hgu95av2GO {hgu95av2}R Documentation

Map between Manufacturer IDs and Gene Ontology (GO)

Description

hgu95av2GO is an R environment that provides mappings between manufacturer ids and GO ids.

Details

Each manufacturer id is mapped to a named vector of GO ids. The name associated with each GO id corresponds to the evidence code for that GO id. 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

Mappings between probe ids and GO information were obtained through their mappings to Entrez Gene ids. NAs are 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:

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

Gene Ontology:http://gopher5/compbio/annotationSourceData/archive.godatabase.org/latest//go_200509-termdb.rdf-xml.gz. Built: 200509

Package built Tue Oct 4 21:31:35 2005

Examples

    # Convert to a list
    xx <- as.list(hgu95av2GO)
    # 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 hgu95av2 version 1.10.0 Index]