Correlation between copy number variations of arm-level result and molecular subtypes
Esophageal Carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C19W0DQ6
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C19W0DQ6
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.

Summary

Testing the association between copy number variation 82 arm-level events and 10 molecular subtypes across 184 patients, 252 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

  • 4q gain cnv correlated to 'RPPA_CNMF' and 'RPPA_CHIERARCHICAL'.

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

  • 6p gain cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 9p gain cnv correlated to 'RPPA_CHIERARCHICAL'.

  • 9q gain cnv correlated to 'RPPA_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • 10p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 10q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 11q gain cnv correlated to 'MIRSEQ_CNMF'.

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

  • 13q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 14q gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 16p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 17p gain cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

  • 18p gain cnv correlated to 'MIRSEQ_CNMF'.

  • 19q gain cnv correlated to 'RPPA_CHIERARCHICAL' and 'MIRSEQ_CNMF'.

  • 20p gain cnv correlated to 'CN_CNMF'.

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

  • 22q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • xq gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 1q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • 2p loss cnv correlated to 'RPPA_CHIERARCHICAL' and 'MIRSEQ_CHIERARCHICAL'.

  • 2q loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 3p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 4p loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

  • 4q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

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

  • 5q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

  • 8p loss cnv correlated to 'CN_CNMF'.

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

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

  • 11q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

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

  • 12q loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 13q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 14q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 15q loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • 18p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 18q loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 19p loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 19q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 21q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

  • xp loss cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.

