I am looking for additional gene sets that can be used to expand the gene sets found in the Molecular Signatures Database (MSigDB). In particular, I am looking for signatures such as the c6 (oncogenic signatures) and c7 (immunologic signatures) gene sets, i.e.: lists of genes up and downregulated across different conditions from a diverse panel of gene expression experiments (micorarray, RNA-seq).
The idea is to then run GSEA using this expanded collection of gene sets and hopefully get some biological insights about the datasets I'm analysing. Ideally, these gene sets would already be in GMT format, but I'm obviously flexible about this.
Hasn't anybody attempted to analyse all of GEO using some fixed thresholds and made a database yet? :)
Thanks very much!