How to group genes as 'gene sets'

Question

[yliueagle]

I want to do some gene set enrichment analysis for Parkinson. But what are the proper ways to attribute genes into functional related groups? I know genes can be put into groups as 'pathways' or 'gene families', whether there are other ways? And which database should I refer to? Thanks.

[Manvendra Singh]

I think you want to perform Gene Set Enrichment Analysis (GSEA).

There are nice R bioconductor packages to do so

http://www.bioconductor.org/packages/release/bioc/html/GSEABase.html

or you go for gene ontologies, group them on the basis of their molecular function

[Devon Ryan]

For what it's worth, you might download a demo copy of IPA from Ingenuity. Their database tends to be better than anything that's public (unfortunately, since it'd be nicer to not pay for IPA).

Answer 1

[smilefreak]

Various resources exist for this.

For example to functionally characterise the genes by GO and pathways using a web resource you could use pantherdb.

Answer 2

[EagleEye]

You should have a look at this: Gene Set Clustering based on Functional annotation (GeneSCF)