beta-arrestins signature

[Elena Borroni]

Dear Gsea support,

I'm a researcher working on G-protein coupled receptors signaling.

I performed a SILAC analysis to detect the phosphoprotemic profile dowstream my receptor of interest. I wonder if it is possibile to identify a beta-arrestins dependent signature using gsea database. 

Thanks for your help!

Best regards,

Elena M Borroni

[Anthony Castanza]

Hi Elena,

For your specific proteomic workflow, you probably want something more like this: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4258137/ than standard GSEA. The links in that paper no longer work, but the lab's website has relocated to here: http://fields.scripps.edu/yates/wp/?page_id=143, I'm still getting a 503 error on the specific link to the PSEA-quant page from their site, so if you want to use that tool you might have to reach out to the lab directly, it does, however, appear to be designed with support for SILAC analysis in mind. One of our collaborators developed an approach called PTM-SEA for phosphoproteomic studies (available from https://github.com/broadinstitute/ssGSEA2.0) but I don't know if it's specifically appropriate for SILAC data.

As to how to identify a beta-arrestin dependent signature, we have a couple sets based on the pathway in MSigDB, but I'm not sure that's what you want here. If you're aware of any transcriptomic studies that target beta-arrestin in relevant models I'd be happy to put together signatures for you that could be included in a future MSigDB release.

Sorry I couldn't be of more help here

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego