Enrichment Map Genesets

Contents

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:
1. Entrez gene ids
2. UniProt accessions
3. 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
IOB	directly from IOB - static (July 2011)	biopax	Entrez gene	sporadically	35 pathways - 10 are the same as CellMap, 1 is the same as NetPath	need biopax pathways fixed so species info is correct but information is still extractable.
Msigdb - c2	static (needs to be updated manually)	gmt	Entrez gene	sporadically	total 880 genesets: Kegg -186, Reactome - 430 , Biocarta - 217, Other - 47	Only need other and Biocarta as all other sources are currently covered
NetPath	www.netpath.org/browse (scripted grab of file numbered 1-25)	biopax	Entrez gene	static	25 pathways - 12 are cancer pathways (10 are CellMap) 13 are immunity 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
NCI	scripted grab from pathwaycommons	gmt	Entrez gene	every 4 months	217 pathways	Still has next step issues in biopax geneset extraction
NCI	NCI	biopax	Entrez gene	sporadically	?	Can't parse biopax level 3
Biocarta	NCI	biopax	Entrez gene	static	386 pathways	Biopax 3 - Complete Mess! - currently getting from Msigdb
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 15,181 with GO IEA	source is direct from original curator of annotations
msigdb - c3 Specialty GMTs mirs, transcription factors	grab from Msigdb	gmt	Entrez gene	sporadically	221 miRs 616 TFs

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