ChIPBase v3.0: the encyclopedia of transcriptional regulations of non-coding RNAs and protein-coding genes.
Nucleic Acids Res
; 51(D1): D46-D56, 2023 01 06.
Article
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| MEDLINE
| ID: mdl-36399495
ABSTRACT
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 â¼151 187 000 regulatory relationships between â¼171 600 genes and â¼3000 regulators by analyzing â¼55 000 ChIP-seq datasets, which represent a 30-fold expansion. Moreover, we de novo identified â¼29 000 motif matrices of transcription factors. In addition, we constructed a novel 'Enhancer' module to predict â¼1 837 200 regulation regions functioning as poised, active or super enhancers under â¼1300 conditions. Importantly, we constructed exhaustive coexpression maps between regulators and their target genes by integrating expression profiles of â¼65 000 normal and â¼15 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.
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MEDLINE
Asunto principal:
Regulación de la Expresión Génica
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Tipo de estudio:
Prognostic_studies
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En
Año:
2023
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Article