using Ensembl Compara
GO_REF:0000035
sequence orthology evidence used in manual assertion
2010-12-10T03:39:41Z
ECO:0000266
GOECO:ISO
Ortholog evidence
Sequence orthology evidence that is employed in a manual assertion.
eco
mchibucos
inferred from sequence orthology
GOECO:ISO
true
true
ECO:MCC
Sequence orthology evidence that is employed in a manual assertion.
enzyme-linked immunoabsorbent assay evidence
2010-12-14T01:57:13Z
A type of protein assay evidence where an antigen is bound to a substrate, and an antibody directly or indirectly linked to an enzyme is utilized to determine the amount of bound antigen which is visualized with a color change in the substrate.
ECO:0000267
ELISA evidence
ELISA is sometimes used in the study of transcriptional regulation to identify a produced protein, especially secreted protein.
PSI-MI:MI:0411
eco
enzyme-linked immunosorbent assay
mchibucos
enzyme linked immunosorbent assay
PSI-MI:MI:0411
A type of protein assay evidence where an antigen is bound to a substrate, and an antibody directly or indirectly linked to an enzyme is utilized to determine the amount of bound antigen which is visualized with a color change in the substrate.
ECO:MCC
ECO:SW
PMID:23949770
flow cytometry evidence
2010-12-14T02:07:08Z
A direct assay that passes a stream of cells or particles past a light source, followed by using a detector to monitor light scatter or fluorochrome excitation to characterize the cells or particles.
ECO:0000268
FCM
eco
mchibucos
A direct assay that passes a stream of cells or particles past a light source, followed by using a detector to monitor light scatter or fluorochrome excitation to characterize the cells or particles.
ECO:MCC
experimental evidence used in manual assertion
2010-12-20T05:36:49Z
A type of experimental evidence that is used in a manual assertion.
ECO:0000269
GOECO:EXP
eco
mchibucos
true
A type of experimental evidence that is used in a manual assertion.
ECO:MCC
inferred from experiment
GOECO:EXP
true
expression evidence used in manual assertion
2010-12-20T05:46:39Z
A type of expression pattern evidence that is used in a manual assertion.
ECO:0000270
GOECO:IEP
eco
mchibucos
A type of expression pattern evidence that is used in a manual assertion.
ECO:MCC
inferred from expression pattern
GOECO:IEP
true
true
array experiment evidence used in manual assertion
2010-12-20T05:51:58Z
A type of array experiment evidence that is used in a manual assertion.
ECO:0000271
eco
mchibucos
true
A type of array experiment evidence that is used in a manual assertion.
ECO:MCC
true
Affymetrix array experiment evidence used in manual assertion
2010-12-20T05:53:36Z
A type of Affymetrix array experiment evidence that is used in a manual assertion.
ECO:0000272
eco
mchibucos
A type of Affymetrix array experiment evidence that is used in a manual assertion.
ECO:MCC
true
true
cDNA microarray evidence used in manual assertion
2010-12-20T05:55:49Z
A type of evidence arising from a cDNA microarray experiment that is used in a manual assertion.
ECO:0000273
eco
mchibucos
A type of evidence arising from a cDNA microarray experiment that is used in a manual assertion.
ECO:MCC
true
true
CpG island microarray evidence used in manual assertion
2010-12-20T05:58:44Z
A type of evidence arising from a CpG island microarray experiment that is used in a manual assertion.
ECO:0000274
eco
mchibucos
true
A type of evidence arising from a CpG island microarray experiment that is used in a manual assertion.
ECO:MCC
true
expression microarray evidence used in manual assertion
2010-12-20T06:01:26Z
A type of expression microarray evidence that is used in a manual assertion.
ECO:0000275
eco
mchibucos
true
true
A type of expression microarray evidence that is used in a manual assertion.
ECO:MCC
genomic microarray evidence used in manual assertion
2010-12-20T06:03:28Z
A type of evidence arising from a genomic microarray experiment that is used in a manual assertion.
ECO:0000276
eco
mchibucos
true
true
A type of evidence arising from a genomic microarray experiment that is used in a manual assertion.
ECO:MCC
Nimblegen array evidence used in manual assertion
2010-12-20T06:05:20Z
A type of evidence arising from a Nimblegen array experiment that is used in a manual assertion.
ECO:0000277
eco
mchibucos
true
A type of evidence arising from a Nimblegen array experiment that is used in a manual assertion.
ECO:MCC
true
oligonucleotide microarray evidence used in manual assertion
2010-12-20T06:09:45Z
A type of evidence arising from an oligonucleotide microarray experiment that is used in a manual assertion.
ECO:0000278
eco
mchibucos
A type of evidence arising from an oligonucleotide microarray experiment that is used in a manual assertion.
ECO:MCC
true
true
western blot evidence used in manual assertion
2010-12-20T06:20:01Z
A type of Western blot assay that is used in a manual assertion.
ECO:0000279
eco
mchibucos
A type of Western blot assay that is used in a manual assertion.
ECO:MCC
true
true
protein expression level evidence used in manual assertion
2010-12-20T06:21:54Z
A type of protein expression level analysis that is used in a manual assertion.
ECO:0000280
eco
mchibucos
true
true
A type of protein expression level analysis that is used in a manual assertion.
ECO:MCC
expression library screen evidence used in manual assertion
2010-12-20T06:24:05Z
A type of expression library screen evidence that is used in a manual assertion.
ECO:0000281
eco
mchibucos
true
true
A type of expression library screen evidence that is used in a manual assertion.
ECO:MCC
heterologous protein expression evidence used in manual assertion
2010-12-20T06:27:04Z
A type of heterologous protein expression analysis that is used in a manual assertion.
ECO:0000282
eco
mchibucos
A type of heterologous protein expression analysis that is used in a manual assertion.
ECO:MCC
true
true
spatial pattern of protein expression evidence used in manual assertion
2010-12-20T06:31:44Z
A type of protein expression spatial pattern analysis that is used in a manual assertion.
ECO:0000283
eco
mchibucos
true
A type of protein expression spatial pattern analysis that is used in a manual assertion.
ECO:MCC
true
protein expression evidence used in manual assertion
2010-12-20T06:33:46Z
A type of protein expression analysis that is used in a manual assertion.
ECO:0000284
eco
mchibucos
true
true
A type of protein expression analysis that is used in a manual assertion.
ECO:MCC
true
microarray RNA expression level evidence used in manual assertion
2010-12-20T06:41:33Z
A type of microarray RNA expression level data that is used in manual assertion.
ECO:0000285
eco
mchibucos
true
true
A type of microarray RNA expression level data that is used in manual assertion.
ECO:MCC
true
transcript expression level evidence used in manual assertion
2010-12-20T06:52:03Z
A type of transcript expression level data that is used in manual assertion.
ECO:0000286
eco
mchibucos
A type of transcript expression level data that is used in manual assertion.
ECO:MCC
true
true
differential hybridization evidence used in manual assertion
2010-12-20T06:55:14Z
A type of differential hybridization experiment that is used in a manual assertion.
ECO:0000287
eco
mchibucos
A type of differential hybridization experiment that is used in a manual assertion.
ECO:MCC
true
true
RNA protection assay evidence used in manual assertion
2010-12-20T06:57:33Z
A type of RNA protection assay that is used in a manual assertion.
ECO:0000288
eco
mchibucos
true
A type of RNA protection assay that is used in a manual assertion.
ECO:MCC
true
spatial pattern of transcript expression evidence used in manual assertion
2010-12-20T06:59:18Z
A type of spatial pattern of transcript expression analysis that is used in a manual assertion.
ECO:0000289
eco
mchibucos
true
true
A type of spatial pattern of transcript expression analysis that is used in a manual assertion.
ECO:MCC
subtractive hybridization evidence used in manual assertion
2010-12-20T07:00:48Z
A type of subtractive hybridization experiment that is used in a manual assertion.
ECO:0000290
eco
mchibucos
true
A type of subtractive hybridization experiment that is used in a manual assertion.
ECO:MCC
true
transcript expression evidence used in manual assertion
2010-12-20T07:02:08Z
A type of transcript expression evidence that is used in a manual assertion.
ECO:0000291
eco
mchibucos
true
true
A type of transcript expression evidence that is used in a manual assertion.
ECO:MCC
morpholino experiment evidence
2011-01-10T03:36:25Z
A type of experimental phenotypic evidence that uses anti-sense by introducing morpholino oligonucleotides into the cytosol of a cell.
ECO:0000292
Morpholino oligonucleotides modify gene expression by blocking access of other molecules to specific, approximately 25-base-long regions of the base-pairing surfaces of ribonucleic acid (RNA). To achieve this anti-sense knockdown technique, delivery of the morpholino can be achieved via microinjection, electroporation, or another method.
anti-sense
eco
mchibucos
A type of experimental phenotypic evidence that uses anti-sense by introducing morpholino oligonucleotides into the cytosol of a cell.
ECO:MCC
systematic evolution of ligands by exponential amplification evidence
2011-01-10T04:23:50Z
A type of evidence arising from a physical interaction analysis where a combinatorial chemistry technique is used to identify oligonucleotides that bind to a target ligand.
ECO:0000293
PSI-MI:MI:0657
SELEX begins with the synthesis of a large oligonucleotide library, either single-stranded DNA or RNA, which consists of random fixed-length sequences flanked by constant 5' and 3' ends that serve as primers. The library is exposed to a target ligand, typically a protein or small organic compound. Unbound sequences are removed, typically with affinity chromatography. Bound sequences are eluted and the nucleic acid is extracted, followed by PCR amplification (RNA is first reverse transcribed). PCR product is converted to single stranded (DNA) or transcribed (RNA). Oligonucleotides are bound to the ligand again and the process is repeated with increasing elution stringency. After several rounds of the process, recovered oligonucleotides are sequenced and analyzed to reveal the binding specificity of the protein.
SELEX evidence
eco
in vitro evolution evidence
in vitro selection evidence
mchibucos
systematic evolution of ligands by exponential enrichment
PSI-MI:MI:0657
A type of evidence arising from a physical interaction analysis where a combinatorial chemistry technique is used to identify oligonucleotides that bind to a target ligand.
ECO:MCC
url:http://en.wikipedia.org/wiki/Systematic_Evolution_of_Ligands_by_Exponential_Enrichment
bacterial one-hybrid evidence
2011-01-10T06:16:20Z
A type of hybrid interaction evidence that uses bacterial transformation with two plasmids to assess in vivo binding of a DNA-binding domain (bait) and DNA target site (prey).
B1H evidence
Bacterial one-hybrid assay is a method for screening a library of candidate proteins (prey plasmid) for the ability to bind to a target, cis-regulatory element or any other short, DNA binding sequence placed 5' to reporter genes (bait plasmid). Transformation of a bacterial host with two different plasmids is required: One is designed to express the "bait". The other plasmid contains a "prey" which, if bound to by the chimeric fusion product, drives expression of downstream reporter genes.
ECO:0000294
eco
mchibucos
A type of hybrid interaction evidence that uses bacterial transformation with two plasmids to assess in vivo binding of a DNA-binding domain (bait) and DNA target site (prey).
ECO:MCC
RNA-seq evidence
2011-01-11T12:54:50Z
A type of transcript expression evidence based on high-throughput (HT) sequencing of fragmented cDNA molecules.
ECO:0000295
RNA sequencing
Total RNA is isolated from cells and mRNA is purified by targeting the 3' polyadenylated (poly(A)) tail with poly(T) oligos covalently attached to a substrate. Next, cDNA fragments are generated either by hydrolysis of RNA into 200-300 base oligonucleotides, preceded by reverse transcription, or by reverse transcription initiated by random primers. The cDNA second strand is synthesized, fragments are adapter ligated and high-throughput sequencing is performed by Roche 454, Illumina, ABI-SOLiD, or another HT sequencing technology. Resulting sort reads are aligned against a reference genome, and downstream analysis is performed.
WTSS
eco
mchibucos
whole transcriptome shotgun sequencing
A type of transcript expression evidence based on high-throughput (HT) sequencing of fragmented cDNA molecules.
ECO:MCC
PMID:18611170
whole transcriptome shotgun sequencing
green fluorescent protein transcript localization evidence
2011-01-11T02:31:19Z
A transcriptional activation assay that uses a green fluorescent protein (GFP) reporter gene.
ECO:0000296
This term describes transcriptional activation; to describe immunolocalization of the protein, use the term "immunolocalization of green fluorescent protein".
eco
localization of GFP transcript
mchibucos
A transcriptional activation assay that uses a green fluorescent protein (GFP) reporter gene.
ECO:MCC
LacZ transcript localization evidence
2011-01-11T02:53:19Z
A transcriptional activation assay that uses a LacZ reporter gene.
ECO:0000297
This term describes transcriptional activation; to describe immunolocalization of the protein, use the term "immunolocalization of LacZ protein".
eco
mchibucos
A transcriptional activation assay that uses a LacZ reporter gene.
ECO:MCC
cleavage arrested development evidence
2011-01-11T03:28:49Z
A type of experimental phenotypic evidence where embryonic development proceeds although cytokinesis is blocked.
ECO:0000298
In the embryos of some organisms, inhibition of cytokinesis blocks neither the cell cycle nor the unfolding of the developmental program. As such, embryonic morphology can be frozen, allowing analysis of the developmental fate of each cell present at the time of cleavage arrest.
eco
mchibucos
A type of experimental phenotypic evidence where embryonic development proceeds although cytokinesis is blocked.
ECO:MCC
cytochalasin experiment evidence
2011-01-11T03:30:29Z
A type of cleavage arrested development that arises after treatment with cytochalasin.
Cytochalasin inhibits cytokinesis by blocking the formation of contractile microfilaments.
ECO:0000299
eco
mchibucos
A type of cleavage arrested development that arises after treatment with cytochalasin.
ECO:MCC
green fluorescent protein immunolocalization evidence
2011-01-11T03:48:50Z
A type of immunolocalization evidence data that was generated using green fluorescent protein (GFP) as a marker.
ECO:0000300
GFP immunolocalization evidence
This term describes immunolocalization of the protein; to describe transcriptional activation, use the term "localization of green fluorescent protein transcript".
eco
mchibucos
A type of immunolocalization evidence data that was generated using green fluorescent protein (GFP) as a marker.
ECO:MCC
beta-galactosidase protein immunolocalization evidence
2011-01-11T04:06:40Z
A type of immunolocalization evidence that was generated using LacZ protein as a marker.
ECO:0000301
LacZ protein immunolocalization evidence
This term describes immunolocalization of the protein; to describe transcriptional activation, use the term "localization of LacZ transcript".
eco
mchibucos
A type of immunolocalization evidence that was generated using LacZ protein as a marker.
ECO:MCC
author statement used in manual assertion
2011-01-20T02:26:47Z
A type of author statement that is used in a manual assertion.
ECO:0000302
eco
mchibucos
true
A type of author statement that is used in a manual assertion.
ECO:MCC
true
non-traceable author statement used in manual assertion
2011-01-20T02:29:50Z
A type of non-traceable author statement that is used in a manual assertion.
ECO:0000303
GOECO:NAS
NAS
eco
mchibucos
non-traceable author statement
GOECO:NAS
non-traceable author statement
GOECO:NAS
NAS
non-traceable author statement
GOECO:NAS
true
A type of non-traceable author statement that is used in a manual assertion.
ECO:MCC
true
traceable author statement used in manual assertion
2011-01-20T02:31:03Z
A type of traceable author statement that is used in a manual assertion.
ECO:0000304
GOECO:TAS
TAS
eco
mchibucos
traceable author statement
GOECO:TAS
TAS
traceable author statement
GOECO:TAS
GOECO:TAS
traceable author statement
A type of traceable author statement that is used in a manual assertion.
ECO:MCC
true
true
curator inference used in manual assertion
2011-01-20T02:33:32Z
A type of curator inference that is used in a manual assertion.
ECO:0000305
GOECO:IC
eco
mchibucos
true
inferred by curator
GOECO:IC
true
A type of curator inference that is used in a manual assertion.
ECO:MCC
inference from background scientific knowledge used in manual assertion
2011-01-20T02:35:11Z
A type of inference from background scientific knowledge that is used in a manual assertion.
ECO:0000306
eco
mchibucos
true
true
A type of inference from background scientific knowledge that is used in a manual assertion.
ECO:MCC
no biological data found used in manual assertion
2011-01-20T02:43:18Z
A type of no biological data found that is used in a manual assertion.
ECO:0000307
GOECO:ND
eco
mchibucos
true
no biological data available
GOECO:ND
A type of no biological data found that is used in a manual assertion.
ECO:MCC
true
biological aspect of ancestor evidence
2011-02-04T05:41:26Z
A type of phylogenetic evidence whereby an aspect of a descendant gene is inferred through the characterization of an aspect of an ancestral gene.
ECO:0000308
First, a characteristic of the most recent common ancestor (MRCA) is inferred from experimental evidence in descendants; this is followed by inferring a characteristic of a descendant of the MRCA. This type of evidence can be used in support of both positive and "not" GO annotations.
eco
mchibucos
A type of phylogenetic evidence whereby an aspect of a descendant gene is inferred through the characterization of an aspect of an ancestral gene.
ECO:MCC
cap analysis of gene expression evidence
2011-02-17T01:33:09Z
A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by a cap-trapper system.
CAGE
Complementary DNA (cDNA) is synthesized from microgram quantities of mRNA using first-strand cDNA primer (oligo dT12-18) and reverse transcriptase in the presence of trehalose and sorbitol, followed by selection of full-length cDNA with biotinylated cap-trapper. Linkers are attached to the 5' ends of full-length enriched cDNAs to introduce a recognition site for the restriction endonuclease MmeI, which creates a two base overhang. After amplification, sequencing tags are concatenated for high-throughput sequencing. Resulting sort reads are aligned against a reference genome, and downstream analysis is performed.
ECO:0000309
eco
mchibucos
CAGE
PMID:16489339
A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by a cap-trapper system.
ECO:MCC
nano-cap analysis of gene expression evidence
2011-02-17T01:33:34Z
A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by reverse transcriptase template switching.
