Table 1.
Summary of differential splicing across cancer types
| Patients (n) | Coverage (106 reads) | Cassette exons | Competing 5′ splice sites | Competing 3′ splice sites | Retained introns | Constitutive introns | Constitutive junctions | Retained intron ratio | |
|---|---|---|---|---|---|---|---|---|---|
| Acute myeloid leukemia | 169 | 75 (8) | 1,219 | 326 | 377 | 973 | 6,239 | 841 | 4.74 (1.2) |
| Bladder | 18 | 56 (14) | 894 | 170 | 211 | 296 | 552 | 456 | 1.83 (2.2) |
| Breast | 104 | 72 (17) | 1,052 | 210 | 268 | 266 | 612 | 569 | -2.01 (2.1) |
| Colon | 37 | 58 (18) | 597 | 165 | 200 | 307 | 376 | 291 | 3.44 (2.6) |
| Endometrium | 21 | 35 (16) | 619 | 171 | 180 | 296 | 370 | 312 | 0.48 (2.4) |
| Head and neck | 40 | 81 (26) | 829 | 153 | 202 | 115 | 290 | 418 | 0.82 (1.7) |
| Kidney (chromophobe) | 25 | 82 (12) | 941 | 184 | 228 | 207 | 481 | 484 | 1.65 (1.4) |
| Kidney (renal clear cell) | 71 | 80 (16) | 729 | 149 | 194 | 143 | 380 | 380 | 1.42 (1.7) |
| Kidney (renal papillary cell) | 30 | 85 (20) | 730 | 155 | 220 | 184 | 440 | 408 | 1.51 (2.1) |
| Liver | 50 | 70 (15) | 413 | 90 | 117 | 106 | 200 | 206 | 0.82 (2.1) |
| Lung (adenocarcinoma) | 51 | 43 (28) | 517 | 115 | 141 | 176 | 277 | 233 | 0.20 (2.6) |
| Lung (squamous cell) | 50 | 83 (31) | 1,068 | 190 | 252 | 236 | 609 | 547 | 0.44 (2.0) |
| Prostate | 43 | 75 (11) | 607 | 133 | 185 | 130 | 358 | 337 | 1.44 (2.4) |
| Stomach | 30 | 105 (21) | 1,048 | 200 | 302 | 206 | 886 | 884 | 0.99 (1.7) |
| Rectum | 8 | 53 (14) | 680 | 123 | 172 | 310 | 390 | 314 | 4.30 (2.3) |
| Thyroid | 58 | 83 (11) | 533 | 132 | 177 | 174 | 488 | 332 | 0.66 (2.4) |
Read coverage, number of differentially spliced isoforms, and bias between intron retention in tumor samples compared to patient-matched normal controls Numbers are medians (standard deviation) across all samples