Correlation between copy number variations of arm-level result and molecular subtypes
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 90 patients, 212 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 2p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 2q gain cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 4q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 5p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 5q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 6p gain cnv correlated to 'CN_CNMF'.

  • 7p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 7q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 8p gain cnv correlated to 'CN_CNMF'.

  • 8q gain cnv correlated to 'CN_CNMF'.

  • 9p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 9q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 10p gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 10q gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 11q gain cnv correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • 12p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 12q gain cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 13q gain cnv correlated to 'MRNASEQ_CNMF'.

  • 14q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 15q gain cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

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

  • 17q gain cnv correlated to 'CN_CNMF'.

  • 19p gain cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 19q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 20p gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • xp gain cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • xq gain cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 1p loss cnv correlated to 'MIRSEQ_MATURE_CNMF'.

  • 1q loss cnv correlated to 'RPPA_CHIERARCHICAL'.

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

  • 2q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

  • 3q loss cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 4p loss cnv correlated to 'MRNASEQ_CNMF'.

  • 4q loss cnv correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 5p loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 8p loss cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 8q loss cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 9p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 9q loss cnv correlated to 'RPPA_CHIERARCHICAL'.

  • 11p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

  • 12p loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 12q loss cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 13q loss cnv correlated to 'CN_CNMF'.

  • 14q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 15q loss cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

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

  • 16q loss cnv correlated to 'MIRSEQ_MATURE_CNMF'.

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

  • 17q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 18p loss cnv correlated to 'CN_CNMF'.

  • 18q loss cnv correlated to 'CN_CNMF'.

  • 19p loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 20p loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 22q loss cnv correlated to 'CN_CNMF'.

