This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.
Testing the association between copy number variation 80 arm-level events and 12 molecular subtypes across 493 patients, 177 significant findings detected with P value < 0.05 and Q value < 0.25.
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1p gain cnv correlated to 'CN_CNMF'.
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2p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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2q gain cnv correlated to 'CN_CNMF'.
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3q gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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4p gain cnv correlated to 'CN_CNMF'.
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5p gain cnv correlated to 'CN_CNMF'.
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6p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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6q gain cnv correlated to 'MIRSEQ_CHIERARCHICAL'.
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7p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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7q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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8p gain cnv correlated to 'CN_CNMF'.
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8q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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10p gain cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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11p gain cnv correlated to 'CN_CNMF'.
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11q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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12p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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12q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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14q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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15q gain cnv correlated to 'MRNASEQ_CNMF'.
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17p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
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17q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
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18p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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18q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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20p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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20q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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21q gain cnv correlated to 'CN_CNMF'.
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1p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
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3p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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4p loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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4q loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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5p loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
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5q loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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6q loss cnv correlated to 'METHLYATION_CNMF'.
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7p loss cnv correlated to 'CN_CNMF'.
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8p loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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8q loss cnv correlated to 'CN_CNMF'.
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9p loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
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9q loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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10p loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
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10q loss cnv correlated to 'CN_CNMF'.
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11p loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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12q loss cnv correlated to 'CN_CNMF'.
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13q loss cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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15q loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
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16p loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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16q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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17p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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17q loss cnv correlated to 'CN_CNMF'.
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18p loss cnv correlated to 'CN_CNMF'.
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18q loss cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', and 'MRNASEQ_CNMF'.
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19p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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19q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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21q loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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22q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 177 significant findings detected.
Clinical Features |
MRNA CNMF |
MRNA CHIERARCHICAL |
CN CNMF |
METHLYATION CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRSEQ MATURE CNMF |
MIRSEQ MATURE CHIERARCHICAL |
||
nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
8q gain | 235 (48%) | 258 |
0.024 (1.00) |
0.0244 (1.00) |
2.34e-20 (2.22e-17) |
1.34e-05 (0.0114) |
0.287 (1.00) |
0.0396 (1.00) |
9.18e-08 (8.35e-05) |
1.93e-05 (0.016) |
4.24e-06 (0.00369) |
2.41e-05 (0.0199) |
0.000199 (0.155) |
1.13e-05 (0.00962) |
12p gain | 131 (27%) | 362 |
0.221 (1.00) |
0.0501 (1.00) |
1.06e-06 (0.000936) |
0.0509 (1.00) |
0.0166 (1.00) |
0.0205 (1.00) |
4.46e-09 (4.13e-06) |
4.3e-11 (4.02e-08) |
1.46e-05 (0.0124) |
1.81e-05 (0.0151) |
6.62e-08 (6.03e-05) |
4.9e-08 (4.48e-05) |
12q gain | 126 (26%) | 367 |
0.221 (1.00) |
0.103 (1.00) |
3.78e-08 (3.47e-05) |
0.0168 (1.00) |
0.17 (1.00) |
0.0399 (1.00) |
1.14e-11 (1.07e-08) |
5.74e-12 (5.39e-09) |
1.19e-05 (0.0101) |
3.13e-06 (0.00273) |
2.22e-07 (0.000201) |
6.19e-07 (0.000554) |
20p gain | 164 (33%) | 329 |
0.0815 (1.00) |
0.191 (1.00) |
6.66e-05 (0.0535) |
0.00644 (1.00) |
0.421 (1.00) |
0.265 (1.00) |
0.000214 (0.166) |
6.56e-06 (0.00566) |
2.82e-05 (0.0231) |
5.4e-06 (0.00468) |
0.000189 (0.148) |
2.77e-05 (0.0227) |
20q gain | 189 (38%) | 304 |
0.01 (1.00) |
0.0239 (1.00) |
1.64e-07 (0.000149) |
0.00114 (0.822) |
0.228 (1.00) |
0.0314 (1.00) |
4.47e-06 (0.00389) |
3.34e-07 (3e-04) |
2.04e-06 (0.00179) |
6.85e-07 (0.000612) |
1.77e-05 (0.0148) |
1.69e-05 (0.0141) |
4q loss | 132 (27%) | 361 |
0.00043 (0.327) |
0.000811 (0.597) |
2.35e-06 (0.00206) |
0.00336 (1.00) |
0.278 (1.00) |
0.0476 (1.00) |
9.39e-08 (8.52e-05) |
7.54e-13 (7.1e-10) |
1.77e-06 (0.00156) |
2.31e-07 (0.000209) |
0.000287 (0.222) |
0.000289 (0.223) |
5q loss | 137 (28%) | 356 |
0.0641 (1.00) |
0.0411 (1.00) |
2.49e-09 (2.31e-06) |
0.000644 (0.479) |
0.00117 (0.84) |
0.00554 (1.00) |
1.55e-06 (0.00137) |
1.44e-08 (1.32e-05) |
9.39e-07 (0.000832) |
2.65e-06 (0.00232) |
6.96e-06 (0.006) |
4.6e-07 (0.000413) |
19p loss | 235 (48%) | 258 |
0.815 (1.00) |
1 (1.00) |
5.34e-08 (4.87e-05) |
1.2e-10 (1.12e-07) |
0.335 (1.00) |
0.522 (1.00) |
7.15e-07 (0.000637) |
2.35e-07 (0.000212) |
2.5e-05 (0.0206) |
3.18e-07 (0.000286) |
0.0062 (1.00) |
1.63e-05 (0.0136) |
22q loss | 212 (43%) | 281 |
0.126 (1.00) |
0.118 (1.00) |
1.06e-09 (9.86e-07) |
2.8e-05 (0.0229) |
0.798 (1.00) |
0.0688 (1.00) |
8.98e-08 (8.17e-05) |
5.38e-07 (0.000482) |
0.000205 (0.159) |
9.04e-07 (0.000803) |
0.000337 (0.259) |
3.35e-05 (0.0273) |
2p gain | 148 (30%) | 345 |
0.301 (1.00) |
0.119 (1.00) |
3.86e-08 (3.53e-05) |
0.000614 (0.46) |
0.444 (1.00) |
0.358 (1.00) |
8.92e-05 (0.0709) |
5.18e-06 (0.0045) |
1.1e-06 (0.000974) |
7.36e-06 (0.00634) |
0.00204 (1.00) |
6.12e-05 (0.0493) |
7p gain | 251 (51%) | 242 |
0.856 (1.00) |
0.535 (1.00) |
1.34e-20 (1.27e-17) |
0.00272 (1.00) |
0.000443 (0.336) |
0.000542 (0.408) |
2.78e-11 (2.61e-08) |
1.01e-11 (9.45e-09) |
4.23e-06 (0.00369) |
0.000908 (0.666) |
0.00032 (0.247) |
1.66e-05 (0.0139) |
11q gain | 112 (23%) | 381 |
0.01 (1.00) |
0.02 (1.00) |
2.8e-08 (2.57e-05) |
0.0742 (1.00) |
0.261 (1.00) |
0.343 (1.00) |
0.00412 (1.00) |
0.000194 (0.151) |
5.15e-05 (0.0416) |
8.66e-05 (0.0691) |
0.000317 (0.245) |
0.0037 (1.00) |
4p loss | 116 (24%) | 377 |
0.186 (1.00) |
0.145 (1.00) |
4.45e-05 (0.036) |
0.212 (1.00) |
0.195 (1.00) |
