Updated November 9, 2007
- Transcript levels or timing (e.g. Northerns, microarray data)
- Protein levels (e.g. Western blots)
The IEP evidence code covers cases where the annotation is inferred from the timing or location of expression of a gene, particularly when comparing a gene that is not yet characterized with the timing or location of expression of genes known to be involved in a particular process. Use this code with caution! It may be difficult to determine whether the expression pattern really indicates that a gene plays a role in a given process, so the IEP evidence code is usually used in conjunction with high level GO terms in the biological process ontology.
Note that we have not yet encountered any examples where we feel it is valid to make annotations to terms from the cellular component or molecular function ontologies on the basis of expression pattern data. Thus we currently recommend that this code be restricted to annotations to terms from the biological process ontology. Also, different annotating groups use different identifiers (gene or protein or gene_product) and no inference should be made as to whether an annotation made using IEP concerns a gene, RNA or protein.
Examples where the IEP evidence code should be used:
- genes upregulated during a stress condition may be annotated to the process of stress response (for example, heat shock proteins)
- genes selectively expressed at specific developmental stages in specific organs may be annotated to xxx development
- PMID:10748035. Both mRNA and protein levels of Atp2a2 (SERCA2) are increased upon ER stress in a pattern highly similar to BiP, a well-characterized endoplasmic reticulum (ER) chaperone with a role in the ER stress response. Therefore Atp2a2 may be annotated to 'response to endoplasmic reticulum stress' with IEP.
- PMID:17627301. Primate IRF2BPL (EAP1) expression increases selectively at puberty in the hypothalamus, and IRF2BPL is expressed in neurons involved in the inhibitory and facilitatory control of reproduction. Ideally there should be additional support for a role of the gene product in the process. In this example, PMID: 17627301 shows that human IRF2BPL (EAP1) activates genes required for reproductive function, and represses inhibitory genes. Therefore primate IRF2BPL may be annotated to 'development of secondary female sexual characteristics' with IEP.
Examples where the IEP evidence code should not be used:
- Function and component annotations should not be made with IEP.
- Exogenous expression or overexpression of a gene should be not annotated using IEP; only the normal expression pattern should lead to an IEP annotation.
- Overexpression of a gene causing increased activity of an enzyme should be annotated to IDA or IMP (see IDA documentation)
- Overexpression (wild type or mutated) of a gene causing an abnormal phenotype should be annotated to IMP
- Exogenous expression of a gene and assaying of its function should be annotated to IDA (like a transcription factor)
- Binding assays with overexpressed proteins or exogenously expressed proteins should be annotated to IPI for protein binding or IDA for binding to other molecules.
- Observation of protein localization for a component annotation should be made using the IDA evidence code.
- Annotation to the molecular function term transcription factor activity where the experimental evidence is that introduction of the gene to be tested into an in vitro assay system leads to expression of the appropriate reporter gene. Annotate using the IDA evidence code.
- Annotation to a binding molecular function term, e.g. calmodulin binding, where the experiment was to screen an expression library (a library expressing various proteins) to identify which of the library proteins interact with a particular protein of interest. Annotate using the IPI evidence code with the accession number of to the interacting protein (or its corresponding gene) in the with/from field.
- Annotating an enzymatic function to a Molecular Function Term based on an overexpression experiment. Since this is not the normal expression pattern, the IEP code does not apply. IDA would be the appropriate evidence code for this annotation. Annotating guanylate cyclase 2f from rat (GC-F), to the Molecular Function term guanylate cyclase activity, based on the experimental result that over-production of GC-E and GC-F in COS cells resulted in production of or increase in of guanylyl cyclase activity (PMID:7831337). IDA would be the appropriate evidence code for this annotation.