  • xp loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • xq loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_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, 212 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
16p gain 49 (54%) 41 1e-05
(0.00041) 		0.0105
(0.0722) 		1
(1.00) 		0.0381
(0.159) 		1e-05
(0.00041) 		1e-05
(0.00041) 		0.0465
(0.183) 		0.0255
(0.124) 		0.0299
(0.136) 		0.273
(0.502)
20p gain 46 (51%) 44 1e-05
(0.00041) 		0.236
(0.463) 		0.00277
(0.0267) 		0.00839
(0.063) 		8e-05
(0.00177) 		0.00012
(0.00252) 		0.00479
(0.0405) 		0.0894
(0.269) 		0.00952
(0.0674) 		0.00468
(0.0403)
10q gain 26 (29%) 64 0.00168
(0.0182) 		0.0702
(0.234) 		0.023
(0.117) 		0.0147
(0.087) 		4e-05
(0.00106) 		0.00049
(0.00731) 		0.0212
(0.111) 		0.342
(0.567) 		0.0298
(0.136) 		0.846
(0.989)
14q gain 21 (23%) 69 0.014
(0.0855) 		0.0563
(0.203) 		0.0706
(0.235) 		0.428
(0.658) 		0.00039
(0.00615) 		0.00122
(0.0143) 		2e-05
(0.000713) 		0.00025
(0.00418) 		2e-05
(0.000713) 		1e-05
(0.00041)
16q gain 47 (52%) 43 1e-05
(0.00041) 		0.00799
(0.0607) 		1
(1.00) 		0.324
(0.553) 		7e-05
(0.00164) 		1e-05
(0.00041) 		0.0257
(0.124) 		0.0125
(0.0808) 		0.014
(0.0855) 		0.461
(0.688)
20q gain 49 (54%) 41 1e-05
(0.00041) 		0.0653
(0.225) 		0.0169
(0.0976) 		0.076
(0.248) 		0.00013
(0.00266) 		0.00024
(0.00418) 		0.0201
(0.108) 		0.274
(0.502) 		0.0113
(0.0757) 		0.0141
(0.0855)
21q gain 31 (34%) 59 0.0207
(0.11) 		0.00914
(0.0663) 		0.208
(0.441) 		0.232
(0.462) 		0.0198
(0.108) 		0.00098
(0.0129) 		0.0141
(0.0855) 		0.0201
(0.108) 		0.0028
(0.0267) 		0.0849
(0.26)
2q gain 12 (13%) 78 0.0523
(0.197) 		0.00238
(0.0238) 		0.665
(0.859) 		0.178
(0.4) 		0.0185
(0.103) 		0.00275
(0.0267) 		0.0548
(0.201) 		0.00472
(0.0403) 		0.0201
(0.108) 		0.0243
(0.12)
9q gain 29 (32%) 61 0.00032
(0.00515) 		0.00111
(0.014) 		0.00121
(0.0143) 		0.0702
(0.234) 		0.0235
(0.118) 		0.00169
(0.0182) 		0.0331
(0.148) 		0.353
(0.578) 		0.0909
(0.27) 		0.0823
(0.254)
10p gain 25 (28%) 65 0.00179
(0.0191) 		0.0585
(0.209) 		0.0106
(0.0722) 		0.0142
(0.0855) 		3e-05
(0.000911) 		0.00015
(0.00286) 		0.0352
(0.153) 		0.508
(0.727) 		0.0557
(0.203) 		0.454
(0.681)
9p loss 20 (22%) 70 0.00183
(0.0192) 		0.0479
(0.187) 		0.514
(0.73) 		0.116
(0.31) 		4e-05
(0.00106) 		0.0011
(0.014) 		0.00922
(0.0663) 		0.139
(0.344) 		0.00437
(0.0385) 		0.936
(1.00)
16p loss 6 (7%) 84 0.126
(0.324) 		0.0489
(0.189) 		0.665
(0.859) 		0.0465
(0.183) 		0.0021
(0.0213) 		0.00437
(0.0385) 		0.0124
(0.0808) 		0.443
(0.67) 		0.0003
(0.00492) 		0.465
(0.688)
17p loss 32 (36%) 58 0.00293
(0.0273) 		0.00019
(0.00346) 		0.353
(0.578) 		0.195
(0.422) 		0.0119
(0.0791) 		0.0132
(0.0838) 		0.0795
(0.254) 		0.00307
(0.0283) 		0.0138
(0.0855) 		0.114
(0.309)
2p gain 13 (14%) 77 0.00703
(0.0544) 		0.0013
(0.015) 		0.0959
(0.278) 		0.343
(0.568) 		0.0124
(0.0808) 		0.00025
(0.00418) 		0.372
(0.599) 		0.0193
(0.106) 		0.125
(0.324) 		0.0735
(0.242)
4p gain 37 (41%) 53 1e-05
(0.00041) 		0.0431
(0.175) 		0.767
(0.927) 		0.464
(0.688) 		3e-05
(0.000911) 		4e-05
(0.00106) 		0.297
(0.523) 		0.00205
(0.021) 		0.344
(0.568) 		0.858
(0.995)
4q gain 33 (37%) 57 1e-05
(0.00041) 		0.0367
(0.157) 		1
(1.00) 		0.727
(0.889) 		3e-05
(0.000911) 		1e-05
(0.00041) 		0.556
(0.761) 		0.00073
(0.00981) 		0.36
(0.585) 		0.948
(1.00)
5p gain 57 (63%) 33 1e-05
(0.00041) 		0.0376
(0.159) 		0.12
(0.316) 		0.0333
(0.148) 		0.00058
(0.00834) 		1e-05
(0.00041) 		0.254
(0.478) 		0.227
(0.461) 		0.0736
(0.242) 		0.355
(0.58)
9p gain 20 (22%) 70 6e-05
(0.00149) 		0.002
(0.0208) 		0.00415
(0.0374) 		0.136
(0.341) 		0.00902
(0.066) 		0.0104
(0.0722) 		0.385
(0.618) 		0.552
(0.76) 		0.465
(0.688) 		0.251
(0.476)
8q loss 12 (13%) 78 0.00468
(0.0403) 		0.0875
(0.266) 		0.243
(0.468) 		0.0341
(0.15) 		0.0332
(0.148) 		0.126
(0.324) 		0.0785
(0.253) 		0.0343
(0.15) 		0.182
(0.405) 		0.0371
(0.158)
5q gain 53 (59%) 37 1e-05
(0.00041) 		0.00845
(0.063) 		0.542
(0.749) 		0.147
(0.352) 		0.00067
(0.00916) 		2e-05
(0.000713) 		0.336
(0.567) 		0.136
(0.341) 		0.209
(0.441) 		0.17
(0.39)
12q gain 64 (71%) 26 1e-05
(0.00041) 		0.312
(0.541) 		0.738
(0.898) 		0.0273
(0.129) 		0.00053
(0.00776) 		0.00015
(0.00286) 		0.237
(0.463) 		0.452
(0.681) 		0.221
(0.454) 		0.589
(0.801)
15q gain 11 (12%) 79 0.094
(0.275) 		0.0451
(0.181) 		0.414
(0.645) 		0.847
(0.989) 		0.0107
(0.0722) 		0.00497
(0.0416) 		0.362
(0.588) 		0.00061
(0.00862) 		0.505
(0.724) 		0.256
(0.478)
19p gain 56 (62%) 34 0.00389
(0.0354) 		0.0544
(0.201) 		0.108
(0.303) 		0.0189
(0.105) 		0.00117
(0.0141) 		0.00047
(0.00714) 		0.467
(0.688) 		0.471
(0.692) 		0.639
(0.841) 		0.215
(0.45)
xp gain 42 (47%) 48 1e-05
(0.00041) 		0.241
(0.467) 		1
(1.00) 		0.03
(0.136) 		0.00099
(0.0129) 		0.00579
(0.0461) 		1
(1.00) 		0.0809
(0.254) 		0.429
(0.658) 		0.217
(0.452)
xq gain 41 (46%) 49 3e-05
(0.000911) 		0.167
(0.385) 		0.768
(0.928) 		0.042
(0.171) 		0.00153
(0.0172) 		0.00892
(0.0659) 		0.798
(0.947) 		0.151
(0.356) 		0.342
(0.567) 		0.139
(0.344)
8p loss 16 (18%) 74 0.00573
(0.0461) 		0.224
(0.459) 		0.284
(0.512) 		0.00062
(0.00862) 		0.179
(0.402) 		0.143
(0.349) 		0.18
(0.403) 		0.0239
(0.12) 		0.255
(0.478) 		0.0291
(0.134)
17q loss 24 (27%) 66 0.0147
(0.087) 		0.00554
(0.0454) 		0.53
(0.744) 		0.515
(0.73) 		0.116
(0.31) 		0.0336
(0.148) 		0.0663
(0.227) 		0.021
(0.11) 		0.225
(0.46) 		0.107
(0.303)
7p gain 48 (53%) 42 1e-05
(0.00041) 		0.118
(0.31) 		0.542
(0.749) 		0.0902
(0.27) 		0.00012
(0.00252) 		0.00156
(0.0173) 		0.915
(1.00) 		0.547
(0.756) 		0.278
(0.507) 		0.29
(0.516)
7q gain 48 (53%) 42 1e-05
(0.00041) 		0.115
(0.31) 		0.542
(0.749) 		0.245
(0.47) 		1e-05
(0.00041) 		0.00015
(0.00286) 		0.916
(1.00) 		0.329
(0.557) 		0.276
(0.504) 		0.189
(0.413)
12p gain 64 (71%) 26 1e-05
(0.00041) 		0.21
(0.441) 		0.749
(0.91) 		0.0676
(0.228) 		0.00016
(0.00298) 		4e-05
(0.00106) 		0.248
(0.474) 		0.209
(0.441) 		0.132
(0.336) 		0.25
(0.476)
19q gain 52 (58%) 38 6e-05
(0.00149) 		0.0503
(0.193) 		0.542
(0.749) 		0.056
(0.203) 		0.00041
(0.00634) 		0.00117
(0.0141) 		0.144
(0.349) 		0.11
(0.305) 		0.522
(0.735) 		0.117
(0.31)
2p loss 17 (19%) 73 0.00683
(0.0537) 		0.0266
(0.127) 		0.722
(0.888) 		0.656
(0.855) 		0.613
(0.826) 		0.266
(0.492) 		0.038
(0.159) 		0.77
(0.928) 		0.229
(0.462) 		0.701
(0.875)
2q loss 15 (17%) 75 0.00529
(0.0438) 		0.00113
(0.014) 		1
(1.00) 		0.886
(1.00) 		0.113
(0.309) 		0.0534
(0.199) 		0.0314
(0.141) 		0.727
(0.889) 		0.0691
(0.232) 		0.537
(0.748)
4q loss 11 (12%) 79 0.239
(0.464) 		0.0957
(0.278) 		0.414
(0.645) 		0.923
(1.00) 		0.00728
(0.0558) 		0.0265
(0.127) 		0.25
(0.476) 		0.813
(0.962) 		0.0128
(0.0822) 		0.902
(1.00)
14q loss 18 (20%) 72 0.0278
(0.131) 		0.445
(0.67) 		0.722
(0.888) 		0.0537
(0.199) 		0.0177
(0.0999) 		0.0478
(0.187) 		0.414
(0.645) 		0.531
(0.745) 		0.216
(0.451) 		0.147
(0.352)
20p loss 9 (10%) 81 0.0412
(0.169) 		0.303
(0.53) 		0.0216
(0.112) 		0.855
(0.993) 		0.212
(0.445) 		0.126
(0.324) 		0.0673
(0.228) 		0.444
(0.67) 		0.021
(0.11) 		0.44
(0.67)
xp loss 16 (18%) 74 7e-05
(0.00164) 		0.395
(0.627) 		0.459
(0.686) 		0.094
(0.275) 		0.0226
(0.116) 		0.0286
