Table 2. Significant (p < 0.05) gene ontologies (GO) enriched for genes within 5-kb flanking region of associated SNP for PRA disease.
| GO ID | GO term | No. of genes | p-value | Genes |
|---|---|---|---|---|
| GO:0007156 | Homophilic cell adhesion via plasma membrane adhesion molecules | 13 | 8.32E-06 | CDH12, CDH8, CDH13, CRTAM, CDH9, PTPRM, FAT3, ROBO1, DSC3, CDHR3, ROBO2, PCDH15, CDH10 |
| GO:0090036 | Regulation of protein kinase C signaling | 4 | 4.86E-04 | AKAP12, SEZ6L, CAPZB, SEZ6 |
| GO:0006915 | Apoptotic process | 10 | 6.46E-04 | DLC1, DCC, ATCAY, PRUNE2, STK24, CLIC4, BNIP2, TFAP2B, VDAC1, HIP1 |
| GO:0035264 | Multicellular organism growth | 9 | 1.17E-03 | SLITRK1, TBL1XR1, STK40, CLIC4, APBA2, H3F3B, PCDH15, PKDCC, WWTR1 |
| GO:0046777 | Protein autophosphorylation | 11 | 1.59E-03 | EPHA4, TNIK, VRK2, STK24, NLK, PEAK1, LRRK2, EIF2AK3, DAPK3, EPHB1, KDR |
| GO:0005509 | Calcium ion binding | 28 | 3.24E-03 | SPOCK3, NELL1, NELL2, FAM20C, DLK1, PRKCSH, KCNIP4, CDH8, CDH9, FAT3, FSTL5, HPCAL1, CNTNAP4, C2CD5, CAPN9, LRP1B, CDHR3, PADI2, PCDH15, MAN1A1, ITPR2, CDH12, CDH13, CBLB, SULF2, DSC3, CACNA1E, CDH10 |
| GO:0042130 | Negative regulation of T cell proliferation | 5 | 3.67E-03 | MAD1L1, IL20RB, FOXJ1, PDE5A, DLG1 |
| GO:0005524 | ATP binding | 49 | 4.50E-03 | CDK19, RAD51C, ATP10B, PEAK1, EPHB1, IARS, GSS, MCM9, ADCK1, VRK2, STK40, MCCC1, CHD2, DHX35, CHD6, ROS1, CDK14, AKT2, ABCA12, ABCA 4, CDK1, TNIK, STK24, FLT3, NLK, MYLK4, CDK8, ATP1A4, RPS6KC1, PKDCC, ATP1A1, DGKI, OXSR1, PRKCE, DAPK3, KDR, MAP4K4, TARS, EPHA4, HUNK, ABCC9, ASCC3, NTRK2, RRM1, MAP3K10, CDC42BPA, LRRK2, EIF2AK3, PCCA |
| GO:0005783 | Endoplasmic reticulum | 24 | 6.31E-03 | MOGAT1, ATP10B, NDFIP2, MAN1A1, SEZ6L, PRKCE, CPED1, VASH1, FDFT1, KDR, VCAM1, NCSTN, PSMF1, TMEM117, BRINP1, SULF2, SRD5A3, SUMF1, SIL1, LRRK2, USP25, SEZ6, ZFYVE1, DLG1 |
| GO:0001701 | In utero embryonic development | 12 | 6.54E-03 | BMI1, NMT1, MSX1, HAND2, FOXF1, EDN1, DSC3, APBA2, SMAD2, PRKCSH, FOXP1, PITX2 |
| GO:0004672 | Protein kinase activity | 10 | 7.97E-03 | CDK19, MAP4K4, ADCK1, VRK2, STK40, STK24, NTRK2, PEAK1, PKDCC, FASTKD5 |
| GO:0010811 | Positive regulation of cell-substrate adhesion | 5 | 8.29E-03 | RSU1, FOXF1, DMP1, VIT, PRKCE |
| GO:0008360 | Regulation of cell shape | 9 | 8.29E-03 | DLC1, VRK2, DIAPH1, ARHGAP18, LIMD1, DAPK3, FN1, KDR, DLG1 |
| GO:0060079 | Excitatory postsynaptic potential | 4 | 8.92E-03 | GRIK2, DGKI, LRRK2, SEZ6 |
| GO:0010575 | Positive regulation of vascular endothelial growth factor production | 4 | 1.15E-02 | CYP1B1, SULF2, RORA, EIF2AK3 |
| GO:0008283 | Cell proliferation | 9 | 1.22E-02 | CDK1, TYR, ASCC3, E2F8, TBX20, UCHL1, H3F3B, ROS1, OCA2 |
| GO:0005925 | Focal adhesion | 16 | 1.77E-02 | ACTB, DLC1, RSU1, PEAK1, AKAP12, ITGA11, ARF6, NCSTN, RND3, CDH13, YWHAQ, GIT2, SNTB1, PPP1R12A, HSPB1, LIMD1 |
| GO:0015459 | Potassium channel regulator activity | 4 | 2.63E-02 | SUMO1, KCNAB1, KCNIP4, DLG1 |
| GO:0001662 | Behavioral fear response | 4 | 2.66E-02 | BRINP1, GRIK2, GABRA5, VDAC1 |
| GO:0072659 | Protein localization to plasma membrane | 5 | 2.69E-02 | TNIK, C2CD5, AKT2, DLG1, ABCA12 |
| GO:0006260 | DNA replication | 5 | 2.70E-02 | POLD3, MCM9, GINS3, RRM1, REV3L |
| GO:0045944 | Positive regulation of transcription from RNA polymerase II promoter | 24 | 2.76E-02 | TBL1XR1, IKZF3, COPS5, EDN1, E2F8, EOMES, FHL5, RORA, WWTR1, FOXP1, CDH13, EPC1, NPAS2, PAX7, GALR2, THRAP3, EBF1, TFAP2B, PPP1R12A, POU3F3, NRG1, TCF4, BCAS3, PIK3R1 |
| GO:0007411 | Axon guidance | 7 | 3.32E-02 | DCC, KLF7, ROBO1, SEMA3C, CNTN4, ROBO2, RELN |
| GO:0048286 | Lung alveolus development | 4 | 3.33E-02 | STK40, FOXF1, PKDCC, ABCA12 |
| GO:0046982 | Protein heterodimerization activity | 4 | 3.38E-02 | PPARD, TFAP2B, ADRA1B, TCF4 |
| GO:0030336 | Negative regulation of cell migration | 6 | 3.53E-02 | DLC1, CYP1B1, STK24, ROBO1, CLIC4, KANK1 |
| GO:0031901 | Early endosome membrane | 4 | 3.53E-02 | MARCH1, EPHA4, PMEPA1, EPHB1 |
SNP, single nucleotide polymorphism; PRA, progressive retinal atrophy; ATP, adenosine triphosphate.