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SEdb 2.0: a comprehensive super-enhancer database of human and mouse.
Wang, Yuezhu; Song, Chao; Zhao, Jun; Zhang, Yuexin; Zhao, Xilong; Feng, Chenchen; Zhang, Guorui; Zhu, Jiang; Wang, Fan; Qian, Fengcui; Zhou, Liwei; Zhang, Jian; Bai, Xuefeng; Ai, Bo; Liu, Xinyu; Wang, Qiuyu; Li, Chunquan.
Afiliação
  • Wang Y; The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.
  • Song C; School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China.
  • Zhao J; The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.
  • Zhang Y; School of Computer, University of South China, Hengyang, Hunan 421001, China.
  • Zhao X; 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; The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.
  • Zhang G; School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China.
  • Zhu J; The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.
  • Wang F; School of Computer, University of South China, Hengyang, Hunan 421001, China.
  • Qian F; The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.
  • Zhou L; School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China.
  • Zhang J; School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China.
  • Bai X; The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.
  • Ai B; School of Computer, University of South China, Hengyang, Hunan 421001, China.
  • Liu X; School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China.
  • Wang Q; School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China.
  • Li C; The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.
Nucleic Acids Res ; 51(D1): D280-D290, 2023 01 06.
Article em En | MEDLINE | ID: mdl-36318264
Super-enhancers (SEs) are cell-specific DNA cis-regulatory elements that can supervise the transcriptional regulation processes of downstream genes. SEdb 2.0 (http://www.licpathway.net/sedb) aims to provide a comprehensive SE resource and annotate their potential roles in gene transcriptions. Compared with SEdb 1.0, we have made the following improvements: (i) Newly added the mouse SEs and expanded the scale of human SEs. SEdb 2.0 contained 1 167 518 SEs from 1739 human H3K27ac chromatin immunoprecipitation sequencing (ChIP-seq) samples and 550 226 SEs from 931 mouse H3K27ac ChIP-seq samples, which was five times that of SEdb 1.0. (ii) Newly added transcription factor binding sites (TFBSs) in SEs identified by TF motifs and TF ChIP-seq data. (iii) Added comprehensive (epi)genetic annotations of SEs, including chromatin accessibility regions, methylation sites, chromatin interaction regions and topologically associating domains (TADs). (iv) Newly embedded and updated search and analysis tools, including 'Search SE by TF-based', 'Differential-Overlapping-SE analysis' and 'SE-based TF-Gene analysis'. (v) Newly provided quality control (QC) metrics for ChIP-seq processing. In summary, SEdb 2.0 is a comprehensive update of SEdb 1.0, which curates more SEs and annotation information than SEdb 1.0. SEdb 2.0 provides a friendly platform for researchers to more comprehensively clarify the important role of SEs in the biological process.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Elementos Facilitadores Genéticos / Bases de Dados Genéticas Tipo de estudo: Prognostic_studies Limite: Animals / Humans Idioma: En Revista: Nucleic Acids Res Ano de publicação: 2023 Tipo de documento: Article País de afiliação: China
Texto completo
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XML
PubMed Links
Buscar no Google

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Elementos Facilitadores Genéticos / Bases de Dados Genéticas Tipo de estudo: Prognostic_studies Limite: Animals / Humans Idioma: En Revista: Nucleic Acids Res Ano de publicação: 2023 Tipo de documento: Article País de afiliação: China