Thanks Julian and Steve.

But I think I am more concerned with some results like after information
retrieval, kind of a one step before text mining. So those genes after
retrieval might just be "associated" with cancer. Is there some online
tools to extract those info from like pubmed?

Best,

Nick


On Sat, May 10, 2014 at 3:20 AM, Julian Gehring <julian.gehring@embl.de>wrote:

> Hi Nick,
>
> COSMIC is generally a well curated source for your purpose.
>
> Going with Steve's suggestion, you can use the 'COSMIC.67' bioconductor
> package to get the cancer gene census list:
>
>   data(cgc_67, package = "COSMIC.67")
>
> The Cancer Gene Census (CGC) is a list of genes that are causal to cancer,
> currently including ~600 genes.
>
> If you want to go a step further, you could parse the mutation calls from
> a number of large scale cancer sequencing studies, mainly the ICGC and
> TCGA.  You can find the somatic mutation calls of 8 TCGA studies in the
> 'SomaticCancerAlterations' package, and could find the genes overlapping
> the mutations.
>
> Best wishes
> Julian
>
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