ECO:0000310
NanoCAGE captures the 5' ends of molecules by template switching. When polymerizing the cDNA of a capped mRNA, the reverse transcriptase adds extra cytosines that are complementary to the cap. Each 5' full length cDNAs is extended upon hybridization of the riboguanosine-tailed template switching oligonucleotides to these extra cytosines. In semisuppressive PCR, the short templates fold intramolecularly and prevent the binding of primers, which precludes amplification; longer molecules are less likely to fold and are thus amplified. Templates derived from reaction artifacts form stable homoduplexes, also precluding amplification. After template switching, semisuppressive PCR, and EcoP151 cleavage, 25-bp tags are ligated to bar code-containing oligonucleotide adaptors. After PCR amplification, the nanoCAGE tags are sequenced by synthesis. NanoCAGE requires as little as 10 nanograms of total RNA.
eco
mchibucos
nanoCAGE
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
PMID:20543846
nanoCAGE
imported information
2011-03-02T05:24:13Z
An evidence type that is based on work performed by a person or group prior to a use by different person or group.
ECO:0000311
eco
mchibucos
An evidence type that is based on work performed by a person or group prior to a use by different person or group.
ECO:MCC
imported information used in manual assertion
2011-03-02T05:29:44Z
A type of imported information that is used in a manual assertion.
ECO:0000312
eco
mchibucos
true
A type of imported information that is used in a manual assertion.
ECO:MCC
true
imported information used in automatic assertion
2011-03-02T05:33:43Z
A type of imported information that is used in an automatic assertion.
ECO:0000313
eco
mchibucos
true
true
A type of imported information that is used in an automatic assertion.
ECO:MCC
direct assay evidence used in manual assertion
2011-10-28T04:59:31Z
A type of direct assay evidence that is used in a manual assertion.
ECO:0000314
GOECO:IDA
IDA
eco
inferred from direct assay
mchibucos
GOECO:IDA
inferred from direct assay
true
GOECO:IDA
IDA
true
inferred from direct assay
GOECO:IDA
A type of direct assay evidence that is used in a manual assertion.
ECO:MCC
mutant phenotype evidence used in manual assertion
2011-10-28T05:12:49Z
A type of mutant phenotype evidence that is used in a manual assertion.
ECO:0000315
GOECO:IMP
IMP
eco
inferred from mutant phenotype
mchibucos
true
true
GOECO:IMP
IMP
A type of mutant phenotype evidence that is used in a manual assertion.
ECO:MCC
inferred from mutant phenotype
GOECO:IMP
GOECO:IMP
inferred from mutant phenotype
genetic interaction evidence used in manual assertion
2011-10-28T05:14:42Z
A type of genetic interaction experiment evidence that is used in a manual assertion.
ECO:0000316
GOECO:IGI
IGI
eco
inferred from genetic interaction
mchibucos
inferred from genetic interaction
GOECO:IGI
true
true
A type of genetic interaction experiment evidence that is used in a manual assertion.
ECO:MCC
GOECO:IGI
inferred from genetic interaction
GOECO:IGI
IGI
genomic context evidence used in manual assertion
2011-10-28T05:22:53Z
A type of genomic context evidence that is used in a manual assertion.
ECO:0000317
GOECO:IGC
IGC
eco
inferred from genomic context
mchibucos
true
A type of genomic context evidence that is used in a manual assertion.
ECO:MCC
inferred from genomic context
GOECO:IGC
true
GOECO:IGC
IGC
GOECO:IGC
inferred from genomic context
biological aspect of ancestor evidence used in manual assertion
2011-10-28T05:23:51Z
A type of biological aspect of ancestor evidence that is used in a manual assertion.
ECO:0000318
GOECO:IBA
IBA
eco
inferred from biological aspect of ancestor
mchibucos
GOECO:IBA
IBA
GOECO:IBA
inferred from biological aspect of ancestor
A type of biological aspect of ancestor evidence that is used in a manual assertion.
ECO:MCC
true
inferred from biological aspect of ancestor
GOECO:IBA
true
biological aspect of descendant evidence used in manual assertion
2011-10-28T05:25:09Z
A type of biological aspect of descendant evidence that is used in a manual assertion.
ECO:0000319
GOECO:IBD
IBD
eco
inferred from biological aspect of descendant
mchibucos
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
GOECO:IBD
IBD
true
inferred from biological aspect of descendant
GOECO:IBD
phylogenetic determination of loss of key residues evidence used in manual assertion
2011-10-28T05:25:48Z
A type of phylogenetic determination of loss of key residues evidence that is used in a manual assertion.
ECO:0000320
GOECO:IKR
GOECO:IMR
IKR
IMR
eco
inferred from key residues
inferred from missing residues
mchibucos
true
GOECO:IKR
inferred from missing residues
GOECO:IKR
inferred from key residues
GOECO:IKR
IMR
inferred from key residues
GOECO:IKR
GOECO:IKR
IKR
A type of phylogenetic determination of loss of key residues evidence that is used in a manual assertion.
ECO:MCC
true
inferred from missing residues
GOECO:IMR
rapid divergence from ancestral sequence evidence used in manual assertion
2011-10-28T05:26:42Z
A type of rapid divergence from ancestral sequence evidence that is used in a manual assertion.
ECO:0000321
GOECO:IRD
IRD
eco
inferred from rapid divergence
mchibucos
true
GOECO:IRD
inferred from rapid divergence
true
A type of rapid divergence from ancestral sequence evidence that is used in a manual assertion.
ECO:MCC
GOECO:IRD
IRD
inferred from rapid divergence
GOECO:IRD
imported manually asserted information used in automatic assertion
2011-12-13T12:04:48Z
ECO:0000322
Evidence that was initially used in manual assertion by one person or group, which is imported by a second person or group and used in automatic assertion.
GO_REF:0000041
eco
mchibucos
IEA (UniProt UniPathway)
GO_REF:0000041
ECO:MCC
Evidence that was initially used in manual assertion by one person or group, which is imported by a second person or group and used in automatic assertion.
imported automatically asserted information used in automatic assertion
2011-12-13T02:06:25Z
ECO:0000323
Evidence 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
mchibucos
ECO:MCC
Evidence 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.
imaging assay evidence
2012-02-23T12:01:43Z
Direct assay evidence derived from analysis of an image.
ECO:0000324
ECO:0001122
eco
mchibucos
radiologic test evidence
Direct assay evidence derived from analysis of an image.
ECO:MCC
chromatography evidence
2012-05-16T11:46:27Z
A type of experimental evidence that is based on separation of constituent parts of a mixture (the mobile phase) as they pass differentially through a stationary phase due to differences in partition coefficient and retention on the stationary phase.
ECO:0000325
chromatographic evidence
eco
mchibucos
A type of experimental evidence that is based on separation of constituent parts of a mixture (the mobile phase) as they pass differentially through a stationary phase due to differences in partition coefficient and retention on the stationary phase.
ECO:MCC
transcript splice pattern evidence
2012-06-08T11:03:59Z
A type of sequence alignment evidence that is based on comparing the position of exon junctions, relative to a reference genome, for a transcript annotation and a supporting transcript.
ECO:0000326
eco
mchibucos
A type of sequence alignment evidence that is based on comparing the position of exon junctions, relative to a reference genome, for a transcript annotation and a supporting transcript.
ECO:MCC
whole transcript splice pattern evidence
2012-06-08T11:11:24Z
A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features.
ECO:0000327
This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that have the same splice pattern as a RefSeq transcript. If such full transcript information is not available, RefSeq reports sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, supported by the evidence term ECO:0000328 or a child.
eco
mchibucos
A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features.
ECO:MCC
coding sequence splice pattern evidence
2012-06-08T11:21:57Z
A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript.
ECO:0000328
This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, but for which full transcript information is unavailable. For sequences that have the same splice pattern as a whole RefSeq transcript, use the evidence term ECO:0000327 or a child.
eco
mchibucos
A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript.
ECO:MCC
whole transcript splice pattern evidence used in manual assertion
2012-06-08T11:40:03Z
A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features, and is used in manual assertion.
ECO:0000329
This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that have the same splice pattern as a RefSeq transcript. If such full transcript information is not available, RefSeq reports sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, supported by the evidence term ECO:0000328 or a child.
eco
mchibucos
A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features, and is used in manual assertion.
ECO:MCC
true
true
coding sequence splice pattern evidence used in manual assertion
2012-06-08T11:43:47Z
A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript, and is used in manual assertion.
ECO:0000330
This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, but for which full transcript information is unavailable. For sequences that have the same splice pattern as a whole RefSeq transcript, use the evidence term ECO:0000327 or a child.
eco
mchibucos
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
true
coding sequence splice pattern evidence used in automatic assertion
2012-06-08T11:48:09Z
A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript, and is used in automatic assertion.
ECO:0000331
This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, but for which full transcript information is unavailable. For sequences that have the same splice pattern as a whole RefSeq transcript, use the evidence term ECO:0000327 or a child.
eco
mchibucos
true
A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript, and is used in automatic assertion.
ECO:MCC
true
whole transcript splice pattern evidence used in automatic assertion
2012-06-08T11:49:17Z
A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features, and is used in automatic assertion.
ECO:0000332
This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that have the same splice pattern as a RefSeq transcript. If such full transcript information is not available, RefSeq reports sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, supported by the evidence term ECO:0000328 or a child.
eco
mchibucos
true
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
true
sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence
2012-07-31T02:56:43Z
A type of gel electrophoresis evidence where proteins are separated according to their electrophoretic mobility.
ECO:0000333
Electrophoretic mobility is a function of both the length and charge of a protein. The protein sample is linearized with sodium dodecyl sulfate (SDS), an anionic detergent. Typically, polypeptides bound with SDS possess an even distribution of charge per unit mass, and subsequent fractionation is by size.
SDS-PAGE evidence
eco
mchibucos
A type of gel electrophoresis evidence where proteins are separated according to their electrophoretic mobility.
ECO:MCC
PubMed:4861258
url:http://www.nature.com/nmeth/journal/v2/n1/full/nmeth0105-83.html
url:http://www.ncbi.nlm.nih.gov/Class/NAWBIS/Modules/Protein/protein18.html
particle size and count assay evidence
2012-07-31T03:19:32Z
A type of direct assay evidence resulting from an assay where both the size of and number of particles in a sample are determined.
An example of an instrument used to analyze particle sizes and counts is the Beckman Coulter® Z Series system.
ECO:0000334
eco
mchibucos
A type of direct assay evidence resulting from an assay where both the size of and number of particles in a sample are determined.
ECO:MCC
substance quantification evidence
2012-07-31T03:52:46Z
A type of direct assay evidence where the quantity of a substance used as part of an assay is measured.
ECO:0000335
Two examples of substance quantification assay are (i) measuring how much of a radiolabelled compound is taken up by a cell and (ii) measuring how much of a substrate is turned over by a given enzyme.
eco
mchibucos
A type of direct assay evidence where the quantity of a substance used as part of an assay is measured.
ECO:MCC
competitive growth assay evidence
2012-08-24T12:03:58Z
A type of biological assay evidence in which a mutated strain of a microorganism, such as a yeast or bacterium, is grown competitively with wild-type cells and the relative fitness of the strains is assessed.
ECO:0000336
eco
fitness profiling
mchibucos
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
GOC:MAH
PMID:20537132
fitness profiling
gel electrophoresis evidence
2012-08-24T12:11:51Z
A type of direct assay evidence where molecules have been sorted according to their size and charge by moving through a gel in the presence of an electric field.
ECO:0000337
Molecules typically separated include DNA, RNA, or protein. The gel is typically made of agarose, polyacrylamide, or starch.
eco
mchibucos
A type of direct assay evidence where molecules have been sorted according to their size and charge by moving through a gel in the presence of an electric field.
ECO:MCC
wikipedia:Gel_electrophoresis
pulsed-field gel electrophoresis evidence
2012-08-24T12:34:01Z
ECO:0000338
Gel electrophoresis evidence that employs alternately pulsed, perpendicularly oriented electrical fields, at least one of which is inhomogeneous, to separate large DNA molecules on an agarose gel.
PFGE
eco
mchibucos
Gel electrophoresis evidence that employs alternately pulsed, perpendicularly oriented electrical fields, at least one of which is inhomogeneous, to separate large DNA molecules on an agarose gel.
PMID:6373014
two-dimensional agarose gel electrophoresis evidence
2-D agarose gel electrophoresis
2012-08-24T12:42:37Z
A type of gel electrophoresis evidence where DNA molecules are electrophoresed on a low percentage agarose gel followed by high voltage electrophoresis on a higher percentage agarose gel in the presence of ethidium bromide.
ECO:0000339
The first dimension gel is intentionally run at low voltage in low percentage agarose to separate DNA molecules in proportion to their mass. The second dimension is run at high voltage in a gel of higher agarose concentration in the presence of ethidium bromide so that the mobility of a non-linear molecule is drastically influenced by its shape.
eco
mchibucos
A type of gel electrophoresis evidence where DNA molecules are electrophoresed on a low percentage agarose gel followed by high voltage electrophoresis on a higher percentage agarose gel in the presence of ethidium bromide.
PMID:16118435
PMID:8594382
plasmid maintenance assay evidence
2012-08-24T01:27:58Z
ECO:0000340
Experimental evidence from an assay in which a mitotically stable plasmid (or minichromosome) is introduced into cells, cells are grown without selection for several generations, the proportion of cells that retain the plasmid is then determined (by comparing colony numbers on selective versus non-selective media), and the loss per generation calculated.
eco
mchibucos
minichromosome maintenance assay evidence
ECO:MCC
Experimental evidence from an assay in which a mitotically stable plasmid (or minichromosome) is introduced into cells, cells are grown without selection for several generations, the proportion of cells that retain the plasmid is then determined (by comparing colony numbers on selective versus non-selective media), and the loss per generation calculated.
PMID:6323245
PMID:6323245
minichromosome maintenance assay evidence
specific protein inhibition by antibody evidence
2012-08-24T01:48:24Z
A type of specific protein inhibition evidence where the molecular function of a protein is inhibited by an antibody.
ECO:0000341
eco
mchibucos
A type of specific protein inhibition evidence where the molecular function of a protein is inhibited by an antibody.
ECO:MCC
Support of intron position by RNA-seq alignment evidence
2013-04-03T04:22:05Z
A type of transcript splice pattern evidence where intron locations in predicted transcripts are compared to intron locations supported by RNA-seq evidence.
ECO:0000342
RNA-seq alignment intron location evidence is used by NCBI RefSeq (http://www.ncbi.nlm.nih.gov/refseq). Exon-exon boundaries (or intron locations) of a RefSeq transcript, as determined by aligning the transcript to a reference chromosome, are compared to intron locations supported by RNAseq data.
eco
mchibucos
A type of transcript splice pattern evidence where intron locations in predicted transcripts are compared to intron locations supported by RNA-seq evidence.
ECO:MCC
Full support of intron position by RNA-seq alignment evidence
2013-04-03T04:41:48Z
A type of support of intron position by RNA-seq alignment evidence where RNA-seq alignment from a single sample supports all of the intron positions (exon pairs) predicted for a transcript.
ECO:0000343
Full support entails that all exon pairs represented in the transcript are supported. For example, for a transcript containing five exons, if liver RNA-seq reads support all four introns but brain RNA-seq supports only three introns, then the liver data fully support the transcript exons whereas the brain data do not.
eco
mchibucos
A type of support of intron position by RNA-seq alignment evidence where RNA-seq alignment from a single sample supports all of the intron positions (exon pairs) predicted for a transcript.
ECO:MCC
Partial support of intron position by RNA-seq alignment evidence
2013-04-03T04:50:46Z
A type of support of intron position by RNA-seq alignment evidence where RNA-seq alignment to a genome supports only some of the intron positions (exon pairs) predicted for a transcript.
ECO:0000344
Partial support can occur in two ways. First, one or more exon-exon pair (intron) is not supported by any RNA-seq sample included in the analysis. Second, no single RNA-seq sample provides support for all exon-exon pairs (introns) represented in a transcript, but all represented exons are supported by at least one sample.
eco
mchibucos
A type of support of intron position by RNA-seq alignment evidence where RNA-seq alignment to a genome supports only some of the intron positions (exon pairs) predicted for a transcript.
ECO:MCC
single exon transcript confirmation via alignment evidence
2013-04-03T05:10:34Z
ECO:0000345
eco
mchibucos
Support of intron position by RNA-seq alignment evidence used in manual assertion
2013-04-04T04:37:35Z
A type of support of intron position by RNA-seq alignment evidence that is used in a manual assertion.
ECO:0000346
eco
mchibucos
true
true
A type of support of intron position by RNA-seq alignment evidence that is used in a manual assertion.
ECO:MCC
Support of intron position by RNA-seq alignment evidence used in automatic assertion
2013-04-04T04:38:45Z
A type of support of intron position by RNA-seq alignment evidence that is used in an automatic assertion.
ECO:0000347
eco
mchibucos
A type of support of intron position by RNA-seq alignment evidence that is used in an automatic assertion.
ECO:MCC
true
true
Full support of intron position by RNA-seq alignment evidence used in automatic assertion
2013-04-04T04:40:19Z
A type of full support of intron position by RNA-seq alignment evidence that is used in an automatic assertion.
ECO:0000348
eco
mchibucos
A type of full support of intron position by RNA-seq alignment evidence that is used in an automatic assertion.
ECO:MCC
true
true
Full support of intron position by RNA-seq alignment evidence used in manual assertion
2013-04-04T04:41:34Z
A type of full support of intron position by RNA-seq alignment evidence that is used in a manual assertion.
ECO:0000349
eco
mchibucos
true
A type of full support of intron position by RNA-seq alignment evidence that is used in a manual assertion.
ECO:MCC
true
Partial support of intron position by RNA-seq alignment evidence used in automatic assertion
2013-04-04T04:42:53Z
A type of partial support of intron position by RNA-seq alignment evidence that is used in an automatic assertion.
ECO:0000350
eco
mchibucos
A type of partial support of intron position by RNA-seq alignment evidence that is used in an automatic assertion.
ECO:MCC
true
true
Partial support of intron position by RNA-seq alignment evidence used in manual assertion
2013-04-04T04:43:56Z
A type of partial support of intron position by RNA-seq alignment evidence that is used in a manual assertion.
ECO:0000351
eco
mchibucos
true
true
A type of partial support of intron position by RNA-seq alignment evidence that is used in a manual assertion.
ECO:MCC
evidence used in manual assertion
A type of evidence that is used in an manual assertion.
