Aix-Marseille University, CNRS, IBDM UMR 7288, 13009 Marseille, France.
Nucleic Acids Res. 2022 Jul 5;50(W1):W490-W499. doi: 10.1093/nar/gkac306.
Mitochondria are subcellular organelles present in almost all eukaryotic cells, which play a central role in cellular metabolism. Different tissues, health and age conditions are characterized by a difference in mitochondrial structure and composition. The visual data mining platform mitoXplorer 1.0 was developed to explore the expression dynamics of genes associated with mitochondrial functions that could help explain these differences. It, however, lacked functions aimed at integrating mitochondria in the cellular context and thus identifying regulators that help mitochondria adapt to cellular needs. To fill this gap, we upgraded the mitoXplorer platform to version 2.0 (mitoXplorer 2.0). In this upgrade, we implemented two novel integrative functions, network analysis and transcription factor enrichment, to specifically help identify signalling or transcriptional regulators of mitochondrial processes. In addition, we implemented several other novel functions to allow the platform to go beyond simple data visualization, such as an enrichment function for mitochondrial processes, a function to explore time-series data, the possibility to compare datasets across species and an IDconverter to help facilitate data upload. We demonstrate the usefulness of these functions in three specific use cases. mitoXplorer 2.0 is freely available without login at http://mitoxplorer2.ibdm.univ-mrs.fr.
线粒体是存在于几乎所有真核细胞中的亚细胞细胞器，在细胞代谢中起着核心作用。不同的组织、健康和年龄状况的特点是线粒体结构和组成的差异。开发了可视化数据挖掘平台 mitoXplorer 1.0，以探索与线粒体功能相关的基因表达动态，这有助于解释这些差异。然而，它缺乏将线粒体整合到细胞环境中的功能，因此无法识别有助于线粒体适应细胞需求的调节剂。为了填补这一空白，我们将 mitoXplorer 平台升级到了 2.0 版本（mitoXplorer 2.0）。在此次升级中，我们实现了两个新的整合功能，即网络分析和转录因子富集，专门用于帮助识别线粒体过程的信号或转录调节剂。此外，我们还实现了其他几个新功能，使该平台不仅能够进行简单的数据可视化，还能够进行例如线粒体过程富集功能、时间序列数据探索功能、跨物种数据集比较功能以及 ID 转换器功能，以帮助促进数据上传。我们在三个具体用例中展示了这些功能的实用性。mitoXplorer 2.0 可在无需登录的情况下免费使用，网址为 http://mitoxplorer2.ibdm.univ-mrs.fr。