(0.134) 		0.69
(0.874) 		0.0886
(0.268) 		0.157
(0.367) 		1
(1.00)
xq loss 15 (17%) 75 0.00277
(0.0267) 		0.153
(0.36) 		0.135
(0.341) 		0.0956
(0.278) 		0.0178
(0.0999) 		0.016
(0.0928) 		0.505
(0.724) 		0.172
(0.393) 		0.183
(0.407) 		0.624
(0.831)
1q gain 8 (9%) 82 0.0441
(0.178) 		0.656
(0.855) 		0.608
(0.82) 		0.557
(0.762) 		0.0462
(0.183) 		0.0785
(0.253) 		0.065
(0.225) 		0.244
(0.469) 		0.147
(0.352) 		0.85
(0.99)
11q gain 6 (7%) 84 0.126
(0.324) 		0.173
(0.393) 		0.346
(0.57) 		0.485
(0.709) 		0.045
(0.181) 		0.0789
(0.253) 		0.188
(0.412) 		0.369
(0.596) 		0.00577
(0.0461) 		0.392
(0.626)
3q loss 20 (22%) 70 0.167
(0.385) 		0.163
(0.381) 		0.284
(0.512) 		0.604
(0.818) 		0.0217
(0.112) 		0.029
(0.134) 		0.192
(0.417) 		0.34
(0.567) 		0.315
(0.542) 		0.117
(0.31)
11p loss 24 (27%) 66 0.00688
(0.0537) 		0.0178
(0.0999) 		1
(1.00) 		0.798
(0.947) 		0.22
(0.454) 		0.19
(0.413) 		0.281
(0.511) 		0.891
(1.00) 		0.691
(0.874) 		1
(1.00)
11q loss 23 (26%) 67 0.0123
(0.0808) 		0.0029
(0.0273) 		1
(1.00) 		0.395
(0.627) 		0.137
(0.343) 		0.124
(0.324) 		0.103
(0.294) 		0.827
(0.972) 		0.492
(0.714) 		0.78
(0.935)
12q loss 4 (4%) 86 0.186
(0.409) 		0.0487
(0.189) 		1
(1.00) 		0.0822
(0.254) 		0.442
(0.67) 		0.00954
(0.0674) 		0.329
(0.557) 		0.239
(0.464) 		0.674
(0.869) 		0.113
(0.309)
6p gain 18 (20%) 72 0.0177
(0.0999) 		0.684
(0.874) 		0.722
(0.888) 		0.873
(1.00) 		0.066
(0.226) 		0.471
(0.692) 		0.165
(0.384) 		0.056
(0.203) 		0.416
(0.645) 		0.235
(0.462)
8p gain 32 (36%) 58 8e-05
(0.00177) 		0.144
(0.349) 		0.337
(0.567) 		0.44
(0.67) 		0.168
(0.385) 		0.145
(0.35) 		0.112
(0.308) 		0.174
(0.394) 		0.243
(0.468) 		0.515
(0.73)
8q gain 38 (42%) 52 0.0002
(0.00357) 		0.294
(0.52) 		0.758
(0.918) 		0.467
(0.688) 		0.415
(0.645) 		0.233
(0.462) 		0.498
(0.716) 		0.262
(0.487) 		0.521
(0.735) 		0.644
(0.846)
13q gain 6 (7%) 84 0.401
(0.634) 		0.466
(0.688) 		1
(1.00) 		0.726
(0.889) 		0.0403
(0.167) 		0.638
(0.841) 		0.141
(0.349) 		0.915
(1.00) 		0.185
(0.409) 		0.699
(0.874)
17q gain 7 (8%) 83 0.025
(0.122) 		0.34
(0.567) 		0.233
(0.462) 		0.686
(0.874) 		0.145
(0.35) 		0.209
(0.441) 		0.793
(0.945) 		0.0611
(0.216) 		0.0611
(0.216)
1p loss 29 (32%) 61 0.118
(0.31) 		0.143
(0.349) 		1
(1.00) 		0.131
(0.334) 		0.439
(0.67) 		0.0642
(0.223) 		0.467
(0.688) 		0.407
(0.641) 		0.029
(0.134) 		0.949
(1.00)
1q loss 20 (22%) 70 0.207
(0.441) 		0.0888
(0.268) 		1
(1.00) 		0.0251
(0.122) 		0.962
(1.00) 		0.599
(0.813) 		0.37
(0.596) 		0.842
(0.986) 		0.0782
(0.253) 		0.487
(0.711)
4p loss 10 (11%) 80 0.0974
(0.281) 		0.235
(0.462) 		0.665
(0.859) 		0.989
(1.00) 		0.023
(0.117) 		0.0811
(0.254) 		0.309
(0.537) 		0.932
(1.00) 		0.0514
(0.196) 		1
(1.00)
5p loss 8 (9%) 82 0.287
(0.515) 		0.0502
(0.193) 		0.608
(0.82) 		0.192
(0.417) 		0.229
(0.462) 		0.00975
(0.0683) 		0.772
(0.929) 		0.298
(0.524) 		0.698
(0.874) 		1
(1.00)
9q loss 11 (12%) 79 0.323
(0.553) 		0.935
(1.00) 		1
(1.00) 		0.0362
(0.155) 		0.0801
(0.254) 		0.323
(0.553) 		0.56
(0.763) 		0.498
(0.716) 		0.219
(0.454) 		0.805
(0.954)
12p loss 5 (6%) 85 0.0907
(0.27) 		0.254
(0.478) 		1
(1.00) 		0.0827
(0.254) 		0.62
(0.83) 		0.0389
(0.162) 		0.102
(0.292) 		0.515
(0.73) 		0.426
(0.658) 		0.15
(0.356)
13q loss 39 (43%) 51 0.0147
(0.087) 		0.0806
(0.254) 		0.365
(0.591) 		0.942
(1.00) 		0.626
(0.831) 		0.886
(1.00) 		0.753
(0.913) 		0.305
(0.533) 		0.615
(0.826) 		0.493
(0.715)
15q loss 21 (23%) 69 0.0815
(0.254) 		0.416
(0.645) 		1
(1.00) 		0.51
(0.728) 		0.109
(0.304) 		0.227
(0.461) 		0.607
(0.82) 		0.0407
(0.168) 		0.29
(0.516) 		0.876
(1.00)
16q loss 5 (6%) 85 0.218
(0.452) 		0.0777
(0.253) 		0.346
(0.57) 		0.175
(0.397) 		0.0568
(0.204) 		0.0862
(0.263) 		0.166
(0.385) 		0.306
(0.533) 		0.00137
(0.0156) 		0.698
(0.874)
18p loss 37 (41%) 53 0.0244
(0.12) 		0.26
(0.484) 		0.554
(0.76) 		0.691
(0.874) 		0.778
(0.934) 		0.646
(0.847) 		0.694
(0.874) 		0.689
(0.874) 		0.356
(0.581) 		0.338
(0.567)
18q loss 35 (39%) 55 0.0359
(0.155) 		0.425
(0.657) 		1
(1.00) 		0.533
(0.746) 		0.825
(0.971) 		0.935
(1.00) 		0.496
(0.716) 		0.914
(1.00) 		0.291
(0.516) 		0.352
(0.578)
19p loss 5 (6%) 85 0.0916
(0.271) 		0.442
(0.67) 		1
(1.00) 		0.157
(0.367) 		0.0139
(0.0855) 		0.139
(0.344) 		0.715
(0.885) 		0.282
(0.511) 		0.111
(0.305)
22q loss 48 (53%) 42 0.0149
(0.0873) 		0.0812
(0.254) 		0.55
(0.758) 		0.482
(0.706) 		0.621
(0.83) 		0.284
(0.512) 		0.875
(1.00) 		0.824
(0.971) 		0.681
(0.874) 		0.227
(0.461)
1p gain 4 (4%) 86 0.186
(0.409) 		1
(1.00)
3p gain 13 (14%) 77 0.285
(0.512) 		0.0666
(0.227) 		0.699
(0.874) 		0.883
(1.00) 		0.329
(0.557) 		0.365
(0.591) 		0.406
(0.64) 		0.106
(0.301) 		0.637
(0.84) 		0.387
(0.619)
3q gain 15 (17%) 75 0.401
(0.634) 		0.0519
(0.197) 		0.722
(0.888) 		0.824
(0.971) 		0.0521
(0.197) 		0.792
(0.945) 		0.655
(0.855) 		0.247
(0.474) 		0.677
(0.871) 		0.708
(0.878)
6q gain 16 (18%) 74 0.0738
(0.242) 		0.457
(0.685) 		0.699
(0.874) 		0.685
(0.874) 		0.199
(0.428) 		0.291
(0.516) 		0.3
(0.527) 		0.197
(0.425) 		0.149
(0.355) 		0.438
(0.67)
11p gain 5 (6%) 85 0.0917
(0.271) 		1
(1.00)
17p gain 5 (6%) 85 0.111
(0.305) 		0.338
(0.567) 		0.233
(0.462) 		0.688
(0.874) 		0.144
(0.349) 		0.205
(0.439) 		0.794
(0.945) 		0.0619
(0.218) 		0.063
(0.22)
18p gain 6 (7%) 84 0.262
(0.487) 		0.233
(0.462)
18q gain 5 (6%) 85 0.495
(0.716) 		0.489
(0.711)
22q gain 3 (3%) 87 0.633
(0.839) 		1
(1.00)
3p loss 20 (22%) 70 0.256
(0.478) 		0.143
(0.349) 		0.459
(0.686) 		0.292
(0.516) 		0.11
(0.305) 		0.135
(0.341) 		0.523
(0.735) 		0.39
(0.623) 		0.686
(0.874) 		0.316
(0.543)
5q loss 7 (8%) 83 0.898
(1.00) 		0.657
(0.855) 		0.489
(0.711) 		0.278
(0.507) 		0.134
(0.341) 		0.661
(0.859) 		0.125
(0.324) 		0.662
(0.859) 		0.85
(0.99)
6p loss 19 (21%) 71 0.151
(0.356) 		0.854
(0.993) 		0.722
(0.888) 		0.232
(0.462) 		0.62
(0.83) 		0.692
(0.874) 		0.623
(0.83) 		0.1
(0.288) 		0.727
(0.889) 		0.522
(0.735)
6q loss 22 (24%) 68 0.0625
(0.219) 		0.859
(0.995) 		0.314
(0.542) 		0.273
(0.502) 		0.634
(0.839) 		0.693
(0.874) 		0.731
(0.892) 		0.176
(0.397) 		0.555
(0.76) 		0.325
(0.553)
7p loss 5 (6%) 85 0.394
(0.627) 		0.582
(0.793) 		0.109
(0.304) 		0.205
(0.439) 		0.908
(1.00) 		0.892
(1.00) 		0.817
(0.965) 		0.415
(0.645) 		0.834
(0.978) 		0.114
(0.309)
7q loss 6 (7%) 84 0.313
(0.542) 		0.303
(0.53) 		0.109
(0.304) 		0.781
(0.935) 		0.622
(0.83) 		0.653
(0.855) 		1
(1.00) 		0.235
(0.462) 		0.733
(0.894) 		0.151
(0.357)
10p loss 12 (13%) 78 0.222
(0.456) 		0.427
(0.658) 		1
(1.00) 		0.0564
(0.203) 		0.264
(0.489) 		1
(1.00) 		0.686
(0.874) 		0.708
(0.878) 		1
(1.00) 		0.328
(0.557)
10q loss 10 (11%) 80 0.538
(0.748) 		0.626
(0.831) 		1
(1.00) 		0.239
(0.464) 		0.536
(0.748) 		1
(1.00) 		1
(1.00) 		0.704
(0.877) 		1
(1.00) 		0.289
(0.516)
19q loss 4 (4%) 86 0.185
(0.409) 		0.708
(0.878) 		1
(1.00) 		0.775
(0.932) 		0.118
(0.31) 		0.784
(0.938) 		0.207
(0.441) 		1
(1.00) 		0.429
(0.658)
20q loss 3 (3%) 87 0.182
(0.405) 		0.233
(0.462)
21q loss 15 (17%) 75 0.115
(0.309) 		0.339
(0.567) 		0.414
(0.645) 		0.0528
(0.198) 		0.256
(0.478) 		0.253
(0.478) 		0.222
(0.456) 		0.509
(0.727) 		0.0824
(0.254) 		0.101
(0.288)
'1q gain' versus 'CN_CNMF'

