Gene Disease (Cancer) Association

Question

[TitoPullo]

I'm a computer scientist, so I don't have a lot of knowledge about biology. I developed a statistical method to highlight some genes from microarray dataset. Now, I'd like to know if the gene I selected are related to the microarray problem. That is, given a microarray dataset about Prostate Cancer (or Leukemia), I'd like to know if genes: X,Y,Z, etc. are already known to be related, in literature, with Prostate cancer. Is there any tool/website that could help me? Is there a way that, given a gene, I know all the disease associated to it? Or, in the other way around, what's the better method to get all the genes associated with a particular disease?

UPDATE:

I'd suggest an interesting tool that I've found: Diseases. It mines the literature to associate genes to diseases or viceversa.

[PoGibas]

Take a look at Where Can I Find Mutation Databases Specialized In Cancer? to a similar question.

[Jeremy Leipzig]

This too Database of tumor suppressors and/or oncogenes

Answer 1

[Arnaud Ceol]

That's exactly what you will find if you download data from the The cancer Gene Census at http://cancer.sanger.ac.uk/cancergenome/projects/census/

[TitoPullo]

But this website list all the studies involving that particular gene. It doesn't tell me if that gene is actually related with the disease.

[Arnaud Ceol]

"The cancer Gene Census is an ongoing effort to catalogue those genes for which mutations have been causally implicated in cancer.": you can download the Excel or tab delimited file, it lists all genes and associated cancer types.

e.g.: Symbol Name GeneID Chr Chr Band Cancer Somatic Mut Cancer Germline Mut Tumour Types (Somatic Mutations) ABI1 abl-interactor 1 10006 10 10p11.2 yes AML

Answer 2

[David Westergaard]

There's some good sources already in a comment, but I'd like to highlight a few more:

• PubMed: Just search for the gene, really, and look at studies. If you're into the more advanced stuff, look at co-mentions (i.e. in how many articles are the gene and the word prostate cancer, or any derivative thereof, co-mentioned)
• ExpressionAtlas: Look at other peoples results, and compare.

I would just like to point out an obvious problem with what you are asking: "to be related to disease X" can have multiple meanings. Related how? A mutation is causing the cancer, it's a prognostic marker of the cancer, overexpression drives the cancer and so on.

Also, be aware that there are a lot of different statistical methods for microarray analysis. If you ever submit a paper using this method, be aware that a lot of reviewers will be very critical about methods they're not familiar with (this is my own opinion, and I only have my own experiences to back it up, and is not meant to be discouraging.)

[TitoPullo]

I think PubMed is the best resource for me.

Answer 3

[Vivek]

Along with the ones already mentioned you could search the OMIM genemap for genes with phenotypes associated with a specific disease.