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Although thousands of ncRNAs have been discovered, the transcriptional mechanisms and networks of the majority of ncRNAs have not been fully investigated. In this study, we updated ChIPBase to version 3.0 (https:\/\/rnasysu.com\/chipbase3\/) to provide the most comprehensive transcriptional regulation atlas of ncRNAs and protein-coding genes (PCGs). ChIPBase has identified \u223c151 187 000 regulatory relationships between \u223c171 600 genes and \u223c3000 regulators by analyzing \u223c55 000 ChIP-seq datasets, which represent a 30-fold expansion. Moreover, we de novo identified \u223c29 000 motif matrices of transcription factors. In addition, we constructed a novel \u2018Enhancer\u2019 module to predict \u223c1 837 200 regulation regions functioning as poised, active or super enhancers under \u223c1300 conditions. Importantly, we constructed exhaustive coexpression maps between regulators and their target genes by integrating expression profiles of \u223c65 000 normal and \u223c15 000 tumor samples. We built a \u2018Disease\u2019 module to obtain an atlas of the disease-associated variations in the regulation regions of genes. We also constructed an \u2018EpiInter\u2019 module to explore potential interactions between epitranscriptome and epigenome. Finally, we designed \u2018Network\u2019 module to provide extensive and gene-centred regulatory networks. ChIPBase will serve as a useful resource to facilitate integrative explorations and expand our understanding of transcriptional regulation.<\/jats:p>","DOI":"10.1093\/nar\/gkac1067","type":"journal-article","created":{"date-parts":[[2022,11,18]],"date-time":"2022-11-18T18:35:29Z","timestamp":1668796529000},"page":"D46-D56","source":"Crossref","is-referenced-by-count":63,"title":["ChIPBase v3.0: the encyclopedia of transcriptional regulations of non-coding RNAs and protein-coding genes"],"prefix":"10.1093","volume":"51","author":[{"given":"Junhong","family":"Huang","sequence":"first","affiliation":[{"name":"Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University , Guangzhou \u00a0510275, P.R. 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