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SEdb 2.0: a comprehensive super-enhancer database of human and mouse
Yuezhu Wang1,2, Chao Song1,3,4, Jun Zhao1,2
1The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.
Nucleic Acids Research
|November 1, 2022
Summary
SEdb 2.0 enhances the study of super-enhancers (SEs) by significantly expanding human and mouse SE data. This updated resource offers new annotations and analysis tools for investigating SE roles in gene regulation.
Area of Science:
- Genomics
- Epigenetics
- Bioinformatics
Background:
- Super-enhancers (SEs) are critical cell-specific cis-regulatory elements controlling gene transcription.
- Understanding SEs is vital for elucidating gene regulation and biological processes.
Purpose of the Study:
- To introduce SEdb 2.0, a significantly updated and expanded resource for super-enhancers.
- To provide comprehensive annotations and advanced analysis tools for SEs.
Main Methods:
- Curated and integrated human and mouse super-enhancer data from H3K27ac ChIP-seq samples.
- Annotated SEs with transcription factor binding sites (TFBSs), epigenetic modifications, and chromatin interactions.
- Developed new search and analysis functionalities within the SEdb 2.0 platform.
Main Results:
- SEdb 2.0 contains over 1.7 million SEs from human and mouse datasets, a fivefold increase from its predecessor.
- Integrated comprehensive epigenetic and genetic annotations, including TFBSs, chromatin accessibility, and methylation data.
- Introduced enhanced tools for TF-based SE searching, differential analysis, and TF-Gene association.
Conclusions:
- SEdb 2.0 represents a substantial advancement, offering a more extensive and richly annotated collection of super-enhancers.
- The platform empowers researchers with improved tools to explore the intricate roles of SEs in biological systems.
