Script that converts MSigDB '.gmt' files into a tab-delimited gene-set ready for use in 'Genomica'
msigdbToGeneSet.pl <msigdbfile.txt> <output.txt>
Tab delimited .txt or .gmt file downloaded from MSigDB (tested on input files with entrezID, but could work with other types of IDs).
Example input:
TRNA_PROCESSING http://www.broadinstitute.org/gsea/msigdb/cards/TRNA_PROCESSING 23536 51095 10667 4234 6301 16 54974
REGULATION_OF_BIOLOGICAL_QUALITY http://www.broadinstitute.org/gsea/msigdb/cards/REGULATION_OF_BIOLOGICAL_QUALITY 10395 57679 84679 5743 5742 4358 259230
DNA_METABOLIC_PROCESS http://www.broadinstitute.org/gsea/msigdb/cards/DNA_METABOLIC_PROCESS 7520 7518 5889 7517 7516 2547 3669
Output is a tab delimited list of genes and their 'hits' in each signature is marked by 1
TRNA_PROCESSING REGULATION_OF_BIOLOGICAL_QUALITY DNA_METABOLIC_PROCESS
23536 1 0 0
51095 1 0 0
10667 1 0 0
4234 1 0 0
6301 1 0 0
16 1 0 0
54974 1 0 0
10395 0 1 0
57679 0 1 0
84679 0 1 0
5743 0 1 0
5742 0 1 0
4358 0 1 0
259230 0 1 0
7520 0 0 1
7518 0 0 1
5889 0 0 1
7517 0 0 1
7516 0 0 1
2547 0 0 1
3669 0 0 1