{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,7]],"date-time":"2026-07-07T23:46:54Z","timestamp":1783468014441,"version":"3.55.0"},"reference-count":48,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2022,10,21]],"date-time":"2022-10-21T00:00:00Z","timestamp":1666310400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2021YFF0703704"],"award-info":[{"award-number":["2021YFF0703704"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Natural Science Foundation for Distinguished Young Scholars of Hubei Province of China","award":["2020CFA070"],"award-info":[{"award-number":["2020CFA070"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32100527"],"award-info":[{"award-number":["32100527"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Transcription factors (TFs) are proteins that interact with specific DNA sequences to regulate gene expression and play crucial roles in all kinds of biological processes. To keep up with new data and provide a more comprehensive resource for TF research, we updated the Animal Transcription Factor Database (AnimalTFDB) to version 4.0 (http:\/\/bioinfo.life.hust.edu.cn\/AnimalTFDB4\/) with up-to-date data and functions. We refined the TF family rules and prediction pipeline to predict TFs in genome-wide protein sequences from Ensembl. As a result, we predicted 274 633 TF genes and 150 726 transcription cofactor genes in AnimalTFDB 4.0 in 183 animal genomes, which are 86 more species than AnimalTFDB 3.0. Besides double data volume, we also added the following new annotations and functions to the database: (i) variations (including mutations) on TF genes in various human cancers and other diseases; (ii) predicted post-translational modification sites (including phosphorylation, acetylation, methylation and ubiquitination sites) on TFs in 8 species; (iii) TF regulation in autophagy; (iv) comprehensive TF expression annotation for 38 species; (v) exact and batch search functions allow users to search AnimalTFDB flexibly. AnimalTFDB 4.0 is a useful resource for studying TF and transcription regulation, which contains comprehensive annotation and classification of TFs and transcription cofactors.<\/jats:p>","DOI":"10.1093\/nar\/gkac907","type":"journal-article","created":{"date-parts":[[2022,10,21]],"date-time":"2022-10-21T10:51:56Z","timestamp":1666349516000},"page":"D39-D45","source":"Crossref","is-referenced-by-count":329,"title":["AnimalTFDB 4.0: a comprehensive animal transcription factor database updated with variation and expression annotations"],"prefix":"10.1093","volume":"51","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9168-4465","authenticated-orcid":false,"given":"Wen-Kang","family":"Shen","sequence":"first","affiliation":[{"name":"Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan, Hubei\u00a0430074, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8076-0576","authenticated-orcid":false,"given":"Si-Yi","family":"Chen","sequence":"additional","affiliation":[{"name":"Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan, Hubei\u00a0430074, China"},{"name":"Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan, Hubei\u00a0430074, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zi-Quan","family":"Gan","sequence":"additional","affiliation":[{"name":"Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan, Hubei\u00a0430074, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu-Zhu","family":"Zhang","sequence":"additional","affiliation":[{"name":"Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan, Hubei\u00a0430074, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tao","family":"Yue","sequence":"additional","affiliation":[{"name":"Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan, Hubei\u00a0430074, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miao-Miao","family":"Chen","sequence":"additional","affiliation":[{"name":"Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan, Hubei\u00a0430074, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9403-6869","authenticated-orcid":false,"given":"Yu","family":"Xue","sequence":"additional","affiliation":[{"name":"Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan, Hubei\u00a0430074, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9208-1041","authenticated-orcid":false,"given":"Hui","family":"Hu","sequence":"additional","affiliation":[{"name":"Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan, Hubei\u00a0430074, China"},{"name":"Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan, Hubei\u00a0430074, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5099-7465","authenticated-orcid":false,"given":"An-Yuan","family":"Guo","sequence":"additional","affiliation":[{"name":"Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan, Hubei\u00a0430074, China"},{"name":"Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan, Hubei\u00a0430074, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,10,21]]},"reference":[{"key":"2023010804302758500_B1","doi-asserted-by":"crossref","first-page":"650","DOI":"10.1016\/j.cell.2018.01.029","article-title":"The human transcription factors","volume":"172","author":"Lambert","year":"2018","journal-title":"Cell"},{"key":"2023010804302758500_B2","doi-asserted-by":"crossref","first-page":"D1040","DOI":"10.1093\/nar\/gkw982","article-title":"PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in 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