P value = 0.0441 (Fisher's exact test), Q value = 0.18

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
1Q GAIN MUTATED 7 0 1 0
1Q GAIN WILD-TYPE 29 26 15 12

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

'1q gain' versus 'MRNASEQ_CNMF'

P value = 0.0462 (Fisher's exact test), Q value = 0.18

Table S2.  Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
1Q GAIN MUTATED 4 2 0 0
1Q GAIN WILD-TYPE 20 11 17 23

Figure S2.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p gain' versus 'CN_CNMF'

P value = 0.00703 (Fisher's exact test), Q value = 0.054

Table S3.  Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
2P GAIN MUTATED 11 1 1 0
2P GAIN WILD-TYPE 25 25 15 12

Figure S3.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p gain' versus 'METHLYATION_CNMF'

P value = 0.0013 (Fisher's exact test), Q value = 0.015

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 11 20 18 11
2P GAIN MUTATED 7 1 0 1 0
2P GAIN WILD-TYPE 11 10 20 17 11

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

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.081

Table S5.  Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
2P GAIN MUTATED 7 0 0 2
2P GAIN WILD-TYPE 17 13 17 21

Figure S5.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.0042

Table S6.  Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
2P GAIN MUTATED 8 0 1 0
2P GAIN WILD-TYPE 15 23 6 24

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

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0193 (Fisher's exact test), Q value = 0.11

Table S7.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 27 11 20 4
2P GAIN MUTATED 0 1 1 6 1
2P GAIN WILD-TYPE 16 26 10 14 3

Figure S7.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'METHLYATION_CNMF'

P value = 0.00238 (Fisher's exact test), Q value = 0.024

Table S8.  Gene #4: '2q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 11 20 18 11
2Q GAIN MUTATED 6 0 0 1 0
2Q GAIN WILD-TYPE 12 11 20 17 11

Figure S8.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.0185 (Fisher's exact test), Q value = 0.1

Table S9.  Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
2Q GAIN MUTATED 6 0 0 1
2Q GAIN WILD-TYPE 18 13 17 22

Figure S9.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00275 (Fisher's exact test), Q value = 0.027

Table S10.  Gene #4: '2q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
2Q GAIN MUTATED 6 0 1 0
2Q GAIN WILD-TYPE 17 23 6 24

Figure S10.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00472 (Fisher's exact test), Q value = 0.04

Table S11.  Gene #4: '2q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 27 11 20 4
2Q GAIN MUTATED 0 0 1 6 0
2Q GAIN WILD-TYPE 16 27 10 14 4

Figure S11.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0201 (Fisher's exact test), Q value = 0.11

Table S12.  Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 22 27
2Q GAIN MUTATED 2 5 0
2Q GAIN WILD-TYPE 26 17 27

Figure S12.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0243 (Fisher's exact test), Q value = 0.12

Table S13.  Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 24 14
2Q GAIN MUTATED 7 0 0
2Q GAIN WILD-TYPE 32 24 14

Figure S13.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00041

Table S14.  Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
4P GAIN MUTATED 4 13 12 8
4P GAIN WILD-TYPE 32 13 4 4

Figure S14.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

'4p gain' versus 'METHLYATION_CNMF'

P value = 0.0431 (Fisher's exact test), Q value = 0.18

Table S15.  Gene #7: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 11 20 18 11
4P GAIN MUTATED 3 4 13 6 5
4P GAIN WILD-TYPE 15 7 7 12 6

Figure S15.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00091

Table S16.  Gene #7: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
4P GAIN MUTATED 1 8 11 10
4P GAIN WILD-TYPE 23 5 6 13

Figure S16.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.0011

Table S17.  Gene #7: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
4P GAIN MUTATED 2 15 0 13
4P GAIN WILD-TYPE 21 8 7 11

Figure S17.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00205 (Fisher's exact test), Q value = 0.021

Table S18.  Gene #7: '4p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 27 11 20 4
4P GAIN MUTATED 11 10 5 2 3
4P GAIN WILD-TYPE 5 17 6 18 1

Figure S18.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00041

Table S19.  Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
4Q GAIN MUTATED 3 12 11 7
4Q GAIN WILD-TYPE 33 14 5 5

Figure S19.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

'4q gain' versus 'METHLYATION_CNMF'

P value = 0.0367 (Fisher's exact test), Q value = 0.16

Table S20.  Gene #8: '4q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 11 20 18 11
4Q GAIN MUTATED 2 4 12 6 4
4Q GAIN WILD-TYPE 16 7 8 12 7

Figure S20.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00091

Table S21.  Gene #8: '4q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
4Q GAIN MUTATED 0 8 9 10
4Q GAIN WILD-TYPE 24 5 8 13

Figure S21.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00041

Table S22.  Gene #8: '4q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
4Q GAIN MUTATED 1 15 0 11
4Q GAIN WILD-TYPE 22 8 7 13

Figure S22.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00073 (Fisher's exact test), Q value = 0.0098

Table S23.  Gene #8: '4q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 27 11 20 4
4Q GAIN MUTATED 10 9 5 1 3
4Q GAIN WILD-TYPE 6 18 6 19 1

Figure S23.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00041

Table S24.  Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
5P GAIN MUTATED 10 24 14 9
5P GAIN WILD-TYPE 26 2 2 3

Figure S24.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.0376 (Fisher's exact test), Q value = 0.16

Table S25.  Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 11 20 18 11
5P GAIN MUTATED 7 5 15 14 9
5P GAIN WILD-TYPE 11 6 5 4 2

Figure S25.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0333 (Fisher's exact test), Q value = 0.15

Table S26.  Gene #9: '5p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 8 7 7 3 4 4 6 6
5P GAIN MUTATED 4 5 6 1 4 4 5 1
5P GAIN WILD-TYPE 4 2 1 2 0 0 1 5

Figure S26.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.0083

Table S27.  Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
5P GAIN MUTATED 7 10 14 18
5P GAIN WILD-TYPE 17 3 3 5

Figure S27.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00041

Table S28.  Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
5P GAIN MUTATED 6 18 3 22
5P GAIN WILD-TYPE 17 5 4 2

Figure S28.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00041

Table S29.  Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
5Q GAIN MUTATED 8 21 14 10
5Q GAIN WILD-TYPE 28 5 2 2

Figure S29.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 0.00845 (Fisher's exact test), Q value = 0.063

Table S30.  Gene #10: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 11 20 18 11
5Q GAIN MUTATED 7 4 17 11 9
5Q GAIN WILD-TYPE 11 7 3 7 2

Figure S30.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0092

Table S31.  Gene #10: '5q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
5Q GAIN MUTATED 7 10 15 15
5Q GAIN WILD-TYPE 17 3 2 8

Figure S31.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00071

Table S32.  Gene #10: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
5Q GAIN MUTATED 5 19 3 20
5Q GAIN WILD-TYPE 18 4 4 4

Figure S32.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 0.0177 (Fisher's exact test), Q value = 0.1

Table S33.  Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
6P GAIN MUTATED 7 1 5 5
6P GAIN WILD-TYPE 29 25 11 7

Figure S33.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00041

Table S34.  Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
7P GAIN MUTATED 8 20 12 8
7P GAIN WILD-TYPE 28 6 4 4

Figure S34.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0025

Table S35.  Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
7P GAIN MUTATED 6 12 13 11
7P GAIN WILD-TYPE 18 1 4 12

Figure S35.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00156 (Fisher's exact test), Q value = 0.017

Table S36.  Gene #13: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
7P GAIN MUTATED 7 19 2 14
7P GAIN WILD-TYPE 16 4 5 10

Figure S36.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00041

Table S37.  Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
7Q GAIN MUTATED 7 20 13 8
7Q GAIN WILD-TYPE 29 6 3 4

Figure S37.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00041

Table S38.  Gene #14: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
7Q GAIN MUTATED 5 13 13 11
7Q GAIN WILD-TYPE 19 0 4 12

Figure S38.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.0029

Table S39.  Gene #14: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
7Q GAIN MUTATED 6 20 2 14
7Q GAIN WILD-TYPE 17 3 5 10

Figure S39.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.0018

Table S40.  Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
8P GAIN MUTATED 5 18 4 5
8P GAIN WILD-TYPE 31 8 12 7

Figure S40.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0036

Table S41.  Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
8Q GAIN MUTATED 9 20 4 5
8Q GAIN WILD-TYPE 27 6 12 7

Figure S41.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'9p gain' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0015

Table S42.  Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
9P GAIN MUTATED 2 4 10 4
9P GAIN WILD-TYPE 34 22 6 8

Figure S42.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 0.002 (Fisher's exact test), Q value = 0.021

Table S43.  Gene #17: '9p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 11 20 18 11
9P GAIN MUTATED 2 5 8 0 1
9P GAIN WILD-TYPE 16 6 12 18 10

Figure S43.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p gain' versus 'RPPA_CNMF'

P value = 0.00415 (Fisher's exact test), Q value = 0.037

Table S44.  Gene #17: '9p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2
ALL 23 22
9P GAIN MUTATED 1 9
9P GAIN WILD-TYPE 22 13

Figure S44.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'9p gain' versus 'MRNASEQ_CNMF'

P value = 0.00902 (Fisher's exact test), Q value = 0.066

Table S45.  Gene #17: '9p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
9P GAIN MUTATED 1 6 5 3
9P GAIN WILD-TYPE 23 7 12 20

Figure S45.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 0.072

Table S46.  Gene #17: '9p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
9P GAIN MUTATED 3 10 0 2
9P GAIN WILD-TYPE 20 13 7 22

Figure S46.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0051

Table S47.  Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
9Q GAIN MUTATED 8 4 12 5
9Q GAIN WILD-TYPE 28 22 4 7

Figure S47.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'9q gain' versus 'METHLYATION_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.014

Table S48.  Gene #18: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 11 20 18 11
9Q GAIN MUTATED 8 5 9 0 1
9Q GAIN WILD-TYPE 10 6 11 18 10

Figure S48.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q gain' versus 'RPPA_CNMF'

