Table 6.
The significant enriched analysis of differentially expressed proteins (DEPs) in ischemic stroke.
| Pathway identifier | Pathway name | #Entities found | #Entities total | Entities ratio | Entities p value | Entities FDR | Submitted entities found |
|---|---|---|---|---|---|---|---|
| Down-regulated | |||||||
| R-HSA-381426 | Regulation of Insulin-like growth factor (IGF) transport and uptake by insulin-like growth factor binding proteins (IGFBPs) | 12 | 127 | 8.43E−03 | 3.89E−12 | 8.53E−10 | TF; ITIH2; PROC; AHSG; FUCA2; SPP2; SPARCL1; APOA1; QSOX1; IGFALS; APOB; HSP90B1 |
| R-HSA-8957275 | Post-translational protein phosphorylation | 11 | 109 | 7.23E−03 | 1.63E−11 | 1.78E−09 | TF; ITIH2; PROC; AHSG; FUCA2; SPP2; SPARCL1; APOA1; QSOX1; APOB; HSP90B1 |
| R-HSA-174824 | Plasma lipoprotein assembly, remodeling, and clearance | 9 | 98 | 6.50E−03 | 2.84E−09 | 2.07E−07 | APOC1; APOA1; LCAT; APOA4; APOB; A2M; PLTP |
| R-HSA-8963899 | Plasma lipoprotein remodeling | 7 | 56 | 3.72E−03 | 2.24E−08 | 1.21E−06 | APOA1; LCAT; APOA4; APOB; PLTP |
| R-HSA-166658 | Complement cascade | 9 | 156 | 1.04E−02 | 1.46E−07 | 6.28E−06 | IGLV2-8; COLEC11; C8G; IGLV5-45; IGKV1-16; CFHR1; CPN2; CPN1; MBL2 |
| R-HSA-168249 | Innate immune system | 23 | 1334 | 8.85E−02 | 2.11E−07 | 7.59E−06 | DSP; COLEC11; JUP; AHSG; FUCA2; GGH; CPN2; CPN1; HSP90B1; IGLV2-8; TF; APOM; C8G; IGLV5-45; IGKV1-16; LAMP1; CFHR1; QSOX1; APOB; CTSD; MBL2 |
| R-HSA-8963898 | Plasma lipoprotein assembly | 5 | 30 | 1.99E−03 | 6.23E−07 | 1.93E−05 | APOC1; APOA1; APOA4; APOB; A2M |
| R-HSA-114608 | Platelet degranulation | 8 | 141 | 9.36E−03 | 8.48E−07 | 2.29E−05 | TF; APOM; LAMP1; AHSG; SPP2; APOA1; QSOX1; A2M |
| R-HSA-76005 | Response to elevated platelet cytosolic Ca2+ | 8 | 148 | 9.82E−03 | 1.21E−06 | 2.91E−05 | TF; APOM; LAMP1; AHSG; SPP2; APOA1; QSOX1; A2M |
| R-HSA-2173782 | Binding and uptake of ligands by scavenger receptors | 8 | 168 | 1.11E−02 | 3.08E−06 | 6.46E−05 | IGLV2-8; COLEC11; IGLV5-45; IGKV1-16; APOA1; APOB; IGHA2; HSP90B1 |
| R-HSA-6798695 | Neutrophil degranulation | 12 | 480 | 3.18E−02 | 7.66E−06 | 1.45E−04 | DSP; TF; APOM; JUP; LAMP1; AHSG; FUCA2; GGH; QSOX1; CTSD; CPN1 |
| R-HSA-8964058 | HDL remodeling | 4 | 24 | 1.59E−03 | 8.78E−06 | 1.47E−04 | APOA1; LCAT; PLTP |
| R-HSA-977606 | Regulation of complement cascade | 7 | 139 | 9.22E−03 | 9.21E−06 | 1.47E−04 | IGLV2-8; C8G; IGLV5-45; IGKV1-16; CFHR1; CPN2; CPN1 |
