Table 4 Fusion detection performance comparison based on cancer cell line data sets
From: FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq
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 | ||