0.218 (1.00) |
8.76e-05 (0.0697) |
8.23e-08 (7.49e-05) |
7.71e-06 (0.00663) |
3.55e-06 (0.0031) |
0.00593 (1.00) |
0.000356 (0.273) |
16q loss | 137 (28%) | 356 |
0.551 (1.00) |
0.707 (1.00) |
9.14e-06 (0.00784) |
0.000321 (0.247) |
0.0738 (1.00) |
0.219 (1.00) |
1.69e-07 (0.000153) |
3.53e-07 (0.000317) |
0.00667 (1.00) |
0.0313 (1.00) |
0.00133 (0.948) |
3.36e-05 (0.0273) |
19q loss | 153 (31%) | 340 |
0.344 (1.00) |
0.475 (1.00) |
1.47e-07 (0.000133) |
8.18e-07 (0.000727) |
0.272 (1.00) |
0.22 (1.00) |
0.000103 (0.0816) |
0.000177 (0.138) |
0.000677 (0.503) |
7.8e-05 (0.0623) |
0.026 (1.00) |
0.000359 (0.275) |
14q gain | 120 (24%) | 373 |
0.803 (1.00) |
0.722 (1.00) |
9.11e-09 (8.4e-06) |
0.0156 (1.00) |
0.229 (1.00) |
0.127 (1.00) |
7.43e-05 (0.0595) |
0.00356 (1.00) |
3.2e-05 (0.0261) |
2.67e-05 (0.0219) |
0.00078 (0.577) |
0.0147 (1.00) |
17q gain | 186 (38%) | 307 |
0.305 (1.00) |
0.312 (1.00) |
1.72e-08 (1.58e-05) |
0.000909 (0.666) |
0.624 (1.00) |
0.172 (1.00) |
4.29e-05 (0.0348) |
6.2e-06 (0.00536) |
8.91e-06 (0.00765) |
0.000367 (0.28) |
0.0606 (1.00) |
0.000637 (0.475) |
18q gain | 66 (13%) | 427 |
0.595 (1.00) |
0.14 (1.00) |
0.000139 (0.109) |
1.61e-06 (0.00142) |
0.0217 (1.00) |
0.0172 (1.00) |
1.81e-05 (0.0151) |
2.6e-05 (0.0214) |
0.0109 (1.00) |
0.00079 (0.583) |
0.0027 (1.00) |
0.00174 (1.00) |
13q loss | 243 (49%) | 250 |
0.105 (1.00) |
0.268 (1.00) |
2.62e-17 (2.47e-14) |
0.157 (1.00) |
0.000538 (0.405) |
2.79e-06 (0.00244) |
3.09e-07 (0.000278) |
5.43e-06 (0.0047) |
0.0137 (1.00) |
0.0103 (1.00) |
0.0428 (1.00) |
0.162 (1.00) |
15q loss | 233 (47%) | 260 |
0.101 (1.00) |
0.176 (1.00) |
7.26e-07 (0.000646) |
0.0201 (1.00) |
0.127 (1.00) |
0.0735 (1.00) |
5.61e-13 (5.28e-10) |
1.49e-06 (0.00132) |
1.59e-05 (0.0134) |
0.00199 (1.00) |
0.0177 (1.00) |
0.00295 (1.00) |
21q loss | 157 (32%) | 336 |
0.184 (1.00) |
0.191 (1.00) |
7.21e-07 (0.000642) |
0.0415 (1.00) |
0.0315 (1.00) |
0.00316 (1.00) |
2.26e-10 (2.1e-07) |
5.86e-09 (5.41e-06) |
0.000425 (0.323) |
1.37e-06 (0.00121) |
0.00698 (1.00) |
0.000996 (0.726) |
7q gain | 207 (42%) | 286 |
0.482 (1.00) |
0.388 (1.00) |
9.72e-11 (9.07e-08) |
0.0349 (1.00) |
0.133 (1.00) |
0.221 (1.00) |
5.7e-09 (5.27e-06) |
1.21e-08 (1.12e-05) |
0.0026 (1.00) |
0.00371 (1.00) |
0.0117 (1.00) |
0.00158 (1.00) |
10p gain | 105 (21%) | 388 |
0.236 (1.00) |
0.308 (1.00) |
0.000641 (0.478) |
1.26e-05 (0.0107) |
0.018 (1.00) |
0.00405 (1.00) |
7.64e-05 (0.0611) |
1.52e-05 (0.0128) |
0.00913 (1.00) |
0.0013 (0.927) |
0.0384 (1.00) |
0.00439 (1.00) |
18p gain | 91 (18%) | 402 |
0.876 (1.00) |
0.751 (1.00) |
3.35e-05 (0.0273) |
2.4e-05 (0.0199) |
0.256 (1.00) |
0.65 (1.00) |
0.0203 (1.00) |
0.00466 (1.00) |
0.0151 (1.00) |
0.00092 (0.673) |
0.00571 (1.00) |
2.67e-05 (0.0219) |
1p loss | 79 (16%) | 414 |
0.0797 (1.00) |
0.14 (1.00) |
1.88e-05 (0.0157) |
0.000138 (0.109) |
0.908 (1.00) |
0.108 (1.00) |
9.66e-05 (0.0766) |
0.00102 (0.743) |
0.521 (1.00) |
0.0491 (1.00) |
0.456 (1.00) |
0.224 (1.00) |
3p loss | 205 (42%) | 288 |
0.343 (1.00) |
0.117 (1.00) |
2.02e-05 (0.0167) |
4.81e-06 (0.00418) |
0.253 (1.00) |
0.323 (1.00) |
0.0311 (1.00) |
5.31e-06 (0.00461) |
0.0219 (1.00) |
0.35 (1.00) |
0.123 (1.00) |
0.11 (1.00) |
8p loss | 191 (39%) | 302 |
0.132 (1.00) |
0.0285 (1.00) |
8.73e-19 (8.25e-16) |
0.241 (1.00) |
0.0496 (1.00) |
0.00995 (1.00) |
0.000101 (0.0797) |
3.94e-05 (0.0319) |
0.00258 (1.00) |
0.0326 (1.00) |
0.00566 (1.00) |
0.0014 (0.994) |
9q loss | 238 (48%) | 255 |
0.499 (1.00) |
1 (1.00) |
2.4e-05 (0.0199) |
0.00361 (1.00) |
0.418 (1.00) |
0.029 (1.00) |
0.139 (1.00) |
9.29e-06 (0.00795) |
0.00642 (1.00) |
0.0025 (1.00) |
0.0259 (1.00) |
0.000173 (0.135) |
16p loss | 108 (22%) | 385 |
0.453 (1.00) |
0.411 (1.00) |
9.33e-06 (0.00797) |
0.000558 (0.419) |
0.232 (1.00) |
0.517 (1.00) |
4.71e-05 (0.0381) |
1.42e-05 (0.0121) |
0.00845 (1.00) |
0.0364 (1.00) |
0.00783 (1.00) |
0.0024 (1.00) |
18q loss | 207 (42%) | 286 |
0.519 (1.00) |
0.668 (1.00) |
3.76e-10 (3.49e-07) |
0.819 (1.00) |
0.00357 (1.00) |
0.000269 (0.209) |
0.000277 (0.215) |
0.00598 (1.00) |
0.0253 (1.00) |
1 (1.00) |
0.687 (1.00) |
0.772 (1.00) |
3q gain | 86 (17%) | 407 |
0.0797 (1.00) |
0.14 (1.00) |
0.00142 (1.00) |
0.146 (1.00) |
0.0265 (1.00) |
0.106 (1.00) |
3.11e-05 (0.0254) |
1.52e-05 (0.0128) |
0.0156 (1.00) |
0.0323 (1.00) |
0.00949 (1.00) |
0.0233 (1.00) |
6p gain | 141 (29%) | 352 |
0.354 (1.00) |
0.0645 (1.00) |
1.59e-05 (0.0134) |
1.94e-06 (0.00171) |
0.0296 (1.00) |
0.742 (1.00) |
0.0965 (1.00) |
0.578 (1.00) |
0.0267 (1.00) |
0.00801 (1.00) |
0.0667 (1.00) |
0.00237 (1.00) |
17p gain | 83 (17%) | 410 |
0.453 (1.00) |
0.411 (1.00) |
6.17e-05 (0.0496) |
0.0911 (1.00) |
0.831 (1.00) |
0.0817 (1.00) |
0.00996 (1.00) |
0.00287 (1.00) |
1.05e-05 (0.00893) |
0.00111 (0.807) |
0.227 (1.00) |
0.0588 (1.00) |
10p loss | 108 (22%) | 385 |
0.816 (1.00) |
0.416 (1.00) |
7.13e-07 (0.000636) |
0.184 (1.00) |
0.0394 (1.00) |
0.0123 (1.00) |
7.29e-05 (0.0584) |
0.0269 (1.00) |
0.00376 (1.00) |
0.0508 (1.00) |
0.00188 (1.00) |
0.0359 (1.00) |
11p loss | 108 (22%) | 385 |
0.144 (1.00) |
0.0799 (1.00) |
7.93e-05 (0.0633) |
0.0147 (1.00) |
0.0356 (1.00) |
0.283 (1.00) |
0.00383 (1.00) |
1.64e-05 (0.0137) |
0.0265 (1.00) |
0.0158 (1.00) |
0.027 (1.00) |
0.0197 (1.00) |
17p loss | 206 (42%) | 287 |
0.549 (1.00) |
0.59 (1.00) |
2.17e-11 (2.03e-08) |
0.00013 (0.102) |
0.132 (1.00) |
0.00627 (1.00) |
0.000942 (0.688) |
0.000625 (0.468) |
0.5 (1.00) |
0.478 (1.00) |
0.606 (1.00) |
0.303 (1.00) |
1p gain | 133 (27%) | 360 |
0.388 (1.00) |
1 (1.00) |
1.26e-08 (1.16e-05) |
0.312 (1.00) |
0.0729 (1.00) |
0.00459 (1.00) |
0.117 (1.00) |
0.00259 (1.00) |
0.073 (1.00) |
0.987 (1.00) |
0.313 (1.00) |
0.654 (1.00) |
2q gain | 135 (27%) | 358 |
0.126 (1.00) |
0.302 (1.00) |
7.89e-06 (0.00678) |
0.0013 (0.926) |
0.694 (1.00) |
0.749 (1.00) |
0.0765 (1.00) |
0.000987 (0.72) |
0.00178 (1.00) |
0.00147 (1.00) |
0.0281 (1.00) |
0.000597 (0.448) |
4p gain | 80 (16%) | 413 |
0.876 (1.00) |
0.869 (1.00) |
1.24e-05 (0.0105) |
0.035 (1.00) |
0.301 (1.00) |
0.0908 (1.00) |
0.0446 (1.00) |
0.0148 (1.00) |
0.088 (1.00) |
0.173 (1.00) |
0.434 (1.00) |
0.284 (1.00) |
5p gain | 267 (54%) | 226 |
0.798 (1.00) |
0.59 (1.00) |
6.75e-11 (6.31e-08) |
0.777 (1.00) |
0.16 (1.00) |
0.571 (1.00) |
0.0236 (1.00) |
0.0322 (1.00) |
0.0446 (1.00) |
0.116 (1.00) |
0.0911 (1.00) |
0.0375 (1.00) |
6q gain | 60 (12%) | 433 |
1 (1.00) |
1 (1.00) |
0.0131 (1.00) |
0.00679 (1.00) |
0.164 (1.00) |
0.944 (1.00) |
0.201 (1.00) |
0.137 (1.00) |
0.00203 (1.00) |
0.000105 (0.0831) |
0.282 (1.00) |
0.00191 (1.00) |
8p gain | 123 (25%) | 370 |
0.151 (1.00) |
0.176 (1.00) |
2.15e-10 (2e-07) |
0.0533 (1.00) |
0.436 (1.00) |
0.376 (1.00) |
0.00126 (0.906) |
0.00674 (1.00) |
0.455 (1.00) |
0.35 (1.00) |
0.842 (1.00) |
0.784 (1.00) |
11p gain | 92 (19%) | 401 |
0.00952 (1.00) |
0.00906 (1.00) |
1.62e-05 (0.0136) |
0.607 (1.00) |
0.545 (1.00) |
0.468 (1.00) |
0.188 (1.00) |
0.0161 (1.00) |
0.000441 (0.335) |
0.000533 (0.403) |
0.000523 (0.395) |
0.00109 (0.789) |
15q gain | 35 (7%) | 458 |
0.192 (1.00) |
0.157 (1.00) |
0.384 (1.00) |
0.343 (1.00) |
0.561 (1.00) |
0.326 (1.00) |
6.84e-09 (6.31e-06) |
0.000513 (0.388) |
0.773 (1.00) |
0.806 (1.00) |
0.194 (1.00) |
0.691 (1.00) |
21q gain | 94 (19%) | 399 |
0.538 (1.00) |
0.466 (1.00) |
5.78e-05 (0.0466) |
0.984 (1.00) |
0.331 (1.00) |
0.0638 (1.00) |
0.0276 (1.00) |
0.13 (1.00) |
0.335 (1.00) |
0.657 (1.00) |
0.639 (1.00) |
0.734 (1.00) |
5p loss | 40 (8%) | 453 |
0.595 (1.00) |
0.453 (1.00) |
0.676 (1.00) |
0.0182 (1.00) |
0.388 (1.00) |
0.287 (1.00) |
0.0289 (1.00) |
2.91e-05 (0.0238) |
0.0711 (1.00) |
0.0641 (1.00) |
0.0169 (1.00) |
0.00112 (0.813) |
6q loss | 208 (42%) | 285 |
0.247 (1.00) |
0.32 (1.00) |
0.0299 (1.00) |
8.96e-05 (0.0711) |
0.813 (1.00) |
0.538 (1.00) |
0.0809 (1.00) |
0.0899 (1.00) |
0.338 (1.00) |
0.0423 (1.00) |
0.726 (1.00) |
0.101 (1.00) |
7p loss | 33 (7%) | 460 |
1 (1.00) |
1 (1.00) |
1.61e-05 (0.0135) |
0.0367 (1.00) |
0.33 (1.00) |
0.713 (1.00) |
0.00529 (1.00) |
0.0184 (1.00) |
0.279 (1.00) |
0.366 (1.00) |
0.867 (1.00) |
0.23 (1.00) |
8q loss | 54 (11%) | 439 |
0.000278 (0.215) |
0.53 (1.00) |
0.293 (1.00) |
0.375 (1.00) |
0.153 (1.00) |
0.133 (1.00) |
0.213 (1.00) |
0.739 (1.00) |
0.412 (1.00) |
0.651 (1.00) |
||
9p loss | 254 (52%) | 239 |
0.0516 (1.00) |
0.465 (1.00) |
0.00182 (1.00) |
0.0411 (1.00) |
0.215 (1.00) |
0.0638 (1.00) |
0.00122 (0.877) |
0.000154 (0.121) |
0.0628 (1.00) |
0.0632 (1.00) |
0.352 (1.00) |
0.0889 (1.00) |
10q loss | 128 (26%) | 365 |
0.816 (1.00) |
0.416 (1.00) |
1.95e-05 (0.0161) |
0.0642 (1.00) |
0.0543 (1.00) |
0.0131 (1.00) |
0.00135 (0.962) |
0.0662 (1.00) |
0.00521 (1.00) |
0.00683 (1.00) |
0.00129 (0.924) |
0.000852 (0.626) |
12q loss | 93 (19%) | 400 |
0.554 (1.00) |
0.418 (1.00) |
1.52e-05 (0.0128) |
0.0817 (1.00) |
0.0947 (1.00) |
0.0175 (1.00) |
0.00126 (0.902) |
0.0105 (1.00) |
0.202 (1.00) |
0.107 (1.00) |
0.555 (1.00) |
0.361 (1.00) |
17q loss | 55 (11%) | 438 |
0.294 (1.00) |
0.546 (1.00) |
0.000114 (0.0899) |
0.0486 (1.00) |
0.0109 (1.00) |
0.00762 (1.00) |
0.129 (1.00) |
0.123 (1.00) |
0.422 (1.00) |
0.16 (1.00) |
0.0822 (1.00) |
0.782 (1.00) |
18p loss | 169 (34%) | 324 |
0.438 (1.00) |
0.631 (1.00) |
1.31e-05 (0.0112) |
0.75 (1.00) |
0.0371 (1.00) |
0.00211 (1.00) |
0.022 (1.00) |
0.00467 (1.00) |
0.0288 (1.00) |
