Table 1.
Gene set databases currently supported by DSEA
| Source | Name | Description | # |
|---|---|---|---|
| BioMart | GO BP | Gene Ontology—Biological Processes | 3262 |
| BioMart | GO MF | Gene Ontology—Molecular Function | 939 |
| BioMart | GO CC | Gene Ontology—Cellular Component | 556 |
| MSigDB | CP | Expert-defined Canonical Pathways | 243 |
| MSigDB | KEGG | Kyoto Encyclopedia of Genes and Genomes | 186 |
| MSigDB | Biocarta | Community-fed molecular relationships | 217 |
| MSigDB | Reactome | Open-source, open access, manually curated and peer-reviewed pathway database | 674 |
| MSigDB | CGP | Genetic and Chemical Perturbations | 2427 |
| Mips | CORUM | Comprehensive Resource of Mammalian protein complexes | 1343 |
| – | SGS | Sets containing single genes mapped from Affymetrix chip U133A | 12012 |
We also added a collection of fictitious sets each containing a single gene from the 12012 obtained after probe reannotation of the cMap raw data. We collected existing gene sets from a number of publicly available databases.