[BioC] intersection between genes and pathways

[Alberto Goldoni]

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