Table 5 Related pathways across transcriptomics, proteomics and metabolomics
S No. | Blood Component | Top 10 pathways affected | Level in PD (compared to healthy controls) |
|---|---|---|---|
Transcriptomics | |||
1 | Whole blood | Nil | Downregulated |
Dilated cardiomyopathy, Hypertrophic cardiomyopathy, Cardiac muscle contraction, ECM-receptor interation, Platelet activation, Arrhythmogenic righ ventricular cardiomyopathy, Antigen processing and presentation, Adrenergic signaling in cardiomyocytes, Focal adhesion, | Upregulated | ||
2 | Whole blood | Nil | Downregulated |
Staphylococcus aureus infection, Complement and coagulation cascades | Upregulated | ||
3 | Whole blood | Nil | Downregulated |
Osteoclast differentiation, Leishmaniasis, Tuberculosis, | Upregulated | ||
4 | Whole blood | Parkinson disease, Alzheimer disease, Pathways of neurodegeneration | Downregulated |
5 | Whole blood | Nil | Downregulated |
Osteoclast differenciation, Natural killer cell mediated cytotoxicity, Antigent processing and presentation, B cell receptor signalling pathway, Graft-versus-host disease, Lysosome, Phagosome, Chemokine signaling pathway, Fc gamma R-mediated phagocytosis, Tuberculosis | Upregulated | ||
6 | Whole blood | Parkinson Disease, Perussis, Prion Disease, Huntington disease, | Downregulated |
Nil | Upregulated | ||
7 | peripheral blood mononuclear cells (PBMCs) | Th1 and Th2 cell differentiation, Th17 cell differentiation, Epstein-Barr virus infection, Toxoplasmosis, Leukocyte transendothelial migration, Human immunodeficiency virus 1 infection, Tuberculosis, Leishmaniasis, Pathways in cancer, Human cytomegalovirus infection | Downregulated |
Porphyrin and chlorophyll metabolism, Amoebiasis | Upregulated | ||
8 | peripheral blood mononuclear cells (PBMCs) | Sulfur metabolism, Collecting duct acid secretion, Glycine, serine and threonine metabolism, Porphyrin and chlorophyll metabolism, Malaria | Downregulated |
9 | Whole blood | Nil | Downregulated |
Endocrine and other factor-regulated calcium reabsorption, Nitrogen metabolism, | Upregulated | ||
10 | Whole blood / leukocytes | Citrate cycle (TCA cycle), Pyruvate metabolism, Cocaine addiction, Aminoacyl-tRNA biosynthesis, Amphetamine addiction, Salmonella infection, Parkinson disease, Prion disease, Huntington Disease, Amyotrophic lateral sclerosis | Downregulated |
Nil | Upregulated | ||
11 | peripheral blood mononuclear cell (PBMC) | Autophagy, Mitophagy, RIG-I-like receptor signaling pathway, NOD-like recptor signaling pathway, Shigellosis | Downregulated |
Lysosome, Glycosaminoglycan degradation, Other glycan degradation, Glycosphingolipid biosynthesis, Phagosome, Sphinagolipid metabolism, Collecting duct acid secretion, Apoptosis, Tuberculosis, Synaptic vesicle cycle | Upregulated | ||
12 | Whole blood | Nil | Downregulated |
Nil | Upregulated | ||
13 | peripheral blood mononuclear cells (PBMCs) | Nil | Downregulated |
Inflammatory bowel disease, Cytokine-cytokin receptor interaction, African trypanosomiasis, Malaria, Perussis, Leishmaniasis, Asthma, IL-17 signaling pathway, Hematopoietic cell lineage, Amoebiasis | Upregulated | ||
14 | Whole blood | Nil | Downregulated |
15 | Whole blood | Ubiquitin mediated proteolysis, Protein processing in endoplasmis reticulum, Parkinson disease | Downregulated |
Fructose and mannose metabolism, Inflammatory bwel disease | Upregulated | ||
16 | Whole blood | Nil | Downregulated |
Arachidonic acid metabolism | Upregulated | ||
17 | Peripheral blood | Nil | Downregulated |
18 | Blood Serum | Nil | Upregulated |
Blood Serum | Viral protein interaction with cytokine and cytokine receptor, | Upregulated | |
Proteomics | |||