ECO:0000352
eco
mchibucos
true
true
A type of evidence that is used in an manual assertion.
ECO:MCC
physical interaction evidence used in manual assertion
2013-10-31T21:01:27Z
A type of physical interaction evidence that is used in a manual assertion.
ECO:0000353
GOECO:IPI
IPI
eco
inferred from physical interaction
mchibucos
true
inferred from physical interaction
GOECO:IPI
GOECO:IPI
inferred from physical interaction
GOECO:IPI
IPI
true
A type of physical interaction evidence that is used in a manual assertion.
ECO:MCC
gene neighbors evidence used in manual assertion
2013-11-19T13:37:24Z
A type of gene neighbors evidence that is used in a manual assertion.
ECO:0000354
GO_REF:0000025
eco
mchibucos
A type of gene neighbors evidence that is used in a manual assertion.
ECO:MCC
true
operon structure as IGC evidence
GO_REF:0000025
phylogenetic distribution evidence
2014-04-22T17:02:31Z
A type of phylogenetic evidence characterized by the mapping of the character states of living organisms onto phylogenies using the method of maximum parsimony.
ECO:0000355
Example of use: "The presence of paired evaginated hemispheres and olfactory bulbs in both agnathan and gnathostome radiations suggests that such hemispheres were also present in the common ancestor." PMID: 7013637. Northcutt RG. (1981) Evolution of the telencephalon in nonmammals. Ann. Rev. Neurosci.
eco
mchibucos
A type of phylogenetic evidence characterized by the mapping of the character states of living organisms onto phylogenies using the method of maximum parsimony.
ECO:MCC
PMID:21238344
differential gene expression evidence from microarray experiment
2014-09-26T16:21:45Z
ECO:0000356
eco
mchibucos
differential gene expression evidence from RNA-seq experiment
2014-09-26T16:22:57Z
ECO:0000357
eco
mchibucos
differential geneset expression evidence from microarray experiment (GSEA, Fisher-exact)
2014-09-26T16:25:47Z
ECO:0000358
eco
mchibucos
differential geneset expression evidence from RNA-seq experiment (GSEA, Fisher-exact)
2014-09-26T16:26:48Z
ECO:0000359
eco
mchibucos
biological target-disease association via drug
2014-09-26T16:39:11Z
ECO:0000360
eco
mchibucos
inferential evidence
2015-07-14T11:19:37Z
A type of evidence where an assertion is derived from another assertion via logical inference or some non-logical but rational means.
ECO:0000361
Inference is the process of deriving logical conclusions from premises known or assumed to be true, or alternatively, arriving at conclusions via some non-logical means of observation of patterns of facts, which can result in identifying new meanings and contexts for understanding. Given the evidence provided by a set of premises, deductive reasoning involves drawing conclusions that necessarily follow, i.e. are certain, whereas inductive reasoning generates conclusions that are likely to be, but are not necessarily, true.
eco
mchibucos
A type of evidence where an assertion is derived from another assertion via logical inference or some non-logical but rational means.
ECO:MCC
evidence based on computational logical inference
2015-07-14T11:24:27Z
A type of inferential evidence based on a computationally derived unary inference or an inference chain in which at least one step is
computationally derived.
ECO:0000362
eco
mchibucos
A type of inferential evidence based on a computationally derived unary inference or an inference chain in which at least one step is
computationally derived.
ECO:MCC
GOC:MC
evidence based on computational logical inference used in automatic assertion
2015-07-14T11:35:08Z
A type of evidence based on computational logical inference that is used in automatic assertion.
ECO:0000363
eco
mchibucos
true
A type of evidence based on computational logical inference that is used in automatic assertion.
ECO:MCC
true
evidence based on logical inference from manual annotation used in automatic assertion
2015-07-14T11:44:19Z
A type of evidence based on logical inference from a manually curated annotation that is used in an automatic assertion.
ECO:0000364
eco
mchibucos
A type of evidence based on logical inference from a manually curated annotation that is used in an automatic assertion.
ECO:MCC
evidence based on logical inference from automatic annotation used in automatic assertion
2015-07-14T11:45:25Z
A type of evidence based on logical inference from an automatically curated annotation that is used in an automatic assertion.
ECO:0000366
eco
mchibucos
A type of evidence based on logical inference from an automatically curated annotation that is used in an automatic assertion.
ECO:MCC
evidence used in automatic assertion
A type of evidence that is used in an automatic assertion.
ECO:0000501
GOECO:IEA
GO_REF:0000004
GO_REF:0000023
IEA
cjm
eco
inferred from electronic annotation
true
GOECO:IEA
IEA
inferred from electronic annotation
GOECO:IEA
Gene Ontology annotation based on Swiss-Prot keyword mapping.
GO_REF:0000004
true
A type of evidence that is used in an automatic assertion.
ECO:cjm
Gene Ontology annotation based on Swiss-Prot Subcellular Location vocabulary mapping.
GO_REF:0000023
GOECO:IEA
inferred from electronic annotation
3D cell culture evidence
2014-03-16T11:30:54Z
ECO:0001001
eco
mchibucos
[3H]arachidonic acid release assay evidence
2014-03-16T11:30:54Z
ECO:0001002
eco
mchibucos
[3H]-thymidine incorporation assay evidence
2014-03-16T11:30:54Z
ECO:0001003
eco
mchibucos
51Cr release assay evidence
2014-03-16T11:30:54Z
ECO:0001004
eco
mchibucos
7-aminoactinomycin staining evidence
2014-03-16T11:30:54Z
7-AAD staining evidence
7-amino-actinomycin D staining evidence
ECO:0001005
eco
mchibucos
adhesion assay evidence
2014-03-16T11:30:54Z
ECO:0001006
eco
mchibucos
adoptive cell transfer evidence
2014-03-16T11:30:54Z
A type of ex vivo assay evidence derived by ex vivo selection of tumor-reactive lymphocytes, and their activation and numerical expansion before re-infusion to the autologous tumor-bearing host.
Adoptive immunotherapy
ECO:0001007
eco
mchibucos
passive immunization
A type of ex vivo assay evidence derived by ex vivo selection of tumor-reactive lymphocytes, and their activation and numerical expansion before re-infusion to the autologous tumor-bearing host.
ECO:SN
url:http://jco.ascopubs.org/content/23/10/2346.full.pdf+html
url:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2305722/pdf/nihms42807.pdf
Alamar blue assay evidence
2014-03-16T11:30:54Z
ECO:0001008
eco
mchibucos
allograft transplantation experiment evidence
2014-03-16T11:30:54Z
A type of anatomical perturbation evidence where an organ or tissue is transplanted from one individual to another of the same species with a different genotype.
Allotransplantation
ECO:0001009
allografting
eco
mchibucos
tissue grafting
A type of anatomical perturbation evidence where an organ or tissue is transplanted from one individual to another of the same species with a different genotype.
ECO:SN
url:http://www.nature.com/subjects/allograft
url:http://www.organdonor.gov/about/terms_and_topics/
anion-exchange chromatography evidence
2014-03-16T11:30:54Z
A type of chromatography evidence where a positively charged ion exchange resin with an affinity for molecules having net negative surface charges is used to separate the molecules.
ECO:0001010
eco
mchibucos
A type of chromatography evidence where a positively charged ion exchange resin with an affinity for molecules having net negative surface charges is used to separate the molecules.
ECO:SN
PMID:20978968
url:http://www.bio-rad.com/en-us/applications-technologies/anion-exchange-chromatography
url:http://www.uta.edu/faculty/sawasthi/Enzymology-4351-5324/Class%20Syllabus%20Enzymology/Ion%20Exchange%20Chromatography-1.pdf
annexin-V staining evidence
2014-03-16T11:30:54Z
ECO:0001011
eco
mchibucos
behavioral assay evidence
2014-03-16T11:30:54Z
ECO:0001012
eco
mchibucos
blocking monoclonal antibody evidence
2014-03-16T11:30:54Z
ECO:0001013
eco
mchibucos
blocking peptide evidence
2014-03-16T11:30:54Z
ECO:0001014
eco
mchibucos
blocking polyclonal antibody evidence
2014-03-16T11:30:54Z
ECO:0001015
eco
mchibucos
blood test evidence
2014-03-16T11:30:54Z
A type of direct assay evidence where a blood sample is extracted from an organism to analyze different blood components.
ECO:0001016
eco
mchibucos
A type of direct assay evidence where a blood sample is extracted from an organism to analyze different blood components.
ECO:SN
url:https://www.nhlbi.nih.gov/health/health-topics/topics/bdt
Boyden chamber assay evidence
2014-03-16T11:30:54Z
ECO:0001017
eco
mchibucos
bromodeoxyuridine incorporation assay evidence
2014-03-16T11:30:54Z
5-bromo-2'-deoxyuridine incorporation assay evidence
BUdR incorporation assay evidence
BrdU incorporation assay evidence
BrdUrd incorporation assay evidence
ECO:0001018
eco
mchibucos
caspase assay evidence
2014-03-16T11:30:54Z
ECO:0001019
eco
mchibucos
cell counting evidence
2014-03-16T11:30:54Z
ECO:0001020
eco
mchibucos
cell permeability assay evidence
2014-03-16T11:30:54Z
ECO:0001021
eco
mchibucos
carboxyfluorescein diacetate succinimidyl ester staining evidence
2014-03-16T11:30:54Z
CFDA-SE staining evidence
CFSE-staining evidence
ECO:0001022
eco
mchibucos
chemiluminescence-linked immunoassay evidence
2014-03-16T11:30:54Z
CLIA evidence
ECO:0001023
eco
mchibucos
chimeric protein evidence
2014-03-16T11:30:54Z
ECO:0001024
eco
mchibucos
co-electrophoresis evidence
2014-03-16T11:30:54Z
ECO:0001025
eco
mchibucos
co-localization evidence
2014-03-16T11:30:54Z
ECO:0001026
eco
mchibucos
colony counting evidence
2014-03-16T11:30:54Z
ECO:0001027
eco
mchibucos
co-sedimentation assay evidence
2014-03-16T11:30:54Z
ECO:0001028
eco
mchibucos
comet assay evidence
2014-03-16T11:30:54Z
ECO:0001029
eco
mchibucos
conditional knockout evidence
2014-03-16T11:30:54Z
ECO:0001030
eco
mchibucos
conditional knockin evidence
2014-03-16T11:30:54Z
ECO:0001031
eco
mchibucos
constitutively active mutant evidence
2014-03-16T11:30:54Z
ECO:0001032
eco
mchibucos
cross-linking evidence
2014-03-16T11:30:54Z
ECO:0001033
eco
mchibucos
crystallography evidence
2014-03-16T11:30:54Z
ECO:0001034
eco
mchibucos
cytochemistry evidence
2014-03-16T11:30:54Z
ECO:0001035
eco
mchibucos
cytochrome C release assay evidence
2014-03-16T11:30:54Z
ECO:0001036
eco
mchibucos
4',6-diamidino-2-phenylindole staining evidence
2014-03-16T11:30:54Z
DAPI staining evidence
ECO:0001037
eco
mchibucos
deletion evidence
2014-03-16T11:30:54Z
ECO:0001038
eco
mchibucos
DNA laddering assay evidence
2014-03-16T11:30:54Z
ECO:0001039
eco
mchibucos
RNA dot blot assay evidence
2014-03-16T11:30:54Z
A type of RNA detection assay evidence based on the direct application of a RNA mixture in a circular motion on a matrix for hybridization with labeled DNA fragments.
ECO:0001040
RNA dot blot
eco
mchibucos
A type of RNA detection assay evidence based on the direct application of a RNA mixture in a circular motion on a matrix for hybridization with labeled DNA fragments.
ECO:SW
PMID:21424648
RNA microarray evidence
2014-03-16T11:30:54Z
ECO:0001041
eco
mchibucos
dominant-negative mutant evidence
2014-03-16T11:30:54Z
ECO:0001042
eco
mchibucos
Edman degradation evidence used in manual assertion
2014-03-17T16:59:00Z
A type of Edman degradation evidence that is used in a manual assertion.
ECO:0001043
eco
mchibucos
true
true
A type of Edman degradation evidence that is used in a manual assertion.
ECO:MCC
Edman degradation evidence
2014-03-16T11:30:54Z
ECO:0001044
eco
mchibucos
eTag assay evidence
2014-03-16T11:30:54Z
ECO:0001045
eco
mchibucos
filter binding assay evidence
2014-03-16T11:30:54Z
ECO:0001046
eco
mchibucos
fluorescence in situ hybridization evidence
2014-03-16T11:30:54Z
ECO:0001047
eco
mchibucos
fluorescence resonance energy transfer evidence
2014-03-16T11:30:54Z
ECO:0001048
FRET
eco
mchibucos
gel-filtration evidence
2014-03-16T11:30:54Z
ECO:0001049
eco
mchibucos
histochemistry evidence
2014-03-16T11:30:54Z
ECO:0001050
eco
mchibucos
histology evidence
2014-03-16T11:30:54Z
ECO:0001051
eco
mchibucos
high-performance liquid chromatography evidence
2014-03-16T11:30:54Z
ECO:0001052
HPLC evidence
eco
mchibucos
immunocytochemistry evidence
2014-03-16T11:30:54Z
ECO:0001053
eco
mchibucos
immunodepletion evidence
2014-03-16T11:30:54Z
ECO:0001054
eco
mchibucos
immunohistochemistry evidence
2014-03-16T11:30:54Z
ECO:0001055
eco
mchibucos
induced mutation evidence
2014-03-16T11:30:54Z
ECO:0001056
eco
mchibucos
in vitro acetylation assay evidence
2014-03-16T11:30:54Z
A type of in vitro assay evidence where acetylated residues are detected in a compound (such as a protein or a nucleic acid) in an in vitro experiment.
ECO:0001057
eco
mchibucos
A type of in vitro assay evidence where acetylated residues are detected in a compound (such as a protein or a nucleic acid) in an in vitro experiment.
ECO:SN
SIB:PG
url:http://www.perkinelmer.com/resources/technicalresources/applicationsupportknowledgebase/radiometric/acetylation.xhtml
in vitro cleavage assay evidence
2014-03-16T11:30:54Z
A type of in vitro assay evidence where the cleavage of a protein by a protease is detected in an in vitro experiment. The cleavage gives rise to protein fragments.
ECO:0001058
eco
mchibucos
A type of in vitro assay evidence where the cleavage of a protein by a protease is detected in an in vitro experiment. The cleavage gives rise to protein fragments.
ECO:SN
PMID:21121091
SIB:PG
in vitro deubiquitination assay evidence
2014-03-16T11:30:54Z
A type of in vitro assay evidence where the removal of ubiquitin groups on a protein is detected in vitro.
ECO:0001059
eco
mchibucos
A type of in vitro assay evidence where the removal of ubiquitin groups on a protein is detected in vitro.
ECO:SN
PMID:19692941
SIB:PG
in vitro deacetylation assay evidence
2014-03-16T11:30:54Z
A type of in vitro assay evidence where the removal of acetyl groups from a compound is detected in an in vitro experiment.
ECO:0001060
eco
mchibucos
A type of in vitro assay evidence where the removal of acetyl groups from a compound is detected in an in vitro experiment.
ECO:SN
SIB:PG
url:http://www.perkinelmer.com/resources/technicalresources/applicationsupportknowledgebase/radiometric/acetylation.xhtml
in vitro defarnesylation assay evidence
2014-03-16T11:30:54Z
A type of in vitro assay evidence where the removal of farnesyl groups from a protein is detected in an in vitro experiment.
ECO:0001061
eco
mchibucos
A type of in vitro assay evidence where the removal of farnesyl groups from a protein is detected in an in vitro experiment.
ECO:SN
PMID:16126733
SIB:PG
in vitro demethylation assay evidence
2014-03-16T11:30:54Z
A type of in vitro assay evidence where the removal of methyl groups from a compound is detected in an in vitro experiment.
ECO:0001062
eco
mchibucos
A type of in vitro assay evidence where the removal of methyl groups from a compound is detected in an in vitro experiment.
ECO:SN
SIB:PG
url:http://en.wikipedia.org/wiki/Demethylation
in vitro desumoylation assay evidence
2014-03-16T11:30:54Z
A type of in vitro assay evidence where the removal of sumo groups is detected on a protein in vitro.
ECO:0001063
eco
mchibucos
A type of in vitro assay evidence where the removal of sumo groups is detected on a protein in vitro.
ECO:SN
SIB:PG
url:http://www.enzolifesciences.com/BML-UW8955/sumoylation-kit/
in vitro farnesylation assay evidence
2014-03-16T11:30:54Z
A type of in vitro assay evidence where farnesylated residues in proteins are detected in an in vitro experiment.
ECO:0001064
eco
mchibucos
A type of in vitro assay evidence where farnesylated residues in proteins are detected in an in vitro experiment.
ECO:SN
SIB:PG
url:http://en.wikipedia.org/wiki/Farnesyltransferase
in vitro methylation assay evidence
2014-03-16T11:30:54Z
A type of in vitro assay evidence where methylated residues are detected in a compound (such as a protein or a nucleic acid) in an in vitro experiment.
ECO:0001065
eco
mchibucos
A type of in vitro assay evidence where methylated residues are detected in a compound (such as a protein or a nucleic acid) in an in vitro experiment.
ECO:SN
SIB:PG
url:http://en.wikipedia.org/wiki/Methylation
in vitro palmitoylation assay evidence
2014-03-16T11:30:54Z
A type of in vitro assay evidence where palmitoylated residues in proteins are detected in an in vitro experiment.
ECO:0001066
eco
mchibucos
A type of in vitro assay evidence where palmitoylated residues in proteins are detected in an in vitro experiment.
ECO:SN
PMID:17077383
SIB:PG
in vitro phosphatase assay evidence
2014-03-16T11:30:54Z
A type of in vitro assay evidence where the removal of phosphatase groups on a protein is detected in an in vitro experiment.
ECO:0001067
eco
mchibucos
A type of in vitro assay evidence where the removal of phosphatase groups on a protein is detected in an in vitro experiment.
ECO:SN
SIB:PG
url:http://en.wikipedia.org/wiki/Phosphatase
in vitro protein kinase assay evidence
2014-03-16T11:30:54Z
A type of in vitro assay evidence where phosphorylated residues in a protein are detected in an in vitro experiment.
