Table 1. Ranked list of CESAM pan-cancer candidate genes.
The list is ranked by FDR-corrected P-value, and is continued as Supplementary Table 1. For each candidate gene, tumor types with at least 3 samples exhibiting upregulation are depicted. FC, dosage-adjusted expression fold-change for SCNA-carrier samples vs. non-carrier controls. Padj, adjusted p-values, according to the Benjamini and Hochberg procedure.
| Gene | Chromosome location of TAD | FC | Padj |
|---|---|---|---|
| IRS4 | chrX: 107,720,001-108,600,000 | 15.0 | 2.47E-18 |
| TBL1X | chrX: 8,640,000-10,080,000 | 4.4 | 1.15E-05 |
| MTHFD1L | chr6: 151,200,000-151,760,000 | 3.4 | 4.01E-05 |
| LIPA | chr10: 91,000,000-91,520,000 | 2.3 | 4.63E-05 |
| PPP3CA | chr4: 101,080,000-103,480,000 | 2.4 | 0.000142 |
| MLLT4 | chr6: 167,400,000-169,000,000 | 6.2 | 0.000150 |
| NCOR1 | chr17: 15,880,000-16,440,000 | 3.1 | 0.000703 |
| GIGYF2 | chr2: 233,160,000-233,840,000 | 3.6 | 0.000822 |
| BTD | chr3: 15,600,000-16,280,000 | 2.6 | 0.00862 |
| SMARCA1 | chrX: 128,400,000-129,200,000 | 11.5 | 0.0127 |
| TERT | chr5: 40,000-1,720,000 | 2.7 | 0.0128 |
| OSGIN1 | chr16: 83,680,000-84,240,000 | 34.5 | 0.0250 |
| TSC22D3 | chrX: 105,560,000-107,240,000 | 2.7 | 0.0260 |
| STUB1 | chr16: 680,000-1,280,000 | 22.6 | 0.0275 |
| FAM135B | chr8: 138,840,001-139,800,000 | 2.9 | 0.0298 |
| KCNQ1 | chr11: 2,160,000-3,600,000 | 2.3 | 0.0353 |
| INSC | chr11: 16,760,001-17,520,000 | 2.1 | 0.0406 |
| PTCHD1 | chrX: 21,720,000-23,560,000 | 2.8 | 0.0463 |