Fig. 5
Pipeline for construction of putative dynamic PPI networks in the exercise and training responses. Each putative contextual PPI network is composed from nodes, V, (genes) and edges, E, (interactions) related to one of the experimental contexts (cohorts). For example, the putative PPI network for the exercise in the untrained rest state, (1): G = (V UE, E UR ), contains the nodes (genes) that are associated with exercise (VUE) and the edges (based on gene expression correlations) from the untrained rest (EUR) cohort that are also supported by known protein-protein interactions (PPIs) in the IntAct molecular interaction database. This can be considered the ‘ground state’ of the dynamic exercise network and can be compared to the exercise ‘active state’, (2): G = (V UE, E UE ), or the sub-network that is exclusive to exercise, (3):G = (V UE – TR ,E UE ) to model how these putative PPI interactions might be re-wired in the exercise response and the exercise-specific response respectively. Networks (1)–(3) are illustrated in Fig. 6(a)-(c) and networks (4)–(6) are illustrated in Fig. 7(a)-(c)