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 |
||||||||
