Table 3

Nineteen candidate fusions reported by TopHat-Fusion in the prostate cell line

Fusion genes (left-right)

Chromosomes (left-right)

5' position

3' position

Spanning reads

Spanning pairs


ZDHHC7-ABCB9

16-12

85023908

123444867

13

69

TMPRSS2-ERG

21-21

42879875

39817542

7

285

HJURP-EIF4E2

2-2

234749254

233421125

3

9

VWA2-PRKCH

10-14

116008521

61909826

1

10

RGS3-PRKAR1B

9-7

116299195

699055

3

11

SPOCK1-TBC1D9B

5-5

136397966

179305324

9

31

LRP4-FBXL20

11-17

46911864

37557613

5

9

INPP4A-HJURP

2-2

99193605

234746297

6

12

C16orf70-C16orf48

16-16

67144140

67700168

2

19

NDUFV2-ENSG00000188699

18-19

9102729

53727808

1

35

NEAT1-ENSG00000229344

11-1

65190281

568419

1

17

ENSG00000011405-TEAD1

11-11

17229396

12883794

7

9

USP10-ZDHHC7

16-16

84733713

85024243

1

22

LMAN2-AP3S1

5-5

176778452

115202366

15

2

WDR45L-ENSG00000224737

17-17

80579516

30439195

1

33

RC3H2-RGS3

9-9

125622198

116299072

3

11

CTNNA1-ENSG00000249026

5-5

138145895

114727795

1

12

IMMTP1-IMMT

21-2

46097128

86389185

1

50

ENSG00000214009-PCNA

X-20

45918367

5098168

1

24


Nineteen candidate fusions found by TopHat-Fusion in the VCaP prostate cell line, with previously reported fusions [11] indicated in boldface. Fusion genes are sorted according to the scoring scheme described in Materials and methods.

Kim and Salzberg Genome Biology 2011 12:R72   doi:10.1186/gb-2011-12-8-r72

Open Data