MSigDB version for Ensembl102

[Zhenyu Zhang]

I am looking for MSigDB version for Ensembl102 (GENCODE v36). From the release notes, it seems that this version is skipped. Could anyone help confirming this?

Another question is that I know I can download the old MSigDB database as zip file from https://www.gsea-msigdb.org/gsea/downloads_archive.jsp. Do you have functional archive mirror pages (similar to Ensembl Archive) that supports browsing?  

[Anthony Castanza]

Hello,

 

Unfortunately we're only able to produce an MSigDB version in sync with ever other Ensembl release. The general recommendation in this case is to use Ensembl Gene IDs for your gene identifiers and to use the Collapse/Remap dataset feature with our provided Ensembl_Gene_ID chip file to convert your data to the symbol versions in the current release of MSigDB. (The collapsing mode in advanced fields should be set to sum_of_probes for standard GSEA with RNA-seq data, in GSEA Preranked this would not need to be changed)

 

-Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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