For more details, see https://github.com/evidenceontology/evidenceontology
GO biological process terms should be used in the GO with/from field
GO cellular component terms should be used in the GO with/from field
Chemical entity IDs should be used in the GO with/from field
Gene IDs should be used in the GO with/from field
GO molecular function terms should be used in the GO with/from field
Protein IDs should be used in the GO with/from field
Protein complex IDs should be used in the GO with/from field
Transcript IDs should be used in the GO with/from field
A relation connecting a piece of evidence to an assertion method, where that assertion method is supported by the evidence.
In the future we may use a more generic relation with weaker domain and range constraints taken from IAO, RO or OBI.
A type of information that is used to support an assertion.
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.
Experimental evidence that is based on direct measurement of some aspect of a biological feature.
A type of direct assay evidence based on reconstructing a biological sample from its disassociated state to its original state.
A type of fractionation evidence where sub-cellular components are separated based on their physical properties such as density in a sucrose density gradient.
If using this term for Gene Ontology annotation, it would be used most typically for annotations to the cellular component ontology.
Used when an annotation is made based on assays that determine the catalytic activity of enzymes.
An evidence type that is based on the results of a laboratory assay.
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.
Experimental evidence that is based on characterization of gene expression.
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.
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.
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
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.
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.
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.
A type of protein assay evidence based on the inhibition of the molecular function of a protein.
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.
A type of physical interaction evidence where a cellular component subunit is isolated as part of purification of its larger complex.
A type of physical interaction evidence that depends on the strength of the interaction between two entities.
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.
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.
A type of similarity evidence based on structural similarity of an annotated gene or gene product to another gene or group of genes.
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.
Used when an annotation is made based on the presence of a recognized domain or motif in a gene product's (usually protein) primary sequence.
match to InterPro member signature evidence
A type of BLAST evidence that is used in a manual assertion.
protein BLAST evidence used in manual assertion
Protein BLAST evidence that is used in a manual assertion.
BLAST search criteria for ISS assignment in PAMGO_GAT
nucleotide BLAST evidence used in manual assertion
Nucleotide BLAST evidence that is used in a manual assertion.
An author statement that is based on a cited reference.
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.
An author statement that is not associated with results presented or a cited reference.
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.
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.
An evidence that reflects an annotation was made before curators began tracking evidence types.
The evidence not_recorded appears in some legacy annotations; it should not be used for new annotations.
An evidence type that is based on comparing likeness of distinct biological entities.
gain-of-function mutant phenotype 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.
inferred from sequence or structural similarity
spatial pattern of protein expression evidence
spatial pattern of transcript expression evidence
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.
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.
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.
suppressor/enhancer interaction evidence
IGI: 'traditional' genetic interactions (e.g. suppressors, synthetic lethals)
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.
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.
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.
A type of similarity based on the expression of a genotype in an environment.
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.
Experimental evidence that is based on the expression of a genotype in an environment.
Used when an annotation is made based on the similarity of the location and or arrangement of structures.
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.
Used when an annotation is made based on the similarity of the histological makeup of structures.
functional complementation in heterologous system evidence
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.
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.
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).
Used when an annotation is made based on the similarity of embryological and/or post-embryonic origin of structures.
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
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.
If performing GO annotation, the interacting protein is referenced in the evidence_with column.
Used when an annotation is made based on the similarity of the shape, structure or overall configuration of structures.
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.
Experimental evidence that characterizes an attribute of the genome underlying a gene product.
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.
Used when an annotation is made based on the similarity of expression of genes in structures.
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
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.
"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.
A type of similarity that indicates common ancestry.
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.
transmembrane domain prediction evidence
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.
Evidence that supports the identity of a gene product on the basis of the identity of neighboring genes.
Genomic cluster analyses include synteny and operon structure.
A type of protein assay evidence that involves precipitation of a multivalent antigen by a bivalent antibody for protein isolation.
Transcription factors isolated in this way can be incubated with a radiolabeled probe to demonstrate binding.
intermethylated site amplification evidence
A type of microscopy evidence where antibodies are used to detect the location of molecules or other structures within cells or tissues.
biological system reconstruction evidence
A type of evidence that is based on a combination of experimental evidences or existing models of that system in a related species used for the reconstruction of a biological system.
The biological system in question might be a multi-step process or pathway or a physical complex comprising several components. The components in the experimental evidence can come from the same species or a mix of species. The experimental evidences may be only partial or weak.
restriction landmark genomic scanning evidence
restriction landmark genome scanning evidence
A type of immunolocalization evidence where the antibodies are labeled with colloidal gold particles whose location is then detected via microscopy.
epitope-tagged protein immunolocalization evidence
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.
Direct assay evidence that is derived by using a living organism to measure the effect of a substance, factor, or condition.
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.
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.
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
IDA: electrophoretic mobility shift assay
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.
Used when an annotation is made based on fractionation of a protein with other compounds, factors, or macromolecules.
microarray RNA expression level evidence
IEP: transcript levels (e.g. microarray data)
Used when an annotation is made based on levels of RNA expression determined by microarray experiment.
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.
reverse transcription polymerase chain reaction transcription evidence
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.
The starting product for PCR, and therefore amplification volume, is directly correlated to the transcription rate.
A type of nuclease protection assay evidence where mRNA is hybridized with radiolabeled RNA probes after which RNAse is added to digest the unbound, nonresistant single-stranded overhang regions, later the remaining probe target hybrids are purified and resolved on denaturing polyacrylamide gel, and quantified by autoradiography.
A type of gel electrophoresis evidence where proteins are separated using gel electrophoresis and then they are blotted on a nitrocellulose or polyvinylidene difluoride (PVDF) membrane, later an antibody with a dye or an enzyme is added to the solution which is able to bind to its specific protein and this product is detected either by chemiluminescent detection technique or fluorescence imaging technique.
IEP: protein levels (e.g. Western blots)
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.
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.
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.
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.
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.
green fluorescent protein fusion protein localization evidence
GFP fusion protein localization evidence
IDA: localization of GFP/YFP fusion protein
yellow fluorescent protein fusion protein localization evidence
YFP fusion protein localization evidence
beta-glucuronidase fusion protein localization evidence
GUS fusion protein localization evidence
beta-galactosidase fusion protein localization evidence
LacZ fusion protein localization 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.
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.
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 transcription reconstitution assay evidence
IDA: in vitro reconstitution assay with recombinant protein
in vitro recombinant protein transcription reconstitution assay evidence
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.
IDA: protein expression in heterologous system
protein separation followed by direct sequencing evidence
IDA: protein separation and direct sequencing
protein separation followed by fragment identification evidence
IDA: protein separation and fragment identification
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.
A type of direct assay evidence where electrical properties of cells or tissues are studied.
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.
two-electrode voltage clamp experiment evidence
A type of electrophysiology assay evidence which involves using two electrodes inserted into a large cell (often a xenopus oocyte) where one electrode is used to measure the internal potential (voltage) of the cell and the other electrode is used to clamp the current.
IDA: two-electrode voltage clamp technique
Used when an annotation is made based on assays that show transcriptional activation of a specific target reporter gene.
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.
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.
Used when an annotation is made based on the visual examination of a mutant phenotype; for example, abnormalities in organism morphology.
An evidence type that is based on the location of a gene, which gives rise to a gene product, within the genome.
This type of evidence might include identity of neighboring genes, operon structure, synteny, phylogenetic analysis, or other whole-genome analysis.
A type of experimental evidence arising from the investigation of an animal model system.
A type of experimental evidence arising from a controlled investigation that uses human subjects.
A type of specific protein inhibition evidence where the protein under study is an enzyme.
A type of sequence similarity evidence where a sequence alignment is the basis for making an annotation, but only when the alignment has been manually reviewed; or if the information is in a published paper, the authors have manually reviewed the evidence. Such alignments may be pairwise alignments or multiple alignments.
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.
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.
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.
An evidence type that is based on an assertion by the author of a paper, which is read by a curator.
A type of inferential evidence that is based on a conclusion drawn by a curator.
A type of pairwise sequence alignment evidence obtained with basic local alignment search tool (BLAST).
BLAST evidence from aligning nucleotide sequence with nucleotide sequence.
BLAST evidence from aligning amino acid or translated nucleotide sequence with amino acid or translated nucleotide sequence.
BLAST evidence used in automatic assertion
A type of BLAST evidence that is used in an automatic assertion.
nucleotide BLAST evidence used in automatic assertion
Nucleotide BLAST evidence that is used in an automatic assertion.
protein BLAST evidence used in automatic assertion
Protein BLAST evidence that is used in an automatic assertion.
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.
combinatorial evidence used in automatic assertion
A type of combinatorial analysis that is used in an automatic assertion.
biological aspect of descendant evidence
A type of phylogenetic evidence whereby an aspect of an ancestral gene is inferred through the characterization of an aspect of a descendant gene.
