{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,3]],"date-time":"2025-09-03T11:09:45Z","timestamp":1756897785987,"version":"3.41.2"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2025,3,3]],"date-time":"2025-03-03T00:00:00Z","timestamp":1740960000000},"content-version":"vor","delay-in-days":2,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000289","name":"Cancer Research UK","doi-asserted-by":"publisher","award":["C476\/A27060"],"award-info":[{"award-number":["C476\/A27060"]}],"id":[{"id":"10.13039\/501100000289","id-type":"DOI","asserted-by":"publisher"}]},{"name":"University of Oxford Returning Carer\u2019s Fund"},{"DOI":"10.13039\/100004440","name":"Wellcome","doi-asserted-by":"publisher","award":["203141\/Z\/16\/Z"],"award-info":[{"award-number":["203141\/Z\/16\/Z"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>GeneFEAST, implemented in Python, is a gene-centric functional enrichment analysis summarization and visualization tool that can be applied to large functional enrichment analysis (FEA) results arising from upstream FEA pipelines. It produces a systematic, navigable HTML report, making it easy to identify sets of genes putatively driving multiple enrichments and to explore gene-level quantitative data first used to identify input genes. Further, GeneFEAST can juxtapose FEA results from multiple studies, making it possible to highlight patterns of gene expression amongst genes that are differentially expressed in at least one of multiple conditions, and which give rise to shared enrichments under those conditions. Thus, GeneFEAST offers a novel, effective way to address the complexities of linking up many overlapping FEA results to their underlying genes and data, advancing gene-centric hypotheses, and providing pivotal information for downstream validation experiments.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>GeneFEAST GitHub repository: https:\/\/github.com\/avigailtaylor\/GeneFEAST; Zenodo record: 10.5281\/zenodo.14753734; Python Package Index: https:\/\/pypi.org\/project\/genefeast; Docker container: ghcr.io\/avigailtaylor\/genefeast.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf100","type":"journal-article","created":{"date-parts":[[2025,3,5]],"date-time":"2025-03-05T00:11:26Z","timestamp":1741133486000},"source":"Crossref","is-referenced-by-count":1,"title":["GeneFEAST: the pivotal, gene-centric step in functional enrichment analysis interpretation"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8199-1007","authenticated-orcid":false,"given":"Avigail","family":"Taylor","sequence":"first","affiliation":[{"name":"Nuffield Department of Medicine, University of Oxford , Oxford OX3 7BN,","place":["United Kingdom"]},{"name":"Centre for Human Genetics, University of Oxford , Oxford OX3 7BN,","place":["United Kingdom"]},{"name":"Nuffield Department of Surgical Sciences, University of Oxford, ORCRB , Oxford OX3 7DQ,","place":["United Kingdom"]}]},{"given":"Valentine M","family":"Macaulay","sequence":"additional","affiliation":[{"name":"Nuffield Department of Surgical Sciences, University of Oxford, ORCRB , Oxford OX3 7DQ,","place":["United Kingdom"]}]},{"given":"Matthieu J","family":"Miossec","sequence":"additional","affiliation":[{"name":"Centre for Human Genetics, University of Oxford , Oxford OX3 7BN,","place":["United Kingdom"]}]},{"given":"Anand K","family":"Maurya","sequence":"additional","affiliation":[{"name":"Nuffield Department of Medicine, University of Oxford , Oxford OX3 7BN,","place":["United Kingdom"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0409-406X","authenticated-orcid":false,"given":"Francesca M","family":"Buffa","sequence":"additional","affiliation":[{"name":"Computational Biology & Integrative Genomics Lab, Department of Oncology, University of Oxford, ORCRB , Oxford OX3 7DQ,","place":["United Kingdom"]}]}],"member":"286","published-online":{"date-parts":[[2025,3,3]]},"reference":[{"key":"2025031823572659700_btaf100-B1","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology. The gene ontology consortium","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat Genet"},{"key":"2025031823572659700_btaf100-B2","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple