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

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

   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   
  1. *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.
  2. $These genes were found to exhibit better agreement with CEF ratios in the analysis of [21].
  3. #CEF ratio was either zero or infinity for these genes. Therefore, they could not be used in the correlation calculation.
  4. § 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.