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.
rapid divergence from ancestral sequence evidence
A type of phylogenetic evidence characterized by long phylogenetic tree branch lengths following a duplication event.
Long branch lengths indicate that descendant sequences may have acquired different or additional functions than the ancestral sequence.
phylogenetic determination of loss of key residues evidence
A type of phylogenetic evidence characterized by the absence of key sequence residues.
The loss of certain residues important for function can indicate that a sequence lacks a particular function.
A means by which a statement is made about an entity.
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.
A sequencing assay result for a biopolymer that comprises nucleotides.
A type of experimental evidence where the order of molecules that constitute a biopolymer is determined.
high throughput nucleotide sequencing assay evidence
A nucleotide sequencing assay result that is derived from a parallelized sequencing technique.
Typically thousands to millions of reads are produced in parallel.
A high throughput nucleotide sequencing result derived by Illumina (Solexa) sequencing technology.
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.
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.
A high throughput nucleotide sequencing result derived by SOLiD sequencing technology.
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.
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.
A type of immunoprecipitation evidence that is used to identify a protein binding site on a genomic DNA sequence.
Chromatin immunoprecipitation (ChIP) is used to investigate protein-DNA interactions in vivo. DNA and proteins are chemically cross-linked in vivo to form chromatin complexes, followed by cell lysis and DNA shearing. Fragmented DNA-protein complexes are selectively enriched for a protein of interest using a specific antibody (immunoprecipitation). Protein digestion and DNA purification are performed prior to DNA detection via molecular cloning and sequencing, polymerase chain reaction (PCR), microarray analysis (ChIP-on-chip), or direct high-throughput sequencing (ChIP-seq).
chromatin immunoprecipitation-PCR evidence
A type of chromatin immunoprecipitation evidence that uses polymerase chain reaction (PCR) where specific primers are used on the pulled-down DNA for DNA detection.
ChIP-PCR is often used to validate ChIP-chip results and less frequently,ChIP-Seq results.
chromatin immunoprecipitation-qPCR evidence
A chromatin immunoprecipitation (ChIP) evidence that uses quantitative polymerase chain reaction (qPCR) for DNA detection.
chromatin immunoprecipitation-seq evidence
A type of chromatin immunoprecipitation evidence that uses high-throughput sequencing where immunoprecipitated DNA fragments are funnelled into a massively parallel sequencer to produce multiple short reads for locating binding sites of DNA-associated proteins.
ChIP-Seq experiments often use the input as a control to eliminate biases. To obtain similar results, ChIP-chip with high-density tiling arrays can be used.
chromatin immunoprecipitation-chip evidence
A fixating agent such as formaldehyde is used to cross link proteins and DNA. Sonication is applied for DNA shearing. For transcription factor tagging, an antibody or epitope is employed. After cross-linking is reversed, the DNA is amplified and labeled with a flourophore for microarray which produces a resolution of aproximately 500 bp.
A type of chromatin immunoprecipitation evidence that uses a tiling microarray for the detection of protein-bound DNA regions where chromatin is immunoprecipitated for protein tagging and DNA is sheared from the cross-linked protein-DNA complex to be arrayed revealing the protein-bound genomic regions.
quantitative polymerase chain reaction evidence
A type of polymerase chain reaction evidence where the reaction product is quantified in real-time across cycles by means of fluorescent dyes for detection and quantification of specific sequences in a DNA sample.
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).
real-time polymerase chain reaction evidence
chromosome conformation capture-based evidence
A type of experimental evidence that is based on a five-step technique of cross-linking DNA in vivo, restriction digestion, intramolecular ligation, reversing DNA cross-links, and DNA processing and quantitation.
Chromosome conformation capture technologies are used to study the structural properties and spatial organization of chromosomes inside cells. All types of chromosome conformation capture technology involve five primary steps: cross-linking of DNA in vivo, restriction digestion, intramolecular ligation, reversing cross-linkages, and DNA enrichment and quantitation. The last step is different for each type of chromosome conformation capture technology, and may include PCR (3C), inverse PCR (4C), or ligation-mediated amplification (5C). Methods for product quantitation can include agarose gel detection or real-time quantitative PCR in the case of 3C, or high-throughput sequencing or microarray analysis for 4C and 5C.
chromosome conformation capture evidence
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.
circularized chromosome conformation capture evidence
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.
carbon-copy chromosome conformation capture evidence
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.
chromosome conformation capture-PCR evidence
A type of chromosome conformation capture evidence that is derived by performing polymerase chain reaction (PCR) in the quantitation step.
chromosome conformation capture-qPCR evidence
A type of chromosome conformation capture evidence that is derived by performing quantitative polymerase chain reaction (qPCR) in the quantitation step.
A type of chromosome conformation capture-based evidence that is derived by performing immunoprecipitation enrichment of ligated fragments events prior to product quantitation.
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.
chromosome conformation capture sequencing evidence
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.
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.
Experimental phenotypic evidence where a structural feature of an organism is disrupted.
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.
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.
A type of anatomical perturbation that is based on adding tissue to an organism through a graft procedure.
combinatorial evidence used in manual assertion
A type of combinatorial analysis that is used in a manual assertion.
computational combinatorial evidence used in manual assertion
A type of computational combinatorial analysis that is used in a manual assertion.
inferred from reviewed computational analysis
computational combinatorial evidence used in automatic assertion
A type of computational combinatorial analysis that is used in an automatic assertion.
sequence alignment evidence used in manual assertion
Sequence alignment evidence that is used in a manual assertion.
sequence alignment evidence used in automatic assertion
Sequence alignment evidence that is used in an automatic assertion.
sequence similarity evidence used in automatic assertion
Sequence similarity evidence that is used in an automatic assertion.
sequence similarity evidence used in manual assertion
Sequence similarity evidence that is used in a manual assertion.
similarity evidence used in automatic assertion
Similarity evidence that is used in an automatic assertion.
similarity evidence used in manual assertion
Similarity evidence that is used in a manual assertion.
genetic similarity evidence used in manual assertion
Genetic similarity evidence that is used in a manual assertion.
genetic similarity evidence used in automatic assertion
Genetic similarity evidence that is used in an automatic assertion.
match to sequence model evidence used in manual assertion
A match to sequence model evidence that is employed in a manual assertion.
match to sequence model evidence used in automatic assertion
A match to sequence model evidence that is employed in an automatic assertion.
Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara
Gene Ontology annotation through association of InterPro records with GO terms.
Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl
motif similarity evidence used in manual assertion
Motif similarity evidence that is employed in a manual assertion.
motif similarity evidence used in automatic assertion
Motif similarity evidence that is employed in an automatic assertion.
match to InterPro member signature evidence used in automatic assertion
A match to InterPro member signature evidence that is employed in an automatic assertion.
match to InterPro member signature evidence used in manual assertion
A match to InterPro member signature evidence that is employed in a manual assertion.
targeting sequence prediction evidence used in automatic assertion
A targeting sequence prediction that is employed in an automatic assertion.
targeting sequence prediction evidence used in manual assertion
A targeting sequence prediction that is employed in a manual assertion.
transmembrane domain prediction evidence used in automatic assertion
Transmembrane domain prediction that is employed in an automatic assertion.
transmembrane domain prediction evidence used in manual assertion
Transmembrane domain prediction that is employed in a manual assertion.
sequence orthology evidence used in automatic assertion
Sequence orthology evidence that is employed in an automatic assertion.
Gene Ontology annotation based on Enzyme Commission mapping.
Automatic transfer of experimentally verified manual GO annotation data to plant orthologs using Ensembl Compara
sequence orthology evidence used in manual assertion
Sequence orthology evidence that is employed in a manual assertion.
enzyme-linked immunoabsorbent assay evidence
A type of protein detection assay evidence where an antigen is bound to a substrate, and an antibody directly or indirectly linked to an enzyme is utilized to determine the amount of bound antigen which is visualized with a color change in the substrate.
ELISA is sometimes used in the study of transcriptional regulation to identify a produced protein, especially secreted protein.
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.
experimental evidence used in manual assertion
A type of experimental evidence that is used in a manual assertion.
expression evidence used in manual assertion
A type of expression pattern evidence that is used in a manual assertion.
array experiment evidence used in manual assertion
A type of array experiment evidence that is used in a manual assertion.
Affymetrix array experiment evidence used in manual assertion
A type of Affymetrix array experiment evidence that is used in a manual assertion.
cDNA microarray evidence used in manual assertion
A type of evidence arising from a cDNA microarray experiment that is used in a manual assertion.
CpG island microarray evidence used in manual assertion
A type of evidence arising from a CpG island microarray experiment that is used in a manual assertion.
expression microarray evidence used in manual assertion
A type of expression microarray evidence that is used in a manual assertion.
genomic microarray evidence used in manual assertion
A type of evidence arising from a genomic microarray experiment that is used in a manual assertion.
