hgu95av2GO2ALLPROBES {hgu95av2}R Documentation

Map Between Gene Ontology (GO) Identifiers and all Manufacturer Identifiers

Description

hgu95av2GO2ALLPROBES is an R environment that provides mappings between a given GO id and all manufacturer ids.

Details

Each GO term maps to a named vector of manufacturer ids. The name associated with each manufacturer id corresponds to the evidence code for that GO id. The evidence code indicates what kind of evidence supports the association between the GO and Entrez Gene ids. Evidence codes currently 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

A GO id may be mapped to the same manufacturer id more than once but the evidence code can be different. Mappings between Gene Ontology ids and Gene Ontology terms and other information are available in a separate data package named GO.

Mappings were based on data provided:

Entrez Gene:http://gopher5/compbio/annotationSourceData/ftp.ncbi.nlm.nih.gov/gene/DATA/. Built: Source data downloaded from Entrez Gene on Tue Oct 4 21:15:59 2005

Package built Tue Oct 4 21:31:35 2005

References

ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/

Examples

    # Convert to a list
    xx <- as.list(hgu95av2GO2ALLPROBES)
    if(length(xx) > 0){
        # Gets the probe ids for the top 2nd and 3nd GO ids
        goids <- xx[2:3]
        # Gets all the probe ids for the first element of goids
        goids[[1]]
        # Evidence code for the mappings
        names(goids[[1]])
    }

[Package hgu95av2 version 1.10.0 Index]