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Table 2 Artificial corynebacterial stimulon

From: CoryneRegNet 4.0 – A reference database for corynebacterial gene regulatory networks

Gene GeneID Operon M-value Regulated by
ramB cg0444 - 1.9 (R) ramB, (A) ramA
sdhCD cg0445 OP_cg 0445 -1.8 (R) ramB, (R) ripA, (A) dtxR, (A) ramA
sdhA cg0446 OP_cg 0445 1.8 (R) ramB, (R) ripA, (A) dtxR, (A) ramA
sdhB cg0447 OP_cg 0445 -2.5 (R) ramB, (R) ripA, (A) dtxR, (A) ramA
- cg0448 OP_cg 0445 -1.7 (R) ramB, (R) ripA, (A) dtxR, (A) ramA
ramA cg2831 - -1.6 (R) ramA
  1. This table shows a small, artificial stimulon, which can be applied to the novel consistency check feature of CoryneRegNet 4.0. Expression values are given as M-values. In the last column, we list that transcription factors, which control the gene in the first column. We denote (R) as repression and (A) as activation respectively. One can see 3 putative contradictions: (1) The gene sdhA is upregulated, while all the other genes in the same predicted operon are downregulated. (2) The gene ramB is upregulated, but the activator ramA is downregulated. (3) The gene sdhA is upregulated, while the activator ramA is downregulated and the repressor ramB is upregulated. Refer figure 3 for a visualization.
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