GOALLENTREZID {GO} | R Documentation

## Annotation of GO identifiers by all the corresponding Entrez Gene identifiers

### Description

This is an R environment (hash table) mapping GO identifiers to all the Entrez Gene identifiers corresponding to the GO identifiers and its direct or indirect offspring. The direct or indirect offspring of a given GO identifier are the nodes that are directly linked to the node for the GO identifier or indirectly linked to the GO identifier through nodes that are linked to the GO identifier based on the directed acyclic graph defined by Gene Ontology Consortium

### Details

GO identifiers are Keys and the corresponding Entrez Gene identifiers are Values. Values are named vectors of length 1 or greater depending on whether a given GO identifier can be mapped to one or more Entrez Gene identifiers. Names for values are the evidence codes for the GO identifier (if an evidence code was provided by source data). The evidence codes that are in use include:

IMP - inferred from mutant phenotype

IGI - inferred from genetic interaction

IPI - inferred from physical interaction

ISS - inferred from sequence similarity

IDA - inferred from direct assay

IEP - inferred from expression pattern

IEA - inferred from electronic annotation

TAS - traceable author statement

NAS - non-traceable author statement

ND - no biological data available

IC - inferred by curator

NA is assigned to GO identifiers that can not be mapped to any Entrez Gene identifier at this time.

Mappings were based on data provided by:

Gene Ontology:ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest. Built: Build Information not available

Entrez Gene:ftp://ftp.ncbi.nlm.nih.gov/gene/DATA. Built: Source data downloaded from Entrez Gene on Wed Aug 29 09:09:16 2007

Package built: Wed Aug 29 09:09:17 2007

### References

http://www.geneontology.org/ and http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene

### Examples

            require("GO") || stop("GO unavailable")
            # Convert the environment object to a list
            xx <- as.list(GOALLENTREZID)
            # Remove GO identifiers that are not mapped to any Entrez Gene identifier
            xx <- xx[!is.na(xx)]
            if(length(xx) > 0){
                    # Get the Entrez Gene identifiers for the first two elents of xx
                    llids  <- xx[1:2]
                    # Get the evidence code llids
                    evds <- sapply(llids, names)
            }

[Package GO version 2.0.1 Index]