[BioC] intersection between genes and pathways

[John Stevens]

Hi Alberto,

There may be a more elegant way to do this, but I think you'll want to make use of the rat2302PATH2PROBE object in the rat2302.db package.  The key is that you first need the path ID, and that's available through the KEGG.db package.  Below is some starter code; I hope it helps.

Regards,

John R. Stevens
Utah State University



# load KEGG pathway information
library(KEGG.db)

# define a function to search for path IDs
# - shouldn't need to change this
KEGGTerm2Tag <- function(term)
{
  KTL <- eapply(KEGGPATHID2NAME,
               function(x){agrep(term,x,value=TRUE)})
  Kl <- sapply(KTL,length); names(KTL[Kl>0]) 
 }

# call this function -- look for path ID of pathways
#    whose name contains 'hyptertroph'
KEGG <- KEGGTerm2Tag("hyptertroph")
KEGG
# "05410"

# see full name of this path ID
KEGGPATHID2NAME$"05410" 
#  "Hypertrophic cardiomyopathy (HCM)"

# get probeset IDs from rat2302 array
#   that are in this pathway
library(rat2302.db)
gn <- rat2302PATH2PROBE$"05410"

# Then look at the intersection of this vector
#   and the vector of probeset IDs
#   from your ExpressionSet object SHR
intersect(gn,featureNames(SHR))




-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Alberto Goldoni
Sent: Wednesday, March 10, 2010 2:45 AM
To: BioC
Subject: [BioC] intersection between genes and pathways

Dear all,
i have a question for you.
If i have a list of 66 genes:

> SHR
ExpressionSet (storageMode: lockedEnvironment)
assayData: 66 features, 4 samples
  element names: exprs
phenoData
  sampleNames: SHR-PUFA5.CEL, SHR-PUFA6.CEL, SHR-st7.CEL, SHR-st8.CEL
  varLabels and varMetadata description:
    DIETA: Con PUFA=OMEGA3 o ST=ALIMENTAZIONE STANDARD
    TYPE: WK=RATTO NORMALE o SHR=RATTO IPERTESO featureData
  featureNames: 1367871_at, 1368692_a_at, ..., 1399089_at  (66 total)
  fvarLabels and fvarMetadata description: none
experimentData: use 'experimentData(object)'
Annotation: rat2302

and i would found which genes are involved in the "hypertrophy" and "cardiac decompensation" pathways.
the only way i have found is to list all the pathways with my probe ids:

paths <- aafPathway(probeids, "rat2302.db")

but now i have to look manually to every pathway.

There is a method in order to do automatically, because now i have only 66 genes, but if i have 1000 genes is too complicated.

Best regards.

--
-----------------------------------------------------
Dr. Alberto Goldoni
Bologna, Italy

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