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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.