Table 2.

Mean fluorescence intensity ratios (i.e., fold-change) for known genes involved in aromatic amino acid metabolism

Gene	Exp. 1	Exp. 2	Exp. 3	Exp. 4	Exp. 5	Exp. 6	Exp. 7
aroA	0.99	1.18	1.24	0.40 (0.0007)†	2.67 (0.0020)*	0.98	1.02
aroB	0.92	1.06	1.37 (0.0003)*	0.95 (0.0012)†	1.31 (0.0166)*	0.96	0.99
aroC	1.04	1.25	0.99	1.02	0.84	1.11 (0.0093)*	1.01
aroD	0.92	1.09	1.83 (0.0003)*	0.99	1.07	0.73 (0.0001)†	0.96
aroE	1.24 (0.0066)*	1.27 (0.0124)*	2.43 (0.0003)*	0.62 (0.0007)†	1.98 (0.0020)*	1.61 (0.0012)*	0.98
aroF	1.16 (0.0106)*	1.11	1.11	0.77	1.25 (0.0068)*	1.23 (0.0012)*	1.01
aroH	1.00	1.05	1.09	0.96	1.18	0.93	0.97
aroK	1.02	0.94	0.99	0.73	1.21 (0.0068)*	1.59 (0.0012)*	0.88 (0.0252)†
folB	1.15	1.03	1.49 (0.0003)*	1.29	0.93	1.03	0.96
folC	1.31 (0.0046)*	1.09	2.08 (0.0003)*	0.85 (0.0007)†	1.79 (0.0020)*	0.67 (0.0001)†	0.95
folD	1.06	0.95	0.89	1.17	0.82	0.98	0.67 (0.0022)†
folK	1.34 (0.0031)*	1.02	1.37	1.02	0.93	1.03	0.98
hisA	1.01	0.85	2.54 (0.0003)*	2.25 (0.0007)*	0.50 (0.0020)†	0.83 (0.0001)†	0.99
hisB	1.19	0.79	2.33 (0.0003)*	1.38 (0.0007)*	0.65 (0.0027)†	0.94	1.07
hisC	1.17	1.36 (0.0033)*	3.70 (0.0003)*	0.83 (0.0007)*	1.73 (0.0020)*	1.56 (0.0001)*	1.09
hisD	1.00	0.83	2.56 (0.0003)*	1.49 (0.0007)*	0.57 (0.0020)†	0.95	0.92
hisF	1.09	0.91	3.06 (0.0003)*	1.91 (0.0007)*	0.56 (0.0020)†	0.71 (0.0001)†	1.02
hisG	1.11	0.83	2.49 (0.0003)*	2.17 (0.0007)*	0.47 (0.0020)†	1.11 (0.0020)*	0.80 (0.0022)†
hisH	0.97	0.89	1.87 (0.0003)*	1.62 (0.0007)*	0.57 (0.0020)†	0.91 (0.0093)†	1.00
hisI	1.14	0.89	3.01 (0.0003)*	2.15 (0.0007)*	0.60 (0.0020)†	0.75 (0.0001)†	1.11
hisJ	0.82 (0.0046)†	1.30 (0.0108)*	1.18 (0.0003)*	0.93	0.92	0.91	1.00
hisS	1.21	1.18	1.97 (0.0003)*	0.79 (0.0012)†	1.15	0.58 (0.0001)†	0.89
hisZ	1.01	1.00	2.04 (0.0003)*	2.26 (0.0007)*	0.44 (0.0020)†	1.01	0.72 (0.0038)†
mtrA	0.99	1.43	1.76 (0.0003)*	0.77 (0.0007)†	1.65 (0.0020)*	0.56 (0.0001)†	1.09
mtrB	0.99	1.36	1.15	0.90 (0.0028)†	1.06	0.54 (0.0001)†	1.16 (0.0127)*
pabA	1.10	1.10	2.64 (0.0003)*	1.02	1.15	0.98	0.95
pabB	1.02	1.09	1.05	1.39 (0.0081)*	0.59 (0.0020)†	ND	0.99
pabC	1.29 (0.0031)*	1.25	3.66 (0.0003)*	1.03	1.15	0.80 (0.0001)†	0.97
pheA	0.91	1.14	1.31 (0.0003)*	0.98 (0.0025)†	1.14	0.80 (0.0004)†	1.12
pheB	1.00	0.98	1.49 (0.0003)*	1.17 (0.0104)*	1.00	1.11 (0.0001)*	1.17
pheS	0.92	2.00 (0.0033)*	2.05 (0.0003)*	0.79 (0.0007)†	1.27 (0.0106)*	0.99	1.29 (0.0022)*
pheT	0.93	1.17	1.66 (0.0003)*	ND	1.00	1.19	0.91
suI	1.12	1.12	1.91 (0.0003)*	1.30 (0.0007)*	0.98	1.17 (0.0019)*	1.01
trpA	1.49 (0.0031)*	1.42	2.13 (0.0003)*	0.95	1.49 (0.0020)*	1.54 (0.0001)*	1.06
trpB	2.34 (0.0031)*	1.91 (0.0033)*	2.24 (0.0003)*	1.39 (0.0012)*	4.40 (0.0020)*	7.94 (0.0001)*	1.50 (0.0022)*
trpC	1.16	1.38 (0.0124)*	1.86 (0.0003)*	1.32 (0.0035)*	1.56 (0.0020)*	2.56 (0.0001)*	1.17 (0.0252)*
trpD	1.29 (0.0031)*	3.56 (0.0033)*	8.71 (0.0003)*	1.38 (0.0104)*	2.45 (0.0020)*	4.68 (0.0001)*	1.38 (0.0022)*
trpE	0.92	5.11 (0.0033)*	6.63 (0.0003)*	1.81 (0.0007)*	1.75 (0.0020)*	3.15 (0.0001)*	1.75 (0.0022)*
trpF	1.38 (0.0031)*	2.42 (0.0033)*	5.13 (0.0003)*	1.20	4.20 (0.0020)*	5.60 (0.0001)*	1.10 (0.0070)*
trpS	1.36 (0.0031)*	2.61 (0.0033)*	0.91	1.33 (0.0007)*	1.13	1.80 (0.0001)*	3.03 (0.0022)*
tyrA	1.09	1.27	2.00 (0.0003)*	0.96 (0.0081)†	1.24	1.13 (0.0008)*	1.56 (0.0022)*
tyrS	0.88	1.42 (0.0124)*	1.31 (0.0021)*	0.94 (0.0035)†	1.08	0.75 (0.0001)†	1.19 (0.0158)*
tyrZ	1.00	0.88	0.80 (0.0007)†	0.89	0.79	1.42 (0.0001)*	1.14
ycbK	0.95	2.87 (0.0033)*	0.61 (0.0003)†	0.9	0.83	1.45 (0.0001)*	3.05 (0.0022)*
rtpA	1.12	3.46 (0.0033)*	0.87	1.00	0.91	ND	1.89 (0.0022)*

The ratios were calculated based on the culture conditions or strain comparisons shown in Table 1. Numbers in parentheses represent the q values determined by sam (similar to P values; refer to text). ND, not determined. 

^*Transcripts that are significantly up-regulated on the basis of sam. 

^† Transcripts that are significantly down-regulated.