  • xq loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 arm-level 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, 252 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 Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
22q gain 31 (17%) 153 2e-05
(0.000586) 		1e-05
(0.000456) 		0.00398
(0.0286) 		0.00052
(0.00609) 		2e-05
(0.000586) 		2e-05
(0.000586) 		2e-05
(0.000586) 		1e-05
(0.000456) 		1e-05
(0.000456) 		3e-05
(0.000683)
14q loss 45 (24%) 139 0.00046
(0.00563) 		0.0052
(0.0344) 		0.00392
(0.0284) 		0.00281
(0.0221) 		0.00696
(0.0414) 		0.0195
(0.0908) 		0.0293
(0.115) 		0.0027
(0.0217) 		0.0369
(0.131) 		0.00129
(0.0126)
16q loss 53 (29%) 131 1e-05
(0.000456) 		2e-05
(0.000586) 		0.0383
(0.136) 		0.0277
(0.111) 		3e-05
(0.000683) 		1e-05
(0.000456) 		1e-05
(0.000456) 		2e-05
(0.000586) 		1e-05
(0.000456) 		1e-05
(0.000456)
16q gain 38 (21%) 146 0.00074
(0.00798) 		0.028
(0.111) 		0.0836
(0.218) 		0.0171
(0.0819) 		0.00315
(0.0235) 		0.0134
(0.0691) 		0.0121
(0.0645) 		0.00674
(0.0414) 		0.00287
(0.0221) 		0.00678
(0.0414)
22q loss 72 (39%) 112 5e-05
(0.00102) 		1e-05
(0.000456) 		0.0311
(0.119) 		0.115
(0.263) 		0.00111
(0.0112) 		0.00035
(0.0047) 		5e-05
(0.00102) 		0.00025
(0.00373) 		1e-05
(0.000456) 		2e-05
(0.000586)
12p gain 58 (32%) 126 0.0237
(0.101) 		0.00411
(0.0293) 		0.32
(0.521) 		0.0551
(0.169) 		0.00391
(0.0284) 		0.00262
(0.0215) 		0.00571
(0.0364) 		0.00312
(0.0235) 		0.00284
(0.0221) 		0.00931
(0.0523)
13q gain 43 (23%) 141 0.00237
(0.02) 		1e-05
(0.000456) 		0.221
(0.422) 		0.11
(0.258) 		5e-05
(0.00102) 		2e-05
(0.000586) 		1e-05
(0.000456) 		3e-05
(0.000683) 		0.00014
(0.0023) 		1e-05
(0.000456)
20q gain 115 (62%) 69 8e-05
(0.00146) 		0.00027
(0.00388) 		0.0724
(0.201) 		0.0547
(0.169) 		0.00573
(0.0364) 		0.00269
(0.0217) 		0.00039
(0.00508) 		0.00064
(0.00739) 		0.00633
(0.0396) 		5e-05
(0.00102)
1p loss 38 (21%) 146 0.00923
(0.0523) 		0.0232
(0.1) 		0.99
(1.00) 		0.878
(0.932) 		0.0145
(0.0727) 		0.0385
(0.136) 		0.0203
(0.0935) 		0.0314
(0.119) 		0.01
(0.0556) 		0.045
(0.15)
3p loss 93 (51%) 91 3e-05
(0.000683) 		7e-05
(0.00137) 		0.107
(0.254) 		0.0859
(0.222) 		3e-05
(0.000683) 		1e-05
(0.000456) 		1e-05
(0.000456) 		2e-05
(0.000586) 		0.00125
(0.0123) 		1e-05
(0.000456)
5p loss 46 (25%) 138 0.00017
(0.00268) 		3e-05
(0.000683) 		0.39
(0.58) 		0.0521
(0.163) 		8e-05
(0.00146) 		7e-05
(0.00137) 		8e-05
(0.00146) 		2e-05
(0.000586) 		0.0002
(0.00309) 		1e-05
(0.000456)
10p loss 50 (27%) 134 0.00188
(0.0171) 		0.0045
(0.0307) 		0.154
(0.318) 		0.479
(0.661) 		0.0234
(0.1) 		0.0144
(0.0727) 		0.00237
(0.02) 		0.00832
(0.0485) 		0.0136
(0.0699) 		0.00237
(0.02)
10q loss 49 (27%) 135 0.00012
(0.00205) 		0.00087
(0.00926) 		0.78
(0.885) 		0.159
(0.327) 		0.00834
(0.0485) 		0.00194
(0.0175) 		0.0016
(0.0153) 		0.00233
(0.02) 		0.0165
(0.0799) 		0.00181
(0.017)
12p loss 33 (18%) 151 0.0992
(0.241) 		0.00094
(0.00976) 		0.0628
(0.182) 		0.0211
(0.0957) 		0.00035
(0.0047) 		0.00071
(0.00798) 		0.00257
(0.0213) 		0.00204
(0.0182) 		0.0145
(0.0727) 		0.0004
(0.00512)
16p loss 54 (29%) 130 0.00051
(0.00606) 		0.00015
(0.00241) 		0.716
(0.839) 		0.686
(0.816) 		0.0007
(0.00797) 		0.00011
(0.00192) 		0.00021
(0.00319) 		0.00031
(0.00431) 		0.00046
(0.00563) 		0.00026
(0.00381)
18p loss 71 (39%) 113 0.0122
(0.0645) 		0.00103
(0.0106) 		0.205
(0.4) 		0.483
(0.661) 		0.00692
(0.0414) 		0.00446
(0.0307) 		0.00117
(0.0117) 		0.0232
(0.1) 		0.0261
(0.109) 		0.00572
(0.0364)
5p gain 76 (41%) 108 3e-05
(0.000683) 		0.0278
(0.111) 		0.5
(0.673) 		0.131
(0.286) 		0.0233
(0.1) 		0.0117
(0.0629) 		0.013
(0.0676) 		0.0328
(0.121) 		0.0513
(0.163) 		0.0161
(0.0791)
12q loss 31 (17%) 153 0.165
(0.338) 		0.00292
(0.0222) 		0.0753
(0.206) 		0.0601
(0.179) 		0.00922
(0.0523) 		0.00546
(0.0355) 		0.0253
(0.107) 		0.0115
(0.0622) 		0.00833
(0.0485) 		0.00697
(0.0414)
17p loss 71 (39%) 113 0.00274
(0.0218) 		0.00011
(0.00192) 		0.277
(0.483) 		0.279
(0.486) 		0.00184
(0.017) 		0.0009
(0.00946) 		3e-05
(0.000683) 		0.00139
(0.0134) 		0.0619
(0.181) 		0.00014
(0.0023)
18q loss 102 (55%) 82 0.0955
(0.236) 		0.0116
(0.0628) 		0.643
(0.79) 		0.791
(0.892) 		0.0265
(0.109) 		0.0273
(0.111) 		0.0218
(0.0969) 		0.00212
(0.0187) 		0.0485
(0.159) 		0.00029
(0.0041)
xq loss 40 (22%) 144 0.0161
(0.0791) 		0.028
(0.111) 		0.00038
(0.00503) 		0.0264
(0.109) 		0.0691
(0.195) 		0.0664
(0.189) 		0.12
(0.27) 		0.00244
(0.0204) 		0.0417
(0.144) 		0.011
(0.06)
14q gain 48 (26%) 136 0.0352
(0.128) 		0.0835
(0.218) 		0.0281
(0.111) 		0.228
(0.427) 		0.0515
(0.163) 		0.022
(0.0969) 		0.0382
(0.135) 		0.0363
(0.131) 		0.138
(0.294) 		0.0533
(0.166)
16p gain 41 (22%) 143 0.00415
(0.0293) 		0.0963
(0.237) 		0.135
(0.289) 		0.145
(0.305) 		0.0199
(0.092) 		0.00359
(0.0265) 		0.0255
(0.107) 		0.0362
(0.131) 		0.0833
(0.218) 		0.0586
(0.177)
xq gain 38 (21%) 146 0.045
(0.15) 		0.0296
(0.115) 		0.0451
(0.15) 		0.176
(0.355) 		0.0957
(0.236) 		0.0531
(0.166) 		0.011
(0.06) 		0.0269
(0.11) 		0.0555
(0.17) 		0.0696
(0.195)
11q loss 58 (32%) 126 0.00047
(0.00567) 		0.0423
(0.144) 		0.958
(0.984) 		0.818
(0.906) 		0.0343
(0.126) 		0.0219
(0.0969) 		0.0143
(0.0727) 		0.134
(0.289) 		0.0766
(0.208) 		0.0684
(0.194)
2p gain 61 (33%) 123 0.0128
(0.0671) 		0.0314
(0.119) 		0.135
(0.289) 		0.0895
(0.228) 		0.0928
(0.233) 		0.0915
(0.232) 		0.0368
(0.131) 		0.338
(0.538) 		0.00289
(0.0221) 		0.506
(0.678)
4q loss 87 (47%) 97 0.00042
(0.0053) 		0.0456
(0.151) 		0.126
(0.278) 		0.825
(0.907) 		0.0448
(0.15) 		0.0947
(0.236) 		0.0403
(0.14) 		0.222
(0.423) 		0.122
(0.271) 		0.0883
(0.226)
15q loss 57 (31%) 127 0.282
(0.486) 		0.0303
(0.116) 		0.196
(0.387) 		0.32
(0.521) 		0.138
(0.294) 		0.0497
(0.162) 		0.0952
(0.236) 		0.00531
(0.0348) 		0.326
(0.527) 		0.00074
(0.00798)
19q loss 52 (28%) 132 0.0048
(0.0325) 		0.111
(0.258) 		0.0729
(0.202) 		0.114
(0.262) 		0.112
(0.259) 		0.0128
(0.0671) 		0.0608
(0.179) 		0.0952
(0.236) 		0.0184
(0.0873) 		0.0094
(0.0524)
21q loss 106 (58%) 78 0.0311
(0.119) 		0.00615
(0.0388) 		0.216
(0.414) 		0.1
(0.242) 		0.0505
(0.163) 		0.0975
(0.239) 		0.0214
(0.0962) 		0.148
(0.31) 		0.042
(0.144) 		0.0846
(0.22)
10p gain 40 (22%) 144 0.0362
(0.131) 		0.0277
(0.111) 		0.354
(0.555) 		0.457
(0.641) 		0.0247
(0.104) 		0.0769
(0.208) 		0.121
(0.27) 		0.214
(0.411) 		0.0564
(0.172) 		0.0767
(0.208)
10q gain 30 (16%) 154 0.0152
(0.0757) 		0.0316
(0.119) 		0.825
(0.907) 		0.848
(0.915) 		0.0549
(0.169) 		0.0592
(0.178) 		0.08
(0.214) 		0.0703
(0.197) 		0.0514
(0.163) 		0.0218
(0.0969)
2q loss 18 (10%) 166 0.358
(0.56) 		0.0325
(0.121) 		0.847
(0.915) 		0.418
(0.605) 		0.119
(0.27) 		0.0322
(0.121) 		0.0647
(0.185) 		0.00683
(0.0414) 		0.282
(0.486) 		0.0864
(0.223)
5q loss 86 (47%) 98 0.0186
(0.0875) 		0.00926
(0.0523) 		0.245
(0.443) 		0.134
(0.289) 		0.201
(0.395) 		0.11
(0.258) 		0.0208
(0.0948) 		0.111
(0.258) 		0.212
(0.409) 		0.0918
(0.232)
13q loss 67 (36%) 117 0.0162
(0.0792) 		0.0644
(0.185) 		0.783
(0.886) 		0.664
(0.803) 		0.115
(0.263) 		0.035
(0.128) 		0.0415
(0.144) 		0.15
(0.313) 		0.0597
(0.179) 		0.105
(0.25)
3q gain 77 (42%) 107 1e-05
(0.000456) 		0.0204
(0.0935) 		0.595
(0.752) 		0.259
(0.462) 		0.229
(0.427) 		0.0828
(0.218) 		0.305
(0.511) 		0.24
(0.439) 		0.165
(0.338) 		0.408
(0.599)
4q gain 18 (10%) 166 0.0846
(0.22) 		0.326
(0.527) 		0.00487
(0.0327) 		0.0325
(0.121) 		0.196
(0.387) 		0.124
(0.274) 		0.312
(0.514) 		0.543
(0.709) 		0.56
(0.721) 		0.491
(0.666)
9q gain 33 (18%) 151 0.395
(0.586) 		0.259
(0.462) 		0.00647
(0.0402) 		0.633
(0.782) 		0.342
(0.543) 		0.416
(0.605) 		0.385
(0.578) 		0.0296
(0.115) 		0.673
(0.806) 		0.0807
(0.216)
17p gain 33 (18%) 151 0.0522
(0.163) 		0.0302
(0.116) 		0.848
(0.915) 		0.415
(0.604) 		0.0463
(0.153) 		0.0516
(0.163) 		0.367
(0.565) 		0.453
(0.637) 		0.541
(0.708) 		0.554
(0.718)
19q gain 38 (21%) 146 0.0989
(0.241) 		0.141
(0.298) 		0.335
(0.536) 		0.0168
(0.0809) 		0.489
(0.664) 		0.156
(0.323) 		0.0441
(0.149) 		0.355
(0.556) 		0.4
(0.589) 		0.111
(0.258)
1q loss 22 (12%) 162 0.04
(0.14) 		0.231
(0.428) 		0.137
(0.292) 		0.587
(0.746) 		0.131
(0.286) 		0.0518
(0.163) 		0.0743
(0.205) 		0.121
(0.27) 		0.0242
(0.103) 		0.125
(0.276)
2p loss 11 (6%) 173 0.854
(0.919) 		0.133
(0.289) 		0.0971
(0.238) 		0.0188
(0.0879) 		0.482
(0.661) 		0.31
(0.514) 		0.376
(0.573) 		0.00182
(0.017) 		0.835
(0.911) 		0.374
(0.572)
4p loss 105 (57%) 79 0.00074
(0.00798) 		0.0776
(0.209) 		0.242
(0.441) 		0.941
(0.971) 		0.109
(0.256) 		0.212
(0.409) 		0.0181
(0.0863) 		0.286
(0.488) 		0.186
(0.371) 		0.411
(0.602)
19p loss 65 (35%) 119 0.0483
(0.158) 		0.392
(0.582) 		0.421
(0.607) 		0.757
(0.87) 		0.272
(0.477) 		0.521
(0.694) 		0.0628
(0.182) 		0.121
(0.27) 		0.0953
(0.236) 		0.00926
(0.0523)
xp loss 60 (33%) 124 0.00439
(0.0305) 		0.174
(0.352) 		0.0432
(0.147) 		0.349
(0.548) 		0.376
(0.573) 		0.806
(0.901) 		0.525
(0.696) 		0.243
(0.442) 		0.322
(0.523) 		0.264
(0.468)
6p gain 38 (21%) 146 0.242
(0.441) 		0.367
(0.565) 		0.12
(0.27) 		0.226
(0.426) 		0.488
(0.664) 		0.27
(0.475) 		0.253
(0.456) 		0.105
(0.249) 		0.116
(0.264) 		0.0296
(0.115)
9p gain 16 (9%) 168 0.798
(0.895) 		0.48
(0.661) 		0.235
(0.432) 		0.039
(0.137) 		0.0637
(0.184) 		0.481
(0.661) 		0.566
(0.727) 		0.186
(0.37) 		0.587
(0.746) 		0.468
(0.651)
11q gain 29 (16%) 155 0.287
(0.488) 		0.313
(0.514) 		0.845
(0.915) 		0.75
(0.864) 		0.0883
(0.226) 		0.103
(0.247) 		0.0481
(0.158) 		0.177
(0.357) 		0.0815
(0.217) 		0.0775
(0.209)
18p gain 50 (27%) 134 0.0614
(0.181) 		0.375
(0.573) 		0.42
(0.606) 		0.67
(0.805) 		0.336
(0.536) 		0.331
(0.532) 		0.0225
(0.0988) 		0.871
(0.926) 		0.937
(0.97) 		0.813
(0.905)
20p gain 108 (59%) 76 0.00507
(0.0338) 		0.0574
(0.174) 		0.344
(0.544) 		0.15
(0.313) 		0.25
(0.452) 		0.224
(0.425) 		0.101
(0.243) 		0.261
(0.464) 		0.388
(0.58) 		0.0581
(0.176)
8p loss 63 (34%) 121 0.00433
(0.0303) 		0.462
(0.647) 		0.655
(0.797) 		0.921
(0.957) 		0.837
(0.911) 		0.504
(0.676) 		0.309
(0.513) 		0.593
(0.751) 		0.385
(0.578) 		0.308
(0.512)
1p gain 37 (20%) 147 0.653
(0.796) 		0.229
(0.427) 		0.695
(0.822) 		0.196
(0.387) 		0.909
(0.952) 		0.776
(0.885) 		1
(1.00) 		0.883
(0.936) 		0.452
(0.637) 		0.966
(0.989)
1q gain 63 (34%) 121 0.062
(0.181) 		0.206
(0.401) 		0.455
(0.639) 		0.0926
(0.233) 		0.825
(0.907) 		0.445
(0.634) 		0.385
(0.578) 		0.488
(0.664) 		0.501
(0.674) 		0.626
(0.775)
2q gain 46 (25%) 138 0.265
(0.468) 		0.071
(0.198) 		0.083
(0.218) 		0.272
(0.477) 		0.53
(0.699) 		0.104
(0.249) 		0.483
(0.661) 		0.77
(0.881) 		0.259
(0.462) 		0.887
(0.939)
3p gain 31 (17%) 153 0.306
(0.511) 		0.444
(0.634) 		0.747
(0.863) 		0.758
(0.87) 		0.414
(0.603) 		0.311
(0.514) 		0.778
(0.885) 		0.611
(0.764) 		0.859
(0.919) 		0.616
(0.769)
4p gain 19 (10%) 165 0.529
(0.699) 		0.857
(0.919) 		0.171
(0.348) 		0.312
(0.514) 		0.623
(0.774) 		0.689
(0.817) 		1
(1.00) 		0.956
(0.984) 		0.98
(0.997) 		1
(1.00)
5q gain 20 (11%) 164 0.407
(0.599) 		0.779
(0.885) 		0.494
(0.669) 		0.67
(0.805) 		0.134
(0.289) 		0.838
(0.911) 		0.699
(0.825) 		0.987
(1.00) 		0.752
(0.866) 		0.794
(0.892)
6q gain 33 (18%) 151 0.235
(0.432) 		0.329
(0.531) 		0.073
(0.202) 		0.235
(0.432) 		0.609
(0.763) 		0.245
(0.443) 		0.377
(0.573) 		0.285
(0.488) 		0.148
(0.31) 		0.0836
(0.218)
7p gain 110 (60%) 74 0.347
(0.546) 		0.236
(0.433) 		0.306
(0.511) 		0.301
(0.509) 		0.0522
(0.163) 		0.178
(0.357) 		0.075
(0.206) 		0.21
(0.408) 		0.556
(0.718) 		0.108
(0.254)
7q gain 89 (48%) 95 0.666
(0.805) 		0.29
(0.491) 		0.55
(0.713) 		0.451
(0.637) 		0.807
(0.901) 		0.305
(0.511) 		0.424
(0.61) 		0.746
(0.863) 		0.836
(0.911) 		0.122
(0.271)
8p gain 68 (37%) 116 0.314
(0.515) 		0.538
(0.707) 		1
(1.00) 		0.847
(0.915) 		0.67
(0.805) 		0.0607
(0.179) 		0.371
(0.571) 		0.833
(0.911) 		0.555
(0.718) 		0.741
(0.86)
8q gain 101 (55%) 83 0.466
(0.65) 		0.287
(0.488) 		0.941
(0.971) 		0.134
(0.289) 		0.785
(0.887) 		0.412
(0.603) 		0.289
(0.491) 		0.726
(0.848) 		0.913
(0.953) 		0.978
(0.997)
11p gain 39 (21%) 145 0.644
(0.791) 		0.915
(0.955) 		1
(1.00) 		0.935
(0.97) 		0.728
(0.848) 		0.63
(0.779) 		0.347
(0.546) 		0.32
(0.521) 		0.874
(0.928) 		0.479
(0.661)
12q gain 38 (21%) 146 0.173
(0.351) 		0.325
(0.526) 		0.98
(0.997) 		0.479
(0.661) 		0.398
(0.587) 		0.625
(0.775) 		0.39
(0.58) 		0.452
(0.637) 		0.264
(0.468) 		0.259
(0.462)
15q gain 30 (16%) 154 0.386
(0.578) 		0.278
(0.483) 		0.53
(0.699) 		0.228
(0.427) 		0.361
(0.562) 		0.0505
(0.163) 		0.453
(0.637) 		0.372
(0.572) 		0.318
(0.52) 		0.362
(0.562)
17q gain 45 (24%) 139 0.141
(0.298) 		0.211
(0.408) 		0.964
(0.988) 		0.617
(0.769) 		0.521
(0.694) 		0.0602
(0.179) 		0.857
(0.919) 		0.936
(0.97) 		0.992
(1.00) 		0.634
(0.782)
18q gain 26 (14%) 158 0.74
(0.859) 		0.815
(0.905) 		0.687
(0.816) 		0.446
(0.634) 		0.524
(0.696) 		0.91
(0.952) 		0.396
(0.586) 		0.306
(0.511) 		0.384
(0.578) 		0.226
(0.426)
19p gain 28 (15%) 156 0.428
(0.613) 		0.283
(0.487) 		0.486
(0.664) 		0.204
(0.399) 		1
(1.00) 		0.73
(0.849) 		0.384
(0.578) 		0.906
(0.952) 		0.541
(0.708) 		0.496
(0.669)
21q gain 18 (10%) 166 1
(1.00) 		0.569
(0.729) 		0.231
(0.428) 		0.61
(0.764) 		0.544
(0.709) 		0.418
(0.605) 		0.209
(0.407) 		0.425
(0.61) 		0.386
(0.578) 		0.226
(0.426)
xp gain 23 (12%) 161 0.452
(0.637) 		0.305
(0.511) 		0.166
(0.34) 		0.192
(0.382) 		0.427
(0.612) 		0.725
(0.848) 		0.384
(0.578) 		0.129
(0.284) 		0.202
(0.397) 		0.151
(0.313)
3q loss 33 (18%) 151 0.859
(0.919) 		0.671
(0.805) 		0.104
(0.249) 		0.661
(0.801) 		0.692
(0.82) 		0.599
(0.754) 		0.653
(0.796) 		0.91
(0.952) 		0.661
(0.801) 		0.89
(0.94)
6p loss 39 (21%) 145 0.343
(0.543) 		0.622
(0.774) 		0.545
(0.709) 		0.835
(0.911) 		0.398
(0.587) 		0.704
(0.83) 		0.373
(0.572) 		0.362
(0.562) 		0.862
(0.92) 		0.463
(0.647)
6q loss 39 (21%) 145 0.332
(0.533) 		0.66
(0.801) 		0.282
(0.486) 		0.596
(0.752) 		0.814
(0.905) 		0.871
(0.926) 		0.49
(0.665) 		0.683
(0.815) 		0.831
(0.911) 		0.273
(0.478)
7p loss 13 (7%) 171 0.817
(0.906) 		0.557
(0.718) 		0.847
(0.915) 		0.115
(0.263) 		0.27
(0.476) 		0.643
(0.79) 		0.579
(0.74) 		0.582
(0.742) 		0.303
(0.511) 		0.647
(0.792)
7q loss 22 (12%) 162 0.173
(0.351) 		0.336
(0.536) 		0.837
(0.911) 		0.286
(0.488) 		0.761
(0.873) 		0.542
(0.708) 		0.59
(0.749) 		0.854
(0.919) 		0.225
(0.426) 		0.806
(0.901)
8q loss 23 (12%) 161 0.779
(0.885) 		1
(1.00) 		0.921
(0.957) 		0.951
(0.98) 		0.964
(0.988) 		0.131
(0.286) 		0.823
(0.907) 		0.258
(0.462) 		0.716
(0.839) 		1
(1.00)
9p loss 101 (55%) 83 0.089
(0.227) 		0.115
(0.263) 		0.713
(0.837) 		0.695
(0.822) 		0.109
(0.256) 		0.172
(0.35) 		0.529
(0.699) 		0.567
(0.727) 		0.784
(0.886) 		0.538
(0.707)
9q loss 65 (35%) 119 0.0643
(0.185) 		0.181
(0.361) 		0.366
(0.565) 		0.342
(0.543) 		0.545
(0.709) 		0.523
(0.696) 		0.647
(0.792) 		0.231
(0.428) 		0.0679
(0.193) 		0.794
(0.892)
11p loss 52 (28%) 132 0.1
(0.242) 		0.226
(0.426) 		0.94
(0.971) 		0.728
(0.848) 		0.472
(0.656) 		0.917
(0.955) 		0.9
(0.947) 		0.648
(0.792) 		0.821
(0.907) 		0.772
(0.882)
17q loss 25 (14%) 159 0.792
(0.892) 		0.603
(0.759) 		0.978
(0.997) 		0.607
(0.762) 		0.968
(0.99) 		0.908
(0.952) 		0.514
(0.687) 		0.891
(0.94) 		0.362
(0.562) 		0.867
(0.924)
20p loss 19 (10%) 165 0.582
(0.742) 		0.855
(0.919) 		0.496
(0.669) 		0.824
(0.907) 		0.813
(0.905) 		0.148
(0.311) 		0.595
(0.752) 		0.418
(0.605) 		0.685
(0.816) 		0.48
(0.661)
20q loss 8 (4%) 176 0.9
(0.947) 		0.706
(0.83) 		0.282
(0.486) 		0.768
(0.879) 		1
(1.00) 		0.671
(0.805) 		1
(1.00) 		0.678
(0.81) 		0.745
(0.863) 		0.446
(0.634)
'2p gain' versus 'CN_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 0.067

