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