ECO:0001068
eco
mchibucos
A type of in vitro assay evidence where phosphorylated residues in a protein are detected in an in vitro experiment.
ECO:SN
SIB:PG
url:http://en.wikipedia.org/wiki/Protein_kinase
url:http://en.wikipedia.org/wiki/Protein_phosphorylation
in vitro polyADP-ribosylation assay evidence
2014-03-16T11:30:54Z
A type of in vitro assay evidence where ADP-ribosylated residues in proteins are detected in an in vitro experiment.
ECO:0001069
eco
mchibucos
A type of in vitro assay evidence where ADP-ribosylated residues in proteins are detected in an in vitro experiment.
ECO:SN
PMID:21870253
SIB:PG
in vitro sumoylation assay evidence
2014-03-16T11:30:54Z
A type of in vitro assay evidence where sumoylated residues are detected on a protein in an in vitro experiment.
ECO:0001070
eco
mchibucos
A type of in vitro assay evidence where sumoylated residues are detected on a protein in an in vitro experiment.
ECO:SN
SIB:PG
url:http://www.enzolifesciences.com/BML-UW8955/sumoylation-kit/
in vitro transcription assay evidence
2014-03-16T11:30:54Z
A type of in vitro assay evidence where transcription is detected in vitro to validate the activation or repression ablity of a transcription factor in the absence of other proteins present in in vivo conditions.
ECO:0001071
eco
mchibucos
A type of in vitro assay evidence where transcription is detected in vitro to validate the activation or repression ablity of a transcription factor in the absence of other proteins present in in vivo conditions.
ECO:SN
ECO:SW
PMID:21125481
SIB:PG
in vitro translation assay evidence
2014-03-16T11:30:54Z
A type of in vitro assay evidence where de novo protein synthesis is detected in an in vitro experiment.
ECO:0001072
eco
mchibucos
A type of in vitro assay evidence where de novo protein synthesis is detected in an in vitro experiment.
ECO:SN
PMID:18230759
SIB:PG
in vitro ubiquitination assay evidence
2014-03-16T11:30:54Z
A type of in vitro assay evidence where ubiquitinated residues are detected on a protein in an in vitro experiment.
ECO:0001073
eco
mchibucos
A type of in vitro assay evidence where ubiquitinated residues are detected on a protein in an in vitro experiment.
ECO:SN
PMID:19692941
SIB:PG
in vivo acetylation assay evidence
2014-03-16T11:30:54Z
A type of in vivo assay evidence where acetylated residues are detected in a compound (such as a protein or a nucleic acid) in cells in vivo.
ECO:0001074
eco
mchibucos
A type of in vivo assay evidence where acetylated residues are detected in a compound (such as a protein or a nucleic acid) in cells in vivo.
ECO:SN
SIB:PG
url:http://www.perkinelmer.com/resources/technicalresources/applicationsupportknowledgebase/radiometric/acetylation.xhtml
in vivo cleavage assay evidence
2014-03-16T11:30:54Z
A type of in vivo assay evidence where the cleavage of a protein by a protease is detected in cells in vivo. The cleavage gives rise to protein fragments.
ECO:0001075
eco
mchibucos
A type of in vivo assay evidence where the cleavage of a protein by a protease is detected in cells in vivo. The cleavage gives rise to protein fragments.
ECO:SN
PMID:22154596
SIB:PG
in vivo deacetylation assay evidence
2014-03-16T11:30:54Z
A type of in vivo assay evidence where the removal of acetyl groups from a compound is detected in cells in vivo.
ECO:0001076
eco
mchibucos
A type of in vivo assay evidence where the removal of acetyl groups from a compound is detected in cells in vivo.
ECO:SN
SIB:PG
url:http://www.perkinelmer.com/resources/technicalresources/applicationsupportknowledgebase/radiometric/acetylation.xhtml
in vivo defarnesylation assay evidence
2014-03-16T11:30:54Z
A type of in vivo assay evidence where removal of farnesyl groups from a protein is detected in cells in vivo.
ECO:0001077
eco
mchibucos
A type of in vivo assay evidence where removal of farnesyl groups from a protein is detected in cells in vivo.
ECO:SN
PMID:15556768
PMID:16507103
SIB:PG
in vivo demethylation assay evidence
2014-03-16T11:30:54Z
A type of in vivo assay evidence where the removal of methyl groups from a compound is detected in cells in vivo.
ECO:0001078
eco
mchibucos
A type of in vivo assay evidence where the removal of methyl groups from a compound is detected in cells in vivo.
ECO:SN
SIB:PG
url:http://en.wikipedia.org/wiki/Demethylation
in vivo deubiquitination assay evidence
2014-03-16T11:30:54Z
A type of in vivo assay evidence where the removal of ubiquitin groups on a protein is detected in cells in vivo.
ECO:0001079
eco
mchibucos
A type of in vivo assay evidence where the removal of ubiquitin groups on a protein is detected in cells in vivo.
ECO:SN
PMID:19692941
SIB:PG
in vivo desumoylation assay evidence
2014-03-16T11:30:54Z
A type of in vivo assay evidence where the removal of sumo groups on a protein is detected in cells in vivo.
ECO:0001080
eco
mchibucos
A type of in vivo assay evidence where the removal of sumo groups on a protein is detected in cells in vivo.
ECO:SN
SIB:PG
url:http://www.enzolifesciences.com/BML-UW8955/sumoylation-kit/
in vivo farnesylation assay evidence
2014-03-16T11:30:54Z
A type of in vivo assay evidence where farnesylated residues in proteins are detected in cells in vivo.
ECO:0001081
eco
mchibucos
A type of in vivo assay evidence where farnesylated residues in proteins are detected in cells in vivo.
ECO:SN
PMID:9030603
SIB:PG
in vivo methylation assay evidence
2014-03-16T11:30:54Z
A type of in vivo assay evidence where methylated residues are detected in a compound (such as a protein or a nucleic acid) in vivo.
ECO:0001082
eco
mchibucos
A type of in vivo assay evidence where methylated residues are detected in a compound (such as a protein or a nucleic acid) in vivo.
ECO:SN
SIB:PG
url:http://en.wikipedia.org/wiki/Methylation
in vivo palmitoylation assay evidence
2014-03-16T11:30:54Z
A type of in vivo assay evidence where palmitoylated residues in proteins are detected in cells in vivo.
ECO:0001083
eco
mchibucos
A type of in vivo assay evidence where palmitoylated residues in proteins are detected in cells in vivo.
ECO:SN
PMID:10329400
SIB:PG
in vivo phosphatase assay evidence
2014-03-16T11:30:54Z
A type of in vivo assay evidence where the removal of phosphate groups on a protein is detected in cells in vivo.
ECO:0001084
eco
mchibucos
A type of in vivo assay evidence where the removal of phosphate groups on a protein is detected in cells in vivo.
ECO:SN
SIB:PG
url:http://en.wikipedia.org/wiki/Phosphatase
in vivo protein kinase assay evidence
2014-03-16T11:30:54Z
A type of in vivo assay evidence where phosphorylated residues in a protein are detected in cells in vivo.
ECO:0001085
eco
mchibucos
A type of in vivo assay evidence where phosphorylated residues in a protein are detected in cells in vivo.
ECO:SN
SIB:PG
url:http://en.wikipedia.org/wiki/Protein_kinase
url:http://en.wikipedia.org/wiki/Protein_phosphorylation
in vivo sumoylation assay evidence
2014-03-16T11:30:54Z
A type of in vivo assay evidence where sumoylated residues are detected on a protein in cells in vivo.
ECO:0001086
eco
mchibucos
A type of in vivo assay evidence where sumoylated residues are detected on a protein in cells in vivo.
ECO:SN
SIB:PG
url:http://www.enzolifesciences.com/BML-UW8955/sumoylation-kit/
in vivo transcription assay evidence
2014-03-16T11:30:54Z
A type of in vivo assay evidence where transcription is detected in cells in vivo.
ECO:0001087
eco
mchibucos
A type of in vivo assay evidence where transcription is detected in cells in vivo.
ECO:SN
PMID:12181418
SIB:PG
in vivo translation assay evidence
2014-03-16T11:30:54Z
A type of in vivo assay evidence where de novo protein synthesis is detected in cells in vivo.
ECO:0001088
eco
mchibucos
A type of in vivo assay evidence where de novo protein synthesis is detected in cells in vivo.
ECO:SN
PMID:24901308
SIB:PG
in vivo ubiquitination assay evidence
2014-03-16T11:30:54Z
A type of in vivo assay evidence where ubiquitinated residues on a protein are detected in cells in vivo.
ECO:0001089
eco
mchibucos
A type of in vivo assay evidence where ubiquitinated residues on a protein are detected in cells in vivo.
ECO:SN
PMID:19692941
SIB:PG
knockin evidence
2014-03-16T11:30:54Z
ECO:0001090
eco
mchibucos
knockout evidence
2014-03-16T11:30:54Z
ECO:0001091
eco
mchibucos
lipid binding assay evidence
2014-03-16T11:30:54Z
ECO:0001092
eco
mchibucos
luminescence-based mammalian interactome mapping assay evidence
2014-03-16T11:30:54Z
ECO:0001093
LUMIER assay
eco
mchibucos
macroscopy evidence
2014-03-16T11:30:54Z
ECO:0001094
eco
mchibucos
mammalian 2-hybrid assay evidence
2014-03-16T11:30:54Z
ECO:0001095
eco
mchibucos
mass spectrometry evidence
2014-03-16T11:30:54Z
ECO:0001096
eco
mchibucos
medical imaging evidence
2014-03-16T11:30:54Z
ECO:0001097
eco
mchibucos
microscopy evidence
2014-03-16T11:30:54Z
A type of direct assay evidence where a microscope was used to view a sample.
ECO:0001098
eco
mchibucos
A type of direct assay evidence where a microscope was used to view a sample.
ECO:MCC
motility wound healing assay evidence
2014-03-16T11:30:54Z
ECO:0001099
eco
mchibucos
MTS assay evidence
2014-03-16T11:30:54Z
3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium
ECO:0001100
eco
mchibucos
MTT assay evidence
2014-03-16T11:30:54Z
3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide
ECO:0001101
eco
mchibucos
multiplex bead-based immunoassay evidence
2014-03-16T11:30:54Z
ECO:0001102
eco
mchibucos
natural variation mutant evidence
2014-03-16T11:30:54Z
ECO:0001103
eco
mchibucos
nuclear fragmentation evidence
2014-03-16T11:30:54Z
ECO:0001104
eco
mchibucos
nuclear magnetic resonance spectroscopy evidence
2014-03-16T11:30:54Z
ECO:0001105
NMR spectroscopy
eco
mchibucos
nuclease protection assay evidence
2014-03-16T11:30:54Z
ECO:0001106
eco
mchibucos
nucleotide analog incorporation evidence
2014-03-16T11:30:54Z
ECO:0001107
eco
mchibucos
phage display evidence
2014-03-16T11:30:54Z
ECO:0001108
eco
mchibucos
phosphoamino acid analysis evidence
2014-03-16T11:30:54Z
ECO:0001109
eco
mchibucos
peptide affinity enrichment evidence
2014-03-16T11:30:54Z
ECO:0001110
eco
mchibucos
phosphopeptide affinity enrichment evidence
physical examination evidence
2014-03-16T11:30:54Z
ECO:0001111
eco
mchibucos
peptide array evidence
2014-03-16T11:30:54Z
ECO:0001112
eco
mchibucos
phosphopeptide array evidence
point mutation evidence
2014-03-16T11:30:54Z
ECO:0001113
eco
mchibucos
propidium iodide staining evidence
2014-03-16T11:30:54Z
ECO:0001114
eco
mchibucos
fluorescence evidence
2014-03-16T11:30:54Z
ECO:0001115
eco
mchibucos
protein dot blot assay evidence
2014-03-16T11:30:54Z
ECO:0001116
eco
mchibucos
protein microarray evidence
2014-03-16T11:30:54Z
ECO:0001117
eco
mchibucos
protein sequencing assay evidence
2014-03-16T11:30:54Z
ECO:0001118
eco
mchibucos
quantitative mass spectrometry evidence
2014-03-16T11:30:54Z
ECO:0001119
eco
mchibucos
radioisotope assay evidence
2014-03-16T11:30:54Z
ECO:0001120
eco
mchibucos
radioassay
radioisotopic assay
radioimmunoassay evidence
2014-03-16T11:30:54Z
ECO:0001121
eco
mchibucos
resonant mirror biosensor evidence
2014-03-16T11:30:54Z
ECO:0001123
eco
mchibucos
restriction fragment detection evidence
2014-03-16T11:30:54Z
ECO:0001124
eco
mchibucos
spectrophotometry evidence
2014-03-16T11:30:54Z
ECO:0001126
eco
mchibucos
surface plasmon resonance evidence
2014-03-16T11:30:54Z
A type of physical interaction evidence based on real-time, rapid plasmon generation on the interface between a planar surface and vacuum that measures changes in refractive index close to the sensor surface when an analyte and its immobilized ligand bind to observe and characterize molecular interaction.
ECO:0001127
Plasmons are generated by an incident light beam.
SPR evidence
eco
mchibucos
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
PMID:11578932
SPR evidence
syngeneic transplantation experiment evidence
2014-03-16T11:30:54Z
ECO:0001128
eco
mchibucos
TACE activity assay evidence
2014-03-16T11:30:54Z
ECO:0001129
Tumor necrosis factor - alpha converting enzyme activity assay
eco
mchibucos
tissue microarray evidence
2014-03-16T11:30:54Z
ECO:0001130
eco
mchibucos
transgenic organism evidence
2014-03-16T11:30:54Z
ECO:0001131
eco
mchibucos
tryptic phosphopeptide mapping assay evidence
2014-03-16T11:30:54Z
ECO:0001132
eco
mchibucos
terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence
2014-03-16T11:30:54Z
ECO:0001133
TUNEL assay evidence
TdT-mediated dUTP-biotin nick end labeling assay
eco
mchibucos
terminal deoxynucleotidyl transferase-dUTP nick end labeling assay evidence
urine test evidence
2014-03-16T11:30:54Z
ECO:0001134
eco
mchibucos
wound healing assay evidence
2014-03-16T11:30:54Z
ECO:0001135
eco
mchibucos
WST-1 assay evidence
2014-03-16T11:30:54Z
ECO:0001136
eco
mchibucos
xenotransplantation experiment evidence
2014-03-16T11:30:54Z
A type of anatomical perturbation evidence where live cells, tissues, or organs from a non-human animal source are transplanted, implanted or infused into a human recipient.
ECO:0001137
Xenograft transplantation
Xenografting
Xenotransplantation
eco
mchibucos
tissue grafting
A type of anatomical perturbation evidence where live cells, tissues, or organs from a non-human animal source are transplanted, implanted or infused into a human recipient.
ECO:SN
url:http://ilarjournal.oxfordjournals.org/content/37/1/16.full.pdf+html
url:http://www.fda.gov/BiologicsBloodVaccines/Xenotransplantation/
3D cell culture evidence used in manual assertion
2014-03-17T15:18:35Z
A type of 3D cell culture evidence that is used in a manual assertion.
ECO:0001138
eco
mchibucos
A type of 3D cell culture evidence that is used in a manual assertion.
ECO:MCC
true
true
51Cr release assay evidence used in manual assertion
2014-03-17T15:20:55Z
A type of 51Cr release assay evidence that is used in a manual assertion.
ECO:0001139
eco
mchibucos
A type of 51Cr release assay evidence that is used in a manual assertion.
ECO:MCC
true
true
7-aminoactinomycin staining evidence used in manual assertion
2014-03-17T15:22:01Z
A type of 7-aminoactinomycin staining evidence that is used in a manual assertion.
ECO:0001140
eco
mchibucos
true
A type of 7-aminoactinomycin staining evidence that is used in a manual assertion.
ECO:MCC
true
[3H]-thymidine incorporation assay evidence used in manual assertion
2014-03-17T15:31:52Z
A type of [3H]-thymidine incorporation assay evidence that is used in a manual assertion.
ECO:0001141
eco
mchibucos
A type of [3H]-thymidine incorporation assay evidence that is used in a manual assertion.
ECO:MCC
true
true
[3H]arachidonic acid release assay evidence used in manual assertion
2014-03-17T15:32:44Z
A type of [3H]arachidonic acid release assay evidence that is used in a manual assertion.
ECO:0001142
eco
mchibucos
true
true
A type of [3H]arachidonic acid release assay evidence that is used in a manual assertion.
ECO:MCC
adhesion assay evidence used in manual assertion
2014-03-17T15:33:38Z
A type of adhesion assay evidence that is used in a manual assertion.
ECO:0001143
eco
mchibucos
true
A type of adhesion assay evidence that is used in a manual assertion.
ECO:MCC
true
adoptive cell transfer evidence used in manual assertion
2014-03-17T15:36:19Z
A type of adoptive cell transfer evidence that is used in a manual assertion.
ECO:0001144
eco
mchibucos
true
A type of adoptive cell transfer evidence that is used in a manual assertion.
ECO:MCC
true
Alamar blue assay evidence used in manual assertion
2014-03-17T15:37:21Z
A type of Alamar blue assay evidence that is used in a manual assertion.
ECO:0001145
eco
mchibucos
A type of Alamar blue assay evidence that is used in a manual assertion.
ECO:MCC
true
true
allograft transplantation experiment evidence used in manual assertion
2014-03-17T15:38:22Z
A type of allograft transplantation experiment evidence that is used in a manual assertion.
ECO:0001146
eco
mchibucos
true
A type of allograft transplantation experiment evidence that is used in a manual assertion.
ECO:MCC
true
anion-exchange chromatography evidence used in manual assertion
2014-03-17T15:44:30Z
A type of anion-exchange chromatography evidence that is used in a manual assertion.
ECO:0001147
eco
mchibucos
true
A type of anion-exchange chromatography evidence that is used in a manual assertion.
ECO:MCC
true
annexin-V staining evidence used in manual assertion
2014-03-17T15:52:01Z
A type of annexin-V staining evidence that is used in a manual assertion.
ECO:0001148
eco
mchibucos
true
true
A type of annexin-V staining evidence that is used in a manual assertion.
ECO:MCC
behavioral assay evidence used in manual assertion
2014-03-17T15:53:38Z
A type of behavioral assay evidence used that is used in a manual assertion.
