Enrichment Map Plugin Download Page
Contents
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 07/06/2011 - Release 1.2 : Compatible with cytoscape 2.6,2.7,2.8
Enrichment Map Plugin (v1.2 Release)
Download the zipped file, move it to the Cytoscape plugin directory and unzip it.
Distributions with source code:
Enrichment Map Plugin with source code, tar and gzipped (v1.2 Release)
Updated at 02/7/2011 - Release 1.1: Compatible with cytoscape 2.6,2.7,2.8
Enrichment Map Plugin (v1.1 Release)
Download the zipped file, move it to the Cytoscape plugin directory and unzip it.
Distributions with source code:
Enrichment Map Plugin with source code, tar and gzipped (v1.1 Release)
Development Versions
Updated at 10/17/2013 - Release 1.3 - DEVELOPMENT Release : Compatible with cytoscape 2.6,2.7,2.8
- Added bug fix with missing leading edge on reloaded sessions files for down regulated gene sets.
- Added command tool support
- Added EDB support
- Added values to heat map
- Added ability to load GSEA class files directly
- fixed misc bugs
Enrichment Map Plugin (v1.3 DEV)
Download the zipped file, move it to the Cytoscape plugin directory and unzip it.
Source code can be found on github: https://github.com/BaderLab/EnrichmentMapApp
Updated at 08/05/2011 - Release 1.3 - DEVELOPMENT Release : Compatible with cytoscape 2.6,2.7,2.8
- Added bug fix with missing leading edge on reloaded sessions files for down regulated gene sets.
Enrichment Map Plugin (v1.3 DEV)
Download the zipped file, move it to the Cytoscape plugin directory and unzip it.
Distributions with source code:
Enrichment Map Plugin with source code, tar and gzipped (v1.3 DEV)
Tutorials and Examples
data used for the tutorials: Estradiol-treated MCF7 cells, 12 and 24hrs (Gene Expression Omnibus: GSE11352)
GSEA format:
Guided GSEA tutorial to load the filed into Enrichment Map
Guided GSEA/EM tutorial to create EM directly from GSEA interface for single analysis (direct link from GSEA Reports frame).
Guided GSEA/EM tutorial for multiple analyses to create an EM directly from GSEA interface for multiple analysis (from "Step in GSEA analysis frame)
Generic format:
- note: the results should be the same as GSEA
DAVID format:
files: EM_David_testData.zip
Guided DAVID Tutorial to load the files into Enrichment Map
BiNGO format:
files: EM_Bingo_testData.zip
Guided BiNGO Tutorial to load the files into Enrichment Map
g:Profiler format:
files: EM_gProfiler_testData.zip
Guided g:Profiler Tutorial to load the files into Enrichment Map
Query-set analysis (aka Post-analysis)
Estrogen targets (Lin CY et al 2007, Plos Genetics; PMID: 17542648)
User Guide
Gene-sets for Enrichment Analysis
directly downloading our monthly updated gene-set collections from Baderlab genesets collections. Description of sources and methods used to create collection can be found 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
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
Papers Citing Enrichment Map
Pathway analysis of expression data: deciphering functional building blocks of complex diseases.
Emmert-Streib F, Glazko GV.
PLoS Comput Biol. 2011 May;7(5):e1002053.
PubMedInflammasome is a central player in the induction of obesity and insulin resistance.
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.
Proc Natl Acad Sci U S A. 2011 Aug 29.
PubMedDelineation of Two Clinically and Molecularly Distinct Subgroups of Posterior Fossa Ependymoma
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
Cancer Cell, Volume 20, Issue 2, 143-157, 16 August 2011
PubMed Abstract - PDF
Report a Bug or a Problem
please make sure you don't have formatting issues (have a look at the 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
- 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)
For Feature requests please send to enrichmentmap-dev@googlegroups.com