ssGSEA signature using combine mode

[Johanna Szychter]

Hello,

I ran a ssGSEA analysis using both Combine.add and Combine.replace modes, and I got a good result for one of the combined signatures.

I usually go on the MSigDB website to download the associated gmx file to then run only the specific signature in the standard GSEA software and got the enrichment curve. However, I can't find a signature associated with the combined mode. 

Would you have an idea of how or where I can find the associated signatures? If not,m how to recreate it?

Thanks for your answer,

Best regards

Johanna

[Anthony Castanza]

Hi Johanna,

 

The combined signatures are created from a union of two signatures with the same base name (e.g. RESPONSE_TO_XYZ_INHIBITION) and the suffixes _UP and _DN, so if you wanted to find the original signatures that made up the combined signature, you'd need to recreate the names (RESPONSE_TO_XYZ_INHIBITION_UP and RESPONSE_TO_XYZ_INHIBITION_DN) then download those signatures from the website and combine them manually.

 

Let me know if that answer is unclear, or you're still unable to find the original signatures.

 

-Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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[Johanna Szychter]

Hi Anthony,

Thanks a lot for your answer! I will combine them manually so.

Have a great day!

Johanna