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

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.

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 Creators:
Yim, Annie1, Author              
Koti, Prasanna1, Author              
Bonnard, Adrien2, Author
Marchiano, Fabio2, Author
Dürrbaum, Milena3, Author              
Garcia-Perez, Cecilia2, Author
Villaveces, Jose1, Author              
Gamal, Salma1, Author              
Cardone, Giovanni4, Author              
Perocchi, Fabiana2, Author
Storchova, Zuzana3, Author              
Habermann, Bianca H.1, Author              
Affiliations:
1Habermann, Bianca / Computational Biology, Max Planck Institute of Biochemistry, Max Planck Society, ou_1832284              
2external, ou_persistent22              
3Storchova, Zuzana / Maintenance of Genome Stability, Max Planck Institute of Biochemistry, Max Planck Society, ou_1565171              
4Scientific Service Groups, Max Planck Institute of Biochemistry, Max Planck Society, ou_1565170              

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Free keywords: DOWN-SYNDROME; GENE-EXPRESSION; OXIDATIVE STRESS; PROTEIN; CARDIOLIPIN; DYSFUNCTION; CELLS; DIVERSITY; DISEASES; NETWORK
 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.

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Language(s): eng - English
 Dates: 2020
 Publication Status: Published in print
 Pages: 28
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Identifiers: ISI: 000518532100014
DOI: 10.1093/nar/gkz1128
 Degree: -

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Project name : DFG grant [HA 6905/2-1]
Grant ID : HA 6905/2-1
Funding program : -
Funding organization : German research foundation
Project name : Munich Center for Systems Neurology [SyNergy EXC 1010]; Bert L & N Kuggie Vallee Foundation (to F.P.); Bavarian Molecular Biosystems Research Network [D2-F5121.2-10c/4822 to C.M.].
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Title: Nucleic Acids Research (London)
  Other : Nucleic Acids Res
Source Genre: Journal
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Publ. Info: Oxford : Oxford University Press
Pages: - Volume / Issue: 48 (2) Sequence Number: - Start / End Page: 605 - 632 Identifier: ISSN: 0305-1048
CoNE: https://pure.mpg.de/cone/journals/resource/110992357379342