Correlation between copy number variation genes (focal events) and molecular subtypes
Stomach Adenocarcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1ZS2TZX
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1ZS2TZX
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.

Summary

Testing the association between copy number variation 40 focal events and 10 molecular subtypes across 331 patients, 226 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 1q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 2p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 2q cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 3p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 3q cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 4p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 4q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 5p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 5q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 6p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 6q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 7p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 7q cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 8p cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • 8q cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • 9p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 9q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 10p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 10q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 11p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 11q cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 12p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 12q cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 13q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 14q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 15q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 16p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 16q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 17p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 17q cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 18p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 18q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 19p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 19q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 20p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 20q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 21q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 22q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • xq cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 40 focal events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 226 significant findings detected.

Clinical
Features 		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 Chi-square 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
19q 118 (36%) 213 4.45e-18
(1.75e-15) 		2.42e-09
(8.5e-07) 		0.00105
(0.192) 		0.0213
(1.00) 		1.24e-10
(4.55e-08) 		1.22e-07
(3.96e-05) 		1.26e-06
(0.000386) 		1.32e-10
(4.82e-08) 		0.000462
(0.0934) 		6.52e-09
(2.27e-06)
5p 115 (35%) 216 5.9e-21
(2.35e-18) 		9.25e-11
(3.4e-08) 		0.695
(1.00) 		0.701
(1.00) 		6.47e-12
(2.42e-09) 		1.16e-08
(3.98e-06) 		7.84e-08
(2.56e-05) 		9.49e-09
(3.27e-06) 		7e-06
(0.00197) 		1.86e-11
(6.91e-09)
5q 101 (31%) 230 3.45e-17
(1.35e-14) 		3.53e-08
(1.18e-05) 		0.356
(1.00) 		0.901
(1.00) 		1.5e-09
(5.34e-07) 		1.56e-07
(5.06e-05) 		3.77e-06
(0.0011) 		3.54e-08
(1.18e-05) 		0.000122
(0.0291) 		2.89e-10
(1.05e-07)
6p 95 (29%) 236 3.08e-16
(1.2e-13) 		2.93e-12
(1.1e-09) 		0.00779
(1.00) 		0.327
(1.00) 		1.54e-06
(0.000465) 		4.83e-07
(0.000154) 		1.77e-05
(0.00479) 		4.47e-08
(1.47e-05) 		6.96e-06
(0.00196) 		2.26e-10
(8.23e-08)
9p 145 (44%) 186 3.67e-16
(1.42e-13) 		6.12e-07
(0.000194) 		0.000205
(0.0463) 		0.217
(1.00) 		3.14e-06
(0.000919) 		8.42e-05
(0.0208) 		0.000134
(0.0314) 		5.53e-06
(0.00159) 		0.109
(1.00) 		3.21e-08
(1.09e-05)
16p 115 (35%) 216 3.55e-17
(1.39e-14) 		4.23e-08
(1.4e-05) 		0.349
(1.00) 		0.528
(1.00) 		1.51e-08
(5.16e-06) 		3.3e-05
(0.00857) 		3.78e-06
(0.0011) 		7.99e-06
(0.00223) 		0.000375
(0.0784) 		1.17e-06
(0.000359)
17p 136 (41%) 195 3.66e-22
(1.46e-19) 		1.26e-09
(4.5e-07) 		0.356
(1.00) 		0.948
(1.00) 		3.23e-08
(1.09e-05) 		6.47e-07
(0.000204) 		1.73e-05
(0.00469) 		3.74e-07
(0.00012) 		0.00108
(0.198) 		1.44e-08
(4.94e-06)
19p 122 (37%) 209 2.37e-21
(9.47e-19) 		8.26e-11
(3.05e-08) 		0.0017
(0.294) 		0.066
(1.00) 		1.87e-11
(6.92e-09) 		6.81e-09
(2.36e-06) 		1.42e-06
(0.000431) 		4.25e-11
(1.57e-08) 		0.000877
(0.167) 		1.13e-09
(4.06e-07)
21q 140 (42%) 191 1.92e-15
(7.38e-13) 		3.41e-08
(1.15e-05) 		0.112
(1.00) 		0.512
(1.00) 		0.000367
(0.0775) 		2.14e-05
(0.00569) 		6.12e-05
(0.0154) 		1.5e-06
(0.000453) 		0.000977
(0.181) 		1.73e-06
(0.000518)
1q 100 (30%) 231 2.13e-14
(8.15e-12) 		2.12e-06
(0.000627) 		0.0198
(1.00) 		0.0421
(1.00) 		1.1e-06
(0.00034) 		0.000117
(0.028) 		0.000143
(0.0334) 		0.00133
(0.234) 		0.00378
(0.59) 		0.000519
(0.104)
4p 134 (40%) 197 4.46e-18
(1.75e-15) 		1.87e-05
(0.00504) 		0.241
(1.00) 		0.465
(1.00) 		0.000229
(0.0516) 		0.000244
(0.0539) 		5.75e-06
(0.00164) 		1.38e-06
(0.00042) 		0.00465
(0.702) 		2.95e-05
(0.00777)
6q 96 (29%) 235 7.26e-13
(2.75e-10) 		4.29e-09
(1.5e-06) 		0.0919
(1.00) 		0.361
(1.00) 		1.27e-05
(0.00346) 		3.68e-05
(0.00942) 		0.0177
(1.00) 		0.000158
(0.0364) 		0.00112
(0.204) 		1.06e-05
(0.00292)
10p 118 (36%) 213 9.98e-21
(3.96e-18) 		3.99e-09
(1.4e-06) 		0.226
(1.00) 		0.284
(1.00) 		4.89e-06
(0.00141) 		0.000173
(0.0395) 		0.000129
(0.0304) 		5.81e-06
(0.00165) 		0.0039
(0.6) 		4.58e-05
(0.0116)
12p 111 (34%) 220 6.47e-13
(2.45e-10) 		4.06e-07
(0.00013) 		0.227
(1.00) 		0.233
(1.00) 		1.8e-06
(0.000537) 		0.00191
(0.322) 		0.000188
(0.0427) 		0.000325
(0.0695) 		0.00029
(0.0629) 		3.56e-05
(0.00919)
15q 93 (28%) 238 1.17e-11
(4.37e-09) 		7.55e-08
(2.47e-05) 		0.00346
(0.544) 		0.265
(1.00) 		8.62e-07
(0.000271) 		9.85e-07
(0.000307) 		0.000711
(0.136) 		9.59e-07
(3e-04) 		0.00175
(0.297) 		2.46e-07
(7.95e-05)
16q 113 (34%) 218 1.2e-14
(4.61e-12) 		4.06e-08
(1.35e-05) 		0.0251
(1.00) 		0.646
(1.00) 		7.07e-09
(2.45e-06) 		1.07e-05
(0.00294) 		7.1e-06
(0.00199) 		5.12e-05
(0.013) 		0.00704
(0.992) 		1.91e-05
(0.00512)
20q 209 (63%) 122 3.87e-16
(1.5e-13) 		9.57e-10
(3.45e-07) 		0.044
(1.00) 		0.971
(1.00) 		1.02e-06
(0.000317) 		7.6e-05
(0.0188) 		2.26e-06
(0.000668) 		1.03e-09
(3.71e-07) 		0.0463
(1.00) 		2.37e-09
(8.33e-07)
1p 80 (24%) 251 5.4e-14
(2.06e-11) 		0.000241
(0.0534) 		0.107
(1.00) 		0.269
(1.00) 		3.76e-05
(0.00958) 		0.0173
(1.00) 		0.000131
(0.0307) 		0.000929
(0.174) 		0.0422
(1.00) 		0.000446
(0.0911)
2p 74 (22%) 257 1.91e-09
(6.75e-07) 		0.000168
(0.0385) 		0.284
(1.00) 		0.956
(1.00) 		0.00281
(0.452) 		0.0749
(1.00) 		3.34e-05
(0.00866) 		0.00127
(0.225) 		0.000455
(0.0924) 		3.07e-05
(0.00804)
4q 129 (39%) 202 1.54e-18
(6.1e-16) 		2.6e-06
(0.000766) 		0.103
(1.00) 		0.316
(1.00) 		0.00379
(0.59) 		0.000499
(0.1) 		0.000244
(0.0539) 		1.54e-06
(0.000465) 		0.0293
(1.00) 		3.65e-05
(0.00938)
10q 99 (30%) 232 8.71e-16
(3.36e-13) 		1.06e-06
(0.00033) 		0.0612
(1.00) 		0.391
(1.00) 		1.93e-06
(0.000573) 		8.98e-05
(0.0221) 		0.0017
(0.294) 		0.000624
(0.122) 		0.0968
(1.00) 		0.000149
(0.0345)
14q 100 (30%) 231 1.29e-09
(4.59e-07) 		0.000623
(0.122) 		0.442
(1.00) 		0.23
(1.00) 		0.000537
(0.106) 		0.000368
(0.0775) 		1.99e-05
(0.00531) 		0.00516
(0.758) 		0.00315
(0.504) 		0.000269
(0.0587)
18q 159 (48%) 172 5.55e-15
(2.13e-12) 		0.000561
(0.11) 		0.0862
(1.00) 		0.352
(1.00) 		0.000893
(0.169) 		0.00973
(1.00) 		4.42e-06
(0.00128) 		1.1e-05
(0.00301) 		0.00704
(0.992) 		0.000128
(0.0304)
20p 198 (60%) 133 1.38e-16
(5.39e-14) 		4.09e-08
(1.35e-05) 		0.0583
(1.00) 		0.386
(1.00) 		0.000237
(0.0531) 		0.009
(1.00) 		3.77e-06
(0.0011) 		8.38e-06
(0.00233) 		0.0068
(0.966) 		6.81e-06
(0.00193)
22q 127 (38%) 204 1.17e-19
(4.63e-17) 		7.26e-08
(2.38e-05) 		0.0508
(1.00) 		0.691
(1.00) 		5.52e-05
(0.0139) 		0.0123
(1.00) 		7.77e-07
(0.000245) 		1.03e-08
(3.56e-06) 		0.00484
(0.722) 		2.49e-07
(8.03e-05)
11p 82 (25%) 249 1.98e-08
(6.73e-06) 		2.23e-05
(0.00588) 		0.0415
(1.00) 		0.959
(1.00) 		0.0166
(1.00) 		0.000327
(0.0696) 		0.00219
(0.363) 		0.000238
(0.0531) 		0.147
(1.00) 		0.000526
(0.105)
13q 141 (43%) 190 1.78e-09
(6.31e-07) 		0.00118
(0.212) 		0.803
(1.00) 		0.12
(1.00) 		0.0449
(1.00) 		0.529
(1.00) 		0.000363
(0.0769) 		0.000902
(0.17) 		0.00845
(1.00) 		0.0001
(0.0243)
18p 154 (47%) 177 1.19e-12
(4.48e-10) 		0.000412
(0.0845) 		0.0706
(1.00) 		0.0884
(1.00) 		0.0042
(0.638) 		0.0387
(1.00) 		2.15e-05
(0.00571) 		3.19e-05
(0.00831) 		0.0101
(1.00) 		0.000113
(0.0272)
xq 83 (25%) 248 4.01e-10
(1.46e-07) 		0.000108
(0.026) 		0.341
(1.00) 		0.527
(1.00) 		0.000877
(0.167) 		0.0458
(1.00) 		0.00026
(0.057) 		0.279
(1.00) 		0.00124
(0.221) 		0.0582
(1.00)
2q 69 (21%) 262 2.73e-08
(9.27e-06) 		0.0052
(0.759) 		0.42
(1.00) 		0.889
(1.00) 		0.00113
(0.205) 		0.0307
(1.00) 		0.00136
(0.238) 		0.00335
(0.533) 		0.00264
(0.43) 		0.000692
(0.134)
9q 124 (37%) 207 8.6e-10
(3.11e-07) 		7.42e-05
(0.0185) 		0.0191
(1.00) 		0.621
(1.00) 		0.000377
(0.0784) 		0.00408
(0.624) 		0.00497
(0.736) 		0.0297
(1.00) 		0.0563
(1.00) 		0.00065
(0.126)
3p 101 (31%) 230 3.44e-08
(1.15e-05) 		1.08e-05
(0.00296) 		0.217
(1.00) 		0.122
(1.00) 		0.0545
(1.00) 		0.0333
(1.00) 		0.00465
(0.702) 		0.0109
(1.00) 		0.0683
(1.00) 		0.000105
(0.0254)
7p 156 (47%) 175 6.53e-14
(2.48e-11) 		1.53e-05
(0.00416) 		0.533
(1.00) 		0.973
(1.00) 		0.0173
(1.00) 		0.0336
(1.00) 		0.077
(1.00) 		0.0137
(1.00) 		0.00948
(1.00) 		6.98e-05
(0.0174)
17q 94 (28%) 237 5.05e-10
(1.83e-07) 		0.0119
(1.00) 		0.538
(1.00) 		0.97
(1.00) 		0.00196
(0.329) 		0.000151
(0.0348) 		0.00121
(0.217) 		0.00255
(0.419) 		0.101
(1.00) 		0.00584
(0.841)
3q 100 (30%) 231 1.15e-06
(0.000354) 		9.63e-05
(0.0235) 		0.273
(1.00) 		0.846
(1.00) 		0.283
(1.00) 		0.276
(1.00) 		0.012
(1.00) 		0.0241
(1.00) 		0.0269
(1.00) 		0.00166
(0.289)
7q 145 (44%) 186 1.88e-12
(7.08e-10) 		9.58e-05
(0.0235) 		0.71
(1.00) 		0.805
(1.00) 		0.378
(1.00) 		0.125
(1.00) 		0.406
(1.00) 		0.183
(1.00) 		0.14
(1.00) 		0.00841
(1.00)
8p 197 (60%) 134 0.000313
(0.0672) 		0.0199
(1.00) 		0.242
(1.00) 		0.473
(1.00) 		0.0412
(1.00) 		0.143
(1.00) 		0.00238
(0.393) 		0.0189
(1.00) 		6.7e-06
(0.0019) 		0.13
(1.00)
8q 203 (61%) 128 0.000405
(0.0834) 		0.00172
(0.294) 		0.718
(1.00) 		0.169
(1.00) 		0.0167
(1.00) 		0.133
(1.00) 		0.0111
(1.00) 		0.0152
(1.00) 		0.000398
(0.0824) 		0.0448
(1.00)
11q 86 (26%) 245 4.13e-07
(0.000132) 		0.000941
(0.175) 		0.849
(1.00) 		0.793
(1.00) 		0.279
(1.00) 		0.00572
(0.83) 		0.00276
(0.447) 		0.00217
(0.362) 		0.0275
(1.00) 		0.00345
(0.544)
12q 92 (28%) 239 1.6e-06
(0.000481) 		0.000302
(0.0652) 		0.196
(1.00) 		0.276
(1.00) 		0.0223
(1.00) 		0.18
(1.00) 		0.215
(1.00) 		0.00654
(0.935) 		0.053
(1.00) 		0.0206
(1.00)
'1p' versus 'CN_CNMF'