1 | Plasma EV | Parkinson disease, MAPK signaling pathway, Alzheimer disease, Pathways of neurodegeneration | Upregulated |
2 | Plasma EV | Parkinson disease, Alzheimer disease, Pathways of neurodegeneration | Upregulated |
3 | Plasma EV | Parkinson disease, Alzheimer disease, Pathways of neurodegeneration | Upregulated |
4 | Plasma EV | Parkinson disease, Alzheimer disease, Pathways of neurodegeneration | Upregulated |
5 | Plasma EV | Parkinson disease, Alzheimer disease, Pathways of neurodegeneration | Upregulated |
6 | Plasma EV | Parkinson disease, Alzheimer disease, Pathways of neurodegeneration | Upregulated |
7 | Plasma EV | Parkinson disease, Alzheimer disease, Pathways of neurodegeneration, | Upregulated |
8 | Plasma EV | Ferroptosis, Prion disease, Pathways of neurodegeneration, | Upregulated |
9 | Plasma EV | Nil | Upregulated |
10 | Plasma EV | Complement and coagulation cascades, Staphylococcus aureus infection, Coronavirus disease, Vitamin digestion and absorption, African trypanosomiasis, Fat digestion and absorption, Cholesterol metabolism, PPAR signaling pathway, Pertussis, Platelet activation, | Downregulated |
11 | Plasma EV | Proteasome, Gastric acid secretion, Endocytosis, Parkinson disease, Phagosome, Aldosterone-regulated sodium reabsorption, Salivary secretion, Adrenergic signaling in cardiomyocytes, Aldosterone synthesis and secretion, Glycolysis / Gluconeogenesis, Endocrine and other factor-regulated calcium reabsorption, | Upregulated |
Proteasome, Pentose phosphate pathway, Spinocerebellar ataxia, Prion disease, Parkinson disease, Amyotrophic lateral sclerosis, Huntington disease, Pathways of neurodegeneration, Glycolysis / Gluconeogenesis, Cysteine and methionine metabolism, | Downregulated | ||
12 | Serum EV | Parkinson disease, Alzheimer disease, Pathways of neurodegeneration | Upregulated |
Nil | Downregulated | ||
13 | Serum EV | Parkinson disease, Alzheimer disease, Pathways of neurodegeneration | Downregulated |
14 | Serum EV | Asthma, African trypanosomiasis, Allograft rejection, Graft-versus-host disease, Type I diabetes mellitus, Type II diabetes mellitus, Malaria, Legionellosis, Inflammatory bowel disease, Fc epsilon RI signaling pathway, | Upregulated |
Thermogenesis, Citrate cycle (TCA cycle), Asthma, Oxidative phosphorylation, Non-alcoholic fatty liver disease, Diabetic cardiomyopathy, Parkinson disease, Melanoma, Prion disease, Huntington disease, | Downregulated | ||
15 | Serum EV | Parkinson disease, Alzheimer disease, Pathways of neurodegeneration | Upregulated |
16 | Serum EV | Parkinson disease, Alzheimer disease, Pathways of neurodegeneration | Upregulated |
17 | Serum EV | Parkinson disease, Alzheimer disease, Pathways of neurodegeneration | Upregulated |
18 | Serum EV | Complement and coagulation cascades, Platelet activation, Pertussis, Systemic lupus erythematosus, Neutrophil extracellular trap formation, ECM-receptor interaction, Hypertrophic cardiomyopathy, Coronavirus disease, Staphylococcus aureus infection, Dilated cardiomyopathy, | Upregulated |
Complement and coagulation cascades, Pertussis, Staphylococcus aureus infection, Systemic lupus erythematosus, Coronavirus disease, Renin-angiotensin system, Ferroptosis, Porphyrin and chlorophyll metabolism, Type II diabetes mellitus, Glutathione metabolism, | Downregulated | ||
19 | Serum EV | Complement and coagulation cascades, Platelet activation, Coronavirus disease, ECM-receptor interaction, Staphylococcus aureus infection, Neutrophil extracellular trap formation, Focal adhesion, , , , | Upregulated |
Allograft rejection, Staphylococcus aureus infection, Autoimmune thyroid disease, Viral myocarditis, Systemic lupus erythematosus, Pertussis, Complement and coagulation cascades, Dilated cardiomyopathy, Chagas disease, Coronavirus disease, | Downregulated | ||
