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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....

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Detalles Bibliográficos
Autores principales: Merico, Daniele, Isserlin, Ruth, Stueker, Oliver, Emili, Andrew, Bader, Gary D.
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
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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/).
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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
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