Comparing the GO enrichment analysis of genes regulated by the first layer hidden nodes with different activation numbers.

Comparing the GO enrichment analysis of genes regulated by the first layer hidden nodes with different activation numbers.</p

Comparing the TF enrichment analysis of genes regulated by the first layer hidden nodes with different activation numbers.

Comparing the TF enrichment analysis of genes regulated by the first layer hidden nodes with different activation numbers.</p

Protein-protein interaction subnetwork of genes in the perturbation module-30.

Protein-protein interaction subnetwork of genes in the perturbation module-30.</p

Comparing the PPI density of genes in perturbation modules obtained from different methods.

Comparing the PPI density of genes in perturbation modules obtained from different methods.</p

Comparing the GO enrichment analysis of genes in perturbation modules obtained using different methods.

Comparing the GO enrichment analysis of genes in perturbation modules obtained using different methods.</p

Numbers of hidden nodes that were set and actually activated in all hidden layers.

Numbers of hidden nodes that were set and actually activated in all hidden layers.</p

Protein-protein interaction subnetwork of genes in the perturbation module-80.

Protein-protein interaction subnetwork of genes in the perturbation module-80.</p

Example perturbation-responding subgraphs.

<p>Two example subgraphs are shown: <b>Panel A</b>, GO:0019236 (<i>response to pheromone</i>) and <b>Panel B</b>, GO:0006826 (<i>iron ion transport</i>). For each subgraph, the perturbation instances (green hexagons) are shown in the top tier; responding genes (blue circles) are shown in the middle tiers; and the transcription factor modules (grey triangles) are shown in the bottom tier. To avoid an overly crowded figure, a red dash line indicates that a perturbation instance and a responding gene are NOT connected.</p

Subgraph connectivity.

<p>Cumulative distribution of within bipartite subgraph connectivity of the modules identified in three experiments: MBSEC with module-based input graphs (red); SAMBA with module-based input graphs (green); and SAMBA with global input graph (blue).</p

Functional coherence of modules.

<p><b>A</b>. The cumulative distribution of functional coherence p-values of the responding modules identified by different methods: MBSEC with module-based input graphs (red); SAMBA with module-based input graphs (green); and SAMBA with the global input graph (blue). <b>B</b>. The cumulative distribution of functional coherence p-values of the perturbation modules identified by different methods: MBSEC with module-based input graphs (red); SAMBA with module-based input graphs (green); and SAMBA with the global input graph (blue).</p