20 | Blood Plasma | Complement and coagulation cascades, Coronavirus disease, Neuroactive ligand-receptor interaction | Upregulated |
Complement and coagulation cascades, Staphylococcus aureus infection, Vitamin digestion and absorption, African trypanosomiasis, Fat digestion and absorption, Cholesterol metabolism, PPAR signaling pathway, Platelet activation, Neutrophil extracellular trap formation, Lipid and atherosclerosis, | Downregulated | ||
21 | Blood Plasma | Nil | Upregulated |
Nil | Downregulated | ||
22 | Blood Plasma | PI3K-Akt signaling pathway, ECM-receptor interaction, Growth hormone synthesis, secretion and action, JAK-STAT signaling pathway, Focal adhesion, Cytokine-cytokine receptor interaction, Human papillomavirus infection, Neuroactive ligand-receptor interaction, | Upregulated |
Arginine biosynthesis | Downregulated | ||
23 | Blood Plasma | ECM-receptor interaction, Staphylococcus aureus infection | Upregulated |
Pantothenate and CoA biosynthesis, Complement and coagulation cascades, | Downregulated | ||
24 | Blood Plasma | African trypanosomiasis, Malaria, AGE-RAGE signaling pathway in diabetic complications, NF-kappa B signaling pathway, TNF signaling pathway, Leukocyte transendothelial migration, Fluid shear stress and atherosclerosis, Cell adhesion molecules, Lipid and atherosclerosis, | Upregulated |
African trypanosomiasis, Graft-versus-host disease, Malaria, Legionellosis, Inflammatory bowel disease, Pertussis, Antigen processing and presentation, Epstein-Barr virus infection, Human T-cell leukemia virus 1 infection, Human cytomegalovirus infection, | Downregulated | ||
25 | Blood Plasma | Sphingolipid signaling pathway, Lysosome, Estrogen signaling pathway, Autophagy, Apoptosis, Protein processing in endoplasmic reticulum, Tuberculosis, Diabetic cardiomyopathy | Downregulated |
26 | Blood Plasma | ECM-receptor interaction | Upregulated |
27 | Blood Plasma | Parkinson disease, Alzheimer disease, Pathways of neurodegeneration, MAPK signaling pathway | Upregulated |
28 | Blood Plasma | Parkinson disease, Alzheimer disease, Pathways of neurodegeneration | Upregulated |
29 | Blood Serum | Nil | Upregulated |
Nil | Downregulated | ||
30 | Blood Serum | Cholesterol metabolism, Thyroid hormone synthesis, Complement and coagulation cascades | Upregulated |
Vasopressin-regulated water reabsorption | Downregulated | ||
31 | Blood Serum | Complement and coagulation cascades, Staphylococcus aureus infection, Platelet activation, Neutrophil extracellular trap formation, Coronavirus disease | Upregulated |
Vitamin digestion and absorption, Fat digestion and absorption, Cholesterol metabolism, African trypanosomiasis, Lipid and atherosclerosis, PPAR signaling pathway, Complement and coagulation cascades, Platelet activation, Phospholipase D signaling pathway, | Downregulated | ||
32 | Blood Serum | Nil | Upregulated |
Asthma, JAK-STAT signaling pathway, Cytokine-cytokine receptor interaction | Downregulated | ||
33 | Blood Serum | Parkinson disease, Alzheimer disease, Pathways of neurodegeneration | Upregulated |
34 | Whole Blood | Parkinson disease, MAPK signaling pathway, Alzheimer disease, Pathways of neurodegeneration | Upregulated |
Parkinson disease, Alzheimer disease, Pathways of neurodegeneration | Downregulated | ||
Metabolomics | |||
1 | Blood plasma | Sphingolipid metabolism | Upregulated |
names not identified | Downregulated | ||
2 | Blood plasma | names not identified | Upregulated |
3 | Blood plasma | Citrate cycle (TCA cycle), Arginine biosynthesis | Upregulated |
NIL | Downregulated | ||