Table S1.  Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
2P GAIN MUTATED 20 8 33
2P GAIN WILD-TYPE 45 36 42

Figure S1.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p gain' versus 'METHLYATION_CNMF'

P value = 0.0314 (Fisher's exact test), Q value = 0.12

Table S2.  Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
2P GAIN MUTATED 22 6 33
2P GAIN WILD-TYPE 54 26 43

Figure S2.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p gain' versus 'MIRSEQ_CNMF'

P value = 0.0368 (Fisher's exact test), Q value = 0.13

Table S3.  Gene #3: '2p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
2P GAIN MUTATED 24 36 1
2P GAIN WILD-TYPE 60 51 11

Figure S3.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00289 (Fisher's exact test), Q value = 0.022

Table S4.  Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
2P GAIN MUTATED 20 32 5 2
2P GAIN WILD-TYPE 46 34 30 9

Figure S4.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00046

Table S5.  Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
3Q GAIN MUTATED 29 5 43
3Q GAIN WILD-TYPE 36 39 32

Figure S5.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 0.0204 (Fisher's exact test), Q value = 0.094

Table S6.  Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
3Q GAIN MUTATED 29 8 40
3Q GAIN WILD-TYPE 47 24 36

Figure S6.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q gain' versus 'RPPA_CNMF'

P value = 0.00487 (Fisher's exact test), Q value = 0.033

Table S7.  Gene #8: '4q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
4Q GAIN MUTATED 1 6 7 0 1
4Q GAIN WILD-TYPE 25 22 23 34 7

Figure S7.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'4q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0325 (Fisher's exact test), Q value = 0.12

Table S8.  Gene #8: '4q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
4Q GAIN MUTATED 1 6 4 3 1
4Q GAIN WILD-TYPE 22 15 18 23 33

