How to group genes as 'gene sets'
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.
2 answers
Various resources exist for this.
For example to functionally characterise the genes by GO and pathways using a web resource you could use pantherdb.
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smilefreak
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smilefreak
You should have a look at this: Gene Set Clustering based on Functional annotation (GeneSCF)
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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
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).