TABLE 1.

Selected discrepant genes up-regulated due to temperature or growth rate effects^a

Locus	Function	n1.25	Value for n1.25		n2.0	Value for n2.0		n5.0	Value for n5.0
			% UN	% MM		% UN	% MM		% UN	% MM
Temperature effects (85°C vs 80°C) (CIRCE regulon)
TM0373	DnaK protein	9	11.1	33.3	18	16.7	38.9	24	16.7	45.8
TM0374	Heat shock protein class I	4	0	100	16	0	100	24	4.2	100
TM0505	GroES	3	0	100	14	0	100	24	4.2	24
TM0506	GroEL	0			5	0	60	24	25	41.7
TM0849	DnaJ protein	0			5	0	0	22	22.7	0
TM0850	GrpE protein	8	0	37.5	18	0	33.3	24	0	25
TM0851	Heat shock operon repressor HrcA	9	0	100	19	0	78.9	24	0	66.7
Growth rate effects (D = 0.17 h−1 vs D = 0.25 h−1)
TM0402	Ammonium transporter	4	100	100	9	100	100	18	100	100
TM0403	Nitrogen regulatory protein P-II	2	100	100	16	81.3	100	18	83.3	100
TM0451	Ribosomal protein L33	4	25	50	13	53.8	53.8	18	33.3	61.1
TM0454	Ribosomal protein L11	3	33.3	100	15	20	100	18	16.7	100
TM0455	Ribosomal protein L1	2	100	0	6	100	0	6	100	0
TM0456	Ribosomal protein L10	5	60	0	15	75	0	18	66.7	0
TM1835	Cyclomaltodextrinase, putative	0			10	0	70	18	0	66.7
TM1840	Alpha-amylase	6	0	100	8	0	100	17	0	88.2
TM1845	Pullulanase	1	0	100	8	0	75	18	0	72.2

^aFor the number of comparisons less than a given simple fold change threshold (n_x refers to the number of occurrences less than an x-fold change), the percentages of occurrence genes that were detected to be differentially expressed using the unnormalized log₂-transformed (% UN) or mixed model (% MM) methods are shown. A total of 24 comparisons were possible for each temperature effect and 18 comparisons were possible for each dilution rate effect (Fig. 1). Genes corresponding to the CIRCE regulon are known to be induced by temperature upshift in T. maritima (7) and were chosen as a benchmark for comparison. D, dilution rate.