Table 6.
Student’s t-test analysis of tear proteome from patients diagnosed with ocular GVHD versus control
| Gene name | Protein | p-value | FDR 5% | FDR 1% | FWER | Control average LFQ log transformed | GVHD average LFQ log transformed | SE of difference |
|---|---|---|---|---|---|---|---|---|
| TKT | Transketolase | 2.75E−05 | Y | Y | Y | 21.2 | 25.4 | 0.6 |
| DEFA1; DEFA3 | Neutrophil defensin 1; HP 1–56; Neutrophil defensin 2; Neutrophil defensin 3; HP 3–56; Neutrophil defensin 2 | 3.90E−05 | Y | Y | Y | 24.7 | 30.1 | 0.9 |
| KRT13§ | Keratin, type I cytoskeletal 13 | 5.89E−05 | Y | Y | Y | 25.8 | 30.1 | 0.8 |
| KRT4 | Keratin, type II cytoskeletal 4 | 6.68E−04 | Y | N | N | 25.5 | 28.9 | 0.8 |
| KRT5 | Keratin, type II cytoskeletal 5 | 7.04E−04 | Y | N | N | 26.2 | 29.2 | 0.7 |
| SAA4 | Serum amyloid A-4 protein | 1.49E−03 | Y | N | N | 22.6 | 23.9 | 0.3 |
| CASP14 | Caspase-14; Caspase-14 subunit p19; Caspase-14 subunit p10 | 2.43E−03 | Y | N | N | 22.2 | 25.2 | 0.7 |
| ANXA1 | Annexin A1; Annexin | 2.47E−03 | Y | N | N | 24.8 | 27.1 | 0.6 |
| KRT19 | Keratin, type I cytoskeletal 19 | 2.48E−03 | Y | N | N | 25.6 | 28.5 | 0.8 |
| A2M | Alpha-2-macroglobulin | 2.89E−03 | Y | N | N | 26.1 | 29.0 | 0.8 |
| CFB | Complement factor B; Complement factor B Ba fragment; Complement factor B Bb fragment | 3.20E−03 | Y | N | N | 24.2 | 26.9 | 0.7 |
| KRT6A; KRT6C | Keratin, type II cytoskeletal 6A; Keratin, type II cytoskeletal 6C | 3.74E−03 | Y | N | N | 28.1 | 30.6 | 0.7 |
| SPRR3 | Small proline-rich protein 3 | 4.04E−03 | Y | N | N | 22.3 | 24.9 | 0.7 |
| PLG | Plasminogen | 4.67E−03 | Y | N | N | 22.7 | 24.7 | 0.5 |
| IGHM | Ig mu chain C region; Ig mu heavy chain disease protein | 4.86E−03 | Y | N | N | 26.3 | 28.2 | 0.6 |
| ANXA2; ANXA2P2 | Annexin A2; Annexin; Putative annexin A2-like protein | 5.22E−03 | Y | N | N | 25.1 | 27.7 | 0.8 |
| HRG | Histidine-rich glycoprotein | 5.85E−03 | Y | N | N | 21.7 | 23.8 | 0.6 |
| H2AFX# | Histone H2AX | 6.76E−03 | N | N | N | 22.0 | 24.4 | 0.7 |
| FLG | Filaggrin | 6.93E−03 | N | N | N | 21.8 | 25.7 | 1.2 |
| MYL6 | Myosin light polypeptide 6 | 8.11E−03 | N | N | N | 21.9 | 24.0 | 0.7 |
| IGHG3 | Ig gamma-3 chain C region | 9.38E−03 | N | N | N | 27.4 | 29.8 | 0.8 |
| CTSG | Cathepsin G | 9.40E−03 | N | N | N | 20.3 | 24.6 | 1.3 |
| HIST1H4A | Histone H4 | 1.00E−02 | N | N | N | 23.2 | 25.2 | 0.6 |