ECO:0001149
eco
mchibucos
A type of behavioral assay evidence used that is used in a manual assertion.
ECO:MCC
true
true
blocking monoclonal antibody evidence used in manual assertion
2014-03-17T15:54:44Z
A type of blocking monoclonal antibody evidence that is used in a manual assertion.
ECO:0001150
eco
mchibucos
true
A type of blocking monoclonal antibody evidence that is used in a manual assertion.
ECO:MCC
true
blocking peptide evidence used in manual assertion
2014-03-17T15:55:33Z
A type of blocking peptide evidence that is used in a manual assertion.
ECO:0001151
eco
mchibucos
true
true
A type of blocking peptide evidence that is used in a manual assertion.
ECO:MCC
blocking polyclonal antibody evidence used in manual assertion
2014-03-17T16:01:39Z
A type of blocking polyclonal antibody evidence tthat is used in a manual assertion.
ECO:0001152
eco
mchibucos
A type of blocking polyclonal antibody evidence tthat is used in a manual assertion.
ECO:MCC
true
true
blood test evidence used in manual assertion
2014-03-17T16:02:47Z
A type of blood test evidence that is used in a manual assertion.
ECO:0001153
eco
mchibucos
A type of blood test evidence that is used in a manual assertion.
ECO:MCC
true
true
Boyden chamber assay evidence used in manual assertion
2014-03-17T16:03:53Z
A type of Boyden chamber assay evidence that is used in a manual assertion.
ECO:0001154
eco
mchibucos
true
true
A type of Boyden chamber assay evidence that is used in a manual assertion.
ECO:MCC
bromodeoxyuridine incorporation assay evidence used in manual assertion
2014-03-17T16:04:49Z
A type of BrdU incorporation assay evidence that is used in a manual assertion.
ECO:0001155
eco
mchibucos
true
A type of BrdU incorporation assay evidence that is used in a manual assertion.
ECO:MCC
true
caspase assay evidence used in manual assertion
2014-03-17T16:06:06Z
A type of caspase assay evidence that is used in a manual assertion.
ECO:0001156
eco
mchibucos
true
true
A type of caspase assay evidence that is used in a manual assertion.
ECO:MCC
cell counting evidence used in manual assertion
2014-03-17T16:07:13Z
A type of cell counting evidence that is used in a manual assertion.
ECO:0001157
eco
mchibucos
A type of cell counting evidence that is used in a manual assertion.
ECO:MCC
true
true
cell permeability assay evidence used in manual assertion
2014-03-17T16:07:58Z
A type of cell permeability assay evidence that is used in a manual assertion.
ECO:0001158
eco
mchibucos
true
A type of cell permeability assay evidence that is used in a manual assertion.
ECO:MCC
true
carboxyfluorescein diacetate succinimidyl ester staining evidence used in manual assertion
2014-03-17T16:08:54Z
A type of carboxyfluorescein diacetate succinimidyl ester staining evidence that is used in a manual assertion.
ECO:0001159
eco
mchibucos
true
A type of carboxyfluorescein diacetate succinimidyl ester staining evidence that is used in a manual assertion.
ECO:MCC
true
chemiluminescence-linked immunoassay evidence used in manual assertion
2014-03-17T16:09:55Z
A type of chemiluminescence-linked immunoassay evidence that is used in a manual assertion.
ECO:0001160
eco
mchibucos
A type of chemiluminescence-linked immunoassay evidence that is used in a manual assertion.
ECO:MCC
true
true
chimeric protein evidence used in manual assertion
2014-03-17T16:10:40Z
A type of chimeric protein evidence that is used in a manual assertion.
ECO:0001161
eco
mchibucos
true
true
A type of chimeric protein evidence that is used in a manual assertion.
ECO:MCC
co-electrophoresis evidence used in manual assertion
2014-03-17T16:11:22Z
A type of co-electrophoresis evidence that is used in a manual assertion.
ECO:0001162
eco
mchibucos
true
true
A type of co-electrophoresis evidence that is used in a manual assertion.
ECO:MCC
co-localization evidence used in manual assertion
2014-03-17T16:12:04Z
A type of co-localization evidence that is used in a manual assertion.
ECO:0001163
eco
mchibucos
A type of co-localization evidence that is used in a manual assertion.
ECO:MCC
true
true
co-sedimentation assay evidence used in manual assertion
2014-03-17T16:12:55Z
A type of co-sedimentation assay evidence that is used in a manual assertion.
ECO:0001164
eco
mchibucos
A type of co-sedimentation assay evidence that is used in a manual assertion.
ECO:MCC
true
true
colony counting evidence used in manual assertion
2014-03-17T16:14:57Z
A type of colony counting evidence that is used in a manual assertion.
ECO:0001165
eco
mchibucos
A type of colony counting evidence that is used in a manual assertion.
ECO:MCC
true
true
comet assay evidence used in manual assertion
2014-03-17T16:16:01Z
A type of comet assay evidence that is used in a manual assertion.
ECO:0001166
eco
mchibucos
true
true
A type of comet assay evidence that is used in a manual assertion.
ECO:MCC
conditional knockin evidence used in manual assertion
2014-03-17T16:17:22Z
A type of conditional knockin evidence that is used in a manual assertion.
ECO:0001167
eco
mchibucos
true
true
A type of conditional knockin evidence that is used in a manual assertion.
ECO:MCC
conditional knockout evidence used in manual assertion
2014-03-17T16:17:58Z
A type of conditional knockout evidence that is used in a manual assertion.
ECO:0001168
eco
mchibucos
true
A type of conditional knockout evidence that is used in a manual assertion.
ECO:MCC
true
constitutively active mutant evidence used in manual assertion
2014-03-17T16:20:23Z
A type of constitutively active mutant evidence that is used a in manual assertion.
ECO:0001169
eco
mchibucos
true
true
A type of constitutively active mutant evidence that is used a in manual assertion.
ECO:MCC
cross-linking evidence used in manual assertion
2014-03-17T16:21:29Z
A type of cross-linking evidence that is used in a manual assertion.
ECO:0001170
eco
mchibucos
A type of cross-linking evidence that is used in a manual assertion.
ECO:MCC
true
true
true
crystallography evidence used in manual assertion
2014-03-17T16:22:20Z
A type of crystallography evidence that is used in a manual assertion.
ECO:0001171
eco
mchibucos
A type of crystallography evidence that is used in a manual assertion.
ECO:MCC
true
true
cytochemistry evidence used in manual assertion
2014-03-17T16:23:10Z
A type of cytochemistry evidence that is used in a manual assertion.
ECO:0001172
eco
mchibucos
true
true
A type of cytochemistry evidence that is used in a manual assertion.
ECO:MCC
cytochrome C release assay evidence used in manual assertion
2014-03-17T16:23:53Z
A type of cytochrome C release assay evidence that is used in a manual assertion.
ECO:0001173
eco
mchibucos
true
A type of cytochrome C release assay evidence that is used in a manual assertion.
ECO:MCC
true
4',6-diamidino-2-phenylindole staining evidence used in manual assertion
2014-03-17T16:25:03Z
A type of 4',6-diamidino-2-phenylindole staining evidence that is used in a manual assertion.
ECO:0001174
eco
mchibucos
A type of 4',6-diamidino-2-phenylindole staining evidence that is used in a manual assertion.
ECO:MCC
true
true
deletion evidence used in manual assertion
2014-03-17T16:25:54Z
A type of deletion evidence that is used in a manual assertion.
ECO:0001175
eco
mchibucos
A type of deletion evidence that is used in a manual assertion.
ECO:MCC
true
true
DNA laddering assay evidence used in manual assertion
2014-03-17T16:26:46Z
A type of DNA laddering assay evidence that is used in a manual assertion.
ECO:0001176
eco
mchibucos
true
true
A type of DNA laddering assay evidence that is used in a manual assertion.
ECO:MCC
RNA dot blot assay evidence used in manual assertion
2014-03-17T16:45:52Z
A type of RNA dot blot assay evidence that is used in a manual assertion.
ECO:0001177
eco
mchibucos
true
A type of RNA dot blot assay evidence that is used in a manual assertion.
ECO:MCC
true
RNA microarray evidence used in manual assertion
2014-03-17T16:46:50Z
A type of RNA microarray evidence that is used in a manual assertion.
ECO:0001178
eco
mchibucos
true
A type of RNA microarray evidence that is used in a manual assertion.
ECO:MCC
true
dominant-negative mutant evidence used in manual assertion
2014-03-17T16:47:44Z
A type of dominant-negative mutant evidence that is used in a manual assertion.
ECO:0001179
eco
mchibucos
true
A type of dominant-negative mutant evidence that is used in a manual assertion.
ECO:MCC
true
eTag assay evidence used in manual assertion
2014-03-17T16:59:39Z
A type of eTag assay evidence that is used in a manual assertion.
ECO:0001180
eco
mchibucos
true
true
A type of eTag assay evidence that is used in a manual assertion.
ECO:MCC
filter binding assay evidence used in manual assertion
2014-03-17T17:03:28Z
A type of filter binding assay evidence that is used in a manual assertion.
ECO:0001181
eco
mchibucos
A type of filter binding assay evidence that is used in a manual assertion.
ECO:MCC
true
true
fluorescence in situ hybridization evidence used in manual assertion
2014-03-17T17:04:20Z
A type of fluorescence in situ hybridization evidence that is used in a manual assertion.
ECO:0001182
eco
mchibucos
A type of fluorescence in situ hybridization evidence that is used in a manual assertion.
ECO:MCC
true
true
fluorescence resonance energy transfer evidence used in manual assertion
2014-03-17T17:05:22Z
A type of fluorescence resonance energy transfer evidence that is used in a manual assertion.
ECO:0001183
eco
mchibucos
A type of fluorescence resonance energy transfer evidence that is used in a manual assertion.
ECO:MCC
true
true
gel-filtration evidence used in manual assertion
2014-03-17T17:06:14Z
A type of gel-filtration evidence that is used in a manual assertion.
ECO:0001184
eco
mchibucos
true
true
A type of gel-filtration evidence that is used in a manual assertion.
ECO:MCC
histochemistry evidence used in manual assertion
2014-03-17T17:07:19Z
A type of histochemistry evidence that is used in a manual assertion.
ECO:0001185
eco
mchibucos
true
A type of histochemistry evidence that is used in a manual assertion.
ECO:MCC
true
immunocytochemistry evidence used in manual assertion
2014-03-17T17:12:39Z
A type of immunocytochemistry evidence that is used in a manual assertion.
ECO:0001186
eco
mchibucos
true
A type of immunocytochemistry evidence that is used in a manual assertion.
ECO:MCC
true
histology evidence used in manual assertion
2014-03-17T17:09:50Z
A type of histology evidence that is used in a manual assertion.
ECO:0001187
eco
mchibucos
true
A type of histology evidence that is used in a manual assertion.
ECO:MCC
true
immunodepletion evidence used in manual assertion
2014-03-17T17:16:19Z
A type of immunodepletion evidence that is used in a manual assertion.
ECO:0001188
eco
mchibucos
true
true
A type of immunodepletion evidence that is used in a manual assertion.
ECO:MCC
immunohistochemistry evidence used in manual assertion
2014-03-17T17:17:22Z
A type of immunohistochemistry evidence that is used in a manual assertion.
ECO:0001189
eco
mchibucos
true
A type of immunohistochemistry evidence that is used in a manual assertion.
ECO:MCC
true
in vitro acetylation assay evidence used in manual assertion
2014-03-17T17:19:24Z
A type of in vitro acetylation assay evidence that is used in a manual assertion.
ECO:0001190
eco
mchibucos
true
A type of in vitro acetylation assay evidence that is used in a manual assertion.
ECO:MCC
true
in vitro cleavage assay evidence used in manual assertion
2014-03-17T17:21:22Z
A type of in vitro cleavage assay evidence that is used in a manual assertion.
ECO:0001191
eco
mchibucos
true
A type of in vitro cleavage assay evidence that is used in a manual assertion.
ECO:MCC
true
in vitro deacetylation assay evidence used in manual assertion
2014-03-17T17:23:42Z
A type of in vitro deacetylation assay evidence that is used in a manual assertion.
ECO:0001192
eco
mchibucos
true
true
A type of in vitro deacetylation assay evidence that is used in a manual assertion.
ECO:MCC
in vitro defarnesylation assay evidence used in manual assertion
2014-03-17T17:25:45Z
A type of in vitro defarnesylation assay evidence that is used in a manual assertion.
ECO:0001193
eco
mchibucos
A type of in vitro defarnesylation assay evidence that is used in a manual assertion.
ECO:MCC
true
true
in vitro demethylation assay evidence used in manual assertion
2014-03-17T17:27:00Z
A type of in vitro demethylation assay evidence that is used in a manual assertion.
ECO:0001194
eco
mchibucos
A type of in vitro demethylation assay evidence that is used in a manual assertion.
ECO:MCC
true
true
in vitro desumoylation assay evidence used in manual assertion
2014-03-17T17:29:01Z
A type of in vitro desumoylation assay evidence that is used in a manual assertion.
ECO:0001195
eco
mchibucos
A type of in vitro desumoylation assay evidence that is used in a manual assertion.
ECO:MCC
true
true
in vitro deubiquitination assay evidence used in manual assertion
2014-03-17T17:29:48Z
A type of in vitro deubiquitination assay evidence that is used in a manual assertion.
ECO:0001196
eco
mchibucos
true
A type of in vitro deubiquitination assay evidence that is used in a manual assertion.
ECO:MCC
true
in vitro farnesylation assay evidence used in manual assertion
2014-03-17T17:30:50Z
A type of in vitro farnesylation assay evidence that is used in a manual assertion.
ECO:0001197
eco
mchibucos
true
true
A type of in vitro farnesylation assay evidence that is used in a manual assertion.
ECO:MCC
in vitro methylation assay evidence used in manual assertion
2014-03-17T17:31:54Z
A type of in vitro methylation assay evidence that is used in a manual assertion.
ECO:0001198
eco
mchibucos
A type of in vitro methylation assay evidence that is used in a manual assertion.
ECO:MCC
true
true
in vitro palmitoylation assay evidence used in manual assertion
2014-03-17T17:32:57Z
A type of in vitro palmitoylation assay evidence that is used in a manual assertion.
ECO:0001199
eco
mchibucos
true
A type of in vitro palmitoylation assay evidence that is used in a manual assertion.
ECO:MCC
true
in vitro phosphatase assay evidence used in manual assertion
2014-03-17T17:34:16Z
A type of in vitro phosphatase assay evidence that is used in a manual assertion.
ECO:0001200
eco
mchibucos
A type of in vitro phosphatase assay evidence that is used in a manual assertion.
ECO:MCC
true
true
in vitro polyADP-ribosylation assay evidence used in manual assertion
2014-03-17T17:34:57Z
A type of in vitro polyADP-ribosylation assay evidence that is used in a manual assertion.
ECO:0001201
eco
mchibucos
A type of in vitro polyADP-ribosylation assay evidence that is used in a manual assertion.
ECO:MCC
true
true
in vitro protein kinase assay evidence used in manual assertion
2014-03-17T17:39:57Z
A type of in vitro protein kinase assay evidence that is used in a manual assertion.
ECO:0001202
eco
mchibucos
A type of in vitro protein kinase assay evidence that is used in a manual assertion.
ECO:MCC
true
true
in vitro sumoylation assay evidence used in manual assertion
2014-03-17T17:41:25Z
A type of in vitro sumoylation assay evidence that is used in a manual assertion.
ECO:0001203
eco
mchibucos
true
A type of in vitro sumoylation assay evidence that is used in a manual assertion.
ECO:MCC
true
in vitro transcription assay used in manual assertion
2014-03-17T17:44:40Z
A type of in vitro transcription assay evidence that is used in a manual assertion.
ECO:0001204
eco
mchibucos
true
true
A type of in vitro transcription assay evidence that is used in a manual assertion.
ECO:MCC
in vitro translation assay evidence used in manual assertion
2014-03-17T17:46:30Z
A type of in vitro translation assay evidence that is used in a manual assertion.
ECO:0001205
eco
mchibucos
true
A type of in vitro translation assay evidence that is used in a manual assertion.
ECO:MCC
true
in vitro ubiquitination assay evidence used in manual assertion
2014-03-17T17:47:18Z
A type of in vitro ubiquitination assay evidence that is used in a manual assertion.
ECO:0001206
eco
mchibucos
true
true
A type of in vitro ubiquitination assay evidence that is used in a manual assertion.
ECO:MCC
in vivo acetylation assay evidence used in manual assertion
2014-03-17T17:48:56Z
A type of in vivo acetylation assay evidence that is used in manual assertion.
ECO:0001207
eco
mchibucos
true
true
A type of in vivo acetylation assay evidence that is used in manual assertion.
ECO:MCC
in vivo cleavage assay evidence used in manual assertion
2014-03-17T17:49:43Z
A type of in vivo cleavage assay evidence that is used in a manual assertion.
ECO:0001208
eco
mchibucos
true
true
A type of in vivo cleavage assay evidence that is used in a manual assertion.
ECO:MCC
in vivo deacetylation assay evidence used in manual assertion
2014-03-17T17:50:47Z
A type of in vivo deacetylation assay evidence that is used in a manual assertion.
ECO:0001209
eco
mchibucos
A type of in vivo deacetylation assay evidence that is used in a manual assertion.
ECO:MCC
true
true
in vivo defarnesylation assay evidence used in manual assertion
2014-03-17T17:52:41Z
A type of in vivo defarnesylation assay evidence that is used in a manual assertion.
ECO:0001210
eco
mchibucos
true
true
A type of in vivo defarnesylation assay evidence that is used in a manual assertion.
ECO:MCC
in vivo demethylation assay evidence used in manual assertion
2014-03-17T17:53:40Z
A type of in vivo demethylation assay evidence that is used in a manual assertion.
ECO:0001211
eco
mchibucos
A type of in vivo demethylation assay evidence that is used in a manual assertion.
ECO:MCC
true
true
in vivo desumoylation assay evidence used in manual assertion
2014-03-17T17:54:36Z
A type of in vivo desumoylation assay evidence that is used in a manual assertion.
ECO:0001212
eco
mchibucos
true
true
A type of in vivo desumoylation assay evidence that is used in a manual assertion.
