Table 3.
The set of 62 differentially expressed genes in seven patients with chronic venous disease vs. seven controls, resulted from DESeq2 analysis (p < 0.00001) with statistical significance confirmed by Uninformative Variable Elimination by Partial Least Squares (UVE-PLS) analysis.
| No. | Gene Symbol | Gene Name | p Value | Fold Change | PLS Coefficient | ROC-AUC |
|---|---|---|---|---|---|---|
| Upregulated Genes | ||||||
| 1. | TSC2 | TSC complex subunit 2 | 4.87 × 10−17 | 1.437 | 8.197 × 10−4 | 1.000 |
| 2. | TBC1D22A | TBC1 domain family member 22A | 4.36 × 10−11 | 1.431 | 7.572 × 10−4 | 1.000 |
| 3. | PPP6R2 | protein phosphatase 6 regulatory subunit 2 | 9.52 × 10−9 | 1.361 | 6.225 × 10−4 | 1.000 |
| 4. | UPF1 | UPF1, RNA helicase and ATPase | 2.82 × 10−7 | 1.247 | 5.077 × 10−4 | 1.000 |
| 5. | WNK1 | WNK lysine deficient protein kinase 1 | 4.59 × 10−7 | 1.258 | 4.134 × 10−4 | 1.000 |
| 6. | CDS2 | CDP-diacylglycerol synthase 2 | 5.31 × 10−7 | 1.241 | 4.756 × 10−4 | 1.000 |
| 7. | PRRC2B | proline rich coiled-coil 2B | 1.56 × 10−6 | 1.273 | 4.693 × 10−4 | 1.000 |
| 8. | HDAC5 | histone deacetylase 5 | 4.89 × 10−6 | 1.432 | 5.694 × 10−4 | 1.000 |
| 9. | INTS11 (CPSF3L) | integrator complex subunit 11 | 5.95 × 10−6 | 1.246 | 4.683 × 10−4 | 1.000 |
| Downregulated genes | ||||||
| 10. | AC078899.1 | Unmatched | 1.18 × 10−13 | 0.393 | −1.586 × 10−3 | 1.000 |
| 11. | RP11-16F15.1 | Unmatched | 1.18 × 10−13 | 0.327 | −2.068 × 10−3 | 1.000 |
| 12. | EEF1A1P19 | eukaryotic translation elongation factor 1 alpha 1 pseudogene 19 | 8.40 × 10−13 | 0.500 | −1.305 × 10−3 | 1.000 |
| 13. | PFN1P1 | profilin 1 pseudogene 1 | 4.04 × 10−11 | 0.367 | −1.457 × 10−3 | 1.000 |
| 14. | RP4-706A16.3 | Unmatched | 4.36 × 10−11 | 0.455 | −1.394 × 10−3 | 1.000 |
| 15. | AC005884.1 | Unmatched | 4.36 × 10−11 | 0.401 | −1.488 × 10−3 | 1.000 |
| 16. | CALM2P2 | calmodulin 2 pseudogene 2 | 4.36 × 10−11 | 0.386 | −1.498 × 10−3 | 1.000 |
| 17. | HSPA8P1 | heat shock protein family A (Hsp70) member 8 pseudogene 1 | 4.36 × 10−11 | 0.379 | −1.575 × 10−3 | 1.000 |
| 18. | RP11-490H24.5 | Unmatched | 4.36 × 10−11 | 0.312 | −1.508 × 10−3 | 1.000 |
| 19. | EIF4A1P10 | eukaryotic translation initiation factor 4A1 pseudogene 10 | 4.66 × 10−11 | 0.461 | −1.286 × 10−3 | 1.000 |
| 20. | RP11-1033A18.1 | Unmatched | 7.00 × 10−11 | 0.381 | −1.495 × 10−3 | 1.000 |
| 21. | EIF3FP3 | eukaryotic translation initiation factor 3 subunit F pseudogene 3 | 1.35 × 10−10 | 0.443 | −1.423 × 10−3 | 1.000 |