Figure S8.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00068

Table S9.  Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
5P GAIN MUTATED 22 9 45
5P GAIN WILD-TYPE 43 35 30

Figure S9.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.0278 (Fisher's exact test), Q value = 0.11

Table S10.  Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
5P GAIN MUTATED 24 12 40
5P GAIN WILD-TYPE 52 20 36

Figure S10.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 0.0233 (Fisher's exact test), Q value = 0.1

Table S11.  Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
5P GAIN MUTATED 25 36 12 3
5P GAIN WILD-TYPE 56 33 10 8

Figure S11.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0117 (Fisher's exact test), Q value = 0.063

Table S12.  Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
5P GAIN MUTATED 23 4 49
5P GAIN WILD-TYPE 44 16 47

Figure S12.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.068

Table S13.  Gene #9: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
5P GAIN MUTATED 26 46 4
5P GAIN WILD-TYPE 58 41 8

Figure S13.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0328 (Fisher's exact test), Q value = 0.12

Table S14.  Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
5P GAIN MUTATED 18 9 33 16
5P GAIN WILD-TYPE 44 17 29 17

Figure S14.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0161 (Fisher's exact test), Q value = 0.079

Table S15.  Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
5P GAIN MUTATED 18 9 49
5P GAIN WILD-TYPE 44 13 45

Figure S15.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0296 (Fisher's exact test), Q value = 0.12

Table S16.  Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
6P GAIN MUTATED 20 2 16
6P GAIN WILD-TYPE 42 20 78

Figure S16.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.039 (Fisher's exact test), Q value = 0.14

Table S17.  Gene #17: '9p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
9P GAIN MUTATED 0 3 4 5 1
9P GAIN WILD-TYPE 23 18 18 21 33

Figure S17.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'9q gain' versus 'RPPA_CNMF'

P value = 0.00647 (Fisher's exact test), Q value = 0.04

Table S18.  Gene #18: '9q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
9Q GAIN MUTATED 1 6 9 6 5
9Q GAIN WILD-TYPE 25 22 21 28 3

Figure S18.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'9q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0296 (Fisher's exact test), Q value = 0.12

Table S19.  Gene #18: '9q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
9Q GAIN MUTATED 6 6 17 3
9Q GAIN WILD-TYPE 56 20 45 30

Figure S19.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 0.0362 (Fisher's exact test), Q value = 0.13

Table S20.  Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
10P GAIN MUTATED 21 8 11
10P GAIN WILD-TYPE 44 36 64

Figure S20.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 0.0277 (Fisher's exact test), Q value = 0.11

Table S21.  Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
10P GAIN MUTATED 24 4 12
10P GAIN WILD-TYPE 52 28 64

Figure S21.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 0.0247 (Fisher's exact test), Q value = 0.1

Table S22.  Gene #19: '10p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
10P GAIN MUTATED 25 10 5 0
10P GAIN WILD-TYPE 56 59 17 11

Figure S22.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q gain' versus 'CN_CNMF'

P value = 0.0152 (Fisher's exact test), Q value = 0.076

Table S23.  Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
10Q GAIN MUTATED 17 7 6
10Q GAIN WILD-TYPE 48 37 69

Figure S23.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

'10q gain' versus 'METHLYATION_CNMF'

P value = 0.0316 (Fisher's exact test), Q value = 0.12

Table S24.  Gene #20: '10q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
10Q GAIN MUTATED 19 3 8
10Q GAIN WILD-TYPE 57 29 68

Figure S24.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0218 (Fisher's exact test), Q value = 0.097

Table S25.  Gene #20: '10q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
10Q GAIN MUTATED 16 4 9
10Q GAIN WILD-TYPE 46 18 85

Figure S25.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CNMF'

P value = 0.0481 (Fisher's exact test), Q value = 0.16

Table S26.  Gene #22: '11q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
11Q GAIN MUTATED 19 10 0
11Q GAIN WILD-TYPE 65 77 12

Figure S26.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 0.0237 (Fisher's exact test), Q value = 0.1

Table S27.  Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
12P GAIN MUTATED 17 9 32
12P GAIN WILD-TYPE 48 35 43

Figure S27.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 0.00411 (Fisher's exact test), Q value = 0.029

Table S28.  Gene #23: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
12P GAIN MUTATED 14 12 32
12P GAIN WILD-TYPE 62 20 44

Figure S28.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 0.00391 (Fisher's exact test), Q value = 0.028

Table S29.  Gene #23: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
12P GAIN MUTATED 15 28 11 4
12P GAIN WILD-TYPE 66 41 11 7

Figure S29.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00262 (Fisher's exact test), Q value = 0.021

Table S30.  Gene #23: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
12P GAIN MUTATED 14 3 41
12P GAIN WILD-TYPE 53 17 55

Figure S30.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 0.00571 (Fisher's exact test), Q value = 0.036

Table S31.  Gene #23: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
12P GAIN MUTATED 17 37 3
12P GAIN WILD-TYPE 67 50 9

Figure S31.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00312 (Fisher's exact test), Q value = 0.023

Table S32.  Gene #23: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
12P GAIN MUTATED 12 5 30 10
12P GAIN WILD-TYPE 50 21 32 23

Figure S32.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00284 (Fisher's exact test), Q value = 0.022

Table S33.  Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
12P GAIN MUTATED 14 32 8 2
12P GAIN WILD-TYPE 52 34 27 9

Figure S33.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00931 (Fisher's exact test), Q value = 0.052

Table S34.  Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
12P GAIN MUTATED 12 5 39
12P GAIN WILD-TYPE 50 17 55

Figure S34.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 0.00237 (Fisher's exact test), Q value = 0.02

Table S35.  Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
13Q GAIN MUTATED 24 10 9
13Q GAIN WILD-TYPE 41 34 66

Figure S35.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00046

Table S36.  Gene #25: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
13Q GAIN MUTATED 31 5 7
13Q GAIN WILD-TYPE 45 27 69

Figure S36.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.001

Table S37.  Gene #25: '13q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
13Q GAIN MUTATED 32 7 2 2
13Q GAIN WILD-TYPE 49 62 20 9

Figure S37.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00059

Table S38.  Gene #25: '13q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
13Q GAIN MUTATED 23 11 9
13Q GAIN WILD-TYPE 44 9 87

Figure S38.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00046

Table S39.  Gene #25: '13q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
13Q GAIN MUTATED 34 9 0
13Q GAIN WILD-TYPE 50 78 12

Figure S39.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'13q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00068

Table S40.  Gene #25: '13q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
13Q GAIN MUTATED 25 9 5 4
13Q GAIN WILD-TYPE 37 17 57 29

Figure S40.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.0023

Table S41.  Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
13Q GAIN MUTATED 28 8 4 3
13Q GAIN WILD-TYPE 38 58 31 8

Figure S41.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'13q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00046

Table S42.  Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
13Q GAIN MUTATED 26 8 9
13Q GAIN WILD-TYPE 36 14 85

Figure S42.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 0.0352 (Fisher's exact test), Q value = 0.13

Table S43.  Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
14Q GAIN MUTATED 14 7 27
14Q GAIN WILD-TYPE 51 37 48

Figure S43.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'RPPA_CNMF'

P value = 0.0281 (Fisher's exact test), Q value = 0.11

Table S44.  Gene #26: '14q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
14Q GAIN MUTATED 4 5 9 16 4
14Q GAIN WILD-TYPE 22 23 21 18 4

Figure S44.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.022 (Fisher's exact test), Q value = 0.097

Table S45.  Gene #26: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
14Q GAIN MUTATED 13 2 33
14Q GAIN WILD-TYPE 54 18 63

Figure S45.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 0.0382 (Fisher's exact test), Q value = 0.14

Table S46.  Gene #26: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
14Q GAIN MUTATED 15 30 2
14Q GAIN WILD-TYPE 69 57 10

Figure S46.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0363 (Fisher's exact test), Q value = 0.13

Table S47.  Gene #26: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
14Q GAIN MUTATED 11 4 24 8
14Q GAIN WILD-TYPE 51 22 38 25

Figure S47.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 0.00415 (Fisher's exact test), Q value = 0.029

Table S48.  Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
16P GAIN MUTATED 10 5 26
16P GAIN WILD-TYPE 55 39 49

Figure S48.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.0199 (Fisher's exact test), Q value = 0.092

Table S49.  Gene #28: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
16P GAIN MUTATED 11 23 6 1
16P GAIN WILD-TYPE 70 46 16 10

Figure S49.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00359 (Fisher's exact test), Q value = 0.027

Table S50.  Gene #28: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
16P GAIN MUTATED 12 0 29
16P GAIN WILD-TYPE 55 20 67

Figure S50.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 0.0255 (Fisher's exact test), Q value = 0.11

Table S51.  Gene #28: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
16P GAIN MUTATED 12 27 2
16P GAIN WILD-TYPE 72 60 10

Figure S51.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0362 (Fisher's exact test), Q value = 0.13

Table S52.  Gene #28: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
16P GAIN MUTATED 8 4 21 8
16P GAIN WILD-TYPE 54 22 41 25

Figure S52.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 0.00074 (Fisher's exact test), Q value = 0.008

Table S53.  Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
16Q GAIN MUTATED 7 5 26
16Q GAIN WILD-TYPE 58 39 49

Figure S53.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 0.028 (Fisher's exact test), Q value = 0.11

Table S54.  Gene #29: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
16Q GAIN MUTATED 9 7 22
16Q GAIN WILD-TYPE 67 25 54

Figure S54.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0171 (Fisher's exact test), Q value = 0.082

Table S55.  Gene #29: '16q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
16Q GAIN MUTATED 0 3 7 8 8
16Q GAIN WILD-TYPE 23 18 15 18 26

Figure S55.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 0.00315 (Fisher's exact test), Q value = 0.023