Nimblegen array evidence used in manual assertion
A type of evidence arising from a Nimblegen array experiment that is used in a manual assertion.
oligonucleotide microarray evidence used in manual assertion
A type of evidence arising from an oligonucleotide microarray experiment that is used in a manual assertion.
western blot evidence used in manual assertion
A type of Western blot assay that is used in a manual assertion.
protein expression level evidence used in manual assertion
A type of protein expression level analysis that is used in a manual assertion.
expression library screen evidence used in manual assertion
A type of expression library screen evidence that is used in a manual assertion.
heterologous protein expression evidence used in manual assertion
A type of heterologous protein expression analysis that is used in a manual assertion.
spatial pattern of protein expression evidence used in manual assertion
A type of protein expression spatial pattern analysis that is used in a manual assertion.
protein expression evidence used in manual assertion
A type of protein expression analysis that is used in a manual assertion.
microarray RNA expression level evidence used in manual assertion
A type of microarray RNA expression level data that is used in manual assertion.
transcript expression level evidence used in manual assertion
A type of transcript expression level data that is used in manual assertion.
differential hybridization evidence used in manual assertion
A type of differential hybridization experiment that is used in a manual assertion.
RNA protection assay evidence used in manual assertion
A type of RNA protection assay that is used in a manual assertion.
spatial pattern of transcript expression evidence used in manual assertion
A type of spatial pattern of transcript expression analysis that is used in a manual assertion.
subtractive hybridization evidence used in manual assertion
A type of subtractive hybridization experiment that is used in a manual assertion.
transcript expression evidence used in manual assertion
A type of transcript expression evidence that is used in a manual assertion.
A type of experimental phenotypic evidence that uses anti-sense by introducing morpholino oligonucleotides into the cytosol of a cell.
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.
systematic evolution of ligands by exponential amplification evidence
A type of evidence arising from a physical interaction analysis where a combinatorial chemistry technique is used to identify oligonucleotides that bind to a target ligand.
SELEX begins with the synthesis of a large oligonucleotide library, either single-stranded DNA or RNA, which consists of random fixed-length sequences flanked by constant 5' and 3' ends that serve as primers. The library is exposed to a target ligand, typically a protein or small organic compound. Unbound sequences are removed, typically with affinity chromatography. Bound sequences are eluted and the nucleic acid is extracted, followed by PCR amplification (RNA is first reverse transcribed). PCR product is converted to single stranded (DNA) or transcribed (RNA). Oligonucleotides are bound to the ligand again and the process is repeated with increasing elution stringency. After several rounds of the process, recovered oligonucleotides are sequenced and analyzed to reveal the binding specificity of the protein.
systematic evolution of ligands by exponential enrichment
A type of hybrid interaction evidence that uses bacterial transformation with two plasmids to assess in vivo binding of a DNA-binding domain (bait) and DNA target site (prey).
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.
A type of transcript expression evidence based on high-throughput (HT) sequencing of fragmented cDNA molecules.
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.
green fluorescent protein transcript localization evidence
A transcriptional activation assay that uses a green fluorescent protein (GFP) reporter gene.
This term describes transcriptional activation; to describe immunolocalization of the protein, use the term "immunolocalization of green fluorescent protein".
A transcriptional activation assay that uses a LacZ reporter gene.
This term describes transcriptional activation; to describe immunolocalization of the protein, use the term "immunolocalization of LacZ protein".
A type of experimental phenotypic evidence where embryonic development proceeds although cytokinesis is blocked.
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.
A type of cleavage arrested development that arises after treatment with cytochalasin.
Cytochalasin inhibits cytokinesis by blocking the formation of contractile microfilaments.
green fluorescent protein immunolocalization evidence
A type of immunolocalization evidence data that was generated using green fluorescent protein (GFP) as a marker.
This term describes immunolocalization of the protein; to describe transcriptional activation, use the term "localization of green fluorescent protein transcript".
beta-galactosidase protein immunolocalization evidence
A type of immunolocalization evidence that was generated using LacZ protein as a marker.
LacZ protein immunolocalization evidence
This term describes immunolocalization of the protein; to describe transcriptional activation, use the term "localization of LacZ transcript".
author statement used in manual assertion
A type of author statement that is used in a manual assertion.
non-traceable author statement used in manual assertion
A type of non-traceable author statement that is used in a manual assertion.
traceable author statement used in manual assertion
A type of traceable author statement that is used in a manual assertion.
curator inference used in manual assertion
A type of curator inference that is used in a manual assertion.
inference from background scientific knowledge used in manual assertion
A type of inference from background scientific knowledge that is used in a manual assertion.
no biological data found used in manual assertion
A type of no biological data found that is used in a manual assertion.
A type of phylogenetic evidence whereby an aspect of a descendant gene is inferred through the characterization of an aspect of an ancestral gene.
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.
cap analysis of gene expression evidence
A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by a cap-trapper system.
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.
nano-cap analysis of gene expression evidence
A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by reverse transcriptase template switching.
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.
An evidence type that is based on work performed by a person or group prior to a use by different person or group.
imported information used in manual assertion
A type of imported information that is used in a manual assertion.
imported information used in automatic assertion
A type of imported information that is used in an automatic assertion.
direct assay evidence used in manual assertion
A type of direct assay evidence that is used in a manual assertion.
mutant phenotype evidence used in manual assertion
A type of mutant phenotype evidence that is used in a manual assertion.
genetic interaction evidence used in manual assertion
A type of genetic interaction experiment evidence that is used in a manual assertion.
genomic context evidence used in manual assertion
A type of genomic context evidence that is used in a manual assertion.
biological aspect of ancestor evidence used in manual assertion
A type of biological aspect of ancestor evidence that is used in a manual assertion.
inferred from biological aspect of ancestor
biological aspect of descendant evidence used in manual assertion
A type of biological aspect of descendant evidence that is used in a manual assertion.
inferred from biological aspect of descendant
phylogenetic determination of loss of key residues evidence used in manual assertion
A type of phylogenetic determination of loss of key residues evidence that is used in a manual assertion.
rapid divergence from ancestral sequence evidence used in manual assertion
A type of rapid divergence from ancestral sequence evidence that is used in a manual assertion.
imported manually asserted information used in automatic assertion
Evidence that was initially used in manual assertion by one person or group, which is imported by a second person or group and used in automatic assertion.
imported automatically asserted information used in automatic assertion
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.
Direct assay evidence derived from analysis of an image.
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.
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.
whole transcript splice pattern evidence
A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features.
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.
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.
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.
whole transcript splice pattern evidence used in manual assertion
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.
coding sequence splice pattern evidence used in manual assertion
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.
coding sequence splice pattern evidence used in automatic assertion
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.
whole transcript splice pattern evidence used in automatic assertion
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.
sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence
A type of gel electrophoresis evidence where proteins are separated according to their electrophoretic mobility.
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.
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.
A type of direct assay evidence where the quantity of a substance used as part of an assay is measured.
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.
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.
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.
Molecules typically separated include DNA, RNA, or protein. The gel is typically made of agarose, polyacrylamide, or starch.
pulsed-field gel electrophoresis evidence
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.
two-dimensional agarose gel electrophoresis evidence
A type of gel electrophoresis evidence where DNA molecules are electrophoresed on a low percentage agarose gel followed by high voltage electrophoresis on a higher percentage agarose gel in the presence of ethidium bromide.
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.
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.
minichromosome maintenance assay evidence
specific protein inhibition by antibody evidence
A type of specific protein inhibition evidence where the molecular function of a protein is inhibited by an antibody.
Support of intron position by RNA-seq alignment evidence
A type of transcript splice pattern evidence where intron locations in predicted transcripts are compared to intron locations supported by RNA-seq evidence.
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.
Full support of intron position by RNA-seq alignment evidence
A type of support of intron position by RNA-seq alignment evidence where RNA-seq alignment from a single sample supports all of the intron positions (exon pairs) predicted for a transcript.
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.
Partial support of intron position by RNA-seq alignment evidence
A type of support of intron position by RNA-seq alignment evidence where RNA-seq alignment to a genome supports only some of the intron positions (exon pairs) predicted for a transcript.
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.
single exon transcript confirmation via alignment evidence
Support of intron position by RNA-seq alignment evidence used in manual assertion
A type of support of intron position by RNA-seq alignment evidence that is used in a manual assertion.
Support of intron position by RNA-seq alignment evidence used in automatic assertion
A type of support of intron position by RNA-seq alignment evidence that is used in an automatic assertion.
Full support of intron position by RNA-seq alignment evidence used in automatic assertion
A type of full support of intron position by RNA-seq alignment evidence that is used in an automatic assertion.
Full support of intron position by RNA-seq alignment evidence used in manual assertion
A type of full support of intron position by RNA-seq alignment evidence that is used in a manual assertion.
Partial support of intron position by RNA-seq alignment evidence used in automatic assertion
A type of partial support of intron position by RNA-seq alignment evidence that is used in an automatic assertion.
