cBioPortal survival analysis help

[doc....@gmail.com]

dear cBioPortal team and users,

In cBioPortal's survival analysis (web portal), when stratifying samples into "with/without Cases with Alteration(s) in Query Gene(s)" based on a gene list, how is the overall with/without Cases with Alteration(s) groups in Query Gene(s) stratified (/calculated?

For example in http://bit.ly/2a4BeLT
Select Genomic Profiles: mRNA Expression z-Scores (RNA Seq V2 RSEM): Enter a z-score threshold ±:2
Tumor Samples with mRNA data (RNA Seq V2) (498 samples) / 40 Genes

I assume alteration here is mRNA Upregulation vs mRNA Downregulation for each gene. So, for each gene each sample has a z-score (indicate relative over- or under-expression for each gene in comparison to the rest of the cohort), but I am not sure where to go from here when it comes to dividing the samples into two distinct groups.

all the best,
doc golly

[JianJiong Gao]

Hi,

The samples were stratified based on your query. Basically in the
oncoprint, the ones with any alteration (mutation, cna, mrna up or
down) will be considered altered; and the other samples unaltered.

For mRNA expression, you may want to use Onco Query Language
(http://www.cbioportal.org/onco_query_lang_desc.jsp) to specify up- or
down-regulation. E.g. PTEN: exp<-2 will query for down-regulation
only.

Best,
-JJ

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