hgu133aGO {hgu133a}R Documentation

Annotation of probe ids by Gene Ontology information

Description

hgu133aGO mappes probe ids to Gene Ontology information including GO ids, evidence codes, and GO categories based on data collected from LocusLink and Gene Ontology consortium for the genes represented by the probe ids.

Details

This is an environment object with key and value pairs. Keys are probe ids and values are lists containing one (mapped to none or one set of GO information) or more (mapped to more than one sets of GO information) elements. When a probe id is mapped to at lest one set of GO information, each element of the list contains a sub list of three elements named "GOID", "Ontology", and "Evidence". Values for element "GOID" gives the Gene Ontology identifiers the key probe ids corresponding to. Values for element "Ontology" can be an abbreviation of MF (mocular function), BP (biological process), or CC (cellular component) for the GO category the GO id belongs to. Values for element "Evidence" contain an evidence code indicating what kind of evidence is found to support the association of the GO id to the key probe id. 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

Mappings between probe ids and GO information were obtained through their mappings to LocusLink ids. NA is assigned to probe identifiers that can not be mapped to any Gene Ontology information. 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 built: March 3, 2004. ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.ga

Gene Ontology Consortium built: 2004-02-01.http://www.godatabase.org/dev/database/archive/2004-02-01/go_200402-termdb.xml.gz

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(hgu133aGO)
    # Remove all the NAs
    xx <- xx[!is.na(xx)]
    if(length(xx) > 0){
            # Try the firest one
            got <- xx[[1]]           
            got[[1]][["GOID"]]
            got[[1]][["Ontology"]]
            got[[1]][["Evidence"]]

    }

[Package hgu133a version 1.5.1 Index]