P value = 0.00121 (Fisher's exact test), Q value = 0.014

Table S49.  Gene #18: '9q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2
ALL 23 22
9Q GAIN MUTATED 2 12
9Q GAIN WILD-TYPE 21 10

Figure S49.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'9q gain' versus 'MRNASEQ_CNMF'

P value = 0.0235 (Fisher's exact test), Q value = 0.12

Table S50.  Gene #18: '9q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
9Q GAIN MUTATED 6 8 5 3
9Q GAIN WILD-TYPE 18 5 12 20

Figure S50.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00169 (Fisher's exact test), Q value = 0.018

Table S51.  Gene #18: '9q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
9Q GAIN MUTATED 8 12 0 2
9Q GAIN WILD-TYPE 15 11 7 22

Figure S51.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_CNMF'

P value = 0.0331 (Fisher's exact test), Q value = 0.15

Table S52.  Gene #18: '9q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 16 26
9Q GAIN MUTATED 13 7 3
9Q GAIN WILD-TYPE 23 9 23

Figure S52.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 0.00179 (Fisher's exact test), Q value = 0.019

Table S53.  Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
10P GAIN MUTATED 7 5 11 2
10P GAIN WILD-TYPE 29 21 5 10

Figure S53.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'RPPA_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.072

Table S54.  Gene #19: '10p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2
ALL 23 22
10P GAIN MUTATED 3 11
10P GAIN WILD-TYPE 20 11

Figure S54.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'10p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0142 (Fisher's exact test), Q value = 0.085

Table S55.  Gene #19: '10p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 8 7 7 3 4 4 6 6
10P GAIN MUTATED 6 3 0 2 1 1 0 1
10P GAIN WILD-TYPE 2 4 7 1 3 3 6 5

Figure S55.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00091

Table S56.  Gene #19: '10p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
10P GAIN MUTATED 6 11 4 2
10P GAIN WILD-TYPE 18 2 13 21

Figure S56.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.0029

Table S57.  Gene #19: '10p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
10P GAIN MUTATED 7 14 1 1
10P GAIN WILD-TYPE 16 9 6 23

Figure S57.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_CNMF'

P value = 0.0352 (Fisher's exact test), Q value = 0.15

Table S58.  Gene #19: '10p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 16 26
10P GAIN MUTATED 13 7 3
10P GAIN WILD-TYPE 23 9 23

Figure S58.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10q gain' versus 'CN_CNMF'

P value = 0.00168 (Fisher's exact test), Q value = 0.018

Table S59.  Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
10Q GAIN MUTATED 9 5 11 1
10Q GAIN WILD-TYPE 27 21 5 11

Figure S59.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

'10q gain' versus 'RPPA_CNMF'

P value = 0.023 (Fisher's exact test), Q value = 0.12

Table S60.  Gene #20: '10q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2
ALL 23 22
10Q GAIN MUTATED 3 10
10Q GAIN WILD-TYPE 20 12

Figure S60.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'10q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0147 (Fisher's exact test), Q value = 0.087

Table S61.  Gene #20: '10q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 8 7 7 3 4 4 6 6
10Q GAIN MUTATED 6 2 0 2 1 1 0 1
10Q GAIN WILD-TYPE 2 5 7 1 3 3 6 5

Figure S61.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'10q gain' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0011

Table S62.  Gene #20: '10q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
10Q GAIN MUTATED 7 11 3 2
10Q GAIN WILD-TYPE 17 2 14 21

Figure S62.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.0073

Table S63.  Gene #20: '10q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
10Q GAIN MUTATED 8 13 1 1
10Q GAIN WILD-TYPE 15 10 6 23

Figure S63.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q gain' versus 'MIRSEQ_CNMF'

P value = 0.0212 (Fisher's exact test), Q value = 0.11

Table S64.  Gene #20: '10q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 16 26
10Q GAIN MUTATED 12 8 3
10Q GAIN WILD-TYPE 24 8 23

Figure S64.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0298 (Fisher's exact test), Q value = 0.14

Table S65.  Gene #20: '10q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 22 27
10Q GAIN MUTATED 8 11 4
10Q GAIN WILD-TYPE 20 11 23

Figure S65.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 0.045 (Fisher's exact test), Q value = 0.18

Table S66.  Gene #22: '11q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
11Q GAIN MUTATED 4 0 0 0
11Q GAIN WILD-TYPE 20 13 17 23

Figure S66.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00577 (Fisher's exact test), Q value = 0.046

Table S67.  Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 22 27
11Q GAIN MUTATED 0 4 0
11Q GAIN WILD-TYPE 28 18 27

Figure S67.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00041

Table S68.  Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
12P GAIN MUTATED 14 26 15 9
12P GAIN WILD-TYPE 22 0 1 3

Figure S68.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.003

Table S69.  Gene #23: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
12P GAIN MUTATED 9 13 14 18
12P GAIN WILD-TYPE 15 0 3 5

Figure S69.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.0011

Table S70.  Gene #23: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
12P GAIN MUTATED 10 20 2 22
12P GAIN WILD-TYPE 13 3 5 2

Figure S70.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00041

Table S71.  Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
12Q GAIN MUTATED 13 26 16 9
12Q GAIN WILD-TYPE 23 0 0 3

Figure S71.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0273 (Fisher's exact test), Q value = 0.13

Table S72.  Gene #24: '12q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 8 7 7 3 4 4 6 6
12Q GAIN MUTATED 7 6 6 3 2 4 5 1
12Q GAIN WILD-TYPE 1 1 1 0 2 0 1 5

Figure S72.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.0078

Table S73.  Gene #24: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
12Q GAIN MUTATED 10 13 14 18
12Q GAIN WILD-TYPE 14 0 3 5

Figure S73.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.0029

Table S74.  Gene #24: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
12Q GAIN MUTATED 11 20 2 22
12Q GAIN WILD-TYPE 12 3 5 2

Figure S74.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 0.0403 (Fisher's exact test), Q value = 0.17

Table S75.  Gene #25: '13q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
13Q GAIN MUTATED 1 1 4 0
13Q GAIN WILD-TYPE 23 12 13 23

Figure S75.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 0.014 (Fisher's exact test), Q value = 0.085

Table S76.  Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
14Q GAIN MUTATED 6 4 9 2
14Q GAIN WILD-TYPE 30 22 7 10

Figure S76.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.0061

Table S77.  Gene #26: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
14Q GAIN MUTATED 2 6 8 1
14Q GAIN WILD-TYPE 22 7 9 22

Figure S77.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00122 (Fisher's exact test), Q value = 0.014

Table S78.  Gene #26: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
14Q GAIN MUTATED 3 12 0 2
14Q GAIN WILD-TYPE 20 11 7 22

Figure S78.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00071

Table S79.  Gene #26: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 16 26
14Q GAIN MUTATED 17 0 1
14Q GAIN WILD-TYPE 19 16 25

Figure S79.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.0042

Table S80.  Gene #26: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 27 11 20 4
14Q GAIN MUTATED 7 0 3 5 3
14Q GAIN WILD-TYPE 9 27 8 15 1

Figure S80.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00071

Table S81.  Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 22 27
14Q GAIN MUTATED 14 2 1
14Q GAIN WILD-TYPE 14 20 26

Figure S81.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00041

Table S82.  Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 24 14
14Q GAIN MUTATED 17 0 0
14Q GAIN WILD-TYPE 22 24 14

Figure S82.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q gain' versus 'METHLYATION_CNMF'

P value = 0.0451 (Fisher's exact test), Q value = 0.18

Table S83.  Gene #27: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 11 20 18 11
15Q GAIN MUTATED 0 2 6 1 1
15Q GAIN WILD-TYPE 18 9 14 17 10

Figure S83.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q gain' versus 'MRNASEQ_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.072

Table S84.  Gene #27: '15q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
15Q GAIN MUTATED 0 3 5 2
15Q GAIN WILD-TYPE 24 10 12 21

Figure S84.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00497 (Fisher's exact test), Q value = 0.042

Table S85.  Gene #27: '15q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
15Q GAIN MUTATED 1 8 0 1
15Q GAIN WILD-TYPE 22 15 7 23

Figure S85.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00061 (Fisher's exact test), Q value = 0.0086

Table S86.  Gene #27: '15q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 27 11 20 4
15Q GAIN MUTATED 6 1 1 0 2
15Q GAIN WILD-TYPE 10 26 10 20 2

Figure S86.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00041

Table S87.  Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
16P GAIN MUTATED 6 26 11 6
16P GAIN WILD-TYPE 30 0 5 6

Figure S87.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.072

Table S88.  Gene #28: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 11 20 18 11
16P GAIN MUTATED 4 6 16 10 6
16P GAIN WILD-TYPE 14 5 4 8 5

Figure S88.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0381 (Fisher's exact test), Q value = 0.16

Table S89.  Gene #28: '16p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 8 7 7 3 4 4 6 6
16P GAIN MUTATED 3 7 4 0 1 3 4 2
16P GAIN WILD-TYPE 5 0 3 3 3 1 2 4

