I am looking to compile a list of resources that provide associations between point mutations, deletions, genes...etc and cancer. Cosmic is great for this but I am looking for additional resources of a similar concept. Aside from downloading all of TCGA and variant calling on this list does anyone know of online resources that provide a cosmic type database? Any help would be greatly appreciated thanks !!
I know of no one-stop shop where you will find everything from genes, variants and chromosomal aberrations all associated with cancer. Cancer is quite broad - which type(s) or all are of interest to you? Do you need to retain that the association is to a specific cancer?
One place to look for SNP-cancer associations is the GWAS catalog at NHGRI. KEGG has pathways for 16 different cancers - a source for genes to add to your list. Documentation on NCI's cancer Gene Index is here.
Here is a start. If other sources of info/data come to mind, I will list them later.
At this link is a review of chromosomal translocations and gene fusions in cancer.
This question might also have stuff that's useful to you.
But also keep an eye on the IGCG.org site. You can get some interesting things out of mining their BioMart if you are up for that. I've seen some pretty good data there.