Issue searching gene expression

[Alexandra Nicole Demetriou]

Hello,

 

I’m trying to use cBioPortal to look at expression of a particular gene across brain tumor cases, and I watched the “cBioPortal: Comparing samples based on expression level of a gene” YouTube video for reference. When I search my gene of interest under Charts > Gene Specific, it says “unable to validate gene symbols.” Under “mutated genes,” I see that the gene is mutated in 4 cases. Does this mean that expression data is not available for that gene? Or is there another way I might assess expression levels across samples?

 

Thanks,

Alexandra

[JJ Gao]

Hi Alexandra,

That's strange. It might be due to some temporary issue in the gene validation service. Would you please give it another try? If it's still not working, would you please let us know the gene and a screenshot?

Thanks,

-JJ

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[Alexandra Nicole Demetriou]

Hi JJ,

 

Thanks for getting back to me. I tried accessing cBioPortal through a different browser and it worked this time. I actually had another question – I’m trying to also look at gain and loss of entire chromosomes and I was having trouble doing so. I have a private dataset and I’m not sure if that makes a difference for what I can/can’t view in cBioPortal. My cBioPortal displays the following genomic data chart options (first screenshot), and when I display structural variant genes, the following comes up (second screenshot). I want to see cases that have gain of entire chromosome 7, for example, and I’m not sure if that’s possible here. Do you have any thoughts on how I might see that data in cBioPortal, or if it’s maybe not possible based on what I have here?

 

Thanks,

Alexandra

 

[JJ Gao]

Hi Alexandra,

You would need the arm-level CNA data in order to do that analysis. For example, in this study, you can add arm-level CNAs in study view (screenshot below). For you local installation, the arm-level CNA data can be imported as Generic Assays data type, see examples here: https://github.com/cBioPortal/datahub/tree/master/public/gbm_tcga_pan_can_atlas_2018

If you don't have arm-level CNA calls but segment data, the CN Segment tab may be useful to identify arm-level CNA events.

-JJ