hgu133aGO2PROBE {hgu133a}R Documentation

Annotation of GO identifiers by probe ids corresponding to the GO ids

Description

A GO id can be associated with a group of genes directly. hgu133aGO2PROBE maps each GO id to the genes represented by probe ids that are directly associated with the GO id.

Details

hgu133aGO2PROBE is an environment object with key and value pairs. Keys are GO ids and values are the probe ids that are directly or associated with the GO ids. Values are vectors of length 1 or greater depending on whether a given GO id can be mapped to only one or more probe ids. Names for values are the evidence codes for the GO ids indicating what kind of evidence is found to support the association. 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

GO ids can not be mapped to any probe identifier are assigned a value of NA. 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 built: March 3, 2004. ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.ga.

Package built Wed Mar 3 16:27:29 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 1.5.1 Index]