Table 3.
Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment for the differentially expressed proteins from AβPP/PS1 transgenic mice treated with tocotrienol-rich fraction (Tg-TRF) compared with the vehicle control group, AβPP/PS1 transgenic mice treated with palm oil stripped of vitamin E (Tg-PO) using KOBAS. The pathways are arranged according to the number of differentially expressed proteins in each pathway. Only the top five enriched pathways (p < 0.05) are listed. ↓ represents significantly downregulated (p < 0.05) protein. ↑ represents significantly upregulated (p < 0.05) protein
| Pathway | Proteins number | p | Corrected p | Accession number | Protein names | Gene names | Proteins expression |
| Hippocampus | |||||||
| Metabolic pathways | 25 | 0.0004 | 0.0099 | P05064 | Fructose-bisphosphate aldolase | ALDOA | ↓ |
| P03911 | NADH-ubiquinone oxidoreductase chain 4 | MTND4 | ↓ | ||||
| Q9Z0J4 | Nitric oxide synthase, brain | NOS1 | ↓ | ||||
| Q91YT0 | NADH dehydrogenase [ubiquinone] flavoprotein 1 | NDUFV1 | ↑ | ||||
| Q8CGC7 | Bifunctional glutamate/proline—tRNA ligase | EPRS | ↓ | ||||
| Q80UP3 | Diacylglycerol kinase zeta | DGKZ | ↓ | ||||
| P62814 | V-type proton ATPase subunit B, brain isoform | ATP6V1B2 | ↑ | ||||
| Q61753 | D-3-phosphoglycerate dehydrogenase | PHGDH | ↑ | ||||
| Q9Z1B3 | 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-1 | PLCB1 | ↓ | ||||
| Q9CZS1 | Aldehyde dehydrogenase X | ALDH1B1 | ↑ | ||||
| Q91WD5 | NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 | NDUFS2 | ↑ | ||||
| Q7TMF3 | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 | NDUFA12 | ↑ | ||||
| Q91YQ5 | Dolichyl-diphosphooligosaccharide—protein glycosyltransferase subunit 1 | RPN1 | ↓ | ||||
| P00397 | Cytochrome c oxidase subunit 1 | MTCO1 | ↓ | ||||
| Q5SUR0 | Phosphoribosylformylglycinamidine synthase | PFAS | ↓ | ||||
| Q91V92 | ATP-citrate synthase | ACLY | ↓ | ||||
| Q920P5 | Adenylate kinase isoenzyme 5 | AK5 | ↑ | ||||
| P56480 | ATP synthase subunit beta | ATP5B | ↑ | ||||
| Q9CQ60 | 6-phosphogluconolactonase | PGLS | ↑ | ||||
| Q9DCS9 | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 | NDUFB10 | ↑ | ||||
| Q924M7 | Mannose-6-phosphate isomerase | MPI | ↑ | ||||
| P24549 | Retinal dehydrogenase 1 | ALDH1A1 | ↑ | ||||
| P61922 | 4-aminobutyrate aminotransferase | ABAT | ↑ | ||||
| P26443 | Glutamate dehydrogenase 1 | GLUD1 | ↑ | ||||
| Q4KWH5 | 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-2 | PLCH2 | ↓ | ||||
| Huntington’s disease | 12 | 3.99E-07 | 6.26E-05 | P00397 | Cytochrome c oxidase subunit 1 | MTCO1 | ↓ |
| Q9DCS9 | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 | NDUFB10 | ↑ | ||||
| Q9Z1B3 | 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-1 | PLCB1 | ↓ | ||||
| Q91WD5 | NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 | NDUFS2 | ↑ | ||||
| Q91YT0 | NADH dehydrogenase [ubiquinone] flavoprotein 1 | NDUFV1 | ↑ | ||||
| P11352 | Glutathione peroxidase 1 | GPX1 | ↓ | ||||
| Q7TMF3 | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 | NDUFA12 | ↑ | ||||
| Q62108 | Disks large homolog 4 | DLG4 | ↓ | ||||
| P56480 | ATP synthase subunit beta | ATP5B | ↑ | ||||
| Q3UVX5 | Metabotropic glutamate receptor 5 | GRM5 | ↓ | ||||
| O08788 | Dynactin subunit 1 | DCTN1 | ↓ | ||||
| Q60931 | Voltage-dependent anion-selective channel protein 3 | VDAC3 | ↑ | ||||
| Alzheimer’s disease | 9 | 5.88E-05 | 0.0023 | P12023 | Amyloid beta A4 protein | APP | ↓ |
| P00397 | Cytochrome c oxidase subunit 1 | MTCO1 | ↓ | ||||
| Q9DCS9 | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 | NDUFB10 | ↑ | ||||
| Q9Z0J4 | Nitric oxide synthase, brain | NOS1 | ↓ | ||||
| Q9Z1B3 | 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-1 | PLCB1 | ↓ | ||||
