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GsmPlot: a web server to visualize epigenome data in NCBI.

Jia Li1, Yue Yin1, Mutian Zhang1

  • 1Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, Texas A&M University College of Medicine, Houston, TX, 77030, USA.

BMC Bioinformatics
|February 14, 2020
PubMed
Summary
This summary is machine-generated.

GsmPlot simplifies epigenetic data analysis by enabling visualization of NCBI data and private files without bioinformatics expertise. This tool promotes epigenetic research by making complex datasets accessible for exploration.

Keywords:
EpigeneticsGsmPlotNCBIVisualizationWebserver

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Area of Science:

  • Genomics
  • Epigenetics
  • Bioinformatics

Background:

  • Epigenetic regulation controls gene expression in biological processes.
  • High-throughput sequencing generates vast epigenetic data (e.g., histone modifications, DNA methylation).
  • NCBI Gene Expression Omnibus (GEO) stores large epigenetic datasets, posing reanalysis challenges for non-experts.

Purpose of the Study:

  • To develop a user-friendly tool for visualizing and exploring epigenetic data.
  • To enable researchers without bioinformatics skills to analyze complex epigenetic datasets.

Main Methods:

  • GsmPlot accepts NCBI GSM IDs or user-provided bigwig files.
  • The tool generates visualizations for specified genomic regions (promoters, exons, custom locations).
  • UCSC genome browser tracks are generated for data visualization.

Main Results:

  • GsmPlot facilitates automatic data download from NCBI.
  • It allows plotting of both public and private epigenetic data.
  • The server generates UCSC visualization tracks for easy interpretation.

Conclusions:

  • GsmPlot provides convenient visualization and exploration of NCBI epigenetic data.
  • It requires no bioinformatics skills or specialized computational resources.
  • The web server promotes epigenetic research by enhancing data accessibility.