{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,15]],"date-time":"2026-04-15T02:29:15Z","timestamp":1776220155637,"version":"3.50.1"},"reference-count":48,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2019,10,10]],"date-time":"2019-10-10T00:00:00Z","timestamp":1570665600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81572341"],"award-info":[{"award-number":["81572341"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61601150"],"award-info":[{"award-number":["61601150"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["YQ2019C013"],"award-info":[{"award-number":["YQ2019C013"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Yu Weihan Outstanding Youth Training Fund of Harbin Medical University"},{"name":"Wu Liande Youth Science Research Fund of Harbin Medical University","award":["DQWLD201703"],"award-info":[{"award-number":["DQWLD201703"]}]},{"name":"Scientific Research Fund of Harbin Medical University","award":["DQXN201707"],"award-info":[{"award-number":["DQXN201707"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,1,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Transcription factors (TFs) and their target genes have important functions in human diseases and biological processes. Gene expression profile analysis before and after knockdown or knockout is one of the most important strategies for obtaining target genes of TFs and exploring TF functions. Human gene expression profile datasets with TF knockdown and knockout are accumulating rapidly. Based on the urgent need to comprehensively and effectively collect and process these data, we developed KnockTF (http:\/\/www.licpathway.net\/KnockTF\/index.html), a comprehensive human gene expression profile database of TF knockdown and knockout. KnockTF provides a number of resources for human gene expression profile datasets associated with TF knockdown and knockout and annotates TFs and their target genes in a tissue\/cell type-specific manner. The current version of KnockTF has 570 manually curated RNA-seq and microarray datasets associated with 308 TFs disrupted by different knockdown and knockout techniques and across multiple tissue\/cell types. KnockTF collects upstream pathway information of TFs and functional annotation results of downstream target genes. It provides details about TFs binding to promoters, super-enhancers and typical enhancers of target genes. KnockTF constructs a TF-differentially expressed gene network and performs network analyses for genes of interest. KnockTF will help elucidate TF-related functions and potential biological effects.<\/jats:p>","DOI":"10.1093\/nar\/gkz881","type":"journal-article","created":{"date-parts":[[2019,10,8]],"date-time":"2019-10-08T04:17:03Z","timestamp":1570508223000},"page":"D93-D100","source":"Crossref","is-referenced-by-count":128,"title":["KnockTF: a comprehensive human gene expression profile database with knockdown\/knockout of transcription factors"],"prefix":"10.1093","volume":"48","author":[{"given":"Chenchen","family":"Feng","sequence":"first","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China"}]},{"given":"Chao","family":"Song","sequence":"additional","affiliation":[{"name":"Department of Pharmacology, Daqing Campus, Harbin Medical University, Daqing 163319, China"}]},{"given":"Yuejuan","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China"}]},{"given":"Fengcui","family":"Qian","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China"}]},{"given":"Yu","family":"Gao","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China"}]},{"given":"Ziyu","family":"Ning","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China"}]},{"given":"Qiuyu","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China"}]},{"given":"Yong","family":"Jiang","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China"}]},{"given":"Yanyu","family":"Li","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China"}]},{"given":"Meng","family":"Li","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China"}]},{"given":"Jiaxin","family":"Chen","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China"}]},{"given":"Jian","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China"}]},{"given":"Chunquan","family":"Li","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China"}]}],"member":"286","published-online":{"date-parts":[[2019,10,10]]},"reference":[{"key":"2020010521380118300_B1","doi-asserted-by":"crossref","first-page":"613","DOI":"10.1038\/nrg3207","article-title":"Transcription factors: from enhancer binding to developmental control","volume":"13","author":"Spitz","year":"2012","journal-title":"Nat. Rev. Genet."},{"key":"2020010521380118300_B2","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1038\/nrg2957","article-title":"Enhancer function: new insights into the regulation of tissue-specific gene expression","volume":"12","author":"Ong","year":"2011","journal-title":"Nat. Rev. Genet."},{"key":"2020010521380118300_B3","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1146\/annurev-genet-110711-155437","article-title":"Disentangling the many layers of eukaryotic transcriptional regulation","volume":"46","author":"Lelli","year":"2012","journal-title":"Annu. Rev. Genet."