Creating co-Mutation Groups

[Mohammed Barakat]

Dear cbioportal group, I hope this email finds you well.

I am a highschool student currently working on an Investigation centered around a comparison of different combinations in oncogene and tumor suppressor gene mutations. I would like to compare the Kaplan-Meier survival curves for a KRAS Mutation group, leaving all others as  Wild Type. In another group B, I would like to look at a triple mutation (KRAS + STK11 + KEAP 1) leaving all other genes as Wildtype. This follows for group C ( KRAS +STK11 mutations leaving TP53 and KEAP1 as wild types), and a KRAS +TP53 mutation leaving KEAP1 AND STK11 as wild types. I would appreciate it if you could provide me with a guide on how to achieve this. Thank you for your time. 

Yours Faithfully, 

Mohammad Barakat 

[Tali Mazor]

Hi Mohammed,

I think the best way to approach this is to run a query for your genes of interest. Here's a query for the genes you listed in the TCGA PanCancer Atlas Lung Adenocarcinoma cohort.

Within the 'Comparison/Survival' tab, there are 2 tabs you'll want to use. The 'Survival' tab will display a Kaplan-Meier plot based on the currently selected groups. The 'Overlap' tab will enable you to create the groups you mentioned. By default, you'll see there are 6 groups: for each query gene, there is a group of all samples/patients with an alteration in that gene. The 'Altered group' contains all samples/patients that have an alteration in one or more of your query genes. The 'Unaltered group' contains all samples/patients that have no alterations in your query genes. You can select subsets of the venn diagram on the Overlap tab to save new groups, eg select the 19 samples that have KRAS+STK11+KEAP1. You can find more details about creating new groups in these tutorial slides.

-Tali

PS Please keep the google group cc'ed on the email if you have further questions.

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[Mohammed Barakat]

Dear Dr. Mazor,

Thank you so much for your help and for the specific guidance on using the 'Comparison/Survival' and 'Overlap' tabs. The link to the tutorial slides was especially helpful for my work.

I really appreciate you taking the time to explain this to me.

Best regards,

Barakat