Table 2 Seventy-six candidate fusions reported by TopHat-Fusion in four breast cancer cell lines
From: TopHat-Fusion: an algorithm for discovery of novel fusion transcripts
SAMPLE ID | Fusion genes (left-right) | Chromosomes (left-right) | 5' position | 3' position | Spanning reads | Spanning pairs |
|---|---|---|---|---|---|---|
BT474 | TRPC4AP-MRPL45 | 20-17 | 33665850 | 36476499 | 2 | 9 |
BT474 | TOB1-SYNRG | 17-17 | 48943418 | 35880750 | 26 | 47 |
SKBR3 | TATDN1-GSDMB | 8-17 | 125551264 | 38066175 | 311 | 555 |
BT474 | THRA-SKAP1 | 17-17 | 38243102 | 46384689 | 28 | 46 |
MCF7 | BCAS4-BCAS3 | 20-17 | 49411707 | 59445685 | 105 | 284 |
BT474 | ACACA-STAC2 | 17-17 | 35479452 | 37374425 | 57 | 59 |
BT474 | STX16-RAE1 | 20-20 | 57227142 | 55929087 | 6 | 24 |
BT474 | MED1-ACSF2 | 17-17 | 37595419 | 48548386 | 10 | 12 |
MCF7 | ENSG00000254868-FOXA1 | 14-14 | 38184710 | 38061534 | 2 | 22 |
SKBR3 | ANKHD1-PCDH1 | 5-5 | 139825557 | 141234002 | 4 | 15 |
BT474 | ZMYND8-CEP250 | 20-20 | 45852972 | 34078459 | 10 | 53 |
BT474 | AHCTF1-NAAA | 1-4 | 247094879 | 76846963 | 10 | 42 |
SKBR3 | SUMF1-LRRFIP2 | 3-3 | 4418012 | 37170638 | 3 | 12 |
KPL4 | BSG-NFIX | 19-19 | 580779 | 13135832 | 12 | 27 |
BT474 | VAPB-IKZF3 | 20-17 | 56964574 | 37922743 | 4 | 14 |
BT474 | DLG2-HFM1 | 11-1 | 85195025 | 91853144 | 2 | 10 |
SKBR3 | CSE1L -ENSG00000236127 | 20-20 | 47688988 | 47956855 | 13 | 31 |
MCF7 | RSBN1-AP4B1 | 1-1 | 114354329 | 114442495 | 6 | 7 |
BT474 | MED13-BCAS3 | 17-17 | 60129899 | 59469335 | 3 | 14 |
MCF7 | ARFGEF2-SULF2 | 20-20 | 47538545 | 46365686 | 17 | 20 |
BT474 | HFM1-ENSG00000225630 | 1-1 | 91853144 | 565937 | 2 | 43 |
KPL4 | MUC20-ENSG00000249796 | 3-3 | 195456606 | 195352198 | 13 | 46 |
KPL4 | MUC20-ENSG00000236833 | 3-3 | 195456612 | 197391649 | 8 | 15 |
MCF7 | RPS6KB1-TMEM49 | 17-17 | 57992061 | 57917126 | 4 | 3 |
SKBR3 | WDR67-ZNF704 | 8-8 | 124096577 | 81733851 | 3 | 3 |
BT474 | CPNE1-PI3 | 20-20 | 34243123 | 43804501 | 2 | 6 |
BT474 | ENSG00000229344-RYR2 | 1-1 | 568361 | 237766339 | 1 | 19 |
BT474 | LAMP1-MCF2L | 13-13 | 113951808 | 113718616 | 2 | 6 |
MCF7 | SULF2-ZNF217 | 20-20 | 46415146 | 52210647 | 11 | 32 |
BT474 | WBSCR17-FBXL20 | 7-17 | 70958325 | 37557612 | 2 | 8 |
MCF7 | ENSG00000224738-TMEM49 | 17-17 | 57184949 | 57915653 | 5 | 6 |
MCF7 | ANKRD30BL-RPS23 | 2-5 | 133012791 | 81574161 | 2 | 6 |
BT474 | ENSG00000251948-SLCO5A1 | 19-8 | 24184149 | 70602608 | 2 | 6 |
BT474 | GLB1-CMTM7 | 3-3 | 33055545 | 32483333 | 2 | 6 |
KPL4 | EEF1DP3-FRY | 13-13 | 32520314 | 32652967 | 2 | 4 |
MCF7 | PAPOLA-AK7 | 14-14 | 96968936 | 96904171 | 3 | 3 |
