CHRONOS: a time-varying method for microRNA-mediated subpathway enrichment analysis
Aristidis G Vrahatis1, Konstantina Dimitrakopoulou2, Panos Balomenos1
1Department of Computer Engineering and Informatics, Department of Medical Physics, School of Medicine, University of Patras, Patras 26500, Greece.
Bioinformatics (Oxford, England)
|November 17, 2015
Summary
We developed CHRONOS, a novel tool for analyzing time-varying gene expression data. It identifies dynamic biological pathways and microRNA impacts, outperforming existing methods in capturing network functionality over time.
Area of Science:
- Bioinformatics
- Systems Biology
- Network Medicine
Background:
- Network medicine and time series mRNA/microRNA expression data are rapidly growing fields.
- Current pathway enrichment methods fail to capture time- and condition-specific biological circuitry and microRNA effects.
- Existing approaches overlook dynamic themes in microRNA-mediated subpathways crucial for signaling network functionality.
Purpose of the Study:
- To develop a novel tool for analyzing time-varying omics data.
- To address the limitations of current methods in capturing dynamic pathway behavior and microRNA impact.
- To provide a method for identifying time- and condition-specific active parts of biological networks.
Main Methods:
- Developed time-vaRying enriCHment integrOmics Subpathway aNalysis tOol (CHRONOS).
- Integrated time series mRNA/microRNA expression data with KEGG pathway maps and microRNA-target interactions.
- Extracted and evaluated microRNA-mediated subpathway topologies based on temporal transitions and gene/microRNA fold-change activity.
Main Results:
- CHRONOS successfully integrates diverse biological data types.
- The tool provides measures for structural and functional subpathway features.
- CHRONOS outperforms existing subpathway methods in revealing dynamic pathway properties on synthetic and real data.
Conclusions:
- CHRONOS offers a powerful approach for analyzing dynamic biological networks.
- The tool enhances understanding of microRNA-mediated regulatory mechanisms over time.
- CHRONOS provides valuable insights into the functional dynamics of signaling pathways.
