Annotations of Human Entrez Genes (EG) by Mammalian Phenotype (MP).

Description

An R object that contains associations between Mammalian Phenotype terms and Human Entrez Genes. This data is prepared based on ftp://ftp.informatics.jax.org/pub/reports/MPheno_OBO.ontology and ftp://ftp.informatics.jax.org/pub/reports/MGI_PhenoGenoMP.rpt, which results in annotations of Mouse Entrez Genes. Then, these annotations are transferred to Human Entrez Genes based on ftp://anonymous@ftp.ncbi.nih.gov/pub/HomoloGene/build67/homologene.data.

Usage

org.Hs.egMP <- dRDataLoader(RData = "org.Hs.egMP")

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. MP 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

Smith et al. (2009) The Mammalian Phenotype Ontology: enabling robust annotation and comparative analysis. Wiley Interdiscip Rev Syst Biol Med, 1:390-399.

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

Examples

org.Hs.egMP <- dRDataLoader(RData='org.Hs.egMP')
'org.Hs.egMP' (from https://github.com/hfang-bristol/RDataCentre/blob/master/dnet/1.0.7/org.Hs.egMP.RData?raw=true) has been loaded into the working environment (at 2017-03-27 20:01:48)
names(org.Hs.egMP)
[1] "gs" "set_info"