Table 2.
Genes with statistically significant differences (based on Welch's t-test) in expression between benign skin lesions vs. all CTCL samples (left panel) and benign skin vs. stage IV CTCL samples (right panel). Average expression is presented as transcripts per million. p or q values for all analyses are reported. The q values that failed to reach statistical significance are presented in light grey font.
| Benign FFPE sample vs. all CTCL samples |
Benign FFPE sample vs. Stage IV CTCL FFPE samples |
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Gene Name | Benign vs. CTCL t-test p value | Benign vs. CTCL q-value | Benign vs. CTCL FFPE log2-ratio (absolute value) | Benign Samples Average Expression | CTCL Samples Average Expression | Benign vs. stage IV CTCL t-test p value | Benign vs stage IV CTCL q-value | Benign vs. stage IV CTCL log2-ratio (absolute value) | Benign samples Average Expression | Stage IV CTCL Samples Average Expression |
| LTA | 2.08E-06 | 1.08E-05 | 2.8 | 189.2 | 1360.0 | 1.13E-03 | 4.61E-03 | 2.9 | 189.2 | 1450.0 |
| TOX | 4.00E-16 | 1.67E-14 | 2.7 | 410.1 | 2669.4 | 1.22E-06 | 5.98E-05 | 3.3 | 410.1 | 3916.4 |
| ITK | 3.67E-08 | 3.40E-07 | 2.6 | 140.1 | 841.3 | 3.41E-05 | 4.77E-04 | 2.7 | 140.1 | 916.4 |
| POU2AF1 | 3.90E-03 | 5.53E-03 | 2.4 | 151.4 | 800.2 | 2.96E-02 | 2.09E-01 | 2.6 | 151.4 | 948.5 |
| CD70 | 4.92E-06 | 2.40E-05 | 2.4 | 813.9 | 4375.0 | 8.24E-04 | 3.84E-03 | 2.5 | 813.9 | 4642.7 |
| SKAP1 | 2.24E-08 | 2.34E-07 | 2.4 | 373.9 | 1970.3 | 2.75E-05 | 4.49E-04 | 2.7 | 373.9 | 2402.8 |
| CCR4 | 3.14E-09 | 5.24E-08 | 2.4 | 1375.9 | 7192.2 | 4.10E-05 | 5.02E-04 | 2.6 | 1375.9 | 8592.0 |
| CCR7 | 8.16E-03 | 9.87E-03 | 2.4 | 91.6 | 492.5 | 3.91E-03 | 1.16E-02 | 2.1 | 91.6 | 396.3 |
| LEF1 | 9.34E-08 | 6.49E-07 | 2.3 | 161.0 | 783.8 | 1.48E-05 | 3.16E-04 | 2.4 | 161.0 | 878.7 |
| FYB | 8.08E-19 | 6.74E-17 | 2.3 | 1337.9 | 6636.5 | 1.72E-07 | 1.69E-05 | 2.9 | 1337.9 | 9750.4 |
| IL21R | 5.64E-05 | 1.57E-04 | 1.9 | 256.3 | 963.6 | 5.32E-04 | 3.66E-03 | 2.1 | 256.3 | 1136.5 |
