Onco Query Language (OQL) AND Operator and conditional gene groups

[Marc Rijksen]

Hi all,

In the cbioportal, I want to use a patient group out of the acute myeloid leukemia (tcga, nejm 2013) dataset, where I want to select patients with NPM1 AND FLT3 mutated genes. However, I can only select NPM1 OR FLT3 if I type NPM1, FLT3. Is there a way for an AND operator?

Second question would be that if I have this defined patient cohort (NPM1 AND FLT3), I want to compare survival outcome between these two goups: mRNA expression Gene group 1: C3AR1 > ADGRG1. Group 2: ADGRG1 > C3AR1. With my knowledge, it is only possible to compare one gene to the unaltered group, but not combine groups like this with that individual condition. Is this possible? If not, how could I proceed to get my research question solved?

Thank you very much for your help! 

[Pieter Lukasse]

Hi Marc,

Thanks for the questions. I don't think OQL supports AND at this moment. But you can run your query and download the tabular data from oncoprint (see screenshot):

From the tabular data, you can select the samples that have mutations in both genes, and then run a query for just these sample ids. 

Alternatively you can go to the study view and select the genes there and choose the "intersection" option in the mutations table (see screenshot):

From this selection, you can run a query.

For your second question, you can go to Plots tab and plot ADGRG1 expression vs C3AR1 (see screenshot):

You could download the plot data to find which samples would fall into group 1 and group 2 and then use these samples to make the groups in cBioPortal to then make the survival plot. 

I hope this helps!

Best,

Pieter

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