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mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dynamics

Annie Yim1, Prasanna Koti1, Adrien Bonnard2

  • 1Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.

Nucleic Acids Research
|December 5, 2019
PubMed
Summary

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This summary is machine-generated.

mitoXplorer is a new web tool for analyzing mitochondrial gene expression and mutations. It reveals significant mitochondrial defects in trisomy 21 cells, impacting oxidative phosphorylation and morphology.

Area of Science:

  • Cell Biology
  • Genomics
  • Bioinformatics

Background:

  • Mitochondria are crucial for cellular metabolism and signaling, adapting to diverse cell types.
  • Studying mitochondrial gene (mito-gene) expression dynamics across various datasets is challenging due to data accessibility limitations.

Purpose of the Study:

  • To develop mitoXplorer, a visual data mining platform for analyzing mitochondrial gene expression and mutation data.
  • To provide user-friendly tools for exploring mitochondrial dynamics across species and conditions.

Main Methods:

  • Integration of expression and mutation data for mito-genes with a curated mitochondrial interactome (∼1200 genes, 38 processes).
  • Development of analysis and visualization tools within the mitoXplorer platform.
  • Application of mitoXplorer to quantify mito-gene expression in trisomy 21 cells and analysis of mitochondrial morphology using the mitoMorph Fiji plugin.

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Main Results:

  • mitoXplorer successfully integrates diverse mitochondrial data, enabling mining of expression dynamics and mutations.
  • Analysis of trisomy 21 cells revealed significant dysregulation of the mitochondrial transcriptome and proteome, affecting the mitochondrial ribosome and oxidative phosphorylation.
  • Mild alterations in mitochondrial morphology were observed in trisomy 21 cells using the mitoMorph plugin.

Conclusions:

  • mitoXplorer is a valuable, accessible web-based tool for researchers studying mitochondrial gene expression dynamics.
  • The study highlights specific mitochondrial defects in trisomy 21, linked to ribosome dysregulation and impacting cellular respiration.