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How Difficult Is Inference of Mammalian Causal Gene Regulatory Networks?

Figure 6

Comparison of the true positive and false positive rates as determined by different network inference approaches on the tooth dataset: Pearson correlation, Pathway Commons database, protein-protein interactions (PPI), the union of the previous three methods and direct effect on genetic perturbation (log fold change cut-off or 0.5 and 1).

Note: the TP and FP rates for the first 4 methods were calculated based on the subset of 686 RTPs that were represented in the microarray, PPI and pathway data. The TP and FP rates for perturbation data were based on the subset of 39 RTPs with a regulator matching the pathway being perturbed.

Figure 6