Table 1 The topological properties of the functional gene co-occurrence networks on four dilution levels and their respective identically sized random networks
From: Specialized metabolic functions of keystone taxa sustain soil microbiome stability
Network indexes | Dilution | |||
|---|---|---|---|---|
Dil = 10-1 | Dil = 10-4 | Dil = 10-7 | Dil = 10-10 | |
Empirical Networks | ||||
Total nodes | 231 | 205 | 184 | 183 |
Total links | 1844 | 1993 | 736 | 603 |
Metabolic process (positive-negative) | 718–712 | 532–394 | 269–276 | 293–277 |
Environmental signal responses (positive-negative) | 368–4 | 893–8 | 188–1 | – |
Average degree (avgK) | 17.67 | 18.39 | 8.01 | 7.59 |
Average clustering coefficient (avgCC) | 0.647 | 0.662 | 0.586 | 0.538 |
Average path distance (APD) | 4.22 | 3.39 | 4.64 | 4.71 |
Modularity (M) | 0.679 | 0.680 | 0.625 | 0.579 |
Graph density (GD) | 0.168 | 0.171 | 0.088 | 0.072 |
Random Networks | ||||
Average clustering coefficient (avgCC) | 0.202 ± 0.008 | 0.198 ± 0.007 | 0.113 ± 0.007 | 0.153 ± 0.014 |
Average path distance (APD) | 2.499 ± 0.025 | 2.365 ± 0.021 | 2.602 ± 0.021 | 2.729 ± 0.023 |
Modularity (M) | 0.265 ± 0.004 | 0.258 ± 0.005 | 0.232 ± 0.006 | 0.223 ± 0.005 |