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.