Figure 4

Time-dependent regulatory network involved in yeast chemical stress response. Microarray results for the kinetics of benomyl action [30] were analyzed using ARTIVA. A hierarchical clustering analysis was carried out for the time-course responses of the wild-type strain and deletion strains for four transcription factors (TFs): Yap1, Pdr1, Pdr3 and Yrr1. The resulting 18 clusters have low intra-cluster variability and comprise genes whose expression is identically modified in TFs deletion strains compared to the wild-type strain (see Methods). Results for cluster #1 are presented here. (A) Gene expression measurements represented using the common color code (black for expression values around 0 and red for positive values). Bayes factors for changepoint (CP) and edge detection are respectively shown in (B) and (C). Two CP were identified at the 4 min and 10 min time-points, and regulatory associations with the TF Yap1 were identified in the second temporal phase (from 4 min to 20 min). (D) All the identified regulatory associations are shown here, after analyzing the 18 clusters of co-expressed genes independently. They are all positive, meaning that each transcription factor activates the expression of their respectives target genes. Regulatory interactions are color-coded according to their starting time-point: orange = 4 minutes, yellow = 10 minutes and green = 20 minutes. We found 62 regulatory interactions for Yap1; 19 for Pdr1; 10 for Pdr3; and 2 for Yrr1. Pink and white segments on the surrounding circle indicate genes belonging to the same gene expression cluster, the clusters are ordered as follows (starting at 4 min): 1, 18, 7, 9, 13, 8, 17, 2, 5, 6, 3, 11, 4, 10, 12, 14, 15, 16.