Supplementary Material

Tian L, Greenberg SA, Kong SW, Altschuler J, Kohane IS, & Park PJ , Proc Natl Acad Sci USA, 2005

R package: sigPathway

Implemented by Weil R. Lai

The latest version is available from the Bioconductor website: http://www.bioconductor.org/packages/bioc/html/sigPathway.html

A "Package" is a Windows binary file. For compiling on non-windows platforms, try"R CMD INSTALL sigPathway_1.1-4.tar.gz"

Expression Data

Gene sets (R object)

Click on the right mouse button and choose 'save link as' to download the files.

UPDATED:


• U74av2 (mouse), 7.7 MB
• U74av2 (mouse), 7.7 MB
• U430v2 (mouse), 7.0 MB
• U95av2 (human), 7.5 MB
• U133a (human), 7.5 MB
• U133plus2 (human), 7.2 MB

OLD:


• U74av2 (mouse), 23.6 MB
• U95av2 (human), 19.3 MB
• U133a (human), 20.6 MB

For other array types, Entrez Gene IDs can be used as identifiers: Genesets_EntrezGeneIDs (all species, 3MB)

How to create your own gene sets

########################################################################
## create_gene_sets_from_Bioconductor_annotations.R
## Weil Lai
## wlai@alum.mit.edu
## August 13, 2007
##
## This R script lets users convert human, mouse, or rat annotations
## from Bioconductor annotation packages to a "G" list, which is
## required for analyzing gene sets in sigPathway. Although the script
## looks a bit convoluted, it takes less than one minute to run the script
## on a Pentium M 1.86 Mhz computer.
##
## The values for egidDir, biocAnnot, and perhaps other variables will
## need to be changed so that the script will run properly. Please
## make sure the Bioconductor annotation package of interest has already
## been installed in R before running this script.
##
## I have tested this script for hgu133a, hgu95av2, hs25kresogen, rat2302,
## and mgu74av2. It should work for other human, mouse, and rat
## Bioconductor annotations. More details regarding the "G" list format
## can be found in the sigPathway vignette.
########################################################################

## "Genesets_EntrezGeneIDs.RData" is an R workspace containing Entrez Gene
## IDs corresponding to gene sets from GO, KEGG, and other pathway
## databases listed in the sigPathway vignette PDF. It can be found at
## http://www.chip.org/~ppark/Supplements/PNAS05/Genesets_EntrezGeneIDs.RData
##
## egidDir stands for the directory name where Genesets_EntrezGeneIDs.RData
## is located
egidDir <- "W:/sigPathway development/pathway lists/egids"
load(file.path(egidDir, "Genesets_EntrezGeneIDs.RData"))

## Give the Bioconductor annotation package name here
biocAnnot <- "rat2302"

## get Entrez Gene IDs for each "probe set" (Affymetrix terminology)
## on the array
library(biocAnnot, character.only = TRUE)
xx <- as.list(get(paste(biocAnnot, "ENTREZID", sep = "")))
xx <- xx[!is.na(xx)]
xx <- unlist(xx)

xxUnique <- unique(xx)

yy <- vector("list", length(xxUnique))

for(i in 1:length(yy))
yy[[i]] <- names(xx)[xx == xxUnique[i]]

## Match probe sets (by Entrez Gene IDs) to master gene list
zz <- vector("list", length(G.EGIDs))

for(i in 1:length(zz)) {
m <- match(G.EGIDs[[i]]$probes, xxUnique)
zz[[i]] <- unlist(yy[m])

if(i %% 1000 == 0)
cat("i = ", i, "\n", sep = "")
}

## Disregard gene sets that did not get represented on the array
idx <- which(sapply(zz, length) > 0)
G.biocAnnot <- G.EGIDs[idx]

for(i in 1:length(idx))
G.biocAnnot[[i]]$probes <- zz[[idx[i]]]

## Save mapped gene set to the directory specified in egidDir
save(G.biocAnnot, file = file.path(egidDir, "G_biocAnnot.RData"))

Please direct your questions to Peter J. Park.