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Supplementary Information Elucidation of Directionality for Co-Expressed Genes

Summary: Supplementary Information
Elucidation of Directionality for Co-Expressed Genes:
Predicting Intra-Operon Termination sites
Anshuman Gupta, Costas D. Maranas, Réka Albert
Co-Expression Network Results
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
metabolism pathway (e.g., argB, argC, argD, argG, argH, carA, carB, rocA, rocF, rocD),
showed an initial peak in expression followed by rapid decay. Tryptophan biosynthesis genes
such as trpB, trpC, trpD, trpE, trpF, trpS along with glycerophospholipid metabolism genes such


Source: Albert, Réka - Departments of Biology & Physics, Pennsylvania State University


Collections: Biology and Medicine