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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_logo_mini.png|Enrichment Map Logo|align="right"}}<<BR>> 
= Enrichment Map Plugin Download Page =
<<TableOfContents(5)>>
== 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 [[Software/EnrichmentMap/Description|more details and an analysis example]]. 

== Legends ==
For easier figure creation download our template legends that contains all the visual properties used in a standard enrichment map.  Download and customize legend to fit your network
  * [[attachment:em_legend.pdf|PDF File]]
  * [[attachment:em_legend.svg|SVG File]]
  * {{attachment:em_example_legend.png|Enrichment Map Example Legend|width=500}}<<BR>> 

== Downloads ==

Cytoscape can be downloaded from: http://cytoscape.org/

EnrichmentMap is available on the Cytoscape App Store: http://apps.cytoscape.org/apps/enrichmentmap

Alternatively download the EnrichmentMap Pipeline Collection. This will install EnrichmentMap as well as a suite of other apps that work well with EnrichmentMap, including AutoAnnotate, WordCloud and clusterMaker2: http://apps.cytoscape.org/apps/enrichmentmappipelinecollection

== Tutorials and Examples ==

Tuturials and protocols for EnrichmentMap 3.0 are here: https://baderlab.github.io/Cytoscape_workflows/EnrichmentMapPipeline/

Tutorials for the older 2.2 version of EnrichmentMap are here: http://enrichmentmap.readthedocs.io/en/docs-2.2/Tutorials.html

== User Guide ==

The EnrichmentMap User Guide has been moved to: http://enrichmentmap.readthedocs.io

User Guide for older 2.2 version of EnrichmentMap (including tutorials) is here: http://enrichmentmap.readthedocs.io/en/docs-2.2/

== Gene-sets for Enrichment Analysis ==
 * directly downloading our monthly updated gene-set collections from [[http://download.baderlab.org/EM_Genesets/current_release/|Baderlab genesets]] collections. Description of sources and methods used to create collection can be found [[http://baderlab.org/GeneSets|here]]
 * 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>>

=== 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>>

 * '''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>>


== Papers Citing Enrichment Map ==

 * [[http://www.ncbi.nlm.nih.gov/pubmed?db=pubmed&cmd=link&linkname=pubmed_pubmed_citedin&uid=21085593|Citations in Pubmed Central]]


 * '''Pathway analysis of expression data: deciphering functional building blocks of complex diseases.'''<<BR>> Emmert-Streib F, Glazko GV.<<BR>> PLoS Comput Biol. 2011 May;7(5):e1002053.<<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/21637797|PubMed]]

 * '''Inflammasome is a central player in the induction of obesity and insulin resistance.'''<<BR>> Stienstra R, van Diepen JA, Tack CJ, Zaki MH, van de Veerdonk FL, Perera D, Neale GA, Hooiveld GJ, Hijmans A, Vroegrijk I, van den Berg S, Romijn J, Rensen PC, Joosten LA, Netea MG, Kanneganti TD.<<BR>> Proc Natl Acad Sci U S A. 2011 Aug 29.<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/21637797|PubMed]]

 * '''Delineation of Two Clinically and Molecularly Distinct Subgroups of Posterior Fossa Ependymoma'''<<BR>> Witt H, Mack SC, Ryzhova M, Bender S, Sill M, '''Isserlin R''', Benner A, Hielscher T, Milde T, Remke M, Jones DTW, Northcott PA, Garzia L, Bertrand KC, Wittmann A, Yao Y, Roberts SS, Massimi L, Van Meter T, Weiss WA, Gupta N, Grajkowska W, Lach B, Cho YJ, von Deimling A, Kulozik AE, Witt O, '''Bader GD''', Hawkins CE, Tabori U, Guha A, Rutka JT, Lichter P, Korshunov A, Taylor MD, Pfister SM <<BR>> [[http://www.sciencedirect.com/science/article/pii/S1535610811002625|Cancer Cell, Volume 20, Issue 2, 143-157, 16 August 2011]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/21840481|PubMed Abstract]] - [[attachment:Publications/ependymoma.pdf|PDF]]<<BR>>

== Report a Bug or a Problem ==
 1. please make sure you don't have formatting issues (have a look at the [[Software/EnrichmentMap/UserManual|User Guide (and FAQ)]]) 
   * if you are still not sure how to handle formats, 
   * or you don't know what's the best suitable analysis for you,
   * please send an email to: daniele[AT]merico[DOT]gmail.com
 1. please check what's your
   * plugin version and build (from the Cytoscape menu / Plugins / Enrichment Map / About)
   * Cytoscape version (from the Cytoscape menu / Cytoscape)
   * Operating System (e.g. Windows Vista)
 and send your bug report to ruth[DOT]isserlin[AT]utoronto.ca<<BR>> OR <<BR>> report the bug to the Enrichment map issue tracker:
   1. go to https://github.com/BaderLab/EnrichmentMapApp
   1. click on "Issues"
   1. click on "New Issue"
   1. write a short description of the issue
   1. attached session file (.cys) file or example input files if applicable
   1. Make sure to enter plugin version and build, cytoscape version and operating system.
   1. click on "Submit new issue"
 1. For Feature requests please send to enrichmentmap-dev@googlegroups.com