Table 1 Gene Ontology evidence codes
From: Experimental-confirmation and functional-annotation of predicted proteins in the chicken genome
Code | Description | Example |
|---|---|---|
Direct experimental evidence codes | ||
IDA | Inferred from Direct Assay | enzyme assays |
| Â | Â | in vitro reconstitution |
| Â | Â | immunofluorescence |
| Â | Â | cell fractionation |
| Â | Â | physical interaction/binding assay |
IGI | Inferred from Genetic Interaction | "traditional" genetic interactions such as suppressors, synthetic lethals, etc. |
| Â | Â | functional complementation |
| Â | Â | rescue experiments |
| Â | Â | inference about one gene drawn from the phenotype of a mutation in a different gene |
IMP | Inferred from Mutant Phenotype | any gene mutation/knockout |
| Â | Â | overexpression/ectopic expression of wild-type or mutant genes |
| Â | Â | anti-sense experiments |
| Â | Â | RNAi experiments |
| Â | Â | specific protein inhibitors |
| Â | Â | polymorphism or allelic variation |
IPI | Inferred from Physical Interaction | 2-hybrid interactions |
| Â | Â | co-purification |
| Â | Â | co-immunoprecipitation |
| Â | Â | ion/protein binding experiments |
IEP | Inferred from Expression Pattern | transcript levels (e.g. Northerns, microarray data) |
| Â | Â | protein levels (e.g. Western blots) |
Indirect evidence codes | ||
NAS | Non-traceable Author Statement | Database entries that don't cite a paper |
TAS | Traceable Author Statement | original experiments are traceable through that article |
IC | Inferred by Curator | inferred by a curator from other GO annotations |
IGC | Inferred from Genomic Context | operon structure |
| Â | Â | syntenic regions |
| Â | Â | pathway analysis |
| Â | Â | genome-scale analysis of processes |
NR | Not Recorded | used for annotations done before curators began tracking evidence types, not used for new annotations |
ND | No biological Data available | "unknown" molecular function, biological process, cellular component |
IEA | Inferred from Electronic Annotation | "hits" in sequence similarity searches, if they have not been reviewed by curators; transferred from database records, if not reviewed by curators |
ISS | Inferred from Sequence or Structural Similarity | sequence similarity (homologue of/most closely related to) |
| Â | Â | recognized domains |
| Â | Â | structural similarity |
| Â | Â | Southern blotting |
| Â | Â | protein features, predicted or observed (e.g. hydrophobicity, sequence composition) |
RCA | Inferred from Reviewed Computational Analysis | predictions based on large-scale experiments (e.g. genome-wide two-hybrid) |
| Â | Â | predictions based on integration of large-scale datasets of several types |
| Â | Â | text-based computation (e.g. text mining) |