ECO:MCC
in vivo deubiquitination assay evidence used in manual assertion
2014-03-17T17:56:28Z
A type of in vivo deubiquitination assay evidence that is used in a manual assertion.
ECO:0001213
eco
mchibucos
true
A type of in vivo deubiquitination assay evidence that is used in a manual assertion.
ECO:MCC
true
in vivo farnesylation assay evidence used in manual assertion
2014-03-17T17:57:18Z
A type of in vivo farnesylation assay evidence that is used in a manual assertion.
ECO:0001214
eco
mchibucos
A type of in vivo farnesylation assay evidence that is used in a manual assertion.
ECO:MCC
true
true
in vivo methylation assay evidence used in manual assertion
2014-03-17T18:03:16Z
A type of in vivo methylation assay evidence that is used in a manual assertion.
ECO:0001215
eco
mchibucos
true
A type of in vivo methylation assay evidence that is used in a manual assertion.
ECO:MCC
true
in vivo palmitoylation assay evidence used in manual assertion
2014-03-17T18:04:07Z
A type of in vivo palmitoylation assay evidence that is used in a manual assertion.
ECO:0001216
eco
mchibucos
A type of in vivo palmitoylation assay evidence that is used in a manual assertion.
ECO:MCC
true
true
in vivo phosphatase assay evidence used in manual assertion
2014-03-17T18:06:08Z
A type of in vivo phosphatase assay evidence that is used in a manual assertion.
ECO:0001217
eco
mchibucos
A type of in vivo phosphatase assay evidence that is used in a manual assertion.
ECO:MCC
true
true
in vivo protein kinase assay evidence used in manual assertion
2014-03-17T18:07:58Z
A type of in vivo protein kinase assay evidence that is used in a manual assertion.
ECO:0001218
eco
mchibucos
true
true
A type of in vivo protein kinase assay evidence that is used in a manual assertion.
ECO:MCC
in vivo sumoylation assay evidence used in manual assertion
2014-03-17T18:09:49Z
A type of in vivo sumoylation assay evidence that is used in a manual assertion.
ECO:0001219
eco
mchibucos
true
true
A type of in vivo sumoylation assay evidence that is used in a manual assertion.
ECO:MCC
in vivo transcription assay evidence used in manual assertion
2014-03-17T18:11:20Z
A type of in vivo transcription assay evidence that is used in a manual assertion.
ECO:0001220
eco
mchibucos
true
true
A type of in vivo transcription assay evidence that is used in a manual assertion.
ECO:MCC
in vivo translation assay evidence used in manual assertion
2014-03-17T18:42:50Z
A type of in vivo translation assay evidence that is used in a manual assertion.
ECO:0001221
eco
mchibucos
A type of in vivo translation assay evidence that is used in a manual assertion.
ECO:MCC
true
true
in vivo ubiquitination assay evidence used in manual assertion
2014-03-17T18:44:11Z
A type of in vivo ubiquitination assay evidence that is used in a manual assertion.
ECO:0001222
eco
mchibucos
A type of in vivo ubiquitination assay evidence that is used in a manual assertion.
ECO:MCC
true
true
induced mutation evidence used in manual assertion
2014-03-17T18:45:56Z
A type of induced mutation evidence that is used in a manual assertion.
ECO:0001223
eco
mchibucos
true
A type of induced mutation evidence that is used in a manual assertion.
ECO:MCC
true
knockin evidence used in manual assertion
2014-03-17T18:49:35Z
A type of knockin evidence that is used in a manual assertion.
ECO:0001224
eco
mchibucos
A type of knockin evidence that is used in a manual assertion.
ECO:MCC
true
true
knockout evidence used in manual assertion
2014-03-17T18:51:31Z
A type of knockout evidence that is used in a manual assertion.
ECO:0001225
eco
mchibucos
A type of knockout evidence that is used in a manual assertion.
ECO:MCC
true
true
lipid binding assay evidence used in manual assertion
2014-03-17T18:52:19Z
A type of lipid binding assay evidence that is used in a manual assertion.
ECO:0001226
eco
mchibucos
true
true
A type of lipid binding assay evidence that is used in a manual assertion.
ECO:MCC
luminescence-based mammalian interactome mapping assay evidence used in manual assertion
2014-03-17T18:55:16Z
A type of LUMIER assay evidence that is used in a manual assertion.
ECO:0001227
eco
mchibucos
A type of LUMIER assay evidence that is used in a manual assertion.
ECO:MCC
true
true
macroscopy evidence used in manual assertion
2014-03-17T18:56:21Z
A type of macroscopy evidence that is used in a manual assertion.
ECO:0001228
eco
mchibucos
A type of macroscopy evidence that is used in a manual assertion.
ECO:MCC
true
true
mammalian 2-hybrid assay evidence used in manual assertion
2014-03-17T18:57:25Z
A type of mammalian 2-hybrid assay evidence that is used in a manual assertion.
ECO:0001229
eco
mchibucos
true
A type of mammalian 2-hybrid assay evidence that is used in a manual assertion.
ECO:MCC
true
mass spectrometry evidence used in manual assertion
2014-03-17T18:59:50Z
A type of mass spectrometry evidence that is used in a manual assertion.
ECO:0001230
eco
mchibucos
A type of mass spectrometry evidence that is used in a manual assertion.
ECO:MCC
true
true
medical imaging evidence used in manual assertion
2014-03-17T19:04:43Z
A type of medical imaging evidence that is used in a manual assertion.
ECO:0001231
eco
mchibucos
true
true
A type of medical imaging evidence that is used in a manual assertion.
ECO:MCC
microscopy evidence used in manual assertion
2014-03-17T19:05:37Z
A type of microscopy evidence that is used in a manual assertion.
ECO:0001232
eco
mchibucos
true
A type of microscopy evidence that is used in a manual assertion.
ECO:MCC
true
motility wound healing assay evidence used in manual assertion
2014-03-17T19:08:13Z
A type of motility wound healing assay evidence that is used in a manual assertion.
ECO:0001233
eco
mchibucos
true
A type of motility wound healing assay evidence that is used in a manual assertion.
ECO:MCC
true
MTS assay evidence used in manual assertion
2014-03-17T19:08:51Z
A type of MTS assay evidence that is used in a manual assertion.
ECO:0001234
eco
mchibucos
true
A type of MTS assay evidence that is used in a manual assertion.
ECO:MCC
true
MTT assay evidence used in manual assertion
2014-03-17T19:13:17Z
A type of MTT assay evidence that is used in a manual assertion.
ECO:0001235
eco
mchibucos
A type of MTT assay evidence that is used in a manual assertion.
ECO:MCC
true
true
multiplex bead-based immunoassay evidence used in manual assertion
2014-03-17T19:14:03Z
A type of multiplex bead-based immunoassay evidence that is used in a manual assertion.
ECO:0001236
eco
mchibucos
true
true
A type of multiplex bead-based immunoassay evidence that is used in a manual assertion.
ECO:MCC
natural variation mutant evidence used in manual assertion
2014-03-17T19:15:48Z
A type of natural variation mutant evidence that is used in a manual assertion.
ECO:0001237
eco
mchibucos
A type of natural variation mutant evidence that is used in a manual assertion.
ECO:MCC
true
true
nuclear magnetic resonance spectroscopy evidence used in manual assertion
2014-03-17T19:18:50Z
A type of nuclear magnetic resonance spectroscopy evidence that is used in a manual assertion.
ECO:0001238
eco
mchibucos
true
A type of nuclear magnetic resonance spectroscopy evidence that is used in a manual assertion.
ECO:MCC
true
nuclear fragmentation evidence used in manual assertion
2014-03-17T19:19:55Z
A type of nuclear fragmentation evidence that is used in a manual assertion.
ECO:0001239
eco
mchibucos
true
true
A type of nuclear fragmentation evidence that is used in a manual assertion.
ECO:MCC
nuclease protection assay evidence used in manual assertion
2014-03-17T19:23:41Z
A type of nuclease protection assay evidence that is used in a manual assertion.
ECO:0001240
eco
mchibucos
A type of nuclease protection assay evidence that is used in a manual assertion.
ECO:MCC
true
true
nucleotide analog incorporation evidence used in manual assertion
2014-03-17T19:25:17Z
A type of nucleotide analog incorporation evidence that is used in a manual assertion.
ECO:0001241
eco
mchibucos
true
true
A type of nucleotide analog incorporation evidence that is used in a manual assertion.
ECO:MCC
phage display evidence used in manual assertion
2014-03-17T19:27:17Z
A type of phage display evidence that is used in a manual assertion.
ECO:0001242
eco
mchibucos
true
true
true
A type of phage display evidence that is used in a manual assertion.
ECO:MCC
phosphoamino acid analysis evidence used in manual assertion
2014-03-17T19:28:59Z
A type of phosphoamino acid analysis evidence that is used in a manual assertion.
ECO:0001243
eco
mchibucos
A type of phosphoamino acid analysis evidence that is used in a manual assertion.
ECO:MCC
true
true
peptide affinity enrichment evidence used in manual assertion
2014-03-17T19:30:13Z
A type of peptide affinity enrichment evidence that is used in a manual assertion.
ECO:0001244
eco
mchibucos
true
A type of peptide affinity enrichment evidence that is used in a manual assertion.
ECO:MCC
true
peptide array evidence used in manual assertion
2014-03-17T20:16:45Z
A type of peptide array evidence that is used in a manual assertion.
ECO:0001245
eco
mchibucos
true
true
A type of peptide array evidence that is used in a manual assertion.
ECO:MCC
physical examination evidence used in manual assertion
2014-03-17T20:17:27Z
A type of physical examination evidence that is used in a manual assertion.
ECO:0001246
eco
mchibucos
true
A type of physical examination evidence that is used in a manual assertion.
ECO:MCC
true
point mutation evidence used in manual assertion
2014-03-17T20:18:10Z
A type of point mutation evidence that is used in a manual assertion.
ECO:0001247
eco
mchibucos
true
A type of point mutation evidence that is used in a manual assertion.
ECO:MCC
true
propidium iodide staining evidence used in manual assertion
2014-03-17T20:18:58Z
A type of propidium iodide staining evidence that is used in a manual assertion.
ECO:0001248
eco
mchibucos
true
A type of propidium iodide staining evidence that is used in a manual assertion.
ECO:MCC
true
fluorescence evidence used in manual assertion
2014-03-17T20:19:35Z
A type of protein detection by fluorescence evidence that is used in a manual assertion.
ECO:0001249
eco
mchibucos
true
true
A type of protein detection by fluorescence evidence that is used in a manual assertion.
ECO:MCC
protein dot blot assay evidence used in manual assertion
2014-03-17T20:20:30Z
A type of protein dot blot assay evidence that is used in a manual assertion.
ECO:0001250
eco
mchibucos
A type of protein dot blot assay evidence that is used in a manual assertion.
ECO:MCC
true
true
protein microarray evidence used in manual assertion
2014-03-17T20:21:11Z
A type of protein microarray evidence that is used in a manual assertion.
ECO:0001251
eco
mchibucos
true
true
A type of protein microarray evidence that is used in a manual assertion.
ECO:MCC
protein sequencing assay evidence used in manual assertion
2014-03-17T20:22:08Z
A type of protein sequencing assay evidence that is used in a manual assertion.
ECO:0001252
eco
mchibucos
true
A type of protein sequencing assay evidence that is used in a manual assertion.
ECO:MCC
true
quantitative mass spectrometry evidence used in manual assertion
2014-03-17T20:23:15Z
A type of quantitative mass spectrometry evidence that is used in a manual assertion.
ECO:0001253
eco
mchibucos
true
true
A type of quantitative mass spectrometry evidence that is used in a manual assertion.
ECO:MCC
radioisotope assay evidence used in manual assertion
2014-03-17T20:27:05Z
A type of radioisotope assay evidence that is used in a manual assertion.
ECO:0001254
eco
mchibucos
true
true
A type of radioisotope assay evidence that is used in a manual assertion.
ECO:MCC
radioimmunoassay evidence used in manual assertion
2014-03-17T20:28:04Z
A type of radioimmunoassay evidence that is used in a manual assertion.
ECO:0001255
eco
mchibucos
A type of radioimmunoassay evidence that is used in a manual assertion.
ECO:MCC
true
true
imaging assay evidence used in manual assertion
2014-03-17T20:29:00Z
A type of imaging assay evidence that is used in a manual assertion.
ECO:0001256
eco
mchibucos
true
A type of imaging assay evidence that is used in a manual assertion.
ECO:MCC
true
restriction fragment detection evidence used in manual assertion
2014-03-17T20:29:05Z
A type of restriction fragment detection evidence that is used in a manual assertion.
ECO:0001257
eco
mchibucos
A type of restriction fragment detection evidence that is used in a manual assertion.
ECO:MCC
true
true
spectrophotometry evidence used in manual assertion
2014-03-17T20:29:09Z
A type of spectrophotometry evidence that is used in a manual assertion.
ECO:0001258
eco
mchibucos
A type of spectrophotometry evidence that is used in a manual assertion.
ECO:MCC
true
true
syngeneic transplantation experiment evidence used in manual assertion
2014-03-17T20:29:13Z
A type of syngeneic transplantation experiment evidence that is used in a manual assertion.
ECO:0001259
eco
mchibucos
true
true
A type of syngeneic transplantation experiment evidence that is used in a manual assertion.
ECO:MCC
xenotransplantation experiment evidence used in manual assertion
2014-03-17T20:29:18Z
A type of xenotransplantation experiment evidence that is used in a manual assertion.
ECO:0001260
eco
mchibucos
true
true
A type of xenotransplantation experiment evidence that is used in a manual assertion.
ECO:MCC
WST-1 assay evidence used in manual assertion
2014-03-17T20:29:22Z
A type of WST-1 assay evidence that is used in a manual assertion.
ECO:0001261
eco
mchibucos
A type of WST-1 assay evidence that is used in a manual assertion.
ECO:MCC
true
true
wound healing assay evidence used in manual assertion
2014-03-17T20:29:26Z
A type of wound healing assay evidence that is used in a manual assertion.
ECO:0001262
eco
mchibucos
true
true
A type of wound healing assay evidence that is used in a manual assertion.
ECO:MCC
urine test evidence used in manual assertion
2014-03-17T20:29:30Z
A type of urine test evidence that is used in a manual assertion.
ECO:0001263
eco
mchibucos
A type of urine test evidence that is used in a manual assertion.
ECO:MCC
true
true
terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence used in manual assertion
2014-03-17T20:29:34Z
A type of TUNEL assay evidence that is used in a manual assertion.
ECO:0001264
eco
mchibucos
true
true
A type of TUNEL assay evidence that is used in a manual assertion.
ECO:MCC
tryptic phosphopeptide mapping assay evidence used in manual assertion
2014-03-17T20:29:38Z
A type of tryptic phosphopeptide mapping assay evidence that is used in a manual assertion.
ECO:0001265
eco
mchibucos
true
A type of tryptic phosphopeptide mapping assay evidence that is used in a manual assertion.
ECO:MCC
true
transgenic organism evidence used in manual assertion
2014-03-17T20:29:41Z
A type of transgenic organism evidence that is used in a manual assertion.
ECO:0001266
eco
mchibucos
true
true
A type of transgenic organism evidence that is used in a manual assertion.
ECO:MCC
tissue microarray evidence used in manual assertion
2014-03-17T20:29:45Z
A type of tissue microarray evidence that is used in a manual assertion.
ECO:0001267
eco
mchibucos
true
A type of tissue microarray evidence that is used in a manual assertion.
ECO:MCC
true
TACE activity assay evidence used in manual assertion
2014-03-17T20:29:49Z
A type of TACE activity assay evidence that is used in a manual assertion.
ECO:0001268
eco
mchibucos
true
A type of TACE activity assay evidence that is used in a manual assertion.
ECO:MCC
true
surface plasmon resonance evidence used in manual assertion
2014-03-17T20:29:54Z
A type of surface plasmon resonance evidence that is used in a manual assertion.
ECO:0001269
eco
mchibucos
true
true
A type of surface plasmon resonance evidence that is used in a manual assertion.
ECO:MCC
restriction landmark genomic scanning evidence used in manual assertion
2014-03-17T20:29:58Z
A type of restriction landmark genome scanning evidence that is used in a manual assertion.
ECO:0001270
eco
mchibucos
A type of restriction landmark genome scanning evidence that is used in a manual assertion.
ECO:MCC
true
true
resonant mirror biosensor evidence used in manual assertion
2014-03-17T20:30:02Z
A type of resonant mirror biosensor evidence that is used in a manual assertion.
ECO:0001271
eco
mchibucos
A type of resonant mirror biosensor evidence that is used in a manual assertion.
ECO:MCC
true
true
high-performance liquid chromatography evidence used in manual assertion
2014-03-16T20:49:54Z
A type of high-performance liquid chromatography evidence that is used in a manual assertion.
ECO:0001272
eco
mchibucos
true
true
A type of high-performance liquid chromatography evidence that is used in a manual assertion.
ECO:MCC
ectopic expression evidence used in manual assertion
2014-03-17T22:34:56Z
A type of ectopic expression evidence that is used in a manual assertion.
ECO:0001273
eco
mchibucos
true
true
A type of ectopic expression evidence that is used in a manual assertion.
ECO:MCC
alkaline phosphatase reporter gene assay evidence
2015-10-29T15:53:45Z
A type of reporter gene assay evidence based on the fusion of selected genes with the phoA gene to express alkaline phosphatase in periplasmic space for protein tracing.
Alkaline phosphatase reporter assay produces a hybrid protein with alkaline phosphatase activity following transportation across the cellular membrane.
ECO:0001801
SEAP reporter assay
Secreted Embryonic Alkaline Phosphatase reporter assay
eco
swolfish
A type of reporter gene assay evidence based on the fusion of selected genes with the phoA gene to express alkaline phosphatase in periplasmic space for protein tracing.
ECO:SW
beta-galactosidase reporter gene assay evidence
2015-10-29T15:57:10Z
A type of reporter gene assay evidence based on the fusion of the lacZ gene to a specific promoter for the expression of beta-galactosidase which will appear blue when grown on a X-gal medium.
ECO:0001802
The assay is often performed using a plasmid borne construction on a lacZ strain.
beta-gal reporter gene assay
eco
lacZ reporter gene assay
swolfish
A type of reporter gene assay evidence based on the fusion of the lacZ gene to a specific promoter for the expression of beta-galactosidase which will appear blue when grown on a X-gal medium.
