mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dynamics and mutations - Archive ouverte HAL Access content directly
Journal Articles Nucleic Acids Research Year : 2020

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

Abstract

Mitochondria participate in metabolism and signal-ing. They adapt to the requirements of various cell types. Publicly available expression data permit to study expression dynamics of genes with mitochon-drial function (mito-genes) in various cell types, conditions and organisms. Yet, we lack an easy way of extracting these data for mito-genes. Here, we introduce the visual data mining platform mitoXplorer, which integrates expression and mutation data of mito-genes with a manually curated mitochondrial interactome containing ∼1200 genes grouped in 38 mitochondrial processes. User-friendly analysis and visualization tools allow to mine mitochondrial expression dynamics and mutations across various datasets from four model species including human. To test the predictive power of mitoXplorer, we quantify mito-gene expression dynamics in trisomy 21 cells, as mitochondrial defects are frequent in tri-somy 21. We uncover remarkable differences in the regulation of the mitochondrial transcriptome and proteome in one of the trisomy 21 cell lines, caused by dysregulation of the mitochondrial ribosome and resulting in severe defects in oxidative phosphory-lation. With the newly developed Fiji plugin mito-Morph, we identify mild changes in mitochondrial morphology in trisomy 21. Taken together, mitoX-plorer (http://mitoxplorer.ibdm.univ-mrs.fr) is a user-friendly, web-based and freely accessible software, aiding experimental scientists to quantify mitochon-drial expression dynamics.
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Dates and versions

hal-02394433 , version 1 (04-12-2019)

Licence

Attribution - CC BY 4.0

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Annie Yim, Prasanna Koti, Adrien Bonnard, Fabio Marchiano, Milena Dürrbaum, et al.. mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dynamics and mutations. Nucleic Acids Research, 2020, ⟨10.1093/nar/gkz1128⟩. ⟨hal-02394433⟩
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