| 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. This mapping and its reverse mapping do NOT associate the child terms from the GO ontology with the gene. Only the directly evidenced terms are represented here.
org.Hs.egGO2ALLEGS is an R object that provides mappings between a given GO identifier and all of the Entrez Gene identifiers annotated at that GO term OR TO ONE OF IT'S CHILD NODES in the GO ontology. Thus, this mapping is much larger and more inclusive than org.Hs.egGO2EG.
If org.Hs.egGO is cast as a list, 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. Some of 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 more complete listing of evidence codes can be found at:
http://www.geneontology.org/GO.evidence.shtml
If org.Hs.egGO2ALLEGS or org.Hs.egGO2EG is cast as a list, each GO term maps to a named vector of entrez gene identifiers and evidence codes. 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.
Whenever any of these mappings are cast as a data.frame, all the results will be output in an appropriate tabular form.
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.
All mappings were based on data provided by: Gene Ontology ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/ With a date stamp from the source of: 2017-Nov01
For GO2ALL style mappings, the intention is to return all the genes that are the same kind of term as the parent term (based on the idea that they are more specific descriptions of the general term). However because of this intent, not all relationship types will be counted as offspring for this mapping. Only "is a" and "has a" style relationships indicate that the genes from the child terms would be the same kind of thing.
ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
AnnotationDb-class for use of
the select() interface.
## select() interface:
## Objects in this package can be accessed using the select() interface
## from the AnnotationDbi package. See ?select for details.
## Bimap interface:
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]])
}
# For org.Hs.egGO2ALLEGS
xx <- as.list(org.Hs.egGO2ALLEGS)
if(length(xx) > 0){
# Gets the Entrez Gene identifiers for the top 2nd and 3nd GO identifiers
goids <- xx[2:3]
# Gets all the Entrez Gene identifiers for the first element of goids
goids[[1]]
# Evidence code for the mappings
names(goids[[1]])
}