Supplementary Table 5.
Summary of correlation between CNAs frequencied and gene expression levels.
| Gene | Amplification | Deletion | Diploid | Total amplification | Total deletion | Amplification and expressed higher (%) | Amplification and expressed lower (%) | Deletion and expressed higher (%) | Deletion and expressed lower (%) | |||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Higher | Lower | Higher | Lower | Higher | Lower | |||||||
| Expression | ||||||||||||
| ASH1L | 19 | 8 | 0 | 8 | 183 | 181 | 27 | 8 | 70.37 | 29.63 | 0.00 | 100.00 |
| DOT1L 4 | 1 | 11 | 19 | 179 | 185 | 5 | 30 | 80.00 | 20.00 | 36.67 | 63.33 | |
| EHMT1 | 35 | 11 | 3 | 5 | 183 | 162 | 46 | 8 | 76.09 | 23.91 | 37.50 | 62.50 |
| EHMT2 | 8 | 4 | 5 | 10 | 185 | 187 | 12 | 15 | 66.67 | 33.33 | 33.33 | 66.67 |
| EZH1 | 3 | 1 | 13 | 37 | 161 | 184 | 4 | 50 | 75.00 | 25.00 | 26.00 | 74.00 |
| EZH2 | 58 | 15 | 2 | 6 | 178 | 140 | 73 | 8 | 79.45 | 20.55 | 25.00 | 75.00 |
| KMT2A | 12 | 10 | 14 | 15 | 174 | 174 | 22 | 29 | 54.55 | 45.45 | 48.28 | 51.72 |
| KMT2B | 6 | 3 | 10 | 6 | 190 | 184 | 9 | 16 | 66.67 | 33.33 | 62.50 | 37.50 |
| KMT2C | 39 | 35 | 10 | 11 | 153 | 151 | 74 | 21 | 52.70 | 47.30 | 47.62 | 58.38 |
| KMT2D | 6 | 5 | 8 | 8 | 186 | 186 | 11 | 16 | 54.55 | 45.45 | 50.00 | 50.00 |
| KMT2E | 39 | 37 | 3 | 4 | 158 | 158 | 76 | 7 | 51.32 | 48.68 | 42.86 | 57.14 |
| MECOM | 36 | 26 | 3 | 4 | 169 | 161 | 62 | 7 | 58.06 | 41.94 | 42.86 | 57.14 |
| NSD1 | 16 | 6 | 5 | 5 | 188 | 179 | 22 | 10 | 72.73 | 27.27 | 50.00 | 50.00 |
| PRDM1 | 2 | 0 | 62 | 60 | 139 | 136 | 2 | 122 | 100.00 | 0.00 | 50.82 | 49.18 |
| PRDM10 | 18 | 6 | 6 | 13 | 180 | 176 | 24 | 19 | 75.00 | 25.00 | 31.58 | 68.42 |
| PRDM11 | 8 | 8 | 6 | 20 | 171 | 186 | 16 | 26 | 50.00 | 50.00 | 23.08 | 76.92 |
| PRDM12 | 33 | 11 | 1 | 9 | 179 | 166 | 44 | 10 | 75.00 | 25.00 | 10.00 | 90.00 |
| PRDM13 | 0 | 5 | 7 | 118 | 189 | 80 | 5 | 125 | 0.00 | 100.00 | 5.60 | 94.40 |
| PRDM14 | 16 | 96 | 0 | 2 | 270 | 15 | 112 | 2 | 14.29 | 85.71 | 0.00 | 100.00 |
| PRDM15 | 14 | 4 | 8 | 18 | 177 | 178 | 18 | 26 | 77.78 | 22.22 | 30.77 | 69.23 |
| PRDM16 | 3 | 4 | 13 | 16 | 179 | 184 | 7 | 29 | 42.86 | 57.14 | 44.83 | 55.17 |
| PRDM2 | 2 | 0 | 9 | 26 | 173 | 189 | 2 | 35 | 100.00 | 0.00 | 25.71 | 74.29 |
| PRDM4 | 18 | 2 | 6 | 13 | 184 | 176 | 20 | 19 | 90.00 | 10.00 | 31.58 | 68.42 |
