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 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)
Updated at 02/14/2011 - DEVELOPMENT Release 1.2:
Compatible with cytoscape 2.6,2.7,2.8
Added Features in DEV version
- Bulk Enrichment map creation - designed for multiple GSEA results where an EM is wanted for each GSEA run. Using the rpt file of each GSEA result a cytoscape session with the EM and a pdf of each network is generated.
- Ability to compare two different species or enrichment results from two different expression platforms. Overlaps are created for each expression set separately.
- Creation of Enrichment maps based solely on a gene set file (for large gmt files requires a lot of memory)
- New similarity metric using combined overlap and jaccard coefficient based on a constant K defined by the user.
Enrichment Map Plugin (v1.2 DEV 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 DEV Release)
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
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)