Partial support of intron position by RNA-seq alignment evidence used in manual assertion
A type of partial support of intron position by RNA-seq alignment evidence that is used in a manual assertion.
A type of evidence that is used in an manual assertion.
physical interaction evidence used in manual assertion
A type of physical interaction evidence that is used in a manual assertion.
gene neighbors evidence used in manual assertion
A type of gene neighbors evidence that is used in a manual assertion.
A type of phylogenetic evidence characterized by the mapping of the character states of living organisms onto phylogenies using the method of maximum parsimony.
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.
differential gene expression evidence from microarray experiment
differential gene expression evidence from RNA-seq experiment
differential geneset expression evidence from microarray experiment (GSEA, Fisher-exact)
differential geneset expression evidence from RNA-seq experiment (GSEA, Fisher-exact)
biological target-disease association via drug
A type of evidence where an assertion is derived from another assertion via logical inference or some non-logical but rational means.
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.
evidence based on computational logical inference
A type of inferential evidence based on a computationally derived unary inference or an inference chain in which at least one step is computationally derived.
evidence based on computational logical inference used in automatic assertion
A type of evidence based on computational logical inference that is used in automatic assertion.
Automatic assignment of GO terms using logical inference, based on on inter-ontology links
evidence based on logical inference from manual annotation used in automatic assertion
A type of evidence based on logical inference from a manually curated annotation that is used in an automatic assertion.
evidence based on logical inference from automatic annotation used in automatic assertion
A type of evidence based on logical inference from an automatically curated annotation that is used in an automatic assertion.
A type of evidence that is used in an automatic assertion.
Gene Ontology annotation based on Swiss-Prot Subcellular Location vocabulary mapping.
Gene Ontology annotation based on Swiss-Prot keyword mapping.
[3H]arachidonic acid release assay evidence
[3H]-thymidine incorporation assay evidence
A type of ex vivo assay evidence derived by ex vivo selection of tumor-reactive lymphocytes, and their activation and numerical expansion before re-infusion to the autologous tumor-bearing host.
allograft transplantation experiment evidence
A type of anatomical perturbation evidence where an organ or tissue is transplanted from one individual to another of the same species with a different genotype.
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.
A type of direct assay evidence where a blood sample is extracted from an organism to analyze different blood components.
bromodeoxyuridine incorporation assay evidence
5-bromo-2'-deoxyuridine incorporation assay evidence
carboxyfluorescein diacetate succinimidyl ester staining evidence
chemiluminescence-linked immunoassay evidence
4',6-diamidino-2-phenylindole staining evidence
A type of RNA detection assay evidence based on the direct application of a RNA mixture in a circular motion on a matrix for hybridization with labeled DNA fragments.
Edman degradation evidence used in manual assertion
A type of Edman degradation evidence that is used in a manual assertion.
fluorescence in situ hybridization evidence
fluorescence resonance energy transfer evidence
high-performance liquid chromatography evidence
A type of in vitro assay evidence where acetylated residues are detected in a compound (such as a protein or a nucleic acid) in an in vitro experiment.
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.
in vitro deubiquitination assay evidence
A type of in vitro assay evidence where the removal of ubiquitin groups on a protein is detected in vitro.
A type of in vitro assay evidence where the removal of acetyl groups from a compound is detected in an in vitro experiment.
A type of in vitro assay evidence where the removal of farnesyl groups from a protein is detected in an in vitro experiment.
A type of in vitro assay evidence where the removal of methyl groups from a compound is detected in an in vitro experiment.
A type of in vitro assay evidence where the removal of sumo groups is detected on a protein in vitro.
A type of in vitro assay evidence where farnesylated residues in proteins are detected in an in vitro experiment.
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.
A type of in vitro assay evidence where palmitoylated residues in proteins are detected in an in vitro experiment.
A type of in vitro assay evidence where the removal of phosphatase groups on a protein is detected in an in vitro experiment.
A type of in vitro assay evidence where phosphorylated residues in a protein are detected in an in vitro experiment.
in vitro polyADP-ribosylation assay evidence
A type of in vitro assay evidence where ADP-ribosylated residues in proteins are detected in an in vitro experiment.
A type of in vitro assay evidence where sumoylated residues are detected on a protein in an in vitro experiment.
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.
A type of in vitro assay evidence where de novo protein synthesis is detected in an in vitro experiment.
A type of in vitro assay evidence where ubiquitinated residues are detected on a protein in an in vitro experiment.
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.
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.
A type of in vivo assay evidence where the removal of acetyl groups from a compound is detected in cells in vivo.
A type of in vivo assay evidence where removal of farnesyl groups from a protein is detected in cells in vivo.
A type of in vivo assay evidence where the removal of methyl groups from a compound is detected in cells in vivo.
A type of in vivo assay evidence where the removal of ubiquitin groups on a protein is detected in cells in vivo.
A type of in vivo assay evidence where the removal of sumo groups on a protein is detected in cells in vivo.
A type of in vivo assay evidence where farnesylated residues in proteins are detected in cells in vivo.
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.
A type of in vivo assay evidence where palmitoylated residues in proteins are detected in cells in vivo.
A type of in vivo assay evidence where the removal of phosphate groups on a protein is detected in cells in vivo.
A type of in vivo assay evidence where phosphorylated residues in a protein are detected in cells in vivo.
A type of in vivo assay evidence where sumoylated residues are detected on a protein in cells in vivo.
A type of in vivo assay evidence where transcription is detected in cells in vivo.
A type of in vivo assay evidence where de novo protein synthesis is detected in cells in vivo.
A type of in vivo assay evidence where ubiquitinated residues on a protein are detected in cells in vivo.
luminescence-based mammalian interactome mapping assay evidence
A type of direct assay evidence where a microscope was used to view a sample.
3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide
multiplex bead-based immunoassay evidence
nuclear magnetic resonance spectroscopy evidence
nucleotide analog incorporation evidence
phosphopeptide affinity enrichment evidence
A type of physical interaction evidence based on real-time, rapid plasmon generation on the interface between a planar surface and vacuum that measures changes in refractive index close to the sensor surface when an analyte and its immobilized ligand bind to observe and characterize molecular interaction.
Plasmons are generated by an incident light beam.
syngeneic transplantation experiment evidence
Tumor necrosis factor - alpha converting enzyme activity assay
tryptic phosphopeptide mapping assay evidence
terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence
TdT-mediated dUTP-biotin nick end labeling assay
terminal deoxynucleotidyl transferase-dUTP nick end labeling assay evidence
A type of anatomical perturbation evidence where live cells, tissues, or organs from a non-human animal source are transplanted, implanted or infused into a human recipient.
3D cell culture evidence used in manual assertion
A type of 3D cell culture evidence that is used in a manual assertion.
51Cr release assay evidence used in manual assertion
A type of 51Cr release assay evidence that is used in a manual assertion.
7-aminoactinomycin staining evidence used in manual assertion
A type of 7-aminoactinomycin staining evidence that is used in a manual assertion.
[3H]-thymidine incorporation assay evidence used in manual assertion
A type of [3H]-thymidine incorporation assay evidence that is used in a manual assertion.
[3H]arachidonic acid release assay evidence used in manual assertion
A type of [3H]arachidonic acid release assay evidence that is used in a manual assertion.
adhesion assay evidence used in manual assertion
A type of adhesion assay evidence that is used in a manual assertion.
adoptive cell transfer evidence used in manual assertion
A type of adoptive cell transfer evidence that is used in a manual assertion.
Alamar blue assay evidence used in manual assertion
A type of Alamar blue assay evidence that is used in a manual assertion.
allograft transplantation experiment evidence used in manual assertion
A type of allograft transplantation experiment evidence that is used in a manual assertion.
anion-exchange chromatography evidence used in manual assertion
A type of anion-exchange chromatography evidence that is used in a manual assertion.
annexin-V staining evidence used in manual assertion
A type of annexin-V staining evidence that is used in a manual assertion.
behavioral assay evidence used in manual assertion
A type of behavioral assay evidence used that is used in a manual assertion.
blocking monoclonal antibody evidence used in manual assertion
A type of blocking monoclonal antibody evidence that is used in a manual assertion.
blocking peptide evidence used in manual assertion
A type of blocking peptide evidence that is used in a manual assertion.
blocking polyclonal antibody evidence used in manual assertion
A type of blocking polyclonal antibody evidence tthat is used in a manual assertion.
blood test evidence used in manual assertion
A type of blood test evidence that is used in a manual assertion.
