Table 4.
Top gene ontology enrichment processes in the PPI.
| Gene ontology term description | Observed gene count | Background gene count | Strength | False discovery rate | Matching proteins in network |
|---|---|---|---|---|---|
| Vesicle fusion | 7 | 95 | 1.32 | 8.84 × 10−5 | VAMP4, STX6, TMEM175, SYT17, STX16, VTI1A, STX10 |
| Cellular component organization | 38 | 5163 | 0.32 | 8.84 × 10−5 | PARD6A, RAB3A, WNT3, APOB, VAMP4, APOE, STX6, BRIP1, TMEM175, MCCC1, BIN3, KPNB1, PRKCI, NDUFAF2, LRRK2, GAK, SNCA, MCCC2, KPNA1, THSD4, SYT17, NUCKS1, SCAF11, STX16, PARD6B, PARD3, NOTCH4, ITGA8, UNC13B, VTI1A, LAMB2, NPNT, PET117, RIMS1, LDLR, CHD9, STX10, CLTC |
| Vesicle-mediated transport | 22 | 1699 | 0.56 | 8.84 × 10−5 | RAB3A, APOB, VAMP4, STBD1, APOE, STX6, TMEM175, KPNB1, PRKCI, LRRK2, GAK, SNCA, CTSB, SYT17, STX16, UNC13B, VTI1A, RIMS1, FAM49B, LDLR, STX10, CLTC |
| Regulation of localization | 26 | 2524 | 0.47 | 8.84 × 10−5 | PARD6A, RAB3A, WNT3, APOB, APOE, STX6, SNCAIP, CRH, CATSPER3, PRKCI, NDUFAF2, LRRK2, SNCA, SYT17, STK39, BAG3, PARD6B, PARD3, UNC13B, GPNMB, TRIM40, CRHR1, RIMS1, LDLR, STX10, CLTC |
| Intracellular transport | 20 | 1390 | 0.61 | 8.84 × 10−5 | RAB3A, STBD1, APOE, STX6, KPNB1, PRKCI, GAK, SNCA, KPNA1, SYT17, STX16, PARD3, DLG2, UNC13B, VTI1A, SNX13, RIMS1, LDLR, STX10, CLTC |
| Regulation of neurotransmitter secretion | 6 | 55 | 1.49 | 8.84 × 10−5 | RAB3A, SNCAIP, LRRK2, SNCA, UNC13B, RIMS1 |
| Regulation of neurotransmitter transport | 7 | 92 | 1.33 | 8.84 × 10−5 | RAB3A, SNCAIP, CRH, LRRK2, SNCA, UNC13B, RIMS1 |
| Regulation of cellular localization | 15 | 766 | 0.74 | 8.84 × 10−5 | PARD6A, RAB3A, STX6, SNCAIP, CRH, PRKCI, NDUFAF2, LRRK2, SNCA, BAG3, PARD3, UNC13B, TRIM40, RIMS1, CLTC |
| Membrane organization | 15 | 729 | 0.77 | 8.84 × 10−5 | APOB, VAMP4, APOE, STX6, TMEM175, PRKCI, GAK, SNCA, SYT17, STX16, VTI1A, RIMS1, LDLR, STX10, CLTC |
| Membrane fusion | 8 | 170 | 1.13 | 8.84 × 10−5 | VAMP4, STX6, TMEM175, SYT17, STX16, VTI1A, RIMS1, STX10 |
| Golgi ribbon formation | 4 | 11 | 2.01 | 8.84 × 10−5 | VAMP4, STX6, STX16, VTI1A |
| Regulation of synaptic vesicle cycle | 5 | 46 | 1.49 | 0.00016 | RAB3A, LRRK2, SNCA, UNC13B, RIMS1 |
| Golgi organization | 6 | 95 | 1.25 | 0.00022 | VAMP4, STX6, LRRK2, GAK, STX16, VTI1A |
| Chemical synaptic transmission | 10 | 402 | 0.85 | 0.00024 | RAB3A, APOE, CRH, LRRK2, SNCA, SYT17, DLG2, UNC13B, RIMS1, GPR19 |
