Table 8.
Differentially expressed pseudogene and parent gene read counts
| Ensemble ID | Gene ID | DON RV MIN | DON RV MAX | DON RV MEAN | DON RV SD | DON RV CORR | HF RV MIN | HF RV MAX | HF RV MEAN | HF RV SD | HF RV CORR | Parent∶TPG ratio P value |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ENSG00000095303 | PTGS1 | 49 | 142 | 100.0 | 33.2 | −0.36 | 18 | 156 | 71.1 | 33.0 | 0.66 | 0.46 |
| ENSG00000230916 | RP11-10B2.1 | 11 | 48 | 23.6 | 15.8 | 6 | 9,631 | 1,028.0 | 2,381.2 | |||
| Ratio | 2 | 12 | 6.3 | 4.5 | 0 | 16 | 4.6 | 4.5 | ||||
| ENSG00000159433 | STARD9 | 464 | 915 | 666.4 | 177.4 | 0.61 | 187 | 606 | 360.5 | 113.3 | 0.12 | 0.02 |
| ENSG00000177359 | RP11-551L14.1 | 17 | 411 | 197.6 | 193.0 | 0 | 21 | 6.8 | 6.1 | |||
| Ratio | 1 | 34 | 12.4 | 13.8 | 12 | 245 | 99.2 | 75.5 | ||||
| ENSG00000153406 | NMRAL1 | 243 | 457 | 350.6 | 79.0 | −0.61 | 163 | 703 | 374.3 | 132.4 | 0.59 | 0.01 |
| ENSG00000171658 | RP11-443P15.2 | 0 | 70 | 35.4 | 30.2 | 0 | 8 | 1.5 | 1.8 | |||
| Ratio | 5 | 35 | 13.2 | 14.8 | 37 | 521 | 239.0 | 148.9 | ||||
| ENSG00000128591 | FLNC | 7,405 | 68,685 | 29,113.8 | 23,179.7 | 0.82 | 12,874 | 85,574 | 34,519.5 | 17,945.1 | 0.00 | 0.15 |
| ENSG00000224163 | RP11-309L24.6 | 3 | 9 | 5.4 | 2.6 | 0 | 256 | 25.2 | 63.9 | |||
| Ratio | 2,468 | 8,265 | 5,194.6 | 2,604.5 | 237 | 38,914 | 12,647.5 | 10,832.6 | ||||
| ENSG00000156509 | FBX043 | 1 | 6 | 3.6 | 2.3 | 0.57 | 0 | 12 | 3.6 | 3.1 | 0.93 | 0.00 |
| ENSG00000236155 | RP11-231P20.2 | 29 | 47 | 37.4 | 6.7 | 70 | 188 | 112.5 | 29.4 | |||
| Ratio | 0 | 0 | 0.1 | 0.1 | 0 | 0 | 0.032 | 0.0 | ||||
| ENSG000000215198 | RP11-182N22.7 | 0 | 2 | 0.6 | 0.9 | 0.83 | 0 | 2 | 0.2 | 0.5 | 0.97 | 0.89 |
| ENSG00000227671 | RP11-488L18.4 | 116 | 318 | 216.4 | 196.1 | 15 | 154 | 62.9 | 34.6 | |||
| Ratio | 0 | 0 | 0.0 | 0.0 | 0 | 0 | 0.004 | 0.0 | ||||
| ENSG00000129048 | CCRL1 | 37 | 676 | 278.4 | 260.0 | 0.77 | 5 | 90 | 44.0 | 23.3 | −0.27 | 0.24 |
| ENSG00000225415 | RP3-509I19.1 | 16 | 397 | 183.0 | 163.8 | 0 | 75 | 17.4 | 18.7 | |||
| Ratio | 1 | 4 | 1.9 | 1.1 | 1 | 27 | 5.6 | 6.7 | ||||
| ENSG00000170606 | HSPA4 | 1,125 | 2,748 | 2,159.8 | 661.6 | 0.81 | 1,512 | 4,215 | 2,394.8 | 710.1 | 0.21 | 0.04 |
| ENSG00000256356 | RP11-320N7.3 | 0 | 3 | 1.6 | 1.1 | 0 | 30 | 9.3 | 8.6 | |||
| Ratio | 916 | 2,379 | 1,392.1 | 682.2 | 88 | 2,422 | 601.2 | 677.1 | ||||
| ENSG00000198938 | MT-CO3 | 412,866 | 1,123,986 | 758,553.2 | 316,252.7 | −0.59 | 524,558 | 1,216,500 | 769,377.6 | 171,110.3 | 0.48 | 0.59 |
