{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T02:41:18Z","timestamp":1780540878598,"version":"3.54.1"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2023,5,1]],"date-time":"2023-05-01T00:00:00Z","timestamp":1682899200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"NIH\/NIGMS","award":["P41 GM132087"],"award-info":[{"award-number":["P41 GM132087"]}]},{"name":"NIH\/NHGRI","award":["U41HG000739"],"award-info":[{"award-number":["U41HG000739"]}]},{"DOI":"10.13039\/501100003122","name":"UK Medical Research Council","doi-asserted-by":"publisher","award":["MR\/W024233\/1"],"award-info":[{"award-number":["MR\/W024233\/1"]}],"id":[{"id":"10.13039\/501100003122","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Gene set enrichment analysis (GSEA) plays an important role in large-scale data analysis, helping scientists discover the underlying biological patterns over-represented in a gene list resulting from, for example, an \u2018omics\u2019 study. Gene Ontology (GO) annotation is the most frequently used classification mechanism for gene set definition. Here we present a new GSEA tool, PANGEA (PAthway, Network and Gene-set Enrichment Analysis; https:\/\/www.flyrnai.org\/tools\/pangea\/), developed to allow a more flexible and configurable approach to data analysis using a variety of classification sets. PANGEA allows GO analysis to be performed on different sets of GO annotations, for example excluding high-throughput studies. Beyond GO, gene sets for pathway annotation and protein complex data from various resources as well as expression and disease annotation from the Alliance of Genome Resources (Alliance). In addition, visualizations of results are enhanced by providing an option to view network of gene set to gene relationships. The tool also allows comparison of multiple input gene lists and accompanying visualisation tools for quick and easy comparison. This new tool will facilitate GSEA for Drosophila and other major model organisms based on high-quality annotated information available for these species.<\/jats:p>","DOI":"10.1093\/nar\/gkad331","type":"journal-article","created":{"date-parts":[[2023,5,1]],"date-time":"2023-05-01T09:55:53Z","timestamp":1682934953000},"page":"W419-W426","source":"Crossref","is-referenced-by-count":101,"title":["PANGEA: a new gene set enrichment tool for <i>Drosophila<\/i> and common research organisms"],"prefix":"10.1093","volume":"51","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1494-1402","authenticated-orcid":false,"given":"Yanhui","family":"Hu","sequence":"first","affiliation":[{"name":"Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University , Boston , MA \u00a002115, USA"},{"name":"Drosophila RNAi Screening Center, Harvard Medical School , 77 Avenue Louis Pasteur, Boston , MA \u00a002115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aram","family":"Comjean","sequence":"additional","affiliation":[{"name":"Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University , Boston , MA \u00a002115, USA"},{"name":"Drosophila RNAi Screening Center, Harvard Medical School , 77 Avenue Louis Pasteur, Boston , MA \u00a002115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3212-6364","authenticated-orcid":false,"given":"Helen","family":"Attrill","sequence":"additional","affiliation":[{"name":"Department of Physiology, Development and Neuroscience, University of Cambridge , Downing Street, Cambridge CB2 3DY, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giulia","family":"Antonazzo","sequence":"additional","affiliation":[{"name":"Department of Physiology, Development and Neuroscience, University of Cambridge , Downing Street, Cambridge CB2 3DY, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jim","family":"Thurmond","sequence":"additional","affiliation":[{"name":"Department of Biology, Indiana University , Bloomington , IN \u00a047405, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weihang","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University , Boston , MA \u00a002115, USA"},{"name":"Drosophila RNAi Screening Center, Harvard Medical School , 77 Avenue Louis Pasteur, Boston , MA \u00a002115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fangge","family":"Li","sequence":"additional","affiliation":[{"name":"Drosophila RNAi Screening Center, Harvard Medical School , 77 Avenue Louis Pasteur, Boston , MA \u00a002115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tiffany","family":"Chao","sequence":"additional","affiliation":[{"name":"Drosophila RNAi Screening Center, Harvard Medical School , 77 Avenue Louis Pasteur, Boston , MA \u00a002115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephanie E","family":"Mohr","sequence":"additional","affiliation":[{"name":"Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University , Boston , MA \u00a002115, USA"},{"name":"Drosophila RNAi Screening Center, Harvard Medical School , 77 Avenue Louis Pasteur, Boston , MA \u00a002115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8958-7017","authenticated-orcid":false,"given":"Nicholas H","family":"Brown","sequence":"additional","affiliation":[{"name":"Department of Physiology, Development and Neuroscience, University of Cambridge , Downing Street, Cambridge CB2 3DY, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7542-472X","authenticated-orcid":false,"given":"Norbert","family":"Perrimon","sequence":"additional","affiliation":[{"name":"Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University , Boston , MA \u00a002115, USA"},{"name":"Drosophila RNAi Screening Center, Harvard Medical School , 77 Avenue Louis Pasteur, Boston , MA \u00a002115, USA"},{"name":"Howard Hughes Medical Institute , Boston , MA \u00a002138, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,5,1]]},"reference":[{"key":"2023070505005046400_B1","doi-asserted-by":"crossref","first-page":"843","DOI":"10.1016\/j.ajhg.2017.04.010","article-title":"MARRVEL: integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome","volume":"100","author":"Wang","year":"2017","journal-title":"Am. 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