P value = 5.4e-14 (Chi-square test), Q value = 2.1e-11

Table S1.  Gene #1: '1p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
1P MUTATED 6 9 21 2 40 2
1P WILD-TYPE 145 18 34 11 42 1

Figure S1.  Get High-res Image Gene #1: '1p' versus Molecular Subtype #1: 'CN_CNMF'

'1p' versus 'METHLYATION_CNMF'

P value = 0.000241 (Fisher's exact test), Q value = 0.053

Table S2.  Gene #1: '1p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
1P MUTATED 3 17 10 31
1P WILD-TYPE 34 63 55 45

Figure S2.  Get High-res Image Gene #1: '1p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p' versus 'MRNASEQ_CNMF'

P value = 3.76e-05 (Chi-square test), Q value = 0.0096

Table S3.  Gene #1: '1p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
1P MUTATED 8 5 12 8 26
1P WILD-TYPE 57 57 34 29 36

Figure S3.  Get High-res Image Gene #1: '1p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1p' versus 'MIRSEQ_CNMF'

P value = 0.000131 (Fisher's exact test), Q value = 0.031

Table S4.  Gene #1: '1p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
1P MUTATED 17 16 43
1P WILD-TYPE 88 85 72

Figure S4.  Get High-res Image Gene #1: '1p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000929 (Fisher's exact test), Q value = 0.17

Table S5.  Gene #1: '1p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
1P MUTATED 19 32 25
1P WILD-TYPE 83 49 113

Figure S5.  Get High-res Image Gene #1: '1p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000446 (Fisher's exact test), Q value = 0.091

Table S6.  Gene #1: '1p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
1P MUTATED 27 26 12
1P WILD-TYPE 37 103 69

Figure S6.  Get High-res Image Gene #1: '1p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q' versus 'CN_CNMF'

P value = 2.13e-14 (Chi-square test), Q value = 8.1e-12

Table S7.  Gene #2: '1q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
1Q MUTATED 11 12 23 6 46 2
1Q WILD-TYPE 140 15 32 7 36 1

Figure S7.  Get High-res Image Gene #2: '1q' versus Molecular Subtype #1: 'CN_CNMF'

'1q' versus 'METHLYATION_CNMF'

P value = 2.12e-06 (Fisher's exact test), Q value = 0.00063

Table S8.  Gene #2: '1q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
1Q MUTATED 6 25 10 41
1Q WILD-TYPE 31 55 55 35

Figure S8.  Get High-res Image Gene #2: '1q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1q' versus 'MRNASEQ_CNMF'

P value = 1.1e-06 (Chi-square test), Q value = 0.00034

Table S9.  Gene #2: '1q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
1Q MUTATED 14 9 12 10 36
1Q WILD-TYPE 51 53 34 27 26

Figure S9.  Get High-res Image Gene #2: '1q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000117 (Fisher's exact test), Q value = 0.028

Table S10.  Gene #2: '1q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
1Q MUTATED 32 35 14
1Q WILD-TYPE 37 78 76

Figure S10.  Get High-res Image Gene #2: '1q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1q' versus 'MIRSEQ_CNMF'

P value = 0.000143 (Fisher's exact test), Q value = 0.033

Table S11.  Gene #2: '1q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
1Q MUTATED 23 23 52
1Q WILD-TYPE 82 78 63

Figure S11.  Get High-res Image Gene #2: '1q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00133 (Fisher's exact test), Q value = 0.23

Table S12.  Gene #2: '1q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
1Q MUTATED 24 38 36
1Q WILD-TYPE 78 43 102

Figure S12.  Get High-res Image Gene #2: '1q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000519 (Fisher's exact test), Q value = 0.1

Table S13.  Gene #2: '1q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
1Q MUTATED 32 38 16
1Q WILD-TYPE 32 91 65

Figure S13.  Get High-res Image Gene #2: '1q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p' versus 'CN_CNMF'

P value = 1.91e-09 (Chi-square test), Q value = 6.8e-07

Table S14.  Gene #3: '2p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
2P MUTATED 10 10 19 1 34 0
2P WILD-TYPE 141 17 36 12 48 3

Figure S14.  Get High-res Image Gene #3: '2p' versus Molecular Subtype #1: 'CN_CNMF'

'2p' versus 'METHLYATION_CNMF'