| ENSG00000249780 | RP11-352E6.2 | 1 | 64 | 14.0 | 28.0 | 0 | 4 | 1.1 | 1.1 | |||
| Ratio | 6,451 | 1,064,846 | 527,405.4 | 385,001.9 | 228,661 | 1,216,500 | 616,128.4 | 289,694.0 | ||||
| ENSG00000146066 | HIGD2A | 1,670 | 3,298 | 2,358.8 | 660.6 | 0.17 | 1,706 | 4,695 | 2,605.8 | 806.0 | −0.51 | 0.09 |
| ENSG00000235695 | RP11-395P16.1 | 0 | 1 | 0.4 | 0.5 | 0 | 32 | 4.4 | 9.6 | |||
| Ratio | 1,670 | 3,298 | 2,484.0 | 1,151.2 | 110 | 2,778 | 732.4 | 1,042.9 | ||||
| ENSG00000008710 | PKD1 | 2,192 | 2,864 | 2,495.2 | 278.1 | 0.68 | 1,555 | 3,434 | 2,371.0 | 473.1 | 0.01 | 0.20 |
| ENSG00000183458 | RP11-958N24.1 | 18 | 87 | 45.6 | 33.1 | 1 | 80 | 16.1 | 17.2 | |||
| Ratio | 33 | 122 | 79.6 | 43.3 | 36 | 2,461 | 408.9 | 549.1 | ||||
| ENSG00000008710 | PKD1 | 2,192 | 2,864 | 2,495.2 | 278.1 | −0.51 | 1,555 | 3,434 | 2,371.0 | 473.1 | 0.09 | 0.13 |
| ENSG00000227827 | RP11-958N24.2 | 20 | 99 | 45.8 | 32.6 | 0 | 24 | 8.5 | 7.0 | |||
| Ratio | 22 | 127 | 77.8 | 44.1 | 78 | 2,399 | 454.9 | 525.6 | ||||
| ENSG00000215817 | ZC3H11B | 2 | 20 | 10.2 | 8.6 | 0.96 | 0 | 6 | 2.5 | 2.3 | 0.35 | 0.51 |
| ENSG00000214558 | RP11-74E24.2 | 6 | 28 | 14.2 | 10.1 | 0 | 10 | 3.0 | 3.2 | |||
| Ratio | 0 | 1 | 0.7 | 0.3 | 0 | 2.5 | 0.9 | 0.7 | ||||
| ENSG00000206149 | HERC2 | 1,061 | 1,675 | 1,371.8 | 232.5 | 0.80 | 546 | 1,161 | 857.1 | 140.9 | −0.41 | 0.13 |
| ENSG00000254398 | RP11-578F21.2 | 18 | 99 | 52.4 | 40.5 | 0 | 35 | 10.1 | 8.7 | |||
| Ratio | 16 | 64 | 39.7 | 22.9 | 33 | 738 | 180.8 | 199.9 | ||||
| ENSG00000157985 | AGAP1 | 133 | 198 | 164.6 | 24.8 | −0.05 | 53 | 132 | 87.9 | 21.3 | N/C | N/C |
| ENSG00000227141 | RP11-545A16.3 | 0 | 5 | 2.0 | 2.1 | 0 | 1 | 0.0 | 0.2 | |||
| Ratio | 31 | 67 | 54.5 | 20.4 | 31 | 65 | 65.0 | N/C | ||||
| ENSG00000077809 | GTF2I | 2,846 | 3,963 | 3,320.2 | 435.7 | 0.25 | 2,064 | 3,218 | 2,719.5 | 343.2 | 0.51 | 0.16 |
| ENSG00000232546 | RP11-458F8.1 | 1 | 15 | 6.0 | 5.3 | 0 | 3 | 0.9 | 1.1 | |||
| Ratio | 225 | 2,993 | 1,081.5 | 1,091.4 | 909 | 3,191 | ||||||
| ENSG00000110696 | C11orf58 | 1,317 | 3,311 | 2,215.4 | 851.8 | 0.45 | 810 | 2,602 | 1,661.6 | 426.5 | 0.38 | 0.02 |
| ENSG00000205898 | RP11-3B12.4 | 0 | 14 | 7.6 | 5.7 | 0 | 5 | 1.3 | 1.6 | |||
| Ratio | 110 | 478 | 296.6 | 158.8 | 308 | 2,593 | 1,236.6 | 719.5 | ||||
| ENSG00000131469 | RPL27 | 8,100 | 11,516 | 9,989.4 | 1,605.8 | 0.65 | 5,944 | 12,985 | 9,044.7 | 1,764.4 | 1.00 | 0.03 |
| ENSG00000232403 | RP11-511I11.1 | 0 | 4 | 1.8 | 1.5 | 0 | 1 | 0.2 | 0.4 | |||
| Ratio | 2,646 | 8,100 | 5,537.7 | 2,235.0 | 7,579 | 10,848 | 8,804.0 | 1,466.4 | ||||