0.694 (1.00) |
0.144 (1.00) |
0.79 (1.00) |
1q gain | 297 (60%) | 196 |
0.121 (1.00) |
1 (1.00) |
0.00169 (1.00) |
0.00125 (0.897) |
0.000756 (0.56) |
0.0208 (1.00) |
0.128 (1.00) |
0.918 (1.00) |
0.518 (1.00) |
0.145 (1.00) |
0.0149 (1.00) |
0.126 (1.00) |
3p gain | 40 (8%) | 453 |
0.0036 (1.00) |
0.0137 (1.00) |
0.108 (1.00) |
0.137 (1.00) |
0.000403 (0.307) |
0.00112 (0.813) |
0.063 (1.00) |
0.181 (1.00) |
0.163 (1.00) |
0.0564 (1.00) |
||
4q gain | 46 (9%) | 447 |
0.329 (1.00) |
0.505 (1.00) |
0.0108 (1.00) |
0.901 (1.00) |
0.399 (1.00) |
0.392 (1.00) |
0.00442 (1.00) |
0.0284 (1.00) |
0.0166 (1.00) |
0.237 (1.00) |
0.16 (1.00) |
0.289 (1.00) |
5q gain | 124 (25%) | 369 |
0.195 (1.00) |
0.453 (1.00) |
0.00558 (1.00) |
0.549 (1.00) |
0.0283 (1.00) |
0.365 (1.00) |
0.00585 (1.00) |
0.0774 (1.00) |
0.146 (1.00) |
0.0135 (1.00) |
0.0362 (1.00) |
0.0592 (1.00) |
9p gain | 42 (9%) | 451 |
0.0143 (1.00) |
0.104 (1.00) |
0.449 (1.00) |
0.45 (1.00) |
0.000998 (0.727) |
0.619 (1.00) |
0.205 (1.00) |
0.648 (1.00) |
0.204 (1.00) |
0.211 (1.00) |
||
9q gain | 30 (6%) | 463 |
0.252 (1.00) |
0.297 (1.00) |
0.572 (1.00) |
0.566 (1.00) |
0.0783 (1.00) |
0.782 (1.00) |
0.494 (1.00) |
0.724 (1.00) |
0.442 (1.00) |
0.255 (1.00) |
||
10q gain | 76 (15%) | 417 |
0.0378 (1.00) |
0.00149 (1.00) |
0.286 (1.00) |
0.0902 (1.00) |
0.000334 (0.257) |
0.0169 (1.00) |
0.372 (1.00) |
0.0827 (1.00) |
0.214 (1.00) |
0.679 (1.00) |
||
13q gain | 43 (9%) | 450 |
0.414 (1.00) |
0.466 (1.00) |
0.736 (1.00) |
0.00258 (1.00) |
0.0486 (1.00) |
0.0577 (1.00) |
0.0513 (1.00) |
0.0854 (1.00) |
0.978 (1.00) |
0.866 (1.00) |
0.81 (1.00) |
0.805 (1.00) |
16p gain | 127 (26%) | 366 |
0.532 (1.00) |
0.235 (1.00) |
0.00312 (1.00) |
1 (1.00) |
0.298 (1.00) |
0.15 (1.00) |
0.178 (1.00) |
0.189 (1.00) |
0.00996 (1.00) |
0.00868 (1.00) |
0.0489 (1.00) |
0.444 (1.00) |
16q gain | 94 (19%) | 399 |
0.437 (1.00) |
0.27 (1.00) |
0.00256 (1.00) |
0.939 (1.00) |
0.0693 (1.00) |
0.0729 (1.00) |
0.426 (1.00) |
0.783 (1.00) |
0.00198 (1.00) |
0.00214 (1.00) |
0.0209 (1.00) |
0.775 (1.00) |
19p gain | 32 (6%) | 461 |
0.192 (1.00) |
0.0514 (1.00) |
0.188 (1.00) |
0.318 (1.00) |
1 (1.00) |
0.791 (1.00) |
0.987 (1.00) |
0.617 (1.00) |
0.44 (1.00) |
0.63 (1.00) |
0.0219 (1.00) |
0.266 (1.00) |
19q gain | 71 (14%) | 422 |
0.0502 (1.00) |
0.0514 (1.00) |
0.00296 (1.00) |
0.00659 (1.00) |
0.946 (1.00) |
0.695 (1.00) |
0.168 (1.00) |
0.0138 (1.00) |
0.382 (1.00) |
0.041 (1.00) |
0.0721 (1.00) |
0.0499 (1.00) |
22q gain | 61 (12%) | 432 |
0.108 (1.00) |
0.132 (1.00) |
0.00348 (1.00) |
0.785 (1.00) |
0.215 (1.00) |
0.191 (1.00) |
0.163 (1.00) |
0.0546 (1.00) |
0.6 (1.00) |
0.758 (1.00) |
0.462 (1.00) |
0.509 (1.00) |
xq gain | 68 (14%) | 425 |
0.658 (1.00) |
0.505 (1.00) |
0.00071 (0.526) |
0.26 (1.00) |
0.274 (1.00) |
0.116 (1.00) |
0.0346 (1.00) |
0.336 (1.00) |
0.114 (1.00) |
0.318 (1.00) |
0.221 (1.00) |
0.474 (1.00) |
1q loss | 28 (6%) | 465 |
0.179 (1.00) |
0.00395 (1.00) |
0.179 (1.00) |
0.463 (1.00) |
0.0696 (1.00) |
0.0121 (1.00) |
0.694 (1.00) |
0.363 (1.00) |
0.294 (1.00) |
0.0763 (1.00) |
||
2p loss | 24 (5%) | 469 |
0.75 (1.00) |
0.591 (1.00) |
0.123 (1.00) |
0.19 (1.00) |
0.611 (1.00) |
1 (1.00) |
0.978 (1.00) |
0.771 (1.00) |
0.0865 (1.00) |
0.133 (1.00) |
0.0686 (1.00) |
0.491 (1.00) |
2q loss | 23 (5%) | 470 |
0.00167 (1.00) |
0.00388 (1.00) |
0.426 (1.00) |
1 (1.00) |
0.268 (1.00) |
0.475 (1.00) |
0.32 (1.00) |
0.144 (1.00) |
0.453 (1.00) |
0.26 (1.00) |
||
3q loss | 140 (28%) | 353 |
0.552 (1.00) |
0.191 (1.00) |
0.0146 (1.00) |
0.000546 (0.41) |
0.916 (1.00) |
0.845 (1.00) |
0.0647 (1.00) |
0.168 (1.00) |
0.674 (1.00) |
0.923 (1.00) |
0.845 (1.00) |
0.647 (1.00) |
6p loss | 101 (20%) | 392 |
0.0126 (1.00) |
0.00838 (1.00) |
0.0538 (1.00) |
0.388 (1.00) |
0.528 (1.00) |
0.58 (1.00) |
0.187 (1.00) |
0.292 (1.00) |
0.538 (1.00) |
0.252 (1.00) |
0.506 (1.00) |
0.403 (1.00) |
7q loss | 39 (8%) | 454 |
0.803 (1.00) |
0.176 (1.00) |
0.00708 (1.00) |
0.291 (1.00) |
0.91 (1.00) |
0.463 (1.00) |
0.0859 (1.00) |
0.291 (1.00) |
0.355 (1.00) |
0.349 (1.00) |
0.269 (1.00) |
0.46 (1.00) |
11q loss | 88 (18%) | 405 |
0.841 (1.00) |
0.411 (1.00) |
0.007 (1.00) |
0.0108 (1.00) |
0.00359 (1.00) |
0.513 (1.00) |
0.00146 (1.00) |
0.000378 (0.288) |
0.0559 (1.00) |
0.026 (1.00) |
0.0285 (1.00) |
0.0273 (1.00) |
12p loss | 106 (22%) | 387 |
0.63 (1.00) |
0.77 (1.00) |
0.00573 (1.00) |
0.357 (1.00) |
0.0473 (1.00) |
0.0982 (1.00) |
0.0065 (1.00) |
0.0576 (1.00) |
0.264 (1.00) |
0.329 (1.00) |
0.607 (1.00) |
0.521 (1.00) |
14q loss | 111 (23%) | 382 |
0.929 (1.00) |
0.466 (1.00) |
0.061 (1.00) |
0.363 (1.00) |
0.171 (1.00) |
0.0602 (1.00) |
0.0217 (1.00) |
0.00162 (1.00) |
0.074 (1.00) |
0.0345 (1.00) |
0.000756 (0.56) |
0.0361 (1.00) |
20p loss | 114 (23%) | 379 |
0.333 (1.00) |
0.631 (1.00) |
0.00036 (0.275) |
0.00384 (1.00) |
0.000631 (0.471) |
0.00272 (1.00) |
0.016 (1.00) |
0.0494 (1.00) |
0.965 (1.00) |
0.95 (1.00) |
0.126 (1.00) |
0.839 (1.00) |
20q loss | 67 (14%) | 426 |
0.513 (1.00) |
0.882 (1.00) |
0.408 (1.00) |
0.614 (1.00) |
0.262 (1.00) |
0.894 (1.00) |
0.625 (1.00) |
0.979 (1.00) |
0.599 (1.00) |
0.896 (1.00) |
0.132 (1.00) |
0.933 (1.00) |
xq loss | 64 (13%) | 429 |
0.276 (1.00) |
0.0398 (1.00) |
0.000824 (0.607) |
0.00294 (1.00) |
0.455 (1.00) |
0.363 (1.00) |
0.44 (1.00) |
0.221 (1.00) |
0.346 (1.00) |
0.252 (1.00) |
0.506 (1.00) |
0.338 (1.00) |
P value = 1.26e-08 (Fisher's exact test), Q value = 1.2e-05
Table S1. Gene #1: '1p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
1P GAIN MUTATED | 79 | 35 | 19 |
1P GAIN WILD-TYPE | 107 | 181 | 72 |
Figure S1. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D1V3.png)
P value = 3.86e-08 (Fisher's exact test), Q value = 3.5e-05
Table S2. Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
2P GAIN MUTATED | 74 | 36 | 38 |
2P GAIN WILD-TYPE | 112 | 180 | 53 |
Figure S2. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D3V3.png)
P value = 8.92e-05 (Chi-square test), Q value = 0.071
Table S3. Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
2P GAIN MUTATED | 40 | 18 | 25 | 49 | 16 |
2P GAIN WILD-TYPE | 98 | 94 | 51 | 57 | 38 |
Figure S3. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D3V7.png)
P value = 5.18e-06 (Fisher's exact test), Q value = 0.0045
Table S4. Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 119 | 211 | 156 |
2P GAIN MUTATED | 34 | 44 | 70 |
2P GAIN WILD-TYPE | 85 | 167 | 86 |
Figure S4. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D3V8.png)
P value = 1.1e-06 (Fisher's exact test), Q value = 0.00097
Table S5. Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 179 | 231 | 78 |
2P GAIN MUTATED | 37 | 96 | 14 |
2P GAIN WILD-TYPE | 142 | 135 | 64 |
Figure S5. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D3V9.png)
P value = 7.36e-06 (Fisher's exact test), Q value = 0.0063
Table S6. Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 51 | 249 | 188 |
2P GAIN MUTATED | 6 | 98 | 43 |
2P GAIN WILD-TYPE | 45 | 151 | 145 |
Figure S6. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D3V10.png)
P value = 6.12e-05 (Fisher's exact test), Q value = 0.049
Table S7. Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 188 | 188 |
2P GAIN MUTATED | 10 | 75 | 38 |
2P GAIN WILD-TYPE | 39 | 113 | 150 |
Figure S7. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
![](D3V12.png)
P value = 7.89e-06 (Fisher's exact test), Q value = 0.0068
Table S8. Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
2Q GAIN MUTATED | 60 | 37 | 38 |
2Q GAIN WILD-TYPE | 126 | 179 | 53 |
Figure S8. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D4V3.png)
P value = 3.11e-05 (Chi-square test), Q value = 0.025
Table S9. Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
3Q GAIN MUTATED | 34 | 2 | 16 | 23 | 10 |
3Q GAIN WILD-TYPE | 104 | 110 | 60 | 83 | 44 |
Figure S9. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D6V7.png)
P value = 1.52e-05 (Fisher's exact test), Q value = 0.013
Table S10. Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 119 | 211 | 156 |
3Q GAIN MUTATED | 29 | 18 | 38 |
3Q GAIN WILD-TYPE | 90 | 193 | 118 |
Figure S10. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D6V8.png)
P value = 1.24e-05 (Fisher's exact test), Q value = 0.011
Table S11. Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
4P GAIN MUTATED | 48 | 18 | 14 |
4P GAIN WILD-TYPE | 138 | 198 | 77 |
Figure S11. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D7V3.png)
P value = 6.75e-11 (Fisher's exact test), Q value = 6.3e-08
Table S12. Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
5P GAIN MUTATED | 135 | 84 | 48 |
5P GAIN WILD-TYPE | 51 | 132 | 43 |
Figure S12. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D9V3.png)
P value = 1.59e-05 (Fisher's exact test), Q value = 0.013
Table S13. Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
6P GAIN MUTATED | 62 | 40 | 39 |
6P GAIN WILD-TYPE | 124 | 176 | 52 |
Figure S13. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D11V3.png)
P value = 1.94e-06 (Fisher's exact test), Q value = 0.0017
Table S14. Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 141 | 140 | 150 |
6P GAIN MUTATED | 56 | 44 | 21 |
6P GAIN WILD-TYPE | 85 | 96 | 129 |
Figure S14. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D11V4.png)
P value = 0.000105 (Fisher's exact test), Q value = 0.083
