Figure 7

Multi-edge simulation study involving 5 gene expression traits ( E 1- E 5) and one clinical trait Trait. The heatmap plot in (a) depicts the true causal model. Note that a red square in the i-th row and j-th column indicates that trait i causally affects trait j, e.g. E 1 → E 2. The rows and columns of the heatmap are ordered according to a hierarchical clustering tree, which was constructed using average linkage hierarchical clustering based on the pairwise correlations of the traits. Figure (b) depicts the corresponding heatmap of the observed network that was reconstructed using the LEO.NB.OCA score. Figure (c) shows an alternative output graph of NEO. Blue edges indicate significant correlations and a LEO.NB.OCA score is added to each edges whose LEO.NB.OCA score passes a user-supplied threshold. We find that all true causal edges are correctly retrieved at the recommended LEO.NB.OCA threshold of 0.3. Figure (d) shows the results of a robustness analysis for the LEO.NB.OCA and LEO.NB.CPA scores for the edge orientation E 4 → Trait. The LEO.NB.OCA scores exceed the recommended threshold of 0.3 (red horizontal line), i.e. they retrieve the orientation correctly. Similarly, the LEO.NB.CPA scores exceed the threshold of 0.8.