Table S56.  Gene #29: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
16Q GAIN MUTATED 9 24 4 1
16Q GAIN WILD-TYPE 72 45 18 10

Figure S56.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0134 (Fisher's exact test), Q value = 0.069

Table S57.  Gene #29: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
16Q GAIN MUTATED 8 2 28
16Q GAIN WILD-TYPE 59 18 68

Figure S57.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.064

Table S58.  Gene #29: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
16Q GAIN MUTATED 10 26 2
16Q GAIN WILD-TYPE 74 61 10

Figure S58.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00674 (Fisher's exact test), Q value = 0.041

Table S59.  Gene #29: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
16Q GAIN MUTATED 5 5 20 8
16Q GAIN WILD-TYPE 57 21 42 25

Figure S59.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00287 (Fisher's exact test), Q value = 0.022

Table S60.  Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
16Q GAIN MUTATED 5 20 7 4
16Q GAIN WILD-TYPE 61 46 28 7

Figure S60.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00678 (Fisher's exact test), Q value = 0.041

Table S61.  Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
16Q GAIN MUTATED 5 5 26
16Q GAIN WILD-TYPE 57 17 68

Figure S61.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p gain' versus 'METHLYATION_CNMF'

P value = 0.0302 (Fisher's exact test), Q value = 0.12

Table S62.  Gene #30: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
17P GAIN MUTATED 11 2 20
17P GAIN WILD-TYPE 65 30 56

Figure S62.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 0.0463 (Fisher's exact test), Q value = 0.15

Table S63.  Gene #30: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
17P GAIN MUTATED 12 19 2 0
17P GAIN WILD-TYPE 69 50 20 11

Figure S63.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18p gain' versus 'MIRSEQ_CNMF'

P value = 0.0225 (Fisher's exact test), Q value = 0.099

Table S64.  Gene #32: '18p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
18P GAIN MUTATED 20 29 0
18P GAIN WILD-TYPE 64 58 12

Figure S64.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0168 (Fisher's exact test), Q value = 0.081

Table S65.  Gene #35: '19q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
19Q GAIN MUTATED 8 0 4 3 9
19Q GAIN WILD-TYPE 15 21 18 23 25

Figure S65.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 0.0441 (Fisher's exact test), Q value = 0.15

Table S66.  Gene #35: '19q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
19Q GAIN MUTATED 23 15 0
19Q GAIN WILD-TYPE 61 72 12

Figure S66.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 0.00507 (Fisher's exact test), Q value = 0.034

Table S67.  Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
20P GAIN MUTATED 47 18 43
20P GAIN WILD-TYPE 18 26 32

Figure S67.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.0015

Table S68.  Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
20Q GAIN MUTATED 54 21 40
20Q GAIN WILD-TYPE 11 23 35

Figure S68.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0039

Table S69.  Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
20Q GAIN MUTATED 60 18 37
20Q GAIN WILD-TYPE 16 14 39

Figure S69.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 0.00573 (Fisher's exact test), Q value = 0.036

Table S70.  Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
20Q GAIN MUTATED 62 36 12 5
20Q GAIN WILD-TYPE 19 33 10 6

Figure S70.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00269 (Fisher's exact test), Q value = 0.022

Table S71.  Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
20Q GAIN MUTATED 51 15 49
20Q GAIN WILD-TYPE 16 5 47

Figure S71.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.0051

Table S72.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
20Q GAIN MUTATED 65 44 5
20Q GAIN WILD-TYPE 19 43 7

Figure S72.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00064 (Fisher's exact test), Q value = 0.0074

Table S73.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
20Q GAIN MUTATED 50 17 33 14
20Q GAIN WILD-TYPE 12 9 29 19

Figure S73.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00633 (Fisher's exact test), Q value = 0.04

Table S74.  Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
20Q GAIN MUTATED 52 33 21 7
20Q GAIN WILD-TYPE 14 33 14 4

Figure S74.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.001

Table S75.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
20Q GAIN MUTATED 52 15 46
20Q GAIN WILD-TYPE 10 7 48

Figure S75.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00059

Table S76.  Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
22Q GAIN MUTATED 3 3 25
22Q GAIN WILD-TYPE 62 41 50

Figure S76.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00046

Table S77.  Gene #39: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
22Q GAIN MUTATED 3 3 25
22Q GAIN WILD-TYPE 73 29 51

Figure S77.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q gain' versus 'RPPA_CNMF'

P value = 0.00398 (Fisher's exact test), Q value = 0.029

Table S78.  Gene #39: '22q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
22Q GAIN MUTATED 1 3 6 14 1
22Q GAIN WILD-TYPE 25 25 24 20 7

Figure S78.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'22q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.0061

Table S79.  Gene #39: '22q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
22Q GAIN MUTATED 1 0 3 9 12
22Q GAIN WILD-TYPE 22 21 19 17 22

Figure S79.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00059

Table S80.  Gene #39: '22q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
22Q GAIN MUTATED 2 22 4 3
22Q GAIN WILD-TYPE 79 47 18 8

Figure S80.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00059

Table S81.  Gene #39: '22q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
22Q GAIN MUTATED 3 0 28
22Q GAIN WILD-TYPE 64 20 68

Figure S81.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00059

Table S82.  Gene #39: '22q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
22Q GAIN MUTATED 3 26 2
22Q GAIN WILD-TYPE 81 61 10

Figure S82.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00046

Table S83.  Gene #39: '22q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
22Q GAIN MUTATED 2 1 22 6
22Q GAIN WILD-TYPE 60 25 40 27

Figure S83.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00046

Table S84.  Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
22Q GAIN MUTATED 2 25 3 1
22Q GAIN WILD-TYPE 64 41 32 10

Figure S84.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00068

Table S85.  Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
22Q GAIN MUTATED 2 1 28
22Q GAIN WILD-TYPE 60 21 66

Figure S85.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 0.045 (Fisher's exact test), Q value = 0.15

Table S86.  Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
XQ GAIN MUTATED 13 4 21
XQ GAIN WILD-TYPE 52 40 54

Figure S86.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 0.0296 (Fisher's exact test), Q value = 0.12

Table S87.  Gene #41: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
XQ GAIN MUTATED 11 4 23
XQ GAIN WILD-TYPE 65 28 53

Figure S87.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq gain' versus 'RPPA_CNMF'

P value = 0.0451 (Fisher's exact test), Q value = 0.15

Table S88.  Gene #41: 'xq gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
XQ GAIN MUTATED 1 9 5 10 2
XQ GAIN WILD-TYPE 25 19 25 24 6

Figure S88.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'xq gain' versus 'MIRSEQ_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.06

Table S89.  Gene #41: 'xq gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
XQ GAIN MUTATED 12 25 0
XQ GAIN WILD-TYPE 72 62 12

Figure S89.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xq gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0269 (Fisher's exact test), Q value = 0.11

Table S90.  Gene #41: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
XQ GAIN MUTATED 11 1 19 6
XQ GAIN WILD-TYPE 51 25 43 27

Figure S90.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 0.00923 (Fisher's exact test), Q value = 0.052

Table S91.  Gene #42: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
1P LOSS MUTATED 21 4 13
1P LOSS WILD-TYPE 44 40 62

Figure S91.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 0.0232 (Fisher's exact test), Q value = 0.1

Table S92.  Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
1P LOSS MUTATED 23 3 12
1P LOSS WILD-TYPE 53 29 64

Figure S92.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 0.0145 (Fisher's exact test), Q value = 0.073

Table S93.  Gene #42: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
1P LOSS MUTATED 25 9 4 0
1P LOSS WILD-TYPE 56 60 18 11

Figure S93.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0385 (Fisher's exact test), Q value = 0.14

Table S94.  Gene #42: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
1P LOSS MUTATED 20 5 13
1P LOSS WILD-TYPE 47 15 83

Figure S94.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 0.0203 (Fisher's exact test), Q value = 0.094

Table S95.  Gene #42: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
1P LOSS MUTATED 25 12 1
1P LOSS WILD-TYPE 59 75 11

Figure S95.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0314 (Fisher's exact test), Q value = 0.12

Table S96.  Gene #42: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
1P LOSS MUTATED 19 6 11 2
1P LOSS WILD-TYPE 43 20 51 31

Figure S96.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.01 (Fisher's exact test), Q value = 0.056

Table S97.  Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
1P LOSS MUTATED 22 11 4 0
1P LOSS WILD-TYPE 44 55 31 11

Figure S97.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.045 (Fisher's exact test), Q value = 0.15

Table S98.  Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
1P LOSS MUTATED 18 6 13
1P LOSS WILD-TYPE 44 16 81

Figure S98.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 0.04 (Fisher's exact test), Q value = 0.14

Table S99.  Gene #43: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
1Q LOSS MUTATED 13 2 7
1Q LOSS WILD-TYPE 52 42 68

Figure S99.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0242 (Fisher's exact test), Q value = 0.1

Table S100.  Gene #43: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
1Q LOSS MUTATED 14 6 1 0
1Q LOSS WILD-TYPE 52 60 34 11

Figure S100.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0188 (Fisher's exact test), Q value = 0.088

Table S101.  Gene #44: '2p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
2P LOSS MUTATED 0 5 0 2 2
2P LOSS WILD-TYPE 23 16 22 24 32

Figure S101.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00182 (Fisher's exact test), Q value = 0.017

Table S102.  Gene #44: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
2P LOSS MUTATED 3 0 1 7
2P LOSS WILD-TYPE 59 26 61 26

Figure S102.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'METHLYATION_CNMF'

P value = 0.0325 (Fisher's exact test), Q value = 0.12

Table S103.  Gene #45: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
2Q LOSS MUTATED 3 6 9
2Q LOSS WILD-TYPE 73 26 67

Figure S103.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0322 (Fisher's exact test), Q value = 0.12