Table S15. Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 51 | 249 | 188 |
6Q GAIN MUTATED | 6 | 44 | 9 |
6Q GAIN WILD-TYPE | 45 | 205 | 179 |
Figure S15. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D12V10.png)
P value = 1.34e-20 (Fisher's exact test), Q value = 1.3e-17
Table S16. Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
7P GAIN MUTATED | 145 | 72 | 34 |
7P GAIN WILD-TYPE | 41 | 144 | 57 |
Figure S16. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D13V3.png)
P value = 2.78e-11 (Chi-square test), Q value = 2.6e-08
Table S17. Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
7P GAIN MUTATED | 103 | 32 | 38 | 47 | 27 |
7P GAIN WILD-TYPE | 35 | 80 | 38 | 59 | 27 |
Figure S17. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D13V7.png)
P value = 1.01e-11 (Fisher's exact test), Q value = 9.5e-09
Table S18. Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 119 | 211 | 156 |
7P GAIN MUTATED | 92 | 79 | 76 |
7P GAIN WILD-TYPE | 27 | 132 | 80 |
Figure S18. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D13V8.png)
P value = 4.23e-06 (Fisher's exact test), Q value = 0.0037
Table S19. Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 179 | 231 | 78 |
7P GAIN MUTATED | 66 | 130 | 52 |
7P GAIN WILD-TYPE | 113 | 101 | 26 |
Figure S19. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D13V9.png)
P value = 0.00032 (Fisher's exact test), Q value = 0.25
Table S20. Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 155 | 192 | 78 |
7P GAIN MUTATED | 59 | 106 | 49 |
7P GAIN WILD-TYPE | 96 | 86 | 29 |
Figure S20. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
![](D13V11.png)
P value = 1.66e-05 (Fisher's exact test), Q value = 0.014
Table S21. Gene #13: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 188 | 188 |
7P GAIN MUTATED | 34 | 108 | 72 |
7P GAIN WILD-TYPE | 15 | 80 | 116 |
Figure S21. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
![](D13V12.png)
P value = 9.72e-11 (Fisher's exact test), Q value = 9.1e-08
Table S22. Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
7Q GAIN MUTATED | 114 | 63 | 30 |
7Q GAIN WILD-TYPE | 72 | 153 | 61 |
Figure S22. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D14V3.png)
P value = 5.7e-09 (Chi-square test), Q value = 5.3e-06
Table S23. Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
7Q GAIN MUTATED | 87 | 27 | 33 | 34 | 22 |
7Q GAIN WILD-TYPE | 51 | 85 | 43 | 72 | 32 |
Figure S23. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D14V7.png)
P value = 1.21e-08 (Fisher's exact test), Q value = 1.1e-05
Table S24. Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 119 | 211 | 156 |
7Q GAIN MUTATED | 77 | 65 | 61 |
7Q GAIN WILD-TYPE | 42 | 146 | 95 |
Figure S24. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D14V8.png)
P value = 2.15e-10 (Fisher's exact test), Q value = 2e-07
Table S25. Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
8P GAIN MUTATED | 33 | 41 | 49 |
8P GAIN WILD-TYPE | 153 | 175 | 42 |
Figure S25. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D15V3.png)
P value = 2.34e-20 (Fisher's exact test), Q value = 2.2e-17
Table S26. Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
8Q GAIN MUTATED | 92 | 64 | 79 |
8Q GAIN WILD-TYPE | 94 | 152 | 12 |
Figure S26. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D16V3.png)
P value = 1.34e-05 (Fisher's exact test), Q value = 0.011
Table S27. Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 141 | 140 | 150 |
8Q GAIN MUTATED | 82 | 76 | 49 |
8Q GAIN WILD-TYPE | 59 | 64 | 101 |
Figure S27. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D16V4.png)
P value = 9.18e-08 (Chi-square test), Q value = 8.3e-05
Table S28. Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
8Q GAIN MUTATED | 68 | 33 | 32 | 74 | 21 |
8Q GAIN WILD-TYPE | 70 | 79 | 44 | 32 | 33 |
Figure S28. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D16V7.png)
P value = 1.93e-05 (Fisher's exact test), Q value = 0.016
Table S29. Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 119 | 211 | 156 |
8Q GAIN MUTATED | 60 | 75 | 93 |
8Q GAIN WILD-TYPE | 59 | 136 | 63 |
Figure S29. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D16V8.png)
P value = 4.24e-06 (Fisher's exact test), Q value = 0.0037
Table S30. Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 179 | 231 | 78 |
8Q GAIN MUTATED | 60 | 134 | 39 |
8Q GAIN WILD-TYPE | 119 | 97 | 39 |
Figure S30. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D16V9.png)
P value = 2.41e-05 (Fisher's exact test), Q value = 0.02
Table S31. Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 51 | 249 | 188 |
8Q GAIN MUTATED | 21 | 144 | 68 |
8Q GAIN WILD-TYPE | 30 | 105 | 120 |
Figure S31. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D16V10.png)
P value = 0.000199 (Fisher's exact test), Q value = 0.16
Table S32. Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 155 | 192 | 78 |
8Q GAIN MUTATED | 56 | 112 | 37 |
8Q GAIN WILD-TYPE | 99 | 80 | 41 |
Figure S32. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
![](D16V11.png)
P value = 1.13e-05 (Fisher's exact test), Q value = 0.0096
Table S33. Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 188 | 188 |
8Q GAIN MUTATED | 23 | 114 | 68 |
8Q GAIN WILD-TYPE | 26 | 74 | 120 |
Figure S33. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
![](D16V12.png)
P value = 1.26e-05 (Fisher's exact test), Q value = 0.011
Table S34. Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 141 | 140 | 150 |
10P GAIN MUTATED | 38 | 41 | 14 |
10P GAIN WILD-TYPE | 103 | 99 | 136 |
Figure S34. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D19V4.png)
P value = 7.64e-05 (Chi-square test), Q value = 0.061
Table S35. Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
10P GAIN MUTATED | 27 | 10 | 20 | 37 | 9 |
10P GAIN WILD-TYPE | 111 | 102 | 56 | 69 | 45 |
Figure S35. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D19V7.png)
P value = 1.52e-05 (Fisher's exact test), Q value = 0.013
Table S36. Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 119 | 211 | 156 |
10P GAIN MUTATED | 21 | 29 | 53 |
10P GAIN WILD-TYPE | 98 | 182 | 103 |
Figure S36. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D19V8.png)
P value = 1.62e-05 (Fisher's exact test), Q value = 0.014
Table S37. Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
11P GAIN MUTATED | 45 | 21 | 26 |
11P GAIN WILD-TYPE | 141 | 195 | 65 |
Figure S37. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D21V3.png)
P value = 2.8e-08 (Fisher's exact test), Q value = 2.6e-05
Table S38. Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
11Q GAIN MUTATED | 63 | 23 | 26 |
11Q GAIN WILD-TYPE | 123 | 193 | 65 |
Figure S38. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D22V3.png)
P value = 0.000194 (Fisher's exact test), Q value = 0.15
Table S39. Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 119 | 211 | 156 |
11Q GAIN MUTATED | 35 | 30 | 47 |
11Q GAIN WILD-TYPE | 84 | 181 | 109 |
Figure S39. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D22V8.png)
P value = 5.15e-05 (Fisher's exact test), Q value = 0.042
Table S40. Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 179 | 231 | 78 |
11Q GAIN MUTATED | 21 | 65 | 23 |
11Q GAIN WILD-TYPE | 158 | 166 | 55 |
Figure S40. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D22V9.png)
P value = 8.66e-05 (Fisher's exact test), Q value = 0.069
Table S41. Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 51 | 249 | 188 |
11Q GAIN MUTATED | 18 | 67 | 24 |
11Q GAIN WILD-TYPE | 33 | 182 | 164 |
Figure S41. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D22V10.png)
P value = 0.000317 (Fisher's exact test), Q value = 0.24
Table S42. Gene #22: '11q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 155 | 192 | 78 |
11Q GAIN MUTATED | 19 | 51 | 25 |
11Q GAIN WILD-TYPE | 136 | 141 | 53 |
Figure S42. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
![](D22V11.png)
P value = 1.06e-06 (Fisher's exact test), Q value = 0.00094
Table S43. Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
12P GAIN MUTATED | 50 | 38 | 43 |
12P GAIN WILD-TYPE | 136 | 178 | 48 |
Figure S43. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D23V3.png)
P value = 4.46e-09 (Chi-square test), Q value = 4.1e-06
Table S44. Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
12P GAIN MUTATED | 40 | 5 | 30 | 42 | 12 |
12P GAIN WILD-TYPE | 98 | 107 | 46 | 64 | 42 |
Figure S44. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D23V7.png)
P value = 4.3e-11 (Fisher's exact test), Q value = 4e-08
Table S45. Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 119 | 211 | 156 |
12P GAIN MUTATED | 30 | 28 | 71 |
12P GAIN WILD-TYPE | 89 | 183 | 85 |
Figure S45. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D23V8.png)
P value = 1.46e-05 (Fisher's exact test), Q value = 0.012
Table S46. Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 179 | 231 | 78 |
12P GAIN MUTATED | 28 | 83 | 18 |
12P GAIN WILD-TYPE | 151 | 148 | 60 |
Figure S46. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D23V9.png)
P value = 1.81e-05 (Fisher's exact test), Q value = 0.015
Table S47. Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 51 | 249 | 188 |
12P GAIN MUTATED | 11 | 88 | 30 |
12P GAIN WILD-TYPE | 40 | 161 | 158 |
Figure S47. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D23V10.png)
P value = 6.62e-08 (Fisher's exact test), Q value = 6e-05
Table S48. Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 155 | 192 | 78 |
