Table 3.
Co-alteration of mutations with Signature #2a.
| Gene | locus | +Sig#2 | −Sig#2 | Log Rc | p-value | q-value |
|---|---|---|---|---|---|---|
| TP53b | 17q13.1 | 560 (52.98%) | 99 (12.24%)e | 2.11 | 3.02e-80 | 5.22e-78 |
| PIK3CAb | 3q26.3 | 362 (34.25%) | 433 (53.52%) | −0.64 | 5.0e-17 | 4.32e-15 |
| CBFBb | 16q22.1 | 21 (1.99%) | 71 (8.78%) | −2.14 | 1.35e-11 | 7.80e-10 |
| MAP3K1b | 5q11.2 | 75 (7.1%) | 123 (15.20%) | −1.1 | 1.53e-8 | 6.64e-7 |
| GATA3b | 10p11 | 94 (8.89%) | 136 (16.81%) | −0.92 | 2.08e-7 | 7.19e-6 |
| CDH1b | 16q22.1 | 70 (6.62%) | 102 (12.61%) | −0.93 | 7.53e-6 | 2.17e-4 |
| DNAH11 | 7p21 | 120 (11.35%) | 55 (6.80%) | 0.74 | 4.73e-4 | 0.0117 |
| RB1b | 13q14.2 | 39 (3.69%) | 10 (1.24%) | 1.58 | 5.74e-4 | 0.0124 |
| GLDC | 9p22 | 29 (2.74%) | 6 (0.74%) | 1.89 | 9.06e-4 | 0.0174 |
| SYNE1b | 6q25 | 152 (14.38%) | 80 (9.89%) | 0.54 | 2.08e-3 | 0.0359 |
| AKAP9b | 7q21–22 | 81 (7.66%) | 36 (4.45%) | 0.78 | 2.73e-3 | 0.0429 |
aCYB5D2 mRNA reduction at levels < −1.5 SD; mutations in co-alteration with Signature #2 were determined using the Curtis dataset (n = 817).
bthese mutations were co-altered with CYB5D2 downregulation (see Table S1).
clog2-based ratio of percentage in altered group/percentage in unchanged group; positive and negative ratios are for co-occurrence and mutual exclusiveness, respectively.