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Table 1 Fusion discoveries in the cancer datasets. The results for TopHat-Fusion, SOAPfuse and JAFFA are collected from a recent study [14]

From: A fast detection of fusion genes from paired-end RNA-seq data

  

FusionMap

TRUP

TopHat-Fusion

JAFFA

SOAPfuse

FuSeq

Breast cancer (TP27)

Total

47

0

261

42

61

53

 

TP

12

0

24

20

24

22

 

Recall

0.44

-

0.89

0.74

0.89

0.81

 

Precision

0.26

-

0.09

0.48

0.39

0.42

 

F1

0.32

-

0.17

0.58

0.55

0.55

 

P-value

0.32

-

9.1e-06

0.71

1

-

Breast cancer (TP99)

Total

47

0

261

42

61

53

 

TP

22

0

35

28

41

36

 

Recall

0.22

-

0.35

0.28

0.41

0.36

 

Precision

0.47

-

0.13

0.67

0.67

0.68

 

F1

0.30

-

0.19

0.40

0.51

0.47

 

P-value

0.32

-

1.1e-08

1

1

-

Melanoma

Total

19

0

29

4

108

21

 

TP

3

0

4

2

10

7

 

Recall

0.27

-

0.36

0.18

0.91

0.64

 

Precision

0.16

-

0.14

0.5

0.09

0.33

 

F1

0.20

-

0.2

0.27

0.17

0.44

 

P-value

0.48

-

0.32

0.62

0.02

-

Glioma

Total

191

209

308

904

299

188

 

TP

28

20

29

30

22

29

 

Recall

0.90

0.65

0.94

0.97

0.71

0.94

 

Precision

0.15

0.10

0.09

0.03

0.07

0.15

 

F1

0.25

0.17

0.12

0.05

0.13

0.26

 

P-value

0.89

0.13

0.09

5.5e-08

0.02

-

  1. We select the best result from the different runs ofcomparison. TP= true positive fusion genes, Total= total discovered fusion-gene candidates, P-value = two-sided p-value of Fisher’s exact test of the difference in precision between FuSeq vs each of the other methods