Querying a large set of genes for mutual exclusivity

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Santiago Enrique Sanchez

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Jul 8, 2021, 4:31:11 AMJul 8
to cbiop...@googlegroups.com
Good afternoon, 

I'm a graduate student at Stanford and was interested in generating a mutual exclusivity query among the Hepatocellular carcinoma patient datasets on the website with a large number of gene combinations for my project. The online portal instructed me to contact you if attempting to query a large number of genes. 

Please let me know if this is possible or how to go about doing this through CBioPortal. 

thank you for your help! 

Santiago E. Sanchez

Stanford Medical School | MD/PhD Student, Artandi Lab
Cambridge University | M.Phil Chemistry '18
UT Austin | BA Plan II | BSA Biochemistry '17

Ino de Bruijn

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Jul 23, 2021, 9:47:20 AMJul 23
to Santiago Enrique Sanchez, cbiop...@googlegroups.com
Hi Santiago,

Thanks for reaching out! Sorry for the delay in replying

cBioPortal's mututal exclusivity analysis works well for subsets of genes. For large number of gene combinations it is better to download the data and perform the calculations in R or Python:

You can find the raw data here: https://www.cbioportal.org/datasets

Best wishes,
Ino



Best wishes,
Ino

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