TABLE 3.

Differentially expressed genes involved in biofilm matrix production and c-di-GMP signaling in ΔcyaA and Δcrp mutants compared to the wild type^a

Gene no.	Designation	Change (fold)
		ΔcyaA/wild type	Δcrp/wild type
Biofilm matrix production genes
VC0916	vpsU	3.76	3.35
VC0917	vpsA	1.51
VC0918	vpsB	2.93	2.16
VC0919	vpsC	2.36	2.37
VC0922	vpsF	2.04
VC0928	rbmA	5.89	5.45
VC0929	rbmB	2.83	3.57
VC0930	rbmC	21.04	8.01
VC0931	rbmD	2.30
VC0932	rbmE	7.46	4.27
VC0933	rbmF	5.89	5.99
VC0935	vpsM	12.75	8.06
VC0936	vpsN	2.63	2.32
VC0937	vpsO	1.61	1.99
VC0939	vpsQ	2.73	2.84
VC0583	hapR	0.11	0.48
VC1888	bap1	7.84	6.28
VCA0952	vpsT	74.62	48.70
c-di-GMP signaling genes: GGDEF and EAL
VC0072		1.91	2.53
VC0653	rocS		1.81
VC0658	cdgI	2.95	3.34
VC0703	mbaA	1.78	1.77
VC1934		0.42	0.44
VC2750			1.70
VCA0785	cdgC	1.53
c-di-GMP signaling genes: only GGDEF
VC1029	cdgB	1.88	2.17
VC1067	cdgH		1.58
VC1216		0.56	0.45
VC1353		0.53
VC1367	cdgE	0.64
VC1370		0.37
VC1376			1.99
VC1599		0.44	0.40
VCA0049		0.58
VCA0074	cdgA	1.61
VCA0165		0.56
VCA0217			1.94
VCA0697	cdgD	0.09	0.11
VCA0956	cgdF	1.90	1.87
VCA0965		0.31	0.50
c-di-GMP signaling genes: only EAL
VC0137		1.69	1.93
VC1086		0.38	0.40
VC1211		1.58
VC1641		1.66	2.56
VC1710		0.21	0.29
c-di-GMP signaling genes: HD-GYP
VC1087		0.43	0.55
VC1348		0.62
VC2340			2.57
VC2497		0.54	0.47
VCA0210			1.76
VCA0895		0.46	0.61
VCA0931		0.48

^aDifferentially expressed genes were determined using the SAM software with a ≥1.5-fold change in gene expression and an FDR of ≤3% as the criteria.