Table S104.  Gene #45: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
2Q LOSS MUTATED 2 2 14
2Q LOSS WILD-TYPE 65 18 82

Figure S104.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00683 (Fisher's exact test), Q value = 0.041

Table S105.  Gene #45: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
2Q LOSS MUTATED 3 1 5 9
2Q LOSS WILD-TYPE 59 25 57 24

Figure S105.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00068

Table S106.  Gene #46: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
3P LOSS MUTATED 24 15 54
3P LOSS WILD-TYPE 41 29 21

Figure S106.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.0014

Table S107.  Gene #46: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
3P LOSS MUTATED 24 18 51
3P LOSS WILD-TYPE 52 14 25

Figure S107.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00068

Table S108.  Gene #46: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
3P LOSS MUTATED 27 51 8 6
3P LOSS WILD-TYPE 54 18 14 5

Figure S108.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00046

Table S109.  Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
3P LOSS MUTATED 18 9 65
3P LOSS WILD-TYPE 49 11 31

Figure S109.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00046

Table S110.  Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
3P LOSS MUTATED 27 60 6
3P LOSS WILD-TYPE 57 27 6

Figure S110.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00059

Table S111.  Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
3P LOSS MUTATED 20 8 42 23
3P LOSS WILD-TYPE 42 18 20 10

Figure S111.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00125 (Fisher's exact test), Q value = 0.012

Table S112.  Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
3P LOSS MUTATED 22 44 18 7
3P LOSS WILD-TYPE 44 22 17 4

Figure S112.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00046

Table S113.  Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
3P LOSS MUTATED 19 8 64
3P LOSS WILD-TYPE 43 14 30

Figure S113.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 0.00074 (Fisher's exact test), Q value = 0.008

Table S114.  Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
4P LOSS MUTATED 42 14 49
4P LOSS WILD-TYPE 23 30 26

Figure S114.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 0.086

Table S115.  Gene #48: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
4P LOSS MUTATED 45 57 3
4P LOSS WILD-TYPE 39 30 9

Figure S115.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.0053

Table S116.  Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
4Q LOSS MUTATED 42 12 33
4Q LOSS WILD-TYPE 23 32 42

Figure S116.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 0.0456 (Fisher's exact test), Q value = 0.15

Table S117.  Gene #49: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
4Q LOSS MUTATED 43 10 34
4Q LOSS WILD-TYPE 33 22 42

Figure S117.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 0.0448 (Fisher's exact test), Q value = 0.15

Table S118.  Gene #49: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
4Q LOSS MUTATED 45 33 7 2
4Q LOSS WILD-TYPE 36 36 15 9

Figure S118.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 0.0403 (Fisher's exact test), Q value = 0.14

Table S119.  Gene #49: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
4Q LOSS MUTATED 46 39 2
4Q LOSS WILD-TYPE 38 48 10

Figure S119.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5p loss' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0027

Table S120.  Gene #50: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
5P LOSS MUTATED 27 10 9
5P LOSS WILD-TYPE 38 34 66

Figure S120.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00068

Table S121.  Gene #50: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
5P LOSS MUTATED 32 2 12
5P LOSS WILD-TYPE 44 30 64

Figure S121.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.0015

Table S122.  Gene #50: '5p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
5P LOSS MUTATED 32 13 0 1
5P LOSS WILD-TYPE 49 56 22 10

Figure S122.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.0014

Table S123.  Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
5P LOSS MUTATED 22 11 13
5P LOSS WILD-TYPE 45 9 83

Figure S123.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.0015

Table S124.  Gene #50: '5p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
5P LOSS MUTATED 33 12 0
5P LOSS WILD-TYPE 51 75 12

Figure S124.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00059

Table S125.  Gene #50: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
5P LOSS MUTATED 29 5 7 4
5P LOSS WILD-TYPE 33 21 55 29

Figure S125.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0031

Table S126.  Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
5P LOSS MUTATED 28 11 3 1
5P LOSS WILD-TYPE 38 55 32 10

Figure S126.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00046

Table S127.  Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
5P LOSS MUTATED 28 4 11
5P LOSS WILD-TYPE 34 18 83

Figure S127.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.087

Table S128.  Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
5Q LOSS MUTATED 39 15 32
5Q LOSS WILD-TYPE 26 29 43

Figure S128.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 0.00926 (Fisher's exact test), Q value = 0.052

Table S129.  Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
5Q LOSS MUTATED 45 9 32
5Q LOSS WILD-TYPE 31 23 44

Figure S129.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 0.0208 (Fisher's exact test), Q value = 0.095

Table S130.  Gene #51: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
5Q LOSS MUTATED 47 37 2
5Q LOSS WILD-TYPE 37 50 10

Figure S130.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 0.00433 (Fisher's exact test), Q value = 0.03

Table S131.  Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
8P LOSS MUTATED 20 8 35
8P LOSS WILD-TYPE 45 36 40

Figure S131.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 0.00188 (Fisher's exact test), Q value = 0.017

Table S132.  Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
10P LOSS MUTATED 11 8 31
10P LOSS WILD-TYPE 54 36 44

Figure S132.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.0045 (Fisher's exact test), Q value = 0.031

Table S133.  Gene #60: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
10P LOSS MUTATED 12 8 30
10P LOSS WILD-TYPE 64 24 46

Figure S133.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.0234 (Fisher's exact test), Q value = 0.1

Table S134.  Gene #60: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
10P LOSS MUTATED 14 26 8 2
10P LOSS WILD-TYPE 67 43 14 9

Figure S134.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0144 (Fisher's exact test), Q value = 0.073

Table S135.  Gene #60: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
10P LOSS MUTATED 12 3 35
10P LOSS WILD-TYPE 55 17 61

Figure S135.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 0.00237 (Fisher's exact test), Q value = 0.02

Table S136.  Gene #60: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
10P LOSS MUTATED 15 34 1
10P LOSS WILD-TYPE 69 53 11

Figure S136.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00832 (Fisher's exact test), Q value = 0.049

Table S137.  Gene #60: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
10P LOSS MUTATED 8 7 24 11
10P LOSS WILD-TYPE 54 19 38 22

Figure S137.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0136 (Fisher's exact test), Q value = 0.07

Table S138.  Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
10P LOSS MUTATED 10 26 10 4
10P LOSS WILD-TYPE 56 40 25 7

Figure S138.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00237 (Fisher's exact test), Q value = 0.02

Table S139.  Gene #60: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
10P LOSS MUTATED 8 7 35
10P LOSS WILD-TYPE 54 15 59

Figure S139.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.002

Table S140.  Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
10Q LOSS MUTATED 9 7 33
10Q LOSS WILD-TYPE 56 37 42

Figure S140.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.0093

Table S141.  Gene #61: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
10Q LOSS MUTATED 11 7 31
10Q LOSS WILD-TYPE 65 25 45

Figure S141.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 0.00834 (Fisher's exact test), Q value = 0.049

Table S142.  Gene #61: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
10Q LOSS MUTATED 12 25 8 4
10Q LOSS WILD-TYPE 69 44 14 7

Figure S142.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00194 (Fisher's exact test), Q value = 0.017

Table S143.  Gene #61: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
10Q LOSS MUTATED 11 2 36
10Q LOSS WILD-TYPE 56 18 60

Figure S143.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 0.0016 (Fisher's exact test), Q value = 0.015

Table S144.  Gene #61: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
10Q LOSS MUTATED 13 34 2
10Q LOSS WILD-TYPE 71 53 10

Figure S144.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00233 (Fisher's exact test), Q value = 0.02

Table S145.  Gene #61: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
10Q LOSS MUTATED 8 5 26 10
10Q LOSS WILD-TYPE 54 21 36 23

Figure S145.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0165 (Fisher's exact test), Q value = 0.08

Table S146.  Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
10Q LOSS MUTATED 10 26 10 3
10Q LOSS WILD-TYPE 56 40 25 8

Figure S146.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00181 (Fisher's exact test), Q value = 0.017

Table S147.  Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
10Q LOSS MUTATED 8 5 36
10Q LOSS WILD-TYPE 54 17 58

Figure S147.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0057

Table S148.  Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
11Q LOSS MUTATED 17 6 35
11Q LOSS WILD-TYPE 48 38 40

Figure S148.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 0.0423 (Fisher's exact test), Q value = 0.14

Table S149.  Gene #63: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
11Q LOSS MUTATED 18 8 32
11Q LOSS WILD-TYPE 58 24 44

Figure S149.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 0.0343 (Fisher's exact test), Q value = 0.13

Table S150.  Gene #63: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
11Q LOSS MUTATED 18 30 7 2
11Q LOSS WILD-TYPE 63 39 15 9

Figure S150.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0219 (Fisher's exact test), Q value = 0.097

Table S151.  Gene #63: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
11Q LOSS MUTATED 13 6 38
11Q LOSS WILD-TYPE 54 14 58

Figure S151.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 0.0143 (Fisher's exact test), Q value = 0.073

Table S152.  Gene #63: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
11Q LOSS MUTATED 19 36 2
11Q LOSS WILD-TYPE 65 51 10

Figure S152.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 0.00094 (Fisher's exact test), Q value = 0.0098

Table S153.  Gene #64: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
12P LOSS MUTATED 22 6 5
12P LOSS WILD-TYPE 54 26 71

Figure S153.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0211 (Fisher's exact test), Q value = 0.096

Table S154.  Gene #64: '12p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
12P LOSS MUTATED 10 3 5 3 3
12P LOSS WILD-TYPE 13 18 17 23 31

Figure S154.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0047

Table S155.  Gene #64: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
12P LOSS MUTATED 25 8 0 0
12P LOSS WILD-TYPE 56 61 22 11

Figure S155.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00071 (Fisher's exact test), Q value = 0.008

Table S156.  Gene #64: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
12P LOSS MUTATED 18 7 8
12P LOSS WILD-TYPE 49 13 88

Figure S156.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_CNMF'

