Doubts in survival plots covariates

[Fabián Robledo]

Hi

I have been using cbioportal for a while and now i want to use the survival plots for one of the data sets available. 

I seem unable to find how to use covariates apropiate or find if its even possible to make cbioportal complex survival plots. make a query with 3 mutations i am interested in in three different genes, and in the plots they appear as 3 different curves, however i cannot see the comparison with the non-altered situation (mutation in TP53 vs non-mutated in that position in TP53). I tried to explicitely find any info about onco query language and logic gates to see if i can select all samples which do not have a paticular mutation, but i didn't find it in the docs.

Any help would be appreciated

Many thanks in advance

Fabián Robledo

[Luke Sikina]

Hi Fabián,

You can use the Overlap subtab within the Group Comparison tab to create groups that capture, for example, all samples without a mutation in TP53. You can see step by step instructions starting on slide 25 of the group comparison tutorial: https://www.cbioportal.org/tutorials#group-comparison 

Here's an example query for 3 genes: https://bit.ly/3dnIfKo

You can use the overlap tab to select samples without TP53 mutation. The altered and unaltered groups take into account all 3 queried genes (altered in one or more genes; unaltered in all genes) - to get only those without TP53 mutation, you want the altered samples that don't have TP53 mutation (40 samples) plus all 173 unaltered samples:

Once I create that group, I can go back to the Survival subtab and compare TP53 mutant to not mutant:

Another option is to query for one gene at a time, in which case the default altered/unaltered groups will be samples with/without alteration in that gene.

[Fabián Robledo]

Hi Luke,

Thank you so much for your answer. That was exactly what I was looking for.

Fabián Robledo