| R-HSA-109582 | Hemostasis | 15 | 803 | 5.33E−02 | 1.65E−05 | 2.47E−04 | F10; AHSG; APOA1; IGLV2-8; TF; PROC; APOM; IGLV5-45; IGKV1-16; LAMP1; SPP2; QSOX1; APOB; A2M; IGHA2 |
| R-HSA-9029569 | NR1H3 and NR1H2 regulate gene expression linked to cholesterol transport and efflux | 5 | 66 | 4.38E−03 | 2.77E−05 | 3.88E−04 | APOC1; PLTP |
| R-HSA-8963888 | Chylomicron assembly | 3 | 14 | 9.29E−04 | 6.01E−05 | 7.82E−04 | APOA1; APOA4; APOB |
| R-HSA-9024446 | NR1H2 and NR1H3-mediated signaling | 5 | 85 | 5.64E−03 | 9.09E−05 | 1.09E−03 | APOC1; PLTP |
| R-HSA-6809371 | Formation of the cornified envelope | 6 | 138 | 9.16E−03 | 9.25E−05 | 1.11E−03 | DSP; JUP; KRT14; KRT9 |
| R-HSA-8963901 | Chylomicron remodeling | 3 | 17 | 1.13E−03 | 1.06E−04 | 1.17E−03 | APOA1; APOA4; APOB |
| R-HSA-3000480 | Scavenging by Class A receptors | 4 | 49 | 3.25E−03 | 1.38E−04 | 1.38E−03 | COLEC11; APOA1; APOB; HSP90B1 |
| R-HSA-76002 | Platelet activation, signaling and aggregation | 8 | 293 | 1.94E−02 | 1.56E−04 | 1.56E−03 | TF; APOM; LAMP1; AHSG; SPP2; APOA1; QSOX1; A2M |
| R-HSA-2168880 | Scavenging of heme from plasma | 5 | 106 | 7.03E−03 | 2.52E−04 | 2.27E−03 | IGLV2-8; IGLV5-45; IGKV1-16; APOA1; IGHA2 |
| R-HSA-166786 | Creation of C4 and C2 activators | 5 | 111 | 7.37E−03 | 3.11E−04 | 2.80E−03 | IGLV2-8; COLEC11; IGLV5-45; IGKV1-16; MBL2 |
| R-HSA-140837 | Intrinsic pathway of fibrin clot formation | 3 | 26 | 1.73E−03 | 3.68E−04 | 3.31E−03 | PROC; F10; A2M |
| R-HSA-166663 | Initial triggering of complement | 5 | 120 | 7.96E−03 | 4.42E−04 | 3.54E−03 | IGLV2-8; COLEC11; IGLV5-45; IGKV1-16; MBL2 |
| R-HSA-975634 | Retinoid metabolism and transport | 4 | 79 | 5.24E−03 | 8.29E−04 | 6.64E−03 | APOM; APOA1; APOA4; APOB |
| R-HSA-8866423 | VLDL assembly | 2 | 9 | 5.97E−04 | 1.07E−03 | 7.46E−03 | APOC1; APOB |
| R-HSA-159763 | Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus | 2 | 9 | 5.97E−04 | 1.07E−03 | 7.46E−03 | PROC; F10 |
| R-HSA-6805567 | Keratinization | 6 | 226 | 1.50E−02 | 1.24E−03 | 7.87E−03 | DSP; JUP; KRT14; KRT9 |
| R-HSA-6806667 | Metabolism of fat-soluble vitamins | 4 | 89 | 5.91E−03 | 1.28E−03 | 7.87E−03 | APOM; APOA1; APOA4; APOB |
| R-HSA-8964046 | VLDL clearance | 2 | 10 | 6.64E−04 | 1.31E−03 | 7.87E−03 | APOC1; APOB |
