Table 1

Significant U-G regions with the associated genes.

regions

chr

cytobands

start

end

Correlation (average r coefficient)

U-G Frequency (average %)

Number of genes

gene symbols


1

7

p22.3,,p22.2,p22.1,...

13912

12407180

0.75

53.13

97

PDGFA,PRKAR1B,HEATR2,...

2

7

p21.2,p21.1

13980952

18581782

0.83

48.34

16

ETV1,DGKB,TMEM195,...

3

7

p21.1

19741898

19786077

0.77

48.44

2

TWISTNB,TMEM196

4

7

p21.1

20735744

20825207

0.81

50.00

2

ABCB5,SP8

5

7

p15.3,p15.2

22277336

26372745

0.85

50.00

28

RAPGEF5,IL6,TOMM7,...

6

7

p15.2

26682190

27829944

0.68

50.00

18

SKAP2,HOXA1,HOXA2,...

7

7

p14.3

29901392

33407268

0.78

50.00

29

WIPF3,SCRN1,FKBP14,...

8

7

p14.3,p14.2

34692740

36658380

0.72

48.44

13

NPSR1,DPY19L1,TBX20,...

9

7

p14.1,p13,p12.3,...

37856706

50759460

0.72

49.60

83

GPR141,TXNDC3,SFRP4,...

10

7

p11.2

54819940

54826939

0.77 *

59.38

1

SEC61G

11

7

p11.2

55086725

55275031

0.77 *

60.94

1

EGFR

12

7

p11.2

55572215

56043680

0.70

59.06

5

VOPP1,SEPT14,ZNF713,...

13

7

p11.2

56125502

56171766

0.70

57.81

4

CCT6A,SUMF2,PHKG1,...

14

7

p11.2,p11.1,q11.21

57269897

66582330

0.66

56.56

25

ERV3,VKORC1L1,GUSB,...

15

7

q11.22,q11.23,q21.11,...

69660980

91851882

0.68

57.74

131

AUTS2,WBSCR17,CALN1,...

16

7

q21.2,q21.3,

92738082

97975672

0.72

56.51

36

SAMD9,SAMD9L,HEPACAM2,...

17

7

q22.1,q22.3,q31.1,...

98456252

141707080

0.71

55.94

343

TMEM130,TRRAP,SMURF1,...

18

7

q34,q35,q36.1,...

141954920

158879258

0.75

56.26

154

TRBV12-2,TRBC1,PRSS1,...

19

20

p13,p12.3,p12.2,...

72762

62897316

0.83

25.62

570

DEFB125,DEFB126,DEFB12,...


Table with the significant Up-regulated and Gained (U-G) regions, indicating: chromosomal bands covered by each region; percentage of samples (%) that are in the U-G 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 * the 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 U-G regions is included as supplementary material: Additional-file-1.

Fontanillo et al. BMC Genomics 2012 13(Suppl 5):S5   doi:10.1186/1471-2164-13-S5-S5

Open Data