hgu133aGO2PROBE {hgu133a}R Documentation

Mappings between GO identifiers and probe identifiers representing genes that are directly associated with the GO ids

Description

The Gene Ontology (GO) Consortium maintains a controlled vocabulary of defined terms to describe gene products. Each of the terms is assigned a GO id that can be associated with a group of genes. hgu133aGO2PROBE maps each GO id to the probe identifiers representing genes that are associated with the GO ids

Details

GO terminologies are presented as a directed acyclic graph with root nodes having more general terms than their children nodes. hgu133aGO2PROBE only maps GO ids to probe ids associated with nodes specified by the GO ids but not their children nodes. The mapped probe ids are named vectors. Names of the vectors are the evidence codes indicating what kind of evidence is found to support the association between GO ids and genes.

The evidence codes 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 LocusLink:ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz. Built: September 15, 2004.

Package built Wed Sep 15 18:48:08 2004

References

ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz

Examples

    # Convert to a list
    xx <- as.list(hgu133aGO2PROBE)
    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 hgu133a version 1.6.5 Index]