Figure S89.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00041

Table S90.  Gene #28: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
16P GAIN MUTATED 3 10 13 16
16P GAIN WILD-TYPE 21 3 4 7

Figure S90.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00041

Table S91.  Gene #28: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
16P GAIN MUTATED 4 20 0 18
16P GAIN WILD-TYPE 19 3 7 6

Figure S91.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 0.0465 (Fisher's exact test), Q value = 0.18

Table S92.  Gene #28: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 16 26
16P GAIN MUTATED 17 6 19
16P GAIN WILD-TYPE 19 10 7

Figure S92.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0255 (Fisher's exact test), Q value = 0.12

Table S93.  Gene #28: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 27 11 20 4
16P GAIN MUTATED 12 16 6 5 3
16P GAIN WILD-TYPE 4 11 5 15 1

Figure S93.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0299 (Fisher's exact test), Q value = 0.14

Table S94.  Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 22 27
16P GAIN MUTATED 15 7 19
16P GAIN WILD-TYPE 13 15 8

Figure S94.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00041

Table S95.  Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
16Q GAIN MUTATED 5 25 11 6
16Q GAIN WILD-TYPE 31 1 5 6

Figure S95.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 0.00799 (Fisher's exact test), Q value = 0.061

Table S96.  Gene #29: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 11 20 18 11
16Q GAIN MUTATED 4 5 16 11 6
16Q GAIN WILD-TYPE 14 6 4 7 5

Figure S96.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.0016

Table S97.  Gene #29: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
16Q GAIN MUTATED 4 9 13 16
16Q GAIN WILD-TYPE 20 4 4 7

Figure S97.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00041

Table S98.  Gene #29: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
16Q GAIN MUTATED 4 19 1 18
16Q GAIN WILD-TYPE 19 4 6 6

Figure S98.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CNMF'

P value = 0.0257 (Fisher's exact test), Q value = 0.12

Table S99.  Gene #29: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 16 26
16Q GAIN MUTATED 18 5 19
16Q GAIN WILD-TYPE 18 11 7

Figure S99.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0125 (Fisher's exact test), Q value = 0.081

Table S100.  Gene #29: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 27 11 20 4
16Q GAIN MUTATED 13 16 6 5 2
16Q GAIN WILD-TYPE 3 11 5 15 2

Figure S100.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.014 (Fisher's exact test), Q value = 0.085

Table S101.  Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 22 27
16Q GAIN MUTATED 17 6 18
16Q GAIN WILD-TYPE 11 16 9

Figure S101.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 0.025 (Fisher's exact test), Q value = 0.12

Table S102.  Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
17Q GAIN MUTATED 4 0 0 3
17Q GAIN WILD-TYPE 32 26 16 9

Figure S102.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 0.00389 (Fisher's exact test), Q value = 0.035

Table S103.  Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
19P GAIN MUTATED 16 16 15 9
19P GAIN WILD-TYPE 20 10 1 3

Figure S103.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0189 (Fisher's exact test), Q value = 0.1

Table S104.  Gene #34: '19p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 8 7 7 3 4 4 6 6
19P GAIN MUTATED 8 7 4 2 1 3 4 2
19P GAIN WILD-TYPE 0 0 3 1 3 1 2 4

Figure S104.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 0.00117 (Fisher's exact test), Q value = 0.014

Table S105.  Gene #34: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
19P GAIN MUTATED 11 13 13 11
19P GAIN WILD-TYPE 13 0 4 12

Figure S105.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.0071

Table S106.  Gene #34: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
19P GAIN MUTATED 14 21 1 12
19P GAIN WILD-TYPE 9 2 6 12

Figure S106.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0015

Table S107.  Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
19Q GAIN MUTATED 13 16 16 7
19Q GAIN WILD-TYPE 23 10 0 5

Figure S107.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.0063

Table S108.  Gene #35: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
19Q GAIN MUTATED 10 13 12 9
19Q GAIN WILD-TYPE 14 0 5 14

Figure S108.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00117 (Fisher's exact test), Q value = 0.014

Table S109.  Gene #35: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
19Q GAIN MUTATED 12 20 1 11
19Q GAIN WILD-TYPE 11 3 6 13

Figure S109.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00041

Table S110.  Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
20P GAIN MUTATED 6 22 11 7
20P GAIN WILD-TYPE 30 4 5 5

Figure S110.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'RPPA_CNMF'

P value = 0.00277 (Fisher's exact test), Q value = 0.027

Table S111.  Gene #36: '20p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2
ALL 23 22
20P GAIN MUTATED 17 6
20P GAIN WILD-TYPE 6 16

Figure S111.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'20p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00839 (Fisher's exact test), Q value = 0.063

Table S112.  Gene #36: '20p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 8 7 7 3 4 4 6 6
20P GAIN MUTATED 5 2 6 1 1 4 4 0
20P GAIN WILD-TYPE 3 5 1 2 3 0 2 6

Figure S112.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.0018

Table S113.  Gene #36: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
20P GAIN MUTATED 4 9 8 18
20P GAIN WILD-TYPE 20 4 9 5

Figure S113.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.0025

Table S114.  Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
20P GAIN MUTATED 6 12 1 20
20P GAIN WILD-TYPE 17 11 6 4

Figure S114.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 0.00479 (Fisher's exact test), Q value = 0.04

Table S115.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 16 26
20P GAIN MUTATED 13 7 20
20P GAIN WILD-TYPE 23 9 6

Figure S115.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00952 (Fisher's exact test), Q value = 0.067

Table S116.  Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 22 27
20P GAIN MUTATED 10 9 20
20P GAIN WILD-TYPE 18 13 7

Figure S116.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00468 (Fisher's exact test), Q value = 0.04

Table S117.  Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 24 14
20P GAIN MUTATED 13 18 8
20P GAIN WILD-TYPE 26 6 6

Figure S117.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00041

Table S118.  Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
20Q GAIN MUTATED 8 22 12 7
20Q GAIN WILD-TYPE 28 4 4 5

Figure S118.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 0.0169 (Fisher's exact test), Q value = 0.098

Table S119.  Gene #37: '20q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2
ALL 23 22
20Q GAIN MUTATED 17 8
20Q GAIN WILD-TYPE 6 14

Figure S119.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.0027

Table S120.  Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
20Q GAIN MUTATED 5 11 8 18
20Q GAIN WILD-TYPE 19 2 9 5

Figure S120.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.0042

Table S121.  Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
20Q GAIN MUTATED 6 14 2 20
20Q GAIN WILD-TYPE 17 9 5 4

Figure S121.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 0.0201 (Fisher's exact test), Q value = 0.11

Table S122.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 16 26
20Q GAIN MUTATED 15 8 20
20Q GAIN WILD-TYPE 21 8 6

Figure S122.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.076

Table S123.  Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 22 27
20Q GAIN MUTATED 12 9 21
20Q GAIN WILD-TYPE 16 13 6

Figure S123.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0141 (Fisher's exact test), Q value = 0.085

Table S124.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 24 14
20Q GAIN MUTATED 15 18 9
20Q GAIN WILD-TYPE 24 6 5

Figure S124.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 0.0207 (Fisher's exact test), Q value = 0.11

Table S125.  Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
21Q GAIN MUTATED 9 8 11 3
21Q GAIN WILD-TYPE 27 18 5 9

Figure S125.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 0.00914 (Fisher's exact test), Q value = 0.066

Table S126.  Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 11 20 18 11
21Q GAIN MUTATED 8 2 12 2 2
21Q GAIN WILD-TYPE 10 9 8 16 9

Figure S126.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 0.0198 (Fisher's exact test), Q value = 0.11

Table S127.  Gene #38: '21q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
21Q GAIN MUTATED 7 9 6 4
21Q GAIN WILD-TYPE 17 4 11 19

Figure S127.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00098 (Fisher's exact test), Q value = 0.013

Table S128.  Gene #38: '21q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
21Q GAIN MUTATED 7 15 1 3
21Q GAIN WILD-TYPE 16 8 6 21

Figure S128.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.085

Table S129.  Gene #38: '21q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 16 26
21Q GAIN MUTATED 18 4 4
21Q GAIN WILD-TYPE 18 12 22

Figure S129.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0201 (Fisher's exact test), Q value = 0.11

Table S130.  Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 27 11 20 4
21Q GAIN MUTATED 10 4 4 6 2
21Q GAIN WILD-TYPE 6 23 7 14 2

Figure S130.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0028 (Fisher's exact test), Q value = 0.027

Table S131.  Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 22 27
21Q GAIN MUTATED 15 7 3
21Q GAIN WILD-TYPE 13 15 24

Figure S131.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xp gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00041

Table S132.  Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
XP GAIN MUTATED 6 22 9 5
XP GAIN WILD-TYPE 30 4 7 7

Figure S132.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

'xp gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.03 (Fisher's exact test), Q value = 0.14

Table S133.  Gene #40: 'xp gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 8 7 7 3 4 4 6 6
XP GAIN MUTATED 6 5 5 0 2 3 4 0
XP GAIN WILD-TYPE 2 2 2 3 2 1 2 6

