Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation
Open accessAbstract
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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Gene set enrichment analysis revealed that the hypoxia pathway is impaired in miR-140G/G, but not in miR-140−/− chondrocytes.
“Furthermore, gene set enrichment analysis (GSEA) revealed that the hypoxia pathway is impaired in miR-140G/G, but not in miR-140−/− chondrocytes”
From Gain-of-function mutation of microRNA-140 in human skeletal dysplasia (2019) · cites this paper as [26]
The Materials and Methods section describes GSEA of breast-cancer-cell data, while the Results section discusses gene sets in early-onset colon cancer; no page numbers are available in our copy. Searches for miR-140 chondrocytes and hypoxia-pathway impairment found no passage addressing the claimed comparison between miR-140G/G and miR-140−/− chondrocytes. (LLM, conf=0.76)
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A Highly Conserved Program of Neuronal Microexons Is Misregulated in Autistic Brains
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MethodMultilevel proteomics reveals host perturbations by SARS-CoV-2 and SARS-CoV
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Accessory subunits are integral for assembly and function of human mitochondrial complex I
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Inhibition of Amino Acid Metabolism Selectively Targets Human Leukemia Stem Cells
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Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake
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GeneMANIA Prediction Server 2013 Update
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B cells sustain inflammation and predict response to immune checkpoint blockade in human melanoma
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AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations
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Self-citationChaperone-mediated autophagy prevents collapse of the neuronal metastable proteome
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Pathway and network analysis of cancer genomes
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Self-citationAssociation analyses identify 31 new risk loci for colorectal cancer susceptibility
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Self-citationThe Proteogenomic Landscape of Curable Prostate Cancer
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The Biotrophic Development of Ustilago maydis Studied by RNA-Seq Analysis
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Therapeutic strategies for diffuse midline glioma from high-throughput combination drug screening
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Microbiota alterations in proline metabolism impact depression
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The blood-brain barrier is dysregulated in COVID-19 and serves as a CNS entry route for SARS-CoV-2
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Self-citation
- Authors
- Merico, D., Isserlin, R., Stueker, O., Emili, A., & Bader, G. D.
- Affiliations
- University of Toronto (CA)
- Corresponding author
- Merico, Daniele
- Bader, Gary D.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2010-11-15
- Volume
- 5
- Issue
- 11
- Pages
- e13984
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC2981572
- OpenAlex
- W2097948046
- Cited by
- 2,235
- References
- 58
- Citations by year
- 2026: 89 · 2025: 145 · 2024: 176 · 2023: 216 · 2022: 238 · 2021: 233 · 2020: 237 · 2019: 164 · 2018: 158 · 2017: 145 · 2016: 127 · 2015: 101 · 2014: 79 · 2013: 69 · 2012: 43
- FWCI
- 16.30
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS ONE (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Funders
- Heart and Stroke Foundation of Canada
- Genome Canada
- Ontario Genomics
- Ontario Genomics Institute
- Hospital for Sick Children
- National Institutes of Health
- National Human Genome Research Institute (P41 P41HG04118, P41HG04118, P41HG004118)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- gene set enrichment analysis, network visualization, gene set overlap, network clustering, pathway over-representation, gene expression data interpretation, Cytoscape plugin
- MeSH terms
- Algorithms, Breast Neoplasms, Colonic Neoplasms, Estrogens, Female, Humans, Software, Reproducibility of Results, Gene Expression Regulation, Neoplastic, Cluster Analysis, Computational Biology, Internet, Gene Expression Profiling, Gene Regulatory Networks
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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