| Vesicle organization | 9 | 318 | 0.9 | 0.00024 | RAB3A, VAMP4, STX6, TMEM175, PRKCI, SYT17, STX16, VTI1A, STX10 |
| Synaptic vesicle cycle | 6 | 100 | 1.23 | 0.00024 | RAB3A, GAK, SNCA, SYT17, UNC13B, RIMS1 |
| Regulation of synaptic vesicle exocytosis | 4 | 24 | 1.67 | 0.00028 | RAB3A, LRRK2, UNC13B, RIMS1 |
| Cell-cell signaling | 15 | 1073 | 0.6 | 0.00042 | PARD6A, RAB3A, WNT3, APOE, CRH, LRRK2, SNCA, SYT17, DLG2, UNC13B, GPNMB, CRHR1, RIMS1, GPR19, CLTC |
| Regulation of synaptic vesicle transport | 4 | 28 | 1.61 | 0.00044 | RAB3A, LRRK2, UNC13B, RIMS1 |
| Regulation of calcium ion-dependent exocytosis | 5 | 66 | 1.33 | 0.00045 | RAB3A, LRRK2, SYT17, UNC13B, RIMS1 |
| Establishment of localization | 32 | 4248 | 0.33 | 0.00045 | RAB3A, APOB, VAMP4, STBD1, APOE, STX6, TMEM175, CATSPER3, KPNB1, PRKCI, LRRK2, GAK, IP6K2, SNCA, KPNA1, CTSB, SYT17, STX16, SLC44A1, PARD3, DLG2, ITGA8, UNC13B, VTI1A, CRHR1, NPNT, SNX13, RIMS1, FAM49B, LDLR, STX10, CLTC |
| Chylomicron remnant clearance | 3 | 8 | 2.03 | 0.00057 | APOB, APOE, LDLR |
| Bicellular tight junction assembly | 4 | 32 | 1.55 | 0.0006 | PARD6A, PRKCI, PARD6B, PARD3 |
| Cytosolic transport | 6 | 132 | 1.11 | 0.00065 | STX6, GAK, STX16, VTI1A, STX10, CLTC |
| Protein localization | 20 | 1966 | 0.46 | 0.00071 | RAB3A, APOB, APOE, STX6, BIN3, KPNB1, PRKCI, LRRK2, GAK, KPNA1, STX16, PARD3, DLG2, ITGA8, VTI1A, NPNT, SNX13, RIMS1, STX10, CLTC |
| Regulation of neurotransmitter levels | 8 | 295 | 0.89 | 0.00073 | RAB3A, SNCAIP, LRRK2, SNCA, SYT17, SLC44A1, UNC13B, RIMS1 |
| Cellular component assembly | 22 | 2343 | 0.43 | 0.00073 | PARD6A, APOB, VAMP4, APOE, BRIP1, TMEM175, MCCC1, BIN3, KPNB1, PRKCI, NDUFAF2, LRRK2, GAK, MCCC2, THSD4, SCAF11, PARD6B, PARD3, UNC13B, PET117, RIMS1, CLTC |
| Retrograde transport, endosome to Golgi | 5 | 79 | 1.25 | 0.00073 | STX6, STX16, VTI1A, STX10, CLTC |
| Establishment of protein localization | 17 | 1467 | 0.52 | 0.00073 | RAB3A, APOB, APOE, STX6, KPNB1, PRKCI, KPNA1, STX16, PARD3, DLG2, ITGA8, VTI1A, NPNT, SNX13, RIMS1, STX10, CLTC |
| Cellular localization | 21 | 2180 | 0.44 | 0.0008 | RAB3A, STBD1, APOE, STX6, KPNB1, PRKCI, LRRK2, GAK, SNCA, KPNA1, SYT17, STX16, PARD3, DLG2, UNC13B, VTI1A, SNX13, RIMS1, LDLR, STX10, CLTC |
The protein products of genes with significant associations are highlighted in bold.