hgu95av2GO2PROBE {hgu95av2}R Documentation

Map Between Gene Ontology (GO) and Manufacturer Identifiers

Description

hgu95av2GO2PROBE is an R environment that provides mappings between GO ids and 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 probe id more than once but the evidence code can be different. Mappings between Gene Ontology ids an Gene Ontology terms and other information are available in a separate data package named GO.

Mappings were based on data provided by:

LocusLink 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(hgu95av2GO2PROBE)
    if(length(xx) > 0){
        # Gets the probe ids for the top 2nd and 3nd GO ids
        goids <- xx[2:3]
        # Gets 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]