Correlation between copy number variation genes (focal events) and molecular subtypes
Overview
Introduction

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

Summary

Testing the association between copy number variation 55 focal events and 10 molecular subtypes across 366 patients, 151 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1p12 cnv correlated to 'CN_CNMF'.

  • amp_1q21.3 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

  • amp_1q44 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_4q12 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • amp_5p15.33 cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_5q35.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CNMF'.

  • amp_6p24.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_7p22.1 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • amp_7q34 cnv correlated to 'CN_CNMF'.

  • amp_8q11.21 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_8q24.21 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • amp_12q14.1 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • amp_13q31.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_15q26.2 cnv correlated to 'CN_CNMF'.

  • amp_17q25.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_19p13.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • amp_20q13.33 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • amp_22q13.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_1p36.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • del_1p22.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_2q37.3 cnv correlated to 'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_4p16.3 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • del_4q34.3 cnv correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_CHIERARCHICAL'.

  • del_5q12.1 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • del_5q31.3 cnv correlated to 'METHLYATION_CNMF'.

  • del_6q22.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • del_6q26 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_8p23.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • del_9p23 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

  • del_9p21.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • del_10p15.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_10q21.1 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_10q23.31 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • del_10q26.3 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_11p15.5 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • del_11q23.3 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_12q23.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_13q34 cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • del_14q23.3 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_14q32.31 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • del_15q13.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_16p13.3 cnv correlated to 'RPPA_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • del_16q12.1 cnv correlated to 'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_16q24.3 cnv correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_17p13.3 cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • del_19p13.3 cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_xp21.1 cnv correlated to 'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 55 focal events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 151 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
amp 6p24 3 210 (57%) 156 1e-05
(0.00025) 		1e-05
(0.00025) 		0.323
(0.525) 		0.0159
(0.0868) 		0.0349
(0.144) 		0.00812
(0.0551) 		0.00083
(0.0104) 		0.0174
(0.0907) 		0.0008
(0.0102) 		0.00187
(0.019)
amp 1q44 201 (55%) 165 1e-05
(0.00025) 		0.00882
(0.0577) 		0.162
(0.367) 		0.142
