| Supplementary Information Elucidation of Directionality for Co-Expressed Genes: Predicting Intra-Operon Termination sites (2008) | |||||||||||||
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| Figure S1 shows the co-expression network at the chosen similarity threshold value of 0.90. The network was composed of 262 nodes connected by a total of 530 edges while the remaining 484 nodes were isolated. There were 47 separate clusters (sub-networks) in the network with the largest connected component consisting of 79 nodes and 260 edges (see Table S1). Figure 3 (main manuscript) shows the characteristic expression signatures of the top 6 clusters. The genes in the largest cluster exhibited an exponentially decaying time profile representing the overall “cradle-to-grave ” design of the experiment. The two main enzyme classes that were highly represented in this cluster were t-RNA synthetases that are indispensable to the translation process and kinases that carry out phosphorylation/dephosphorylation. In particular, we found 8 genes (argS, thrS, serS, ileS, proS, alaS, aspS, hisS) involved in aminoacyl-tRNA biosynthesis and 9 kinases (adk, udk, pyk, pfk, ackA, thrB, pgk, thiD, dapG) involved in carbohydrate and amino acid metabolism. Cluster 2 genes, most of which belong to the urea cycle and amino group | |||||||||||||
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