},{"key":"2020010521380118300_B4","doi-asserted-by":"crossref","first-page":"1190","DOI":"10.1126\/science.1222794","article-title":"Systematic localization of common disease-associated variation in regulatory DNA","volume":"337","author":"Maurano","year":"2012","journal-title":"Science"},{"key":"2020010521380118300_B5","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1126\/science.1127677","article-title":"Activated signal transduction kinases frequently occupy target genes","volume":"313","author":"Pokholok","year":"2006","journal-title":"Science"},{"key":"2020010521380118300_B6","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1038\/nmeth1068","article-title":"Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing","volume":"4","author":"Robertson","year":"2007","journal-title":"Nat. Methods"},{"key":"2020010521380118300_B7","doi-asserted-by":"crossref","first-page":"662","DOI":"10.1016\/j.devcel.2010.02.014","article-title":"Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming","volume":"18","author":"Cao","year":"2010","journal-title":"Dev. Cell"},{"key":"2020010521380118300_B8","doi-asserted-by":"crossref","first-page":"1497","DOI":"10.1126\/science.1141319","article-title":"Genome-wide mapping of in vivo protein-DNA interactions","volume":"316","author":"Johnson","year":"2007","journal-title":"Science"},{"key":"2020010521380118300_B9","doi-asserted-by":"crossref","first-page":"1106","DOI":"10.1016\/j.cell.2008.04.043","article-title":"Integration of external signaling pathways with the core transcriptional network in embryonic stem cells","volume":"133","author":"Chen","year":"2008","journal-title":"Cell"},{"key":"2020010521380118300_B10","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1038\/nature11245","article-title":"Architecture of the human regulatory network derived from ENCODE data","volume":"489","author":"Gerstein","year":"2012","journal-title":"Nature"},{"key":"2020010521380118300_B11","doi-asserted-by":"crossref","first-page":"683","DOI":"10.1038\/ng2012","article-title":"Genetic reconstruction of a functional transcriptional regulatory network","volume":"39","author":"Hu","year":"2007","journal-title":"Nat. Genet."},{"key":"2020010521380118300_B12","doi-asserted-by":"crossref","first-page":"2172","DOI":"10.1101\/gr.098921.109","article-title":"Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression","volume":"19","author":"Cheng","year":"2009","journal-title":"Genome Res."},{"key":"2020010521380118300_B13","doi-asserted-by":"crossref","first-page":"11494","DOI":"10.1073\/pnas.1618091114","article-title":"Breast tumor cell-specific knockout of Twist1 inhibits cancer cell plasticity, dissemination, and lung metastasis in mice","volume":"114","author":"Xu","year":"2017","journal-title":"PNAS"},{"key":"2020010521380118300_B14","doi-asserted-by":"crossref","first-page":"636","DOI":"10.1126\/science.1105136","article-title":"The ENCODE (ENCyclopedia Of DNA Elements) Project","volume":"306","author":"Consortium","year":"2004","journal-title":"Science"},{"key":"2020010521380118300_B15","doi-asserted-by":"crossref","first-page":"D61","DOI":"10.1093\/nar\/gkw951","article-title":"GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments","volume":"45","author":"Yevshin","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2020010521380118300_B16","doi-asserted-by":"crossref","first-page":"D178","DOI":"10.1093\/nar\/gkt1254","article-title":"DPRP: a database of phenotype-specific regulatory programs derived from transcription factor binding data","volume":"42","author":"Tzeng","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2020010521380118300_B17","doi-asserted-by":"crossref","first-page":"D71","DOI":"10.1093\/nar\/gkx796","article-title":"dbCoRC: a database of core transcriptional regulatory circuitries modeled by H3K27ac ChIP-seq signals","volume":"46","author":"Huang","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2020010521380118300_B18","doi-asserted-by":"crossref","first-page":"e19","DOI":"10.1158\/0008-5472.CAN-17-0327","article-title":"Cistrome cancer: a web resource for integrative gene regulation modeling in cancer","volume":"77","author":"Mei","year":"2017","journal-title":"Cancer Res."},{"key":"2020010521380118300_B19","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":"Cheneby","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2020010521380118300_B20","doi-asserted-by":"crossref","first-page":"e46255","DOI":"10.15252\/embr.201846255","article-title":"ChIP-Atlas: a data-mining suite powered by full integration of public ChIP-seq data","volume":"19","author":"Oki","year":"2018","journal-title":"EMBO Rep."},{"key":"2020010521380118300_B21","doi-asserted-by":"crossref","first-page":"D171","DOI":"10.1093\/nar\/gks1221","article-title":"Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium","volume":"41","author":"Wang","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2020010521380118300_B22","doi-asserted-by":"crossref","first-page":"1869","DOI":"10.1101\/gr.173039.114","article-title":"Linking signaling pathways to transcriptional programs in breast cancer","volume":"24","author":"Osmanbeyoglu","year":"2014","journal-title":"Genome Res."},{"key":"2020010521380118300_B23","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1038\/nrg2538","article-title":"A census of human transcription factors: function, expression and evolution","volume":"10","author":"Vaquerizas","year":"2009","journal-title":"Nat. Rev. Genet."},{"key":"2020010521380118300_B24","doi-asserted-by":"crossref","first-page":"D76","DOI":"10.1093\/nar\/gku887","article-title":"AnimalTFDB 2.0: a resource for expression, prediction and functional study of animal transcription factors","volume":"43","author":"Zhang","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2020010521380118300_B25","doi-asserted-by":"crossref","first-page":"D145","DOI":"10.1093\/nar\/gkw1007","article-title":"TcoF-DB v2: update of the database of human and mouse transcription co-factors and transcription factor interactions","volume":"45","author":"Schmeier","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2020010521380118300_B26","doi-asserted-by":"crossref","first-page":"D343","DOI":"10.1093\/nar\/gkx987","article-title":"TFClass: expanding the classification of human transcription factors to their mammalian orthologs","volume":"46","author":"Wingender","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2020010521380118300_B27","doi-asserted-by":"crossref","first-page":"D991","DOI":"10.1093\/nar\/gks1193","article-title":"NCBI GEO: archive for functional genomics data sets\u2013update","volume":"41","author":"Barrett","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2020010521380118300_B28","doi-asserted-by":"crossref","first-page":"948","DOI":"10.1101\/gad.981002","article-title":"Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells","volume":"16","author":"Paddison","year":"2002","journal-title":"Genes Dev."