gahgu95cGO {gahgu95c} | R Documentation

## Map between custom probeset IDs and Gene Ontology (GO)

### Description

gahgu95cGO is an R environment that provides mappings between custom probeset identifiers and the GO identifiers that they are directly associated with.

### Details

Each custom probeset identifier is mapped to a list of lists. The names on the outer list are GO identifiers. Each inner list contains of five named elements: GOID, Ontology, Term, Evidence and PMIDS.

The GOID element matches the GO identifier named in the outer list.

The Ontology element indicates which of the three Gene Ontology categories this identifier belongs to. The categories are biological process (BP), cellular component (CC), and molecular function (MF).

The Term element indicates the name of GO cathegory correspoding to the GO identifier named in the outer list.

The Evidence element contains a code indicating what kind of evidence supports the association of the GO identifier to the Entrez Gene 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

The PMIDS element indicates the Pubmed IDs of references in the literature, if relevant, obtained from EntrezGene.

NAs are assigned to probe identifiers that can not be mapped to any Gene Ontology information. Other information concerning Gene Ontology classification are available in a separate data package named GO.

Mappings were based on data provided by:

GeneCards database - www.genecards.org

Package built Tue Feb 26 00:16:28 2008

### References

www.genecards.org

### Examples

        # Convert to a list
        xx <- as.list(gahgu95cGO)
        # Remove all the NAs
        xx <- xx[!is.na(xx)]
        if(length(xx) > 0){
                # Try the first one
                got <- xx[[1]]
                got[[1]][["GOID"]]
                got[[1]][["Ontology"]]
                got[[1]][["Evidence"]]

        }

[Package gahgu95c version 1.4.0 Index]