Network topological characteristics
Using functional gene data, we generated fMENs for control and warmed samples. Both networks were scale-free (power-law R2> 0.85), and possessed other typical properties of biological networks such as small-world and modularity (Table 3). In line with Hypothesis 1, the fMEN of warmed samples had significantly different topological characteristics with the fMEN of control (P < 0.001). The average path distance of warmed samples (18.718) was significantly higher than that of control (10.325) (P < 0.001), whereas the average clustering coefficient of warmed samples (0.298) was significantly lower than that of control (0.329) (P < 0.001). A lower percentage of negative links was found in the fMEN of warmed samples (19.78%) than in control (36.32%) (Fig. 2 & Table 3).
Based on Zi and Pi values of both networks, 12 genes were identified as key genes (9 module hubs and 3 connectors) of warmed samples, while 14 genes were identified as key genes (11 module hubs and 3 connectors) of control samples (Fig. 2 & Table S4). A much higher percentage of key genes were associated with C degradation in warmed samples (91.7%, 11 out of 12 genes) than in control (64.3%, 9 out of 14 genes) (Table S4). Partial Mantel tests revealed that thaw depth was significantly linked to network connectivity of key genes (P < 0.01).