| 22. | PDIA3P1 (PDIA3P) | protein disulfide isomerase family A member 3 pseudogene 1 | 2.38 × 10−10 | 0.465 | −1.240 × 10−3 | 1.000 |
| 23. | HSPA9P1 | heat shock protein family A (Hsp70) member 9 pseudogene 1 | 2.76 × 10−10 | 0.420 | −1.414 × 10−3 | 1.000 |
| 24. | AC007238.1 | Unmatched | 3.62 × 10−10 | 0.422 | −1.398 × 10−3 | 1.000 |
| 25. | HNRNPA1P7 | heterogeneous nuclear ribonucleoprotein A1 pseudogene 7 | 3.72 × 10−10 | 0.462 | −1.232 × 10−3 | 1.000 |
| 26. | RP11-159C21.4 | Unmatched | 4.81 × 10−10 | 0.390 | −1.552 × 10−3 | 1.000 |
| 27. | PABPC3 | poly(A) binding protein cytoplasmic 3 | 1.70 × 10−9 | 0.414 | −1.468 × 10−3 | 1.000 |
| 28. | RP11-74E24.2 | Unmatched | 1.94 × 10−9 | 0.537 | −1.067 × 10−3 | 1.000 |
| 29. | EEF1A1P6 | eukaryotic translation elongation factor 1 alpha 1 pseudogene 6 | 1.94 × 10−9 | 0.441 | −1.375 × 10−3 | 1.000 |
| 30. | XRCC6P2 | X-ray repair cross complementing 6 pseudogene 2 | 2.89 × 10−9 | 0.373 | −1.535 × 10−3 | 1.000 |
| 31. | HNRNPKP2 | heterogeneous nuclear ribonucleoprotein K pseudogene 2 | 3.13 × 10−9 | 0.424 | −1.163 × 10 ^-3 | 1.000 |
| 32. | EEF1A1P11 | eukaryotic translation elongation factor 1 alpha 1 pseudogene 11 | 8.40 × 10−9 | 0.448 | −1.369 × 10−3 | 1.000 |
| 33. | UBA52P5 | ubiquitin A-52 residue ribosomal protein fusion product 1 pseudogene 5 | 8.40 × 10−9 | 0.397 | −1.306 × 10−3 | 1.000 |
| 34. | RPL9P7 | ribosomal protein L9 pseudogene 7 | 9.10 × 10−9 | 0.414 | −1.417 × 10−3 | 1.000 |
| 35. | RPS21P4 | ribosomal protein S21 pseudogene 4 | 1.37 × 10−8 | 0.376 | −1.531 × 10−3 | 1.000 |
| 36. | RP11-334L9.1 | Unmatched | 1.37 × 10−8 | 0.333 | −1.206 × 10−3 | 1.000 |
| 37. | HNRNPKP4 | heterogeneous nuclear ribonucleoprotein K pseudogene 4 | 1.38 × 10−8 | 0.462 | −1.120 × 10−3 | 1.000 |
| 38. | RPL9P9 | ribosomal protein L9 pseudogene 9 | 1.38 × 10−8 | 0.418 | −1.302 × 10−3 | 1.000 |
| 39. | AC138123.2 | Unmatched | 1.38 × 10−8 | 0.407 | −1.422 × 10−3 | 1.000 |
| 40. | HNRNPA1P10 | heterogeneous nuclear ribonucleoprotein A1 pseudogene 10 | 1.39 × 10−8 | 0.475 | −1.227 × 10−3 | 1.000 |
| 41. | MORF4L1P1 | mortality factor 4 like 1 pseudogene 1 | 3.98 × 10−8 | 0.535 | −1.045 × 10−3 | 1.000 |
| 42. | RP11-676M6.1 | Unmatched | 8.19 × 10−8 | 0.498 | −1.208 × 10−3 | 1.000 |
| 43, | RPL7AP66 | ribosomal protein L7a pseudogene 66 | 9.71 × 10−8 | 0.485 | −1.089 × 10−3 | 1.000 |
| 44. | RP11-680H20.1 | Unmatched | 9.99 × 10−8 | 0.411 | −1.155 × 10−3 | 1.000 |
