{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T04:20:42Z","timestamp":1768450842101,"version":"3.49.0"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2020,1,24]],"date-time":"2020-01-24T00:00:00Z","timestamp":1579824000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Ontario Research Fund","award":["34876"],"award-info":[{"award-number":["34876"]}]},{"name":"Natural Sciences Research Council"},{"DOI":"10.13039\/501100000038","name":"NSERC","doi-asserted-by":"publisher","award":["203475"],"award-info":[{"award-number":["203475"]}],"id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000196","name":"Canada Foundation for Innovation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000196","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008176","name":"CFI","doi-asserted-by":"publisher","award":["225404"],"award-info":[{"award-number":["225404"]}],"id":[{"id":"10.13039\/100008176","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008176","name":"CFI","doi-asserted-by":"publisher","award":["30865"],"award-info":[{"award-number":["30865"]}],"id":[{"id":"10.13039\/100008176","id-type":"DOI","asserted-by":"publisher"}]},{"name":"IBM and Ian Lawson van Toch Fund"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Gene sets over-representation analysis (GSOA) is a common technique of enrichment analysis that measures the overlap between a gene set and selected instances (e.g. pathways). Despite its popularity, there is currently no established standard for visualization of GSOA results.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we propose a visual exploration of the GSOA results by showing the relationships among the enriched instances, while highlighting important instance attributes, such as significance, closeness (centrality) and clustering.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>GSOAP is implemented as an R package and is available at https:\/\/github.com\/tomastokar\/gsoap.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa001","type":"journal-article","created":{"date-parts":[[2020,1,21]],"date-time":"2020-01-21T20:10:09Z","timestamp":1579637409000},"page":"2923-2925","source":"Crossref","is-referenced-by-count":14,"title":["GSOAP: a tool for visualization of gene set over-representation analysis"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4873-0032","authenticated-orcid":false,"given":"Tomas","family":"Tokar","sequence":"first","affiliation":[{"name":"Krembil Research Institute , UHN, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada"}]},{"given":"Chiara","family":"Pastrello","sequence":"additional","affiliation":[{"name":"Krembil Research Institute , UHN, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada"}]},{"given":"Igor","family":"Jurisica","sequence":"additional","affiliation":[{"name":"Krembil Research Institute , UHN, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada"},{"name":"Department of Computer Science , University of Toronto, Toronto, ON M5T 3A1, Canada"},{"name":"Department of Medical Biophysics , University of Toronto, Toronto, ON M5G 1L7, Canada"},{"name":"Institute of Neuroimmunology , Slovak Academy of Sciences, Dubravska cesta 9, SK-84510, Bratislava, Slovakia"}]}],"member":"286","published-online":{"date-parts":[[2020,1,24]]},"reference":[{"key":"2023013111494310700_btaa001-B1","author":"Alexa","year":"2016"},{"key":"2023013111494310700_btaa001-B2","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1111\/j.1745-3984.2003.tb01108.x","article-title":"Modern multidimensional scaling: theory and applications","volume":"40","author":"Borg","year":"2003","journal-title":"J. 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Neural Netw"},{"key":"2023013111494310700_btaa001-B5","doi-asserted-by":"crossref","first-page":"D419","DOI":"10.1093\/nar\/gkw1082","article-title":"PathDIP: an annotated resource for known and predicted human gene-pathway associations and pathway enrichment analysis","volume":"45","author":"Rahmati","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2023013111494310700_btaa001-B6","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1177\/1525822X0001200104","article-title":"A multidimensional scaling stress evaluation table","volume":"12","author":"Sturrock","year":"2000","journal-title":"Field Methods"},{"key":"2023013111494310700_btaa001-B7","doi-asserted-by":"crossref","first-page":"2319","DOI":"10.1126\/science.290.5500.2319","article-title":"A global geometric framework for nonlinear dimensionality reduction","volume":"290","author":"Tenenbaum","year":"2000","journal-title":"Science"},{"key":"2023013111494310700_btaa001-B8","doi-asserted-by":"crossref","first-page":"9137","DOI":"10.18632\/oncotarget.24070","article-title":"Differentially expressed microRNAs in lung adenocarcinoma invert effects of copy number aberrations of prognostic genes","volume":"9","author":"Tokar","year":"2018","journal-title":"Oncotarget"},{"key":"2023013111494310700_btaa001-B9","first-page":"2579","article-title":"Visualizing data using t-SNE","volume":"9","author":"van der Maaten","year":"2008","journal-title":"J. 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