P value = 0.000168 (Fisher's exact test), Q value = 0.038

Table S15.  Gene #3: '2p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
2P MUTATED 5 17 7 31
2P WILD-TYPE 32 63 58 45

Figure S15.  Get High-res Image Gene #3: '2p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p' versus 'MIRSEQ_CNMF'

P value = 3.34e-05 (Fisher's exact test), Q value = 0.0087

Table S16.  Gene #3: '2p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
2P MUTATED 15 14 42
2P WILD-TYPE 90 87 73

Figure S16.  Get High-res Image Gene #3: '2p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00127 (Fisher's exact test), Q value = 0.23

Table S17.  Gene #3: '2p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
2P MUTATED 19 30 22
2P WILD-TYPE 83 51 116

Figure S17.  Get High-res Image Gene #3: '2p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000455 (Fisher's exact test), Q value = 0.092

Table S18.  Gene #3: '2p' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 131 79
2P MUTATED 11 44 9
2P WILD-TYPE 53 87 70

Figure S18.  Get High-res Image Gene #3: '2p' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.07e-05 (Fisher's exact test), Q value = 0.008

Table S19.  Gene #3: '2p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
2P MUTATED 27 29 8
2P WILD-TYPE 37 100 73

Figure S19.  Get High-res Image Gene #3: '2p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q' versus 'CN_CNMF'

P value = 2.73e-08 (Chi-square test), Q value = 9.3e-06

Table S20.  Gene #4: '2q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
2Q MUTATED 10 10 16 1 32 0
2Q WILD-TYPE 141 17 39 12 50 3

Figure S20.  Get High-res Image Gene #4: '2q' versus Molecular Subtype #1: 'CN_CNMF'

'2q' versus 'MRNASEQ_CNMF'

P value = 0.00113 (Chi-square test), Q value = 0.21

Table S21.  Gene #4: '2q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
2Q MUTATED 10 7 9 5 24
2Q WILD-TYPE 55 55 37 32 38

Figure S21.  Get High-res Image Gene #4: '2q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q' versus 'MIRSEQ_CNMF'

P value = 0.00136 (Fisher's exact test), Q value = 0.24

Table S22.  Gene #4: '2q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
2Q MUTATED 15 15 37
2Q WILD-TYPE 90 86 78

Figure S22.  Get High-res Image Gene #4: '2q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000692 (Fisher's exact test), Q value = 0.13

Table S23.  Gene #4: '2q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
2Q MUTATED 24 26 9
2Q WILD-TYPE 40 103 72

Figure S23.  Get High-res Image Gene #4: '2q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p' versus 'CN_CNMF'

P value = 3.44e-08 (Chi-square test), Q value = 1.2e-05

Table S24.  Gene #5: '3p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
3P MUTATED 19 11 26 5 39 1
3P WILD-TYPE 132 16 29 8 43 2

Figure S24.  Get High-res Image Gene #5: '3p' versus Molecular Subtype #1: 'CN_CNMF'

'3p' versus 'METHLYATION_CNMF'

P value = 1.08e-05 (Fisher's exact test), Q value = 0.003

Table S25.  Gene #5: '3p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
3P MUTATED 8 27 8 38
3P WILD-TYPE 29 53 57 38

Figure S25.  Get High-res Image Gene #5: '3p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000105 (Fisher's exact test), Q value = 0.025

Table S26.  Gene #5: '3p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
3P MUTATED 34 35 17
3P WILD-TYPE 30 94 64

Figure S26.  Get High-res Image Gene #5: '3p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q' versus 'CN_CNMF'

P value = 1.15e-06 (Chi-square test), Q value = 0.00035

Table S27.  Gene #6: '3q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
3Q MUTATED 21 13 24 5 36 1
3Q WILD-TYPE 130 14 31 8 46 2

Figure S27.  Get High-res Image Gene #6: '3q' versus Molecular Subtype #1: 'CN_CNMF'

'3q' versus 'METHLYATION_CNMF'

P value = 9.63e-05 (Fisher's exact test), Q value = 0.023

Table S28.  Gene #6: '3q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
3Q MUTATED 11 23 8 36
3Q WILD-TYPE 26 57 57 40

Figure S28.  Get High-res Image Gene #6: '3q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p' versus 'CN_CNMF'

P value = 4.46e-18 (Chi-square test), Q value = 1.8e-15

Table S29.  Gene #7: '4p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
4P MUTATED 23 14 40 2 52 3
4P WILD-TYPE 128 13 15 11 30 0

Figure S29.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #1: 'CN_CNMF'

'4p' versus 'METHLYATION_CNMF'

P value = 1.87e-05 (Fisher's exact test), Q value = 0.005

Table S30.  Gene #7: '4p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
4P MUTATED 6 27 22 46
4P WILD-TYPE 31 53 43 30

Figure S30.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p' versus 'MRNASEQ_CNMF'

P value = 0.000229 (Chi-square test), Q value = 0.052

Table S31.  Gene #7: '4p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
4P MUTATED 13 22 17 13 37
4P WILD-TYPE 52 40 29 24 25

Figure S31.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000244 (Fisher's exact test), Q value = 0.054

Table S32.  Gene #7: '4p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
4P MUTATED 40 32 30
4P WILD-TYPE 29 81 60

Figure S32.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p' versus 'MIRSEQ_CNMF'

P value = 5.75e-06 (Fisher's exact test), Q value = 0.0016

Table S33.  Gene #7: '4p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
4P MUTATED 27 36 66
4P WILD-TYPE 78 65 49

Figure S33.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.38e-06 (Fisher's exact test), Q value = 0.00042

Table S34.  Gene #7: '4p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
4P MUTATED 37 52 40
4P WILD-TYPE 65 29 98

Figure S34.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.95e-05 (Fisher's exact test), Q value = 0.0078

Table S35.  Gene #7: '4p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
4P MUTATED 41 39 29
4P WILD-TYPE 23 90 52

Figure S35.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q' versus 'CN_CNMF'

P value = 1.54e-18 (Chi-square test), Q value = 6.1e-16

Table S36.  Gene #8: '4q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
4Q MUTATED 22 12 43 2 47 3
4Q WILD-TYPE 129 15 12 11 35 0

Figure S36.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #1: 'CN_CNMF'

'4q' versus 'METHLYATION_CNMF'

P value = 2.6e-06 (Fisher's exact test), Q value = 0.00077

Table S37.  Gene #8: '4q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
4Q MUTATED 5 29 21 47
4Q WILD-TYPE 32 51 44 29

Figure S37.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000499 (Fisher's exact test), Q value = 0.1

Table S38.  Gene #8: '4q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
4Q MUTATED 38 30 30
4Q WILD-TYPE 31 83 60

Figure S38.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q' versus 'MIRSEQ_CNMF'

P value = 0.000244 (Fisher's exact test), Q value = 0.054

Table S39.  Gene #8: '4q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
4Q MUTATED 28 36 61
4Q WILD-TYPE 77 65 54

Figure S39.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.54e-06 (Fisher's exact test), Q value = 0.00047

Table S40.  Gene #8: '4q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
4Q MUTATED 35 51 39
4Q WILD-TYPE 67 30 99

Figure S40.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.65e-05 (Fisher's exact test), Q value = 0.0094

Table S41.  Gene #8: '4q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
4Q MUTATED 41 40 28
4Q WILD-TYPE 23 89 53

Figure S41.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p' versus 'CN_CNMF'

P value = 5.9e-21 (Chi-square test), Q value = 2.3e-18

Table S42.  Gene #9: '5p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
5P MUTATED 16 8 23 4 63 1
5P WILD-TYPE 135 19 32 9 19 2

Figure S42.  Get High-res Image Gene #9: '5p' versus Molecular Subtype #1: 'CN_CNMF'

'5p' versus 'METHLYATION_CNMF'

P value = 9.25e-11 (Fisher's exact test), Q value = 3.4e-08

Table S43.  Gene #9: '5p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
5P MUTATED 7 27 6 47
5P WILD-TYPE 30 53 59 29

Figure S43.  Get High-res Image Gene #9: '5p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p' versus 'MRNASEQ_CNMF'

P value = 6.47e-12 (Chi-square test), Q value = 2.4e-09

Table S44.  Gene #9: '5p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
5P MUTATED 16 7 10 13 44
5P WILD-TYPE 49 55 36 24 18

Figure S44.  Get High-res Image Gene #9: '5p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.16e-08 (Fisher's exact test), Q value = 4e-06

Table S45.  Gene #9: '5p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
5P MUTATED 42 34 14
5P WILD-TYPE 27 79 76

Figure S45.  Get High-res Image Gene #9: '5p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p' versus 'MIRSEQ_CNMF'

P value = 7.84e-08 (Fisher's exact test), Q value = 2.6e-05

Table S46.  Gene #9: '5p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
5P MUTATED 31 19 63
5P WILD-TYPE 74 82 52

Figure S46.  Get High-res Image Gene #9: '5p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.49e-09 (Fisher's exact test), Q value = 3.3e-06

Table S47.  Gene #9: '5p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
5P MUTATED 22 51 40
5P WILD-TYPE 80 30 98

Figure S47.  Get High-res Image Gene #9: '5p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-06 (Fisher's exact test), Q value = 0.002

Table S48.  Gene #9: '5p' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 131 79
5P MUTATED 21 62 12
5P WILD-TYPE 43 69 67

Figure S48.  Get High-res Image Gene #9: '5p' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.86e-11 (Fisher's exact test), Q value = 6.9e-09

Table S49.  Gene #9: '5p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
5P MUTATED 45 37 13
5P WILD-TYPE 19 92 68

Figure S49.  Get High-res Image Gene #9: '5p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q' versus 'CN_CNMF'

