Module Anchored Network Inference: A Sequential Module-Based Approach to Novel Gene Network Construction from Genomic Expression Data on Human Disease Mechanism

Figure 8

Comparison of MANI inferred DREAM3 network with the correct answer. (a) The 10-gene DREAM3 network that was perturbed by DREAM3 organizers to produce the time- series data. (b) Network inference by MANI. , , and were external inputs. The edges inferred between genes were either stimulating () or inhibitory (). The parameters for the different regulatory relationships followed the same convention described in Figure 3. Genes in the network were grouped according to their likely times of activation within the cascade as estimated from the durations of lag observed in their expression data. (c) The accuracy of the DREAM3 network inferred by the MANI approach in (b) was evaluated by comparing it to the correct answer shown in (a). Comparisons were based on the presence or absence of edges between genes rather than directions of interactions. Among the MANI inferred edges in (b), there were 4 TPs, 7 FNs, 6 FPs, and 28 True Negatives (TNs).

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