Clairom Arrays support with MSigDB 7.0

[Anthony Castanza]

With MSigDB 7.0 we changed our platform annotations to be derived from the ENSEMBL biomart database, and as such we only generate chip files for platforms deposited in ENSEMBL's biomart by default. The Clariom arrays are not platforms supported by ENSEMBL and so were omitted from the initial build process. Since MSigDB previously supported a very large number of platforms that are not present in ENSEMBL, and the process for updating these is rather crude (relying on the Old-Current Gene Symbol mappings in our Symbol_with_Remapping CHIP which, due to symbol reuse over the years, is not perfectly comprehensive plus some additional massaging with our NCBI_Gene_ID chip to pick up some of the dropped LOC IDs which slip through this initial mapping step), we made the decision to not convert these other platforms unless they were explicitly requested.

As we have recently received a number of requests for CHIP files for these Clariom arrays, versions of the old annotations updated via the patching method described briefly above are available here: https://drive.google.com/drive/folders/1Zrlscdx6JKzC1FkhmVZknCGvSdZbmS0G?usp=sharing

These files are provided without any additional support, validation or warranty of any kind.

-Anthony

Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego

[David Eby]

Just an update: for longer-term stability, these arrays have been moved to our Legacy Annotations file share at https://data.broadinstitute.org/gsea-msigdb/msigdb/annotations_legacy/

- David

David Eby
www.gsea-msigdb.org
igv.org
genepattern.org

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