| R-HSA-159782 | Removal of aminoterminal propeptides from gamma-carboxylated proteins | 2 | 10 | 6.64E−04 | 1.31E−03 | 7.87E−03 | PROC; F10 |
| R-HSA-8964043 | Plasma lipoprotein clearance | 3 | 42 | 2.79E−03 | 1.46E−03 | 8.77E−03 | APOC1; APOA1; APOB |
| R-HSA-140877 | Formation of fibrin clot (clotting cascade) | 3 | 43 | 2.85E−03 | 1.56E−03 | 9.37E−03 | PROC; F10; A2M |
| R-HSA-202733 | Cell surface interactions at the vascular wall | 6 | 257 | 1.71E−02 | 2.36E−03 | 1.42E−02 | IGLV2-8; PROC; IGLV5-45; IGKV1-16; APOB; IGHA2 |
| R-HSA-166662 | Lectin pathway of complement activation | 2 | 15 | 9.95E−04 | 2.90E−03 | 1.45E−02 | COLEC11; MBL2 |
| R-HSA-159740 | Gamma-carboxylation of protein precursors | 2 | 15 | 9.95E−04 | 2.90E−03 | 1.45E−02 | PROC; F10 |
| R-HSA-381183 | ATF6 (ATF6-alpha) activates chaperone genes | 2 | 15 | 9.95E−04 | 2.90E−03 | 1.45E−02 | HSP90B1 |
| R-HSA-159854 | Gamma-carboxylation, transport, and amino-terminal cleavage of proteins | 2 | 16 | 1.06E−03 | 3.29E−03 | 1.64E−02 | PROC; F10 |
| R-HSA-381033 | ATF6 (ATF6-alpha) activates chaperones | 2 | 17 | 1.13E−03 | 3.70E−03 | 1.85E−02 | HSP90B1 |
| R-HSA-8963896 | HDL assembly | 2 | 18 | 1.19E−03 | 4.13E−03 | 2.07E−02 | APOA1; A2M |
| R-HSA-9006931 | Signaling by nuclear receptors | 7 | 387 | 2.57E−02 | 4.25E−03 | 2.13E−02 | APOC1; PLTP; CTSD |
| R-HSA-3000471 | Scavenging by Class B receptors | 2 | 21 | 1.39E−03 | 5.57E−03 | 2.23E−02 | APOA1; APOB |
| R-HSA-140875 | Common pathway of fibrin clot formation | 2 | 25 | 1.66E−03 | 7.79E−03 | 3.12E−02 | PROC; F10 |
| R-HSA-392499 | Metabolism of proteins | 20 | 2207 | 1.46E−01 | 8.85E−03 | 3.54E−02 | ITIH2; F10; AHSG; COG4; FUCA2; APOA1; APOA4; HSP90B1; DPP4; TF; PROC; SPP2; SPARCL1; QSOX1; IGFALS; APOB; CTSD; GAPDH |
| R-HSA-168256 | Immune system | 23 | 2684 | 1.78E−01 | 9.29E−03 | 3.71E−02 | DSP; COLEC11; JUP; AHSG; FUCA2; GGH; CPN2; CPN1; HSP90B1; IGLV2-8; TF; APOM; C8G; IGLV5-45; IGKV1-16; LAMP1; CFHR1; QSOX1; APOB; CTSD; MBL2 |
| R-HSA-8963889 | Assembly of active LPL and LIPC lipase complexes | 2 | 30 | 1.99E−03 | 1.10E−02 | 4.41E−02 | APOA4 |
| R-HSA-5653656 | Vesicle-mediated transport | 10 | 827 | 5.49E−02 | 1.11E−02 | 4.45E−02 | IGLV2-8; COLEC11; TF; IGLV5-45; IGKV1-16; COG4; APOA1; APOB; IGHA2; HSP90B1 |
| R-HSA-977225 | Amyloid fiber formation | 3 | 89 | 5.91E−03 | 1.17E−02 | 4.67E−02 | TF; APOA1; APOA4 |
