Break-down (decomposition) of the composite regulatory network. The input for our algorithm (upper panel) includes: a) a composite regulatory network published by Milo et al  (or a joint network obtained by integrating the literature driven gene regulatory networks compiled by Milo et al.  and Herrgard et al ). The edges (black links) and nodes of the composite network are illustrated by a graph with 11 genes, where yellow and blue circles represent TFs and non regulating genes respectively (b) microarray gene expression profiles from 387 different experimental conditions involving diploid cells. This is a subset of the experiments stored in a compendium of S. cerevisiae gene expression datasets compiled by Ihmels et al . The expression dataset is illustrated by a miniature matrix consisting of 11 genes and 15 experimental conditions, whose red, blue and yellow entries correspond to up-regulation, down-regulation and intermediate expression levels, respectively. The output of our algorithm allows us to read out condition specific regulatory networks, as illustrated in the lower panel.