Predicting and validating condition specific networks. To find a condition specific network associated with treatment with rapamycin, we first analyzed all the local networks and identified from the respective UTMs all the links associated with this condition [see Additional files 3]. Here we show the sub-network consisting of links in the literature-driven gene regulatory networks [21, 22] and predicted links, which are supported by ChIP-on-chip binding assays (P ≤ 0.001) with rapamycin treatment. Blue links represent pairs of TF-target genes bound to each other and predicted to be active in this condition (46/55). Dotted gray links (9/55) correspond to pairs bound to each other, in which our model failed to predict a condition-specific regulatory relationship.