TCGA FPKM and Beta values for colon cancer vs controls

[Stuckel, Alexei]

Hi guys, thanks for your great database. I have referenced you in a recent paper I published.

My question is that for instance, in the past for colorectal adenocarcinoma datasets, I would select all datasets and then query for a given gene. I liked that you guys provided TCGA FPKM expression and methylation beta value comparisons of colon cancers vs the control group. Is this function still available? I haven't been able to find it or use your FAQs for guidance.

Thanks again!

Alex

[David Higgins]

Hello Alexei,

 

Thank you for your kind words, we’re glad to hear cBioPortal has been useful in your research.

 

Unfortunately you cannot query for expression in combined studies of multiple datasets, that feature is not supported. Because the Z-scores for each gene are normalized within their own studies, cross-study comparisons are not supported for this data type.

 

More information for how we process expression data is available in our FAQ and on our Github page.

 

Best,

 

David M. Higgins, Ph.D. | (he/him)
Informatics Program Manager
Center for Data-Driven Discovery in Biomedicine (D3b)
Children’s Hospital of Philadelphia, USA

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