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## page was renamed from Software/EnrichmentMaps ## IMPORTANT EDITING NOTE (by Daniele Merico, 12/10/2010) ## - links to this page and its subsection have been included in a book chapter ## - if the URL of this page needs to be changed, please keep the current URL and auto-direct to the new one {{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 01/5/2011 - Two versions of Release 1.0: 1. '''Compatible with cytoscape 2.8''' * [[attachment:EnrichmentMapPlugin_v1.0_28.zip|Enrichment Map Plugin (v1.0 Release)- cytoscape 2.8 compatible]] Download the zipped file, move it to the Cytoscape plugin directory and unzip it. |
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| Updated at 01/07/2009: attachment:EnrichmentMap.jar (Build from SVN revision XXX) | Distributions with source code: * [[attachment:EnrichmentMapPlugin_v1.0_28_src.zip|Enrichment Map Plugin with source code (v1.0 Release)- cytoscape 2.8 compatible]] * [[attachment:EnrichmentMapPlugin_v1.0_28_src.tar.gz|Enrichment Map Plugin with source code, tar and gzipped (v1.0 Release)- cytoscape 2.8 compatible]] |
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| 1. '''Compatible with Cytoscape 2.7, and 2.6''' * [[attachment:EnrichmentMapPlugin_v1.0_27.zip|Enrichment Map Plugin (v1.0 Release)- cytoscape 2.7/6 compatible]] Download the zipped file, move it to the Cytoscape plugin directory and unzip it. Distributions with source code: * [[attachment:EnrichmentMapPlugin_v1.0_27_src.zip|Enrichment Map Plugin with source code (v1.0 Release)- cytoscape 2.7/6 compatible]] * [[attachment:EnrichmentMapPlugin_v1.0_27_src.tar.gz|Enrichment Map Plugin with source code, tar and gzipped (v1.0 Release)- cytoscape 2.7/6 compatible]] |
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| === Main analysis === * Estradiol-treated MCF7 cells, 12 and 24hrs (Gene Expression Omnibus: GSE11352) * ''GSEA format:'' * files: [[attachment:EM_EstrogenMCF7_TestData.zip]] * [[Software/EnrichmentMap/Tutorial|Guided tutorial]] to load the files into Enrichment Map * ''Generic format:'' * files: [[attachment:EM_EstrogenMCF7_TestData_Generic.zip]] * note: the results should be the same as GSEA |
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| Estradiol-treated MCF7 breast cancer cells, 12hrs and 24hrs. attachment:EstradiolTreatedMCF7_v2.zip |
=== Query-set analysis (aka Post-analysis) === * [[attachment:estrogenTargetsLin2007.GMT|Estrogen targets]] (Lin CY et al 2007, Plos Genetics; PMID: 17542648) == User Guide == [[Software/EnrichmentMap/UserManual|User Guide Link]] |
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| Guided tutorial for the test data: [:EnrichmentMap/Background/Tutorial: here] | == 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 == === Cite EM === * '''Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation'''<<BR>> '''Merico D''', '''Isserlin R''', '''Stueker O''', Emili A, '''Bader GD'''<<BR>>[[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0013984|PLoS One. 2010 Nov 15;5(11):e13984]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/21085593|PubMed Abstract]] -[[attachment:2010_MericoIsserlinStuekerBader-EnrichmentMap_PLoSOne.pdf|PDF]]<<BR>> |
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| == User Guide == | === Examples of Use === * '''Functional impact of global rare copy number variation in autism spectrum disorders.'''<<BR>>Pinto D, Pagnamenta AT, Klei L, Anney R, '''Merico D''', Regan R, Conroy J, Magalhaes TR, Correia C, Abrahams BS, Almeida J, Bacchelli E, '''Bader GD''', ''et al.''<<BR>>[[http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature09146.html|Nature. 2010 Jun 9 (Epub ahead of print)]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/20531469|PubMed Abstract]] - [[attachment:Publications/2010_AutismNature.pdf|PDF]]<<BR>>[[http://blogs.nature.com/news/thegreatbeyond/2010/06/rare_genetic_variants_linked_t.html|Nature Blogs]] - [[http://www.theglobeandmail.com/news/national/autism-caused-by-wide-array-of-rare-gene-changes-study/article1597861/|In the news (The Globe and Mail)]]<<BR>> |
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| [:Software/EnrichmentMaps/UserManual: User Guide Link] | * '''Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps'''<<BR>>'''Isserlin R''', '''Merico D''', Alikhani-Koupaei R, Gramolini A, '''Bader GD''', Emili A.<<BR>>[[http://www3.interscience.wiley.com/journal/123269335/abstract|Proteomics 2010, March 10(6):1316-27]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/20127684|Pubmed Abstract]] - [[attachment:Publications/2010_EM_proteomics.pdf|PDF]]<<BR>> |
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 01/5/2011 - Two versions of Release 1.0:
Compatible with cytoscape 2.8
Download the zipped file, move it to the Cytoscape plugin directory and unzip it.
Distributions with source code:
Enrichment Map Plugin with source code (v1.0 Release)- cytoscape 2.8 compatible
Enrichment Map Plugin with source code, tar and gzipped (v1.0 Release)- cytoscape 2.8 compatible
Compatible with Cytoscape 2.7, and 2.6
Download the zipped file, move it to the Cytoscape plugin directory and unzip it.
Distributions with source code:
Enrichment Map Plugin with source code (v1.0 Release)- cytoscape 2.7/6 compatible
Enrichment Map Plugin with source code, tar and gzipped (v1.0 Release)- cytoscape 2.7/6 compatible
Sample Data Download
Main analysis
- Estradiol-treated MCF7 cells, 12 and 24hrs (Gene Expression Omnibus: GSE11352)
GSEA format:
files: EM_EstrogenMCF7_TestData.zip
Guided tutorial to load the files into Enrichment Map
Generic format:
- note: the results should be the same as GSEA
Query-set analysis (aka Post-analysis)
Estrogen targets (Lin CY et al 2007, Plos Genetics; PMID: 17542648)
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
Cite EM
Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation
Merico D, Isserlin R, Stueker O, Emili A, Bader GD
PLoS One. 2010 Nov 15;5(11):e13984
PubMed Abstract -PDF
Examples of Use
Functional impact of global rare copy number variation in autism spectrum disorders.
Pinto D, Pagnamenta AT, Klei L, Anney R, Merico D, Regan R, Conroy J, Magalhaes TR, Correia C, Abrahams BS, Almeida J, Bacchelli E, Bader GD, et al.
Nature. 2010 Jun 9 (Epub ahead of print)
PubMed Abstract - PDF
Nature Blogs - In the news (The Globe and Mail)
Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps
Isserlin R, Merico D, Alikhani-Koupaei R, Gramolini A, Bader GD, Emili A.
Proteomics 2010, March 10(6):1316-27
Pubmed Abstract - PDF