12P GAIN MUTATED | 18 | 73 | 23 |
12P GAIN WILD-TYPE | 137 | 119 | 55 |
Figure S48. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
![](D23V11.png)
P value = 4.9e-08 (Fisher's exact test), Q value = 4.5e-05
Table S49. Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 188 | 188 |
12P GAIN MUTATED | 13 | 75 | 26 |
12P GAIN WILD-TYPE | 36 | 113 | 162 |
Figure S49. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
![](D23V12.png)
P value = 3.78e-08 (Fisher's exact test), Q value = 3.5e-05
Table S50. Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
12Q GAIN MUTATED | 41 | 39 | 46 |
12Q GAIN WILD-TYPE | 145 | 177 | 45 |
Figure S50. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D24V3.png)
P value = 1.14e-11 (Chi-square test), Q value = 1.1e-08
Table S51. Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
12Q GAIN MUTATED | 31 | 6 | 29 | 49 | 9 |
12Q GAIN WILD-TYPE | 107 | 106 | 47 | 57 | 45 |
Figure S51. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D24V7.png)
P value = 5.74e-12 (Fisher's exact test), Q value = 5.4e-09
Table S52. Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 119 | 211 | 156 |
12Q GAIN MUTATED | 27 | 26 | 71 |
12Q GAIN WILD-TYPE | 92 | 185 | 85 |
Figure S52. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D24V8.png)
P value = 1.19e-05 (Fisher's exact test), Q value = 0.01
Table S53. Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 179 | 231 | 78 |
12Q GAIN MUTATED | 27 | 81 | 16 |
12Q GAIN WILD-TYPE | 152 | 150 | 62 |
Figure S53. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D24V9.png)
P value = 3.13e-06 (Fisher's exact test), Q value = 0.0027
Table S54. Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 51 | 249 | 188 |
12Q GAIN MUTATED | 12 | 86 | 26 |
12Q GAIN WILD-TYPE | 39 | 163 | 162 |
Figure S54. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D24V10.png)
P value = 2.22e-07 (Fisher's exact test), Q value = 2e-04
Table S55. Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 155 | 192 | 78 |
12Q GAIN MUTATED | 17 | 68 | 24 |
12Q GAIN WILD-TYPE | 138 | 124 | 54 |
Figure S55. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
![](D24V11.png)
P value = 6.19e-07 (Fisher's exact test), Q value = 0.00055
Table S56. Gene #24: '12q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 188 | 188 |
12Q GAIN MUTATED | 16 | 68 | 25 |
12Q GAIN WILD-TYPE | 33 | 120 | 163 |
Figure S56. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
![](D24V12.png)
P value = 9.11e-09 (Fisher's exact test), Q value = 8.4e-06
Table S57. Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
14Q GAIN MUTATED | 47 | 30 | 43 |
14Q GAIN WILD-TYPE | 139 | 186 | 48 |
Figure S57. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D26V3.png)
P value = 7.43e-05 (Chi-square test), Q value = 0.059
Table S58. Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
14Q GAIN MUTATED | 37 | 19 | 9 | 42 | 11 |
14Q GAIN WILD-TYPE | 101 | 93 | 67 | 64 | 43 |
Figure S58. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D26V7.png)
P value = 3.2e-05 (Fisher's exact test), Q value = 0.026
Table S59. Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 179 | 231 | 78 |
14Q GAIN MUTATED | 23 | 69 | 25 |
14Q GAIN WILD-TYPE | 156 | 162 | 53 |
Figure S59. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D26V9.png)
P value = 2.67e-05 (Fisher's exact test), Q value = 0.022
Table S60. Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 51 | 249 | 188 |
14Q GAIN MUTATED | 18 | 74 | 25 |
14Q GAIN WILD-TYPE | 33 | 175 | 163 |
Figure S60. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D26V10.png)
P value = 6.84e-09 (Chi-square test), Q value = 6.3e-06
Table S61. Gene #27: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
15Q GAIN MUTATED | 3 | 5 | 19 | 6 | 2 |
15Q GAIN WILD-TYPE | 135 | 107 | 57 | 100 | 52 |
Figure S61. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D27V7.png)
P value = 6.17e-05 (Fisher's exact test), Q value = 0.05
Table S62. Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
17P GAIN MUTATED | 28 | 25 | 30 |
17P GAIN WILD-TYPE | 158 | 191 | 61 |
Figure S62. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D30V3.png)
P value = 1.05e-05 (Fisher's exact test), Q value = 0.0089
Table S63. Gene #30: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 179 | 231 | 78 |
17P GAIN MUTATED | 16 | 58 | 7 |
17P GAIN WILD-TYPE | 163 | 173 | 71 |
Figure S63. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D30V9.png)
P value = 1.72e-08 (Fisher's exact test), Q value = 1.6e-05
Table S64. Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
17Q GAIN MUTATED | 91 | 50 | 45 |
17Q GAIN WILD-TYPE | 95 | 166 | 46 |
Figure S64. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D31V3.png)
P value = 4.29e-05 (Chi-square test), Q value = 0.035
Table S65. Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
17Q GAIN MUTATED | 72 | 28 | 20 | 44 | 18 |
17Q GAIN WILD-TYPE | 66 | 84 | 56 | 62 | 36 |
Figure S65. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D31V7.png)
P value = 6.2e-06 (Fisher's exact test), Q value = 0.0054
Table S66. Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 119 | 211 | 156 |
17Q GAIN MUTATED | 62 | 55 | 65 |
17Q GAIN WILD-TYPE | 57 | 156 | 91 |
Figure S66. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D31V8.png)
P value = 8.91e-06 (Fisher's exact test), Q value = 0.0076
Table S67. Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 179 | 231 | 78 |
17Q GAIN MUTATED | 46 | 112 | 26 |
17Q GAIN WILD-TYPE | 133 | 119 | 52 |
Figure S67. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D31V9.png)
P value = 3.35e-05 (Fisher's exact test), Q value = 0.027
Table S68. Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
18P GAIN MUTATED | 47 | 21 | 23 |
18P GAIN WILD-TYPE | 139 | 195 | 68 |
Figure S68. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D32V3.png)
P value = 2.4e-05 (Fisher's exact test), Q value = 0.02
Table S69. Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 141 | 140 | 150 |
18P GAIN MUTATED | 40 | 27 | 12 |
18P GAIN WILD-TYPE | 101 | 113 | 138 |
Figure S69. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D32V4.png)
P value = 2.67e-05 (Fisher's exact test), Q value = 0.022
Table S70. Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 188 | 188 |
18P GAIN MUTATED | 7 | 53 | 19 |
18P GAIN WILD-TYPE | 42 | 135 | 169 |
Figure S70. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
![](D32V12.png)
P value = 0.000139 (Fisher's exact test), Q value = 0.11
Table S71. Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
18Q GAIN MUTATED | 29 | 15 | 22 |
18Q GAIN WILD-TYPE | 157 | 201 | 69 |
Figure S71. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D33V3.png)
P value = 1.61e-06 (Fisher's exact test), Q value = 0.0014
Table S72. Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 141 | 140 | 150 |
18Q GAIN MUTATED | 34 | 16 | 6 |
18Q GAIN WILD-TYPE | 107 | 124 | 144 |
Figure S72. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D33V4.png)
P value = 1.81e-05 (Chi-square test), Q value = 0.015
Table S73. Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
18Q GAIN MUTATED | 14 | 8 | 9 | 30 | 4 |
18Q GAIN WILD-TYPE | 124 | 104 | 67 | 76 | 50 |
Figure S73. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D33V7.png)
P value = 2.6e-05 (Fisher's exact test), Q value = 0.021
Table S74. Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 119 | 211 | 156 |
18Q GAIN MUTATED | 13 | 15 | 37 |
18Q GAIN WILD-TYPE | 106 | 196 | 119 |
Figure S74. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D33V8.png)
P value = 6.66e-05 (Fisher's exact test), Q value = 0.053
Table S75. Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
20P GAIN MUTATED | 62 | 55 | 47 |
20P GAIN WILD-TYPE | 124 | 161 | 44 |
Figure S75. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D36V3.png)
P value = 0.000214 (Chi-square test), Q value = 0.17
Table S76. Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
20P GAIN MUTATED | 45 | 27 | 24 | 53 | 11 |
20P GAIN WILD-TYPE | 93 | 85 | 52 | 53 | 43 |
Figure S76. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D36V7.png)
P value = 6.56e-06 (Fisher's exact test), Q value = 0.0057
Table S77. Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 119 | 211 | 156 |
20P GAIN MUTATED | 43 | 46 | 71 |
20P GAIN WILD-TYPE | 76 | 165 | 85 |
Figure S77. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D36V8.png)
P value = 2.82e-05 (Fisher's exact test), Q value = 0.023
Table S78. Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 179 | 231 | 78 |
20P GAIN MUTATED | 37 | 92 | 33 |
20P GAIN WILD-TYPE | 142 | 139 | 45 |
Figure S78. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D36V9.png)
P value = 5.4e-06 (Fisher's exact test), Q value = 0.0047
Table S79. Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 51 | 249 | 188 |
20P GAIN MUTATED | 21 | 103 | 38 |
20P GAIN WILD-TYPE | 30 | 146 | 150 |
Figure S79. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D36V10.png)
P value = 0.000189 (Fisher's exact test), Q value = 0.15
Table S80. Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 155 | 192 | 78 |
20P GAIN MUTATED | 33 | 75 | 34 |
20P GAIN WILD-TYPE | 122 | 117 | 44 |
Figure S80. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
![](D36V11.png)
P value = 2.77e-05 (Fisher's exact test), Q value = 0.023
Table S81. Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 188 | 188 |
