Figure 2

Local network approach for identifying the experimental conditions for gene regulation by its known direct regulator. As in Fig. 1, the input includes the composite network and a gene expression compendium dataset. For each link in the network, as illustrated for the link TF→Gene1 highlighted in yellow, we identify conditions in which the target gene (Gene1) is directly controlled by its regulator (TF), by extracting two types of condition subsets: a) subset of states in which the expression profile of the target gene (highlighted in pink) is positively or negatively correlated with the expression profile of its regulator, b) subset of states in which the expression profile of the target gene (highlighted in pink) is correlated with the expression profiles of other genes (highlighted in light blue) that are known to be regulated by the same TF. In the illustration shown in the lower panel the conditions in which the TF directly regulates the target gene are indicated below the gene expression patterns across these conditions. These conditions are also displayed in the braces shown next to the sub-networks. To differentiate between conditions in which the link is functional/not-functional due to the activation/deactivation of the TF, we mark these conditions in red and blue respectively.