| ENSG00000147274 | RBMX | 1,515 | 2,375 | 1,907.6 | 383.7 | 0.95 | 1,241 | 2,443 | 1,911.7 | 277.4 | −0.03 | 0.00 |
| ENSG00000225400 | RP11-1114A5.5 | 15 | 36 | 25.6 | 8.4 | 25 | 79 | 50.5 | 16.2 | |||
| Ratio | 66 | 101 | 77.9 | 14.7 | 17 | 73 | 41.4 | 12.7 | ||||
| ENSG00000198105 | ZNF248 | 379 | 615 | 510.6 | 489.7 | −0.09 | 227 | 624 | 425.0 | 93.7 | −0.01 | 0.13 |
| ENSG00000215452 | RP5-981L23.1 | 2 | 35 | 12.2 | 13.4 | 0 | 9 | 2.9 | 2.8 | |||
| Ratio | 14 | 205 | 102.3 | 88.3 | 56 | 484 | 208.1 | 142.6 | ||||
| Unknown | Novel rRNA | 0 | N/C | N/C | N/C | N/C | N/C | N/C | N/C | |||
| ENSG00000240831.1 | AC112777.1 | 2,366 | 5,431 | 3,743.8 | 3,406.4 | 2,502 | 25,096 | 7,494.8 | 6,133.6 | |||
| Ratio | 0 | N/C | N/C | N/C | N/C | |||||||
| Unknown | Unknown/novel | 0 | N/C | N/C | N/C | N/C | N/C | N/C | N/C | |||
| ENSG00000249214 | AC022558.1 | 0 | 1 | 0.8 | 0.4 | 0 | 95 | 5.0 | 20.1 | |||
| Ratio | 0 | N/C | N/C | N/C | N/C | |||||||
| ENSG00000153207 | AHCTF1 | 420 | 1,075 | 724.8 | 260.6 | 0.82 | 237 | 602 | 376.8 | 96.2 | −0.34 | 0.13 |
| ENSG00000226121 | AC009487.6 | 14 | 80 | 40.8 | 29.3 | 1 | 20 | 9.0 | 5.2 | |||
| Ratio | 11 | 47 | 23.8 | 13.8 | 21 | 267 | 61.0 | 52.5 | ||||
| ENSG00000211460 | TSN | 638 | 1,179 | 943.2 | 216.8 | −0.66 | 695 | 1,340 | 989.3 | 165.3 | 1.00 | 0.39 |
| ENSG00000225898 | AC002075.3 | 0 | 9 | 3.0 | 3.7 | 0 | 1 | 0.1 | 0.3 | |||
| Ratio | 92 | 1,100 | 581.1 | 529.2 | 0 | 965 | 961.0 | 5.7 | ||||
| ENSG00000122026 | RPL21 | 266 | 448 | 367.0 | 76.0 | −0.06 | 261 | 516 | 332.4 | 67.7 | 0.79 | 0.02 |
| ENSG00000236732 | AC094019.4 | 3 | 19 | 7.0 | 6.8 | 0 | 7 | 0.9 | 1.6 | |||
| Ratio | 20 | 149 | 85.6 | 57.3 | 38 | 516 | 266.8 | 138.4 | ||||
| ENSG00000139985 | ADAM21 | 2 | 11 | 6.0 | 3.6 | 0.13 | 1 | 11 | 5.0 | 2.9 | 0.66 | 0.18 |
| ENSG00000226469 | AC003029.4 | 18 | 106 | 58.8 | 37.4 | 6 | 39 | 19.9 | 8.5 | |||
| Ratio | 0 | 0 | 0.1 | 0.2 | 0 | 1 | 0.3 | 0.2 | ||||
| ENSG00000124357 | NAGK | 603 | 870 | 695.4 | 103.6 | −0.79 | 538 | 890 | 681.5 | 90.7 | 0.62 | 0.01 |
| ENSG00000233870 | AC007881.4 | 1 | 8 | 4.0 | 2.7 | 0 | 2 | 0.5 | 0.6 | |||
| Ratio | 75 | 870 | 316.4 | 324.4 | 351 | 890 | 690.7 | 147.1 |
Note
CORR: read count correlation; DON RV: unused donor right ventricle; Ensembl: Ensembl release 73; MAX: read count maximum; MEAN: read count mean; MIN: read count minimum; SD: read count standard deviation; HF RV: heart failure right ventricle; N/C: not calculated due to absence of sufficient read counts; P value: parent∶pseudogene (TPG) ratio P value by t test.