Table 1.
Genes consistently in top 50 up- or downregulated in UM models vs. NM
| Gene name | Consistently up- or downregulated | Ranked Log2FC in MP46 | MP41 vs. NM: Log2FC | MP41 vs. NM: padj | Ranked Log2FC in MP46 | MP46 vs. NM: Log2FC | MP46 vs. NM: padj |
|---|---|---|---|---|---|---|---|
| HAGLR | up | 1 | 12.16 | 2.44E-63 | 1 | 12.48 | 3.56E-62 |
| TRPM2-AS | up | 2 | 12.12 | 9.08E-29 | 14 | 9.33 | 3.29E-17 |
| PRAME* | up | 3 | 12.11 | 3.78E-138 | 2 | 11.92 | 1.46E-113 |
| MT1M | up | 4 | 11.7 | 1.77E-25 | 16 | 8.93 | 6.35E-15 |
| ASB11 | up | 5 | 11.24 | 5.77E-55 | 6 | 10.59 | 3.51E-47 |
| KLHL30 | up | 6 | 10.73 | 8.10E-118 | 8 | 10.16 | 9.85E-100 |
| NRN1 | up | 7 | 10.56 | 2.21E-19 | 23 | 7.68 | 3.35E-09 |
| TRPM2 | up | 8 | 10.44 | 5.56E-16 | 22 | 7.73 | 5.83E-08 |
| CCSER1 | up | 9 | 9.98 | 9.12E-53 | 10 | 9.74 | 1.10E-48 |
| RASGRP3* | up | 10 | 9.96 | 1.95E-77 | 4 | 10.84 | 5.23E-77 |
| HIF3A | up | 11 | 9.46 | 1.41E-57 | 25 | 7.48 | 1.31E-34 |
| HOXA9//HOXA10 | up | 12 | 9.45 | 2.59E-87 | 3 | 10.85 | 9.40E-108 |
| PAQR5 | up | 13 | 9.38 | 7.74E-33 | 29 | 7.14 | 7.21E-19 |
| LMX1B | up | 14 | 9.31 | 3.28E-30 | 19 | 8.09 | 2.54E-22 |
| HOXA11 | up | 15 | 9.29 | 8.02E-38 | 9 | 10.1 | 5.99E-42 |
| EPHA4 | up | 16 | 9.04 | 7.55E-124 | 18 | 8.1 | 5.07E-90 |
| HOXC4//HOXC5//HOXC6 | up | 17 | 8.91 | 1.65E-09 | 21 | 7.75 | 1.82E-06 |
| IGLL3P | up | 18 | 8.79 | 4.08E-24 | 12 | 9.59 | 7.85E-26 |
| LINC00482 | up | 19 | 8.6 | 2.51E-103 | 36 | 6.4 | 1.90E-49 |
| PLCB4* | up | 21 | 8.59 | 1.43E-13 | 7 | 10.28 | 3.01E-16 |
| PNLDC1 | up | 22 | 8.56 | 1.19E-99 | 42 | 6.2 | 2.55E-46 |
| MAL2 | up | 23 | 8.43 | 3.04E-24 | 5 | 10.6 | 2.43E-32 |
| TTC39A | up | 24 | 8.17 | 1.72E-164 | 26 | 7.42 | 2.68E-120 |
| SERPINB9P1 | up | 25 | 8.01 | 1.98E-65 | 32 | 6.69 | 2.66E-41 |
| LINC01531 | up | 27 | 7.77 | 5.71E-106 | 11 | 9.65 | 9.41E-141 |
| RAPGEF4* | up | 28 | 7.71 | 3.11E-39 | 15 | 9.09 | 5.34E-46 |
| CACNA2D2 | up | 32 | 7.58 | 6.51E-70 | 43 | 6.09 | 1.45E-38 |
| EPHA8 | up | 33 | 7.51 | 6.15E-53 | 24 | 7.52 | 1.83E-48 |
| TWIST1 | up | 34 | 7.46 | 2.18E-48 | 20 | 8.01 | 1.59E-52 |
| LRRN2 | up | 35 | 7.12 | 1.89E-38 | 46 | 5.93 | 1.01E-22 |
| PITX2 | up | 37 | 6.82 | 5.05E-19 | 30 | 6.89 | 1.88E-16 |
| CYP26B1 | up | 38 | 6.79 | 1.94E-35 | 17 | 8.34 | 3.88E-49 |
| ITGB2 | up | 39 | 6.67 | 7.50E-31 | 27 | 7.37 | 5.36E-32 |
| LTK | up | 43 | 6.57 | 1.09E-19 | 33 | 6.55 | 1.25E-16 |
| GABRA3 | up | 44 | 6.56 | 2.94E-05 | 41 | 6.21 | 2.80E-04 |
| MGAT4A | up | 47 | 6.38 | 3.23E-44 | 50 | 5.71 | 7.25E-30 |
| HAS2 | up | 50 | 6.17 | 5.40E-44 | 38 | 6.32 | 8.15E-39 |
| ZNF667 | down | 10 | −9.6 | 2.32E-44 | 19 | −8.96 | 1.89E-50 |
| GFRA3 | down | 23 | −8.52 | 1.13E-13 | 24 | −8.56 | 1.58E-13 |
| ABCA8 | down | 24 | −8.4 | 2.02E-47 | 10 | −9.91 | 3.14E-43 |
| SCN1B | down | 25 | −8.31 | 5.38E-97 | 26 | −8.45 | 2.62E-86 |
| PMEPA1 | down | 28 | −8.13 | 2.64E-72 | 28 | −8.43 | 1.34E-64 |
| FAM19A5 | down | 29 | −8.1 | 1.39E-65 | 3 | −12.13 | 1.92E-49 |
| HS3ST1 | down | 36 | −7.56 | 3.29E-21 | 8 | −10.2 | 2.13E-15 |
| MGMT | down | 49 | −7.11 | 1.78E-28 | 20 | −8.86 | 7.47E-35 |
Genes found in top 50 overexpressed or underexpressed in both MP41 and MP46 compared to normal uveal melanocytes. Genes are ranked by log2 fold changes for each comparison.
*
Genes previously identified in UM studies are indicated with.