BT474 | ZNF185-GABRA3 | X-X | 152114004 | 151468336 | 2 | 3 |
KPL4 | PPP1R12A-SEPT10 | 12-2 | 80211173 | 110343414 | 3 | 8 |
BT474 | SKA2-MYO19 | 17-17 | 57232490 | 34863349 | 5 | 12 |
MCF7 | LRP1B-PLXDC1 | 2-17 | 142237963 | 37265642 | 2 | 5 |
BT474 | NDUFB8-TUBD1 | 10-17 | 102289117 | 57962592 | 1 | 49 |
BT474 | ENSG00000225630-NOTCH2NL | 1-1 | 565870 | 145277319 | 1 | 18 |
SKBR3 | CYTH1-EIF3H | 17-8 | 76778283 | 117768257 | 18 | 37 |
BT474 | PSMD3-ENSG00000237973 | 17-1 | 38151673 | 566925 | 1 | 12 |
BT474 | STARD3-DOK5 | 17-20 | 37793479 | 53259992 | 2 | 10 |
BT474 | DIDO1-TTI1 | 20-20 | 61569147 | 36634798 | 1 | 10 |
BT474 | RAB22A-MYO9B | 20-19 | 56886176 | 17256205 | 8 | 20 |
KPL4 | PCBD2-ENSG00000240967 | 5-5 | 134259840 | 99382129 | 1 | 32 |
SKBR3 | RARA-PKIA | 17-8 | 38465535 | 79510590 | 1 | 5 |
BT474 | MED1-STXBP4 | 17-17 | 37607288 | 53218672 | 13 | 11 |
KPL4 | C1orf151-ENSG00000224237 | 1-3 | 19923605 | 27256479 | 1 | 5 |
SKBR3 | RNF6-FOXO1 | 13-13 | 26795971 | 41192773 | 2 | 13 |
SKBR3 | BAT1-ENSG00000254406 | 6-11 | 31499072 | 119692419 | 2 | 30 |
BT474 | KIAA0825-PCBD2 | 5-5 | 93904985 | 134259811 | 1 | 19 |
SKBR3 | PCBD2-ANKRD30BL | 5-2 | 134263179 | 133012790 | 1 | 5 |
BT474 | ENSG00000225630-MTRNR2L8 | 1-11 | 565457 | 10530147 | 1 | 35 |
BT474 | PCBD2-ENSG00000251948 | 5-19 | 134260431 | 24184146 | 2 | 6 |
BT474 | ANKRD30BL-ENSG00000237973 | 2-1 | 133012085 | 567103 | 2 | 8 |
KPL4 | ENSG00000225972-HSP90AB1 | 1-6 | 564639 | 44220780 | 1 | 7 |
BT474 | MTIF2-ENSG00000228826 | 2-1 | 55470625 | 121244943 | 1 | 11 |
BT474 | ENSG00000224905-PCBD2 | 21-5 | 15457432 | 134263223 | 2 | 7 |
BT474 | RPS6KB1-SNF8 | 17-17 | 57970686 | 47021335 | 48 | 57 |
BT474 | MTRNR2L8-PCBD2 | 11-5 | 10530146 | 134263156 | 1 | 6 |
BT474 | RPL23-ENSG00000225630 | 17-1 | 37009355 | 565697 | 3 | 19 |
BT474 | MTRNR2L2-PCBD2 | 5-5 | 79946288 | 134259832 | 1 | 5 |
SKBR3 | ENSG00000240409-PCBD2 | 1-5 | 569005 | 134260124 | 2 | 4 |
SKBR3 | PCBD2-ENSG00000239776 | 5-12 | 134263289 | 127650986 | 2 | 3 |
BT474 | ENSG00000239776-MTRNR2L2 | 12-5 | 127650981 | 79946277 | 2 | 3 |
BT474 | JAK2-TCF3 | 9-19 | 5112849 | 1610500 | 1 | 46 |
KPL4 | NOTCH1-NUP214 | 9-9 | 139438475 | 134062675 | 3 | 5 |
BT474 | MTRNR2L8-TRBV25OR92 | 11-9 | 10530594 | 33657801 | 4 | 4 |
BT474 | MTRNR2L8-AKAP6 | 11-14 | 10530179 | 32953468 | 1 | 5 |
BT474 | ENSG00000230916-PCBD2 | X-5 | 125606246 | 134263219 | 1 | 5 |
MCF7 | ENSG00000226505-MRPL36 | 2-5 | 70329650 | 1799907 | 5 | 20 |
SKBR3 | CCDC85C-SETD3 | 14-14 | 100002351 | 99880270 | 5 | 6 |
BT474 | RPL23-ENSG00000230406 | 17-2 | 37009955 | 222457168 | 109 | 5 |