},{"key":"2020010521380118300_B29","doi-asserted-by":"crossref","first-page":"494","DOI":"10.1038\/35078107","article-title":"Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells","volume":"411","author":"Elbashir","year":"2001","journal-title":"Nature"},{"key":"2020010521380118300_B30","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1038\/nprot.2015.137","article-title":"Antibody-coupled siRNA as an efficient method for in vivo mRNA knockdown","volume":"11","author":"Baumer","year":"2016","journal-title":"Nat. Protoc."},{"key":"2020010521380118300_B31","doi-asserted-by":"crossref","first-page":"819","DOI":"10.1126\/science.1231143","article-title":"Multiplex genome engineering using CRISPR\/Cas systems","volume":"339","author":"Cong","year":"2013","journal-title":"Science"},{"key":"2020010521380118300_B32","doi-asserted-by":"crossref","first-page":"442","DOI":"10.1016\/j.cell.2013.06.044","article-title":"CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes","volume":"154","author":"Gilbert","year":"2013","journal-title":"Cell"},{"key":"2020010521380118300_B33","doi-asserted-by":"crossref","first-page":"420","DOI":"10.1038\/nature17946","article-title":"Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage","volume":"533","author":"Komor","year":"2016","journal-title":"Nature"},{"key":"2020010521380118300_B34","doi-asserted-by":"crossref","first-page":"e47","DOI":"10.1093\/nar\/gkv007","article-title":"limma powers differential expression analyses for RNA-sequencing and microarray studies","volume":"43","author":"Ritchie","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2020010521380118300_B35","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":"PNAS"},{"key":"2020010521380118300_B36","doi-asserted-by":"crossref","first-page":"D1049","DOI":"10.1093\/nar\/gku1179","article-title":"Gene ontology consortium: going forward","volume":"43","author":"Gene Ontology, C","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2020010521380118300_B37","doi-asserted-by":"crossref","first-page":"D330","DOI":"10.1093\/nar\/gky1055","article-title":"The gene ontology resource: 20 years and still GOing strong","volume":"47","author":"The Gene Ontology, C","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020010521380118300_B38","doi-asserted-by":"crossref","first-page":"D353","DOI":"10.1093\/nar\/gkw1092","article-title":"KEGG: new perspectives on genomes, pathways, diseases and drugs","volume":"45","author":"Kanehisa","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2020010521380118300_B39","doi-asserted-by":"crossref","first-page":"D235","DOI":"10.1093\/nar\/gky1025","article-title":"SEdb: a comprehensive human super-enhancer database","volume":"47","author":"Jiang","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020010521380118300_B40","doi-asserted-by":"crossref","first-page":"320","DOI":"10.1016\/j.cell.2013.03.036","article-title":"Selective inhibition of tumor oncogenes by disruption of super-enhancers","volume":"153","author":"Loven","year":"2013","journal-title":"Cell"},{"key":"2020010521380118300_B41","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1101\/gr.197590.115","article-title":"Models of human core transcriptional regulatory circuitries","volume":"26","author":"Saint-Andre","year":"2016","journal-title":"Genome Res."},{"key":"2020010521380118300_B42","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"2020010521380118300_B43","doi-asserted-by":"crossref","first-page":"D108","DOI":"10.1093\/nar\/gkj143","article-title":"TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes","volume":"34","author":"Matys","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2020010521380118300_B44","doi-asserted-by":"crossref","first-page":"W39","DOI":"10.1093\/nar\/gkv416","article-title":"The MEME Suite","volume":"43","author":"Bailey","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2020010521380118300_B45","doi-asserted-by":"crossref","first-page":"1017","DOI":"10.1093\/bioinformatics\/btr064","article-title":"FIMO: scanning for occurrences of a given motif","volume":"27","author":"Grant","year":"2011","journal-title":"Bioinformatics"},{"key":"2020010521380118300_B46","doi-asserted-by":"crossref","first-page":"580","DOI":"10.1038\/ng.2653","article-title":"The Genotype-Tissue Expression (GTEx) project","volume":"45","author":"Consortium","year":"2013","journal-title":"Nat. Genet."},{"key":"2020010521380118300_B47","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1038\/nature11003","article-title":"The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity","volume":"483","author":"Barretina","year":"2012","journal-title":"Nature"},{"key":"2020010521380118300_B48","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"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/48\/D1\/D93\/31697142\/gkz881.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/48\/D1\/D93\/31697142\/gkz881.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,1,5]],"date-time":"2020-01-05T21:38:25Z","timestamp":1578260305000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/48\/D1\/D93\/5584524"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,10,10]]},"references-count":48,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2019,10,10]]},"published-print":{"date-parts":[[2020,1,8]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkz881","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,1,8]]},"published":{"date-parts":[[2019,10,10]]}}}