P value = 3.45e-17 (Chi-square test), Q value = 1.4e-14

Table S50.  Gene #10: '5q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
5Q MUTATED 11 8 24 4 52 2
5Q WILD-TYPE 140 19 31 9 30 1

Figure S50.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #1: 'CN_CNMF'

'5q' versus 'METHLYATION_CNMF'

P value = 3.53e-08 (Fisher's exact test), Q value = 1.2e-05

Table S51.  Gene #10: '5q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
5Q MUTATED 4 27 8 41
5Q WILD-TYPE 33 53 57 35

Figure S51.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q' versus 'MRNASEQ_CNMF'

P value = 1.5e-09 (Chi-square test), Q value = 5.3e-07

Table S52.  Gene #10: '5q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
5Q MUTATED 13 7 8 11 38
5Q WILD-TYPE 52 55 38 26 24

Figure S52.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.56e-07 (Fisher's exact test), Q value = 5.1e-05

Table S53.  Gene #10: '5q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
5Q MUTATED 37 28 12
5Q WILD-TYPE 32 85 78

Figure S53.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q' versus 'MIRSEQ_CNMF'

P value = 3.77e-06 (Fisher's exact test), Q value = 0.0011

Table S54.  Gene #10: '5q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
5Q MUTATED 26 18 55
5Q WILD-TYPE 79 83 60

Figure S54.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.54e-08 (Fisher's exact test), Q value = 1.2e-05

Table S55.  Gene #10: '5q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
5Q MUTATED 18 46 35
5Q WILD-TYPE 84 35 103

Figure S55.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000122 (Fisher's exact test), Q value = 0.029

Table S56.  Gene #10: '5q' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 131 79
5Q MUTATED 17 57 13
5Q WILD-TYPE 47 74 66

Figure S56.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.89e-10 (Fisher's exact test), Q value = 1.1e-07

Table S57.  Gene #10: '5q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
5Q MUTATED 42 32 13
5Q WILD-TYPE 22 97 68

Figure S57.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p' versus 'CN_CNMF'

P value = 3.08e-16 (Chi-square test), Q value = 1.2e-13

Table S58.  Gene #11: '6p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
6P MUTATED 10 8 26 2 48 1
6P WILD-TYPE 141 19 29 11 34 2

Figure S58.  Get High-res Image Gene #11: '6p' versus Molecular Subtype #1: 'CN_CNMF'

'6p' versus 'METHLYATION_CNMF'

P value = 2.93e-12 (Fisher's exact test), Q value = 1.1e-09

Table S59.  Gene #11: '6p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
6P MUTATED 1 19 6 43
6P WILD-TYPE 36 61 59 33

Figure S59.  Get High-res Image Gene #11: '6p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p' versus 'MRNASEQ_CNMF'

P value = 1.54e-06 (Chi-square test), Q value = 0.00047

Table S60.  Gene #11: '6p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
6P MUTATED 12 7 14 8 33
6P WILD-TYPE 53 55 32 29 29

Figure S60.  Get High-res Image Gene #11: '6p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.83e-07 (Fisher's exact test), Q value = 0.00015

Table S61.  Gene #11: '6p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
6P MUTATED 35 28 11
6P WILD-TYPE 34 85 79

Figure S61.  Get High-res Image Gene #11: '6p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6p' versus 'MIRSEQ_CNMF'

P value = 1.77e-05 (Fisher's exact test), Q value = 0.0048

Table S62.  Gene #11: '6p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
6P MUTATED 24 17 51
6P WILD-TYPE 81 84 64

Figure S62.  Get High-res Image Gene #11: '6p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.47e-08 (Fisher's exact test), Q value = 1.5e-05

Table S63.  Gene #11: '6p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
6P MUTATED 17 44 31
6P WILD-TYPE 85 37 107

Figure S63.  Get High-res Image Gene #11: '6p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6p' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.96e-06 (Fisher's exact test), Q value = 0.002

Table S64.  Gene #11: '6p' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 131 79
6P MUTATED 12 54 10
6P WILD-TYPE 52 77 69

Figure S64.  Get High-res Image Gene #11: '6p' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.26e-10 (Fisher's exact test), Q value = 8.2e-08

Table S65.  Gene #11: '6p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
6P MUTATED 38 30 8
6P WILD-TYPE 26 99 73

Figure S65.  Get High-res Image Gene #11: '6p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q' versus 'CN_CNMF'

P value = 7.26e-13 (Chi-square test), Q value = 2.7e-10

Table S66.  Gene #12: '6q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
6Q MUTATED 15 6 27 2 45 1
6Q WILD-TYPE 136 21 28 11 37 2

Figure S66.  Get High-res Image Gene #12: '6q' versus Molecular Subtype #1: 'CN_CNMF'

'6q' versus 'METHLYATION_CNMF'

P value = 4.29e-09 (Fisher's exact test), Q value = 1.5e-06

Table S67.  Gene #12: '6q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
6Q MUTATED 2 18 8 40
6Q WILD-TYPE 35 62 57 36

Figure S67.  Get High-res Image Gene #12: '6q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q' versus 'MRNASEQ_CNMF'

P value = 1.27e-05 (Chi-square test), Q value = 0.0035

Table S68.  Gene #12: '6q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
6Q MUTATED 11 8 17 9 31
6Q WILD-TYPE 54 54 29 28 31

Figure S68.  Get High-res Image Gene #12: '6q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.68e-05 (Fisher's exact test), Q value = 0.0094

Table S69.  Gene #12: '6q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
6Q MUTATED 34 26 16
6Q WILD-TYPE 35 87 74

Figure S69.  Get High-res Image Gene #12: '6q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000158 (Fisher's exact test), Q value = 0.036

Table S70.  Gene #12: '6q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
6Q MUTATED 20 38 34
6Q WILD-TYPE 82 43 104

Figure S70.  Get High-res Image Gene #12: '6q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00112 (Fisher's exact test), Q value = 0.2

Table S71.  Gene #12: '6q' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 131 79
6Q MUTATED 11 49 14
6Q WILD-TYPE 53 82 65

Figure S71.  Get High-res Image Gene #12: '6q' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.06e-05 (Fisher's exact test), Q value = 0.0029

Table S72.  Gene #12: '6q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
6Q MUTATED 32 30 12
6Q WILD-TYPE 32 99 69

Figure S72.  Get High-res Image Gene #12: '6q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p' versus 'CN_CNMF'

P value = 6.53e-14 (Chi-square test), Q value = 2.5e-11

Table S73.  Gene #13: '7p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
7P MUTATED 37 26 34 6 52 1
7P WILD-TYPE 114 1 21 7 30 2

Figure S73.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #1: 'CN_CNMF'

'7p' versus 'METHLYATION_CNMF'

P value = 1.53e-05 (Fisher's exact test), Q value = 0.0042

Table S74.  Gene #13: '7p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
7P MUTATED 18 43 15 48
7P WILD-TYPE 19 37 50 28

Figure S74.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.98e-05 (Fisher's exact test), Q value = 0.017

Table S75.  Gene #13: '7p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
7P MUTATED 45 55 29
7P WILD-TYPE 19 74 52

Figure S75.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q' versus 'CN_CNMF'

P value = 1.88e-12 (Chi-square test), Q value = 7.1e-10

Table S76.  Gene #14: '7q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
7Q MUTATED 36 26 34 6 42 1
7Q WILD-TYPE 115 1 21 7 40 2

Figure S76.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #1: 'CN_CNMF'

'7q' versus 'METHLYATION_CNMF'

P value = 9.58e-05 (Fisher's exact test), Q value = 0.023

Table S77.  Gene #14: '7q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
7Q MUTATED 18 39 13 42
7Q WILD-TYPE 19 41 52 34

Figure S77.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p' versus 'CN_CNMF'

P value = 0.000313 (Chi-square test), Q value = 0.067

Table S78.  Gene #15: '8p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
8P MUTATED 72 21 35 13 54 2
8P WILD-TYPE 79 6 20 0 28 1

Figure S78.  Get High-res Image Gene #15: '8p' versus Molecular Subtype #1: 'CN_CNMF'

'8p' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.7e-06 (Fisher's exact test), Q value = 0.0019

Table S79.  Gene #15: '8p' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 131 79
8P MUTATED 37 93 29
8P WILD-TYPE 27 38 50

Figure S79.  Get High-res Image Gene #15: '8p' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8q' versus 'CN_CNMF'

P value = 0.000405 (Chi-square test), Q value = 0.083

Table S80.  Gene #16: '8q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
8Q MUTATED 77 21 31 13 59 2
8Q WILD-TYPE 74 6 24 0 23 1

Figure S80.  Get High-res Image Gene #16: '8q' versus Molecular Subtype #1: 'CN_CNMF'

'8q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000398 (Fisher's exact test), Q value = 0.082

Table S81.  Gene #16: '8q' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 131 79
8Q MUTATED 39 91 33
8Q WILD-TYPE 25 40 46

Figure S81.  Get High-res Image Gene #16: '8q' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9p' versus 'CN_CNMF'

P value = 3.67e-16 (Chi-square test), Q value = 1.4e-13

Table S82.  Gene #17: '9p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
9P MUTATED 29 12 42 7 55 0
9P WILD-TYPE 122 15 13 6 27 3

Figure S82.  Get High-res Image Gene #17: '9p' versus Molecular Subtype #1: 'CN_CNMF'

'9p' versus 'METHLYATION_CNMF'

P value = 6.12e-07 (Fisher's exact test), Q value = 0.00019

Table S83.  Gene #17: '9p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
9P MUTATED 6 34 22 51
9P WILD-TYPE 31 46 43 25

Figure S83.  Get High-res Image Gene #17: '9p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p' versus 'RPPA_CNMF'

