Gene Regulatory Networks
The first thing that people tend to think of when they hear the word “graph theory” is social networks. However, graph theory is applicable to more than just social media websites or person-person relations. In an article called Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression, regulatory interactions between genes are modeled using nodes and directed edges. Some genes have robust regulation and expression, meaning that their expression is invariable. For example, genes in development are robust. Other genes have more stochastic regulation and expression, meaning that their expression is variable. For example, responses to stress such as environmental stress tend to be stochastic.
Putting all of this information into gene regulatory networks allows for an easier visualization of these complex relationships, as gene regulatory networks essentially involve visually diagramming interactions between genes and their regulators. This method of organizing biological data allows scientists to better understand the flow of information in regulatory relationships between genes with similar phenotypes.
An example in gene regulatory networks is that the nodes are the genes and their regulators, and the edges represent the physical or regulatory interactions. Since there are two types of nodes in these networks–genes and transcription factors (TFs), these networks are bipartite, which makes the network a bit more complex. The edges are directional because usually, TFs regulate their targets, and targets do not regulate TFs.
In social networks, there may be positive relationships between some nodes and negative edges between others–similarly, when generally examining genes and regulators, it may be true that a gene could be positively regulated by a regulator or negatively regulated (keeping in mind that there is a directed edge, different from a social network), showing that like in social networks, there could potentially be a way to apply the structural balance theory to genes and regulators, to add an analysis of balance and imbalance in biological systems.
Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3083081/