Differential gene correlation analysis to investigate evolutionary divergence between Cardamine hirsuta and Arabidopsis thaliana

Dissecting the intricate regulatory dynamics between genes stands as a critical step towards the development of precise predictive models within biological systems. A highly effective strategy in this pursuit involves an examination of variations in correlation among gene pairs across different conditions trough differential gene correlation analysis. We anticipated that the application of this method to phylogenetically close plant species could reveal powerful insights on how genes' relationships have a fundamental role in evolutionary dynamics. Building upon this principle, our investigation focused primarily on conducting a comprehensive differential correlation analysis of the roots' orthologous genes of two closely related plant species: Cardamine hirsuta and Arabidopsis thaliana. By leveraging their shared phylogenetic proximity, we were able to draw comparisons that shed light on how evolutionary pressures might have shaped their gene regulatory networks. By integrating differential expression analysis, differential correlation analysis and functional enrichment analysis, we offer a robust framework for future studies aiming to unravel the complexities of adaptation and evolution across a wide range of biological systems.