Enriched gene signatures - (Jun/30/2011 )
I have a gene expression signature (ie list of genes up and down) which I would like to check against a gene expression profile to see if the signature is enriched in a particular subset of samples in the profile. I was thinking I'd use GenePattern to extract the signature genes from my expression profile or perhaps from a hierarchical cluster of my expression profile to see if they are enriched in a particular subset of samples. Does this sound like a reasonable approach?
Many thanks in advance for any advice,
I think what you need is Gene Ontology analysis. To do so, you just need to compile a list of genes (IDs or symbols) and then choose an online or locally installed GO analysis program to run the assay. The program will return a list of categories in which your genes are enriched or depleted. To find out a list of such program, http://www.geneontology.org/GO.tools.microarray.shtml