[BioC] runSPIA() in graphite package
array chip
arrayprofile at yahoo.com
Fri Feb 8 19:46:52 CET 2013
Hi all, I am using runSPIA() from graphite package to analyze a gene list against biocarta pathway database.
> library(graphite)
> prepareSPIA(biocarta, "biocartaEx")
> obj<-runSPIA(de=siggenes, all=allgenes, "biocartaEx")
where "siggenes" are a list of 1332 significant genes selected from "allgenes" (a list of 17138 genes). The running process verbose indicated a total of 178 pathways analyzed.
One of the pathways I am particularly interested is "estrogen responsive protein efp controls cell cycle and breast tumors growth":
> p <- biocarta[["estrogen responsive protein efp controls cell cycle and breast tumors growth"]]
> nodes(p)
[1] "CDKs" "Cyclin B1/2" "EntrezGene:2099" "EntrezGene:2810" "EntrezGene:57154" "EntrezGene:7157" "EntrezGene:7706" "ubiquitin"
And my siggenes contains 2 of genes involved in this pathway:
> siggenes[c('7706','2099')]
7706 2099
4.347012 -3.792425
So I would assume that runSPIA will examine this pathway during the calculation, but surprisingly I didn't see this particular way being examined. Here is the section of runSPIA() verbose output that started with "e":
Done pathway 42 : e2f1 destruction pathway..
Done pathway 43 : effects of calcineurin in kera..
Done pathway 44 : egf signaling pathway..
Done pathway 45 : endocytotic role of ndk phosph..
Done pathway 46 : epo signaling pathway..
Done pathway 47 : erk and pi-3 kinase are necess..
Done pathway 48 : erk1/erk2 mapk signaling pathw..
Done pathway 49 : eukaryotic protein translation..
Done pathway 50 : extrinsic prothrombin activati..
Can anyone tell me why runSPIA() missed this pathway? Attached are siggenes and allgenes for you to try.
> siggenes<-as.matrix(read.table("siggenes.txt",row.names=1))[,1]
> allgenes<-as.matrix(read.table("H:\\test\\allgenes.txt", row.names=NULL, header=T, colClasses='character'))[,1]
Many thanks
John
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