Are There Any Pre-Defined Gene Sets For Different Cancers

Question

[jack]

Hi all,

I'm looking for the pre-defined gene sets for different type of cancers. is there any database that I can dowload this gene sets? for example gene sets for Breast Cancer.

[Giovanni M Dall'Olio]

related discussion: Database of tumor suppressors and/or oncogenes

Answer 1

[Giovanni M Dall'Olio]

The standard resource is the list of Consensus Cancer Genes (also known as CGCs) provided by the Sanger Welcome Trust. This is a list of 518 genes (*), manually annotated from the literature, and representing a conservative list of genes for which the association to cancer is well known and characterized. You should download the excel or the csv table, and use it as your reference dataset.

Alternatively, in my new lab, I work on the database Network of Cancer Genes, which provides a list of about 2,000 candidate cancer genes annotated for 23 tumor types. This list of cancer genes is manually curated after carefully reading literature and after comparing with other similar databases, and the last update is from last year, when we published a paper on the last version. You can use our Advanced Search Form, to select only the genes from a given cancer type, and also to apply other filters.

Finally, the web interface at ICGC is very good and easy to use, but if I am not wrong, they do not provide a manually annotated list of genes known to be associated with cancer. You will have to download the list of genes for each tumor type, and then apply a filter to select only the genes most commonly mutated in cancer.

• note that the CGC list currently uploaded on the website contains four duplicated entries, so the total is 518. I also think that

Answer 2

[dunordavind]

You can consider GWAS catalog, at http://www.genome.gov/gwastudies/. You can select one or multiple diseases. I have used it for similar purposes before.

Answer 3

[B. Arman Aksoy]

MSigDB's C2 collection has such gene sets that are curated and obtained from different databases, such as Reactome and KEGG:

http://www.broadinstitute.org/gsea/msigdb/genesets.jsp?collection=C2

Additionally C4's CM module might also be of interest to you, but that is a computational set that is inferred from various gene expression assay -- hence, probably less of interest to you.

Answer 4

[Mary]

I really like the data that's available at ICGC: http://dcc.icgc.org/

Answer 5

[jeffk8900]

Here are some links to resources that may help.

GeneSigDB http://compbio.dfci.harvard.edu/genesigdb/ allows one for downloading sets from publications so would be complementary to a certain extant with MSigDB c2 and c6

Which Genes http://www.whichgenes.org This references a number of gene set/pathway datasources that allows you to combine and build custom data sets.

MelanomaDB http://genesetdb.auckland.ac.nz/melanomadb/chooseSets.php This is great resource for what I think you might be looking for, however, it is only for Melanoma.

Glad4U http://bioinfo.vanderbilt.edu/glad4u/ I really like this resource. It is pretty simple, just plug in a pubmed search term, for example 'basal breast cancer' and it will return a weighted list of genes based on literature recovered. The result will not be a 'signature' per se, but will be a list of genes, based on prior knowledge, associated with a cancer type. The difference is subtle but should be taken into account for what you plan to use the lists for.