ECO:SW
PMID:20439410
chloramphenicol acetyltransferase reporter gene assay evidence
2015-10-29T16:06:42Z
A type of reporter gene assay evidence based on the fusion of the CAT gene to a specific promoter for the expression of chloramphenicol acetyltransferase which confers resistance to the chloramphenicol antibiotic.
CAT reporter gene assay
ECO:0001803
The amount of acetylated chloramphenicol is directly proportional to the amount of CAT enzyme present.
eco
swolfish
CAT reporter gene assay
PMID:1630936
A type of reporter gene assay evidence based on the fusion of the CAT gene to a specific promoter for the expression of chloramphenicol acetyltransferase which confers resistance to the chloramphenicol antibiotic.
ECO:SW
PMID:1630936
beta-glucuronidase reporter gene assay evidence
2015-10-29T16:11:02Z
A type of reporter gene assay evidence where the beta-glucuronidase enzyme from Escherichia coli is used as the reporter to transform non-fluorescent substrates into fluorescents for detection.
ECO:0001804
GUS reporter gene assay
eco
swolfish
A type of reporter gene assay evidence where the beta-glucuronidase enzyme from Escherichia coli is used as the reporter to transform non-fluorescent substrates into fluorescents for detection.
ECO:SW
luciferase reporter gene assay evidence
2015-10-29T16:15:39Z
A type of reporter gene assay evidence where luciferase, an oxidative enzyme, is used as the reporter to detect a gene product with bioluminescence.
ECO:0001805
eco
swolfish
A type of reporter gene assay evidence where luciferase, an oxidative enzyme, is used as the reporter to detect a gene product with bioluminescence.
ECO:SW
PMID:17623934
chromatin immunoprecipitation- exonuclease evidence
2015-10-29T16:37:36Z
A type of chromatin immunoprecipitation evidence that uses gama-exonuclease to digest TF-unbound DNA after ChIP for the identification of transcription factor binding site locations with high-resolution data.
ChIP-exo
ECO:0001806
eco
swolfish
A type of chromatin immunoprecipitation evidence that uses gama-exonuclease to digest TF-unbound DNA after ChIP for the identification of transcription factor binding site locations with high-resolution data.
ECO:SW
PMID:25249628
ChIP-exo
PMID:25249628
electrophoretic mobility shift assay evidence used in manual assertion
2015-11-03T12:13:17Z
A type of electrophoretic mobility shift that is used in a manual assertion.
ECO:0001807
eco
swolfish
true
A type of electrophoretic mobility shift that is used in a manual assertion.
ECO:SW
true
reverse transcription polymerase chain reaction evidence used in manual assertion
2015-11-03T12:22:46Z
A type of reverse transcription polymerase chain reaction evidence that is used in a manual assertion.
ECO:0001808
eco
swolfish
A type of reverse transcription polymerase chain reaction evidence that is used in a manual assertion.
ECO:SW
true
true
DNA affinity chromatography evidence
2015-11-03T13:48:49Z
A type of chromatography evidence where immobilized promoter DNA is labeled and bound to a matrix through which a protein mixture is poured and then eluted to purify specific DNA binding proteins.
Biotinylation is commonly used for labeling and beads are commonly used as the matrix. Bound protein will remain attached to the beads. Results can be detected through gel electrophoresis and then sequenced by mass-spectrometry. This technique can be used to demonstrate binding of a purified protein, or to purify the binding protein from crude extract or protein mixture.
DNA affinity purification
ECO:0001809
eco
swolfish
A type of chromatography evidence where immobilized promoter DNA is labeled and bound to a matrix through which a protein mixture is poured and then eluted to purify specific DNA binding proteins.
ECO:SW
PMID:11694305
PMID:11725488
DNAse footprinting evidence
2015-11-03T13:55:15Z
A type of nucleic acid binding evidence where proteins that have been bound to DNA protect a binding site from enzymatic cleavage with DNAse, thereby detecting protein-DNA interactions.
DNase protection
ECO:0001810
In DNAse footingprinting amplified DNA combined with TF and DNAse is electrophoresed for fragment comparison with a non-TF control sample. TF-bound fragments do not appear in the gel. Such fragments can be isolated, purified, and sequenced. This technique is often used to identify the binding motif of a TF resolving the protected region to 50-100 bp which can be further examined for TF-binding sites.
eco
swolfish
A type of nucleic acid binding evidence where proteins that have been bound to DNA protect a binding site from enzymatic cleavage with DNAse, thereby detecting protein-DNA interactions.
ECO:SW
PMID:212715
PMID:22194258
fluorescence anisotropy evidence
2015-11-03T14:01:36Z
A type of fluorescence evidence based on rapid and quantitative analysis of diverse molecular interactions, enzyme activities, and nucleic acid hybridization which uses a fluorophore to measure the binding constants and kinetics of reactions that cause a change in the rotational time of the molecules.
ECO:0001811
FA
FP
Fluorescence polarization
The degree of polarization of a fluorophore is inversely related to its molecular rotation. When the fluorophore is bound to a small molecule, the rate at which it tumbles can decrease significantly from when it is bound tightly to a large protein. If the fluorophore is attached to the larger protein in a binding pair, the difference in polarization between bound and unbound states will be smaller and less accurate. The degree of binding is calculated by using the difference in anisotropy of the partially bound, free, and fully bound states measured by titrating the two binding partners. Fluorescence polarixation assays are homogeneous.
eco
swolfish
Fluorescence polarization
PMCID:3277431
PMID:20232898
A type of fluorescence evidence based on rapid and quantitative analysis of diverse molecular interactions, enzyme activities, and nucleic acid hybridization which uses a fluorophore to measure the binding constants and kinetics of reactions that cause a change in the rotational time of the molecules.
ECO:SW
PMID:20232898
FP
PMCID:3277431
PMID:20232898
genomic systematic evolution of ligands by exponential amplification evidence
2015-11-03T14:05:37Z
A type of systematic evolution of ligands by exponential amplification evidence based on a restricted genomic DNA library to identify naturally occurring genomic aptamers and RNA-protein interaction networks with RNA-binding protein as bait and high-throughput sequencing.
ECO:0001812
The reported sequences should always be verified for presence in the genome sequence.
eco
genomic SELEX
swolfish
PMID:20541015
genomic SELEX
A type of systematic evolution of ligands by exponential amplification evidence based on a restricted genomic DNA library to identify naturally occurring genomic aptamers and RNA-protein interaction networks with RNA-binding protein as bait and high-throughput sequencing.
ECO:SW
PMID:20541015
PMID:21720957
heteronuclear single quantum coherence spectroscopy evidence
2015-11-03T14:11:06Z
A type of nuclear magnetic resonance based on two-dimensional NMR for elucidation of the chemical structure of an isolated or synthesized chemical compound where the characteristic transfer magnetization of a proton to a nitrogen or carbon isotope is monitored by NMR, generating a specific peak in the spectrum.
Chemical shifts in the spectrum indicating binding can be detected from analysis of a protein spectrum in the presence or absence of its cognate DNA binding site.
ECO:0001813
HSQC
eco
swolfish
A type of nuclear magnetic resonance based on two-dimensional NMR for elucidation of the chemical structure of an isolated or synthesized chemical compound where the characteristic transfer magnetization of a proton to a nitrogen or carbon isotope is monitored by NMR, generating a specific peak in the spectrum.
ECO:SW
PMID:19856946
HSQC
PMID:19856946
methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence
2015-11-03T14:24:04Z
A type of nucleic acid binding evidence where the synthetic molecule methidiumpropyl-EDTA (MPE) is used to cleave ligand-protected DNA, followed by analysis of the restriction fragments to generate a footprint (i.e. size and location) of small molecule binding sites on the DNA.
ECO:0001814
MPE Fe(II) footprinting
MPE-EDTA Fe(II) footprinting
Methidiumpropyl-EDTA Fe(II) footprinting
eco
swolfish
MPE Fe(II) footprinting
PMID:6225070
Methidiumpropyl-EDTA Fe(II) footprinting
PMID:6225070
MPE-EDTA Fe(II) footprinting
PMID:6225070
A type of nucleic acid binding evidence where the synthetic molecule methidiumpropyl-EDTA (MPE) is used to cleave ligand-protected DNA, followed by analysis of the restriction fragments to generate a footprint (i.e. size and location) of small molecule binding sites on the DNA.
ECO:SW
PMID:6225070
copper-phenanthroline footprinting evidence
1,10-Phenanthroline-copper footprinting
2015-11-04T08:37:51Z
A type of nucleic acid binding evidence
where nucleic acid that has been bound to protein is cleaved with 1,10-phenanthroline-copper complex resulting in a high-resolution footprint of sequence-specific protein-DNA contacts.
ECO:0001815
OP-Cu Complex
eco
swolfish
OP-Cu Complex
PMID:1384472
1,10-Phenanthroline-copper footprinting
PMID:1384472
A type of nucleic acid binding evidence
where nucleic acid that has been bound to protein is cleaved with 1,10-phenanthroline-copper complex resulting in a high-resolution footprint of sequence-specific protein-DNA contacts.
ECO:SW
PMID:11691942
green fluorescent protein reporter gene assay evidence
2015-11-04T08:58:42Z
A type of reporter gene assay evidence based on the fusion of select genes with the green fluorescent protein (GFP) gene for detection with bioluminescence of the gene product when exposed to blue ultraviolet light.
ECO:0001816
GFP promoter fusion
GFP reporter gene assay
eco
green fluorescent protein promoter fusion
swolfish
A type of reporter gene assay evidence based on the fusion of select genes with the green fluorescent protein (GFP) gene for detection with bioluminescence of the gene product when exposed to blue ultraviolet light.
ECO:SW
PMID:11989662
GFP reporter gene assay
PMID:11989662
glutathione S-transferase pull-down assay evidence
2015-11-04T09:05:56Z
A type of protein binding evidence where a gene is fused with the GST gene and the resulting recombinant bait protein is captured on an immobilized Glutathione affinity ligand and incubated with prey protein to identify and characterize protein-protein interactions.
ECO:0001817
GST pull-down assay
The recombinant protein can also be eluted following the pull-down and analyzed further with qPCR or sequencing.
eco
swolfish
GST pull-down assay
PMID:26096507
A type of protein binding evidence where a gene is fused with the GST gene and the resulting recombinant bait protein is captured on an immobilized Glutathione affinity ligand and incubated with prey protein to identify and characterize protein-protein interactions.
ECO:SW
PMID:26096507
hydroxyl-radical footprinting evidence
2015-11-04T09:20:26Z
A type of nucleic acid binding evidence used to identify protein-binding sites on the DNA molecule where DNA that has been bound to protein is digested with hydroxyl radical produced by reduction of hydrogen peroxide with iron (II), followed by separating the cleavage products on a denaturing electrophoresis gel.
ECO:0001818
eco
swolfish
A type of nucleic acid binding evidence used to identify protein-binding sites on the DNA molecule where DNA that has been bound to protein is digested with hydroxyl radical produced by reduction of hydrogen peroxide with iron (II), followed by separating the cleavage products on a denaturing electrophoresis gel.
ECO:SW
PMID:18546600
PMID:19378159
PMID:3090544
primer extension assay evidence
2015-11-04T09:33:18Z
A type of transcript expression level evidence used to determine expression levels of mRNA where a radiolabeled synthetic oligonucleotide primer is annealed to mRNA at the transcription start site of a gene and the mRNA is extended with reverse transcriptase producing cDNA which is electrophoresed on a polyacrylamide gel and autoradiographed, and the band size is proportional to the initial RNA.
ECO:0001819
The most commonly used radiolabel is 32P.
eco
swolfish
A type of transcript expression level evidence used to determine expression levels of mRNA where a radiolabeled synthetic oligonucleotide primer is annealed to mRNA at the transcription start site of a gene and the mRNA is extended with reverse transcriptase producing cDNA which is electrophoresed on a polyacrylamide gel and autoradiographed, and the band size is proportional to the initial RNA.
ECO:SW
PMID:23378648
rapid amplification of cDNA ends polymerase chain reaction evidence
2015-11-04T09:48:38Z
A type of polymerase chain reaction evidence used to obtain the full length sequence of a RNA transcript 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.
ECO:0001820
RACE PCR
RACE PCR is frequently used to verify transcription start sites relevant to the function of transcription factor binding sites such as repression.
eco
swolfish
A type of polymerase chain reaction evidence used to obtain the full length sequence of a RNA transcript 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.
ECO:SW
PMID:17498297
PMI:17498297
RACE PCR
RNA sequencing assay evidence
2015-11-04T10:15:57Z
A type of nucleotide sequencing assay evidence where RNA is extracted from a cell, reverse transcribed to cDNA, and sequenced for a snapshot of an organism's transcriptome with precise measurement of transcript levels and their isoforms.
ECO:0001821
RNA-Seq
WTTS
Whole Transcriptome Shotgun Sequencing
eco
swolfish
PMID:23851085
Whole Transcriptome Shotgun Sequencing
PMID:23851085
RNA-Seq
A type of nucleotide sequencing assay evidence where RNA is extracted from a cell, reverse transcribed to cDNA, and sequenced for a snapshot of an organism's transcriptome with precise measurement of transcript levels and their isoforms.
ECO:SW
PMID:19015660
survival analysis evidence
2015-11-04T10:48:59Z
A type of knockout evidence based on the survival of an organism in a particular environment where a gene for an enzyme or regulator is knocked out and results are used as a natural reporter.
ECO:0001822
eco
swolfish
A type of knockout evidence based on the survival of an organism in a particular environment where a gene for an enzyme or regulator is knocked out and results are used as a natural reporter.
ECO:SW
X-ray crystallography evidence
2015-11-04T10:56:22Z
A type of crystallography evidence based on X-ray diffraction of a crystal to determine molecular structure.
ECO:0001823
X-ray crystallography can be used for a crystal used to probe at the tridimensional structure of proteins. In some cases, it is possible to co-crystallize the protein bound to its DNA binding site, providing detail on the particular arrangement of the two components.
eco
swolfish
A type of crystallography evidence based on X-ray diffraction of a crystal to determine molecular structure.
ECO:SW
PMID:23135450
PMID:24648090
DNA adenine methyltransferase identification evidence
2015-11-05T15:56:13Z
A type of affinity evidence used to identify DNA binding sites in eukaryotes where Escherichia coli DNA adenine methyltransferase (Dam) is fused to a transcription factor, co-factor, chromatin-associated protein, or nuclear-associated protein, followed by a methyl-dependent PCR to localize methyltransferase in the region of the binding site.
DamID
ECO:0001824
The methylation tag is detected with methylation-sensitive restriction enzymes, DpnI and DpnII.
eco
swolfish
DamID
PMID:19588092
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
isothermal titration calorimetry evidence
2015-11-05T16:06:20Z
A type of affinity evidence where the absorbed or released heat of a biomolecular binding event is directly measured in a reference cell and sample cell after the addition of a ligand using a microcalorimeter for a complete thermodynamic profile of the molecular interaction.
ECO:0001825
ITC
When ITC is used to study TF, the temperature of two identical cells containing a known concentration of TF is monitored. After the ligand is added to the cells in precisely measured aliquots, the temperature difference in each cell is observed to determine target binding. This value can be used to compute the energetics of the reaction and hence, binding affinity of the TF for the DNA fragment. The thermodynamic profile that is measured includes the values of binding constant (K(a)), stoichiometry (n), and the enthalpy of binding (DeltaH(b)).
eco
swolfish
A type of affinity evidence where the absorbed or released heat of a biomolecular binding event is directly measured in a reference cell and sample cell after the addition of a ligand using a microcalorimeter for a complete thermodynamic profile of the molecular interaction.
ECO:SW
PMID:10527727
ITC
PMID:10527727
ultraviolet light footprinting evidence
2015-11-05T16:13:36Z
A type of nucleic acid binding evidence where DNA is non-specifically fragmented with ultraviolet light while protein-bound regions are protected from UV damage and strand breakage patterns are analyzed by PAGE and sequenced to detect protein-DNA contacts.
ECO:0001826
UV footprinting
eco
swolfish
ultraviolet footprinting
A type of nucleic acid binding evidence where DNA is non-specifically fragmented with ultraviolet light while protein-bound regions are protected from UV damage and strand breakage patterns are analyzed by PAGE and sequenced to detect protein-DNA contacts.
ECO:SW
PMID:2842760
PMID:7602584
premethylation interference footprinting evidence
2015-11-05T16:16:27Z
A type of nucleic acid binding evidence used to identify protein binding sites on the DNA molecule where multiple copies of a DNA fragment containing a putative TF-binding site are randomly methylated with dimethyl sulfate (DMS) and cleaved at the methyl group, followed by separating the cleavage products on a denaturing electrophoresis gel.
ECO:0001827
eco
methylation interference footprinting
swolfish
A type of nucleic acid binding evidence used to identify protein binding sites on the DNA molecule where multiple copies of a DNA fragment containing a putative TF-binding site are randomly methylated with dimethyl sulfate (DMS) and cleaved at the methyl group, followed by separating the cleavage products on a denaturing electrophoresis gel.
ECO:SW
PMID:1583685
visual sequence inspection evidence
2015-11-10T14:40:16Z
A type of inference from background scientific knowledge used in manual assertion based on the visual inspection of promoter region to identify putative binding sites.
ECO:0001828
eco
swolfish
A type of inference from background scientific knowledge used in manual assertion based on the visual inspection of promoter region to identify putative binding sites.
ECO:SW
ferric uptake regulator titration assay evidence
2015-11-10T14:55:36Z
A type of reporter gene assay evidence used to locate and isolate Fur sites where a plasmid library is created and cloned into a cell line with a ferric uptake regulator (Fur)-repressed reporter and the Fur protein is titrated away from its binding site on the reporter, after which the cell is isolated and plasmid extracted for further sequence analysis.