| R-HSA-382551 | Transport of small molecules | 11 | 966 | 6.41E−02 | 1.19E−02 | 4.76E−02 | TF; APOC1; APOA1; LCAT; APOA4; APOB; A2M; NEO1; PLTP |
| R-HSA-2187338 | Visual phototransduction | 4 | 169 | 1.12E−02 | 1.22E−02 | 4.88E−02 | APOM; APOA1; APOA4; APOB |
| Up-regulated | |||||||
| R-HSA-977606 | Regulation of complement cascade | 5 | 135 | 1.16E−02 | 2.87E−06 | 1.55E−04 | IGHV2-5; IGLV3-21; IGLL1; CFHR4; IGLV10-54 |
| R-HSA-166658 | Complement cascade | 5 | 146 | 1.26E−02 | 4.20E−06 | 1.55E−04 | IGHV2-5; IGLV3-21; IGLL1; CFHR4; IGLV10-54 |
| R-HSA-173623 | Classical antibody-mediated complement activation | 4 | 95 | 8.20E−03 | 1.97E−05 | 2.70E−04 | IGHV2-5; IGLV3-21; IGLL1; IGLV10-54 |
| R-HSA-2168880 | Scavenging of heme from plasma | 4 | 99 | 8.54E−03 | 2.31E−05 | 2.70E−04 | IGHV2-5; IGLV3-21; IGLL1; IGLV10-54 |
| R-HSA-2029481 | FCGR activation | 4 | 101 | 8.72E−03 | 2.50E−05 | 2.70E−04 | IGHV2-5; IGLV3-21; IGLL1; IGLV10-54 |
| R-HSA-2730905 | Role of LAT2/NTAL/LAB on calcium mobilization | 4 | 102 | 8.80E−03 | 2.60E−05 | 2.70E−04 | IGHV2-5; IGLV3-21; IGLL1; IGLV10-54 |
| R-HSA-166786 | Creation of C4 and C2 activators | 4 | 103 | 8.89E−03 | 2.70E−05 | 2.70E−04 | IGHV2-5; IGLV3-21; IGLL1; IGLV10-54 |
| R-HSA-166663 | Initial triggering of complement | 4 | 111 | 9.58E−03 | 3.61E−05 | 2.83E−04 | IGHV2-5; IGLV3-21; IGLL1; IGLV10-54 |
| R-HSA-2029485 | Role of phospholipids in phagocytosis | 4 | 114 | 9.84E−03 | 4.00E−05 | 2.83E−04 | IGHV2-5; IGLV3-21; IGLL1; IGLV10-54 |
| R-HSA-2871809 | FCERI mediated Ca + 2 mobilization | 4 | 117 | 1.01E−02 | 4.42E−05 | 2.83E−04 | IGHV2-5; IGLV3-21; IGLL1; IGLV10-54 |
| R-HSA-2871796 | FCERI mediated MAPK activation | 4 | 119 | 1.03E−02 | 4.72E−05 | 2.83E−04 | IGHV2-5; IGLV3-21; IGLL1; IGLV10-54 |
| R-HSA-202733 | Cell surface interactions at the vascular wall | 5 | 246 | 2.12E−02 | 5.12E−05 | 3.07E−04 | IGHV2-5; IGLV3-21; IGLL1; IGLV10-54 |
| R-HSA-9664323 | FCGR3A-mediated IL10 synthesis | 4 | 128 | 1.10E−02 | 6.26E−05 | 3.13E−04 | IGHV2-5; IGLV3-21; IGLL1; IGLV10-54 |
| R-HSA-2173782 | Binding and uptake of ligands by scavenger receptors | 4 | 129 | 1.11E−02 | 6.45E−05 | 3.22E−04 | IGHV2-5; IGLV3-21; IGLL1; IGLV10-54 |
| R-HSA-9664417 | Leishmania phagocytosis | 4 | 149 | 1.29E−02 | 1.12E−04 | 4.49E−04 | IGHV2-5; IGLV3-21; IGLL1; IGLV10-54 |
| R-HSA-9664407 | Parasite infection | 4 | 149 | 1.29E−02 | 1.12E−04 | 4.49E−04 | IGHV2-5; IGLV3-21; IGLL1; IGLV10-54 |
