Skip to main content

Table 1 Summary of differential splicing across cancer types

From: Widespread intron retention diversifies most cancer transcriptomes

  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)
  1. 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
\