Table 4

Fusion detection performance comparison based on cancer cell line data sets
Library Name Fusion genes deFuse TopHat-Fusion FusionQ
split reads spanning reads split reads spanning reads split reads spanning reads
SKBR3 TATDN1-GSDMB 67 51 94 27 144 19
SKBR3 RARA-PKIA 7 12 6 7 4 11
SKBR3 ANKHD1-PCDH1 7 14 4 7 6 8
SKBR3 CCDC85C-SETD3 4 6 3 5
SKBR3 SUMF1-LRRFIP2 9 16 3 9
SKBR3 CSE1L-ENSG00000236127 7 19
SKBR3 WDR67-ZNF704 2 1
SKBR3 CYTH1-EIF3H 5 27 7 22
SKBR3 DHX35-ITCH 4 5 4 1
SKBR3 NFS1-PREX1
BT474 ACACA-STAC2 20 20 14 44 8 27
BT474 RPS6KB1-SNF8 28 31 24 32 9 11
BT474 VAPB-IKZF3 13 31 26 27 8 17
BT474 ZMYND8-CEP250 7 16 10 11 8 17
BT474 RAB22A-MYO9B 9 5 10 1 3 4
BT474 SKA2-MYO19 5 6 10 5 3 3
BT474 DIDO1-KIAA0406 1 3
BT474 STARD3-DOK5 3 3 1 3
BT474 LAMP1-MCF2L
BT474 GLB1-CMTM7 2 6 1 3
BT474 CPNE1-PI3
MCF7 BCAS4-BCAS3 67 77 54 39 14 40
MCF7 ARFGEF2-SULF2 25 24 5 8 13 11
MCF7 RPS6KB1-TMEM49 6 8 3 3 2 1
KPL4 BSG-NFIX 23 18 4 11 3 13
KPL4 PPP1R12A-SEPT10 6 8 5 2
KPL4 NOTCH1-NUP214 2 6 3 3

Liu et al.

Liu et al. BMC Bioinformatics 2013 14:193   doi:10.1186/1471-2105-14-193

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