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One major interest of the lab is to understand mitochondrial heterogeneity and diversity of structure, function and expression dynamics across different tissues, but also in different disease conditions.
Mitochondria are the power-houses of our cells, producing cellular energy in the form of ATP. They however are also involved in a multitude of other cellular and metabolic functions, including metabolism of amino acids, nucleotides or lipids, fructose, nitrogen or pyruvate metabolism, mitochondrial signaling, apoptosis ROS defense and many more. Depending on the cellular demand, mitochondria come in many different forms and shapes and also their content varies by cell type or tissue. Likewise, in different mito-diseases, mitochondrial function is perturbed, accompanied by different mitochondrial shapes and/or content. Currently, we do not understand how this variety is regulated, nor how mito-gene expression dynamics varies from one tissue to another.
mitoXplorer - a visual data mining platform for deep mining of mitochondrial expression dynamics
mitoXplorer - a visual data mining platform for deep mining of mitochondrial expression dynamics
the mitoXplorer visual data mining platform integrates a manually curated mitochondrial interactome with publicly available or user-provided expression and mutation data. A set of highly interactive analysis and visualization methods is provided for data discovery.
Mitochondrial structure and content differs from one cell type to the other. Mitochondrial variability is also at the heart of many disease conditions, often related to the nervous system or the muscle.
We are interested in understanding the dynamics of mitochondria in different species, tissues, disease states and throughout ageing. We look at the expression dynamics - reflected in systematic transcriptomic and proteomic data - from a variety of different tissues, disease states, ages and in 4 different species to get an idea of what portion of mito-genes are dynamically expressed.
We have developed the mitoXplorer platform, an interactive, visual data mining platform to integrate large-scale expression and mutation data with a mitochondrial interactome and mitochondrial processes.
A manually curated, mitochondrial interactome is at the heart of mitoXplorer, which contains all proteins that have mitochondrial function, irrespective of their genomic localization (mitochondrial or nuclear gnome). We integrate this manually curated and annotated mito-interactome with -omics data from large public repositories, such as TAGC or with data from Gene Expression Omnibus (GEO). Using specialized pipelines for NGS-data analysis, we extract mutation and expression data for all mito-proteins. mitoXplorer offers a set of powerful, highly interactive analysis and visualization tools to explore the dynamics of mito-associated expression changes and mutations in a variety of data sets from different experimental or disease conditions. This enables us to rapidly and visually compare a large variety of -omics data-sets with respect to their mitochondrial expression and mutation dynamics.
Check out mitoXplorer here!
Download your own version of mitoXplorer here.
mitoXplorer is now published in NAR!
This project was supported by DFG grant ‘CancerSysDB’ and is currently supported by ANR grant ‘MITO-DYNAMICS’ and the CNRS.
ataxiaXplorer - deep data mining of cerebellar ataxias
ataxiaXplorer - deep data mining of cerebellar ataxias
In an FRM-funded project we hold together with the team of Helene Puccio, we will soon start to develop ataxiaXplorer. AtaxiaXplorer will be based on the mitoXplorer 2.0 web-server, with an ataxia-specific interactome and enhanced functionalities to mine single-cell RNA-seq data. More information will follow soon.
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