Table 2. Genes showing high level of CN alteration and corresponding values in TCGA.
CNAs DETECTED IN 37 CC | TCGA | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Gene symbol | Chromosome band |
Number of samples showing CNA |
Percentage of samples showing CNA | Log2 (CNA)* |
Mean CN Ratio** | Range of CN ratio | Type of CNA | Percentage of samples showing CN GAIN | Number of samples showing CN GAIN |
Percentage of samples showing CN LOSS | Number of samples showing CN LOSS |
CCND1 | 11q13.3 | 1 | 2.70 | 2.58 | 6 | 5.99–5.99 | GAIN | 41 | 11.45 | 51 | 14.25 |
CCNE1 | 19q12 | 1 | 2.70 | 2.03 | 4.09 | 4.09–4.09 | GAIN | 72 | 20.11 | 25 | 6.98 |
MAF | 16q23.2 | 6 | 16.21 | 1.52 | 2.92 | 2.48–4.16 | GAIN | 84 | 23.46 | 23 | 6.42 |
BCL2L1 | 20q11.21 | 2 | 5.40 | 1.41 | 2.66 | 2.63–2.68 | GAIN | 254 | 70.95 | 0 | 0 |
SRC | 20q11.23 | 2 | 5.40 | 1.39 | 2.92 | 1.62–4.21 | GAIN | 255 | 71.23 | 1 | 0.28 |
IRS2 | 13q34 | 1 | 2.70 | 1.35 | 2.55 | 2.54–2.54 | GAIN | 211 | 58.94 | 7 | 1.96 |
CEBPA | 19q13.11 | 6 | 16.21 | 1.31 | 2.53 | 1.95–3.54 | GAIN | 69 | 19.27 | 25 | 6.98 |
PMS2 | 7p22.1 | 1 | 2.70 | 1.11 | 2.16 | 2.15–2.15 | GAIN | 195 | 54.47 | 1 | 0.28 |
FANCA | 16q24.3 | 1 | 2.70 | 1.11 | 2.15 | 2.15–2.15 | GAIN | 85 | 23.74 | 27 | 7.54 |
CDK8 | 13q12.13 | 3 | 8.10 | 1.09 | 2.18 | 1.57–2.69 | GAIN | 214 | 59.78 | 8 | 2.23 |
CDKN2A | 9p21.3 | 1 | 2.70 | −2.13 | 0.23 | 0.22–0.22 | LOSS | 60 | 16.76 | 48 | 13.41 |
NPM1 | 5q35.1 | 1 | 2.70 | −1.26 | 0.42 | 0.41–0.41 | LOSS | 24 | 6.7 | 67 | 18.72 |
TCL1A | 14q32.13 | 1 | 2.70 | −1.24 | 0.42 | 0.42–0.42 | LOSS | 25 | 6.98 | 118 | 32.96 |
CHEK2 | 22q12.1 | 1 | 2.70 | −1.19 | 0.44 | 0.43–0.43 | LOSS | 9 | 2.51 | 117 | 32.68 |
PAX5 | 9p13.2 | 1 | 2.70 | −1.17 | 0.45 | 0.44–0.44 | LOSS | 59 | 16.48 | 41 | 11.45 |
SUFU | 10q24.32 | 1 | 2.70 | −1.07 | 0.48 | 0.47–0.47 | LOSS | 12 | 3.35 | 80 | 22.35 |
HSP90AA1 | 14q32.31 | 1 | 2.70 | −1.03 | 0.49 | 0.48–0.48 | LOSS | 24 | 6.7 | 118 | 32.96 |
FOXO3 | 6q21 | 3 | 8.10 | −1 | 0.5 | 0.47–0.51 | LOSS | 51 | 14.25 | 49 | 13.69 |
NRAS | 1p13.2 | 1 | 2.70 | −0.99 | 0.5 | 0.50–0.50 | LOSS | 15 | 4.19 | 88 | 24.58 |
FBXW7 | 4q31.3 | 2 | 5.40 | −0.94 | 0.52 | 0.49–0.55 | LOSS | 13 | 3.63 | 101 | 28.21 |
*Base 2 logarithm of CN ratio.
**Ratio of the Tumor Vs Normal intensity signal.