Effect of carbon source perturbations on transcriptional regulation of metabolic fluxes in Saccharomyces cerevisiae

Table 3 Results of simulations for genes belonging to central carbon metabolism. Corresponding figures are given in figure 2 and 3.

		Qualitative	Quantitative
	Actual EFM number used in simulations	Qualitative agreement*	Omissions for R²:0.60	Slope	Correlation coefficient (R²)	Omitted Genes	Not Applicable Genes^#
Glucose/Ethanol, batch	127,872/11,427	0.82 (36/44)	3^$	1.06	0.65	PFK12 ^$ FBP1 ^$ PYC12	(GPP1-HOR2)
Glucose/Ethanol, chemostat	9,600/7,051	0.77 (33/43)	6	0.81	0.60	PFK12 PYC12 ALD45 (PDA12-PDB1) FBA1^§TPI1^§, TDH1^§	(GPP1-HOR2) BPH1
Glucose/Acetate, batch	127,872/4,238	0.76 (31/41)	3	1.11	0.63	MAE1 IDP23 RPE1	(GPP1-HOR2) BPH1 PYC12 PFK12
Glucose/Acetate, chemostat	9,600/4,190	0.78 (32/41)	6	1.18	0.61	ADH145 RKI1 LSC12 SOL34 FBA1 ZWF1	(GPP1-HOR2) BPH1 PYC12 PFK12
Glucose/Lactate, batch	127,872/25,482	0.84 (38/45)	4	0.89	0.60	PFK12 IDP23 PYK12 MAE1	-
Aerobic/Anaerobic, chemostat	9,600/8,363	0.80 (33/41)	19	1.23	0.60

*Data points in first/third quadrants of the plots. The points with a fold change between 0.95–1.05 for either of model or experiment were considered to be in qualitative agreement.
^$These genes were found to exhibit better agreement with CEF ratios in the analysis of [21].
^#CEF ratio was either zero or infinity for these genes. Therefore, they could not be used in the correlation calculation.
^§ Omission of any two of these there points additional to the other four reported points is enough to get a correlation above the cut-off value, resulting in the same slope.

ISSN: 1752-0509