| PRDM5 | 4 | 6 | 7 | 29 | 164 | 189 | 10 | 36 | 40.00 | 60.00 | 19.44 | 80.56 |
| PRDM6 | 7 | 6 | 6 | 26 | 167 | 187 | 13 | 32 | 53.85 | 46.15 | 18.75 | 81.25 |
| PRDM7 | 1 | 3 | 42 | 103 | 160 | 90 | 40 | 145 | 25.00 | 75.00 | 28.97 | 71.03 |
| PRDM8 | 4 | 7 | 5 | 10 | 182 | 191 | 11 | 15 | 36.36 | 63.64 | 33.33 | 66.67 |
| PRDM9 | 6 | 19 | 2 | 8 | 347 | 17 | 25 | 10 | 24.00 | 76.00 | 20.00 | 80.00 |
| SETD1A | 20 | 3 | 14 | 11 | 185 | 166 | 23 | 25 | 86.96 | 13.04 | 56.00 | 44.00 |
| SETD1B | 13 | 3 | 11 | 17 | 179 | 176 | 16 | 28 | 81.25 | 18.75 | 39.29 | 60.71 |
| SETD2 | 17 | 7 | 3 | 16 | 176 | 180 | 24 | 19 | 70.83 | 29.17 | 15.79 | 84.21 |
| SETD3 | 8 | 2 | 6 | 25 | 172 | 186 | 10 | 31 | 80.00 | 20.00 | 19.35 | 80.65 |
| SETD4 | 14 | 3 | 4 | 13 | 183 | 182 | 17 | 17 | 82.35 | 17.65 | 23.53 | 76.47 |
| SETD5 | 17 | 8 | 3 | 25 | 166 | 180 | 25 | 28 | 68.00 | 32.00 | 10.71 | 89.29 |
| SETD6 | 6 | 0 | 15 | 78 | 121 | 179 | 6 | 93 | 100.00 | 0.00 | 16.13 | 83.87 |
| SETD7 | 7 | 4 | 3 | 14 | 181 | 190 | 11 | 17 | 63.64 | 36.36 | 17.65 | 82.35 |
| SETD8 | 11 | 3 | 6 | 25 | 171 | 183 | 14 | 31 | 78.57 | 21.43 | 19.35 | 80.65 |
| SETDB1 | 26 | 2 | 1 | 1 | 196 | 173 | 28 | 2 | 92.86 | 7.14 | 50.00 | 50.00 |
| SETDB2 | 1 | 1 | 34 | 131 | 67 | 165 | 2 | 165 | 50.00 | 50.00 | 20.61 | 79.39 |
| SETMAR | 17 | 8 | 5 | 16 | 175 | 178 | 25 | 21 | 68.00 | 32.00 | 23.81 | 76.19 |
| SMYD1 | 2 | 10 | 4 | 16 | 279 | 88 | 12 | 20 | 16.67 | 83.33 | 20.00 | 80.00 |
| SMYD2 | 12 | 9 | 4 | 16 | 174 | 184 | 21 | 20 | 57.14 | 42.86 | 20.00 | 80.00 |
| SMYD3 | 18 | 3 | 3 | 11 | 185 | 179 | 21 | 14 | 85.71 | 14.29 | 21.43 | 78.57 |
| SMYD4 | 5 | 0 | 9 | 58 | 141 | 186 | 5 | 67 | 100.00 | 0.00 | 13.43 | 86.57 |
| SMYD5 | 11 | 1 | 5 | 19 | 179 | 184 | 12 | 24 | 91.67 | 8.33 | 20.83 | 79.17 |
| SUV39H1 | 4 | 5 | 13 | 7 | 187 | 183 | 9 | 20 | 44.44 | 55.56 | 65.00 | 35.00 |
| SUV39H2 | 12 | 2 | 4 | 29 | 168 | 184 | 14 | 33 | 85.71 | 14.29 | 12.12 | 87.88 |
| SUV420H1 | 26 | 7 | 0 | 6 | 186 | 174 | 33 | 6 | 174.79 | 21.21 | 0.00 | 100.0 |
| SUV420H2 | 13 | 1 | 10 | 4 | 194 | 177 | 14 | 14 | 92.86 | 7.114 | 71.43 | 28.57 |
| WHSC1 | 14 | 2 | 9 | 12 | 185 | 177 | 16 | 21 | 87.50 | 12.50 | 42.86 | 57.14 |
| WHSC1L1 | 44 | 7 | 18 | 111 | 81 | 138 | 51 | 129 | 86.27 | 13.73 | 13.95 | 86.05 |