{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,11]],"date-time":"2026-07-11T15:34:31Z","timestamp":1783784071012,"version":"3.55.0"},"reference-count":28,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,7,24]],"date-time":"2025-07-24T00:00:00Z","timestamp":1753315200000},"content-version":"vor","delay-in-days":210,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["P41 RR031228"],"award-info":[{"award-number":["P41 RR031228"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U24 HG012107"],"award-info":[{"award-number":["U24 HG012107"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,12,26]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>EnrichmentMap: RNASeq (enrichmentmap.org) is an intuitive, web-based app for gene-set enrichment analysis and visualization, specifically supporting two-case RNA-Seq experiments for Homo sapiens. The web app introduces a simplified user interface, faster processing times, and eliminates the need for software installation compared to running similar workflows in the Cytoscape desktop software, catering to biologists with minimal computational experience. EnrichmentMap: RNASeq is a new type of Cytoscape web app that is interoperable with Cytoscape.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The app is available to use at enrichmentmap.org and the source code is available at github.com\/cytoscape\/enrichment-map-webapp.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioadv\/vbaf178","type":"journal-article","created":{"date-parts":[[2025,7,23]],"date-time":"2025-07-23T11:52:29Z","timestamp":1753271549000},"source":"Crossref","is-referenced-by-count":3,"title":["Gene-set enrichment analysis and visualization on the web using EnrichmentMap:RNASeq"],"prefix":"10.1093","volume":"5","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0169-0480","authenticated-orcid":false,"given":"Max","family":"Franz","sequence":"first","affiliation":[{"name":"The Donnelly Centre, University of Toronto , Toronto, ON M5S 3E1,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christian T","family":"Lopes","sequence":"additional","affiliation":[{"name":"The Donnelly Centre, University of Toronto , Toronto, ON M5S 3E1,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mike","family":"Kucera","sequence":"additional","affiliation":[{"name":"The Donnelly Centre, University of Toronto , Toronto, ON M5S 3E1,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Veronique","family":"Voisin","sequence":"additional","affiliation":[{"name":"Princess Margaret Cancer Centre, University Health Network , Toronto, ON M5G 2M9,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruth","family":"Isserlin","sequence":"additional","affiliation":[{"name":"The Donnelly Centre, University of Toronto , Toronto, ON M5S 3E1,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gary D","family":"Bader","sequence":"additional","affiliation":[{"name":"The Donnelly Centre, University of Toronto , Toronto, ON M5S 3E1,","place":["Canada"]},{"name":"Princess Margaret Cancer Centre, University Health Network , Toronto, ON M5G 2M9,","place":["Canada"]},{"name":"Department of Molecular Genetics, University of Toronto , Toronto, ON M5S 1A8,","place":["Canada"]},{"name":"Department of Computer Science, University of Toronto , Toronto, ON M5S 3G4,","place":["Canada"]},{"name":"The Lunenfeld-Tanenbaum Research Institute, Sinai Health System , Toronto, ON M5T 1V4,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,7,24]]},"reference":[{"key":"2025082301115580400_vbaf178-B1","doi-asserted-by":"crossref","first-page":"R106","DOI":"10.1186\/gb-2010-11-10-r106","article-title":"Differential expression analysis for sequence count data","volume":"11","author":"Anders","year":"2010","journal-title":"Genome Biol"},{"key":"2025082301115580400_vbaf178-B2","doi-asserted-by":"crossref","first-page":"D36","DOI":"10.1093\/nar\/gku1055","article-title":"Gene: a gene-centered information resource at NCBI","volume":"43","author":"Brown","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2025082301115580400_vbaf178-B3","author":"Chen"},{"key":"2025082301115580400_vbaf178-B4","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.1109\/TVCG.2009.122","article-title":"Bubble sets: revealing set relations with isocontours over existing visualizations","volume":"15","author":"Collins","year":"2009","journal-title":"IEEE Trans Vis Comput Graph"},{"key":"2025082301115580400_vbaf178-B5","doi-asserted-by":"crossref","first-page":"P3","DOI":"10.1186\/gb-2003-4-5-p3","article-title":"DAVID: database for annotation, visualization, and integrated discovery","volume":"4","author":"Dennis","year":"2003","journal-title":"Genome Biol"},{"key":"2025082301115580400_vbaf178-B6","author":"Isserlin"},{"key":"2025082301115580400_vbaf178-B7","first-page":"D498","article-title":"The reactome pathway knowledgebase","volume":"48","author":"Jassal","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2025082301115580400_vbaf178-B8","doi-asserted-by":"publisher","author":"Korotkevich","year":"2016","DOI":"10.1101\/060012,"},{"key":"2025082301115580400_vbaf178-B9","doi-asserted-by":"crossref","first-page":"1717","DOI":"10.12688\/f1000research.9090.1","article-title":"AutoAnnotate: a cytoscape app for summarizing networks with semantic annotations. 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