Table 1 Overview of specifications for inferred regulatory networks. In order: the adaptive correlation threshold set to retain significant correlations; average detected genes, number of edges, and percentage of negative edges; number of nodes and percentage of nodes being “regulators of transcription”; network density (ratio edges/nodes), number of connected components, average shortest path, and modularity
From: Single-cell transcriptomics unveils gene regulatory network plasticity
Network | Corr. Tresh. | Avg. det. genes | Edges | Edges < 0 (%) | Nodes | RT % | E/N | Conn. Comp. | Avg. short. path | Modularity |
|---|---|---|---|---|---|---|---|---|---|---|
Marrow | 0.95 | 3152 | 48,748 | 0.0 | 3221 | 27.5 | 15.13 | 3 | 4.06 | 0.37 |
Intestine | 0.94 | 4046 | 60,941 | 0.0 | 5858 | 24.4 | 10.40 | 1 | 6.33 | 0.49 |
Heart | 0.94 | 2682 | 3460 | 0.4 | 1519 | 23.7 | 2.28 | 3 | 6.71 | 0.75 |
Brain | 0.92 | 3195 | 23,492 | 0.0 | 5131 | 27.3 | 4.58 | 2 | 9.84 | 0.73 |
Fat | 0.89 | 3409 | 35,495 | 1.4 | 4814 | 26.7 | 7.37 | 3 | 5.27 | 0.42 |
Mammary | 0.95 | 3623 | 38,088 | 1.2 | 5978 | 26.0 | 6.37 | 2 | 7.92 | 0.64 |
Skin | 0.85 | 3410 | 42,965 | 8.6 | 5361 | 28.6 | 8.01 | 1 | 5.56 | 0.59 |
Spleen | 0.88 | 1839 | 30,424 | 3.4 | 4560 | 28.8 | 6.67 | 1 | 6.95 | 0.43 |
Pancreas | 0.92 | 4408 | 30,191 | 0.5 | 6586 | 24.6 | 4.58 | 1 | 8.84 | 0.75 |
Bladder | 0.99 | 4873 | 46,136 | 26.2 | 5729 | 22.8 | 8.05 | 5 | 7.19 | 0.52 |
Lung | 0.90 | 2546 | 15,008 | 0.6 | 2921 | 25.7 | 5.14 | 2 | 7.73 | 0.66 |
Pancreas, healthy | 0.90 | 5580 | 48,540 | 1.1 | 7432 | 28.0 | 6.53 | 2 | 7.06 | 0.58 |
Pancreas, T2D | 0.91 | 6636 | 52,035 | 6.7 | 7501 | 27.0 | 6.94 | 1 | 6.63 | 0.57 |
Microglia, healthy | 0.89 | 625 | 32,064 | 0.0 | 2665 | 31.6 | 12.03 | 3 | 4.16 | 0.45 |
Microglia, AD | 0.84 | 676 | 20,970 | 0.0 | 2774 | 26.7 | 7.56 | 1 | 6.74 | 0.65 |