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Previously, we developed a widely used method, BETA, to integrate TF ChIP-seq peaks with differential gene expression (DGE) data to infer direct target genes. Here, we provide Cistrome-GO, a website implementation of this method with enhanced features to conduct ontology analyses of gene regulation by TFs in human and mouse. Cistrome-GO has two working modes: solo mode for ChIP-seq peak analysis; and ensemble mode, which integrates ChIP-seq peaks with DGE data. Cistrome-GO is freely available at http:\/\/go.cistrome.org\/.<\/jats:p>","DOI":"10.1093\/nar\/gkz332","type":"journal-article","created":{"date-parts":[[2019,5,2]],"date-time":"2019-05-02T15:13:13Z","timestamp":1556809993000},"page":"W206-W211","source":"Crossref","is-referenced-by-count":97,"title":["Cistrome-GO: a web server for functional enrichment analysis of transcription factor ChIP-seq peaks"],"prefix":"10.1093","volume":"47","author":[{"given":"Shaojuan","family":"Li","sequence":"first","affiliation":[{"name":"Shanghai Key Laboratory of Tuberculosis, Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China"}]},{"given":"Changxin","family":"Wan","sequence":"additional","affiliation":[{"name":"Shanghai Key Laboratory of Tuberculosis, Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China"}]},{"given":"Rongbin","family":"Zheng","sequence":"additional","affiliation":[{"name":"Shanghai Key Laboratory of Tuberculosis, Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China"}]},{"given":"Jingyu","family":"Fan","sequence":"additional","affiliation":[{"name":"Shanghai Key Laboratory of Tuberculosis, Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China"}]},{"given":"Xin","family":"Dong","sequence":"additional","affiliation":[{"name":"Shanghai Key Laboratory of Tuberculosis, Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China"}]},{"given":"Clifford A","family":"Meyer","sequence":"additional","affiliation":[{"name":"Department of Data Sciences, Dana-Farber Cancer Institute and Harvard T.H. 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