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Table 1 Genetic metabolic networks used in this study

From: How to identify essential genes from molecular networks?

Network name Over-linked metabolites Vertices:Edges Overlap (%)
KEGG H2O, ATP, ADP, NAD+, NADH, NADP+, NADPH, Oxygen 636:10038 33.85
KEGGtype Ibid 629:6590 26.81
KEGGpath Ibid 634:7752 31.57
KEGGtypepath ibid 621:5223 25.11
KEGG2 Ibid 609:10518 34.24
KEGG2type Ibid 602:7099 27.44
KEGG2path Ibid 608:8130 31.89
KEGG2typepath Ibid 595:5691 25.65
iND750_0 H2O, H+ 990:8427 19.19
iND750_1 H2O, H+, Pi 976:6995 18.27
iND750_2 H2O, H+, Pi, ATP 976:6278 17.85
iND750_3 H2O, H+, Pi, ATP, Glu-L 974:5742 17.60
iND750_4 H2O, H+, Pi, ATP, Glu-L, ADP 969:5186 17.18
iND750_0nh H2O, H+ 634:4761 19.19
iND750_1nh H2O, H+, Pi 619:3963 18.27
iND750_2nh H2O, H+, Pi, ATP 618:3387 17.85
iND750_3nh H2O, H+, Pi, ATP, Glu-L 617:3122 17.60
iND750_4nh H2O, H+, Pi, ATP, Glu-L, ADP 613:2720 17.18
  1. The names of the KEGG and the iND750-derived networks are indicated under the "Network name" column. Note that the last five networks end with an "nh", indicating that hypothetical reactions were not included in these networks. The column labeled "Over-linked metabolites" indicates the metabolites being removed while reconstructing the network: H2O: water; H+: a proton; Pi: inorganic phosphorus; ATP: adenosine triphosphate; Glu-L: L-glutamate and ADP: adenosine diphosphate, NADP+/NADPH: Nicotinamide adenine dinucleotide phosphate, NAD/NADH: Nicotinamide adenine dinucleotide. The number of genes (values in bold) and gene-to-gene relationships (values in italics) of each graph are indicated separated by a colon in the Vertices:Edges column. The column labeled "Overlap (%)" indicates the percentage of known gene-to-gene relationships (network links) found in each reconstructed network reported in the probabilistic functional network of yeast genes [4] that included two metabolic genes. According to the procedure to build these networks, KEGG, KEGGpath, KEGG2 and KEGG2path networks are undirected.