Differences between revisions 25 and 26

Enrichment Map Gene Sets

Contents

Summary

Enrichment Map Gene Sets 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
The GMT File format contains one Gene Set per line. Each line contains:
- Name (tab) Description (tab) Gene (tab) Gene (tab) ...
- In our format:
  - Name = Gene Set Name | Gene Set Source | Gene Set Source identifier
    - Example --> ATP-dependent protein binding|GO|GO:0043008 OR arginine biosynthesis IV|HUMANCYC|ARGININE-SYN4-PWY
  - Description = Gene Set Name
    - Example --> ATP-dependent protein binding OR arginine biosynthesis IV
  - Gene = identified by one of the three possible identifiers (Entrez gene id, UniProt accession or gene symbols)

Source	File Origin	File Type	ID extracted	Frequency source is updated	Number of pathways
KEGG	KEGG ftp site (July 2011)	GMT	Symbol	static as of July 1, 2011	236
Msigdb - c2 (other + Biocarta)	manual download from Msigdb	GMT	Entrez gene	sporadically	Biocarta - 217 Other - 47
NCI	scripted download of zipped release from website	BioPAX	Entrez gene	sporadically	219 pathways
IOB	received directly from IOB - static (July 2011)	BioPAX	Entrez gene	sporadically	35 pathways - 10 are the same as CellMap, 1 is the same as NetPath
NetPath	scripted download of files numbered 1-25	BioPAX	Entrez gene	static	25 pathways - 12 are cancer pathways (10 are CellMap) 13 are immunity pathways
HumanCyc	scripted download of zipped release from password protected website.	BioPAX	UniProt	updated periodically	249 Pathways
Reactome	scripted download of zipped release from website	BioPAX	UniProt	updated release	1117 pathways (release 37)
GO	scripted download from EBI ftp site (human)	GAF	Uniprot	released once a month	13,034 no GO IEA 15,181 with GO IEA
Msigdb - c3 Specialty GMTs mirs, transcription factors	manual download from Msigdb	GMT	Entrez gene	sporadically	221 miRs 616 TFs

Source	File Origin	File Type	ID extracted	Frequency source is updated	Number of pathways
Reactome	scripted download of zipped release from website	BioPAX	UniProt	updated release	946 pathways (release 37)
GO	scripted download from MGI ftp site (mouse)	GAF	MGI	released once a month	14,563 no GO IEA 15,041 with GO IEA
KEGG	translated from Human using Homologene	GMT	Entrez gene	static as of July 1, 2011	236
Msigdb - c2 (other + Biocarta)	translated from Human using Homologene	GMT	Entrez gene	sporadically	total 880: Kegg -186 Reactome - 430 Biocarta - 217 Other - 47
NCI	translated from Human using Homologene	GMT	Entrez gene	sporadically	219 pathways
IOB	translated from Human using Homologene	GMT	Entrez gene	sporadically	35 pathways - 10 are the same as CellMap, 1 is the same as NetPath
NetPath	translated from Human using Homologene	GMT	Entrez gene	static	25 pathways - 12 are cancer pathways (10 are CellMap) 13 are immunity pathways
HumanCyc	translated from Human using Homologene	GMT	Entrez gene	updated periodically	249 Pathways

< > 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.

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

-  ⇤ ← Revision 25 as of 2011-11-15 16:59:32 → 
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  Editor: RuthIsserlin
  Comment:
+   ← Revision 26 as of 2011-11-15 17:00:34 → ⇥
  Size: 6085
  Editor: RuthIsserlin
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
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-|| [[http://pid.nci.nih.gov/|NCI]] || [[http://pid.nci.nih.gov/download.shtml|NCI]] || BioPAX || Entrez gene || sporadically || 219 pathways ||
+|| [[http://pid.nci.nih.gov/|NCI]] || scripted download of zipped release from website || BioPAX || Entrez gene || sporadically || 219 pathways ||