Table 2.
Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment for the differentially expressed proteins from AβPP/PS1 transgenic mice control (Tg-ctrl) compared with wild type mice (WT-ctrl) 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 | |||||||
| Alzheimer’s disease | 3 | 0.0073 | 0.2502 | P12023 | Amyloid beta A4 protein | APP | ↑ |
| Q63810 | Calcineurin subunit B type 1 | PPP3R1 | ↑ | ||||
| Q9D0M3 | Cytochrome c1 | CYC1 | ↓ | ||||
| Glutamatergic synapse | 3 | 0.003 | 0.2064 | Q63810 | Calcineurin subunit B type 1 | PPP3R1 | ↑ |
| Q99MK8 | Beta-adrenergic receptor kinase 1 | ADRBK1 | ↑ | ||||
| Q61011 | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-3 | GNB3 | ↓ | ||||
| Oxidative phosphorylation | 2 | 0.035 | 0.3776 | Q9D819 | Inorganic pyrophosphatase | PPA1 | ↓ |
| Q9D0M3 | Cytochrome c1 | CYC1 | ↓ | ||||
| Cholinergic synapse | 2 | 0.0317 | 0.3776 | P21278 | Guanine nucleotide-binding protein subunit alpha-11 | GNA11 | ↓ |
| Q61011 | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-3 | GNB3 | ↓ | ||||
| Serotonergic synapse | 2 | 0.0413 | 0.3776 | P12023 | Amyloid beta A4 protein | APP | ↑ |
| Q61011 | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-3 | GNB3 | ↓ | ||||
| Medial prefrontal cortex | |||||||
| Metabolic pathways | 11 | 0.0284 | 0.2045 | P56382 | ATP synthase subunit epsilon | ATP5E | ↑ |
| P12787 | Cytochrome c oxidase subunit 5A | COX5A | ↑ | ||||
| P48758 | Carbonyl reductase [NADPH] 1 | CBR1 | ↓ | ||||
| Q922Q4 | Pyrroline-5-carboxylate reductase 2 | PYCR2 | ↓ | ||||
| Q99LB2 | Dehydrogenase/reductase SDR family member 4 | DHRS4 | ↓ | ||||
| Q91VR2 | ATP synthase subunit gamma | ATP5C1 | ↓ | ||||
| O70250 | Phosphoglycerate mutase 2 | PGAM2 | ↓ | ||||
| Q91XF0 | Pyridoxine-5-phosphate oxidase | PNPO | ↓ | ||||
| Q80XN0 | D-beta-hydroxybutyrate dehydrogenase | BDH1 | ↓ | ||||
| Q99LS3 | Phosphoserine phosphatase | PSPH | ↓ | ||||
| Q9DCC4 | Pyrroline-5-carboxylate reductase 3 | PYCRL | ↓ | ||||
| Parkinson’s disease | 5 | 0.0005 | 0.0164 | Q8CGK7 | Guanine nucleotide-binding protein G(olf) subunit alpha | GNAL | ↑ |
| P56382 | ATP synthase subunit epsilon | ATP5E | ↑ | ||||
| P12787 | Cytochrome c oxidase subunit 5A | COX5A | ↑ | ||||
| Q60930 | Voltage-dependent anion-selective channel protein 2 | VDAC2 | ↓ | ||||
| Q91VR2 | ATP synthase subunit gamma | ATP5C1 | ↓ | ||||
| Ribosome | 5 | 0.0007 | 0.0164 | Q9D1P0 | 39S ribosomal protein L13 | MRPL13 | ↑ |
| P62908 | 40S ribosomal protein S3 | RPS3 | ↓ | ||||
| P62754 | 40S ribosomal protein S6 | RPS6 | ↓ | ||||
| P12970 | 60S ribosomal protein L7a | RPL7A | ↓ | ||||
| P84099 | 60S ribosomal protein L19 | RPL19 | ↓ | ||||
| Alzheimer’s disease | 4 | 0.009 | 0.1298 | P56382 | ATP synthase subunit epsilon | ATP5E | ↑ |
| P12787 | Cytochrome c oxidase subunit 5A | COX5A | ↑ | ||||
| Q91VR2 | ATP synthase subunit gamma | ATP5C1 | ↓ | ||||
| P49615 | Cyclin-dependent-like kinase 5 | CDK5 | ↓ | ||||
| Biosynthesis of amino acids | 4 | 0.0005 | 0.0164 | O70250 | Phosphoglycerate mutase 2 | PGAM2 | ↓ |
| Q922Q4 | Pyrroline-5-carboxylate reductase 2 | PYCR2 | ↓ | ||||
| Q99LS3 | Phosphoserine phosphatase | PSPH | ↓ | ||||
| Q9DCC4 | Pyrroline-5-carboxylate reductase 3 | PYCRL | ↓ | ||||
| Striatum | |||||||
| Metabolic pathways | 5 | 0.0004 | 0.0067 | P12787 | Cytochrome c oxidase subunit 5A | COX5A | ↑ |
| P99028 | Cytochrome b-c1 complex subunit 6 | UQCRH | ↑ | ||||
| Q91XF0 | Pyridoxine-5-phosphate oxidase | PNPO | ↑ | ||||
| P10518 | Delta-aminolevulinic acid dehydratase | ALAD | ↑ | ||||
| Q9D020 | Cytosolic 5-nucleotidase 3A | NT5C3A | ↓ | ||||
| Alzheimer’s disease | 2 | 0.0044 | 0.0122 | P12787 | Cytochrome c oxidase subunit 5A | COX5A | ↑ |
| P99028 | Cytochrome b-c1 complex subunit 6 | UQCRH | ↑ | ||||
| Oxidative phosphorylation | 2 | 0.0025 | 0.0121 | P12787 | Cytochrome c oxidase subunit 5A | COX5A | ↑ |
| P99028 | Cytochrome b-c1 complex subunit 6 | UQCRH | ↑ | ||||
| Parkinson’s disease | 2 | 0.0028 | 0.0121 | P12787 | Cytochrome c oxidase subunit 5A | COX5A | ↑ |
| P99028 | Cytochrome b-c1 complex subunit 6 | UQCRH | ↑ | ||||
| Huntington’s disease | 2 | 0.005 | 0.0122 | P12787 | Cytochrome c oxidase subunit 5A | COX5A | ↑ |
| P99028 | Cytochrome b-c1 complex subunit 6 | UQCRH | ↑ |