Figure 1.
A real-world biological network and some network motifs.
(a) A Drosophila developmental transcriptional network with 119 nodes and 306 directed edges. (b) Some representative 2, 3 and 4-node motifs.
Figure 2.
(a) A simple network with six nodes. (b) Subgraphs that are assumed to be motifs in network (a). (c) Members that compose the three types of motifs. (d) Appearances of nodes in each motif as shown in panel (b). (e) Frequency histograms for the six nodes. (f) Cluster analysis reveals that the six nodes can be remarkably classified into three classes. v1, v3, v5 are the most important nodes, and v2 forms the least important group, v4, v6 form another group, which is more important than v2.
Table 1.
Statistical indexes for the five directed biological networks.
Figure 3.
Cluster analysis for the identified top-30 nodes in the five networks based on the Iscore.
Table 2.
Clusters, members, rankings and statistical characteristics of the identified top-30 nodes in the CEN.
Table 3.
Clusters, members, rankings and statistical characteristics of the identified top-30 nodes in the ECT.
Table 4.
Clusters, members, rankings and statistical characteristics of the identified top-30 ranked nodes in the YT.
Figure 4.
ROC curves based on the available information in the CEN and ECT.
(a) Performance of different indexes in identifying (a) the 10 command interneurons in the CEN, (b) the 117 interneurons in the CEN, (c) the 7 key global regulators in the ECT, (d) the 18 global regulators in the ECT.
Figure 5.
Evaluation of Iscore via ROC curves with composite reference standards for the five networks.
(a) T0 = 10%. A node is defined as important if either its rankings by the in, out, total degree, PageRank, motif centrality or the betweenness are at the top-T0 level. (b) Similarly to (a), but with T0 = 20%.
Figure 6.
Topological neighborhoods of several nodes.
(a) Topological neighborhood of a hub but not top-ranked node: node 209 in the YT. (b) Topological neighborhood of a non-hub but top-ranked node: node 546 in the YT. (c) Topological neighborhood of a not top-ranked node but with the highest betweenness: node 293 in the YT.
Figure 7.
The curves of connectivity density against
for different ranking measures in the ECT and HST.