Figure 4. Comparison of qpgraph with qtlhot/CMST. Precision-recall curves calculated from predicted regulatory relationships inferred from a yeast cross data set using the approach introduced in this paper (qpgraph) and 6 different configurations of the qtlhot/CMST method. In (A) predictions are compared against a bronze standard formed by relationships formed by knocked-out genes and their putative targets derived from differential expression (Hughes et al., 2000; Zhu et al., 2008). In (B) this bronze standard is further restricted to relationships also present in the Yeastract database (Teixeira et al., 2014) of curated transcriptional regulatory associations. The horizontal gray dotted line indicates the baseline precision attained by a random predictor.