Is there a way I can download the mutation data at once?

[Kun-Lin Ho]

Hi, my name is Kun-Lin Ho, a bioinformatics graduate student at the University of Georgia.

Thanks for developing cbioportal so that we can look at the human data more easily.

I have a question about downloading the data.

In your query interface, we can select the dataset and type the gene name to see the mutation results from the dataset and download the dataset.

For example (use PIK3CA gene as an example):

https://www.cbioportal.org/results/mutations?tab_index=tab_visualize&Action=Submit&session_id=614b98e7e6ebe01a6ee32c59&plots_horz_selection=%7B%7D&plots_vert_selection=%7B%7D&plots_coloring_selection=%7B%7D 

My question is, is there a place on the website I can download all of the human gene mutation results (either in a single file or several files)? 

Many thanks

Sincerely

Kun-Lin Ho

[Benjamin Gross]

Hi Kun-Lin,

The only way I know how to do this is to go back to the original data files for each study and combine entries from the respective MAF files that meet your search criteria (like pick only MAF records with PIK3CA variants).

You can find the data files in the repository below, where each folder represents a published study found in cbioportal.org.  The mutation data is found in data_mutation_extended.txt files.

https://github.com/cBioPortal/datahub/tree/master/public

Hope this helps,

Benjamin

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