|
Size: 4306
Comment:
|
Size: 4093
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 13: | Line 13: |
| || Msigdb - c2|| static (needs to be updated manually) || gmt || Entrez gene || sporadically || total 880 genesets:<<BR>> Kegg -186,<<BR>> Reactome - 430 ,<<BR>> Biocarta - 217, <<BR>> Other - 47 || Only need other and Biocarta as all other sources are currently covered || || NCI || scripted grab from pathwaycommons || gmt || Entrez gene || every 4 months || 217 pathways || '''Still has next step issues in biopax geneset extraction'''|| || {X} NCI || [[http://pid.nci.nih.gov/download.shtml|NCI]] || biopax || Entrez gene || sporadically || ? || Can't parse biopax level 3 || |
|| Msigdb - c2|| static (needs to be updated manually) || gmt || Entrez gene || sporadically || total 880:<<BR>> Kegg -186<<BR>> Reactome - 430<<BR>> Biocarta - 217<<BR>> Other - 47 || Only need other and Biocarta as all other sources are currently covered || || NCI || [[http://pid.nci.nih.gov/download.shtml|NCI]] || biopax || Entrez gene || sporadically || ? || || |
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 |
Frequency source is updated |
Number of pathwayss |
Notes |
KEGG |
KEGG ftp site (July 2011) |
gmt |
symbol |
static as of July 1, 2011 |
236 |
Not available in biopax, available in flatfile, translated into gmt files |
Msigdb - c2 |
static (needs to be updated manually) |
gmt |
Entrez gene |
sporadically |
total 880: |
Only need other and Biocarta as all other sources are currently covered |
NCI |
biopax |
Entrez gene |
sporadically |
? |
|
|
|
biopax |
Entrez gene |
static |
386 pathways |
Biopax 3 - Complete Mess! - currently getting from Msigdb |
|
IOB |
directly from IOB - static (July 2011) |
biopax |
Entrez gene |
sporadically |
35 pathways - |
need biopax pathways fixed so species info is correct but information is still extractable. |
NetPath |
www.netpath.org/browse (scripted grab of file numbered 1-25) |
biopax |
Entrez gene |
static |
25 pathways - |
need biopax pathways fixed so species info is correct but information is still extractable. |
HumanCyc |
scripted grab of zipped release from password protected website. |
biopax |
Uniprot |
updated periodically |
249 Pathways |
available in biopax level 2 and level 3 |
Reactome |
scripted grab of zipped release from website |
biopax |
Uniprot |
updated release |
1117 pathways (release 37) |
No way of getting version of release from biopax file |
GO |
scripted grab from EBI ftp site (human) |
GAF |
Uniprot |
released once a month |
13,034 no GO IEA |
source is direct from original curator of annotations |
msigdb - c3 |
grab from Msigdb |
gmt |
Entrez gene |
sporadically |
221 miRs |
|
Biocarta
File Structure
< > denotes directory
<Release> - directory is named according to date sets were updated.
<Species>
<Identifier> - (either Entrez gene, UniProt, Gene symbol)
<GO>
- BP = biological process
- MF = molecular function
- CC = Cellular component
- All = BP + MF + CC
no_GO_IEA - indicates that the file excludes GO annotations with evidence codes - 'IEA' (inferred from electronic annotation), 'ND' (No biological data available), 'RCA' (inferred from reviewed computational analysis)
with_GO_IEA - indicates that the file includes GO annotations with evidence codes - 'IEA' (inferred from electronic annotation), 'ND' (No biological data available), 'RCA' (inferred from reviewed computational analysis)
<Pathways>
<miRs>
<TF>
<Disease phenotypes>
In each <identifier> directory There are amalgamated gene set files:
AllPathways - contains all pathway sources in the Pathways directory
- GOPathways - contains all GO (mf, bp, cc) and all Pathway sources in the Pathways directory.
Creating customized Genesets
Download the desired gene set files you would like to use in your customized set. (For example Human_IOB_Entrezgene.gmt Human_NetPath_Entrezgene.gmt )
cat Human_IOB_Entrezgene.gmt Human_NetPath_Entrezgene.gmt > MyCustomizedSet.gmt