Rapamycin treatment can induce the dephosphorylation and subsequent activation of GLN3 [35]. Figure 5 displays the layout of all the biclusters containing these two transcription factors. We note that all but one bicluster also includes either the transcription factor GAT1 or the transcription factor GCN4. GAT1 is a transcriptional activator of genes involved in nitrogen catabolite repression; the activity and localization of these genes is regulated by nitrogen limitation. GCN4 is another transcription activator that is a master regulator of gene expression during amino acid starvation in S. cerevisiae and is activated in multiple stress responses [36]. Thus, it is not surprising that GAT1 and GCN4 co-regulate genes with GLN3 and RTG3. The functional annotations of the set of nine genes targeted by GCN4, GLN3, and RTG3 is enriched in the Gene Ontology biological process "glutamine family amino acid biosynthesis" (p-value of 2 × 10-8, based on the hypergeometric distribution), indicating that this pathway may be activated by the three transcription factors upon rapamycin treatment.