| Q91WD5 | NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 | NDUFS2 | ↑ | ||||
| Q91YT0 | NADH dehydrogenase [ubiquinone] flavoprotein 1 | NDUFV1 | ↑ | ||||
| Q7TMF3 | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 | NDUFA12 | ↑ | ||||
| P56480 | ATP synthase subunit beta | ATP5B | ↑ | ||||
| Oxidative phosphorylation | 8 | 4.62E-05 | 0.0023 | P00397 | Cytochrome c oxidase subunit 1 | MTCO1 | ↓ |
| Q9DCS9 | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 | NDUFB10 | ↑ | ||||
| P03911 | NADH-ubiquinone oxidoreductase chain 4 | MTND4 | ↓ | ||||
| Q91WD5 | NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 | NDUFS2 | ↑ | ||||
| Q91YT0 | NADH dehydrogenase [ubiquinone] flavoprotein 1 | NDUFV1 | ↑ | ||||
| Q7TMF3 | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 | NDUFA12 | ↑ | ||||
| P56480 | ATP synthase subunit beta | ATP5B | ↑ | ||||
| P62814 | V-type proton ATPase subunit B, brain isoform | ATP6V1B2 | ↑ | ||||
| Parkinson’s disease | 8 | 7.53E-05 | 0.0024 | P00397 | Cytochrome c oxidase subunit 1 | MTCO1 | ↓ |
| Q9DCS9 | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 | NDUFB10 | ↑ | ||||
| P03911 | NADH-ubiquinone oxidoreductase chain 4 | MTND4 | ↓ | ||||
| Q60931 | Voltage-dependent anion-selective channel protein 3 | VDAC3 | ↑ | ||||
| Q91WD5 | NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 | NDUFS2 | ↑ | ||||
| Q91YT0 | NADH dehydrogenase [ubiquinone] flavoprotein 1 | NDUFV1 | ↑ | ||||
| Q7TMF3 | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 | NDUFA12 | ↑ | ||||
| P56480 | ATP synthase subunit beta | ATP5B | ↑ | ||||
| Medial prefrontal cortex | |||||||
| Metabolic pathways | 7 | 0.0018 | 0.0315 | P30275 | Creatine kinase U-type | CKMT1 | ↑ |
| Q9CQZ6 | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 | NDUFB3 | ↑ | ||||
| Q8K183 | Pyridoxal kinase | PDXK | ↑ | ||||
| P54071 | Isocitrate dehydrogenase [NADP] | IDH2 | ↑ | ||||
| P05202 | Aspartate aminotransferase | GOT2 | ↑ | ||||
| O35435 | Dihydroorotate dehydrogenase (quinone) | DHODH | ↓ | ||||
| P16858 | Glyceraldehyde-3-phosphate dehydrogenase | GAPDH | ↓ | ||||
| Biosynthesis of amino acids | 3 | 0.0002 | 0.0132 | P05202 | Aspartate aminotransferase | GOT2 | ↑ |
| P54071 | Isocitrate dehydrogenase [NADP] | IDH2 | ↑ | ||||
| P16858 | Glyceraldehyde-3-phosphate dehydrogenase | GAPDH | ↓ | ||||
| Carbon metabolism | 3 | 0.0006 | 0.0138 | P05202 | Aspartate aminotransferase | GOT2 | ↑ |
| P54071 | Isocitrate dehydrogenase [NADP] | IDH2 | ↑ | ||||
| P16858 | Glyceraldehyde-3-phosphate dehydrogenase | GAPDH | ↓ | ||||
| Alzheimer’s disease | 2 | 0.0271 | 0.1603 | Q9CQZ6 | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 | NDUFB3 | ↑ |
| P16858 | Glyceraldehyde-3-phosphate dehydrogenase | GAPDH | ↓ | ||||
| Arginine and proline metabolism | 2 | 0.0029 | 0.0407 | P05202 | Aspartate aminotransferase | GOT2 | ↑ |
| P30275 | Creatine kinase U-type | CKMT1 | ↑ | ||||
| Striatum | |||||||
| Glycerolipid metabolism | 2 | 0.0027 | 0.0275 | Q9JII6 | Alcohol dehydrogenase [NADP(+)] | AKR1A1 | ↑ |
| Q9CZS1 | Aldehyde dehydrogenase X | ALDH1B1 | ↑ | ||||
| Glycolysis/Gluconeogenesis | 2 | 0.0035 | 0.0290 | Q9JII6 | Alcohol dehydrogenase [NADP(+)] | AKR1A1 | ↑ |
| Q9CZS1 | Aldehyde dehydrogenase X | ALDH1B1 | ↑ | ||||
| Proteasome | 2 | 0.0016 | 0.0265 | Q9WVJ2 | 26S proteasome non-ATPase regulatory subunit 13 | PSMD13 | ↑ |
| O55234 | Proteasome subunit beta type-5 | PSMB5 | ↑ | ||||
| Valine, leucine and isoleucine degradation | 2 | 0.0019 | 0.0265 | Q9CZS1 | Aldehyde dehydrogenase X | ALDH1B1 | ↑ |
| P38060 | Hydroxymethylglutaryl-CoA lyase | HMGCL | ↑ | ||||
| Pentose and glucuronate interconversions | 2 | 0.0008 | 0.0265 | Q9JII6 | Alcohol dehydrogenase [NADP(+)] | AKR1A1 | ↑ |
| Q9CZS1 | Aldehyde dehydrogenase X | ALDH1B1 | ↑ |