Boyden chamber assay evidence used in manual assertion
A type of Boyden chamber assay evidence that is used in a manual assertion.
bromodeoxyuridine incorporation assay evidence used in manual assertion
A type of BrdU incorporation assay evidence that is used in a manual assertion.
caspase assay evidence used in manual assertion
A type of caspase assay evidence that is used in a manual assertion.
cell counting evidence used in manual assertion
A type of cell counting evidence that is used in a manual assertion.
cell permeability assay evidence used in manual assertion
A type of cell permeability assay evidence that is used in a manual assertion.
carboxyfluorescein diacetate succinimidyl ester staining evidence used in manual assertion
A type of carboxyfluorescein diacetate succinimidyl ester staining evidence that is used in a manual assertion.
chemiluminescence-linked immunoassay evidence used in manual assertion
A type of chemiluminescence-linked immunoassay evidence that is used in a manual assertion.
chimeric protein evidence used in manual assertion
A type of chimeric protein evidence that is used in a manual assertion.
co-electrophoresis evidence used in manual assertion
A type of co-electrophoresis evidence that is used in a manual assertion.
co-localization evidence used in manual assertion
A type of co-localization evidence that is used in a manual assertion.
co-sedimentation assay evidence used in manual assertion
A type of co-sedimentation assay evidence that is used in a manual assertion.
colony counting evidence used in manual assertion
A type of colony counting evidence that is used in a manual assertion.
comet assay evidence used in manual assertion
A type of comet assay evidence that is used in a manual assertion.
conditional knockin evidence used in manual assertion
A type of conditional knockin evidence that is used in a manual assertion.
conditional knockout evidence used in manual assertion
A type of conditional knockout evidence that is used in a manual assertion.
constitutively active mutant evidence used in manual assertion
A type of constitutively active mutant evidence that is used a in manual assertion.
cross-linking evidence used in manual assertion
A type of cross-linking evidence that is used in a manual assertion.
crystallography evidence used in manual assertion
A type of crystallography evidence that is used in a manual assertion.
cytochemistry evidence used in manual assertion
A type of cytochemistry evidence that is used in a manual assertion.
cytochrome C release assay evidence used in manual assertion
A type of cytochrome C release assay evidence that is used in a manual assertion.
4',6-diamidino-2-phenylindole staining evidence used in manual assertion
A type of 4',6-diamidino-2-phenylindole staining evidence that is used in a manual assertion.
deletion evidence used in manual assertion
A type of deletion evidence that is used in a manual assertion.
DNA laddering assay evidence used in manual assertion
A type of DNA laddering assay evidence that is used in a manual assertion.
RNA dot blot assay evidence used in manual assertion
A type of RNA dot blot assay evidence that is used in a manual assertion.
RNA microarray evidence used in manual assertion
A type of RNA microarray evidence that is used in a manual assertion.
dominant-negative mutant evidence used in manual assertion
A type of dominant-negative mutant evidence that is used in a manual assertion.
eTag assay evidence used in manual assertion
A type of eTag assay evidence that is used in a manual assertion.
filter binding assay evidence used in manual assertion
A type of filter binding assay evidence that is used in a manual assertion.
fluorescence in situ hybridization evidence used in manual assertion
A type of fluorescence in situ hybridization evidence that is used in a manual assertion.
fluorescence resonance energy transfer evidence used in manual assertion
A type of fluorescence resonance energy transfer evidence that is used in a manual assertion.
gel-filtration evidence used in manual assertion
A type of gel-filtration evidence that is used in a manual assertion.
histochemistry evidence used in manual assertion
A type of histochemistry evidence that is used in a manual assertion.
immunocytochemistry evidence used in manual assertion
A type of immunocytochemistry evidence that is used in a manual assertion.
histology evidence used in manual assertion
A type of histology evidence that is used in a manual assertion.
immunodepletion evidence used in manual assertion
A type of immunodepletion evidence that is used in a manual assertion.
immunohistochemistry evidence used in manual assertion
A type of immunohistochemistry evidence that is used in a manual assertion.
in vitro acetylation assay evidence used in manual assertion
A type of in vitro acetylation assay evidence that is used in a manual assertion.
in vitro cleavage assay evidence used in manual assertion
A type of in vitro cleavage assay evidence that is used in a manual assertion.
in vitro deacetylation assay evidence used in manual assertion
A type of in vitro deacetylation assay evidence that is used in a manual assertion.
in vitro defarnesylation assay evidence used in manual assertion
A type of in vitro defarnesylation assay evidence that is used in a manual assertion.
in vitro demethylation assay evidence used in manual assertion
A type of in vitro demethylation assay evidence that is used in a manual assertion.
in vitro desumoylation assay evidence used in manual assertion
A type of in vitro desumoylation assay evidence that is used in a manual assertion.
in vitro deubiquitination assay evidence used in manual assertion
A type of in vitro deubiquitination assay evidence that is used in a manual assertion.
in vitro farnesylation assay evidence used in manual assertion
A type of in vitro farnesylation assay evidence that is used in a manual assertion.
in vitro methylation assay evidence used in manual assertion
A type of in vitro methylation assay evidence that is used in a manual assertion.
in vitro palmitoylation assay evidence used in manual assertion
A type of in vitro palmitoylation assay evidence that is used in a manual assertion.
in vitro phosphatase assay evidence used in manual assertion
A type of in vitro phosphatase assay evidence that is used in a manual assertion.
in vitro polyADP-ribosylation assay evidence used in manual assertion
A type of in vitro polyADP-ribosylation assay evidence that is used in a manual assertion.
in vitro protein kinase assay evidence used in manual assertion
A type of in vitro protein kinase assay evidence that is used in a manual assertion.
in vitro sumoylation assay evidence used in manual assertion
A type of in vitro sumoylation assay evidence that is used in a manual assertion.
in vitro transcription assay used in manual assertion
A type of in vitro transcription assay evidence that is used in a manual assertion.
in vitro translation assay evidence used in manual assertion
A type of in vitro translation assay evidence that is used in a manual assertion.
in vitro ubiquitination assay evidence used in manual assertion
A type of in vitro ubiquitination assay evidence that is used in a manual assertion.
in vivo acetylation assay evidence used in manual assertion
A type of in vivo acetylation assay evidence that is used in manual assertion.
in vivo cleavage assay evidence used in manual assertion
A type of in vivo cleavage assay evidence that is used in a manual assertion.
in vivo deacetylation assay evidence used in manual assertion
A type of in vivo deacetylation assay evidence that is used in a manual assertion.
in vivo defarnesylation assay evidence used in manual assertion
A type of in vivo defarnesylation assay evidence that is used in a manual assertion.
in vivo demethylation assay evidence used in manual assertion
A type of in vivo demethylation assay evidence that is used in a manual assertion.
in vivo desumoylation assay evidence used in manual assertion
A type of in vivo desumoylation assay evidence that is used in a manual assertion.
in vivo deubiquitination assay evidence used in manual assertion
A type of in vivo deubiquitination assay evidence that is used in a manual assertion.
in vivo farnesylation assay evidence used in manual assertion
A type of in vivo farnesylation assay evidence that is used in a manual assertion.
in vivo methylation assay evidence used in manual assertion
A type of in vivo methylation assay evidence that is used in a manual assertion.
in vivo palmitoylation assay evidence used in manual assertion
A type of in vivo palmitoylation assay evidence that is used in a manual assertion.
in vivo phosphatase assay evidence used in manual assertion
A type of in vivo phosphatase assay evidence that is used in a manual assertion.
in vivo protein kinase assay evidence used in manual assertion
A type of in vivo protein kinase assay evidence that is used in a manual assertion.
in vivo sumoylation assay evidence used in manual assertion
A type of in vivo sumoylation assay evidence that is used in a manual assertion.
in vivo transcription assay evidence used in manual assertion
A type of in vivo transcription assay evidence that is used in a manual assertion.
in vivo translation assay evidence used in manual assertion
A type of in vivo translation assay evidence that is used in a manual assertion.
in vivo ubiquitination assay evidence used in manual assertion
A type of in vivo ubiquitination assay evidence that is used in a manual assertion.
induced mutation evidence used in manual assertion
A type of induced mutation evidence that is used in a manual assertion.
knockin evidence used in manual assertion
A type of knockin evidence that is used in a manual assertion.
knockout evidence used in manual assertion
A type of knockout evidence that is used in a manual assertion.
lipid binding assay evidence used in manual assertion
A type of lipid binding assay evidence that is used in a manual assertion.
luminescence-based mammalian interactome mapping assay evidence used in manual assertion
A type of LUMIER assay evidence that is used in a manual assertion.
macroscopy evidence used in manual assertion
A type of macroscopy evidence that is used in a manual assertion.
mammalian 2-hybrid assay evidence used in manual assertion
A type of mammalian 2-hybrid assay evidence that is used in a manual assertion.
mass spectrometry evidence used in manual assertion
A type of mass spectrometry evidence that is used in a manual assertion.
medical imaging evidence used in manual assertion
A type of medical imaging evidence that is used in a manual assertion.
microscopy evidence used in manual assertion
A type of microscopy evidence that is used in a manual assertion.
motility wound healing assay evidence used in manual assertion
A type of motility wound healing assay evidence that is used in a manual assertion.
