The mitoXplorer 2.0 update: integrating and interpreting mitochondrial expression dynamics within a cellular context.

Area of Science:

• Cell Biology
• Bioinformatics
• Systems Biology

Background:

• Mitochondria are vital organelles involved in cellular metabolism, with structure and composition varying across tissues, health, and age.
• The initial mitoXplorer 1.0 platform facilitated exploration of mitochondrial gene expression but lacked cellular context integration.
• Understanding mitochondrial regulation is crucial for explaining cellular adaptation and diverse physiological states.

Purpose of the Study:

• To upgrade the mitoXplorer platform to version 2.0 (mitoXplorer 2.0) by incorporating novel functions for integrating mitochondria within the cellular context.
• To identify signaling or transcriptional regulators of mitochondrial processes through network analysis and transcription factor enrichment.
• To enhance the platform's capabilities beyond data visualization, including enrichment analysis, time-series exploration, cross-species comparison, and data upload facilitation.

Main Methods:

• Development and implementation of mitoXplorer 2.0, an upgraded visual data mining platform.
• Integration of network analysis and transcription factor enrichment functions for identifying regulatory mechanisms.
• Addition of functions for mitochondrial process enrichment, time-series data exploration, cross-species dataset comparison, and an ID converter.

Main Results:

• mitoXplorer 2.0 provides enhanced capabilities for exploring mitochondrial gene expression dynamics within the cellular environment.
• The new integrative functions successfully identify potential signaling and transcriptional regulators of mitochondrial functions.
• The platform's utility was demonstrated through three specific use cases, highlighting its effectiveness.

Conclusions:

• mitoXplorer 2.0 significantly advances the analysis of mitochondrial biology by enabling the integration of mitochondrial data into the broader cellular context.
• The platform offers powerful tools for discovering regulators that govern mitochondrial adaptation to cellular demands.
• mitoXplorer 2.0 is freely accessible, promoting wider research in mitochondrial function and regulation.