20P GAIN MUTATED | 21 | 80 | 41 |
20P GAIN WILD-TYPE | 28 | 108 | 147 |
Figure S81. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
![](D36V12.png)
P value = 1.64e-07 (Fisher's exact test), Q value = 0.00015
Table S82. Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
20Q GAIN MUTATED | 80 | 56 | 53 |
20Q GAIN WILD-TYPE | 106 | 160 | 38 |
Figure S82. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D37V3.png)
P value = 4.47e-06 (Chi-square test), Q value = 0.0039
Table S83. Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
20Q GAIN MUTATED | 59 | 24 | 27 | 59 | 16 |
20Q GAIN WILD-TYPE | 79 | 88 | 49 | 47 | 38 |
Figure S83. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D37V7.png)
P value = 3.34e-07 (Fisher's exact test), Q value = 3e-04
Table S84. Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 119 | 211 | 156 |
20Q GAIN MUTATED | 54 | 52 | 79 |
20Q GAIN WILD-TYPE | 65 | 159 | 77 |
Figure S84. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D37V8.png)
P value = 2.04e-06 (Fisher's exact test), Q value = 0.0018
Table S85. Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 179 | 231 | 78 |
20Q GAIN MUTATED | 42 | 109 | 34 |
20Q GAIN WILD-TYPE | 137 | 122 | 44 |
Figure S85. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D37V9.png)
P value = 6.85e-07 (Fisher's exact test), Q value = 0.00061
Table S86. Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 51 | 249 | 188 |
20Q GAIN MUTATED | 23 | 118 | 44 |
20Q GAIN WILD-TYPE | 28 | 131 | 144 |
Figure S86. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D37V10.png)
P value = 1.77e-05 (Fisher's exact test), Q value = 0.015
Table S87. Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 155 | 192 | 78 |
20Q GAIN MUTATED | 38 | 92 | 35 |
20Q GAIN WILD-TYPE | 117 | 100 | 43 |
Figure S87. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
![](D37V11.png)
P value = 1.69e-05 (Fisher's exact test), Q value = 0.014
Table S88. Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 188 | 188 |
20Q GAIN MUTATED | 22 | 93 | 50 |
20Q GAIN WILD-TYPE | 27 | 95 | 138 |
Figure S88. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
![](D37V12.png)
P value = 5.78e-05 (Fisher's exact test), Q value = 0.047
Table S89. Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
21Q GAIN MUTATED | 54 | 31 | 9 |
21Q GAIN WILD-TYPE | 132 | 185 | 82 |
Figure S89. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'
![](D38V3.png)
P value = 1.88e-05 (Fisher's exact test), Q value = 0.016
Table S90. Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
1P LOSS MUTATED | 17 | 33 | 29 |
1P LOSS WILD-TYPE | 169 | 183 | 62 |
Figure S90. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D41V3.png)
P value = 0.000138 (Fisher's exact test), Q value = 0.11
Table S91. Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 141 | 140 | 150 |
1P LOSS MUTATED | 34 | 22 | 10 |
1P LOSS WILD-TYPE | 107 | 118 | 140 |
Figure S91. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D41V4.png)
P value = 9.66e-05 (Chi-square test), Q value = 0.077
Table S92. Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
1P LOSS MUTATED | 19 | 10 | 14 | 30 | 2 |
1P LOSS WILD-TYPE | 119 | 102 | 62 | 76 | 52 |
Figure S92. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D41V7.png)
P value = 2.02e-05 (Fisher's exact test), Q value = 0.017
Table S93. Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
3P LOSS MUTATED | 83 | 68 | 54 |
3P LOSS WILD-TYPE | 103 | 148 | 37 |
Figure S93. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D45V3.png)
P value = 4.81e-06 (Fisher's exact test), Q value = 0.0042
Table S94. Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 141 | 140 | 150 |
3P LOSS MUTATED | 82 | 48 | 48 |
3P LOSS WILD-TYPE | 59 | 92 | 102 |
Figure S94. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D45V4.png)
P value = 5.31e-06 (Fisher's exact test), Q value = 0.0046
Table S95. Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 119 | 211 | 156 |
3P LOSS MUTATED | 44 | 69 | 90 |
3P LOSS WILD-TYPE | 75 | 142 | 66 |
Figure S95. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D45V8.png)
P value = 4.45e-05 (Fisher's exact test), Q value = 0.036
Table S96. Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
4P LOSS MUTATED | 50 | 32 | 34 |
4P LOSS WILD-TYPE | 136 | 184 | 57 |
Figure S96. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D47V3.png)
P value = 8.76e-05 (Chi-square test), Q value = 0.07
Table S97. Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
4P LOSS MUTATED | 30 | 12 | 22 | 40 | 11 |
4P LOSS WILD-TYPE | 108 | 100 | 54 | 66 | 43 |
Figure S97. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D47V7.png)
P value = 8.23e-08 (Fisher's exact test), Q value = 7.5e-05
Table S98. Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 119 | 211 | 156 |
4P LOSS MUTATED | 23 | 30 | 62 |
4P LOSS WILD-TYPE | 96 | 181 | 94 |
Figure S98. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D47V8.png)
P value = 7.71e-06 (Fisher's exact test), Q value = 0.0066
Table S99. Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 179 | 231 | 78 |
4P LOSS MUTATED | 23 | 76 | 16 |
4P LOSS WILD-TYPE | 156 | 155 | 62 |
Figure S99. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D47V9.png)
P value = 3.55e-06 (Fisher's exact test), Q value = 0.0031
Table S100. Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 51 | 249 | 188 |
4P LOSS MUTATED | 6 | 82 | 27 |
4P LOSS WILD-TYPE | 45 | 167 | 161 |
Figure S100. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D47V10.png)
P value = 2.35e-06 (Fisher's exact test), Q value = 0.0021
Table S101. Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
4Q LOSS MUTATED | 56 | 36 | 40 |
4Q LOSS WILD-TYPE | 130 | 180 | 51 |
Figure S101. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D48V3.png)
P value = 9.39e-08 (Chi-square test), Q value = 8.5e-05
Table S102. Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
4Q LOSS MUTATED | 33 | 12 | 25 | 49 | 11 |
4Q LOSS WILD-TYPE | 105 | 100 | 51 | 57 | 43 |
Figure S102. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D48V7.png)
P value = 7.54e-13 (Fisher's exact test), Q value = 7.1e-10
Table S103. Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 119 | 211 | 156 |
4Q LOSS MUTATED | 24 | 30 | 76 |
4Q LOSS WILD-TYPE | 95 | 181 | 80 |
Figure S103. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D48V8.png)
P value = 1.77e-06 (Fisher's exact test), Q value = 0.0016
Table S104. Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 179 | 231 | 78 |
4Q LOSS MUTATED | 26 | 85 | 20 |
4Q LOSS WILD-TYPE | 153 | 146 | 58 |
Figure S104. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D48V9.png)
P value = 2.31e-07 (Fisher's exact test), Q value = 0.00021
Table S105. Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 51 | 249 | 188 |
4Q LOSS MUTATED | 11 | 93 | 27 |
4Q LOSS WILD-TYPE | 40 | 156 | 161 |
Figure S105. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D48V10.png)
P value = 0.000287 (Fisher's exact test), Q value = 0.22
Table S106. Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 155 | 192 | 78 |
4Q LOSS MUTATED | 26 | 68 | 17 |
4Q LOSS WILD-TYPE | 129 | 124 | 61 |
Figure S106. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
![](D48V11.png)
P value = 0.000289 (Fisher's exact test), Q value = 0.22
Table S107. Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 188 | 188 |
4Q LOSS MUTATED | 11 | 67 | 33 |
4Q LOSS WILD-TYPE | 38 | 121 | 155 |
Figure S107. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
![](D48V12.png)
P value = 2.91e-05 (Fisher's exact test), Q value = 0.024
Table S108. Gene #49: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 119 | 211 | 156 |
5P LOSS MUTATED | 8 | 6 | 25 |
5P LOSS WILD-TYPE | 111 | 205 | 131 |
Figure S108. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D49V8.png)
P value = 2.49e-09 (Fisher's exact test), Q value = 2.3e-06
Table S109. Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
5Q LOSS MUTATED | 69 | 30 | 38 |
5Q LOSS WILD-TYPE | 117 | 186 | 53 |
Figure S109. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D50V3.png)
P value = 1.55e-06 (Chi-square test), Q value = 0.0014
Table S110. Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
5Q LOSS MUTATED | 47 | 12 | 22 | 44 | 9 |
5Q LOSS WILD-TYPE | 91 | 100 | 54 | 62 | 45 |
Figure S110. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D50V7.png)
P value = 1.44e-08 (Fisher's exact test), Q value = 1.3e-05
Table S111. Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 119 | 211 | 156 |
5Q LOSS MUTATED | 37 | 31 | 66 |
5Q LOSS WILD-TYPE | 82 | 180 | 90 |
Figure S111. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D50V8.png)
P value = 9.39e-07 (Fisher's exact test), Q value = 0.00083
Table S112. Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 179 | 231 | 78 |
5Q LOSS MUTATED | 27 | 88 | 20 |
5Q LOSS WILD-TYPE | 152 | 143 | 58 |
Figure S112. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D50V9.png)
P value = 2.65e-06 (Fisher's exact test), Q value = 0.0023
Table S113. Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 51 | 249 | 188 |
5Q LOSS MUTATED | 12 | 93 | 30 |
5Q LOSS WILD-TYPE | 39 | 156 | 158 |
Figure S113. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D50V10.png)
P value = 6.96e-06 (Fisher's exact test), Q value = 0.006
Table S114. Gene #50: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 155 | 192 | 78 |
