gahgu133plus2GO {gahgu133plus2} | R Documentation |
gahgu133plus2GO is an R environment that provides mappings between custom probeset identifiers and the GO identifiers that they are directly associated with.
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 Mon Feb 25 23:53:26 2008
# Convert to a list xx <- as.list(gahgu133plus2GO) # 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"]] }