| SH2D1A | 9.15E-06 | 3.47E-05 | 1.9 | 162.9 | 602.5 | 6.89E-03 | 1.69E-02 | 2.0 | 162.9 | 668.3 |
| MMP9 | 7.23E-03 | 8.87E-03 | 1.8 | 149.2 | 533.1 | 7.54E-03 | 1.69E-02 | 2.8 | 149.2 | 1038.3 |
| SERPINB4 | 1.23E-02 | 1.37E-02 | 1.8 | 37557.1 | 10458.7 | 2.54E-02 | 4.15E-02 | 1.6 | 37557.1 | 12550.8 |
| TRAF1 | 6.20E-06 | 2.64E-05 | 1.7 | 221.1 | 741.6 | 6.61E-04 | 3.81E-03 | 2.2 | 221.1 | 1048.3 |
| ZAP70 | 1.64E-05 | 5.07E-05 | 1.7 | 915.7 | 3006.2 | 3.40E-03 | 1.07E-02 | 1.8 | 915.7 | 3219.1 |
| EED | 6.07E-10 | 1.69E-08 | 1.6 | 1110.6 | 3364.1 | 5.60E-04 | 3.66E-03 | 1.5 | 1110.6 | 3047.6 |
| IL7R | 1.20E-05 | 4.01E-05 | 1.6 | 523.8 | 1567.4 | 3.80E-03 | 1.16E-02 | 1.7 | 523.8 | 1697.3 |
| PDCD1 | 5.51E-03 | 7.54E-03 | 1.6 | 199.9 | 621.3 | 3.74E-02 | 5.31E-02 | 2.1 | 199.9 | 860.0 |
| TBX3 | 2.70E-02 | 2.62E-02 | 1.6 | 164.6 | 497.9 | 3.47E-02 | 5.15E-02 | 1.7 | 164.6 | 549.4 |
| PSORS1C2 | 3.18E-03 | 4.74E-03 | 1.5 | 56092.9 | 19852.0 | 1.21E-02 | 2.42E-02 | 1.2 | 56092.9 | 24132.8 |
| CNOT3 | 6.32E-06 | 2.64E-05 | 1.5 | 268.2 | 754.1 | 2.99E-03 | 9.77E-03 | 1.5 | 268.2 | 762.8 |
| STAT1 | 1.46E-08 | 1.74E-07 | 1.5 | 1714.1 | 4796.4 | 9.97E-05 | 1.09E-03 | 1.6 | 1714.1 | 5279.1 |
| STAG3 | 5.47E-08 | 4.56E-07 | 1.5 | 1118.5 | 3149.1 | 8.25E-06 | 2.69E-04 | 1.8 | 1118.5 | 3848.8 |
| PILRB | 1.55E-09 | 3.23E-08 | 1.5 | 2562.3 | 7305.2 | 7.99E-04 | 3.84E-03 | 1.4 | 2562.3 | 6818.3 |
| NKG7 | 2.83E-03 | 4.29E-03 | 1.5 | 2964.4 | 8484.3 | 4.02E-02 | 5.62E-02 | 1.2 | 2964.4 | 6967.7 |
| PTPN6 | 6.59E-09 | 9.16E-08 | 1.4 | 746.3 | 2021.7 | 2.51E-04 | 2.24E-03 | 1.4 | 746.3 | 1981.0 |
| IRF4 | 8.00E-08 | 6.07E-07 | 1.4 | 192.3 | 505.3 | 6.27E-04 | 3.81E-03 | 1.3 | 192.3 | 477.6 |
| NFKB2 | 1.50E-05 | 4.81E-05 | 1.4 | 320.1 | 852.4 | 4.33E-03 | 1.25E-02 | 1.6 | 320.1 | 966.2 |
| IL32 | 1.09E-06 | 6.50E-06 | 1.4 | 2781.6 | 7520.3 | 1.48E-04 | 1.45E-03 | 1.5 | 2781.6 | 7979.7 |
| LCP2 | 1.00E-05 | 3.48E-05 | 1.4 | 536.0 | 1421.1 | 1.61E-05 | 3.16E-04 | 1.7 | 536.0 | 1696.3 |
| ZFX | 5.38E-07 | 3.45E-06 | 1.3 | 116.1 | 295.5 | 1.48E-02 | 2.84E-02 | 1.1 | 116.1 | 253.0 |
