org.Hs.egGO {org.Hs.eg.db} | R Documentation |
org.Hs.egGO is an R object that provides mappings between entrez gene identifiers and the GO identifiers that they are directly associated with.
Each Entrez Gene identifier is mapped to a list of lists. The names on the outer list are GO identifiers. Each inner list consists of three named elements: GOID, Ontology, and Evidence.
The GOID element matches the GO identifier named in the outer list and is included for convenience when processing the data using 'lapply'.
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 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
Mappings between entrez gene identifiers and GO information were obtained through their mappings to Entrez Gene identifiers. NAs are assigned to entrez gene identifiers that can not be mapped to any Gene Ontology information. Mappings between Gene Ontology identifiers an Gene Ontology terms and other information are available in a separate data package named GO.
Mappings were based on data provided by: Gene Ontology ( ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest ) on 200803
For the reverse map GO2EG, each GO term maps to a named vector of entrez gene identifiers. A GO identifier may be mapped to the same entrez gene identifier more than once but the evidence code can be different. Mappings between Gene Ontology identifiers and Gene Ontology terms and other information are available in a separate data package named GO.
ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
x <- org.Hs.egGO # Get the entrez gene identifiers that are mapped to a GO ID mapped_genes <- mappedkeys(x) # Convert to a list xx <- as.list(x[mapped_genes]) if(length(xx) > 0) { # Try the first one got <- xx[[1]] got[[1]][["GOID"]] got[[1]][["Ontology"]] got[[1]][["Evidence"]] } # For the reverse map: # Convert to a list xx <- as.list(org.Hs.egGO2EG) if(length(xx) > 0){ # Gets the entrez gene ids for the top 2nd and 3nd GO identifiers goids <- xx[2:3] # Gets the entrez gene ids for the first element of goids goids[[1]] # Evidence code for the mappings names(goids[[1]]) }