1. Dynamic regulatory map and static network for yeast response to AA starvation.
Dynamic regulatory map and static network for yeast response to AA starvation. (A) Dynamic map of yeast response to AA starvation using static input from condition‐specific binding experiments and time‐series expression data. TFs with split score below appear next to the split they regulate, in ranked order of scores. Nodes in the graph represent hidden states. The area of a node is proportional to the s.d. of the expression of the genes assigned to that node. Green nodes represent split nodes. Many of the TFs were correctly assigned to the time points they are known to regulate. For example, Gcn4, which is a known master regulator of AA starvation response, is correctly assigned to the first split. Many of the TFs assigned to the second split regulate specific AA biosynthesis pathways. (B) Dynamic map of yeast response to AA starvation using input from both condition‐ and non‐condition‐specific ChIP‐chip experiments. Several additional TFs not profiled with a condition‐specific ChIP‐chip experiment under the AA condition were determined to be participating in the response and recovery processes. These included Abf1, Swi4, Mbp1, and Ino4. In addition to identifying these TFs as potential participants in the response, DREM also identifies their time of influence. (C) Static regulatory graph for AA starvation. Nodes correspond to genes or TFs. An edge implies that the TF binds the gene with a P‐value <0.005 in an AA starvation ChIP‐chip experiment. Blue edges represent interactions between TFs. Whereas some properties of the networks can be derived from the static representation, many of the dynamic aspects of the system are lost when not using the time‐series data.
Jason Ernst et al. Mol Syst Biol 2007;3:74
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