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Table 4 Results from Flux Variability Analysis (FVA) of 3 knockout models for genes with a confirmed normal phenotype (PGM1, FUT9, SORD) and one essential gene (DHCR7).

From: A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1

  PGM1 FUT9 SORD DHCR7
  down up p-value down up p-value down up p-value down up p-value
Amino Acid Metabolism 61 160 <0.00001 85 133 0.00115 122 98 0.10560 68 152 <0.00001
Carbohydrate Metabolism 35 55 0.03501 48 48 1.00000 40 55 0.12380 22 75 <0.00001
Cofactor and Vitamin Metabolism 20 75 <0.00001 53 45 0.41900 60 37 0.01953 25 71 <0.00001
Energy Metabolism 12 34 0.001180 19 27 0.23820 27 19 0.23820 13 32 0.00462
Glycan Metabolism 60 283 <0.00001 118 229 <0.00001 166 182 0.39110 49 294 <0.00001
Lipid Metabolism 109 243 <0.00001 165 189 0.20210 196 162 0.07234 128 225 <0.00001
Nucleotide Metabolism 64 103 0.00255 80 91 0.40020 87 90 0.82160 45 122 <0.00001
Other Amino Acids Metabolism 6 19 0.00932 11 14 0.54850 12 13 0.84150 7 18 0.02781
Secondary Metabolites Metabolism 0 0 1.00000 0 0 1.00000 0 0 1.00000 0 0 1.00000
Transporters 368 437 0.01502 397 422 0.38240 393 443 0.08376 337 479 <0.00001
  1. For each reaction within the model, FVA determines the minimum and maximum flux resulting in the optimal solution for the objective function (here: biomass production). Only those solutions that resulted in the same maximum biomass yield as the wild type model were used for the analysis. By comparing the flux range (the span between vmax,i and vmin,i for each reaction i) between the knockout model and a wild type model, each reaction was assigned a status of decreased (down), non-changing or increased (up) flux capacity (representing metabolic activity). For each metabolism subsystem, the number of reactions with decreased and increased flux capacity are shown. Significance testing was done by performing a single value Chi-Square test with 1 degree of freedom comparing against even probability of increased and decreased flux capacity. Significant p-values (p < 0.05/10) are typeset in bold.