P value = 0.00257 (Fisher's exact test), Q value = 0.021

Table S157.  Gene #64: '12p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
12P LOSS MUTATED 24 8 1
12P LOSS WILD-TYPE 60 79 11

Figure S157.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00204 (Fisher's exact test), Q value = 0.018

Table S158.  Gene #64: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
12P LOSS MUTATED 15 10 5 3
12P LOSS WILD-TYPE 47 16 57 30

Figure S158.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0145 (Fisher's exact test), Q value = 0.073

Table S159.  Gene #64: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
12P LOSS MUTATED 20 6 5 2
12P LOSS WILD-TYPE 46 60 30 9

Figure S159.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.0051

Table S160.  Gene #64: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
12P LOSS MUTATED 16 9 8
12P LOSS WILD-TYPE 46 13 86

Figure S160.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q loss' versus 'METHLYATION_CNMF'

P value = 0.00292 (Fisher's exact test), Q value = 0.022

Table S161.  Gene #65: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
12Q LOSS MUTATED 20 6 5
12Q LOSS WILD-TYPE 56 26 71

Figure S161.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q loss' versus 'MRNASEQ_CNMF'

P value = 0.00922 (Fisher's exact test), Q value = 0.052

Table S162.  Gene #65: '12q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
12Q LOSS MUTATED 22 5 3 1
12Q LOSS WILD-TYPE 59 64 19 10

Figure S162.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00546 (Fisher's exact test), Q value = 0.036

Table S163.  Gene #65: '12q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
12Q LOSS MUTATED 15 7 9
12Q LOSS WILD-TYPE 52 13 87

Figure S163.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_CNMF'

P value = 0.0253 (Fisher's exact test), Q value = 0.11

Table S164.  Gene #65: '12q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
12Q LOSS MUTATED 21 9 1
12Q LOSS WILD-TYPE 63 78 11

Figure S164.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0115 (Fisher's exact test), Q value = 0.062

Table S165.  Gene #65: '12q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
12Q LOSS MUTATED 14 8 8 1
12Q LOSS WILD-TYPE 48 18 54 32

Figure S165.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00833 (Fisher's exact test), Q value = 0.049

Table S166.  Gene #65: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
12Q LOSS MUTATED 20 7 3 1
12Q LOSS WILD-TYPE 46 59 32 10

Figure S166.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00697 (Fisher's exact test), Q value = 0.041

Table S167.  Gene #65: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
12Q LOSS MUTATED 15 7 9
12Q LOSS WILD-TYPE 47 15 85

Figure S167.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.079

Table S168.  Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
13Q LOSS MUTATED 21 10 36
13Q LOSS WILD-TYPE 44 34 39

Figure S168.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.035 (Fisher's exact test), Q value = 0.13

Table S169.  Gene #66: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
13Q LOSS MUTATED 22 3 42
13Q LOSS WILD-TYPE 45 17 54

Figure S169.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 0.0415 (Fisher's exact test), Q value = 0.14

Table S170.  Gene #66: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
13Q LOSS MUTATED 24 40 3
13Q LOSS WILD-TYPE 60 47 9

Figure S170.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q loss' versus 'CN_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0056

Table S171.  Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
14Q LOSS MUTATED 27 7 11
14Q LOSS WILD-TYPE 38 37 64

Figure S171.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 0.0052 (Fisher's exact test), Q value = 0.034

Table S172.  Gene #67: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
14Q LOSS MUTATED 27 8 10
14Q LOSS WILD-TYPE 49 24 66

Figure S172.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CNMF'

P value = 0.00392 (Fisher's exact test), Q value = 0.028

Table S173.  Gene #67: '14q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
14Q LOSS MUTATED 10 12 7 3 0
14Q LOSS WILD-TYPE 16 16 23 31 8

Figure S173.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'14q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00281 (Fisher's exact test), Q value = 0.022

Table S174.  Gene #67: '14q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
14Q LOSS MUTATED 7 11 6 6 2
14Q LOSS WILD-TYPE 16 10 16 20 32

Figure S174.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 0.00696 (Fisher's exact test), Q value = 0.041

Table S175.  Gene #67: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
14Q LOSS MUTATED 29 13 1 2
14Q LOSS WILD-TYPE 52 56 21 9

Figure S175.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0195 (Fisher's exact test), Q value = 0.091

Table S176.  Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
14Q LOSS MUTATED 24 5 16
14Q LOSS WILD-TYPE 43 15 80

Figure S176.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 0.0293 (Fisher's exact test), Q value = 0.12

Table S177.  Gene #67: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
14Q LOSS MUTATED 28 14 3
14Q LOSS WILD-TYPE 56 73 9

Figure S177.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0027 (Fisher's exact test), Q value = 0.022

Table S178.  Gene #67: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
14Q LOSS MUTATED 26 4 10 5
14Q LOSS WILD-TYPE 36 22 52 28

Figure S178.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0369 (Fisher's exact test), Q value = 0.13

Table S179.  Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
14Q LOSS MUTATED 25 12 6 2
14Q LOSS WILD-TYPE 41 54 29 9

Figure S179.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00129 (Fisher's exact test), Q value = 0.013

Table S180.  Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
14Q LOSS MUTATED 26 4 15
14Q LOSS WILD-TYPE 36 18 79

Figure S180.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.0303 (Fisher's exact test), Q value = 0.12

Table S181.  Gene #68: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
15Q LOSS MUTATED 31 10 16
15Q LOSS WILD-TYPE 45 22 60

Figure S181.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0497 (Fisher's exact test), Q value = 0.16

Table S182.  Gene #68: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
15Q LOSS MUTATED 28 6 23
15Q LOSS WILD-TYPE 39 14 73

Figure S182.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00531 (Fisher's exact test), Q value = 0.035

Table S183.  Gene #68: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
15Q LOSS MUTATED 18 16 14 9
15Q LOSS WILD-TYPE 44 10 48 24

Figure S183.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00074 (Fisher's exact test), Q value = 0.008

Table S184.  Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
15Q LOSS MUTATED 19 15 23
15Q LOSS WILD-TYPE 43 7 71

Figure S184.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.0061

Table S185.  Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
16P LOSS MUTATED 30 12 12
16P LOSS WILD-TYPE 35 32 63

Figure S185.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0024

Table S186.  Gene #69: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
16P LOSS MUTATED 35 7 12
16P LOSS WILD-TYPE 41 25 64

Figure S186.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 7e-04 (Fisher's exact test), Q value = 0.008

Table S187.  Gene #69: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
16P LOSS MUTATED 36 11 6 1
16P LOSS WILD-TYPE 45 58 16 10

Figure S187.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.0019

Table S188.  Gene #69: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
16P LOSS MUTATED 27 11 16
16P LOSS WILD-TYPE 40 9 80

Figure S188.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0032

Table S189.  Gene #69: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
16P LOSS MUTATED 37 14 2
16P LOSS WILD-TYPE 47 73 10

Figure S189.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.0043

Table S190.  Gene #69: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
16P LOSS MUTATED 30 8 10 5
16P LOSS WILD-TYPE 32 18 52 28

Figure S190.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0056

Table S191.  Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
16P LOSS MUTATED 31 10 7 3
16P LOSS WILD-TYPE 35 56 28 8

Figure S191.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.0038

Table S192.  Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
16P LOSS MUTATED 28 8 15
16P LOSS WILD-TYPE 34 14 79

Figure S192.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00046

Table S193.  Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
16Q LOSS MUTATED 33 12 8
16Q LOSS WILD-TYPE 32 32 67

Figure S193.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00059

Table S194.  Gene #70: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
16Q LOSS MUTATED 35 8 10
16Q LOSS WILD-TYPE 41 24 66

Figure S194.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'RPPA_CNMF'

P value = 0.0383 (Fisher's exact test), Q value = 0.14

Table S195.  Gene #70: '16q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
16Q LOSS MUTATED 10 10 4 4 2
16Q LOSS WILD-TYPE 16 18 26 30 6

Figure S195.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'16q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0277 (Fisher's exact test), Q value = 0.11

Table S196.  Gene #70: '16q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
16Q LOSS MUTATED 9 9 3 3 6
16Q LOSS WILD-TYPE 14 12 19 23 28

Figure S196.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00068

Table S197.  Gene #70: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
16Q LOSS MUTATED 38 8 7 0
16Q LOSS WILD-TYPE 43 61 15 11

Figure S197.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00046

Table S198.  Gene #70: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
16Q LOSS MUTATED 31 9 13
16Q LOSS WILD-TYPE 36 11 83

Figure S198.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00046

Table S199.  Gene #70: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
16Q LOSS MUTATED 40 12 0
16Q LOSS WILD-TYPE 44 75 12

Figure S199.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00059

Table S200.  Gene #70: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
16Q LOSS MUTATED 31 9 8 4
16Q LOSS WILD-TYPE 31 17 54 29

Figure S200.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00046

Table S201.  Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
16Q LOSS MUTATED 35 10 4 1
16Q LOSS WILD-TYPE 31 56 31 10

Figure S201.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00046

Table S202.  Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
16Q LOSS MUTATED 31 7 12
16Q LOSS WILD-TYPE 31 15 82

Figure S202.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 0.00274 (Fisher's exact test), Q value = 0.022

Table S203.  Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
17P LOSS MUTATED 35 17 19
17P LOSS WILD-TYPE 30 27 56

Figure S203.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.0019

Table S204.  Gene #71: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
17P LOSS MUTATED 43 10 18
17P LOSS WILD-TYPE 33 22 58

Figure S204.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 0.00184 (Fisher's exact test), Q value = 0.017

Table S205.  Gene #71: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
17P LOSS MUTATED 44 18 6 3
17P LOSS WILD-TYPE 37 51 16 8

Figure S205.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-04 (Fisher's exact test), Q value = 0.0095