| STAT2 | 2.05E-05 | 6.11E-05 | 1.3 | 324.8 | 803.3 | 9.39E-03 | 1.96E-02 | 1.6 | 324.8 | 968.0 |
| IL15 | 1.91E-03 | 3.01E-03 | 1.3 | 274.7 | 694.3 | 4.08E-02 | 5.62E-02 | 1.6 | 274.7 | 843.3 |
| ZBTB16 | 1.24E-04 | 3.34E-04 | 1.2 | 1100.6 | 2606.4 | 7.02E-04 | 3.82E-03 | 1.5 | 1100.6 | 3168.9 |
| RAC2 | 1.31E-03 | 2.45E-03 | 1.2 | 4324.0 | 10279.5 | 1.22E-03 | 4.78E-03 | 1.4 | 4324.0 | 11662.1 |
| CXCL9 | 5.80E-03 | 7.81E-03 | 1.2 | 2507.9 | 5798.2 | 8.66E-03 | 1.89E-02 | 1.5 | 2507.9 | 6862.0 |
| ANKRD11 | 1.47E-06 | 8.18E-06 | 1.2 | 987.6 | 2236.8 | 1.46E-02 | 2.84E-02 | 1.0 | 987.6 | 2001.2 |
| EZH2 | 5.95E-04 | 1.31E-03 | 1.1 | 466.1 | 996.7 | 2.87E-02 | 4.50E-02 | 0.9 | 466.1 | 876.4 |
| CDKN2B | 1.31E-03 | 2.45E-03 | 1.1 | 476.2 | 1024.1 | 4.13E-02 | 5.62E-02 | 1.2 | 476.2 | 1065.9 |
| CCL5 | 1.33E-03 | 2.45E-03 | 1.1 | 18304.2 | 38736.5 | 3.18E-04 | 2.60E-03 | 1.3 | 18304.2 | 43788.2 |
| HDAC1 | 5.18E-06 | 2.40E-05 | 1.1 | 1225.0 | 2568.8 | 1.04E-03 | 4.43E-03 | 1.2 | 1225.0 | 2906.2 |
| NME1 | 1.50E-03 | 2.50E-03 | 1.1 | 1861.2 | 3878.3 | 3.73E-02 | 5.31E-02 | 1.1 | 1861.2 | 3929.5 |
| CD52 | 3.72E-04 | 8.87E-04 | 1.1 | 39313.9 | 81513.5 | 7.47E-04 | 3.84E-03 | 1.2 | 39313.9 | 90909.3 |
| MTF2 | 3.05E-04 | 7.49E-04 | 1.1 | 217.4 | 453.9 | 1.82E-03 | 6.37E-03 | 1.2 | 217.4 | 498.4 |
| ITGA3 | 6.71E-03 | 8.61E-03 | 1.0 | 182.7 | 369.1 | 1.02E-02 | 2.08E-02 | 1.9 | 182.7 | 665.6 |
| RASA1 | 9.05E-04 | 1.85E-03 | 1.0 | 338.1 | 677.7 | 9.12E-04 | 4.06E-03 | 1.1 | 338.1 | 745.1 |
| SUZ12 | 1.00E-05 | 3.48E-05 | 1.0 | 340.2 | 676.1 | 4.65E-04 | 3.51E-03 | 1.2 | 340.2 | 795.6 |
| IRF7 | 3.91E-03 | 5.53E-03 | 1.0 | 841.7 | 1658.5 | 1.82E-02 | 3.11E-02 | 1.0 | 841.7 | 1660.2 |
| PRDM2 | 1.83E-02 | 1.91E-02 | 1.0 | 37.1 | 72.2 | 4.49E-02 | 5.84E-02 | 1.4 | 37.1 | 95.6 |
| MAP2K1 | 1.38E-03 | 2.45E-03 | 0.9 | 412.6 | 794.8 | 8.94E-03 | 1.90E-02 | 1.0 | 412.6 | 803.8 |
| KLHL42 | 1.73E-03 | 2.78E-03 | 0.9 | 136.5 | 260.4 | 5.18E-03 | 1.45E-02 | 1.0 | 136.5 | 273.5 |
| EP400 | 1.40E-03 | 2.45E-03 | 0.9 | 1879.3 | 3608.5 | 1.46E-03 | 5.50E-03 | 1.1 | 1879.3 | 4107.7 |
