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

MPS-Authors
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Yim,  Annie
Habermann, Bianca / Computational Biology, Max Planck Institute of Biochemistry, Max Planck Society;

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Koti,  Prasanna
Habermann, Bianca / Computational Biology, Max Planck Institute of Biochemistry, Max Planck Society;

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Dürrbaum,  Milena
Storchova, Zuzana / Maintenance of Genome Stability, Max Planck Institute of Biochemistry, Max Planck Society;

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Villaveces,  Jose
Habermann, Bianca / Computational Biology, Max Planck Institute of Biochemistry, Max Planck Society;

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Gamal,  Salma
Habermann, Bianca / Computational Biology, Max Planck Institute of Biochemistry, Max Planck Society;

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Cardone,  Giovanni
Scientific Service Groups, Max Planck Institute of Biochemistry, Max Planck Society;

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Storchova,  Zuzana
Storchova, Zuzana / Maintenance of Genome Stability, Max Planck Institute of Biochemistry, Max Planck Society;

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Habermann,  Bianca H.
Habermann, Bianca / Computational Biology, Max Planck Institute of Biochemistry, Max Planck Society;

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Citation

Yim, A., Koti, P., Bonnard, A., Marchiano, F., Dürrbaum, M., Garcia-Perez, C., et al. (2020). mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dynamics and mutations. Nucleic Acids Research (London), 48(2), 605-632. doi:10.1093/nar/gkz1128.


Cite as: http://hdl.handle.net/21.11116/0000-0005-FB74-E
Abstract
Mitochondria participate in metabolism and signaling. They adapt to the requirements of various cell types. Publicly available expression data permit to study expression dynamics of genes with mitochondrial 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 similar to 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 trisomy 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 phosphorylation. With the newly developed Fiji plugin mitoMorph, we identify mild changes in mitochondrial morphology in trisomy 21. Taken together, mitoXplorer (http://mitoxplorer.ibdm.univ-mrs.fr) is a user-friendly, web-based and freely accessible software, aiding experimental scientists to quantify mitochondrial expression dynamics.