Therapy response for multiple cancer types

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12 months ago

ysnuye ▴ 20

I need help with accessing some kind of analysis. I will appreciate any comment, advice or recommendation about it.

I need to learn how expression levels of some genes are associated with therapy (chemo and immunotherapy) response (binary or survival time) for a wide range of cancer types and I need this information for each cancer type or dataset separately (not a fusion of datasets).

I checked TCGA (https://gdac.broadinstitute.org/), but I couldn't find therapy response or survival data in there. I also checked the GDC data portal but what I could find was mutation data only (eg: https://portal.gdc.cancer.gov/genes/ENSG00000134323). CBioPortal (https://www.cbioportal.org/) seems more comprehensive; however, you need to check each dataset and gene one by one, limiting the practicality.

Does anybody have any recommendation for this purpose? CBioPortal visualization is closest to what I need; but if there is a more practical portal or tool anybody can recommend, that will be appreciated.

Thanks.

cancer dataset expression gene therapy response • 604 views

ADD COMMENT • link 12 months ago by ysnuye ▴ 20

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You can check multiple genes at once in cBioportal. See their Onco Query Language tutorial below:

OQL

ADD REPLY • link 12 months ago by Jeremy ▴ 890

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GDC has a lot of clinical data elements that are available via API or custom filter. You can check the supported clinical data via dictionary viewer https://docs.gdc.cancer.gov/Data_Dictionary/viewer/ and then query the GDC for data completeness.