merge multiple samples' or genes' mutations

[frans frans]

Hi, I am wondering whether this is possible? When I go to a sample's page or a gene query, I can see the mutations table for that one sample or gene.

Is there a way to be able to merge multiple sample's/gene's mutations data and display them in the same table? I also need to be able to download this merged table's tsv at the end. Thanks in advance!

[Tim Kuijpers]

Hi Frans,

Thank you for your question. I'm not sure if cBioPortal supports everything you’d like to do, but here are a few things you can try:

• Multiple samples in the mutation table: The patient summary page shows multiple samples per mutation when a patient has more than one sample carrying that mutation. For example, in the MSK-Impact study, the mutation table displays which samples contain a specific mutation: https://www.cbioportal.org/patient?studyId=msk_impact_2017&caseId=P-0000377 
• OncoPrint view: In the OncoPrint (although this is not a table), it’s possible to show events per sample (such as genetic alterations). If you sort the OncoPrint track by “Sort by case ID (alphabetical)”, you’ll get a view where samples from the same patient are grouped together. This makes it possible to explore genetic alterations across samples from the same patient: https://www.cbioportal.org/results/oncoprint?cancer_study_list=msk_impact_2017&tab_index=tab_visualize&case_set_id=msk_impact_2017_all&Action=Submit&gene_list=TP53%250AKRAS&show_samples=true&oncoprint_sortby=case_id
• Mutations table: Unfortunately, it’s not possible to sort by case ID in the mutation table. When a patient has multiple samples, they are included in the table, but they may not appear in alphabetical order.

I  hope this helps! If you have any further questions, please hit reply all, so our continued conversation is captured by the cBioPortal Google groups.

Best,

Tim

[frans frans]

Hi Tim,

Thanks for the response! What I need is a mutation table (or something like an exportable tsv file) of mutations across different patients. Like all the patients of a given cancer type, or only patients with OS < 5 months ,etc. I can go through the mutation table one by one, download the tsv and concatenate them, but I do have a lot of patients so it will be pretty time consuming. Which is why I am wondering if there is a way to get a mutation table that lists all the mutations in a group (may be from different patients).

Thanks again for the help!

Sincerely,
Frans Budiman

--
You received this message because you are subscribed to the Google Groups "cBioPortal for Cancer Genomics Discussion Group" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cbioportal+...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/cbioportal/bc111c44-d393-485c-9c88-0667332d1eabn%40googlegroups.com.