How To Search Disease Association For A List Of Gene Fusions?

Question

[vdtbioinfo]

Hello,

I would like some help regarding the following issue:

I have a list of 30 gene fusions and I would like to perform a web search to see if any of them is associated with a specific trait/ diseases.

Do you know of any web tool to paste my gene fusion list and provide me results or scores for each of the genes?

Thanks in advance,

Answer 1

[mikhail.shugay]

As there are only 30 fusions in your list, I would first do a manual mining using google/pubmed. Fusions are quite rare events and the set of known fusion pairs is really sparse, so you are going to get few publication hits that could read in a reasonable time. I also advice to check if your fusion is not a common read-through event that are typical for healthy cells.

If you're interested in fusion genes in cancer, check out Mitelman DB, TICdb and ChimerDB 2.0

For a set of novel fusions, you can try out ranking them according to their oncogenic potential and look at the resulting expression change/domain composition. This would give you some insights on their possible functional role. Have a look at Oncofuse, Chimera package and Pegasus

Good luck!