Figure S133.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'xp gain' versus 'MRNASEQ_CNMF'

P value = 0.00099 (Fisher's exact test), Q value = 0.013

Table S134.  Gene #40: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
XP GAIN MUTATED 4 10 11 12
XP GAIN WILD-TYPE 20 3 6 11

Figure S134.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00579 (Fisher's exact test), Q value = 0.046

Table S135.  Gene #40: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
XP GAIN MUTATED 5 14 2 16
XP GAIN WILD-TYPE 18 9 5 8

Figure S135.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00091

Table S136.  Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
XQ GAIN MUTATED 7 21 8 5
XQ GAIN WILD-TYPE 29 5 8 7

Figure S136.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.042 (Fisher's exact test), Q value = 0.17

Table S137.  Gene #41: 'xq gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 8 7 7 3 4 4 6 6
XQ GAIN MUTATED 6 4 5 0 2 3 4 0
XQ GAIN WILD-TYPE 2 3 2 3 2 1 2 6

Figure S137.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 0.00153 (Fisher's exact test), Q value = 0.017

Table S138.  Gene #41: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
XQ GAIN MUTATED 4 10 10 12
XQ GAIN WILD-TYPE 20 3 7 11

Figure S138.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00892 (Fisher's exact test), Q value = 0.066

Table S139.  Gene #41: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
XQ GAIN MUTATED 5 13 2 16
XQ GAIN WILD-TYPE 18 10 5 8

Figure S139.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.029 (Fisher's exact test), Q value = 0.13

Table S140.  Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 22 27
1P LOSS MUTATED 4 10 11
1P LOSS WILD-TYPE 24 12 16

Figure S140.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0251 (Fisher's exact test), Q value = 0.12

Table S141.  Gene #43: '1q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 8 7 7 3 4 4 6 6
1Q LOSS MUTATED 0 0 0 2 1 0 2 2
1Q LOSS WILD-TYPE 8 7 7 1 3 4 4 4

Figure S141.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 0.00683 (Fisher's exact test), Q value = 0.054

Table S142.  Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
2P LOSS MUTATED 4 2 5 6
2P LOSS WILD-TYPE 32 24 11 6

Figure S142.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 0.0266 (Fisher's exact test), Q value = 0.13

Table S143.  Gene #44: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 11 20 18 11
2P LOSS MUTATED 1 1 7 2 5
2P LOSS WILD-TYPE 17 10 13 16 6

Figure S143.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 0.038 (Fisher's exact test), Q value = 0.16

Table S144.  Gene #44: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 16 26
2P LOSS MUTATED 8 0 8
2P LOSS WILD-TYPE 28 16 18

Figure S144.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2q loss' versus 'CN_CNMF'

P value = 0.00529 (Fisher's exact test), Q value = 0.044

Table S145.  Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
2Q LOSS MUTATED 3 2 4 6
2Q LOSS WILD-TYPE 33 24 12 6

Figure S145.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 0.00113 (Fisher's exact test), Q value = 0.014

Table S146.  Gene #45: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 11 20 18 11
2Q LOSS MUTATED 0 0 7 2 5
2Q LOSS WILD-TYPE 18 11 13 16 6

Figure S146.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 0.0314 (Fisher's exact test), Q value = 0.14

Table S147.  Gene #45: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 16 26
2Q LOSS MUTATED 6 0 8
2Q LOSS WILD-TYPE 30 16 18

Figure S147.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 0.0217 (Fisher's exact test), Q value = 0.11

Table S148.  Gene #47: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
3Q LOSS MUTATED 7 0 7 3
3Q LOSS WILD-TYPE 17 13 10 20

Figure S148.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.029 (Fisher's exact test), Q value = 0.13

Table S149.  Gene #47: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
3Q LOSS MUTATED 8 7 1 1
3Q LOSS WILD-TYPE 15 16 6 23

Figure S149.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.023 (Fisher's exact test), Q value = 0.12

Table S150.  Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
4P LOSS MUTATED 7 0 1 1
4P LOSS WILD-TYPE 17 13 16 22

Figure S150.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 0.00728 (Fisher's exact test), Q value = 0.056

Table S151.  Gene #49: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
4Q LOSS MUTATED 8 0 1 1
4Q LOSS WILD-TYPE 16 13 16 22

Figure S151.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0265 (Fisher's exact test), Q value = 0.13

Table S152.  Gene #49: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
4Q LOSS MUTATED 7 1 1 1
4Q LOSS WILD-TYPE 16 22 6 23

Figure S152.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 0.082

Table S153.  Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 22 27
4Q LOSS MUTATED 2 7 1
4Q LOSS WILD-TYPE 26 15 26

Figure S153.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00975 (Fisher's exact test), Q value = 0.068

Table S154.  Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
5P LOSS MUTATED 6 1 0 0
5P LOSS WILD-TYPE 17 22 7 24

Figure S154.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 0.00573 (Fisher's exact test), Q value = 0.046

Table S155.  Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
8P LOSS MUTATED 8 0 6 2
8P LOSS WILD-TYPE 28 26 10 10

Figure S155.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.0086

Table S156.  Gene #56: '8p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 8 7 7 3 4 4 6 6
8P LOSS MUTATED 1 1 0 2 0 0 0 5
8P LOSS WILD-TYPE 7 6 7 1 4 4 6 1

Figure S156.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0239 (Fisher's exact test), Q value = 0.12

Table S157.  Gene #56: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 27 11 20 4
8P LOSS MUTATED 2 2 1 5 3
8P LOSS WILD-TYPE 14 25 10 15 1

Figure S157.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0291 (Fisher's exact test), Q value = 0.13

Table S158.  Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 24 14
8P LOSS MUTATED 11 1 1
8P LOSS WILD-TYPE 28 23 13

Figure S158.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 0.00468 (Fisher's exact test), Q value = 0.04

Table S159.  Gene #57: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
8Q LOSS MUTATED 4 0 6 2
8Q LOSS WILD-TYPE 32 26 10 10

Figure S159.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0341 (Fisher's exact test), Q value = 0.15

Table S160.  Gene #57: '8q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 8 7 7 3 4 4 6 6
8Q LOSS MUTATED 1 1 0 2 0 0 0 3
8Q LOSS WILD-TYPE 7 6 7 1 4 4 6 3

Figure S160.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 0.0332 (Fisher's exact test), Q value = 0.15

Table S161.  Gene #57: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
8Q LOSS MUTATED 3 2 5 0
8Q LOSS WILD-TYPE 21 11 12 23

Figure S161.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0343 (Fisher's exact test), Q value = 0.15

Table S162.  Gene #57: '8q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 27 11 20 4
8Q LOSS MUTATED 1 1 1 5 2
8Q LOSS WILD-TYPE 15 26 10 15 2

Figure S162.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0371 (Fisher's exact test), Q value = 0.16

Table S163.  Gene #57: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 24 14
8Q LOSS MUTATED 9 1 0
8Q LOSS WILD-TYPE 30 23 14

Figure S163.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 0.00183 (Fisher's exact test), Q value = 0.019

Table S164.  Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
9P LOSS MUTATED 15 2 3 0
9P LOSS WILD-TYPE 21 24 13 12

Figure S164.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 0.0479 (Fisher's exact test), Q value = 0.19

Table S165.  Gene #58: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 11 20 18 11
9P LOSS MUTATED 9 3 2 4 1
9P LOSS WILD-TYPE 9 8 18 14 10

Figure S165.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0011

Table S166.  Gene #58: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
9P LOSS MUTATED 14 1 3 1
9P LOSS WILD-TYPE 10 12 14 22

Figure S166.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0011 (Fisher's exact test), Q value = 0.014

Table S167.  Gene #58: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
9P LOSS MUTATED 12 4 2 1
9P LOSS WILD-TYPE 11 19 5 23

Figure S167.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 0.00922 (Fisher's exact test), Q value = 0.066

Table S168.  Gene #58: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 16 26
9P LOSS MUTATED 9 8 2
9P LOSS WILD-TYPE 27 8 24

Figure S168.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00437 (Fisher's exact test), Q value = 0.039

Table S169.  Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 22 27
9P LOSS MUTATED 4 11 3
9P LOSS WILD-TYPE 24 11 24

Figure S169.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0362 (Fisher's exact test), Q value = 0.16

Table S170.  Gene #59: '9q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 8 7 7 3 4 4 6 6
9Q LOSS MUTATED 0 0 0 0 1 0 3 1
9Q LOSS WILD-TYPE 8 7 7 3 3 4 3 5

Figure S170.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 0.00688 (Fisher's exact test), Q value = 0.054

Table S171.  Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
11P LOSS MUTATED 7 3 7 7
11P LOSS WILD-TYPE 29 23 9 5

Figure S171.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 0.0178 (Fisher's exact test), Q value = 0.1

Table S172.  Gene #62: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 11 20 18 11
11P LOSS MUTATED 4 1 11 2 4
11P LOSS WILD-TYPE 14 10 9 16 7

Figure S172.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.081

Table S173.  Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
11Q LOSS MUTATED 7 3 6 7
11Q LOSS WILD-TYPE 29 23 10 5