| JARID2 | 5.21E-03 | 7.25E-03 | 0.9 | 698.2 | 1292.2 | 1.87E-02 | 3.11E-02 | 0.9 | 698.2 | 1326.6 |
| NFKB1 | 9.07E-04 | 1.85E-03 | 0.9 | 498.1 | 915.7 | 7.38E-03 | 1.69E-02 | 1.0 | 498.1 | 979.2 |
| WWOX | 8.98E-03 | 1.06E-02 | 0.9 | 953.4 | 1733.4 | 7.15E-03 | 1.69E-02 | 1.1 | 953.4 | 2071.6 |
| NUB1 | 8.89E-03 | 1.06E-02 | 0.8 | 5078.1 | 8783.1 | 1.82E-02 | 3.11E-02 | 0.9 | 5078.1 | 9771.0 |
| STAT5B | 4.80E-02 | 3.86E-02 | 0.8 | 210.0 | 369.8 | 7.01E-03 | 1.69E-02 | 1.2 | 210.0 | 498.2 |
| SMAD2 | 3.99E-02 | 3.43E-02 | 0.8 | 139.7 | 238.3 | 4.44E-02 | 5.84E-02 | 1.1 | 139.7 | 292.7 |
| IL17RA | 2.33E-03 | 3.60E-03 | 0.8 | 455.6 | 809.4 | 3.04E-02 | 4.65E-02 | 0.8 | 455.6 | 783.5 |
| MCL1 | 6.99E-06 | 2.78E-05 | 0.9 | 1349.3 | 2433.9 | 1.80E-03 | 6.37E-03 | 0.8 | 1349.3 | 2360.7 |
| TRAF2 | 2.37E-02 | 2.35E-02 | 0.8 | 2425.2 | 4113.7 | 1.56E-02 | 2.85E-02 | 0.9 | 2425.2 | 4613.1 |
| MYC | 1.41E-03 | 2.45E-03 | 0.8 | 380.8 | 663.6 | 2.35E-03 | 7.94E-03 | 1.2 | 380.8 | 873.1 |
| SOCS3 | 3.32E-02 | 3.04E-02 | 0.8 | 1008.8 | 1713.3 | 2.89E-02 | 4.50E-02 | 1.1 | 1008.8 | 2102.9 |
| E2F4 | 5.97E-03 | 7.91E-03 | 0.8 | 773.6 | 1314.5 | 1.87E-02 | 3.11E-02 | 1.0 | 773.6 | 1566.6 |
| TRRAP | 5.38E-04 | 1.25E-03 | 0.8 | 113.8 | 199.2 | 1.57E-02 | 2.85E-02 | 0.9 | 113.8 | 211.1 |
| NME4 | 1.38E-02 | 1.50E-02 | 0.8 | 3075.1 | 5452.4 | 4.53E-02 | 5.84E-02 | 0.9 | 3075.1 | 5723.2 |
| TGFB1 | 9.62E-03 | 1.11E-02 | 0.7 | 394.7 | 649.9 | 5.47E-03 | 1.49E-02 | 0.9 | 394.7 | 759.3 |
| ACVRL1 | 3.44E-02 | 3.08E-02 | 0.7 | 414.1 | 659.3 | 2.71E-02 | 4.35E-02 | 0.9 | 414.1 | 789.9 |
| ANPEP | 7.20E-03 | 8.87E-03 | 0.7 | 820.7 | 1308.1 | 7.58E-03 | 1.69E-02 | 0.9 | 820.7 | 1512.5 |
| NOTCH1 | 3.78E-02 | 3.29E-02 | 0.5 | 393.3 | 557.5 | 1.64E-02 | 2.92E-02 | 0.9 | 393.3 | 712.9 |
| GTSF1 | 3.35E-05 | 9.64E-05 | ∞ | 0 | 1852.2 | 1.73E-03 | 1.57E-02 | ∞ | 0 | 2573.3 |
| BLK | 1.96E-04 | 5.11E-04 | ∞ | 0 | 416.7 | 3.97E-02 | 6.21E-02 | ∞ | 0 | 283.5 |
| IL26 | 1.61E-03 | 2.63E-03 | ∞ | 0 | 1373.4 | 4.88E-01 | 2.16E-01 | ∞ | 0 | 144.6 |
| TNFSF11 | 4.76E-02 | 3.86E-02 | ∞ | 0 | 243.6 | 1.59E-01 | 1.42E-01 | ∞ | 0 | 280.3 |