Question

Retrieving Background Mutation Rate with Biomart

0

Entering edit mode

9.7 years ago

marcusmgoldberg • 0

I have used biomart quite a bit in the past to convert gene ID's or get dN/dS values, but I can't find any attribute in any obvious mart or dataset to retrieve background mutation rate.

This may just be a terminology problem, but I have dug around to no avail. Is there a way to access background mutation rate from biomart given a gene ID (say, TP53)?

Thanks very much for your help,

Marcus G.

biomart bioconductor • 2.4k views

ADD COMMENT • link updated 2.4 years ago by Ram 43k • written 9.7 years ago by marcusmgoldberg • 0

0

Entering edit mode

What do you mean by background mutation rate? In what context are you working (e.g., cancer)?

ADD REPLY • link updated 2.4 years ago by Ram 43k • written 9.7 years ago by Sean Davis 26k

0

Entering edit mode

Sorry - I should I have more specific. I want to compare mutation rate in cancer cells vs normal human mutation rates (specifically synonymous, silent substitutions).

ADD REPLY • link updated 2.4 years ago by Ram 43k • written 9.7 years ago by marcusmgoldberg • 0

0

Entering edit mode

Background mutation rate over the entire genome would be sufficient, but it would obviously be better if it is possible to get gene specific rates, as well.

ADD REPLY • link 9.7 years ago by marcusmgoldberg • 0

Ram · Answer 1 · 2014-08-20

I think background mutation rates are typically estimated from the data, not from population estimates. The reason for this is that different cancers will have different mutational profiles--there isn't a "normal human mutation rate" in that sense.

There are a number of tools for performing such analysis looking for evidence of mutational burden. MutSig and genome music are a couple of them. You might start by looking at these tools before rolling your own.