hypothesis testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J R Stat Soc B"},{"key":"2025031823572659700_btaf100-B3","doi-asserted-by":"crossref","first-page":"066111","DOI":"10.1103\/PhysRevE.70.066111","article-title":"Finding community structure in very large networks","volume":"70","author":"Clauset","year":"2004","journal-title":"Phys Rev E Stat Nonlin Soft Matter Phys"},{"key":"2025031823572659700_btaf100-B4","doi-asserted-by":"crossref","first-page":"R183","DOI":"10.1186\/gb-2007-8-9-r183","article-title":"The DAVID gene functional classification tool: a novel biological module-centric algorithm to functionally analyze large gene lists","volume":"8","author":"Huang","year":"2007","journal-title":"Genome Biol"},{"key":"2025031823572659700_btaf100-B5","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: kyoto encyclopedia of genes and genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"2025031823572659700_btaf100-B6","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1101\/gr.092759.109","article-title":"Circos: an information aesthetic for comparative genomics","volume":"19","author":"Krzywinski","year":"2009","journal-title":"Genome Res"},{"key":"2025031823572659700_btaf100-B7","doi-asserted-by":"crossref","first-page":"1983","DOI":"10.1109\/TVCG.2014.2346248","article-title":"UpSet: visualisation of intersecting sets","volume":"20","author":"Lex","year":"2014","journal-title":"IEEE Trans Vis Comput Graph"},{"key":"2025031823572659700_btaf100-B8","doi-asserted-by":"crossref","first-page":"e13984","DOI":"10.1371\/journal.pone.0013984","article-title":"Enrichment map: a network-based method for gene-set enrichment visualisation and interpretation","volume":"5","author":"Merico","year":"2010","journal-title":"PLoS One"},{"key":"2025031823572659700_btaf100-B9","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1038\/ng1180","article-title":"PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes","volume":"34","author":"Mootha","year":"2003","journal-title":"Nat Genet"},{"key":"2025031823572659700_btaf100-B10","doi-asserted-by":"crossref","first-page":"105895","DOI":"10.1016\/j.isci.2022.105895","article-title":"Multi-OMICs landscape of SARS-CoV-2-induced host responses in human lung epithelial cells","volume":"26","author":"Pinto","year":"2023","journal-title":"iScience"},{"key":"2025031823572659700_btaf100-B11","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/0377-0427(87)90125-7","article-title":"Silhouettes: a graphical aid to the interpretation and validation of cluster analysis","volume":"20","author":"Rousseeuw","year":"1987","journal-title":"J Comput Appl Math"},{"key":"2025031823572659700_btaf100-B12","doi-asserted-by":"crossref","first-page":"D10","DOI":"10.1093\/nar\/gkaa892","article-title":"Database resources of the national center for biotechnology information","volume":"49","author":"Sayers","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2025031823572659700_btaf100-B13","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"Subramanian","year":"2005","journal-title":"Proc Natl Acad Sci USA"},{"key":"2025031823572659700_btaf100-B14","first-page":"100141","article-title":"clusterProfiler 4.0: a universal enrichment tool for interpreting omics data","volume":"2","author":"Wu","year":"2021","journal-title":"Innovation (Camb)"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaf100\/62244023\/btaf100.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/3\/btaf100\/62244023\/btaf100.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/3\/btaf100\/62244023\/btaf100.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,3,18]],"date-time":"2025-03-18T23:57:47Z","timestamp":1742342267000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btaf100\/8051116"}},"subtitle":[],"editor":[{"given":"Anthony","family":"Mathelier","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2025,3]]},"references-count":14,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2025,3,4]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaf100","relation":{},"ISSN":["1367-4811"],"issn-type":[{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2025,3]]},"published":{"date-parts":[[2025,3]]},"article-number":"btaf100"}}