MTS assay evidence used in manual assertion
A type of MTS assay evidence that is used in a manual assertion.
MTT assay evidence used in manual assertion
A type of MTT assay evidence that is used in a manual assertion.
multiplex bead-based immunoassay evidence used in manual assertion
A type of multiplex bead-based immunoassay evidence that is used in a manual assertion.
natural variation mutant evidence used in manual assertion
A type of natural variation mutant evidence that is used in a manual assertion.
nuclear magnetic resonance spectroscopy evidence used in manual assertion
A type of nuclear magnetic resonance spectroscopy evidence that is used in a manual assertion.
nuclear fragmentation evidence used in manual assertion
A type of nuclear fragmentation evidence that is used in a manual assertion.
nuclease protection assay evidence used in manual assertion
A type of nuclease protection assay evidence that is used in a manual assertion.
nucleotide analog incorporation evidence used in manual assertion
A type of nucleotide analog incorporation evidence that is used in a manual assertion.
phage display evidence used in manual assertion
A type of phage display evidence that is used in a manual assertion.
phosphoamino acid analysis evidence used in manual assertion
A type of phosphoamino acid analysis evidence that is used in a manual assertion.
peptide affinity enrichment evidence used in manual assertion
A type of peptide affinity enrichment evidence that is used in a manual assertion.
peptide array evidence used in manual assertion
A type of peptide array evidence that is used in a manual assertion.
physical examination evidence used in manual assertion
A type of physical examination evidence that is used in a manual assertion.
point mutation evidence used in manual assertion
A type of point mutation evidence that is used in a manual assertion.
propidium iodide staining evidence used in manual assertion
A type of propidium iodide staining evidence that is used in a manual assertion.
fluorescence evidence used in manual assertion
A type of protein detection by fluorescence evidence that is used in a manual assertion.
protein dot blot assay evidence used in manual assertion
A type of protein dot blot assay evidence that is used in a manual assertion.
protein microarray evidence used in manual assertion
A type of protein microarray evidence that is used in a manual assertion.
protein sequencing assay evidence used in manual assertion
A type of protein sequencing assay evidence that is used in a manual assertion.
quantitative mass spectrometry evidence used in manual assertion
A type of quantitative mass spectrometry evidence that is used in a manual assertion.
radioisotope assay evidence used in manual assertion
A type of radioisotope assay evidence that is used in a manual assertion.
radioimmunoassay evidence used in manual assertion
A type of radioimmunoassay evidence that is used in a manual assertion.
imaging assay evidence used in manual assertion
A type of imaging assay evidence that is used in a manual assertion.
restriction fragment detection evidence used in manual assertion
A type of restriction fragment detection evidence that is used in a manual assertion.
spectrophotometry evidence used in manual assertion
A type of spectrophotometry evidence that is used in a manual assertion.
syngeneic transplantation experiment evidence used in manual assertion
A type of syngeneic transplantation experiment evidence that is used in a manual assertion.
xenotransplantation experiment evidence used in manual assertion
A type of xenotransplantation experiment evidence that is used in a manual assertion.
WST-1 assay evidence used in manual assertion
A type of WST-1 assay evidence that is used in a manual assertion.
wound healing assay evidence used in manual assertion
A type of wound healing assay evidence that is used in a manual assertion.
urine test evidence used in manual assertion
A type of urine test evidence that is used in a manual assertion.
terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence used in manual assertion
A type of TUNEL assay evidence that is used in a manual assertion.
tryptic phosphopeptide mapping assay evidence used in manual assertion
A type of tryptic phosphopeptide mapping assay evidence that is used in a manual assertion.
transgenic organism evidence used in manual assertion
A type of transgenic organism evidence that is used in a manual assertion.
tissue microarray evidence used in manual assertion
A type of tissue microarray evidence that is used in a manual assertion.
TACE activity assay evidence used in manual assertion
A type of TACE activity assay evidence that is used in a manual assertion.
surface plasmon resonance evidence used in manual assertion
A type of surface plasmon resonance evidence that is used in a manual assertion.
restriction landmark genomic scanning evidence used in manual assertion
A type of restriction landmark genome scanning evidence that is used in a manual assertion.
resonant mirror biosensor evidence used in manual assertion
A type of resonant mirror biosensor evidence that is used in a manual assertion.
high-performance liquid chromatography evidence used in manual assertion
A type of high-performance liquid chromatography evidence that is used in a manual assertion.
ectopic expression evidence used in manual assertion
A type of ectopic expression evidence that is used in a manual assertion.
alkaline phosphatase reporter gene assay evidence
A type of reporter gene assay evidence based on the fusion of selected genes with the phoA gene to express alkaline phosphatase in periplasmic space for protein tracing.
Alkaline phosphatase reporter assay produces a hybrid protein with alkaline phosphatase activity following transportation across the cellular membrane.
Secreted Embryonic Alkaline Phosphatase reporter assay
beta-galactosidase reporter gene assay evidence
A type of reporter gene assay evidence based on the fusion of the lacZ gene to a specific promoter for the expression of beta-galactosidase which will appear blue when grown on a X-gal medium.
The assay is often performed using a plasmid borne construction on a lacZ strain.
chloramphenicol acetyltransferase reporter gene assay evidence
A type of reporter gene assay evidence based on the fusion of the CAT gene to a specific promoter for the expression of chloramphenicol acetyltransferase which confers resistance to the chloramphenicol antibiotic.
The amount of acetylated chloramphenicol is directly proportional to the amount of CAT enzyme present.
beta-glucuronidase reporter gene assay evidence
A type of reporter gene assay evidence where the beta-glucuronidase enzyme from Escherichia coli is used as the reporter to transform non-fluorescent substrates into fluorescents for detection.
A type of reporter gene assay evidence where luciferase, an oxidative enzyme, is used as the reporter to detect a gene product with bioluminescence.
chromatin immunoprecipitation- exonuclease evidence
A type of chromatin immunoprecipitation evidence that uses gama-exonuclease to digest TF-unbound DNA after ChIP for the identification of transcription factor binding site locations with high-resolution data.
electrophoretic mobility shift assay evidence used in manual assertion
A type of electrophoretic mobility shift that is used in a manual assertion.
reverse transcription polymerase chain reaction evidence used in manual assertion
A type of reverse transcription polymerase chain reaction evidence that is used in a manual assertion.
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.
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.
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.
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.
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.
genomic systematic evolution of ligands by exponential amplification evidence
A type of systematic evolution of ligands by exponential amplification evidence based on a restricted genomic DNA library to identify naturally occurring genomic aptamers and RNA-protein interaction networks with RNA-binding protein as bait and high-throughput sequencing.
The reported sequences should always be verified for presence in the genome sequence.
heteronuclear single quantum coherence spectroscopy evidence
A type of nuclear magnetic resonance spectroscopy evidence based on two-dimensional NMR for elucidation of the chemical structure of an isolated or synthesized chemical compound where the characteristic transfer magnetization of a proton to a nitrogen or carbon isotope is monitored by NMR, generating a specific peak in the spectrum.
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.
methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence
A type of nucleic acid binding evidence where the synthetic molecule methidiumpropyl-EDTA (MPE) is used to cleave ligand-protected DNA, followed by analysis of the restriction fragments to generate a footprint (i.e. size and location) of small molecule binding sites on the DNA.
Methidiumpropyl-EDTA Fe(II) footprinting
copper-phenanthroline footprinting evidence
A type of nucleic acid binding evidence where nucleic acid that has been bound to protein is cleaved with 1,10-phenanthroline-copper complex resulting in a high-resolution footprint of sequence-specific protein-DNA contacts.
green fluorescent protein reporter gene assay evidence
A type of reporter gene assay evidence based on the fusion of select genes with the green fluorescent protein (GFP) gene for detection with bioluminescence of the gene product when exposed to blue ultraviolet light.
green fluorescent protein promoter fusion
glutathione S-transferase pull-down assay evidence
A type of protein binding evidence where a gene is fused with the GST gene and the resulting recombinant bait protein is captured on an immobilized Glutathione affinity ligand and incubated with prey protein to identify and characterize protein-protein interactions.
The recombinant protein can also be eluted following the pull-down and analyzed further with qPCR or sequencing.
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.
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.
The most commonly used radiolabel is 32P.
rapid amplification of cDNA ends polymerase chain reaction evidence
A type of polymerase chain reaction evidence where a mRNA primer is used for RT-PCR and terminal deoxynucleotidyl transferase (TdT) is used to add identical nucleotides to the 3' end of the cDNA after which PCR with a different primer and TdT-oligomer are performed in the other sense to obtain the full length sequence of a RNA transcript.
RACE PCR is frequently used to verify transcription start sites relevant to the function of transcription factor binding sites such as repression.
