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With the rapid accumulation of TcoF associated chromatin immunoprecipitation sequencing (ChIP-seq) data, the comprehensive collection and integrative analyses of these data are urgently required. Here, we developed the TcoFBase database (http:\/\/tcof.liclab.net\/TcoFbase), which aimed to document a large number of available resources for mammalian TcoFs and provided annotations and enrichment analyses of TcoFs. TcoFBase curated 2322 TcoFs and 6759 TcoFs associated ChIP-seq data from over 500 tissues\/cell types in human and mouse. Importantly, TcoFBase provided detailed and abundant (epi) genetic annotations of ChIP-seq based TcoF binding regions. Furthermore, TcoFBase supported regulatory annotation information and various functional annotations for TcoFs. Meanwhile, TcoFBase embedded five types of TcoF regulatory analyses for users, including TcoF gene set enrichment, TcoF binding genomic region annotation, TcoF regulatory network analysis, TcoF-TF co-occupancy analysis and TcoF regulatory axis analysis. TcoFBase was designed to be a useful resource that will help reveal the potential biological effects of TcoFs and elucidate TcoF-related regulatory mechanisms.<\/jats:p>","DOI":"10.1093\/nar\/gkab950","type":"journal-article","created":{"date-parts":[[2021,10,5]],"date-time":"2021-10-05T20:48:04Z","timestamp":1633466884000},"page":"D391-D401","source":"Crossref","is-referenced-by-count":25,"title":["TcoFBase: a comprehensive database for decoding the regulatory transcription co-factors in human and mouse"],"prefix":"10.1093","volume":"50","author":[{"given":"Yuexin","family":"Zhang","sequence":"first","affiliation":[{"name":"The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan\u00a0421001, China"},{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University,\u00a0Daqing\u00a0163319, China"}]},{"given":"Chao","family":"Song","sequence":"additional","affiliation":[{"name":"The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan\u00a0421001, China"},{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University,\u00a0Daqing\u00a0163319, China"}]},{"given":"Yimeng","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University,\u00a0Daqing\u00a0163319, China"},{"name":"The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou\u00a0515041, China"}]},{"given":"Yuezhu","family":"Wang","sequence":"additional","affiliation":[{"name":"The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan\u00a0421001, China"},{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University,\u00a0Daqing\u00a0163319, China"}]},{"given":"Chenchen","family":"Feng","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University,\u00a0Daqing\u00a0163319, China"}]},{"given":"Jiaxin","family":"Chen","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University,\u00a0Daqing\u00a0163319, China"}]},{"given":"Ling","family":"Wei","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University,\u00a0Daqing\u00a0163319, China"}]},{"given":"Qi","family":"Pan","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University,\u00a0Daqing\u00a0163319, China"}]},{"given":"Desi","family":"Shang","sequence":"additional","affiliation":[{"name":"The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan\u00a0421001, China"},{"name":"School of Computer, University of South China, Hengyang, Hunan\u00a0421001, China"},{"name":"The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial\u00a0Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan\u00a0421001, China"},{"name":"Hunan Provincial Base for Scientific and Technological\u00a0Innovation Cooperation, University of South China, Hengyang, Hunan\u00a0421001, China"}]},{"given":"Yanbing","family":"Zhu","sequence":"additional","affiliation":[{"name":"Experimental and Translational Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing\u00a0100050, China"}]},{"given":"Jiang","family":"Zhu","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University,\u00a0Daqing\u00a0163319, China"}]},{"given":"Shuangsang","family":"Fang","sequence":"additional","affiliation":[{"name":"Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing\u00a0100029, China"}]},{"given":"Jun","family":"Zhao","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University,\u00a0Daqing\u00a0163319, China"}]},{"given":"Yongsan","family":"Yang","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University,\u00a0Daqing\u00a0163319, China"}]},{"given":"Xilong","family":"Zhao","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University,\u00a0Daqing\u00a0163319, China"}]},{"given":"Xiaozheng","family":"Xu","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University,\u00a0Daqing\u00a0163319, China"}]},{"given":"Qiuyu","family":"Wang","sequence":"additional","affiliation":[{"name":"The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan\u00a0421001, China"},{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University,\u00a0Daqing\u00a0163319, China"},{"name":"School of Computer, University of South China, Hengyang, Hunan\u00a0421001, China"},{"name":"The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial\u00a0Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan\u00a0421001, China"},{"name":"Hunan Provincial Base for Scientific and Technological\u00a0Innovation Cooperation, University of South China, Hengyang, Hunan\u00a0421001, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5616-6910","authenticated-orcid":false,"given":"Jincheng","family":"Guo","sequence":"additional","affiliation":[{"name":"Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing\u00a0100029, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4700-5496","authenticated-orcid":false,"given":"Chunquan","family":"Li","sequence":"additional","affiliation":[{"name":"The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan\u00a0421001, China"},{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University,\u00a0Daqing\u00a0163319, China"},{"name":"School of Computer, University of South China, Hengyang, Hunan\u00a0421001, China"},{"name":"The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial\u00a0Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan\u00a0421001, China"},{"name":"Hunan