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XDeathDB: a visualization platform for cell death molecular interactions.

Venkat Sundar Gadepalli1, Hangil Kim2, Yueze Liu3

  • 1Research Information Technology, College of Medicine, Ohio State University, 1585 Neil Ave, Columbus, OH, 43210, USA.

Cell Death & Disease
|December 15, 2021
PubMed
Summary
This summary is machine-generated.

XDeathDB is a new platform visualizing cell death interactions across 1461 cancer types and COVID-19. It aids in understanding cell death mechanisms and discovering new cancer drugs by mapping gene-disease and pathway associations.

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Area of Science:

  • Oncology
  • Systems Biology
  • Bioinformatics

Background:

  • Cell death mechanisms are crucial in cancer, involving numerous molecules, pathways, and subcellular sites.
  • Understanding the complex crosstalk between different cell death modes is essential for cancer research and drug discovery.

Purpose of the Study:

  • To develop XDeathDB, a comprehensive visualization platform for cell death and crosstalk.
  • To decipher signaling network organization of cell death interactions in 1461 cancer types and COVID-19.
  • To facilitate systems-oriented drug discovery by understanding molecular mechanisms of cell death.

Main Methods:

  • Collected big data on gene-disease, gene-cell death pathway, pathway-cell death mode, and cell death-cell death associations from literature and public databases.
  • Built an interactive webtool, XDeathDB, using R-Shiny, JavaScript, and Shiny Server.
  • Employed a multilayer spectral graph clustering method for identifying crosstalk among cell death modes.

Main Results:

  • XDeathDB systematically visualizes 12 cell death modes and their crosstalk, including apoptosis, ferroptosis, necroptosis, and pyroptosis.
  • The platform displays associations for 1461 cancer types and COVID-19, highlighting 147 hallmark cell death genes.
  • Identified potential druggable targets and enabled tailored network visualization for user-specific needs.

Conclusions:

  • XDeathDB provides a valuable resource for exploring cell death networks and their implications in cancer and disease.
  • The platform facilitates the understanding of molecular mechanisms underlying cell death and aids in novel drug discovery.
  • XDeathDB is freely accessible, empowering researchers to investigate complex cell death interactions.