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

Table 2

Network analysis serum functions prevalence. Twenty-nine functions filtered by prevalence (cutoff ≥ 2%) from the original 166 functions derived from GeneMania® network analysis of the serum-protein dataset. 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
Blood microparticle	22	97	22.68%	apcs, hp, c3, tf, apoa1, cfb, apoe, serping1, fga, alb, itih4, gc, ahsg, c9, hpx, fgb, pon1, ambp, apoa2, f2, c4bpa, fgg
Glycerolipid metabolic process	9	211	4.27%	c3, apoa1, apoe, apoa5, apoh, pon1, cps1, apoa2, apoc3
Phospholipid binding	9	222	4.05%	apoe, apoa1, apoa5, apoh, fabp1, pon1, cps1, apoa2, apoc3
Negative regulation of hydrolase activity	9	264	3.41%	fetub, kng2, apoa1, serping1, serpina1, fabp1, ambp, apoa2, apoc3
Lipid transport	8	174	4.60%	apoe, apoa1, apoa5, apoh, fabp1, pon1, apoa2, apoc3
Regeneration	8	184	4.35%	fga, hp, apoa1, apoe, apoa5, ahsg, apoa2, apoh
Enzyme inhibitor activity	8	197	4.06%	fetub, apoa1, serping1, serpina1, ahsg, ambp, apoa2, apoc3
Wound healing	8	287	2.79%	fga, c3, apoe, apoa5, c9, fgb, f2, apoh
High-density lipoprotein particle	7	15	46.67%	apoe, apoa1, apoa5, apoh, pon1, apoa2, apoc3
Plasma lipoprotein particle	7	19	36.84%	apoe, apoa1, apoa5, apoh, pon1, apoa2, apoc3
Protein-lipid complex	7	20	35.00%	apoe, apoa1, apoa5, apoh, pon1, apoa2, apoc3
Acylglycerol metabolic process	7	75	9.33%	c3, apoe, apoa5, apoh, apoc3, apoa2, cps1
Neutral lipid metabolic process	7	77	9.09%	c3, apoe, apoa5, apoh, apoc3, apoa2, cps1
Acute inflammatory response	7	96	7.29%	hp, c3, tf, itih4, serping1, ahsg, apoa2
Lipid localization	7	136	5.15%	apoe, apoa1, apoa5, apoh, fabp1, apoa2, apoc3
Regulation of lipid metabolic process	7	229	3.06%	c3, apoa1, apoe, apoa5, fabp1, apoa2, apoc3
Regulation of body fluid levels	7	246	2.85%	c3, apoe, gc, fga, c9, f2, apoh
Extracellular matrix	7	262	2.67%	apcs, alb, tf, rbp3, f2, apoh, ahsg
Triglyceride-rich lipoprotein particle	6	14	42.86%	apoe, apoa1, apoa5, apoh, apoc3, apoa2
Very-low-density lipoprotein particle	6	14	42.86%	apoe, apoa1, apoa5, apoh, apoc3, apoa2
Triglyceride metabolic process	6	67	8.96%	c3, apoe, apoa5, apoh, apoc3, cps1
Organ regeneration	6	92	6.52%	hp, apoa1, apoa5, ahsg, apoa2, apoh
Blood coagulation	6	110	5.45%	c3, apoe, fga, c9, f2, apoh
Hemostasis	6	112	5.36%	c3, apoe, fga, c9, f2, apoh
Coagulation	6	115	5.22%	c3, apoe, fga, c9, f2, apoh
Negative regulation of endopeptidase activity	6	156	3.85%	fetub, kng2, serping1, serpina1, fabp1, ambp
Lipid catabolic process	6	157	3.82%	apoe, apoa5, fabp1, cps1, apoa2, apoc3
Negative regulation of peptidase activity	6	159	3.77%	fetub, kng2, serping1, serpina1, fabp1, ambp
Steroid metabolic process	6	200	3.00%	gc, apoa1, apoe, apoc3, pon1, apoa2
Alcohol metabolic process	6	211	2.84%	gc, apoa1, apoe, apoc3, pon1, apoa2
Regulation of endopeptidase activity	6	276	2.17%	fetub, kng2, serping1, serpina1, fabp1, ambp
Organic anion transport	6	279	2.15%	dpysl2, apoa1, apoe, apoc3, fabp1, apoa2
Regulation of peptidase activity	6	288	2.08%	fetub, kng2, serping1, serpina1, fabp1, ambp