SEanalysis 2.0: a comprehensive super-enhancer regulatory network analysis tool for human and mouse

Abstract Super-enhancers (SEs) play an essential regulatory role in various biological processes and diseases through their specific interaction with transcription factors (TFs). Here, we present the release of SEanalysis 2.0 (http://licpathway.net/SEanalysis), an updated version of the SEanalysis w...

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Published inNucleic acids research Vol. 51; no. W1; pp. W520 - W527
Main Authors Qian, Feng-Cui, Zhou, Li-Wei, Li, Yan-Yu, Yu, Zheng-Min, Li, Li-Dong, Wang, Yue-Zhu, Xu, Ming-Cong, Wang, Qiu-Yu, Li, Chun-Quan
Format Journal Article
LanguageEnglish
Published England Oxford University Press 05.07.2023
Subjects
Animals
Enhancer Elements, Genetic
Gene Expression Regulation
Gene Regulatory Networks
Genomics
Humans
Mice
Software
Transcription Factors - genetics
Transcription Factors - metabolism
Web Server Issue
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Summary:Abstract Super-enhancers (SEs) play an essential regulatory role in various biological processes and diseases through their specific interaction with transcription factors (TFs). Here, we present the release of SEanalysis 2.0 (http://licpathway.net/SEanalysis), an updated version of the SEanalysis web server for the comprehensive analyses of transcriptional regulatory networks formed by SEs, pathways, TFs, and genes. The current version added mouse SEs and further expanded the scale of human SEs, documenting 1 167 518 human SEs from 1739 samples and 550 226 mouse SEs from 931 samples. The SE-related samples in SEanalysis 2.0 were more than five times that in version 1.0, which significantly improved the ability of original SE-related network analyses (‘pathway downstream analysis’, ‘upstream regulatory analysis’ and ‘genomic region annotation’) for understanding context-specific gene regulation. Furthermore, we designed two novel analysis models, ‘TF regulatory analysis’ and ‘Sample comparative analysis’ for supporting more comprehensive analyses of SE regulatory networks driven by TFs. Further, the risk SNPs were annotated to the SE regions to provide potential SE-related disease/trait information. Hence, we believe that SEanalysis 2.0 has significantly expanded the data and analytical capabilities of SEs, which helps researchers in an in-depth understanding of the regulatory mechanisms of SEs. Graphical Abstract Graphical Abstract
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The authors wish it to be known that, in their opinion, the first three authors should be regarded as Joint First Authors.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkad408