Hello, I need to download genes related to particular cellular processes, such as cancer. I tried to download from OMIM (with search terms from two words), but the returns are very unspecific. Anyone can suggest, how to get particular genesets in model organisms? Thank you!
1 answer
Hi, the first resource I usually check for any kind of signatures is the MSigDB https://www.gsea-msigdb.org/gsea/msigdb/index.jsp
They have a HALLMARK_DNA_REPAIR set and probably others that are of interest here as well, e.g. https://www.gsea-msigdb.org/gsea/msigdb/cards/HALLMARK_DNA_REPAIR
The old-fashion way would be to browse relevant papers and see whether they defined gene sets related to what you need given they performed the respective experiments, e.g. RNA-seq between control and a knockout of any factor that is related to genome integrity.
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You just edited the question, removing the initial question towards
HALLMARK_DNA_REPAIR, it is good practice to indicate that, otherwise it makes answers mentioning that particilar signature looks nonsensish.For the current question, cancer is not a specific cellular process, it is in fact a highly heterogeneous molecular state even within the same cancer entity, therefore there is not a single "cancer" signature. I think you will first clarify (to yourself) what question you want to answer.