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Table 2 Significant D-L regions with the associated genes.

From: Combined analysis of genome-wide expression and copy number profiles to identify key altered genomic regions in cancer

regions

chr

cytobands

start

end

Correlation (average r coefficient)

U-G Frequency (average %)

Number of genes

gene symbols

1

10

p14

9365826

11653762

0.62

57.19

5

CUGBP2,C10orf31,USP6NL,...

2

10

p13,p12.33,p12.31,...

16746068

24410224

0.64

59.98

39

RSU1,CUBN,TRDMT1,...

3

10

p12.1,p11.23,p11.22,...

25189544

47921720

0.63

60.50

103

PRTFDC1,ENKUR,THNSL1,...

4

10

p11.2

38238795

38265453

0.60 *

60.94

1

ZNF25

5

10

q11.22,,q11.23

49203737

53404614

0.68

62.91

42

FAM25C,BMS1P7,PTPN20C,...

6

10

q21.1,q21.2,q21.3,...

59989486

82351987

0.65

64.07

152

IPMK,CISD1,UBE2D1,...

7

10

q23.1,

84190870

87742781

0.66

65.63

9

NRG3,GHITM,PCDH21,...

8

10

q23.31,q23.32,q23.33

91498034

97024055

0.62

67.19

39

KIF20B,HTR7,RPP30,...

9

10

q24.1

97391080

97763109

0.62

66.41

6

ALDH18A1,TCTN3,ENTPD1,...

10

10

q24.1,q24.2,q24.31,...

98081203

134474152

0.67

68.70

253

DNTT,OPALIN,TLL2,...

11

13

q12.13,q12.2

27693163

28017254

0.60

28.13

5

USP12,RPL21,RASL11A,...

12

13

q12.2,,q12.3

28367434

30381664

0.61

30.29

13

GSX1,PDX1,ATP5EP2,...

13

13

q13.3,q14.11,q14.12,...

35881808

61059301

0.73

35.48

124

NBEA,MAB21L1,DCLK1,...

14

13

q21.32,q21.33

67340716

70478658

0.62

35.94

2

PCDH9,KLHL1

15

13

q22.2,q22.3,q31.1

76451567

80912598

0.63

37.40

15

KCTD12,IRG1,CLN5,...

16

13

q31.3,

92785210

94467454

0.62

34.38

2

GPC5,GPC6

17

13

q32.1,q32.2,q32.3,...

95812885

106130800

0.64

33.35

38

ABCC4,CLDN10,DZIP1,...

18

13

q33.3

108170700

108931486

0.95

27.73

4

FAM155A,LIG4,ABHD13,...

19

13

q34

110422550

111549152

0.89

23.44

9

IRS2,COL4A1,COL4A2,...

20

14

q11.2,q12,q13.1,...

19686156

70583360

0.75

18.44

389

TTC5,CCNB1IP1,PARP2,...

21

14

q24.2

71478110

72101080

0.74

17.19

2

PCNX,SIPA1L1

22

14

q24.2,,q24.3

73223406

76274521

0.69

17.19

52

DPF3,DCAF4,ZFYVE1,...

23

14

q24.3,,q31.1

77825772

80673424

0.75

17.19

14

TMED8,AHSA1,ISM2,...

24

22

q11.1,q11.21,q11.22,...

16157622

51224902

0.73

24.93

490

POTEH,CESK1,XKR3,...

  1. Table with the significant Down-regulated and Lost (D-L) regions, indicating: chromosomal bands covered by each region; percentage of samples (%) that are in the D-L category in each region (calculated as average frequency for all the gene loci in the region); correlation between GE and CN for each region (calculated as average correlation of the gene loci in the region); number of genes located in each region. Total number of GBM samples analysed: N = 64. Marked with * : correlations calculated between unsegmented GE and segmented CN. Due to size limitations the table only includes a maximum of 3 cytobands or 3 genes. Complete information corresponding to this D-L regions is included as supplementary material: Additional-file-2.
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BMC Genomics

ISSN: 1471-2164

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