R - Generating a list of genes according to family or function

Question

[NLP]

I'm analyzing some old array data I've inherited and I have a question about filtering the list of genes/probes from which I want to do subsequent analysis, such as generating a heat map or producing a list of deferentially expressed genes. I am comfortable so far in using quantitative metrics to filter out genes (e.g. using TopTable or rowSds).

However, what I'd really like to do is filter out genes according to family or function, i.e. filter out only those genes associated with fatty acid metabolism or cellular metabolism. Or say, cancer related genes. Then from those genes generating a heat map or deferentially expressed genes.

Is there a tool available to do that with Affymetrix arrays? Specifically I am using the HT MG-430 PM array. I've tried searching how to do this but I'm concerned part of the problem for me is that I'm probably using the wrong search terms, so if this is a familiar topic I sincerely apologize. Thank you for your help!

Answer 1

[Friederike]

Note: Typically, one first does the differential expression analysis and then the tests for enrichments of certain categories!

In any case, you will have to map the Affymetrix probes to gene names. Once you have the gene names, you can use myriad packages for functional annotations, e.g. biomartr, Blast2GO, DAVID etc.

[NLP]

Thanks for the reply. I've completed the DE analysis and mapped the gene names to my probes. Do you have a personal preference out of any of those functional annotation packages you listed?

[Friederike]

That depends a lot on the question. What exactly do you want to achieve? And are you familiar with R or do you prefer a GUI/web-interface?