Comparing gene signatures

[MSK INTERN]

Hello,

I recently learned how to search for specific genes using cbioportal, is there a way to search for gene signatures?

Thanks,

Alan Hirshaut

[debr...@mskcc.org]

Hi Alan,

 

Thanks for reaching out!

 

We currently do not allow for searching by gene signatures, but we are working on enabling that feature

 

Note that on the results view it is already possible to add a “Mutation Spectrum” track to the Oncoprint so you can get an idea of the type of base changes in a sample. See attached screenshot

 

Hope that helps!

 

Best wishes,

Ino

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[debr...@mskcc.org]

Hi Alan,

 

Apologies. I misread mutational signatures, rather than gene expression signatures

 

That said, we do not provide a way to query by that either in the public portal. If you are using a local version however it is possible to query and cluster by e.g. gene sets from MSigDB. CC’ing Sjoerd in case he wants to add anything

 

See also:

 

https://www.thehyve.nl/articles/gene-set-visualization-in-cbioportal-oncoprint

 

Thank you!
Ino

To view this discussion on the web visit https://groups.google.com/d/msgid/cbioportal/2884CA43-5F20-49A7-A00B-274A9B4AB06A%40mskcc.org.

[Sjoerd van Hagen]

Hi Alan,

Depending on what you would like to do, here are some options:

- You probably know that you can query for multiple genes at the same time. If there is any alteration in any of the genes for a sample, this sample is considered altered throughout the results view. This would allow you to compare samples that have an alteration in a pathway to the samples that do not. Simply query for a set of genes, e.g. CDKN2A MDM2 MDM4 TP53

- If you would like to combine all alterations in a single track in the oncoprint you can use 'merged tracks'. Simply query for [CDKN2A MDM2 MDM4 TP53]. You can name the tracks like this [ "P53 PATHWAY" CDKN2A MDM2 MDM4 TP53].

- If you really want to do genset variation/enrichment analysis, you can use the geneset visualization that we built. See the link in Ino's email to our blog about it. You do need to set up your own cBioPortal installation for that and prepare the GSVA scores yourself.

- There is also the pathway mapper in the pathways tab in the results view that could be of interest:

Best of luck,

Sjoerd.

---

Sjoerd van Hagen

Team Lead cBioPortal & Open Targets

E sjo...@thehyve.nl

T +31 30 700 9713

W thehyve.nl