| R-HSA-9664422 | FCGR3A-mediated phagocytosis | 4 | 149 | 1.29E−02 | 1.12E−04 | 4.49E−04 | IGHV2-5; IGLV3-21; IGLL1; IGLV10-54 |
| R-HSA-2029482 | Regulation of actin dynamics for phagocytic cup formation | 4 | 150 | 1.29E−02 | 1.15E−04 | 4.61E−04 | IGHV2-5; IGLV3-21; IGLL1; IGLV10-54 |
| R-HSA-2871837 | FCERI mediated NF-kB activation | 4 | 167 | 1.44E−02 | 1.74E−04 | 5.21E−04 | IGHV2-5; IGLV3-21; IGLL1; IGLV10-54 |
| R-HSA-2029480 | Fcgamma receptor (FCGR) dependent phagocytosis | 4 | 175 | 1.51E−02 | 2.08E−04 | 6.23E−04 | IGHV2-5; IGLV3-21; IGLL1; IGLV10-54 |
| R-HSA-5690714 | CD22 mediated BCR regulation | 3 | 70 | 6.04E−03 | 2.33E−04 | 6.98E−04 | IGHV2-5; IGLV3-21; IGLL1 |
| R-HSA-2454202 | Fc epsilon receptor (FCERI) signaling | 4 | 218 | 1.88E−02 | 4.77E−04 | 1.43E−03 | IGHV2-5; IGLV3-21; IGLL1; IGLV10-54 |
| R-HSA-983695 | Antigen activates B cell receptor (BCR) leading to generation of second messengers | 3 | 95 | 8.20E−03 | 5.66E−04 | 1.70E−03 | IGHV2-5; IGLV3-21; IGLL1 |
| R-HSA-9664433 | Leishmania parasite growth and survival | 4 | 259 | 2.23E−02 | 9.07E−04 | 1.81E−03 | IGHV2-5; IGLV3-21; IGLL1; IGLV10-54 |
| R-HSA-9662851 | Anti-inflammatory response favouring Leishmania parasite infection | 4 | 259 | 2.23E−02 | 9.07E−04 | 1.81E−03 | IGHV2-5; IGLV3-21; IGLL1; IGLV10-54 |
| R-HSA-198933 | Immunoregulatory interactions between a lymphoid and a non-lymphoid cell | 4 | 297 | 2.56E−02 | 1.50E−03 | 3.01E−03 | IGHV2-5; IGLV3-21; IGLL1; IGLV10-54 |
| R-HSA-9673163 | Oleoyl-phe metabolism | 1 | 1 | 8.63E−05 | 1.72E−03 | 3.45E−03 | PM20D1 |
| R-HSA-5619050 | Defective SLC4A1 causes hereditary spherocytosis type 4 (HSP4), distal renal tubular acidosis (dRTA) and dRTA with hemolytic anemia (dRTA-HA) | 1 | 1 | 8.63E−05 | 1.72E−03 | 3.45E−03 | SLC4A1 |
| R-HSA-9658195 | Leishmania infection | 4 | 345 | 2.98E−02 | 2.60E−03 | 5.19E−03 | IGHV2-5; IGLV3-21; IGLL1; IGLV10-54 |
| R-HSA-168249 | Innate immune system | 7 | 1191 | 1.03E−01 | 2.79E−03 | 5.59E−03 | CHIT1; LRG1; IGHV2-5; IGLV3-21; IGLL1; CFHR4; IGLV10-54 |
| R-HSA-983705 | Signaling by the B cell receptor (BCR) | 3 | 176 | 1.52E−02 | 3.29E−03 | 6.58E−03 | IGHV2-5; IGLV3-21; IGLL1 |
| R-HSA-5619049 | Defective SLC40A1 causes hemochromatosis 4 (HFE4) (macrophages) | 1 | 2 | 1.73E−04 | 3.45E−03 | 6.89E−03 | CP |
