tGeCoNet: a framework for constructing temporal gene co-expression networks

Biological systems, composed of interconnected biological objects, can be effectively represented through a network graph-model where nodes and edges denote biological objects and their interactions/associations, respectively. In this context, Gene Co-expression Networks (GCNs) are widely studied, however, since they rely on a static representation of interactions, they fail to represent the evolution of time-dependent phenomena. The dynamic nature of gene expression is crucial for unravelling complex biological processes. To address this issue, we designed an open-source framework for constructing real-world Temporal Gene Co-expression Networks (tGeCoNet). Temporal Gene Co-expression Networks (TGCNs) are modelled based on real-world data. Gene expression data, along with metadata (e.g., age groups) is used to build a temporal network that captures the time-varying associations between genes (i.e., nodes), based on the statistical significance computed for each age group (i.e., time point). Designed as a scalable and reproducible solution, tGeCoNet can serve as a valuable data source for studies on time-dependent biological phenomena, especially for those exploring the temporal evolution of gene co-expression within the framework of network science.