eRNAbase: a comprehensive database for decoding the regulatory eRNAs in human and mouse.

Autor:	Song C; The First Affiliated Hospital & Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.; The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China., Zhang G; The First Affiliated Hospital & Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.; The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.; Department of Cell Biology and Genetics, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China., Mu X; The First Affiliated Hospital & Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.; The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China., Feng C; School of Computer, University of South China, Hengyang, Hunan, 421001, China., Zhang Q; The First Affiliated Hospital & Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.; The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.; Department of Cell Biology and Genetics, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China., Song S; The First Affiliated Hospital & Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.; The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.; Department of Cell Biology and Genetics, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China., Zhang Y; The First Affiliated Hospital & Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.; The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China., Yin M; The First Affiliated Hospital & Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.; The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.; Department of Cell Biology and Genetics, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China., Zhang H; The First Affiliated Hospital & Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.; School of Computer, University of South China, Hengyang, Hunan, 421001, China.; The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China., Tang H; The First Affiliated Hospital & Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.; The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, China.; The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.; The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.; Clinical Research Center for Myocardial Injury in Hunan Province, Hengyang, Hunan, 421001, China., Li C; The First Affiliated Hospital & Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.; Hunan Provincial Maternal and Child Health Care Hospital, National Health Commission Key Laboratory of Birth Defect Research and Prevention, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.; School of Computer, University of South China, Hengyang, Hunan, 421001, China.; The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, China.
Jazyk:	angličtina
Zdroj:	Nucleic acids research [Nucleic Acids Res] 2024 Jan 05; Vol. 52 (D1), pp. D81-D91.
DOI:	10.1093/nar/gkad925
Abstrakt:	Enhancer RNAs (eRNAs) transcribed from distal active enhancers serve as key regulators in gene transcriptional regulation. The accumulation of eRNAs from multiple sequencing assays has led to an urgent need to comprehensively collect and process these data to illustrate the regulatory landscape of eRNAs. To address this need, we developed the eRNAbase (http://bio.liclab.net/eRNAbase/index.php) to store the massive available resources of human and mouse eRNAs and provide comprehensive annotation and analyses for eRNAs. The current version of eRNAbase cataloged 10 399 928 eRNAs from 1012 samples, including 858 human samples and 154 mouse samples. These eRNAs were first identified and uniformly processed from 14 eRNA-related experiment types manually collected from GEO/SRA and ENCODE. Importantly, the eRNAbase provides detailed and abundant (epi)genetic annotations in eRNA regions, such as super enhancers, enhancers, common single nucleotide polymorphisms, expression quantitative trait loci, transcription factor binding sites, CRISPR/Cas9 target sites, DNase I hypersensitivity sites, chromatin accessibility regions, methylation sites, chromatin interactions regions, topologically associating domains and RNA spatial interactions. Furthermore, the eRNAbase provides users with three novel analyses including eRNA-mediated pathway regulatory analysis, eRNA-based variation interpretation analysis and eRNA-mediated TF-target gene analysis. Hence, eRNAbase is a powerful platform to query, browse and visualize regulatory cues associated with eRNAs. (© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.)
Databáze:	MEDLINE
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