Cargando…
Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation
BACKGROUND: 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....
Autores principales: | , , , , |
---|---|
Formato: | Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2010
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981572/ https://www.ncbi.nlm.nih.gov/pubmed/21085593 http://dx.doi.org/10.1371/journal.pone.0013984 |
_version_ | 1782191689227567104 |
---|---|
author | Merico, Daniele Isserlin, Ruth Stueker, Oliver Emili, Andrew Bader, Gary D. |
author_facet | Merico, Daniele Isserlin, Ruth Stueker, Oliver Emili, Andrew Bader, Gary D. |
author_sort | Merico, Daniele |
collection | PubMed |
description | BACKGROUND: 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. PRINCIPAL FINDINGS: 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. CONCLUSIONS: 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/). |
format | Text |
id | pubmed-2981572 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-29815722010-11-17 Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation Merico, Daniele Isserlin, Ruth Stueker, Oliver Emili, Andrew Bader, Gary D. PLoS One Research Article BACKGROUND: 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. PRINCIPAL FINDINGS: 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. CONCLUSIONS: 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/). Public Library of Science 2010-11-15 /pmc/articles/PMC2981572/ /pubmed/21085593 http://dx.doi.org/10.1371/journal.pone.0013984 Text en Merico et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Merico, Daniele Isserlin, Ruth Stueker, Oliver Emili, Andrew Bader, Gary D. Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation |
title | Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation |
title_full | Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation |
title_fullStr | Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation |
title_full_unstemmed | Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation |
title_short | Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation |
title_sort | enrichment map: a network-based method for gene-set enrichment visualization and interpretation |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981572/ https://www.ncbi.nlm.nih.gov/pubmed/21085593 http://dx.doi.org/10.1371/journal.pone.0013984 |
work_keys_str_mv | AT mericodaniele enrichmentmapanetworkbasedmethodforgenesetenrichmentvisualizationandinterpretation AT isserlinruth enrichmentmapanetworkbasedmethodforgenesetenrichmentvisualizationandinterpretation AT stuekeroliver enrichmentmapanetworkbasedmethodforgenesetenrichmentvisualizationandinterpretation AT emiliandrew enrichmentmapanetworkbasedmethodforgenesetenrichmentvisualizationandinterpretation AT badergaryd enrichmentmapanetworkbasedmethodforgenesetenrichmentvisualizationandinterpretation |