Barelvi Altaf, Anderson Oliver, Ritz Anna
Biology Department, Reed College, Portland, OR 97202, United States.
Bioinform Adv. 2025 Jul 21;5(1):vbaf176. doi: 10.1093/bioadv/vbaf176. eCollection 2025.
Graphs are powerful tools for modeling and analyzing molecular interaction networks. Graphs typically represent either undirected physical interactions or directed regulatory relationships, which can obscure a particular protein's functional context. Graphlets can describe local topologies and patterns within graphs, and combining physical and regulatory interactions offer new graphlet configurations that can provide biological insights.
We present GRPhIN, a tool for characterizing graphlets and protein roles within graphlets in mixed physical and regulatory interaction networks. We describe the graphlets of mixed networks in , , , , and and examine local topologies of proteins and subnetworks related to the oxidative stress response pathway. We found a number of graphlets that were abundant in all species, specific node positions (orbits) within graphlets that were overrepresented in stress-associated proteins, and rarely-occurring graphlets that were overrepresented in oxidative stress subnetworks. These results showcase the potential for using graphlets in mixed physical and regulatory interaction networks to identify new patterns beyond a single interaction type.
GRPhIN is available at https://github.com/Reed-CompBio/grphin.
图形是用于建模和分析分子相互作用网络的强大工具。图形通常表示无向的物理相互作用或有向的调控关系，这可能会模糊特定蛋白质的功能背景。图元可以描述图形中的局部拓扑结构和模式，将物理相互作用和调控相互作用相结合可提供新的图元配置，从而能够提供生物学见解。
我们展示了GRPhIN，这是一种用于在混合物理和调控相互作用网络中表征图元以及图元内蛋白质作用的工具。我们描述了在[具体情况未提及，原文此处可能有误，推测为某些特定条件下]混合网络的图元，并研究了与氧化应激反应途径相关的蛋白质和子网的局部拓扑结构。我们发现了许多在所有物种中都丰富的图元、在与应激相关的蛋白质中过度代表的图元内的特定节点位置（轨道），以及在氧化应激子网中过度代表的罕见图元。这些结果展示了在混合物理和调控相互作用网络中使用图元来识别超越单一相互作用类型的新模式的潜力。
