egSymb: Mapping between Entrez Gene IDs and official symbols

In gage: Generally Applicable Gene-set Enrichment for Pathway Analysis

Description

A two column matrix listing the Entrez IDs and official symbols for all currently known human genes.

Usage

data(egSymb)

Format

The format is: chr [1:40784, 1:2] "1" "10" "100" "1000" ... - attr(*, "dimnames")=List of 2 ..$ : NULL ..$ : chr [1:2] "eg" "sym"

Details

This mapping matrix is commonly used together with functions eg2sym and sym2eg. Check the examples below.

Source

This mapping data matrix were compiled using the gene data from NCBI Entrez Gene database.

Similar information can also be derived from Bioconductor package org.Hs.eg.db. Please check the package for more information.

References

Entrez Gene <URL: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene>

Examples

#genes in gse16873 was label by Entrez IDs
data(gse16873)
head(rownames(gse16873))
#may convert the gene IDs to official symbols
gse16873.sym<-gse16873
data(egSymb)
rownames(gse16873.sym)<-eg2sym(rownames(gse16873.sym))
head(rownames(gse16873.sym))

#convert kegg.gs correspondingly
data(kegg.gs)
kegg.gs.sym<-lapply(kegg.gs, eg2sym)
lapply(kegg.gs.sym[1:3],head)
#GAGE analysis with the converted data
cn=colnames(gse16873)
hn=grep('HN',cn, ignore.case =TRUE)
dcis=grep('DCIS',cn, ignore.case =TRUE)
gse16873.kegg.p2 <- gage(gse16873.sym, gsets = kegg.gs.sym,
    ref = hn, samp = dcis)

Example output

[1] "10000"     "10001"     "10002"     "10003"     "100048912" "10004"    
[1] "AKT3"     "MED6"     "NR2E3"    "NAALAD2"  "CDKN2BAS" "NAALADL1"
$`hsa00010 Glycolysis / Gluconeogenesis`
[1] "AKR1A1" "ADH1A"  "ADH1B"  "ADH1C"  "ADH4"   "ADH5"  

$`hsa00020 Citrate cycle (TCA cycle)`
[1] "CS"   "DLAT" "DLD"  "DLST" "FH"   "IDH1"

$`hsa00030 Pentose phosphate pathway`
[1] "FBP1"    "PRPS1L1" "ALDOA"   "ALDOB"   "RPIA"    "ALDOC"  

gage documentation built on Dec. 13, 2020, 2:01 a.m.