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SEdb: a comprehensive human super-enhancer database.

Yong Jiang1, Fengcui Qian1, Xuefeng Bai1

  • 1School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China.

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|October 30, 2018
PubMed
Summary
This summary is machine-generated.

We created SEdb, a comprehensive database of human super-enhancers, crucial for cell-specific gene expression. SEdb integrates genetic and epigenetic data to aid research into super-enhancer functions and their role in human diseases.

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Area of Science:

  • Genomics
  • Epigenetics
  • Molecular Biology

Background:

  • Super-enhancers regulate cell-specific gene expression.
  • Human H3K27ac ChIP-seq datasets are rapidly growing, necessitating efficient data management.
  • Super-enhancer-associated genetic variations and transcription factors impact human diseases.

Purpose of the Study:

  • To develop a comprehensive human super-enhancer database (SEdb).
  • To provide a centralized resource for human super-enhancers and their functional annotations.
  • To facilitate in-depth analysis of super-enhancer roles in biological processes and diseases.

Main Methods:

  • Manual curation and classification of 410 H3K27ac ChIP-seq samples from NCBI GEO/SRA.
  • Development of the SEdb database (http://www.licpathway.net/sedb).
  • Annotation of super-enhancers with genetic and epigenetic information.

Main Results:

  • SEdb currently contains 331,601 super-enhancers from 542 samples.
  • Detailed annotations include SNPs, TF binding sites, eQTLs, and DHSs.
  • Manual curation of H3K27ac samples distinguishes SEdb from existing databases.

Conclusions:

  • SEdb offers a valuable resource for studying human super-enhancers.
  • The database aids in elucidating super-enhancer functions and their involvement in diseases.
  • SEdb supports research into genetic and epigenetic regulation by super-enhancers.