ECO:0001829
FURTA
Fluorescence polarization
eco
swolfish
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
cell viability assay evidence
2015-02-13T12:08:01Z
ECO:0005004
eco
snadendla
cell proliferation assay evidence
2015-02-11T16:27:13Z
ECO:0005007
eco
snadendla
DNA synthesis cell proliferation assay evidence
2015-02-11T16:30:10Z
ECO:0005008
eco
snadendla
metabolic cell proliferation assay evidence
2015-02-11T16:36:33Z
ECO:0005009
eco
snadendla
cell proliferation marker detection assay evidence
2015-02-11T16:37:23Z
ECO:0005010
eco
snadendla
ATP bioluminescence assay evidence
2015-02-11T16:47:30Z
ECO:0005011
eco
snadendla
cytotoxicity assay evidence
2015-02-12T11:39:35Z
ECO:0005012
eco
snadendla
in vitro cell based assay evidence
2015-02-12T13:26:55Z
ECO:0005014
eco
snadendla
staining evidence
2015-02-19T11:48:57Z
ECO:0005019
eco
snadendla
chemotaxis assay evidence
2015-02-19T13:10:20Z
ECO:0005021
eco
snadendla
genetic transformation evidence
2015-03-16T15:33:50Z
ECO:0005027
eco
snadendla
structure determination evidence
2015-03-20T12:16:17Z
ECO:0005031
eco
snadendla
electron microscopy evidence
2015-03-20T12:21:48Z
ECO:0005033
eco
snadendla
apoptotic assay evidence
2015-04-07T21:58:24Z
ECO:0005034
eco
snadendla
in vivo polyADP-ribosylation assay evidence
2015-06-15T15:35:05Z
A type of in vivo assay evidence where ADP-ribosylated residues in proteins are detected in cells in vivo.
ECO:0005500
eco
snadendla
A type of in vivo assay evidence where ADP-ribosylated residues in proteins are detected in cells in vivo.
ECO:SN
PMID:2820766
SIB:PG
in vivo polyADP-ribosylation assay evidence used in manual assertion
2015-06-15T15:37:23Z
A type of in vivo polyADP-ribosylation assay evidence that is used in a manual assertion.
ECO:0005501
eco
snadendla
A type of in vivo polyADP-ribosylation assay evidence that is used in a manual assertion.
ECO:SN
true
true
ex vivo assay evidence
2015-06-26T11:46:15Z
A type of biological assay evidence derived by studying an organ, tissues, or cells taken from an organism in an external environment with the minimum alteration of natural conditions.
ECO:0005502
eco
snadendla
A type of biological assay evidence derived by studying an organ, tissues, or cells taken from an organism in an external environment with the minimum alteration of natural conditions.
ECO:SN
PMID:16305312
url:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2305722/pdf/nihms42807.pdf
two-dimensional polyacrylamide gel electrophoresis evidence
2015-10-01T16:23:20Z
2D-PAGE
A type of gel electrophoresis beginning with one dimension electrophoresis where biomolecules are electrophoresed on a low percentage polyacrylamide gel to be separated in proportion to their mass or isoelectric point, followed by high voltage electrophoresis on a higher percentage gel in the presence of ethidium bromide to alter non-linear molecular shape.
ECO:0005503
Two-dimensional polyacrylamide gel electrophoresis is commonly employed to establish a proteome for an organism and demonstrate expression changes.
eco
snadendla
A type of gel electrophoresis beginning with 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
spectrometry evidence
2015-08-14T15:48:08Z
ECO:0005504
eco
snadendla
regular expression motif search evidence
2015-10-09T13:51:52Z
A type of motif similarity evidence where the motif, a local alignment of sequences, is represented by a regular expression, which captures the variability of nucleotides at each position in a discrete form and can then be used to search genetic sequences by identifying matches to the regular expression.
ECO:0005505
Regular expression is a computational tool used for determining whether a given genome contains a DNA region resembling a transcription factor binding motif. For example A/T=W indicates A or T may be present in a column of the alignment. (PMID: 20708667).
eco
snadendla
A type of motif similarity evidence where the motif, a local alignment of sequences, is represented by a regular expression, which captures the variability of nucleotides at each position in a discrete form and can then be used to search genetic sequences by identifying matches to the regular expression.
ECO:SW
PMID:17337630
missense mutation evidence
2015-09-18T16:52:34Z
ECO:0005506
eco
snadendla
nonsense mutation evidence
2015-09-18T16:55:32Z
ECO:0005507
eco
snadendla
silent mutation evidence
2015-09-18T17:01:12Z
ECO:0005508
eco
snadendla
insertion mutation evidence
2015-09-18T17:02:03Z
ECO:0005509
eco
snadendla
deletion mutation evidence
2015-09-18T17:02:45Z
ECO:0005510
eco
snadendla
duplication mutation evidence
2015-09-18T17:03:25Z
ECO:0005511
eco
snadendla
frameshift mutation evidence
2015-09-18T17:05:49Z
ECO:0005512
eco
snadendla
repeat expansion mutation evidence
2015-09-18T17:06:34Z
ECO:0005513
eco
snadendla
splice site mutation evidence
2015-09-18T17:07:29Z
ECO:0005514
eco
snadendla
translocation mutation evidence
2015-09-18T17:08:01Z
ECO:0005515
eco
snadendla
molecule detection assay evidence
2015-09-24T15:54:21Z
ECO:0005516
eco
snadendla
protein detection assay evidence
2015-09-25T14:27:40Z
ECO:0005517
eco
snadendla
RNA detection assay evidence
2015-09-25T14:43:53Z
ECO:0005518
eco
snadendla
DNA detection assay evidence
2015-09-25T19:33:25Z
ECO:0005519
eco
snadendla
interferometric reflectance imaging sensor evidence
2015-09-28T16:01:01Z
A type of molecule detection assay evidence based on changes in surface-reflected light due to ligand binding on the surface of a semi-transparent substrate to detect proteins, DNA, and other biological material in a multiplexed, high-throughput microarray format without labels.
Differences in the optical path lengths between a surface layer and a buried silica layer can be measured very precisely allowing optical height information to be converted to accumulated mass on the surface. For the purpose of TF-binding site identification, IRIS is coupled with DNA-arrays with immobilized potential binding regions exposed to the protein of interest and eluted. Protein-bound fragments exhibit changes in reflectance that can be used to gauge binding quantitatively.
ECO:0005520
IRIS
SRIB
Spectral Reflectance Imaging Biosensor
eco
snadendla
A type of molecule detection assay evidence based on changes in surface-reflected light due to ligand binding on the surface of a semi-transparent substrate to detect proteins, DNA, and other biological material in a multiplexed, high-throughput microarray format without labels.
ECO:SW
PMID:21587155
PMID:24271115
S1 nuclease protection assay evidence
2015-09-28T17:16:56Z
A type of nuclease protection assay evidence where RNA is hybridized with complementary DNA probes and exposed to S1 nuclease for unbound RNA degradation after which the intact RNA is run on a gel for probe size determination and RNA identification to detect and map specific RNAs in a complex mixture of total cellular RNA.
ECO:0005521
eco
snadendla
A type of nuclease protection assay evidence where RNA is hybridized with complementary DNA probes and exposed to S1 nuclease for unbound RNA degradation after which the intact RNA is run on a gel for probe size determination and RNA identification to detect and map specific RNAs in a complex mixture of total cellular RNA.
ECO:SW
PMID:21390683
DNA dot blot assay evidence
2015-09-30T10:03:03Z
ECO:0005522
eco
snadendla
DNA dot blot assay evidence used in manual assertion
2015-09-30T10:04:00Z
A type of DNA dot blot assay evidence that is used in a manual assertion.
ECO:0005523
eco
snadendla
true
A type of DNA dot blot assay evidence that is used in a manual assertion.
ECO:SN
ECO:SW
true
DNA microarray evidence
2015-09-30T10:12:48Z
A type of DNA detection assay evidence where complimentary ssDNA is attached to a solid glass, silicon, or plastic surface and is hybridized with a labeled sample of extracted mRNA or amplified cDNA and stimulated with a laser for fluorescence detected with a scanner.
DNA chip
DNA-array expression analysis
ECO:0005524
The mRNA extraction is performed in induced and non-induced cells and reverse transcribed with different fluorophore labeling for controls and experiment. Fluorescence is measured at two different wavelengths and the ratio between the two fluorescence intensities corresponds to the induction level.
eco
snadendla
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
DNA microarray evidence used in manual assertion
2015-09-30T10:13:09Z
A type of DNA microarray evidence that is used in a manual assertion.
ECO:0005525
eco
snadendla
true
A type of DNA microarray evidence that is used in a manual assertion.
ECO:SN
ECO:SW
true
matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence
2015-09-30T10:51:56Z
A type of protein detection assay evidence where soft ionization is used for the analysis of biomolecules for mass determination in a three step process of plate preparation, radiation, and ionization with high throughput technology.
ECO:0005526
MALDI-TOF MS is commonly used for protein identification in constructing a proteome where protein fingerprints obtained by microbial cells are compared with a database of reference spectra by means of various algorithms integrated in systems recently made commercially available.
MALDI-TOF-MS
eco
snadendla
A type of protein detection assay evidence where soft ionization is used for the analysis of biomolecules for mass determination in a three step process of plate preparation, radiation, and ionization with high throughput technology.
ECO:SW
PMID:21964792
PMID:25354905
matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence used in manual assertion
2015-09-30T10:58:51Z
A type of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence that is used in a manual assertion.
ECO:0005527
eco
snadendla
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
true
site-directed mutagenesis evidence
2015-09-30T11:34:41Z
A type of experimental phenotypic evidence based on target-specified mutagenesis for the characterization of various gene and protein interactions, structures, and functions where oligonucleotide primers are used to alter a nucleotide sequence.
ECO:0005528
Site-directed mutagenesis is often performed in tandem with EMSA. It is often implemented only in conserved motif positions or serially through all positions of a site.
eco
site directed mutagenesis
snadendla
A type of experimental phenotypic evidence based on target-specified mutagenesis for the characterization of various gene and protein interactions, structures, and functions where oligonucleotide primers are used to alter a nucleotide sequence.
ECO:SW
PMID:21204030
PMID:24011050
PMID:3541892
random mutagenesis evidence
2015-09-30T11:55:03Z
A type of experimental phenotypic evidence where radiation or a DNA-damaging agent in vivo, or PCR with degenerate primers in vitro are used for non-targeted mutagenesis.
ECO:0005529
Random mutagenesis is not often used in TF-binding site determination; however, it is sometimes used to investigate the effect of mutations in TF binding domains in conjunction with expression assays. Random mutations can also be introduced via chemicals, error-prone PCR (EP-PCR), degenerate oligonucleotides-Pfu(DOP), UV irradiation, mutator strains, nucleotide analogs, or DNA recombination.
eco
snadendla
A type of experimental phenotypic evidence where radiation or a DNA-damaging agent in vivo, or PCR with degenerate primers in vitro are used for non-targeted mutagenesis.
ECO:SW
PMID:15153637
PMID:18265275
random mutagenesis evidence used in manual assertion
2015-09-30T11:57:00Z
A type of random mutagenesis evidence that is used in a manual assertion.
ECO:0005530
eco
snadendla
true
true
motif discovery evidence
2015-09-30T15:04:45Z
A type of sequence alignment evidence based on a set of algorithms that infer over-represented motifs from a set of biological sequences returning one or more local multiple sequence alignment defining the inferred motifs.
ECO:0005531
Relationship type between sequences (e.g. orthologs from multiple genomes or co-expressed genes in the same genome) is not necessarily assumed. The local multiple sequence alignment is typically ungapped. A common application of motif discovery is to infer the binding motif of a given transcription factor (TF). This can be based on the results of a whole-genome expression analysis, assuming that co-expressed genes are co-regulated by the same TF (PMID: 19892760), from peaks in ChIP-seq experiments with the TF (PMID: 16264194), or from the comparative genomics analysis of the promoter regions of orthologs (PMID: 23032607).
eco
snadendla
A type of sequence alignment evidence based on a set of algorithms that infer over-represented motifs from a set of biological sequences returning one or more local multiple sequence alignment defining the inferred motifs.
ECO:SW
PMID:10812473
PMID:16845028
PMID:8211139
consensus search evidence
2015-10-09T14:12:54Z
A type of motif similarity evidence where the motif is represented by a consensus sequence which incorporates the most frequent nucleotide at each position acting as a generic representative for the sequences in the alignment, and is compared to the genetic sequence for a perfect or imperfect match.
ECO:0005532
This technique is used to identify transcription factor binding sites by searching a bacterial genome for DNA regions resembling a given TF-binding motif. PMID: 17085555.
eco
snadendla
A type of motif similarity evidence where the motif is represented by a consensus sequence which incorporates the most frequent nucleotide at each position acting as a generic representative for the sequences in the alignment, and is compared to the genetic sequence for a perfect or imperfect match.
ECO:SW
PMID:15130839
phylogenetic footprinting evidence
2015-09-30T16:23:02Z
A type of motif discovery evidence based on a set of algorithms that infer motifs in non-coding DNA sequences from the conservation of functional regulatory sites through evolution at a higher rate than their local surroundings for the identification of an evolutionary 'footprint'.
ECO:0005533
The name derives to experimental footprinting techniques where transcription factor (TF)-binding sites are identified by sequencing the region of DNA protected from biochemical agents by the bound TF. This technique is used to identify or verify transcription factor-binding motifs, most commonly in the Eukaryota (PMID: 11997340).
eco
snadendla
A type of motif discovery evidence based on a set of algorithms that infer motifs in non-coding DNA sequences from the conservation of functional regulatory sites through evolution at a higher rate than their local surroundings for the identification of an evolutionary 'footprint'.
ECO:SW
PMID:16477324
PMID:3199442
comparative genomics motif search evidence
2015-10-09T14:30:38Z
A type of motif similarity evidence based on comparative genomics which uses a search method to scan a set of genomes for instances of a specific motif, and then applies a comparative criterion to analyze the collective strength of these predictions, based on the assumption that functional instances of the motif will be preserved by natural selection and their prediction will therefore be consistent across genomes.
ECO:0005534
This technique is used to predict transcription factor binding sites in gene promoter regions by identifying conserved DNA regions across multiple genomes. PMID: 22305460. Orthology is a typical comparative criterion used.
eco
snadendla
A type of motif similarity evidence based on comparative genomics which uses a search method to scan a set of genomes for instances of a specific motif, and then applies a comparative criterion to analyze the collective strength of these predictions, based on the assumption that functional instances of the motif will be preserved by natural selection and their prediction will therefore be consistent across genomes.
ECO:SW
PMID:10854408
machine learning prediction of motif instance evidence
2015-10-01T11:58:36Z
A type of match to sequence model evidence which captures the application of a broad suite of supervised and unsupervised machine learning algorithms trained on known motif instances and applied to the prediction of novel putative instances of a motif in a set of biological sequences.
ECO:0005535
Machine learning algorithms include, but are not limited to artificial neural networks, random-forest, k-means clustering, hidden Markov models. This suite of methods can be used to identify or verify transcription factor-binding sites in genomic sequences (PMID: 15703297).
eco
snadendla
A type of match to sequence model evidence which captures the application of a broad suite of supervised and unsupervised machine learning algorithms trained on known motif instances and applied to the prediction of novel putative instances of a motif in a set of biological sequences.
ECO:SW
PMID:17117497
PMID:2014171
position-specific scoring matrix motif search evidence
2015-10-09T15:04:35Z
A type of motif similarity evidence where the motif is represented by a position-specific frequency matrix (PSFM) that specifies the frequency of each base at each position of the motif, from which a position-specific scoring matrix (PSSM) can be derived under the framework of a log-likelihood ratio providing a scoring system based on the likelihood of a sequence given the motif, versus a genomic-frequency based null hypothesis.
ECO:0005536
PSSM
PSSM motif search
This technique is used to predict transcription factor binding sites in gene promoter regions by using a position weight matrix approach. (PMID: 15604457).
eco
snadendla
A type of motif similarity evidence where the motif is represented by a position-specific frequency matrix (PSFM) that specifies the frequency of each base at each position of the motif, from which a position-specific scoring matrix (PSSM) can be derived under the framework of a log-likelihood ratio providing a scoring system based on the likelihood of a sequence given the motif, versus a genomic-frequency based null hypothesis.
ECO:SW
PMID:10812473
xylE reporter gene assay evidence
2015-10-28T15:31:28Z
A type of reporter gene assay evidence based on the fusion of the xylE gene to a specific promoter for the expression of catechol 2,3-dioxygenase that converts the colorless catechol substrate to yellow 2-hydroxymuconic semialdehyde for identification of the expression of a particular gene.
ECO:0005537
eco
snadendla
A type of reporter gene assay evidence based on the fusion of the xylE gene to a specific promoter for the expression of catechol 2,3-dioxygenase that converts the colorless catechol substrate to yellow 2-hydroxymuconic semialdehyde for identification of the expression of a particular gene.
ECO:SW
PMID:2592344
computationally derived logical inference
2015-11-17T15:15:50Z
ECO:0005538
eco
snadendla
computationally derived logical inference used in automatic assertion
2015-11-17T15:17:47Z
ECO:0005539
eco
snadendla
true
true
computationally derived logical inference from automatic assertion used in automatic assertion
2015-11-17T15:24:42Z
ECO:0005540
eco
snadendla
computationally derived logical inference from manual assertion used in automatic assertion
2015-11-17T15:32:03Z
ECO:0005541
eco
snadendla
protein-binding microarray evidence
2015-06-05T14:36:00Z
A type of oligonucleotide microarray evidence that detects binding of a tagged protein to an array of oligonucleotide probes representing potential binding sites.
ID:0001601
PBM evidence
eco
swolfish
A type of oligonucleotide microarray evidence that detects binding of a tagged protein to an array of oligonucleotide probes representing potential binding sites.
PMID:22146299
in vivo cell staining evidence
2015-06-08T11:51:37Z
A type of in vivo assay evidence in which living cells are stained with a vital stain, i.e. dye that can be used on living cells without causing cell death.
ID:0001603
eco
swolfish
vital staining evidence
GOC:MAH
vital staining evidence
A type of in vivo assay evidence in which living cells are stained with a vital stain, i.e. dye that can be used on living cells without causing cell death.
GOC:MAH
computational image-based phenotypic evidence
2015-06-09T16:13:20Z
A type of phenotypic evidence based on unsupervised computational examination of a visual mutant phenotype such as abnormalities in organism morphology.
ID:0001706
eco
kvillanova
true
A type of phenotypic evidence based on unsupervised computational examination of a visual mutant phenotype such as abnormalities in organism morphology.
ECO:KIM
PMID:25373780