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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
  1. The 76 candidate fusion genes found by TopHat-Fusion in four breast cancer cell lines (BT474, SKBR3, KPL4, MCF7), with previously reported fusions [12] shown in boldface. The remaining 51 fusion genes are novel. The fusions are sorted by the scoring scheme described in Materials and methods.