4 | Blood plasma | Nicotinate and nicotinamide metabolism, Tyrosine metabolism | Upregulated |
Tryptophan metabolism | Downregulated | ||
5 | Blood Plasma | Steroid hormone biosynthesis | Upregulated |
NIL | Downregulated | ||
6 | Blood Serum | Arginine biosynthesis, Aminoacyl-tRNA biosynthesis, Pantothenate and CoA biosynthesis, beta-Alanine metabolism, Glutathione metabolism, Alanine, aspartate and glutamate metabolism ,Pyrimidine metabolism Phenylalanine, tyrosine and tryptophan biosynthesis, Tyrosine metabolism, D-Glutamine and D-glutamate metabolism, Nitrogen metabolism | Upregulated |
Thiamine metabolism ,Taurine and hypotaurine metabolism, Pantothenate and Co biosynthesis, Glutathione metabolism, Glycine, serine and threonine metabolism, Cysteine and methionine metabolism | Downregulated | ||
7 | Blood Plasma | Arginine biosynthesis, Butanoate metabolism | Upregulated |
Taurine and hypotaurine metabolism, Biotin metabolism, Lysine degradation | Downregulated | ||
8 | Blood Plasma | Linoleic acid metabolism, alpha-Linolenic acid metabolism | Upregulated |
Glycerophospholipid metabolism, Glycosylphosphatidylinositol (GPI)-anchor biosynthesis | Downregulated | ||
9 | Blood Plasma | Valine, leucine and isoleucine biosynthesis, Aminoacyl-tRNA biosynthesis | Upregulated |
Biosynthesis of unsaturated fatty acids, Linoleic acid metabolism | Downregulated | ||
10 | Blood Plasma | Phenylalanine, tyrosine and tryptophan biosynthesis, Phenylalanine metabolism | Upregulated |
NIL | Downregulated | ||
11 | Plasma EV | names not identified | Upregulated |
names not identified | Downregulated | ||
12 | Serum EV | names not identified | Upregulated |
names not identified | Downregulated | ||
13 | Whole blood | Glutathione metabolism | Upregulated |
Purine metabolism | Downregulated | ||
14 | Whole blood | names not identified | Downregulated |
15 | Whole blood | NIL | Upregulated |
NIL | Downregulated | ||
16 | Blood Plasma | Glycerophospholipid metabolism | Upregulated |
Biosynthesis of unsaturated fatty acids, Linoleic acid metabolism, Arachidonic acid metabolism, Synthesis and degradation of ketone bodies, Tryptophan metabolism | Downregulated | ||
17 | Whole blood | Biosynthesis of unsaturated fatty acids, Arachidonic acid metabolism | Upregulated |
Biosynthesis of unsaturated fatty acids | Downregulated | ||
18 | Blood Plasma | Purine metabolism | Downregulated |
19 | Blood Plasma | NIL | Upregulated |
20 | Blood Serum | D-Glutamine and D-glutamate metabolism, Nitrogen metabolism, Arginine biosynthesis | Upregulated |
Arginine and proline metabolism | Downregulated | ||
21 | Blood Serum | Arginine and proline metabolism, Arginine biosynthesis | Upregulated |
Arginine biosynthesis | Downregulated | ||
22 | Blood Serum | Histidine metabolism | Upregulated |
NIL | Downregulated | ||
23 | Blood Serum | Sphingolipid metabolism, Glycerophospholipid metabolism, Arginine and proline metabolism | Upregulated |
Arginine biosynthesis | Downregulated | ||
24 | Whole blood | Biosynthesis of unsaturated fatty acids | Upregulated |
Butanoate metabolism, Alanine, aspartate and glutamate metabolism, Arginine and proline metabolism, Nitrogen metabolism, D-Glutamine and D-glutamate metabolism | Downregulated | ||
25 | Blood Serum | Tyrosine metabolism, Phenylalanine, tyrosine and tryptophan biosynthesis, Ubiquinone and other terpenoid-quinone biosynthesis, Phenylalanine metabolism, Arginine biosynthesis | Upregulated |
Tryptophan metabolism, caffeine metabolism | Downregulated | ||
26 | Whole blood | Citrate cycle (TCA cycle), Glyoxylate and dicarboxylate metabolism, Pyruvate metabolism, Galactose metabolism,Alanine, aspartate and glutamate metabolism | Downregulated |
27 | Blood Serum | NIL | Upregulated |