P value = 0.000205 (Fisher's exact test), Q value = 0.046

Table S84.  Gene #17: '9p' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 90 91
9P MUTATED 21 41 51
9P WILD-TYPE 61 49 40

Figure S84.  Get High-res Image Gene #17: '9p' versus Molecular Subtype #3: 'RPPA_CNMF'

'9p' versus 'MRNASEQ_CNMF'

P value = 3.14e-06 (Chi-square test), Q value = 0.00092

Table S85.  Gene #17: '9p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
9P MUTATED 17 18 23 16 43
9P WILD-TYPE 48 44 23 21 19

Figure S85.  Get High-res Image Gene #17: '9p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.42e-05 (Fisher's exact test), Q value = 0.021

Table S86.  Gene #17: '9p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
9P MUTATED 45 42 30
9P WILD-TYPE 24 71 60

Figure S86.  Get High-res Image Gene #17: '9p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p' versus 'MIRSEQ_CNMF'

P value = 0.000134 (Fisher's exact test), Q value = 0.031

Table S87.  Gene #17: '9p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
9P MUTATED 32 41 67
9P WILD-TYPE 73 60 48

Figure S87.  Get High-res Image Gene #17: '9p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.53e-06 (Fisher's exact test), Q value = 0.0016

Table S88.  Gene #17: '9p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
9P MUTATED 40 54 46
9P WILD-TYPE 62 27 92

Figure S88.  Get High-res Image Gene #17: '9p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.21e-08 (Fisher's exact test), Q value = 1.1e-05

Table S89.  Gene #17: '9p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
9P MUTATED 49 47 27
9P WILD-TYPE 15 82 54

Figure S89.  Get High-res Image Gene #17: '9p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q' versus 'CN_CNMF'

P value = 8.6e-10 (Chi-square test), Q value = 3.1e-07

Table S90.  Gene #18: '9q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
9Q MUTATED 28 10 33 6 47 0
9Q WILD-TYPE 123 17 22 7 35 3

Figure S90.  Get High-res Image Gene #18: '9q' versus Molecular Subtype #1: 'CN_CNMF'

'9q' versus 'METHLYATION_CNMF'

P value = 7.42e-05 (Fisher's exact test), Q value = 0.018

Table S91.  Gene #18: '9q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
9Q MUTATED 6 31 18 43
9Q WILD-TYPE 31 49 47 33

Figure S91.  Get High-res Image Gene #18: '9q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q' versus 'MRNASEQ_CNMF'

P value = 0.000377 (Chi-square test), Q value = 0.078

Table S92.  Gene #18: '9q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
9Q MUTATED 16 16 20 12 36
9Q WILD-TYPE 49 46 26 25 26

Figure S92.  Get High-res Image Gene #18: '9q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00065 (Fisher's exact test), Q value = 0.13

Table S93.  Gene #18: '9q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
9Q MUTATED 37 46 22
9Q WILD-TYPE 27 83 59

Figure S93.  Get High-res Image Gene #18: '9q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p' versus 'CN_CNMF'

P value = 9.98e-21 (Chi-square test), Q value = 4e-18

Table S94.  Gene #19: '10p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
10P MUTATED 14 11 39 2 51 1
10P WILD-TYPE 137 16 16 11 31 2

Figure S94.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #1: 'CN_CNMF'

'10p' versus 'METHLYATION_CNMF'

P value = 3.99e-09 (Fisher's exact test), Q value = 1.4e-06

Table S95.  Gene #19: '10p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
10P MUTATED 4 24 14 48
10P WILD-TYPE 33 56 51 28

Figure S95.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p' versus 'MRNASEQ_CNMF'

P value = 4.89e-06 (Chi-square test), Q value = 0.0014

Table S96.  Gene #19: '10p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
10P MUTATED 14 16 15 10 39
10P WILD-TYPE 51 46 31 27 23

Figure S96.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000173 (Fisher's exact test), Q value = 0.04

Table S97.  Gene #19: '10p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
10P MUTATED 38 34 22
10P WILD-TYPE 31 79 68

Figure S97.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p' versus 'MIRSEQ_CNMF'

P value = 0.000129 (Fisher's exact test), Q value = 0.03

Table S98.  Gene #19: '10p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
10P MUTATED 27 28 58
10P WILD-TYPE 78 73 57

Figure S98.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.81e-06 (Fisher's exact test), Q value = 0.0017

Table S99.  Gene #19: '10p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
10P MUTATED 30 47 36
10P WILD-TYPE 72 34 102

Figure S99.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.58e-05 (Fisher's exact test), Q value = 0.012

Table S100.  Gene #19: '10p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
10P MUTATED 37 37 20
10P WILD-TYPE 27 92 61

Figure S100.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q' versus 'CN_CNMF'

P value = 8.71e-16 (Chi-square test), Q value = 3.4e-13

Table S101.  Gene #20: '10q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
10Q MUTATED 12 8 33 3 43 0
10Q WILD-TYPE 139 19 22 10 39 3

Figure S101.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #1: 'CN_CNMF'

'10q' versus 'METHLYATION_CNMF'

P value = 1.06e-06 (Fisher's exact test), Q value = 0.00033

Table S102.  Gene #20: '10q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
10Q MUTATED 4 18 12 40
10Q WILD-TYPE 33 62 53 36

Figure S102.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q' versus 'MRNASEQ_CNMF'

P value = 1.93e-06 (Chi-square test), Q value = 0.00057

Table S103.  Gene #20: '10q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
10Q MUTATED 12 11 10 9 35
10Q WILD-TYPE 53 51 36 28 27

Figure S103.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.98e-05 (Fisher's exact test), Q value = 0.022

Table S104.  Gene #20: '10q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
10Q MUTATED 33 29 15
10Q WILD-TYPE 36 84 75

Figure S104.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000624 (Fisher's exact test), Q value = 0.12

Table S105.  Gene #20: '10q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
10Q MUTATED 24 38 33
10Q WILD-TYPE 78 43 105

Figure S105.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000149 (Fisher's exact test), Q value = 0.035

Table S106.  Gene #20: '10q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
10Q MUTATED 31 32 14
10Q WILD-TYPE 33 97 67

Figure S106.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p' versus 'CN_CNMF'

P value = 1.98e-08 (Chi-square test), Q value = 6.7e-06

Table S107.  Gene #21: '11p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
11P MUTATED 15 6 19 2 39 1
11P WILD-TYPE 136 21 36 11 43 2

Figure S107.  Get High-res Image Gene #21: '11p' versus Molecular Subtype #1: 'CN_CNMF'

'11p' versus 'METHLYATION_CNMF'

P value = 2.23e-05 (Fisher's exact test), Q value = 0.0059

Table S108.  Gene #21: '11p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
11P MUTATED 7 13 8 34
11P WILD-TYPE 30 67 57 42

Figure S108.  Get High-res Image Gene #21: '11p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000327 (Fisher's exact test), Q value = 0.07

Table S109.  Gene #21: '11p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
11P MUTATED 27 18 13
11P WILD-TYPE 42 95 77

Figure S109.  Get High-res Image Gene #21: '11p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000238 (Fisher's exact test), Q value = 0.053

Table S110.  Gene #21: '11p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
11P MUTATED 15 33 30
11P WILD-TYPE 87 48 108

Figure S110.  Get High-res Image Gene #21: '11p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000526 (Fisher's exact test), Q value = 0.1

Table S111.  Gene #21: '11p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
11P MUTATED 27 23 14
11P WILD-TYPE 37 106 67

Figure S111.  Get High-res Image Gene #21: '11p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q' versus 'CN_CNMF'

P value = 4.13e-07 (Chi-square test), Q value = 0.00013

Table S112.  Gene #22: '11q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
11Q MUTATED 18 6 22 2 37 1
11Q WILD-TYPE 133 21 33 11 45 2

Figure S112.  Get High-res Image Gene #22: '11q' versus Molecular Subtype #1: 'CN_CNMF'

'11q' versus 'METHLYATION_CNMF'

P value = 0.000941 (Fisher's exact test), Q value = 0.17

Table S113.  Gene #22: '11q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
11Q MUTATED 8 14 9 31
11Q WILD-TYPE 29 66 56 45

Figure S113.  Get High-res Image Gene #22: '11q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p' versus 'CN_CNMF'

P value = 6.47e-13 (Chi-square test), Q value = 2.5e-10

Table S114.  Gene #23: '12p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
12P MUTATED 20 10 27 2 51 1
12P WILD-TYPE 131 17 28 11 31 2

Figure S114.  Get High-res Image Gene #23: '12p' versus Molecular Subtype #1: 'CN_CNMF'

'12p' versus 'METHLYATION_CNMF'

P value = 4.06e-07 (Fisher's exact test), Q value = 0.00013

Table S115.  Gene #23: '12p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
12P MUTATED 11 20 11 45
12P WILD-TYPE 26 60 54 31

Figure S115.  Get High-res Image Gene #23: '12p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p' versus 'MRNASEQ_CNMF'

P value = 1.8e-06 (Chi-square test), Q value = 0.00054

Table S116.  Gene #23: '12p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
12P MUTATED 14 12 13 12 38
12P WILD-TYPE 51 50 33 25 24

Figure S116.  Get High-res Image Gene #23: '12p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p' versus 'MIRSEQ_CNMF'

P value = 0.000188 (Fisher's exact test), Q value = 0.043

Table S117.  Gene #23: '12p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
12P MUTATED 29 23 55
12P WILD-TYPE 76 78 60

Figure S117.  Get High-res Image Gene #23: '12p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000325 (Fisher's exact test), Q value = 0.07

Table S118.  Gene #23: '12p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
12P MUTATED 27 42 38
12P WILD-TYPE 75 39 100