5Q LOSS MUTATED | 25 | 75 | 18 |
5Q LOSS WILD-TYPE | 130 | 117 | 60 |
Figure S114. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'
![](D50V11.png)
P value = 4.6e-07 (Fisher's exact test), Q value = 0.00041
Table S115. Gene #50: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 188 | 188 |
5Q LOSS MUTATED | 9 | 77 | 32 |
5Q LOSS WILD-TYPE | 40 | 111 | 156 |
Figure S115. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
![](D50V12.png)
P value = 8.96e-05 (Fisher's exact test), Q value = 0.071
Table S116. Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 141 | 140 | 150 |
6Q LOSS MUTATED | 65 | 75 | 44 |
6Q LOSS WILD-TYPE | 76 | 65 | 106 |
Figure S116. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D52V4.png)
P value = 1.61e-05 (Fisher's exact test), Q value = 0.014
Table S117. Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
7P LOSS MUTATED | 5 | 11 | 17 |
7P LOSS WILD-TYPE | 181 | 205 | 74 |
Figure S117. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D53V3.png)
P value = 8.73e-19 (Fisher's exact test), Q value = 8.2e-16
Table S118. Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
8P LOSS MUTATED | 119 | 45 | 27 |
8P LOSS WILD-TYPE | 67 | 171 | 64 |
Figure S118. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D55V3.png)
P value = 0.000101 (Chi-square test), Q value = 0.08
Table S119. Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
8P LOSS MUTATED | 76 | 36 | 23 | 41 | 14 |
8P LOSS WILD-TYPE | 62 | 76 | 53 | 65 | 40 |
Figure S119. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D55V7.png)
P value = 3.94e-05 (Fisher's exact test), Q value = 0.032
Table S120. Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 119 | 211 | 156 |
8P LOSS MUTATED | 67 | 66 | 57 |
8P LOSS WILD-TYPE | 52 | 145 | 99 |
Figure S120. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D55V8.png)
P value = 0.000278 (Fisher's exact test), Q value = 0.22
Table S121. Gene #56: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
8Q LOSS MUTATED | 34 | 16 | 4 |
8Q LOSS WILD-TYPE | 152 | 200 | 87 |
Figure S121. Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D56V3.png)
P value = 0.000154 (Fisher's exact test), Q value = 0.12
Table S122. Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 119 | 211 | 156 |
9P LOSS MUTATED | 53 | 96 | 102 |
9P LOSS WILD-TYPE | 66 | 115 | 54 |
Figure S122. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D57V8.png)
P value = 2.4e-05 (Fisher's exact test), Q value = 0.02
Table S123. Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
9Q LOSS MUTATED | 101 | 80 | 57 |
9Q LOSS WILD-TYPE | 85 | 136 | 34 |
Figure S123. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D58V3.png)
P value = 9.29e-06 (Fisher's exact test), Q value = 0.0079
Table S124. Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 119 | 211 | 156 |
9Q LOSS MUTATED | 53 | 83 | 100 |
9Q LOSS WILD-TYPE | 66 | 128 | 56 |
Figure S124. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D58V8.png)
P value = 0.000173 (Fisher's exact test), Q value = 0.14
Table S125. Gene #58: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 188 | 188 |
9Q LOSS MUTATED | 22 | 109 | 69 |
9Q LOSS WILD-TYPE | 27 | 79 | 119 |
Figure S125. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
![](D58V12.png)
P value = 7.13e-07 (Fisher's exact test), Q value = 0.00064
Table S126. Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
10P LOSS MUTATED | 64 | 27 | 17 |
10P LOSS WILD-TYPE | 122 | 189 | 74 |
Figure S126. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D59V3.png)
P value = 7.29e-05 (Chi-square test), Q value = 0.058
Table S127. Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
10P LOSS MUTATED | 46 | 18 | 5 | 23 | 15 |
10P LOSS WILD-TYPE | 92 | 94 | 71 | 83 | 39 |
Figure S127. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D59V7.png)
P value = 1.95e-05 (Fisher's exact test), Q value = 0.016
Table S128. Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
10Q LOSS MUTATED | 69 | 36 | 23 |
10Q LOSS WILD-TYPE | 117 | 180 | 68 |
Figure S128. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D60V3.png)
P value = 7.93e-05 (Fisher's exact test), Q value = 0.063
Table S129. Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
11P LOSS MUTATED | 53 | 28 | 27 |
11P LOSS WILD-TYPE | 133 | 188 | 64 |
Figure S129. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D61V3.png)
P value = 1.64e-05 (Fisher's exact test), Q value = 0.014
Table S130. Gene #61: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 119 | 211 | 156 |
11P LOSS MUTATED | 31 | 25 | 48 |
11P LOSS WILD-TYPE | 88 | 186 | 108 |
Figure S130. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D61V8.png)
P value = 1.52e-05 (Fisher's exact test), Q value = 0.013
Table S131. Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
12Q LOSS MUTATED | 54 | 32 | 7 |
12Q LOSS WILD-TYPE | 132 | 184 | 84 |
Figure S131. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D64V3.png)
P value = 2.62e-17 (Fisher's exact test), Q value = 2.5e-14
Table S132. Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
13Q LOSS MUTATED | 122 | 59 | 62 |
13Q LOSS WILD-TYPE | 64 | 157 | 29 |
Figure S132. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D65V3.png)
P value = 2.79e-06 (Fisher's exact test), Q value = 0.0024
Table S133. Gene #65: '13q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 106 | 70 | 59 |
13Q LOSS MUTATED | 64 | 16 | 31 |
13Q LOSS WILD-TYPE | 42 | 54 | 28 |
Figure S133. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
![](D65V6.png)
P value = 3.09e-07 (Chi-square test), Q value = 0.00028
Table S134. Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
13Q LOSS MUTATED | 87 | 40 | 24 | 66 | 24 |
13Q LOSS WILD-TYPE | 51 | 72 | 52 | 40 | 30 |
Figure S134. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D65V7.png)
P value = 5.43e-06 (Fisher's exact test), Q value = 0.0047
Table S135. Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 119 | 211 | 156 |
13Q LOSS MUTATED | 76 | 79 | 86 |
13Q LOSS WILD-TYPE | 43 | 132 | 70 |
Figure S135. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D65V8.png)
P value = 7.26e-07 (Fisher's exact test), Q value = 0.00065
Table S136. Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
15Q LOSS MUTATED | 107 | 73 | 53 |
15Q LOSS WILD-TYPE | 79 | 143 | 38 |
Figure S136. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D67V3.png)
P value = 5.61e-13 (Chi-square test), Q value = 5.3e-10
Table S137. Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
15Q LOSS MUTATED | 92 | 36 | 13 | 61 | 26 |
15Q LOSS WILD-TYPE | 46 | 76 | 63 | 45 | 28 |
Figure S137. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D67V7.png)
P value = 1.49e-06 (Fisher's exact test), Q value = 0.0013
Table S138. Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 119 | 211 | 156 |
15Q LOSS MUTATED | 79 | 78 | 71 |
15Q LOSS WILD-TYPE | 40 | 133 | 85 |
Figure S138. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D67V8.png)
P value = 1.59e-05 (Fisher's exact test), Q value = 0.013
Table S139. Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 179 | 231 | 78 |
15Q LOSS MUTATED | 60 | 126 | 45 |
15Q LOSS WILD-TYPE | 119 | 105 | 33 |
Figure S139. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D67V9.png)
P value = 9.33e-06 (Fisher's exact test), Q value = 0.008
Table S140. Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
16P LOSS MUTATED | 49 | 27 | 32 |
16P LOSS WILD-TYPE | 137 | 189 | 59 |
Figure S140. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D68V3.png)
P value = 4.71e-05 (Chi-square test), Q value = 0.038
Table S141. Gene #68: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
16P LOSS MUTATED | 42 | 10 | 14 | 34 | 8 |
16P LOSS WILD-TYPE | 96 | 102 | 62 | 72 | 46 |
Figure S141. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D68V7.png)
P value = 1.42e-05 (Fisher's exact test), Q value = 0.012
Table S142. Gene #68: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 119 | 211 | 156 |
16P LOSS MUTATED | 37 | 26 | 45 |
16P LOSS WILD-TYPE | 82 | 185 | 111 |
Figure S142. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D68V8.png)
P value = 9.14e-06 (Fisher's exact test), Q value = 0.0078
Table S143. Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
16Q LOSS MUTATED | 64 | 37 | 36 |
16Q LOSS WILD-TYPE | 122 | 179 | 55 |
Figure S143. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D69V3.png)
P value = 0.000321 (Fisher's exact test), Q value = 0.25
Table S144. Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 141 | 140 | 150 |
16Q LOSS MUTATED | 45 | 49 | 24 |
16Q LOSS WILD-TYPE | 96 | 91 | 126 |
Figure S144. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D69V4.png)
P value = 1.69e-07 (Chi-square test), Q value = 0.00015
Table S145. Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
16Q LOSS MUTATED | 59 | 15 | 16 | 39 | 8 |
16Q LOSS WILD-TYPE | 79 | 97 | 60 | 67 | 46 |
Figure S145. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D69V7.png)
P value = 3.53e-07 (Fisher's exact test), Q value = 0.00032
Table S146. Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 119 | 211 | 156 |
16Q LOSS MUTATED | 52 | 35 | 50 |
16Q LOSS WILD-TYPE | 67 | 176 | 106 |
Figure S146. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D69V8.png)
P value = 3.36e-05 (Fisher's exact test), Q value = 0.027
