Table 1

Gene Ontology evidence codes

Code

Description

Example

Direct experimental evidence codes

IDA

Inferred from Direct Assay

enzyme assays

in vitro reconstitution

immunofluorescence

cell fractionation

physical interaction/binding assay

IGI

Inferred from Genetic Interaction

"traditional" genetic interactions such as suppressors, synthetic lethals, etc.

functional complementation

rescue experiments

inference about one gene drawn from the phenotype of a mutation in a different gene

IMP

Inferred from Mutant Phenotype

any gene mutation/knockout

overexpression/ectopic expression of wild-type or mutant genes

anti-sense experiments

RNAi experiments

specific protein inhibitors

polymorphism or allelic variation

IPI

Inferred from Physical Interaction

2-hybrid interactions

co-purification

co-immunoprecipitation

ion/protein binding experiments

IEP

Inferred from Expression Pattern

transcript levels (e.g. Northerns, microarray data)

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

syntenic regions

pathway analysis

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)

recognized domains

structural similarity

Southern blotting

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)

predictions based on integration of large-scale datasets of several types

text-based computation (e.g. text mining)

Buza et al. BMC Genomics 2007 8:425   doi:10.1186/1471-2164-8-425