I am trying to figure out whether the list of my somatic coding mutation activates genes in cancer. I was trying to get this info from polyphen, however it seems that polyphen does not provide this information. Is it possible to get this information from somewhere else.
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written
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avinash.sahu •
1 answer
Hi Avinash,
If you're still looking, consider using CRAVAT. From this post - "Cancer-specific annotations include COSMIC mutation frequencies by tumor type, Vogelstein/Kinzler oncogene/tumor suppessor gene assignments and PubMed hits. Variant- and gene-level annotations and bioinformatic scores are provided to enable interpretation and prioritization of variants identified in sequencing studies, including frameshift and in-frame insertions/deletions, splice site, missense and nonsense. Variants can be submitted either as a Variant Call File (vcf) or in a simple tab-delimited format, based on genome coordinates, by uploading through a graphical web interface or a RESTful web services API." In addition, CRAVAT also provides a CHASM score which is cancer specific and might help you determine whether your mutations activate cancer genes or not.
Sounds like what you might need!
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