How to identify essential genes from molecular networks?

BMC Systems Biology

Table 1 Genetic metabolic networks used in this study

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

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.

ISSN: 1752-0509