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| {{attachment:Software/EnrichmentMap/UserManual/enrichmentmap_logo3.png|Enrichment Map Logo|align="right"}}<<BR>> | |
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| == Brief Description == Enrichment Map is a Cytoscape plugin for functional enrichment visualization. Enrichment results have to be generated outside Enrichment Map, using any of the available methods. Gene-sets, such as pathways and Gene Ontology terms, are organized into a network (i.e. the "enrichment map"). In this way, mutually overlapping gene-sets cluster together, making interpretation easier. Enrichment Map also enables the comparison of two different enrichment results in the same map. |
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| Follow this link for [[Software/EnrichmentMap/Description|more details and an analysis example]]. | |
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| Updated at 07/20/2010 | |
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| Updated at 01/07/2009: attachment:EnrichmentMap.jar (Build from SVN revision XXX) | * [[attachment:EnrichmentMapPlugin_v1.00-RC7.zip|Enrichment Map Plugin (v1.00 Release Candidate 7)]] Download the zipped file, move it to the Cytoscape plugin directory and unzip it. == Sample Data Download == Standard analysis: * Estradiol-treated MCF7 breast cancer cells, 12hrs and 24hrs: [[attachment:EM_EstrogenMCF7_TestData.zip]] * [[Software/EnrichmentMap/Tutorial|Guided tutorial]] to load the test data into Enrichment Map |
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| == Sample Data Download == | Post-analysis: * [[attachment:estrogenTargetsLin2007.GMT|Estrogen targets]] == User Guide == [[Software/EnrichmentMap/UserManual|User Guide Link]] |
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| Estradiol-treated MCF7 breast cancer cells, 12hrs and 24hrs. attachment:EstradiolTreatedMCF7_v2.zip |
== Gene-sets for Enrichment Analysis == * we generate gene-set files for enrichment analysis (e.g. GSEA) by querying public resources such as Gene Ontology and KEGG, and using Entrez-Gene ID for genes [[GeneSetDB_02|download page]] * how to convert DAVID gene-sets to GMT: [[/DAVIDgs_R|R script]] == Publications == |
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| Guided tutorial for the test data: [:EnrichmentMap/Background/Tutorial: here] == User Guide == [:Software/EnrichmentMaps/UserManual: User Guide Link] |
* Isserlin R, Merico D, Alikhani-Koupaei R, Gramolini A, Bader GD, Emili A. <<BR>> '''''Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps.''''' <<BR>> Proteomics. '''''2010''''' Feb 1. <<BR>> PMID: 20127684 |
Enrichment Map Plugin Download Page
Brief Description
Enrichment Map is a Cytoscape plugin for functional enrichment visualization. Enrichment results have to be generated outside Enrichment Map, using any of the available methods. Gene-sets, such as pathways and Gene Ontology terms, are organized into a network (i.e. the "enrichment map"). In this way, mutually overlapping gene-sets cluster together, making interpretation easier. Enrichment Map also enables the comparison of two different enrichment results in the same map.
Follow this link for more details and an analysis example.
Plugin Download
Updated at 07/20/2010
Download the zipped file, move it to the Cytoscape plugin directory and unzip it.
Sample Data Download
Standard analysis:
Estradiol-treated MCF7 breast cancer cells, 12hrs and 24hrs: EM_EstrogenMCF7_TestData.zip
Guided tutorial to load the test data into Enrichment Map
Post-analysis:
User Guide
Gene-sets for Enrichment Analysis
- we generate gene-set files for enrichment analysis (e.g. GSEA) by querying public resources such as Gene Ontology and KEGG, and using Entrez-Gene ID for genes
how to convert DAVID gene-sets to GMT: R script
Publications
Isserlin R, Merico D, Alikhani-Koupaei R, Gramolini A, Bader GD, Emili A.
Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps.
Proteomics. 2010 Feb 1.
PMID: 20127684