Annotations of Mouse Entrez Genes (EG) by Disease Ontology (DO).

Description

An R object that contains associations between Disease Ontology terms and Mouse Entrez Genes. This data is first prepared based on http://sourceforge.net/p/diseaseontology/code/HEAD/tree/trunk/HumanDO.obo?format=raw and http://dga.nubic.northwestern.edu/ajax/Download.ajax.php, which results in annotations of Human Entrez Genes. Then, these annotations are transferred to Mouse Entrez Genes based on ftp://anonymous@ftp.ncbi.nih.gov/pub/HomoloGene/build67/homologene.data.

Usage

org.Mm.egDO <- dRDataLoader(RData = "org.Mm.egDO")

Value

an object of class "GS", a list with following components:

  • set_info: a matrix of nSet X 4 containing gene set information, where nSet is the number of gene sets (i.e. DO terms), and the 4 columns are "setID" (i.e. "Term ID"), "name" (i.e. "Term Name"), "namespace" and "distance"
  • gs: a list of gene sets, each storing gene members thereof. Always, gene sets are identified by "setID" and gene members identified by "Entrez ID"

References

Schriml et al. (2012) Disease Ontology: a backbone for disease semantic integration. Nucleic Acids Res, 40:D940-946.

Peng et al. (2012) The Disease and Gene Annotations (DGA): an annotation resource for human disease. Nucleic Acids Res, 41:D553-560.

Sayers et al. (2011) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res, 39:D38-51.

Examples

org.Mm.egDO <- dRDataLoader(RData='org.Mm.egDO')
'org.Mm.egDO' (from https://github.com/hfang-bristol/RDataCentre/blob/master/dnet/1.0.7/org.Mm.egDO.RData?raw=true) has been loaded into the working environment (at 2017-03-27 20:02:20)
names(org.Mm.egDO)
[1] "gs" "set_info"