Chromosomal Information For Gene List In Microarray Data

Question

[aditi.qamra]

Hi,

I have an expression profile dataset with a list of genes and normalized expression data. What i want is to only look at genes on the Y chromosome.

Most of the gene annotation packages with R or otherwise look for gene ids/probe-set ID to map to chromosomal information. Can you please help me out with a way to extract chromosomal information ( preferably through an R package) with only the gene names ?

Thanks !

Answer 1

[Sean Davis]

The trick is to use the "org" package for your organism. Here I show human, but you can substitute....

library(org.Hs.eg.db)
symbols = c('BRCA1','TP53','GAPDH')
select(org.Hs.eg.db,keys=symbols,cols=c('SYMBOL','CHR'),keytype='SYMBOL')

Which will return:

  SYMBOL CHR
1  BRCA1  17
2   TP53  17
3  GAPDH  12

[Neilfws]

R/biomaRt is another option.