Help with querying data

[Dario Dilernia]

Hello CBioPortal team!

I'm new to the portal and I'm struggling to figure out how to extract the list of known oncogenic mutations by disease. Particularly interested in breast cancer.

Can you guide me on this?

Thanks in advance,

Dario

[Nikolaus Schultz]

Hi Dario,

There is currently no simple way to identify just oncogenic mutations in a given disease. The best way to start with would be to go to the study view for a study of interest for you, e.g. Breast Cancer from TCGA, then look at the table of mutated genes on the study view. This shows the frequency of all mutations for each gene. You could then start a query for a subset of these genes, e.g. the 10 genes with the highest frequencies. As a next step, you can select “Only drivers” via the settings icon next to the modify query button. You should then see the frequencies of oncogenic alterations. (Note this still includes oncogenic copy-number changes, which you can remove from he query via the “Modify Query” button.)

I hope this is helpful.

Niki.

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[Dario Dilernia]

Thank you, Niki. This is very helpful.

I still need to explore the API but can that type of information be fetched via cBioPortal's REST API? Thinking that I could write a wrapper to access it for the diseases a need and minimize human error...