| 45. | CTB-13H5.1 | Unmatched | 1.41 × 10−7 | 0.418 | −1.175 × 10−3 | 1.000 |
| 46. | HNRNPA1P35 | heterogeneous nuclear ribonucleoprotein A1 pseudogene 35 | 1.49 × 10−7 | 0.350 | −1.223 × 10−3 | 1.000 |
| 47. | PTBP1P | polypyrimidine tract binding protein 1 pseudogene | 1.53 × 10−7 | 0.443 | −1.095 × 10−3 | 1.000 |
| 48. | API5P1 | apoptosis inhibitor 5 pseudogene 1 | 1.57 × 10−7 | 0.347 | −1.204 × 10−3 | 1.000 |
| 49. | UBE2D3P1 | ubiquitin conjugating enzyme E2 D3 pseudogene 1 | 1.69 × 10−7 | 0.485 | −8.801 × 10−4 | 1.000 |
| 50. | AL162151.3 | Unmatched | 1.94 × 10−7 | 0.431 | −1.258 × 10−3 | 1.000 |
| 51. | RPL9P8 | ribosomal protein L9 pseudogene 8 | 2.34 × 10−7 | 0.446 | −1.253 × 10−3 | 1.000 |
| 52. | EEF1A1P13 | eukaryotic translation elongation factor 1 alpha 1 pseudogene 13 | 2.51 × 10−7 | 0.521 | −1.211 × 10−3 | 1.000 |
| 53. | PABPC1P4 | poly(A) binding protein cytoplasmic 1 pseudogene 4 | 2.60 × 10−7 | 0.465 | −1.031 × 10−3 | 1.000 |
| 54. | HNRNPUP1 | heterogeneous nuclear ribonucleoprotein U pseudogene 1 | 2.73 × 10−7 | 0.441 | −1.106 × 10−3 | 1.000 |
| 55. | ARPC3P1 | actin related protein 2/3 complex subunit 3 pseudogene 1 | 3.72 × 10−7 | 0.331 | −1.272 × 10−3 | 1.000 |
| 56. | PTP4A2P1 | protein tyrosine phosphatase type IVA, member 2 pseudogene 1 | 4.59 × 10−7 | 0.500 | −9.014 × 10−4 | 1.000 |
| 57. | CTC-451P13.1 | Unmatched | 4.77 × 10−7 | 0.513 | −9.263 × 10−4 | 1.000 |
| 58. | BZW1P2 | basic leucine zipper and W2 domains 1 pseudogene 2 | 7.97 × 10−7 | 0.445 | −9.598 × 10−4 | 1.000 |
| 59. | RP11-318C24.1 | Unmatched | 1.94 × 10−6 | 0.314 | −1.062 × 10−3 | 0.980 |
| 60. | OTUD4P1 (HIN1L) | OTUD4 pseudogene 1 | 2.08 × 10−6 | 0.480 | −9.962 × 10−4 | 1.000 |
| 61. | EIF3LP2 | eukaryotic translation initiation factor 3 subunit L pseudogene 2 | 2.33 × 10−6 | 0.457 | −9.995 × 10−4 | 1.000 |
| 62. | RAC1P2 | Rac family small GTPase 1 pseudogene 2 | 3.29 × 10−6 | 0.489 | −8.192 × 10−4 | 0.980 |
P (FDR with Benjamini–Hochberg correction) and fold change values were obtained from DESeq2 analysis. PLS coefficients were obtained from UVE-PLS analysis. Areas under Receiver Operating Characteristics (ROC) curves (ROC-AUC) were received from ROC analysis. Genes were ordered according to increasing p values across groups of upregulated and downregulated genes. Genes without names assigned by HUGO Multi-symbol checker were termed as “Unmatched”. Synonyms or previous gene symbols were put into brackets.