Figure S118.  Get High-res Image Gene #23: '12p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.063

Table S119.  Gene #23: '12p' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 131 79
12P MUTATED 20 58 14
12P WILD-TYPE 44 73 65

Figure S119.  Get High-res Image Gene #23: '12p' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.56e-05 (Fisher's exact test), Q value = 0.0092

Table S120.  Gene #23: '12p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
12P MUTATED 36 39 17
12P WILD-TYPE 28 90 64

Figure S120.  Get High-res Image Gene #23: '12p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q' versus 'CN_CNMF'

P value = 1.6e-06 (Chi-square test), Q value = 0.00048

Table S121.  Gene #24: '12q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
12Q MUTATED 20 9 24 2 36 1
12Q WILD-TYPE 131 18 31 11 46 2

Figure S121.  Get High-res Image Gene #24: '12q' versus Molecular Subtype #1: 'CN_CNMF'

'12q' versus 'METHLYATION_CNMF'

P value = 0.000302 (Fisher's exact test), Q value = 0.065

Table S122.  Gene #24: '12q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
12Q MUTATED 13 16 11 35
12Q WILD-TYPE 24 64 54 41

Figure S122.  Get High-res Image Gene #24: '12q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q' versus 'CN_CNMF'

P value = 1.78e-09 (Chi-square test), Q value = 6.3e-07

Table S123.  Gene #25: '13q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
13Q MUTATED 38 21 25 5 52 0
13Q WILD-TYPE 113 6 30 8 30 3

Figure S123.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #1: 'CN_CNMF'

'13q' versus 'METHLYATION_CNMF'

P value = 0.00118 (Fisher's exact test), Q value = 0.21

Table S124.  Gene #25: '13q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
13Q MUTATED 10 29 21 45
13Q WILD-TYPE 27 51 44 31

Figure S124.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q' versus 'MIRSEQ_CNMF'

P value = 0.000363 (Fisher's exact test), Q value = 0.077

Table S125.  Gene #25: '13q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
13Q MUTATED 35 36 66
13Q WILD-TYPE 70 65 49

Figure S125.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'13q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000902 (Fisher's exact test), Q value = 0.17

Table S126.  Gene #25: '13q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
13Q MUTATED 36 49 52
13Q WILD-TYPE 66 32 86

Figure S126.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'13q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.024

Table S127.  Gene #25: '13q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
13Q MUTATED 41 45 26
13Q WILD-TYPE 23 84 55

Figure S127.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q' versus 'CN_CNMF'

P value = 1.29e-09 (Chi-square test), Q value = 4.6e-07

Table S128.  Gene #26: '14q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
14Q MUTATED 19 9 28 2 41 1
14Q WILD-TYPE 132 18 27 11 41 2

Figure S128.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #1: 'CN_CNMF'

'14q' versus 'METHLYATION_CNMF'

P value = 0.000623 (Fisher's exact test), Q value = 0.12

Table S129.  Gene #26: '14q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
14Q MUTATED 5 19 14 35
14Q WILD-TYPE 32 61 51 41

Figure S129.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q' versus 'MRNASEQ_CNMF'

P value = 0.000537 (Chi-square test), Q value = 0.11

Table S130.  Gene #26: '14q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
14Q MUTATED 11 17 11 6 30
14Q WILD-TYPE 54 45 35 31 32

Figure S130.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000368 (Fisher's exact test), Q value = 0.077

Table S131.  Gene #26: '14q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
14Q MUTATED 32 22 21
14Q WILD-TYPE 37 91 69

Figure S131.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q' versus 'MIRSEQ_CNMF'

P value = 1.99e-05 (Fisher's exact test), Q value = 0.0053

Table S132.  Gene #26: '14q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
14Q MUTATED 16 28 50
14Q WILD-TYPE 89 73 65

Figure S132.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000269 (Fisher's exact test), Q value = 0.059

Table S133.  Gene #26: '14q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
14Q MUTATED 32 29 19
14Q WILD-TYPE 32 100 62

Figure S133.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q' versus 'CN_CNMF'

P value = 1.17e-11 (Chi-square test), Q value = 4.4e-09

Table S134.  Gene #27: '15q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
15Q MUTATED 13 10 28 2 39 1
15Q WILD-TYPE 138 17 27 11 43 2

Figure S134.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #1: 'CN_CNMF'

'15q' versus 'METHLYATION_CNMF'

P value = 7.55e-08 (Fisher's exact test), Q value = 2.5e-05

Table S135.  Gene #27: '15q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
15Q MUTATED 6 17 8 41
15Q WILD-TYPE 31 63 57 35

Figure S135.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q' versus 'MRNASEQ_CNMF'

P value = 8.62e-07 (Chi-square test), Q value = 0.00027

Table S136.  Gene #27: '15q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
15Q MUTATED 13 5 10 9 32
15Q WILD-TYPE 52 57 36 28 30

Figure S136.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.85e-07 (Fisher's exact test), Q value = 0.00031

Table S137.  Gene #27: '15q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
15Q MUTATED 33 26 10
15Q WILD-TYPE 36 87 80

Figure S137.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q' versus 'MIRSEQ_CNMF'

P value = 0.000711 (Fisher's exact test), Q value = 0.14

Table S138.  Gene #27: '15q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
15Q MUTATED 24 18 46
15Q WILD-TYPE 81 83 69

Figure S138.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.59e-07 (Fisher's exact test), Q value = 3e-04

Table S139.  Gene #27: '15q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
15Q MUTATED 18 41 29
15Q WILD-TYPE 84 40 109

Figure S139.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.46e-07 (Fisher's exact test), Q value = 7.9e-05

Table S140.  Gene #27: '15q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
15Q MUTATED 35 31 11
15Q WILD-TYPE 29 98 70

Figure S140.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p' versus 'CN_CNMF'

P value = 3.55e-17 (Chi-square test), Q value = 1.4e-14

Table S141.  Gene #28: '16p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
16P MUTATED 20 5 31 2 55 2
16P WILD-TYPE 131 22 24 11 27 1

Figure S141.  Get High-res Image Gene #28: '16p' versus Molecular Subtype #1: 'CN_CNMF'

'16p' versus 'METHLYATION_CNMF'

P value = 4.23e-08 (Fisher's exact test), Q value = 1.4e-05

Table S142.  Gene #28: '16p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
16P MUTATED 5 19 15 46
16P WILD-TYPE 32 61 50 30

Figure S142.  Get High-res Image Gene #28: '16p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p' versus 'MRNASEQ_CNMF'

P value = 1.51e-08 (Chi-square test), Q value = 5.2e-06

Table S143.  Gene #28: '16p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
16P MUTATED 12 15 17 7 41
16P WILD-TYPE 53 47 29 30 21

Figure S143.  Get High-res Image Gene #28: '16p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.3e-05 (Fisher's exact test), Q value = 0.0086

Table S144.  Gene #28: '16p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
16P MUTATED 39 28 25
16P WILD-TYPE 30 85 65

Figure S144.  Get High-res Image Gene #28: '16p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p' versus 'MIRSEQ_CNMF'

P value = 3.78e-06 (Fisher's exact test), Q value = 0.0011

Table S145.  Gene #28: '16p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
16P MUTATED 25 25 60
16P WILD-TYPE 80 76 55

Figure S145.  Get High-res Image Gene #28: '16p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.99e-06 (Fisher's exact test), Q value = 0.0022

Table S146.  Gene #28: '16p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
16P MUTATED 28 46 36
16P WILD-TYPE 74 35 102

Figure S146.  Get High-res Image Gene #28: '16p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000375 (Fisher's exact test), Q value = 0.078

Table S147.  Gene #28: '16p' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 131 79
16P MUTATED 12 59 21
16P WILD-TYPE 52 72 58

Figure S147.  Get High-res Image Gene #28: '16p' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.17e-06 (Fisher's exact test), Q value = 0.00036

Table S148.  Gene #28: '16p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
16P MUTATED 39 35 18
16P WILD-TYPE 25 94 63

Figure S148.  Get High-res Image Gene #28: '16p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q' versus 'CN_CNMF'

P value = 1.2e-14 (Chi-square test), Q value = 4.6e-12

Table S149.  Gene #29: '16q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
16Q MUTATED 22 5 29 2 53 2
16Q WILD-TYPE 129 22 26 11 29 1

Figure S149.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #1: 'CN_CNMF'

'16q' versus 'METHLYATION_CNMF'

P value = 4.06e-08 (Fisher's exact test), Q value = 1.3e-05

Table S150.  Gene #29: '16q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
16Q MUTATED 5 18 16 46
16Q WILD-TYPE 32 62 49 30

Figure S150.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q' versus 'MRNASEQ_CNMF'

P value = 7.07e-09 (Chi-square test), Q value = 2.4e-06

Table S151.  Gene #29: '16q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
16Q MUTATED 11 17 18 6 41
16Q WILD-TYPE 54 45 28 31 21

Figure S151.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.07e-05 (Fisher's exact test), Q value = 0.0029

Table S152.  Gene #29: '16q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
16Q MUTATED 40 27 26
16Q WILD-TYPE 29 86 64

Figure S152.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q' versus 'MIRSEQ_CNMF'

P value = 7.1e-06 (Fisher's exact test), Q value = 0.002

Table S153.  Gene #29: '16q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
16Q MUTATED 24 26 59
16Q WILD-TYPE 81 75 56

Figure S153.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.12e-05 (Fisher's exact test), Q value = 0.013

Table S154.  Gene #29: '16q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
16Q MUTATED 30 44 35
16Q WILD-TYPE 72 37 103

Figure S154.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.91e-05 (Fisher's exact test), Q value = 0.0051

Table S155.  Gene #29: '16q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
16Q MUTATED 37 34 20
16Q WILD-TYPE 27 95 61