| R-HSA-5619060 | Defective CP causes aceruloplasminemia (ACERULOP) | 1 | 2 | 1.73E−04 | 3.45E−03 | 6.89E−03 | CP |
| R-HSA-109582 | Hemostasis | 5 | 726 | 6.26E−02 | 6.76E−03 | 1.35E−02 | IGHV2-5; IGLV3-21; IGLL1; IGLV10-54 |
| R-HSA-209905 | Catecholamine biosynthesis | 1 | 4 | 3.45E−04 | 6.88E−03 | 1.37E−02 | DBH |
| R-HSA-166187 | Mitochondrial uncoupling | 1 | 6 | 5.18E−04 | 1.03E−02 | 1.37E−02 | PM20D1 |
| R-HSA-5619102 | SLC transporter disorders | 2 | 103 | 8.89E−03 | 1.35E−02 | 1.37E−02 | SLC4A1; CP |
| R-HSA-1247673 | Erythrocytes take up oxygen and release carbon dioxide | 1 | 8 | 6.90E−04 | 1.37E−02 | 1.37E−02 | SLC4A1 |
| R-HSA-159763 | Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus | 1 | 9 | 7.77E−04 | 1.54E−02 | 1.54E−02 | PROZ |
| R-HSA-425381 | Bicarbonate transporters | 1 | 10 | 8.63E−04 | 1.71E−02 | 1.71E−02 | SLC4A1 |
| R-HSA-159782 | Removal of aminoterminal propeptides from gamma-carboxylated proteins | 1 | 10 | 8.63E−04 | 1.71E−02 | 1.71E−02 | PROZ |
| R-HSA-159740 | Gamma-carboxylation of protein precursors | 1 | 10 | 8.63E−04 | 1.71E−02 | 1.71E−02 | PROZ |
| R-HSA-2534343 | Interaction with cumulus cells and the zona pellucida | 1 | 11 | 9.49E−04 | 1.88E−02 | 1.88E−02 | CHIT1 |
| R-HSA-159854 | Gamma-carboxylation, transport, and amino-terminal cleavage of proteins | 1 | 11 | 9.49E−04 | 1.88E−02 | 1.88E−02 | PROZ |
| R-HSA-1480926 | O2/CO2 exchange in erythrocytes | 1 | 12 | 1.04E−03 | 2.05E−02 | 2.05E−02 | SLC4A1 |
| R-HSA-1237044 | Erythrocytes take up carbon dioxide and release oxygen | 1 | 12 | 1.04E−03 | 2.05E−02 | 2.05E−02 | SLC4A1 |
| R-HSA-189085 | Digestion of dietary carbohydrate | 1 | 12 | 1.04E−03 | 2.05E−02 | 2.05E−02 | CHIT1 |
| R-HSA-209776 | Metabolism of amine-derived hormones | 1 | 18 | 1.55E−03 | 3.06E−02 | 3.06E−02 | DBH |
| R-HSA-5619115 | Disorders of transmembrane transporters | 2 | 181 | 1.56E−02 | 3.85E−02 | 3.85E−02 | SLC4A1; CP |
| R-HSA-5653656 | Vesicle-mediated transport | 4 | 761 | 6.57E−02 | 3.86E−02 | 3.86E−02 | IGHV2-5; IGLV3-21; IGLL1; IGLV10-54 |
| R-HSA-8935690 | Digestion | 1 | 24 | 2.07E−03 | 4.06E−02 | 4.06E−02 | CHIT1 |
| R-HSA-1187000 | Fertilization | 1 | 26 | 2.24E−03 | 4.39E−02 | 4.39E−02 | CHIT1 |
| R-HSA-425410 | Metal ion SLC transporters | 1 | 26 | 2.24E−03 | 4.39E−02 | 4.39E−02 | CP |
| R-HSA-8963743 | Digestion and absorption | 1 | 29 | 2.50E−03 | 4.89E−02 | 4.89E−02 | CHIT1 |