rae230aGO2ALLPROBES {rae230a}R Documentation

Mappings between GO identifiers and all the probe idifiers representing genes 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 directly or indirectly through the children GO ids of the GO id. rae230aGO2ALLPROBES maps GO ids to genes (represented by probe identifiers) that are directly or indirectly mapped to the GO ids by traversing the GO tree.

Details

GO terminologies are presented as a directed acyclic graph with root nodes having more general terms than their children nodes. Therefore, a GO id can be mapped to genes corresponding to the term of that particular GO id as well as genes corresponding to the terms of all the children GO ids.

rae230aGO2ALLPROBES maps a GO id to all the probe ids representing genes mapped by traversing the GO tree. 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 and Gene Ontology terms and other information are available in a separate data package named GO.

Mappings were based on data provided:

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

Package built Thu Sep 16 09:31:44 2004

References

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

Examples

    # Convert to a list
    xx <- as.list(rae230aGO2ALLPROBES)
    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 rae230a version 1.6.5 Index]