Figure S155.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p' versus 'CN_CNMF'

P value = 3.66e-22 (Chi-square test), Q value = 1.5e-19

Table S156.  Gene #30: '17p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
17P MUTATED 18 18 35 3 59 3
17P WILD-TYPE 133 9 20 10 23 0

Figure S156.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #1: 'CN_CNMF'

'17p' versus 'METHLYATION_CNMF'

P value = 1.26e-09 (Fisher's exact test), Q value = 4.5e-07

Table S157.  Gene #30: '17p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
17P MUTATED 7 31 14 53
17P WILD-TYPE 30 49 51 23

Figure S157.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p' versus 'MRNASEQ_CNMF'

P value = 3.23e-08 (Chi-square test), Q value = 1.1e-05

Table S158.  Gene #30: '17p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
17P MUTATED 16 12 21 14 43
17P WILD-TYPE 49 50 25 23 19

Figure S158.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.47e-07 (Fisher's exact test), Q value = 2e-04

Table S159.  Gene #30: '17p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
17P MUTATED 45 39 22
17P WILD-TYPE 24 74 68

Figure S159.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p' versus 'MIRSEQ_CNMF'

P value = 1.73e-05 (Fisher's exact test), Q value = 0.0047

Table S160.  Gene #30: '17p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
17P MUTATED 39 27 66
17P WILD-TYPE 66 74 49

Figure S160.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.74e-07 (Fisher's exact test), Q value = 0.00012

Table S161.  Gene #30: '17p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
17P MUTATED 30 54 48
17P WILD-TYPE 72 27 90

Figure S161.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00108 (Fisher's exact test), Q value = 0.2

Table S162.  Gene #30: '17p' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 131 79
17P MUTATED 24 68 21
17P WILD-TYPE 40 63 58

Figure S162.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.44e-08 (Fisher's exact test), Q value = 4.9e-06

Table S163.  Gene #30: '17p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
17P MUTATED 47 43 23
17P WILD-TYPE 17 86 58

Figure S163.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q' versus 'CN_CNMF'

P value = 5.05e-10 (Chi-square test), Q value = 1.8e-07

Table S164.  Gene #31: '17q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
17Q MUTATED 15 11 22 3 41 2
17Q WILD-TYPE 136 16 33 10 41 1

Figure S164.  Get High-res Image Gene #31: '17q' versus Molecular Subtype #1: 'CN_CNMF'

'17q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000151 (Fisher's exact test), Q value = 0.035

Table S165.  Gene #31: '17q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
17Q MUTATED 31 26 14
17Q WILD-TYPE 38 87 76

Figure S165.  Get High-res Image Gene #31: '17q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q' versus 'MIRSEQ_CNMF'

P value = 0.00121 (Fisher's exact test), Q value = 0.22

Table S166.  Gene #31: '17q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
17Q MUTATED 27 18 46
17Q WILD-TYPE 78 83 69

Figure S166.  Get High-res Image Gene #31: '17q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18p' versus 'CN_CNMF'

P value = 1.19e-12 (Chi-square test), Q value = 4.5e-10

Table S167.  Gene #32: '18p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
18P MUTATED 38 14 39 3 57 3
18P WILD-TYPE 113 13 16 10 25 0

Figure S167.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #1: 'CN_CNMF'

'18p' versus 'METHLYATION_CNMF'

P value = 0.000412 (Fisher's exact test), Q value = 0.085

Table S168.  Gene #32: '18p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
18P MUTATED 14 29 24 50
18P WILD-TYPE 23 51 41 26

Figure S168.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p' versus 'MIRSEQ_CNMF'

P value = 2.15e-05 (Fisher's exact test), Q value = 0.0057

Table S169.  Gene #32: '18p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
18P MUTATED 34 42 72
18P WILD-TYPE 71 59 43

Figure S169.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.19e-05 (Fisher's exact test), Q value = 0.0083

Table S170.  Gene #32: '18p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
18P MUTATED 40 55 53
18P WILD-TYPE 62 26 85

Figure S170.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000113 (Fisher's exact test), Q value = 0.027

Table S171.  Gene #32: '18p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
18P MUTATED 45 52 32
18P WILD-TYPE 19 77 49

Figure S171.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q' versus 'CN_CNMF'

P value = 5.55e-15 (Chi-square test), Q value = 2.1e-12

Table S172.  Gene #33: '18q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
18Q MUTATED 37 15 41 3 61 2
18Q WILD-TYPE 114 12 14 10 21 1

Figure S172.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #1: 'CN_CNMF'

'18q' versus 'METHLYATION_CNMF'

P value = 0.000561 (Fisher's exact test), Q value = 0.11

Table S173.  Gene #33: '18q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
18Q MUTATED 16 28 25 50
18Q WILD-TYPE 21 52 40 26

Figure S173.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q' versus 'MRNASEQ_CNMF'

P value = 0.000893 (Chi-square test), Q value = 0.17

Table S174.  Gene #33: '18q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
18Q MUTATED 23 22 23 12 41
18Q WILD-TYPE 42 40 23 25 21

Figure S174.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18q' versus 'MIRSEQ_CNMF'

P value = 4.42e-06 (Fisher's exact test), Q value = 0.0013

Table S175.  Gene #33: '18q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
18Q MUTATED 38 39 76
18Q WILD-TYPE 67 62 39

Figure S175.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.1e-05 (Fisher's exact test), Q value = 0.003

Table S176.  Gene #33: '18q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
18Q MUTATED 39 57 57
18Q WILD-TYPE 63 24 81

Figure S176.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000128 (Fisher's exact test), Q value = 0.03

Table S177.  Gene #33: '18q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
18Q MUTATED 45 54 31
18Q WILD-TYPE 19 75 50

Figure S177.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p' versus 'CN_CNMF'

P value = 2.37e-21 (Chi-square test), Q value = 9.5e-19

Table S178.  Gene #34: '19p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
19P MUTATED 14 12 32 3 59 2
19P WILD-TYPE 137 15 23 10 23 1

Figure S178.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #1: 'CN_CNMF'

'19p' versus 'METHLYATION_CNMF'

P value = 8.26e-11 (Fisher's exact test), Q value = 3e-08

Table S179.  Gene #34: '19p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
19P MUTATED 9 23 9 51
19P WILD-TYPE 28 57 56 25

Figure S179.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p' versus 'MRNASEQ_CNMF'

P value = 1.87e-11 (Chi-square test), Q value = 6.9e-09

Table S180.  Gene #34: '19p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
19P MUTATED 15 9 16 9 45
19P WILD-TYPE 50 53 30 28 17

Figure S180.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.81e-09 (Fisher's exact test), Q value = 2.4e-06

Table S181.  Gene #34: '19p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
19P MUTATED 44 34 16
19P WILD-TYPE 25 79 74

Figure S181.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p' versus 'MIRSEQ_CNMF'

P value = 1.42e-06 (Fisher's exact test), Q value = 0.00043

Table S182.  Gene #34: '19p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
19P MUTATED 31 24 64
19P WILD-TYPE 74 77 51

Figure S182.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.25e-11 (Fisher's exact test), Q value = 1.6e-08

Table S183.  Gene #34: '19p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
19P MUTATED 23 56 40
19P WILD-TYPE 79 25 98

Figure S183.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000877 (Fisher's exact test), Q value = 0.17

Table S184.  Gene #34: '19p' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 131 79
19P MUTATED 19 63 19
19P WILD-TYPE 45 68 60

Figure S184.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.13e-09 (Fisher's exact test), Q value = 4.1e-07

Table S185.  Gene #34: '19p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
19P MUTATED 45 39 17
19P WILD-TYPE 19 90 64

Figure S185.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q' versus 'CN_CNMF'

P value = 4.45e-18 (Chi-square test), Q value = 1.8e-15

Table S186.  Gene #35: '19q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
19Q MUTATED 16 12 26 4 58 2
19Q WILD-TYPE 135 15 29 9 24 1

Figure S186.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #1: 'CN_CNMF'

'19q' versus 'METHLYATION_CNMF'

P value = 2.42e-09 (Fisher's exact test), Q value = 8.5e-07

Table S187.  Gene #35: '19q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
19Q MUTATED 10 21 9 48
19Q WILD-TYPE 27 59 56 28

Figure S187.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q' versus 'RPPA_CNMF'

P value = 0.00105 (Fisher's exact test), Q value = 0.19

Table S188.  Gene #35: '19q' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 90 91
19Q MUTATED 23 20 43
19Q WILD-TYPE 59 70 48

Figure S188.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #3: 'RPPA_CNMF'

'19q' versus 'MRNASEQ_CNMF'

P value = 1.24e-10 (Chi-square test), Q value = 4.6e-08

Table S189.  Gene #35: '19q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
19Q MUTATED 15 8 16 9 43
19Q WILD-TYPE 50 54 30 28 19

Figure S189.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.22e-07 (Fisher's exact test), Q value = 4e-05

Table S190.  Gene #35: '19q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
19Q MUTATED 40 37 14
19Q WILD-TYPE 29 76 76

Figure S190.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q' versus 'MIRSEQ_CNMF'

P value = 1.26e-06 (Fisher's exact test), Q value = 0.00039

Table S191.  Gene #35: '19q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
19Q MUTATED 30 22 62
19Q WILD-TYPE 75 79 53

Figure S191.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.32e-10 (Fisher's exact test), Q value = 4.8e-08

Table S192.  Gene #35: '19q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
19Q MUTATED 22 54 38
19Q WILD-TYPE 80 27 100

Figure S192.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000462 (Fisher's exact test), Q value = 0.093

Table S193.  Gene #35: '19q' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 131 79
19Q MUTATED 18 61 17
19Q WILD-TYPE 46 70 62

