ChIPBase v3.0: the encyclopedia of transcriptional regulations of non-coding RNAs and protein-coding genes

Non-coding RNAs (ncRNAs) are emerging as key regulators of various biological processes. 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 similar to 151 187 000 regulatory relationships between similar to 171 600 genes and similar to 3000 regulators by analyzing similar to 55 000 ChIP-seq datasets, which represent a 30-fold expansion. Moreover, we de novo identified similar to 29 000 motif matrices of transcription factors. In addition, we constructed a novel 'Enhancer' module to predict similar to 1 837 200 regulation regions functioning as poised, active or super enhancers under similar to 1300 conditions. Importantly, we constructed exhaustive co-expression maps between regulators and their target genes by integrating expression profiles of similar to 65 000 normal and similar to 15 000 tumor samples. We built a 'Disease' module to obtain an atlas of the disease-associated variations in the regulation regions of genes. We also constructed an 'EpiInter' module to explore potential interactions between epitranscriptome and epigenome. Finally, we designed 'Network' 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.