CoryneRegNet 4.0 – A reference database for corynebacterial gene regulatory networks

BMC Bioinformatics

Table 2 Artificial corynebacterial stimulon

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

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.

ISSN: 1471-2105