Table 2.

Identification of known fusion genes by various fusion detection tools

Sample	Known (Gold) fusion genes	FS	SF	dF	FH	FM	THF
NCI-H660 (2)	TMPRSS2-ERG	●	●	●	●	●	●
	EEF2-SLC25A42	●	●	●	●	-	●
	TP/FP	2/0	2/16	2/11	2/1	1/1	2/1
	Precision	1.0	0.11	0.15	0.67	0.50	0.67
	Recall	1.0	1.0	1.0	1.0	0.50	1.0
K562 (3)	BCR-ABL1	●	●	●	-	●	●
	NUP214-XKR3	●	●	○	●	●	●
	BAT3-SLC44A4	●	●	○	-	●	●
	TP/FP	3/1	3/7	3/27	1/1	3/12	3/0
	Precision	0.75	0.30	0.10	1.0	0.20	1.0
	Recall	1.0	1.0	1.0	0.33	1.0	1.0
MCF-7 (23)	USP31-CRYL1	●	●	○	○	○	●
	ARFGEF2-SULF2	●	●	○	-	○	●
	TXLNG-SYAP1	●	●	●	-	○	●
	DEPDC1B-ELOVL7	●	●	●	○	●	●
	SYTL2-PICALM	●	●	●	○	●	●
	RPS6KB1-DIAPH3	-	●	●	-	-	-
	AHCYL1-RAD51C	-	●	-	●	●	●
	TAF4-BRIP1	-	●	-	-	○	-
	POP1-MATN2	●	●	●	-	○	-
	GCN1L1-MSI1	●	●	●	-	-	●
	ESR1-CCDC170	●	●	●	●	○	●
	SMARCA4-CARM1	●	●	●	-	○	●
	MYO6-SENP6	●	●	●	●	○	●
	ADAMTS19-SLC27A6	●	●	●	●	○	●
	GATAD2B-NUP210L	-	●	●	-	○	●
	SLC25A24-NBPF6	●	●	●	-	●	-
	ATXN7L3-FAM171A2	●	●	●	-	●	-
	C16orf62-IQCK	●	●	●	-	●	●
	TBL1XR1-RGS17	●	-		-	-	-
	BCAS4-BCAS3	●	●	●	●	-	●
	RPS6KB1-TMEM49	●	●	●	-	○	●
	ABCA5-PPP4R1L	-	●	-	-	-	-
	C16orf45-ABCC1	-	-	-	-	-	-
	TP/FP	17/14	21/83	18/132	8/11	17/126	15/26
	Precision	0.55	0.18	0.12	0.42	0.12	0.37
	Recall	0.74	0.91	0.78	0.35	0.74	0.65
Overall	Precision	0.60	0.20	0.12	0.46	0.13	0.43
	Recall	0.79	0.93	0.82	0.39	0.75	0.71
	F1 score	0.68	0.33	0.21	0.42	0.22	0.53
Mapping program		SSAHA2	SOAP2	GMAP	Bowtie	GSNAP	Bowtie
			BWA
Transcriptome		RefGene	Ensembl	Ensembl	RefGene	RefGene	Ensembl

‘●’ and ‘○’ indicate that the case was predicted successfully, with direction reversed in ‘○’. Precision = TP/(TP + FP), Recall = TP/(TP + FN), F₁ score = 2 × precision×recall/(precision + recall).

FS, FusionScan; SF, SOAPfuse; dF, defuse; FH, FusionHunter; FM, FusionMap; THF, TopHat-Fusion; TP, true-positive; FP, false-positive; FN, false-negative.