A type of nucleotide sequencing assay evidence where RNA is extracted from a cell, reverse transcribed to cDNA for a snapshot of an organism's transcriptome with precise measurement of transcript levels and their isoforms.
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.
A type of crystallography evidence where a purified sample at high concentration is crystallised and the crystals are exposed to an x ray beam to obtain three dimensional molecular structure of proteins and biological macromolecules.
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.
DNA adenine methyltransferase identification evidence
A type of affinity evidence used to identify DNA binding sites in eukaryotes where Escherichia coli DNA adenine methyltransferase (Dam) is fused to a transcription factor, co-factor, chromatin-associated protein, or nuclear-associated protein, followed by a methyl-dependent PCR to localize methyltransferase in the region of the binding site.
The methylation tag is detected with methylation-sensitive restriction enzymes, DpnI and DpnII.
isothermal titration calorimetry evidence
A type of affinity evidence where the absorbed or released heat of a biomolecular binding event is directly measured in a reference cell and sample cell after the addition of a ligand using a microcalorimeter for a complete thermodynamic profile of the molecular interaction.
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)).
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.
premethylation interference footprinting evidence
A type of nucleic acid binding evidence used to identify protein binding sites on the DNA molecule where multiple copies of a DNA fragment containing a putative TF-binding site are randomly methylated with dimethyl sulfate (DMS) and cleaved at the methyl group, followed by separating the cleavage products on a denaturing electrophoresis gel.
A type of inference from background scientific knowledge used in manual assertion where a visual inspection of promoter region is made to identify putative binding sites.
ferric uptake regulator titration assay evidence
A type of reporter gene assay evidence used to locate and isolate Fur sites where a plasmid library is created and cloned into a cell line with a ferric uptake regulator (Fur)-repressed reporter and the Fur protein is titrated away from its binding site on the reporter, after which the cell is isolated and plasmid extracted for further sequence analysis.
DNA synthesis cell proliferation assay evidence
metabolic cell proliferation assay evidence
cell proliferation marker detection assay evidence
in vivo polyADP-ribosylation assay evidence
A type of in vivo assay evidence where ADP-ribosylated residues in proteins are detected in cells in vivo.
in vivo polyADP-ribosylation assay evidence used in manual assertion
A type of in vivo polyADP-ribosylation assay evidence that is used in a manual assertion.
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.
two-dimensional polyacrylamide gel electrophoresis evidence
A type of gel electrophoresis evidence that involves one dimension electrophoresis where biomolecules are electrophoresed on a low percentage polyacrylamide gel to be separated in proportion to their mass or isoelectric point, followed by high voltage electrophoresis on a higher percentage gel in the presence of ethidium bromide to alter non-linear molecular shape.
Two-dimensional polyacrylamide gel electrophoresis is commonly employed to establish a proteome for an organism and demonstrate expression changes.
regular expression motif search evidence
A type of motif similarity evidence where the motif, a local alignment of sequences, is represented by a regular expression, which captures the variability of nucleotides at each position in a discrete form and can then be used to search genetic sequences by identifying matches to the regular expression.
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).
interferometric reflectance imaging sensor evidence
A type of molecule detection assay evidence based on changes in surface-reflected light due to ligand binding on the surface of a semi-transparent substrate to detect proteins, DNA, and other biological material in a multiplexed, high-throughput microarray format without labels.
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.
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.
DNA dot blot assay evidence used in manual assertion
A type of DNA dot blot assay evidence that is used in a manual assertion.
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.
The mRNA extraction is performed in induced and non-induced cells and reverse transcribed with different fluorophore labeling for controls and experiment. Fluorescence is measured at two different wavelengths and the ratio between the two fluorescence intensities corresponds to the induction level.
DNA microarray evidence used in manual assertion
A type of DNA microarray evidence that is used in a manual assertion.
matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence
A type of protein detection assay evidence where soft ionization is used for the analysis of biomolecules for mass determination in a three step process of plate preparation, radiation, and ionization with high throughput technology.
MALDI-TOF MS is commonly used for protein identification in constructing a proteome where protein fingerprints obtained by microbial cells are compared with a database of reference spectra by means of various algorithms integrated in systems recently made commercially available.
matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence used in manual assertion
A type of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence that is used in a manual assertion.
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.
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.
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.
Random mutagenesis is not often used in TF-binding site determination; however, it is sometimes used to investigate the effect of mutations in TF binding domains in conjunction with expression assays. Random mutations can also be introduced via chemicals, error-prone PCR (EP-PCR), degenerate oligonucleotides-Pfu(DOP), UV irradiation, mutator strains, nucleotide analogs, or DNA recombination.
random mutagenesis evidence used in manual assertion
A type of random mutagenesis evidence that is used in a manual assertion.
A type of multiple sequence alignment evidence based on a set of algorithms that infer over-represented motifs from a set of biological sequences returning one or more local multiple sequence alignment defining the inferred motifs.
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).
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.
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.
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'.
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).
comparative genomics motif search evidence
A type of motif similarity evidence based on comparative genomics which uses a search method to scan a set of genomes for instances of a specific motif, and then applies a comparative criterion to analyze the collective strength of these predictions, based on the assumption that functional instances of the motif will be preserved by natural selection and their prediction will therefore be consistent across genomes.
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.
machine learning prediction of motif instance evidence
A type of match to sequence model evidence which captures the application of a broad suite of supervised and unsupervised machine learning algorithms trained on known motif instances and applied to the prediction of novel putative instances of a motif in a set of biological sequences.
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).
position-specific scoring matrix motif search evidence
A type of motif similarity evidence where the motif is represented by a position-specific frequency matrix (PSFM) that specifies the frequency of each base at each position of the motif, from which a position-specific scoring matrix (PSSM) can be derived under the framework of a log-likelihood ratio providing a scoring system based on the likelihood of a sequence given the motif, versus a genomic-frequency based null hypothesis.
This technique is used to predict transcription factor binding sites in gene promoter regions by using a position weight matrix approach. (PMID: 15604457).
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.
computationally derived logical inference
computationally derived logical inference used in automatic assertion
computationally derived logical inference from automatic assertion used in automatic assertion
computationally derived logical inference from manual assertion used in automatic assertion
biological system reconstruction evidence by experimental evidence from single species used in manual assertion
A type of biological system reconstruction evidence by experimental evidence from single species that is used in a manual assertion.
Processes, pathways and complexes shown by a single experiment should not be annotated with this term but with ECO:0000353 or a child thereof.
biological system reconstruction evidence by experimental evidence from mixed species used in manual assertion
A type of biological system reconstruction evidence by experimental evidence from mixed species that is used in a manual assertion.
Inference is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. The evidence may originate from a combination of several experiments.
biological system reconstruction evidence based on orthology evidence used in manual assertion
A type of biological system reconstruction evidence based on orthology evidence that is used in a manual assertion.
biological system reconstruction evidence based on orthology evidence
A type of biological system reconstruction evidence based on homology evidence where the evidence is inferred by orthology from an existing experimentally supported model to a process, pathway or complex in another species.
Inference is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. Evidence may originate from a combination of several experiments.
biological system reconstruction based on paralogy evidence used in manual assertion
A type of biological system reconstruction evidence based on paralogy evidence that is used in a manual assertion.
biological system reconstruction evidence based on inference from background scientific knowledge used in manual assertion
A type of biological system reconstruction evidence based on inference from background scientific knowledge that is used in a manual assertion.
Functional studies or ligand binding evidence are often used for the reconstruction of biological systems. It does not provide physical interaction evidence but uses proxies such a ligand binding evidences to infer the presence or absence of the complex components.
biological system reconstruction evidence based on inference from background scientific knowledge
A type of biological system reconstruction based solely on background scientific knowledge of that biological system.
The available knowledge is usually a combination of partial or weak experimental evidence where either some components are missing or no physical interaction evidence can be found but the system is inferred by similarity to related systems in taxonomically-disparate organisms with experimental evidence. Functional studies or ligand binding evidence are often used for the reconstruction of biological systems. It does not provide physical interaction evidence but uses proxies such a ligand binding evidences to infer the presence or absence of the complex components.
biological system reconstruction evidence based on homology evidence
A type of biological system reconstruction where the evidence is inferred by homology based on conservation of sequence, function, and composition from an existing experimentally supported model to a process, pathway, or complex.
Inference may be based on paralogy or orthology of the genome-encoded components and is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. Evidence may originate from a combination of several experiments in the same or another species.
biological system reconstruction evidence based on paralogy evidence
A type of biological system reconstruction evidence based on homology evidence where the evidence is inferred by paralogy from an existing experimentally supported model to a process, pathway, or complex in the same species.
biological system reconstruction evidence by experimental evidence
A type of biological system reconstruction evidence that uses experimental evidence as support.
biological system reconstruction evidence by experimental evidence from mixed species
A type of biological system reconstruction evidence where the experimental evidence is derived by using a mix of species used in the same experiment.
biological system reconstruction evidence by experimental evidence from single species
A type of biological system reconstruction where the experimental evidence is derived by using multiple experiments in a single species.
