Open Access
PLoS ONE, volume 5, issue 11, pages e13984
Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation
Daniele Merico
1
,
Ruth Isserlin
1
,
Oliver Stueker
1
,
Andrew Emili
1
,
Gary D. Bader
1
Publication type: Journal Article
Publication date: 2010-11-15
Multidisciplinary
Abstract
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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Merico D. et al. Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation // PLoS ONE. 2010. Vol. 5. No. 11. p. e13984.
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Merico D., Isserlin R., Stueker O., Emili A., Bader G. D. Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation // PLoS ONE. 2010. Vol. 5. No. 11. p. e13984.
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TY - JOUR
DO - 10.1371/journal.pone.0013984
UR - https://doi.org/10.1371/journal.pone.0013984
TI - Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation
T2 - PLoS ONE
AU - Merico, Daniele
AU - Isserlin, Ruth
AU - Stueker, Oliver
AU - Emili, Andrew
AU - Bader, Gary D.
PY - 2010
DA - 2010/11/15
PB - Public Library of Science (PLoS)
SP - e13984
IS - 11
VL - 5
SN - 1932-6203
ER -
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BibTex (up to 50 authors)
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@article{2010_Merico,
author = {Daniele Merico and Ruth Isserlin and Oliver Stueker and Andrew Emili and Gary D. Bader},
title = {Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation},
journal = {PLoS ONE},
year = {2010},
volume = {5},
publisher = {Public Library of Science (PLoS)},
month = {nov},
url = {https://doi.org/10.1371/journal.pone.0013984},
number = {11},
pages = {e13984},
doi = {10.1371/journal.pone.0013984}
}
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MLA
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Merico, Daniele, et al. “Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation.” PLoS ONE, vol. 5, no. 11, Nov. 2010, p. e13984. https://doi.org/10.1371/journal.pone.0013984.
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Publisher
Journal
scimago Q1
wos Q1
SJR
0.839
CiteScore
6.2
Impact factor
2.9
ISSN
19326203
(Print, Electronic)