Journal Article

Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation

Stueker, Oliver, Merico, Daniele, Isserlin, Ruth, Emili, Andrew, Bader, Gary D.

2010

Overview

Gene-set enrichment analysis is a useful technique to help functionally characterize large gene lists, such as the results of gene expression experiments. This technique finds functionally coherent gene-sets, such as pathways, that are statistically over-represented in a given gene list. Ideally, the number of resulting sets is smaller than the number of genes in the list, thus simplifying interpretation. However, the increasing number and redundancy of gene-sets used by many current enrichment analysis software works against this ideal. To overcome gene-set redundancy and help in the interpretation of large gene lists, we developed \"Enrichment Map\", a network-based visualization method for gene-set enrichment results. Gene-sets are organized in a network, where each set is a node and edges represent gene overlap between sets. Automated network layout groups related gene-sets into network clusters, enabling the user to quickly identify the major enriched functional themes and more easily interpret the enrichment results. Enrichment Map is a significant advance in the interpretation of enrichment analysis. Any research project that generates a list of genes can take advantage of this visualization framework. Enrichment Map is implemented as a freely available and user friendly plug-in for the Cytoscape network visualization software (http://baderlab.org/Software/EnrichmentMap/).

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Algorithms / Analysis / Autism / Bioinformatics / Biology / Breast cancer / Breast Neoplasms - genetics / Cardiomyopathy / Cluster Analysis / Colonic Neoplasms - genetics / Colorectal cancer / Computational Biology / Computational Biology - methods / Computational Biology/Genomics / Computational Biology/Systems Biology / Computer programs / Enrichment / Estrogens - pharmacology / Female / Gene expression / Gene Expression Profiling / Gene Expression Regulation, Neoplastic - drug effects / Gene Regulatory Networks / Gene set enrichment analysis / Genes / Genetics / Genomes / Genomics / Humans / Impact analysis / Information sharing / Internet / Lists / Medical research / Methods / Problems / Redundancy / Reproducibility of Results / Research projects / Software / Statistical analysis / Statistical methods / Stem cells / Tumors / Visualization / Visualization (Computer)