Table S206.  Gene #71: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
17P LOSS MUTATED 36 10 25
17P LOSS WILD-TYPE 31 10 71

Figure S206.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00068

Table S207.  Gene #71: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
17P LOSS MUTATED 46 25 0
17P LOSS WILD-TYPE 38 62 12

Figure S207.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00139 (Fisher's exact test), Q value = 0.013

Table S208.  Gene #71: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
17P LOSS MUTATED 33 14 17 7
17P LOSS WILD-TYPE 29 12 45 26

Figure S208.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.0023

Table S209.  Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
17P LOSS MUTATED 33 13 23
17P LOSS WILD-TYPE 29 9 71

Figure S209.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.064

Table S210.  Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
18P LOSS MUTATED 34 16 21
18P LOSS WILD-TYPE 31 28 54

Figure S210.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 0.00103 (Fisher's exact test), Q value = 0.011

Table S211.  Gene #73: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
18P LOSS MUTATED 41 11 19
18P LOSS WILD-TYPE 35 21 57

Figure S211.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 0.00692 (Fisher's exact test), Q value = 0.041

Table S212.  Gene #73: '18p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
18P LOSS MUTATED 42 19 5 4
18P LOSS WILD-TYPE 39 50 17 7

Figure S212.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00446 (Fisher's exact test), Q value = 0.031

Table S213.  Gene #73: '18p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
18P LOSS MUTATED 34 10 26
18P LOSS WILD-TYPE 33 10 70

Figure S213.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 0.00117 (Fisher's exact test), Q value = 0.012

Table S214.  Gene #73: '18p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
18P LOSS MUTATED 43 22 6
18P LOSS WILD-TYPE 41 65 6

Figure S214.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0232 (Fisher's exact test), Q value = 0.1

Table S215.  Gene #73: '18p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
18P LOSS MUTATED 32 12 19 8
18P LOSS WILD-TYPE 30 14 43 25

Figure S215.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0261 (Fisher's exact test), Q value = 0.11

Table S216.  Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
18P LOSS MUTATED 34 17 14 4
18P LOSS WILD-TYPE 32 49 21 7

Figure S216.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00572 (Fisher's exact test), Q value = 0.036

Table S217.  Gene #73: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
18P LOSS MUTATED 32 11 26
18P LOSS WILD-TYPE 30 11 68

Figure S217.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q loss' versus 'METHLYATION_CNMF'

P value = 0.0116 (Fisher's exact test), Q value = 0.063

Table S218.  Gene #74: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
18Q LOSS MUTATED 52 14 36
18Q LOSS WILD-TYPE 24 18 40

Figure S218.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 0.0265 (Fisher's exact test), Q value = 0.11

Table S219.  Gene #74: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
18Q LOSS MUTATED 54 33 8 6
18Q LOSS WILD-TYPE 27 36 14 5

Figure S219.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0273 (Fisher's exact test), Q value = 0.11

Table S220.  Gene #74: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
18Q LOSS MUTATED 43 14 44
18Q LOSS WILD-TYPE 24 6 52

Figure S220.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 0.0218 (Fisher's exact test), Q value = 0.097

Table S221.  Gene #74: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
18Q LOSS MUTATED 56 40 6
18Q LOSS WILD-TYPE 28 47 6

Figure S221.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00212 (Fisher's exact test), Q value = 0.019

Table S222.  Gene #74: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
18Q LOSS MUTATED 35 22 33 12
18Q LOSS WILD-TYPE 27 4 29 21

Figure S222.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0485 (Fisher's exact test), Q value = 0.16

Table S223.  Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
18Q LOSS MUTATED 43 29 23 5
18Q LOSS WILD-TYPE 23 37 12 6

Figure S223.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.0041

Table S224.  Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
18Q LOSS MUTATED 36 20 44
18Q LOSS WILD-TYPE 26 2 50

Figure S224.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 0.0483 (Fisher's exact test), Q value = 0.16

Table S225.  Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
19P LOSS MUTATED 25 9 31
19P LOSS WILD-TYPE 40 35 44

Figure S225.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00926 (Fisher's exact test), Q value = 0.052

Table S226.  Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
19P LOSS MUTATED 27 2 35
19P LOSS WILD-TYPE 35 20 59

Figure S226.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 0.0048 (Fisher's exact test), Q value = 0.033

Table S227.  Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
19Q LOSS MUTATED 18 5 29
19Q LOSS WILD-TYPE 47 39 46

Figure S227.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0128 (Fisher's exact test), Q value = 0.067

Table S228.  Gene #76: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
19Q LOSS MUTATED 17 1 34
19Q LOSS WILD-TYPE 50 19 62

Figure S228.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0184 (Fisher's exact test), Q value = 0.087

Table S229.  Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
19Q LOSS MUTATED 15 27 5 4
19Q LOSS WILD-TYPE 51 39 30 7

Figure S229.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0094 (Fisher's exact test), Q value = 0.052

Table S230.  Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
19Q LOSS MUTATED 17 1 33
19Q LOSS WILD-TYPE 45 21 61

Figure S230.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 0.0311 (Fisher's exact test), Q value = 0.12

Table S231.  Gene #79: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
21Q LOSS MUTATED 43 18 45
21Q LOSS WILD-TYPE 22 26 30

Figure S231.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 0.00615 (Fisher's exact test), Q value = 0.039

Table S232.  Gene #79: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
21Q LOSS MUTATED 54 14 38
21Q LOSS WILD-TYPE 22 18 38

Figure S232.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 0.0214 (Fisher's exact test), Q value = 0.096

Table S233.  Gene #79: '21q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
21Q LOSS MUTATED 57 45 4
21Q LOSS WILD-TYPE 27 42 8

Figure S233.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'21q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.042 (Fisher's exact test), Q value = 0.14

Table S234.  Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
21Q LOSS MUTATED 45 34 15 8
21Q LOSS WILD-TYPE 21 32 20 3

Figure S234.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.001

Table S235.  Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
22Q LOSS MUTATED 40 13 19
22Q LOSS WILD-TYPE 25 31 56

Figure S235.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00046

Table S236.  Gene #80: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
22Q LOSS MUTATED 45 10 17
22Q LOSS WILD-TYPE 31 22 59

Figure S236.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CNMF'

P value = 0.0311 (Fisher's exact test), Q value = 0.12

Table S237.  Gene #80: '22q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
22Q LOSS MUTATED 15 10 11 7 1
22Q LOSS WILD-TYPE 11 18 19 27 7

Figure S237.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.011

Table S238.  Gene #80: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 69 22 11
22Q LOSS MUTATED 45 19 5 3
22Q LOSS WILD-TYPE 36 50 17 8

Figure S238.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.0047

Table S239.  Gene #80: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 20 96
22Q LOSS MUTATED 38 9 25
22Q LOSS WILD-TYPE 29 11 71

Figure S239.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.001

Table S240.  Gene #80: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 87 12
22Q LOSS MUTATED 47 24 1
22Q LOSS WILD-TYPE 37 63 11

Figure S240.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.0037

Table S241.  Gene #80: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
22Q LOSS MUTATED 37 11 14 10
22Q LOSS WILD-TYPE 25 15 48 23

Figure S241.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00046

Table S242.  Gene #80: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
22Q LOSS MUTATED 43 18 7 3
22Q LOSS WILD-TYPE 23 48 28 8

Figure S242.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00059

Table S243.  Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
22Q LOSS MUTATED 39 9 23
22Q LOSS WILD-TYPE 23 13 71

Figure S243.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'CN_CNMF'

P value = 0.00439 (Fisher's exact test), Q value = 0.031

Table S244.  Gene #81: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
XP LOSS MUTATED 27 6 27
XP LOSS WILD-TYPE 38 38 48

Figure S244.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

'xp loss' versus 'RPPA_CNMF'

P value = 0.0432 (Fisher's exact test), Q value = 0.15

Table S245.  Gene #81: 'xp loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
XP LOSS MUTATED 14 7 7 15 1
XP LOSS WILD-TYPE 12 21 23 19 7

Figure S245.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 0.079

Table S246.  Gene #82: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 44 75
XQ LOSS MUTATED 22 6 12
XQ LOSS WILD-TYPE 43 38 63

Figure S246.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.028 (Fisher's exact test), Q value = 0.11

Table S247.  Gene #82: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 32 76
XQ LOSS MUTATED 24 4 12
XQ LOSS WILD-TYPE 52 28 64

Figure S247.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'RPPA_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.005

Table S248.  Gene #82: 'xq loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
XQ LOSS MUTATED 14 4 2 8 0
XQ LOSS WILD-TYPE 12 24 28 26 8

Figure S248.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'xq loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0264 (Fisher's exact test), Q value = 0.11

Table S249.  Gene #82: 'xq loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
XQ LOSS MUTATED 11 4 2 6 5
XQ LOSS WILD-TYPE 12 17 20 20 29

Figure S249.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00244 (Fisher's exact test), Q value = 0.02

Table S250.  Gene #82: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 26 62 33
XQ LOSS MUTATED 22 3 6 9
XQ LOSS WILD-TYPE 40 23 56 24

Figure S250.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0417 (Fisher's exact test), Q value = 0.14

Table S251.  Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 66 35 11
XQ LOSS MUTATED 21 12 3 2
XQ LOSS WILD-TYPE 45 54 32 9

Figure S251.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.011 (Fisher's exact test), Q value = 0.06

Table S252.  Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 22 94
XQ LOSS MUTATED 21 2 15
XQ LOSS WILD-TYPE 41 20 79

Figure S252.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ESCA-TP/19782631/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/ESCA-TP/20125286/ESCA-TP.transferedmergedcluster.txt

  • Number of patients = 184

  • Number of significantly arm-level cnvs = 82

  • Number of molecular subtypes = 10

  • Exclude genes that fewer than K tumors have mutations, K = 3

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] 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)
[2] 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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