= Enrichment Map Genesets =
Summary
Enrichment Map Genesets are a set of Gene Set files in GMT format (compatible with GSEA) updated monthly from original source locations available with:
- Entrez gene ids
UniProt accessions
- Gene symbols
Sources
Source |
File Origin |
File Type |
ID extracted |
|
KEGG |
static (July 2011) |
gmt |
symbol |
|
IOB |
static (July 2011) |
biopax |
Entrez gene |
|
Msigdb - c2 |
static (needs to be updated manually) |
gmt |
Entrez gene |
|
NetPath |
website (scripted grab of file numbered 1-25) |
biopax |
Entrez gene |
|
HumanCyc |
scripted grab of zipped release from password protected website. |
biopax |
Uniprot |
|
NCI |
scripted grab from pathwaycommons |
gmt |
Entrez gene |
|
Biocarta |
- |
- |
- |
|
Reactome |
scripted grab of zipped release from website |
biopax |
Uniprot |
|
GO |
scripted grab from ftp site |
GAF |
Uniprot |
|
Specialty GMTs |
grab from Msigdb |
gmt |
Entrez gene |
- found in msigdb c2
File Structure
<Release> - directory is named according to date sets were updated.
<Species>
<Identifier> - (either Entrez gene, UniProt, Gene symbol)
- GO
- Pathways
- miRs
- TF
- Disease phenotypes