Figure S193.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.52e-09 (Fisher's exact test), Q value = 2.3e-06

Table S194.  Gene #35: '19q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
19Q MUTATED 43 36 17
19Q WILD-TYPE 21 93 64

Figure S194.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p' versus 'CN_CNMF'

P value = 1.38e-16 (Chi-square test), Q value = 5.4e-14

Table S195.  Gene #36: '20p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
20P MUTATED 51 24 47 7 67 2
20P WILD-TYPE 100 3 8 6 15 1

Figure S195.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #1: 'CN_CNMF'

'20p' versus 'METHLYATION_CNMF'

P value = 4.09e-08 (Fisher's exact test), Q value = 1.4e-05

Table S196.  Gene #36: '20p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
20P MUTATED 24 39 25 64
20P WILD-TYPE 13 41 40 12

Figure S196.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p' versus 'MRNASEQ_CNMF'

P value = 0.000237 (Chi-square test), Q value = 0.053

Table S197.  Gene #36: '20p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
20P MUTATED 27 29 28 22 49
20P WILD-TYPE 38 33 18 15 13

Figure S197.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p' versus 'MIRSEQ_CNMF'

P value = 3.77e-06 (Fisher's exact test), Q value = 0.0011

Table S198.  Gene #36: '20p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
20P MUTATED 54 48 89
20P WILD-TYPE 51 53 26

Figure S198.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.38e-06 (Fisher's exact test), Q value = 0.0023

Table S199.  Gene #36: '20p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
20P MUTATED 47 65 79
20P WILD-TYPE 55 16 59

Figure S199.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.81e-06 (Fisher's exact test), Q value = 0.0019

Table S200.  Gene #36: '20p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
20P MUTATED 54 67 41
20P WILD-TYPE 10 62 40

Figure S200.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q' versus 'CN_CNMF'

P value = 3.87e-16 (Chi-square test), Q value = 1.5e-13

Table S201.  Gene #37: '20q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
20Q MUTATED 57 25 45 8 72 2
20Q WILD-TYPE 94 2 10 5 10 1

Figure S201.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #1: 'CN_CNMF'

'20q' versus 'METHLYATION_CNMF'

P value = 9.57e-10 (Fisher's exact test), Q value = 3.4e-07

Table S202.  Gene #37: '20q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
20Q MUTATED 25 42 28 69
20Q WILD-TYPE 12 38 37 7

Figure S202.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q' versus 'MRNASEQ_CNMF'

P value = 1.02e-06 (Chi-square test), Q value = 0.00032

Table S203.  Gene #37: '20q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
20Q MUTATED 29 31 27 24 56
20Q WILD-TYPE 36 31 19 13 6

Figure S203.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.6e-05 (Fisher's exact test), Q value = 0.019

Table S204.  Gene #37: '20q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
20Q MUTATED 57 63 47
20Q WILD-TYPE 12 50 43

Figure S204.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q' versus 'MIRSEQ_CNMF'

P value = 2.26e-06 (Fisher's exact test), Q value = 0.00067

Table S205.  Gene #37: '20q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
20Q MUTATED 56 53 93
20Q WILD-TYPE 49 48 22

Figure S205.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.03e-09 (Fisher's exact test), Q value = 3.7e-07

Table S206.  Gene #37: '20q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
20Q MUTATED 49 73 80
20Q WILD-TYPE 53 8 58

Figure S206.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.37e-09 (Fisher's exact test), Q value = 8.3e-07

Table S207.  Gene #37: '20q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
20Q MUTATED 60 73 41
20Q WILD-TYPE 4 56 40

Figure S207.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q' versus 'CN_CNMF'

P value = 1.92e-15 (Chi-square test), Q value = 7.4e-13

Table S208.  Gene #38: '21q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
21Q MUTATED 26 13 38 6 54 3
21Q WILD-TYPE 125 14 17 7 28 0

Figure S208.  Get High-res Image Gene #38: '21q' versus Molecular Subtype #1: 'CN_CNMF'

'21q' versus 'METHLYATION_CNMF'

P value = 3.41e-08 (Fisher's exact test), Q value = 1.1e-05

Table S209.  Gene #38: '21q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
21Q MUTATED 3 38 21 48
21Q WILD-TYPE 34 42 44 28

Figure S209.  Get High-res Image Gene #38: '21q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q' versus 'MRNASEQ_CNMF'

P value = 0.000367 (Chi-square test), Q value = 0.077

Table S210.  Gene #38: '21q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
21Q MUTATED 20 19 16 14 40
21Q WILD-TYPE 45 43 30 23 22

Figure S210.  Get High-res Image Gene #38: '21q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'21q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.14e-05 (Fisher's exact test), Q value = 0.0057

Table S211.  Gene #38: '21q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
21Q MUTATED 44 38 27
21Q WILD-TYPE 25 75 63

Figure S211.  Get High-res Image Gene #38: '21q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'21q' versus 'MIRSEQ_CNMF'

P value = 6.12e-05 (Fisher's exact test), Q value = 0.015

Table S212.  Gene #38: '21q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
21Q MUTATED 33 35 67
21Q WILD-TYPE 72 66 48

Figure S212.  Get High-res Image Gene #38: '21q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'21q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.5e-06 (Fisher's exact test), Q value = 0.00045

Table S213.  Gene #38: '21q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
21Q MUTATED 33 54 48
21Q WILD-TYPE 69 27 90

Figure S213.  Get High-res Image Gene #38: '21q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'21q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000977 (Fisher's exact test), Q value = 0.18

Table S214.  Gene #38: '21q' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 131 79
21Q MUTATED 19 71 27
21Q WILD-TYPE 45 60 52

Figure S214.  Get High-res Image Gene #38: '21q' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'21q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.73e-06 (Fisher's exact test), Q value = 0.00052

Table S215.  Gene #38: '21q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
21Q MUTATED 45 47 25
21Q WILD-TYPE 19 82 56

Figure S215.  Get High-res Image Gene #38: '21q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q' versus 'CN_CNMF'

P value = 1.17e-19 (Chi-square test), Q value = 4.6e-17

Table S216.  Gene #39: '22q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
22Q MUTATED 17 12 38 4 53 3
22Q WILD-TYPE 134 15 17 9 29 0

Figure S216.  Get High-res Image Gene #39: '22q' versus Molecular Subtype #1: 'CN_CNMF'

'22q' versus 'METHLYATION_CNMF'

P value = 7.26e-08 (Fisher's exact test), Q value = 2.4e-05

Table S217.  Gene #39: '22q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
22Q MUTATED 5 29 17 49
22Q WILD-TYPE 32 51 48 27

Figure S217.  Get High-res Image Gene #39: '22q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q' versus 'MRNASEQ_CNMF'

P value = 5.52e-05 (Chi-square test), Q value = 0.014

Table S218.  Gene #39: '22q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
22Q MUTATED 13 19 17 14 38
22Q WILD-TYPE 52 43 29 23 24

Figure S218.  Get High-res Image Gene #39: '22q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q' versus 'MIRSEQ_CNMF'

P value = 7.77e-07 (Fisher's exact test), Q value = 0.00024

Table S219.  Gene #39: '22q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
22Q MUTATED 24 33 65
22Q WILD-TYPE 81 68 50

Figure S219.  Get High-res Image Gene #39: '22q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.03e-08 (Fisher's exact test), Q value = 3.6e-06

Table S220.  Gene #39: '22q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
22Q MUTATED 29 54 39
22Q WILD-TYPE 73 27 99

Figure S220.  Get High-res Image Gene #39: '22q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.49e-07 (Fisher's exact test), Q value = 8e-05

Table S221.  Gene #39: '22q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
22Q MUTATED 44 40 23
22Q WILD-TYPE 20 89 58

Figure S221.  Get High-res Image Gene #39: '22q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq' versus 'CN_CNMF'

P value = 4.01e-10 (Chi-square test), Q value = 1.5e-07

Table S222.  Gene #40: 'xq' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
XQ MUTATED 10 10 20 5 36 2
XQ WILD-TYPE 141 17 35 8 46 1

Figure S222.  Get High-res Image Gene #40: 'xq' versus Molecular Subtype #1: 'CN_CNMF'

'xq' versus 'METHLYATION_CNMF'

P value = 0.000108 (Fisher's exact test), Q value = 0.026

Table S223.  Gene #40: 'xq' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
XQ MUTATED 2 24 7 26
XQ WILD-TYPE 35 56 58 50

Figure S223.  Get High-res Image Gene #40: 'xq' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq' versus 'MRNASEQ_CNMF'

P value = 0.000877 (Chi-square test), Q value = 0.17

Table S224.  Gene #40: 'xq' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
XQ MUTATED 6 10 13 14 22
XQ WILD-TYPE 59 52 33 23 40

Figure S224.  Get High-res Image Gene #40: 'xq' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq' versus 'MIRSEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.057

Table S225.  Gene #40: 'xq' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
XQ MUTATED 23 14 43
XQ WILD-TYPE 82 87 72

Figure S225.  Get High-res Image Gene #40: 'xq' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xq' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00124 (Fisher's exact test), Q value = 0.22

Table S226.  Gene #40: 'xq' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 131 79
XQ MUTATED 11 45 11
XQ WILD-TYPE 53 86 68

Figure S226.  Get High-res Image Gene #40: 'xq' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

  • Molecular subtype file = STAD-TP.transferedmergedcluster.txt

  • Number of patients = 331

  • Number of significantly focal cnvs = 40

  • Number of molecular subtypes = 10

  • Exclude genes that fewer than K tumors have alterations, K = 3

Chi-square test

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

Fisher's exact test

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

Q value calculation

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.

Download Results

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.

References
[1] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[2] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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