Differences between revisions 23 and 25 (spanning 2 versions)

Enrichment Map Gene Sets

Contents

Enrichment Map Gene Sets

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)

Sources

Human

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	NCI	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

Mouse

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

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 Gene Sets

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 23 as of 2011-11-15 16:40:39 → 
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  Editor: RuthIsserlin
  Comment:
+   ← Revision 25 as of 2011-11-15 16:59:32 → ⇥
  Size: 6082
  Editor: RuthIsserlin
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
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-= Enrichment Map Genesets =
+= Enrichment Map Gene Sets =
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-  * Enrichment Map Genesets are a set of Gene Set files in GMT format (compatible with [[http://www.broadinstitute.org/gsea/index.jsp| GSEA]]) updated '''monthly''' from original source locations available with:
+  * Enrichment Map Gene Sets are a set of Gene Set files in GMT format (compatible with [[http://www.broadinstitute.org/gsea/index.jsp| GSEA]]) updated '''monthly''' from original source locations available with:
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-  * The GMT File format contains one gene set per line.  Each line contains:
+  * The GMT File format contains one Gene Set per line.  Each line contains:
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-      * Name = Gene set Name | Gene set Source | Gene set Source identifier
+      * Name = Gene Set Name | Gene Set Source | Gene Set Source identifier
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-      * Description = Gene set Name
+      * Description = Gene Set Name
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-|| [[http://www.broadinstitute.org/gsea/msigdb/index.jsp|Msigdb - c2]] <<BR>> (other + Biocarta) || static (needs to be updated manually) || GMT || Entrez gene || sporadically ||  Biocarta - 217<<BR>> Other - 47 ||
+|| [[http://www.broadinstitute.org/gsea/msigdb/index.jsp|Msigdb - c2]] <<BR>> (other + Biocarta) || manual download from Msigdb || GMT || Entrez gene || sporadically ||  Biocarta - 217<<BR>> Other - 47 ||
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-|| IOB || directly from IOB - static (July 2011) || BioPAX || Entrez gene || sporadically  || 35 pathways -  <<BR>> 10 are the same as !CellMap,<<BR>> 1 is the same as !NetPath||
|| [[http://www.netpath.org/browse/|NetPath]] || (scripted grab of file numbered 1-25) || BioPAX || Entrez gene || static ||  25 pathways - <<BR>> 12 are cancer pathways (10 are !CellMap) <<BR>> 13 are immunity pathways ||
|| [[http://humancyc.org/|HumanCyc]] || scripted grab of zipped release from password protected website. || BioPAX || !UniProt || updated periodically || 249 Pathways  ||
|| [[http://www.reactome.org/ReactomeGWT/entrypoint.html|Reactome]] || scripted grab of zipped release from website || BioPAX || !UniProt || updated release ||  1117 pathways (release 37) ||
|| [[http://www.ebi.ac.uk/GO/|GO]] || scripted grab from EBI ftp site (human) || GAF || Uniprot || released once a month || 13,034 no GO IEA <<BR>> 15,181 with GO IEA  ||
|| [[http://www.broadinstitute.org/gsea/msigdb/index.jsp|Msigdb - c3]] <<BR>> Specialty GMTs <<BR>> mirs, transcription factors || grab from Msigdb || GMT || Entrez gene || sporadically || 221 miRs <<BR>> 616 TFs ||
+|| IOB || received directly from IOB - static (July 2011) || BioPAX || Entrez gene || sporadically  || 35 pathways -  <<BR>> 10 are the same as !CellMap,<<BR>> 1 is the same as !NetPath||
|| [[http://www.netpath.org/browse/|NetPath]] || scripted download of files numbered 1-25 || BioPAX || Entrez gene || static ||  25 pathways - <<BR>> 12 are cancer pathways (10 are !CellMap) <<BR>> 13 are immunity pathways ||
|| [[http://humancyc.org/|HumanCyc]] || scripted download of zipped release from password protected website. || BioPAX || !UniProt || updated periodically || 249 Pathways  ||
|| [[http://www.reactome.org/ReactomeGWT/entrypoint.html|Reactome]] || scripted download of zipped release from website || BioPAX || !UniProt || updated release ||  1117 pathways (release 37) ||
|| [[http://www.ebi.ac.uk/GO/|GO]] || scripted download from EBI ftp site (human) || GAF || Uniprot || released once a month || 13,034 no GO IEA <<BR>> 15,181 with GO IEA  ||
|| [[http://www.broadinstitute.org/gsea/msigdb/index.jsp|Msigdb - c3]] <<BR>> Specialty GMTs <<BR>> mirs, transcription factors || manual download from Msigdb || GMT || Entrez gene || sporadically || 221 miRs <<BR>> 616 TFs ||
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-|| [[http://www.reactome.org/ReactomeGWT/entrypoint.html|Reactome]] || scripted grab of zipped release from website || BioPAX || !UniProt || updated release ||  946 pathways (release 37) ||
|| [[http://www.informatics.jax.org/mgihome/GO/project.shtml|GO]] || scripted grab from MGI ftp site (mouse) || GAF || MGI || released once a month || 14,563 no GO IEA <<BR>> 15,041 with GO IEA  ||
+|| [[http://www.reactome.org/ReactomeGWT/entrypoint.html|Reactome]] || scripted download of zipped release from website || BioPAX || !UniProt || updated release ||  946 pathways (release 37) ||
|| [[http://www.informatics.jax.org/mgihome/GO/project.shtml|GO]] || scripted download from MGI ftp site (mouse) || GAF || MGI || released once a month || 14,563 no GO IEA <<BR>> 15,041 with GO IEA  ||
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-  * In each <identifier> directory There are amalgamated gene set files:
+  * In each <identifier> directory There are amalgamated Gene Set files:
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-== Creating customized Genesets ==
+== Creating customized Gene Sets ==