A type of sequence alignment evidence where two sequences are aligned to identify regions of similarity that may indicate functional, structural and/or evolutionary relationships between two biological sequences (protein or nucleic acid).
A type of sequence alignment evidence where three or more biological sequences (protein or nucleic acid) of similar length are aligned to infer homology and the evolutionary relationships between the sequences studied.
multiple sequence alignment evidence used in manual assertion
A type of multiple sequence alignment evidence that is used in a manual assertion.
multiple sequence alignment evidence used in automatic assertion
A type of multiple sequence alignment evidence that is used in an automatic assertion.
motif discovery evidence used in manual assertion
A type of motif discovery evidence that is used in a manual assertion.
motif discovery evidence used in automatic assertion
A type of motif discovery evidence that is used in an automatic assertion.
pairwise sequence alignment evidence used in manual assertion
A type of pairwise sequence alignment evidence that is used in a manual assertion.
pairwise sequence alignment evidence used in automatic assertion
A type of pairwise sequence alignment evidence that is used in an automatic evidence.
A type of electrophysiology assay evidence that involves recording trace of the current (pA) going through the analyzed ion channels determined from voltage clamp current recording.
A type of electrophysiology assay evidence that involves measuring the amount of current (pA) going through the ion channels per unit of membrane.
A type of electrophysiology assay evidence that involves the measurement of the current that persists after the fast and slow inactivation of the analyzed channels.
steady state inactivation curve evidence
A type of electrophysiology assay evidence in which the amount of current remaining after a series of depolarization at different frequencies described as the normalized current related to the time course.
current clamp voltage recording evidence
A type of electrophysiology assay evidence that involves recording the change in membrane potential caused by applying specific current to the cell.
current clamp voltage recording protocol
whole-cell voltage clamp recording evidence
A type of electrophysiology assay evidence that involves direct measurement of ionic current across a membrane while controlling the membrane potential by maintaining the voltage.
whole-cell voltage clamp recording protocol
cell-attached single-channel recording evidence
A type of electrophysiology assay evidence that involves isolation of a patch of membrane electrically from the external solution and to record current flowing into the patch and this is achieved by pressing a fire-polished glass pipette, which has been filled with a suitable electrolyte solution, against the surface of a cell and applying light suction.
cell-attached single-channel recording protocol
cell-detached inside-out single-channel recording evidence
A type of electrophysiology assay evidence that involves study of individual ion channels by gently pulling the patch of membrane away from the cell, and the patch remains attached to the pipette with its cytoplasmic surface exposed to the bathing solution.
cell-detached inside-out single-channel recording protocol
reconstituted bilayer single-channel patch recording evidence
A type of electrophysiology assay evidence that involves ion channel analysis by incorporating the ion channels into liposomes suitable for patch-clamping which allows isolation and study of a specific population of channels into that bilayer membrane.
reconstituted bilayer single-channel patch recording protocol
voltage clamp current recording evidence
A type of electrophysiology assay evidence that involves recording membrane potential by controlling the membrane voltage and measuring the transmembrane current required to maintain that voltage.
voltage clamp current recording protocol
electroencephalography recording evidence
A type of electrophysiology assay evidence that involves recording the electrical activity of the brain by means of electrodes placed on the surface of the head.
electroencephalography recording protocol
A type of microscopy evidence where the images are taken with a higher resolution than the diffraction limit that help in studying nanoscopic sub-cellular structures.
immunogold labelling evidence used in manual assertion
A type of immunogold labelling evidence that is used in a manual assertion.
flow cytometry evidence used in manual assertion
A type of flow cytometry evidence that is used in a manual assertion.
enzyme-linked immunoabsorbent assay evidence used in manual assertion
A type of enzyme-linked immunoabsorbent assay evidence that is used in a manual assertion.
cell-detached outside-out single-channel recording evidence
A type of electrophysiology assay evidence where a part of cellular membrane is detached from the cell and whose external face is exposed to the extracellular medium which allows isolating and studying a single or at least a small number of channels into that fragment (patch).
cut-open oocyte voltage clamp recording evidence
A type of electrophysiology assay evidence that involves inserting the oocyte in a chamber that separates the surface into 3 regions where the top portion of the oocyte membrane is the region that is clamped from which currents are actually recorded while the bottom portion is the region of the oocyte that is cut-open, making it possible to inject current intracellularly through a low resistance pathway.
macropatch voltage clamp recording evidence
A type of electrophysiology assay evidence where recording is done on a fragment of the cell membrane (attached to or detached from the cell) using a large tip diameter pipette that allows isolating and studying a small number of channels into that fragment (patch).
high throughput mass spectrometry evidence
A type of mass spectrometry evidence where mass-to-charge ratio (m/z) of gas-phase ions is measured which is used to identify and quantify molecules in complex solutions within the framework of high throughput studies.
There are significant differences in data analysis and data evaluation if to compare a HTP mass-spec and a regular mass-spec. The regular mass spec method is quite a reliable technique for identifying a protein molecular weight and analysing its post-modifications, other mass-spec applications might require the additional quality controls and more stringent data evaluation. More complex sample mixture is processed, more quality questions should be addressed, such as a sample contamination and sensitivity of the mass spectrometer while using HTP mass-spec. For HTP mass-spec, the analysis of the small data sets allows to manually assign the spectra to proteins or peptides, but for large data sets only the statistical tools can be used instead.
high throughput mass spectrometry evidence used in manual assertion
A type of high throughput mass spectrometry evidence that is used in a manual assertion.
A type of microscopy evidence where sharp images are taken by excluding most of the light from the specimen that is not from the microscope's focal plane, thus allowing better contrast and less haze, which makes it possible to build three-dimensional reconstructions of a volume of the specimen by assembling a series of thin slices taken along the vertical axis.
A type of microscopy evidence where imaging of a thin cell or a tissue specimen is performed by full aperture emission of light gathered by the microscope's objective, which maximizes the recorded signal and simultaneously minimizes the required exposure times.
confocal microscopy evidence used in manual assertion
A type confocal microscopy evidence that is used in a manual assertion.
wide-field microscopy evidence used in manual assertion
A type of wide-field microscopy evidence that is used in a manual assertion.
immunogold labelling electron microscopy assay evidence
A type of immunogold labelling evidence where electron microscopy technique is used to detect the location of the antibodies labeled with colloidal gold particles.
immunogold labelling electron microscopy assay evidence used in manual assertion
A type of immunogold labelling electron microscopy assay evidence that is used in a manual assertion.
A type of direct assay evidence that involves the use of antibodies to detect biomolecules.
immunoperoxidase immunolocalization evidence
A type of immunolocalization evidence involving enzymatic detection of a peroxidase tagged antibody.
immunoperoxidase immunolocalization evidence used in manual assertion
A type of immunoperoxidase immunolocalization evidence that is used in a manual assertion.
immunoperoxidase immunolocalization electron microscopy evidence
A type of immunoperoxidase immunolocalization evidence where electron microscopy technique is used for enzymatic detection of a peroxidase tagged antibody.
Immunoperoxidase labelling electron microscopy
immunoperoxidase immunolocalization electron microscopy evidence used in manual assertion
A type of immunoperoxidase immunolocalization electron microscopy evidence that is used in a manual assertion.
wide-field fluorescence microscopy evidence
A type of wide-field microscopy evidence where pure white and ultraviolet light are produced by a mercury lamp, passed through an optical filter (excitation filter), and directed to a sample via a dichroic mirror, followed by detection of the fluorescent light by a camera after it passes through an emission filter.
The optical filter is used to select the wavelength of excitation light. The detection camera is typically a CCD camera. Both topographical and dynamic information of a sample are obtained.
immunofluorescence wide-field microscopy evidence
A type of wide-field fluorescence microscopy evidence where fluorescently tagged antibodies are imaged that are used to bind to their antigens.
immunofluorescence confocal microscopy evidence
A type of confocal microscopy evidence where light passes through immunofluorescent-stained tissue sections or cells and then the emitted light passes through the dichroic mirror and is focused onto the pinhole for subsequent detection.
This allows visualization of sub cellular distribution of biomolecules of interest.
immunofluorescence confocal microscopy evidence used in manual assertion
A type of immunofluorescence confocal microscopy evidence that is used in a manual assertion.
protein expression level evidence based on western blot
A type of protein expression level evidence where the level of expression of a protein is determined in a cell or tissue extract by western blot technique.
A type of mass spectrometry evidence where one or more protein analyses are performed.
A type of oligonucleotide microarray evidence that detects binding of a tagged protein to an array of oligonucleotide probes representing potential binding sites.
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.
computational image-based phenotypic evidence
A type of phenotypic evidence based on unsupervised computational examination of a visual mutant phenotype such as abnormalities in organism morphology.