Provincial Base for Scientific and Technological\u00a0Innovation Cooperation, University of South China, Hengyang, Hunan\u00a0421001, China"}]}],"member":"286","published-online":{"date-parts":[[2021,10,30]]},"reference":[{"key":"2022010507394082900_B1","doi-asserted-by":"crossref","first-page":"1237","DOI":"10.1016\/j.cell.2013.02.014","article-title":"Transcriptional regulation and its misregulation in disease","volume":"152","author":"Lee","year":"2013","journal-title":"Cell"},{"key":"2022010507394082900_B2","doi-asserted-by":"crossref","first-page":"801","DOI":"10.1016\/j.tig.2016.10.003","article-title":"Regulatory enhancer-core-promoter communication via transcription factors and cofactors","volume":"32","author":"Zabidi","year":"2016","journal-title":"Trends Genet.: TIG"},{"key":"2022010507394082900_B3","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1038\/cdd.2016.161","article-title":"Epigenetic regulation of HDAC1 SUMOylation as an endogenous neuroprotection against Abeta toxicity in a mouse model of Alzheimer's disease","volume":"24","author":"Tao","year":"2017","journal-title":"Cell Death 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Cardiol."},{"key":"2022010507394082900_B6","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1016\/j.immuni.2019.08.006","article-title":"Unique and shared epigenetic programs of the CREBBP and EP300 acetyltransferases in germinal center B cells reveal targetable dependencies in lymphoma","volume":"51","author":"Meyer","year":"2019","journal-title":"Immunity"},{"key":"2022010507394082900_B7","doi-asserted-by":"crossref","first-page":"1490","DOI":"10.1158\/2159-8290.CD-19-1028","article-title":"androgen receptor interaction with mediator complex is enhanced in castration-resistant prostate cancer by CDK7 phosphorylation of MED1","volume":"9","author":"Russo","year":"2019","journal-title":"Cancer Discov."},{"key":"2022010507394082900_B8","doi-asserted-by":"crossref","first-page":"1164","DOI":"10.1002\/hep.24155","article-title":"Transcription coactivator mediator subunit MED1 is required for the development of fatty liver in the 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Res."},{"key":"2022010507394082900_B12","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":"2022010507394082900_B13","doi-asserted-by":"crossref","first-page":"baz094","DOI":"10.1093\/database\/baz094","article-title":"ApicoTFdb: the comprehensive web repository of apicomplexan transcription factors and transcription-associated co-factors","volume":"2019","author":"Sardar","year":"2019","journal-title":"Database"},{"key":"2022010507394082900_B14","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1016\/j.gpb.2019.09.006","article-title":"hTFtarget: a comprehensive database for regulations of human transcription factors and their targets","volume":"18","author":"Zhang","year":"2020","journal-title":"Genomics Proteomics 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atlas","volume":"507","author":"Consortium, F., the, R.P., Clst, Forrest, A.R.","year":"2014","journal-title":"Nature"},{"key":"2022010507394082900_B22","doi-asserted-by":"crossref","first-page":"D106","DOI":"10.1093\/nar\/gky864","article-title":"HACER: an atlas of human active enhancers to interpret regulatory variants","volume":"47","author":"Wang","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2022010507394082900_B23","doi-asserted-by":"crossref","first-page":"bav085","DOI":"10.1093\/database\/bav085","article-title":"DENdb: database of integrated human enhancers","volume":"2015","author":"Ashoor","year":"2015","journal-title":"Database : the journal of biological databases and curation"},{"key":"2022010507394082900_B24","first-page":"D51","article-title":"ENdb: a manually curated database of experimentally supported enhancers for human and mouse","volume":"48","author":"Bai","year":"2020","journal-title":"Nucleic Acids 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Latinoam."},{"key":"2022010507394082900_B40","doi-asserted-by":"crossref","first-page":"D1001","DOI":"10.1093\/nar\/gkt1229","article-title":"The NHGRI GWAS Catalog, a curated resource of SNP-trait associations","volume":"42","author":"Welter","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2022010507394082900_B41","doi-asserted-by":"crossref","first-page":"D869","DOI":"10.1093\/nar\/gkv1317","article-title":"GWASdb v2: an update database for human genetic variants identified by genome-wide association studies","volume":"44","author":"Li","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2022010507394082900_B42","doi-asserted-by":"crossref","first-page":"D971","DOI":"10.1093\/nar\/gkx861","article-title":"PancanQTL: systematic identification of cis-eQTLs and trans-eQTLs in 33 cancer types","volume":"46","author":"Gong","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2022010507394082900_B43","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1093\/bioinformatics\/btr678","article-title":"seeQTL: a searchable database for human eQTLs","volume":"28","author":"Xia","year":"2012","journal-title":"Bioinformatics"},{"key":"2022010507394082900_B44","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1093\/bioinformatics\/btp644","article-title":"SCAN: SNP and copy number annotation","volume":"26","author":"Gamazon","year":"2010","journal-title":"Bioinformatics"},{"key":"2022010507394082900_B45","doi-asserted-by":"crossref","first-page":"D1044","DOI":"10.1093\/nar\/gky1139","article-title":"OncoBase: a platform for decoding regulatory somatic mutations in human cancers","volume":"47","author":"Li","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2022010507394082900_B46","doi-asserted-by":"crossref","first-page":"2560","DOI":"10.1093\/bioinformatics\/btv158","article-title":"4DGenome: a comprehensive database of chromatin interactions","volume":"31","author":"Teng","year":"2015","journal-title":"Bioinformatics"},{"key":"2022010507394082900_B47","doi-asserted-by":"crossref","first-page":"2502","DOI":"10.1038\/nprot.2013.150","article-title":"Target analysis by integration of transcriptome and ChIP-seq data with BETA","volume":"8","author":"Wang","year":"2013","journal-title":"Nat. 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