Table S147. Gene #69: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 188 | 188 |
16Q LOSS MUTATED | 10 | 72 | 34 |
16Q LOSS WILD-TYPE | 39 | 116 | 154 |
Figure S147. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
![](D69V12.png)
P value = 2.17e-11 (Fisher's exact test), Q value = 2e-08
Table S148. Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
17P LOSS MUTATED | 111 | 55 | 40 |
17P LOSS WILD-TYPE | 75 | 161 | 51 |
Figure S148. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D70V3.png)
P value = 0.00013 (Fisher's exact test), Q value = 0.1
Table S149. Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 141 | 140 | 150 |
17P LOSS MUTATED | 56 | 77 | 46 |
17P LOSS WILD-TYPE | 85 | 63 | 104 |
Figure S149. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D70V4.png)
P value = 0.000114 (Fisher's exact test), Q value = 0.09
Table S150. Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
17Q LOSS MUTATED | 30 | 10 | 15 |
17Q LOSS WILD-TYPE | 156 | 206 | 76 |
Figure S150. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D71V3.png)
P value = 1.31e-05 (Fisher's exact test), Q value = 0.011
Table S151. Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
18P LOSS MUTATED | 88 | 55 | 26 |
18P LOSS WILD-TYPE | 98 | 161 | 65 |
Figure S151. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D72V3.png)
P value = 3.76e-10 (Fisher's exact test), Q value = 3.5e-07
Table S152. Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
18Q LOSS MUTATED | 113 | 68 | 26 |
18Q LOSS WILD-TYPE | 73 | 148 | 65 |
Figure S152. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D73V3.png)
P value = 0.000269 (Fisher's exact test), Q value = 0.21
Table S153. Gene #73: '18q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 106 | 70 | 59 |
18Q LOSS MUTATED | 63 | 20 | 26 |
18Q LOSS WILD-TYPE | 43 | 50 | 33 |
Figure S153. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
![](D73V6.png)
P value = 0.000277 (Chi-square test), Q value = 0.22
Table S154. Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
18Q LOSS MUTATED | 79 | 39 | 33 | 33 | 20 |
18Q LOSS WILD-TYPE | 59 | 73 | 43 | 73 | 34 |
Figure S154. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D73V7.png)
P value = 5.34e-08 (Fisher's exact test), Q value = 4.9e-05
Table S155. Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
19P LOSS MUTATED | 99 | 74 | 62 |
19P LOSS WILD-TYPE | 87 | 142 | 29 |
Figure S155. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D74V3.png)
P value = 1.2e-10 (Fisher's exact test), Q value = 1.1e-07
Table S156. Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 141 | 140 | 150 |
19P LOSS MUTATED | 96 | 60 | 44 |
19P LOSS WILD-TYPE | 45 | 80 | 106 |
Figure S156. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D74V4.png)
P value = 7.15e-07 (Chi-square test), Q value = 0.00064
Table S157. Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
19P LOSS MUTATED | 63 | 39 | 42 | 73 | 17 |
19P LOSS WILD-TYPE | 75 | 73 | 34 | 33 | 37 |
Figure S157. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D74V7.png)
P value = 2.35e-07 (Fisher's exact test), Q value = 0.00021
Table S158. Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 119 | 211 | 156 |
19P LOSS MUTATED | 55 | 77 | 102 |
19P LOSS WILD-TYPE | 64 | 134 | 54 |
Figure S158. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D74V8.png)
P value = 2.5e-05 (Fisher's exact test), Q value = 0.021
Table S159. Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 179 | 231 | 78 |
19P LOSS MUTATED | 65 | 134 | 31 |
19P LOSS WILD-TYPE | 114 | 97 | 47 |
Figure S159. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D74V9.png)
P value = 3.18e-07 (Fisher's exact test), Q value = 0.00029
Table S160. Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 51 | 249 | 188 |
19P LOSS MUTATED | 15 | 147 | 68 |
19P LOSS WILD-TYPE | 36 | 102 | 120 |
Figure S160. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D74V10.png)
P value = 1.63e-05 (Fisher's exact test), Q value = 0.014
Table S161. Gene #74: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 188 | 188 |
19P LOSS MUTATED | 18 | 112 | 69 |
19P LOSS WILD-TYPE | 31 | 76 | 119 |
Figure S161. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
![](D74V12.png)
P value = 1.47e-07 (Fisher's exact test), Q value = 0.00013
Table S162. Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
19Q LOSS MUTATED | 76 | 39 | 38 |
19Q LOSS WILD-TYPE | 110 | 177 | 53 |
Figure S162. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D75V3.png)
P value = 8.18e-07 (Fisher's exact test), Q value = 0.00073
Table S163. Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 141 | 140 | 150 |
19Q LOSS MUTATED | 60 | 47 | 23 |
19Q LOSS WILD-TYPE | 81 | 93 | 127 |
Figure S163. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D75V4.png)
P value = 0.000103 (Chi-square test), Q value = 0.082
Table S164. Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
19Q LOSS MUTATED | 48 | 23 | 22 | 50 | 10 |
19Q LOSS WILD-TYPE | 90 | 89 | 54 | 56 | 44 |
Figure S164. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D75V7.png)
P value = 0.000177 (Fisher's exact test), Q value = 0.14
Table S165. Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 119 | 211 | 156 |
19Q LOSS MUTATED | 43 | 46 | 64 |
19Q LOSS WILD-TYPE | 76 | 165 | 92 |
Figure S165. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D75V8.png)
P value = 7.8e-05 (Fisher's exact test), Q value = 0.062
Table S166. Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 51 | 249 | 188 |
19Q LOSS MUTATED | 12 | 98 | 39 |
19Q LOSS WILD-TYPE | 39 | 151 | 149 |
Figure S166. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D75V10.png)
P value = 7.21e-07 (Fisher's exact test), Q value = 0.00064
Table S167. Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
21Q LOSS MUTATED | 50 | 56 | 51 |
21Q LOSS WILD-TYPE | 136 | 160 | 40 |
Figure S167. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D78V3.png)
P value = 2.26e-10 (Chi-square test), Q value = 2.1e-07
Table S168. Gene #78: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
21Q LOSS MUTATED | 40 | 14 | 30 | 58 | 11 |
21Q LOSS WILD-TYPE | 98 | 98 | 46 | 48 | 43 |
Figure S168. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D78V7.png)
P value = 5.86e-09 (Fisher's exact test), Q value = 5.4e-06
Table S169. Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 119 | 211 | 156 |
21Q LOSS MUTATED | 33 | 42 | 78 |
21Q LOSS WILD-TYPE | 86 | 169 | 78 |
Figure S169. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D78V8.png)
P value = 1.37e-06 (Fisher's exact test), Q value = 0.0012
Table S170. Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 51 | 249 | 188 |
21Q LOSS MUTATED | 9 | 105 | 40 |
21Q LOSS WILD-TYPE | 42 | 144 | 148 |
Figure S170. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D78V10.png)
P value = 1.06e-09 (Fisher's exact test), Q value = 9.9e-07
Table S171. Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 186 | 216 | 91 |
22Q LOSS MUTATED | 94 | 60 | 58 |
22Q LOSS WILD-TYPE | 92 | 156 | 33 |
Figure S171. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'
![](D79V3.png)
P value = 2.8e-05 (Fisher's exact test), Q value = 0.023
Table S172. Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 141 | 140 | 150 |
22Q LOSS MUTATED | 70 | 74 | 43 |
22Q LOSS WILD-TYPE | 71 | 66 | 107 |
Figure S172. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'
![](D79V4.png)
P value = 8.98e-08 (Chi-square test), Q value = 8.2e-05
Table S173. Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 138 | 112 | 76 | 106 | 54 |
22Q LOSS MUTATED | 70 | 30 | 34 | 63 | 11 |
22Q LOSS WILD-TYPE | 68 | 82 | 42 | 43 | 43 |
Figure S173. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
![](D79V7.png)
P value = 5.38e-07 (Fisher's exact test), Q value = 0.00048
Table S174. Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 119 | 211 | 156 |
22Q LOSS MUTATED | 59 | 62 | 87 |
22Q LOSS WILD-TYPE | 60 | 149 | 69 |
Figure S174. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
![](D79V8.png)
P value = 0.000205 (Fisher's exact test), Q value = 0.16
Table S175. Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 179 | 231 | 78 |
22Q LOSS MUTATED | 56 | 119 | 33 |
22Q LOSS WILD-TYPE | 123 | 112 | 45 |
Figure S175. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
![](D79V9.png)
P value = 9.04e-07 (Fisher's exact test), Q value = 8e-04
Table S176. Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 51 | 249 | 188 |
22Q LOSS MUTATED | 12 | 134 | 62 |
22Q LOSS WILD-TYPE | 39 | 115 | 126 |
Figure S176. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
![](D79V10.png)
P value = 3.35e-05 (Fisher's exact test), Q value = 0.027
Table S177. Gene #79: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 188 | 188 |
22Q LOSS MUTATED | 16 | 104 | 63 |
22Q LOSS WILD-TYPE | 33 | 84 | 125 |
Figure S177. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'
![](D79V12.png)
-
Copy number data file = transformed.cor.cli.txt
-
Molecular subtypes file = LUAD-TP.transferedmergedcluster.txt
-
Number of patients = 493
-
Number of significantly arm-level cnvs = 80
-
Number of molecular subtypes = 12
-
Exclude genes that fewer than K tumors have mutations, K = 3
For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R
For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R
For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.
In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.