Figure S173.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 0.0029 (Fisher's exact test), Q value = 0.027

Table S174.  Gene #63: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 11 20 18 11
11Q LOSS MUTATED 2 1 11 2 5
11Q LOSS WILD-TYPE 16 10 9 16 6

Figure S174.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0389 (Fisher's exact test), Q value = 0.16

Table S175.  Gene #64: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
12P LOSS MUTATED 2 1 2 0
12P LOSS WILD-TYPE 21 22 5 24

Figure S175.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'METHLYATION_CNMF'

P value = 0.0487 (Fisher's exact test), Q value = 0.19

Table S176.  Gene #65: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 11 20 18 11
12Q LOSS MUTATED 0 2 0 2 0
12Q LOSS WILD-TYPE 18 9 20 16 11

Figure S176.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00954 (Fisher's exact test), Q value = 0.067

Table S177.  Gene #65: '12q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
12Q LOSS MUTATED 2 0 2 0
12Q LOSS WILD-TYPE 21 23 5 24

Figure S177.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 0.0147 (Fisher's exact test), Q value = 0.087

Table S178.  Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
13Q LOSS MUTATED 19 5 7 8
13Q LOSS WILD-TYPE 17 21 9 4

Figure S178.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'CN_CNMF'

P value = 0.0278 (Fisher's exact test), Q value = 0.13

Table S179.  Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
14Q LOSS MUTATED 8 3 1 6
14Q LOSS WILD-TYPE 28 23 15 6

Figure S179.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 0.0177 (Fisher's exact test), Q value = 0.1

Table S180.  Gene #67: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
14Q LOSS MUTATED 7 0 1 8
14Q LOSS WILD-TYPE 17 13 16 15

Figure S180.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0478 (Fisher's exact test), Q value = 0.19

Table S181.  Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
14Q LOSS MUTATED 5 1 3 7
14Q LOSS WILD-TYPE 18 22 4 17

Figure S181.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0407 (Fisher's exact test), Q value = 0.17

Table S182.  Gene #68: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 27 11 20 4
15Q LOSS MUTATED 0 7 2 8 1
15Q LOSS WILD-TYPE 16 20 9 12 3

Figure S182.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'METHLYATION_CNMF'

P value = 0.0489 (Fisher's exact test), Q value = 0.19

Table S183.  Gene #69: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 11 20 18 11
16P LOSS MUTATED 4 0 0 2 0
16P LOSS WILD-TYPE 14 11 20 16 11

Figure S183.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0465 (Fisher's exact test), Q value = 0.18

Table S184.  Gene #69: '16p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 8 7 7 3 4 4 6 6
16P LOSS MUTATED 2 0 0 1 2 0 0 0
16P LOSS WILD-TYPE 6 7 7 2 2 4 6 6

Figure S184.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 0.0021 (Fisher's exact test), Q value = 0.021

Table S185.  Gene #69: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
16P LOSS MUTATED 6 0 0 0
16P LOSS WILD-TYPE 18 13 17 23

Figure S185.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00437 (Fisher's exact test), Q value = 0.039

Table S186.  Gene #69: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
16P LOSS MUTATED 4 0 2 0
16P LOSS WILD-TYPE 19 23 5 24

Figure S186.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.081

Table S187.  Gene #69: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 16 26
16P LOSS MUTATED 2 4 0
16P LOSS WILD-TYPE 34 12 26

Figure S187.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0049

Table S188.  Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 22 27
16P LOSS MUTATED 0 6 0
16P LOSS WILD-TYPE 28 16 27

Figure S188.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00137 (Fisher's exact test), Q value = 0.016

Table S189.  Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 22 27
16Q LOSS MUTATED 0 5 0
16Q LOSS WILD-TYPE 28 17 27

Figure S189.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 0.00293 (Fisher's exact test), Q value = 0.027

Table S190.  Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
17P LOSS MUTATED 16 3 10 3
17P LOSS WILD-TYPE 20 23 6 9

Figure S190.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0035

Table S191.  Gene #71: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 11 20 18 11
17P LOSS MUTATED 11 0 12 4 1
17P LOSS WILD-TYPE 7 11 8 14 10

Figure S191.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.079

Table S192.  Gene #71: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
17P LOSS MUTATED 14 4 7 3
17P LOSS WILD-TYPE 10 9 10 20

Figure S192.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0132 (Fisher's exact test), Q value = 0.084

Table S193.  Gene #71: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
17P LOSS MUTATED 12 11 2 3
17P LOSS WILD-TYPE 11 12 5 21

Figure S193.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00307 (Fisher's exact test), Q value = 0.028

Table S194.  Gene #71: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 27 11 20 4
17P LOSS MUTATED 5 8 0 13 2
17P LOSS WILD-TYPE 11 19 11 7 2

Figure S194.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0138 (Fisher's exact test), Q value = 0.085

Table S195.  Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 22 27
17P LOSS MUTATED 9 13 5
17P LOSS WILD-TYPE 19 9 22

Figure S195.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17q loss' versus 'CN_CNMF'

P value = 0.0147 (Fisher's exact test), Q value = 0.087

Table S196.  Gene #72: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
17Q LOSS MUTATED 10 3 9 2
17Q LOSS WILD-TYPE 26 23 7 10

Figure S196.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 0.00554 (Fisher's exact test), Q value = 0.045

Table S197.  Gene #72: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 11 20 18 11
17Q LOSS MUTATED 7 1 12 3 1
17Q LOSS WILD-TYPE 11 10 8 15 10

Figure S197.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0336 (Fisher's exact test), Q value = 0.15

Table S198.  Gene #72: '17q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
17Q LOSS MUTATED 9 11 1 3
17Q LOSS WILD-TYPE 14 12 6 21

Figure S198.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.021 (Fisher's exact test), Q value = 0.11

Table S199.  Gene #72: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 27 11 20 4
17Q LOSS MUTATED 6 6 0 10 2
17Q LOSS WILD-TYPE 10 21 11 10 2

Figure S199.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 0.0244 (Fisher's exact test), Q value = 0.12

Table S200.  Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
18P LOSS MUTATED 16 5 8 8
18P LOSS WILD-TYPE 20 21 8 4

Figure S200.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 0.0359 (Fisher's exact test), Q value = 0.16

Table S201.  Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
18Q LOSS MUTATED 15 5 7 8
18Q LOSS WILD-TYPE 21 21 9 4

Figure S201.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0139 (Fisher's exact test), Q value = 0.085

Table S202.  Gene #75: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
19P LOSS MUTATED 1 0 2 0
19P LOSS WILD-TYPE 22 23 5 24

Figure S202.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 0.0412 (Fisher's exact test), Q value = 0.17

Table S203.  Gene #77: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
20P LOSS MUTATED 6 0 3 0
20P LOSS WILD-TYPE 30 26 13 12

Figure S203.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

'20p loss' versus 'RPPA_CNMF'

P value = 0.0216 (Fisher's exact test), Q value = 0.11

Table S204.  Gene #77: '20p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2
ALL 23 22
20P LOSS MUTATED 0 5
20P LOSS WILD-TYPE 23 17

Figure S204.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'20p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.021 (Fisher's exact test), Q value = 0.11

Table S205.  Gene #77: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 22 27
20P LOSS MUTATED 2 5 0
20P LOSS WILD-TYPE 26 17 27

Figure S205.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 0.0149 (Fisher's exact test), Q value = 0.087

Table S206.  Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
22Q LOSS MUTATED 22 7 11 8
22Q LOSS WILD-TYPE 14 19 5 4

Figure S206.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'xp loss' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.0016

Table S207.  Gene #81: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
XP LOSS MUTATED 14 0 0 2
XP LOSS WILD-TYPE 22 26 16 10

Figure S207.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

'xp loss' versus 'MRNASEQ_CNMF'

P value = 0.0226 (Fisher's exact test), Q value = 0.12

Table S208.  Gene #81: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
XP LOSS MUTATED 9 0 2 3
XP LOSS WILD-TYPE 15 13 15 20

Figure S208.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0286 (Fisher's exact test), Q value = 0.13

Table S209.  Gene #81: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
XP LOSS MUTATED 9 2 1 2
XP LOSS WILD-TYPE 14 21 6 22

Figure S209.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 0.00277 (Fisher's exact test), Q value = 0.027

Table S210.  Gene #82: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
XQ LOSS MUTATED 12 1 0 2
XQ LOSS WILD-TYPE 24 25 16 10

Figure S210.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 0.0178 (Fisher's exact test), Q value = 0.1

Table S211.  Gene #82: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
XQ LOSS MUTATED 9 0 3 2
XQ LOSS WILD-TYPE 15 13 14 21

Figure S211.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.016 (Fisher's exact test), Q value = 0.093

Table S212.  Gene #82: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
XQ LOSS MUTATED 9 3 1 1
XQ LOSS WILD-TYPE 14 20 6 23

Figure S212.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_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/ACC-TP/19778621/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/ACC-TP/20124001/ACC-TP.transferedmergedcluster.txt

  • Number of patients = 90

  • 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.

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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