Bioinformatical Analysis of Organ-Related (Heart, Brain, Liver, and Kidney) and Serum Proteomic Data to Identify Protein Regulation Patterns and Potential Sepsis Biomarkers

Table 1

Thirty-eight functions filtered by prevalence (cutoff ≥ 12%) from the original 159 functions derived from GeneMania network analysis of the whole dataset without the serum proteins. Column 1 shows the functions names. Columns 2 and 3 show, respectively, the number of annotated genes in the displayed network and the number of genes with that annotation in the genome. In column 5, names in bold letters represent the genes predicted by the software.

Function	Genes in network	Genes in genome	Ratio	Names
NADH metabolic process	6	12	50.00%	gpd1, dlst, ogdh, mdh2, mdh1, aldob
Oxaloacetate metabolic process	4	11	36.36%	got1, mdh1, mdh2, pc
Tricarboxylic acid cycle	5	15	33.33%	dlst, ogdh, aco2, suclg2, mdh2
Tricarboxylic acid cycle enzyme complex	3	11	27.27%	dlst, ogdh, suclg2
NAD metabolic process	6	24	25.00%	gpd1, dlst, ogdh, aldob, mdh2, mdh1
Aerobic respiration	5	25	20.00%	dlst, ogdh, aco2, suclg2, mdh2
Fatty-acyl-CoA binding	3	15	20.00%	acadl, pitpna, acadm
Succinate metabolic process	2	10	20.00%	aldh5a1, suclg2
Pentose-phosphate shunt	2	10	20.00%	g6pd, taldo1
Ribonucleoside diphosphate biosynthetic process	2	10	20.00%	atp5a1, atp5b
Pentose metabolic process	2	10	20.00%	g6pd, taldo1
NADPH regeneration	2	10	20.00%	g6pd, taldo1
2-Oxoglutarate metabolic process	3	16	18.75%	got1, dlst, ogdh
Nicotinamide nucleotide metabolic process	8	43	18.60%	gpd1, dlst, ogdh, g6pd, mdh2, mdh1, taldo1, aldob
Pyridine nucleotide metabolic process	8	43	18.60%	gpd1, dlst, ogdh, g6pd, mdh2, mdh1, taldo1, aldob
MHC class I protein binding	2	11	18.18%	atp5a1, atp5b
ADP metabolic process	2	11	18.18%	atp5a1, atp5b
Positive regulation of glycolysis	2	11	18.18%	gpd1, mif
Oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor	4	25	16.00%	aldh5a1, ogdh, gapdh, aldh7a1
Monosaccharide catabolic process	10	63	15.87%	aldoa, akr1a1, gapdh, eno1, g6pd, fbp1, gpd1, taldo1, mif, aldob
Glucose catabolic process	9	57	15.79%	fbp1, gpd1, aldoa, gapdh, eno1, g6pd, taldo1, mif, aldob
Neurotransmitter metabolic process	3	19	15.79%	aldh5a1, glul, pebp1
Pyridine-containing compound metabolic process	8	51	15.69%	gpd1, dlst, ogdh, g6pd, mdh2, mdh1, taldo1, aldob
Monosaccharide biosynthetic process	8	51	15.69%	gnmt, akr1a1, gapdh, g6pd, fbp1, gpd1, pc, acadm
Oxidoreduction coenzyme metabolic process	8	51	15.69%	gpd1, dlst, ogdh, g6pd, mdh2, mdh1, taldo1, aldob
Acetyl-CoA metabolic process	4	26	15.38%	acss1, fasn, dlat, acaa2
Glycolysis	7	46	15.22%	fbp1, gpd1, aldoa, gapdh, eno1, mif, aldob
Glutamate metabolic process	3	20	15.00%	aldh5a1, got1, glul
Hexose catabolic process	9	61	14.75%	fbp1, gpd1, aldoa, gapdh, eno1, g6pd, taldo1, mif, aldob
Gluconeogenesis	6	44	13.64%	gnmt, gapdh, fbp1, gpd1, pc, acadm
Dicarboxylic acid metabolic process	10	76	13.16%	gnmt, ogdh, glul, suclg2, aldh5a1, got1, dlst, mdh1, mdh2, pc
Hexose biosynthetic process	6	46	13.04%	gnmt, gapdh, fbp1, gpd1, pc, acadm
Purine nucleoside triphosphate biosynthetic process	3	23	13.04%	adk, aldoa, atp5b
Oxidoreductase activity, acting on the aldehyde or oxo group of donors	4	31	12.90%	aldh5a1, ogdh, gapdh, aldh7a1
Single-organism carbohydrate catabolic process	11	90	12.22%	cps1, aldoa, akr1a1, gapdh, eno1, c6pd, fbp1, gpd1, taldo1, mif, aldob
Regulation of glycolysis	3	25	12.00%	fbp1, gpd1, mif
Proton-transporting two-sector ATPase complex	3	25	12.00%	atp6v1b1, atp5a1, atp5b
Hydro-lyase activity	3	25	12.00%	uroc1, aco2, eno1