{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T02:24:36Z","timestamp":1773109476101,"version":"3.50.1"},"reference-count":58,"publisher":"Oxford University Press (OUP)","issue":"D1","funder":[{"DOI":"10.13039\/100000069","name":"National Institute of Arthritis and Musculoskeletal and Skin Diseases","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000069","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>In mammals, transcriptional factors (TFs) drive gene expression by binding to regulatory elements in a cooperative manner. Deciphering the rules of such cooperation is crucial to obtain a full understanding of cellular homeostasis and development. Although this is a long-standing topic, there is no comprehensive database for biologists to access the syntax of TF binding sites. Here we present TFSyntax (https:\/\/tfsyntax.zhaopage.com), a database focusing on the arrangement of TF binding sites. TFSyntax maps the binding motif of 1299 human TFs and 890 mouse TFs across 382 cells and tissues, representing the most comprehensive TF binding map to date. In addition to location, TFSyntax defines motif positional preference, density and colocalization within accessible elements. Powered by a series of functional modules based on web interface, users can freely search, browse, analyze, and download data of interest. With comprehensive characterization of TF binding syntax across distinct tissues and cell types, TFSyntax represents a valuable resource and platform for studying the mechanism of transcriptional regulation and exploring how regulatory DNA variants cause disease.<\/jats:p>","DOI":"10.1093\/nar\/gkac849","type":"journal-article","created":{"date-parts":[[2022,10,6]],"date-time":"2022-10-06T13:33:19Z","timestamp":1665063199000},"page":"D306-D314","source":"Crossref","is-referenced-by-count":10,"title":["TFSyntax: a database of transcription factors binding syntax in mammalian genomes"],"prefix":"10.1093","volume":"51","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9917-7425","authenticated-orcid":false,"given":"Yongbing","family":"Zhao","sequence":"first","affiliation":[{"name":"Lymphocyte Nuclear Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health , Bethesda , MD 20892 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,10,6]]},"reference":[{"key":"2023010804313092000_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":"2023010804313092000_B2","doi-asserted-by":"crossref","first-page":"D33","DOI":"10.1093\/nar\/gky822","article-title":"AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors","volume":"47","author":"Hu","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2023010804313092000_B3","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1038\/nature08531","article-title":"Combinatorial binding predicts spatio-temporal cis-regulatory activity","volume":"462","author":"Zinzen","year":"2009","journal-title":"Nature"},{"key":"2023010804313092000_B4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.sbi.2017.03.006","article-title":"Structural perspective of cooperative transcription factor binding","volume":"47","author":"Morgunova","year":"2017","journal-title":"Curr. 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