| CFH | Complement factor H | 1.22E−02 | N | N | N | 24.2 | 26.4 | 0.7 |
| YWHAZ | 14–3-3 protein zeta/delta | 1.25E−02 | N | N | N | 24.7 | 26.6 | 0.6 |
| EZR | Ezrin | 1.80E−02 | N | N | N | 24.6 | 25.9 | 0.5 |
| HSPA8 | Heat shock cognate 71 kDa protein | 1.94E−02 | N | N | N | 23.2 | 25.0 | 0.7 |
| ACTN4 | Alpha-actinin-4 | 1.98E−02 | N | N | N | 22.6 | 25.0 | 0.9 |
| LRG1 | Leucine-rich alpha-2-glycoprotein | 2.05E−02 | N | N | N | 21.9 | 23.2 | 0.5 |
| S100A14 | Protein S100-A14 | 2.09E−02 | N | N | N | 19.5 | 21.7 | 0.8 |
| KRT14 | Keratin, type I cytoskeletal 14 | 2.30E−02 | N | N | N | 24.8 | 27.8 | 1.1 |
| C4BPA | C4b-binding protein alpha chain | 2.41E−02 | N | N | N | 21.6 | 23.7 | 0.8 |
| TF | Serotransferrin | 2.41E−02 | N | N | N | 28.3 | 30.9 | 1.0 |
| YWHAB | 14–3-3 protein beta/alpha; 14–3-3 protein beta/alpha, N-terminally processed | 2.51E−02 | N | N | N | 23.7 | 25.3 | 0.6 |
| ITIH1 | Inter-alpha-trypsin inhibitor heavy chain H1 | 2.58E−02 | N | N | N | 21.8 | 22.9 | 0.4 |
| C3Φ | Complement C3 | 2.61E−02 | N | N | N | 27.6 | 29.2 | 0.6 |
| TFF1 | Trefoil factor 1 | 2.65E−02 | N | N | N | 22.9 | 25.8 | 1.1 |
| ALB | Serum albumin | 2.82E−02 | N | N | N | 33.5 | 35.3 | 0.7 |
| ACTB | Actin, cytoplasmic 1; Actin, cytoplasmic 1, N-terminally processed | 3.14E−02 | N | N | N | 27.3 | 29.0 | 0.7 |
| CFL1 | Cofilin-1 | 3.62E−02 | N | N | N | 21.9 | 24.0 | 0.9 |
| KNG1 | Kininogen-1 | 4.37E−02 | N | N | N | 23.8 | 25.3 | 0.7 |
| S100A9 | Protein S100-A9 | 4.40E−02 | N | N | N | 24.6 | 26.6 | 0.9 |
| UPK3BL; POLR2J3 | Uroplakin-3b-like protein | 4.44E−02 | N | N | N | 21.9 | 23.0 | 0.5 |
| TXN | Thioredoxin | 4.96E−02 | N | N | N | 22.9 | 24.7 | 0.8 |
Proteins with increased abundance in GVHD in comparison with controls are shown
FDR: false discovery rate. FEWR: family-wise error rate (Holm-Sidak method). Y: yes, still significant after multiple comparisons correction. N: no, not significant after multiple comparisons correction. SE: standard error. § keratin cluster (P13646-1; K7EQH6; P35900; P35900; K7EMJ2; A0A140TA69; Q8IUT8; O76011; Q6IFU5; Q6A162; O76009; Q6NTB9; O76009; A0A140TA62; O76011; G3V1C2; J3QR55). # histone cluster (H2AFX; HIST1H2AA; HIST1H2AB; HIST1H2AG; HIST1H2AD; HIST2H2AA3; HIST3H2A; HIST1H2AC; HIST2H2AC; H2AFJ; HIST1H2AH; HIST1H2AJ; HIST2H2AB; H2AFZ; H2AFV). Φ complement cluster (P01024; Q2UVX4; M0QXZ3; M0QYC8; M0R0Q9)