The 29 GRMs identified in this study. Each rectangle stands for a module and the ovals in a rectangle indicate the TFs that regulate the module. A TF name is colored blue if it is known to be involved in heat shock response but black otherwise. The periphery of a rectangle is colored purple if the module has at least one enriched MIPS functional category but black otherwise. An oval is colored green if the TF's function is consistent with at least one of the module's enriched MIPS functional categories. Two ovals are connected by an undirected red line if these two TFs have physical interactions indicated by the current protein-protein interaction data . Two ovals are connected by a directed black line if the two TFs have genetic interactions indicated by mutant or ChIP-chip data [20, 21]. For example, Msn2→Yap1 means that either TF Msn2 binds to the promoter of gene YAP1 or the disruption of TF Msn2 results in a significant change of the expression of gene YAP1.