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SEanalysis: a web tool for super-enhancer associated regulatory analysis.

Feng-Cui Qian1, Xue-Cang Li1, Jin-Cheng Guo2

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This summary is machine-generated.

SEanalysis is a new web server for analyzing super-enhancers (SEs) and their regulatory networks. It provides comprehensive downstream and upstream regulatory analyses, aiding biological and pathological process research.

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Area of Science:

  • Genomics
  • Systems Biology
  • Bioinformatics

Background:

  • Super-enhancers (SEs) are critical regulators of gene transcription in biological and pathological processes.
  • Existing SE databases lack comprehensive downstream and upstream regulatory network analyses.
  • Understanding the complex interplay between SEs, transcription factors (TFs), and pathways is crucial.

Purpose of the Study:

  • To develop a novel web server, SEanalysis, for comprehensive SE-associated regulatory network analysis.
  • To integrate diverse data types including SEs, TF binding data, and pathway information.
  • To provide interactive visualization tools for exploring complex regulatory networks.

Main Methods:

  • Developed the SEanalysis web server integrating data from >330,000 SEs across >540 cell/tissue types.
  • Incorporated 5042 TF ChIP-seq datasets, motifs for ~700 human TFs, and 2880 pathways from 10 databases.
  • Implemented search functionalities by SEs, samples, TFs, pathways, or genes.
  • Developed a customizable genome browser with >6000 tracks for data visualization.

Main Results:

  • SEanalysis characterizes SE-associated genes, TF binding sites on target SEs, and upstream pathways.
  • The server enables interactive visualization of complex regulatory networks.
  • A customizable genome browser enhances data exploration and visualization.

Conclusions:

  • SEanalysis provides a powerful, integrated platform for comprehensive SE-associated regulatory network analysis.
  • The tool facilitates deeper understanding of gene regulation in biological and pathological contexts.
  • Freely available at http://licpathway.net/SEanalysis, SEanalysis supports diverse research needs.