{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,17]],"date-time":"2026-03-17T00:57:50Z","timestamp":1773709070996,"version":"3.50.1"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2019,7,26]],"date-time":"2019-07-26T00:00:00Z","timestamp":1564099200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Spanish Ministry of Economy and Competitiveness","award":["SAF2014-53819-R"],"award-info":[{"award-number":["SAF2014-53819-R"]}]},{"name":"Spanish Ministry of Economy and Competitiveness","award":["SAF2017-88771-R"],"award-info":[{"award-number":["SAF2017-88771-R"]}]},{"DOI":"10.13039\/501100003403","name":"Fundaci\u00f3n Caja Madrid","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003403","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100012818","name":"Autonomous Community of Madrid","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100012818","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>The computational identification of the transcription factors (TFs) [more generally, transcription regulators, (TR)] responsible for the co-regulation of a specific set of genes is a common problem found in genomic analysis. Herein, we describe TFEA.ChIP, a tool that makes use of ChIP-seq datasets to estimate and visualize TR enrichment in gene lists representing transcriptional profiles. We validated TFEA.ChIP using a wide variety of gene sets representing signatures of genetic and chemical perturbations as input and found that the relevant TR was correctly identified in 126 of a total of 174 analyzed. Comparison with other TR enrichment tools demonstrates that TFEA.ChIP is an highly customizable package with an outstanding performance.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>TFEA.ChIP is implemented as an R package available at Bioconductor https:\/\/www.bioconductor.org\/packages\/devel\/bioc\/html\/TFEA.ChIP.html and github https:\/\/github.com\/LauraPS1\/TFEA.ChIP_downloads. A web-based GUI to the package is also available at https:\/\/www.iib.uam.es\/TFEA.ChIP\/<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz573","type":"journal-article","created":{"date-parts":[[2019,7,24]],"date-time":"2019-07-24T07:27:00Z","timestamp":1563953220000},"page":"5339-5340","source":"Crossref","is-referenced-by-count":51,"title":["TFEA.ChIP: a tool kit for transcription factor binding site enrichment analysis capitalizing on ChIP-seq datasets"],"prefix":"10.1093","volume":"35","author":[{"given":"Laura","family":"Puente-Santamaria","sequence":"first","affiliation":[{"name":"Departamento de Bioqu\u00edmica, Universidad Aut\u00f3noma de Madrid (UAM) and Instituto de Investigaciones Biom\u00e9dicas \u2019Alberto Sols\u2019 (CSIC-UAM) , Madrid, Spain"}]},{"given":"Wyeth W","family":"Wasserman","sequence":"additional","affiliation":[{"name":"Department of Medical Genetics, University of British Columbia Vancouver, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute , Vancouver, BC V5Z 4H4, Canada"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4014-5688","authenticated-orcid":false,"given":"Luis","family":"del Peso","sequence":"additional","affiliation":[{"name":"Departamento de Bioqu\u00edmica, Universidad Aut\u00f3noma de Madrid (UAM) and Instituto de Investigaciones Biom\u00e9dicas \u2019Alberto Sols\u2019 (CSIC-UAM) , Madrid, Spain"},{"name":"IdiPaz, Instituto de Investigaci\u00f3n Sanitaria del Hospital Universitario La Paz"},{"name":"CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III , Madrid, Spain"}]}],"member":"286","published-online":{"date-parts":[[2019,7,26]]},"reference":[{"key":"2023013108411818000_btz573-B1","doi-asserted-by":"crossref","first-page":"1922","DOI":"10.1093\/bioinformatics\/btt316","article-title":"Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool","volume":"29","author":"Auerbach","year":"2013","journal-title":"Bioinformatics"},{"key":"2023013108411818000_btz573-B2","doi-asserted-by":"crossref","first-page":"128.","DOI":"10.1186\/1471-2105-14-128","article-title":"Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool","volume":"14","author":"Chen","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"2023013108411818000_btz573-B3","doi-asserted-by":"crossref","first-page":"D267","DOI":"10.1093\/nar\/gkx1092","article-title":"ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments","volume":"46","author":"Ch\u00e8neby","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023013108411818000_btz573-B4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/database\/bax028","article-title":"GeneHancer: genome-wide integration of enhancers and target genes in GeneCards","volume":"2017","author":"Fishilevich","year":"2017","journal-title":"Database"},{"key":"2023013108411818000_btz573-B5","doi-asserted-by":"crossref","first-page":"769","DOI":"10.1158\/0008-5472.CAN-17-1679","article-title":"Transcription factor activities enhance markers of drug sensitivity in cancer","volume":"78","author":"Garcia-Alonso","year":"2018","journal-title":"Cancer Res"},{"key":"2023013108411818000_btz573-B6","doi-asserted-by":"crossref","first-page":"e1003731.","DOI":"10.1371\/journal.pcbi.1003731","article-title":"iRegulon: from a gene list to a gene regulatory network using large motif and track collections","volume":"10","author":"Janky","year":"2014","journal-title":"PLoS Comput. 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