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Table 3 Number of knockouts for the biomass reaction in selected networks

From: Double and multiple knockout simulations for genome-scale metabolic network reconstructions

Model

 

Single knockouts

Double knockouts

reaction id

cl. size

classes

reactions

cl. pairs

reac. pairs

E. coli iJO1366

     

Ec_biomass_iJO1366_WT_53p95M

20

101

343

130

339

Ec_biomass_iJO1366_core_53p95M

1

80

288

90

268

S. cerevisiae iND750

     

biomass_SC4_bal

26

54

156

60

142

M. tuberculosis iNJ661

     

biomass_Mtb_9_60atp

160

64

154

48

83

S. aureus iSB619

     

SA_biomass_1a

8

25

63

59

157

SA_biomass_5a

1

58

215

54

100

H. pylori iIT341

     

BiomassHP_published

189

36

76

41

81

  1. class size: Number of reactions in the same coupling class as the biomass reaction, i.e., number of reactions that carry flux if and only if the biomass reaction carries flux.
  2. Single Knockouts: Number of different single knockouts (classes and reactions) that block the biomass reaction. Only reactions that are not partially coupled to the biomass (from a different reaction class) are counted.
  3. Double Knockouts: Number of different double knockouts (class pairs and reaction pairs) that block the biomass reaction when combined. Only reactions that are not directionally coupled to the biomass are counted.
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Algorithms for Molecular Biology

ISSN: 1748-7188