(0.336) 		0.00872
(0.0577) 		0.368
(0.561) 		0.00437
(0.0358) 		0.0062
(0.0449) 		0.0199
(0.0975) 		0.00221
(0.0217)
del xp21 1 87 (24%) 279 0.121
(0.301) 		1e-05
(0.00025) 		0.0469
(0.174) 		0.11
(0.284) 		0.00463
(0.0364) 		0.00219
(0.0217) 		0.00086
(0.0105) 		0.048
(0.177) 		0.00106
(0.0119) 		0.239
(0.457)
del 2q37 3 93 (25%) 273 0.419
(0.611) 		0.0963
(0.261) 		0.165
(0.369) 		0.0195
(0.0975) 		0.00494
(0.0377) 		0.0177
(0.091) 		0.0305
(0.135) 		0.0101
(0.0606) 		0.264
(0.471) 		0.308
(0.51)
del 9p21 3 278 (76%) 88 1e-05
(0.00025) 		0.00792
(0.0544) 		0.756
(0.846) 		0.701
(0.813) 		2e-05
(0.000423) 		0.00741
(0.0516) 		0.034
(0.144) 		0.799
(0.87) 		0.411
(0.603) 		0.122
(0.301)
del 11q23 3 202 (55%) 164 1e-05
(0.00025) 		0.336
(0.537) 		0.904
(0.929) 		0.261
(0.468) 		0.043
(0.164) 		0.00046
(0.00649) 		0.444
(0.633) 		0.0337
(0.144) 		0.00986
(0.0606) 		0.0845
(0.247)
del 14q23 3 120 (33%) 246 2e-05
(0.000423) 		0.779
(0.856) 		0.553
(0.705) 		0.247
(0.463) 		0.00592
(0.0434) 		0.0354
(0.144) 		0.00059
(0.00811) 		0.178
(0.383) 		0.112
(0.286) 		0.0388
(0.154)
amp 5q35 3 59 (16%) 307 0.00021
(0.0035) 		0.00032
(0.00489) 		0.0913
(0.255) 		0.0327
(0.143) 		0.0142
(0.0782) 		0.525
(0.693) 		0.273
(0.479) 		0.352
(0.551) 		0.356
(0.554) 		0.455
(0.638)
amp 8q11 21 163 (45%) 203 1e-05
(0.00025) 		0.00145
(0.0153) 		0.569
(0.713) 		0.246
(0.463) 		0.0181
(0.0921) 		0.0105
(0.0616) 		0.837
(0.886) 		0.857
(0.896) 		0.761
(0.847) 		0.747
(0.846)
amp 13q31 3 104 (28%) 262 1e-05
(0.00025) 		1e-05
(0.00025) 		0.75
(0.846) 		0.27
(0.477) 		0.00021
(0.0035) 		0.00121
(0.0133) 		0.679
(0.796) 		0.513
(0.686) 		0.0585
(0.208) 		0.789
(0.862)
amp 17q25 3 122 (33%) 244 0.00017
(0.00312) 		0.0409
(0.16) 		0.0296
(0.133) 		0.0737
(0.234) 		0.429
(0.62) 		0.00729
(0.0516) 		0.56
(0.706) 		0.0656
(0.217) 		0.239
(0.457) 		0.194
(0.402)
del 1p22 1 97 (27%) 269 0.00096
(0.011) 		1e-05
(0.00025) 		0.591
(0.734) 		0.211
(0.429) 		0.00022
(0.00356) 		0.023
(0.108) 		0.0803
(0.243) 		0.769
(0.849) 		0.196
(0.406) 		0.258
(0.467)
del 6q26 221 (60%) 145 1e-05
(0.00025) 		0.00981
(0.0606) 		0.841
(0.887) 		0.537
(0.698) 		9e-05
(0.00171) 		0.0487
(0.179) 		0.324
(0.525) 		0.602
(0.744) 		0.837
(0.886) 		0.458
(0.64)
del 10p15 3 199 (54%) 167 1e-05
(0.00025) 		0.0448
(0.17) 		0.886
(0.914) 		0.221
(0.438) 		0.00064
(0.00859) 		0.00094
(0.011) 		0.0714
(0.23) 		0.453
(0.638) 		0.327
(0.529) 		0.275
(0.481)
del 10q23 31 230 (63%) 136 1e-05
(0.00025) 		0.125
(0.306) 		0.881
(0.912) 		0.206
(0.421) 		0.00394
(0.0333) 		0.0172
(0.0907) 		0.0299
(0.134) 		0.688
(0.803) 		0.342
(0.539) 		0.776
(0.855)
del 14q32 31 117 (32%) 249 1e-05
(0.00025) 		0.622
(0.753) 		0.588
(0.733) 		0.186
(0.391) 		0.00449
(0.0358) 		0.0344
(0.144) 		0.00372
(0.0325) 		0.188
(0.391) 		0.42
(0.611) 		0.187
(0.391)
del 15q13 3 84 (23%) 282 0.0496
(0.181) 		0.0101
(0.0606) 		0.0897
(0.254) 		0.306
(0.509) 		0.4
(0.593) 		0.0175
(0.0907) 		0.651
(0.775) 		0.869
(0.905) 		0.0162
(0.0874) 		0.762
(0.847)
del 16q24 3 133 (36%) 233 0.113
(0.286) 		0.62
(0.753) 		0.146
(0.344) 		0.906
(0.929) 		0.00945
(0.0597) 		0.0024
(0.0228) 		0.0821
(0.243) 		0.0944
(0.258) 		0.0128
(0.0726) 		0.0413
(0.16)
del 19p13 3 104 (28%) 262 0.0215
(0.104) 		0.705
(0.815) 		0.00236
(0.0228) 		0.0623
(0.214) 		0.00079
(0.0102) 		0.00124
(0.0134) 		0.785
(0.86) 		0.101
(0.269) 		0.186
(0.391) 		0.462
(0.643)
amp 1q21 3 203 (55%) 163 1e-05
(0.00025) 		0.0741
(0.234) 		0.339
(0.538) 		0.523
(0.693) 		0.00393
(0.0333) 		0.47
(0.648) 		0.0228
(0.108) 		0.0631
(0.215) 		0.173
(0.378) 		0.0829
(0.244)
amp 5p15 33 110 (30%) 256 1e-05
(0.00025) 		0.134
(0.321) 		0.693
(0.808) 		0.74
(0.84) 		0.0617
(0.214) 		0.563
(0.707) 		0.00546
(0.0411) 		0.739
(0.84) 		0.246
(0.463) 		0.0235
(0.109)
amp 8q24 21 191 (52%) 175 1e-05
(0.00025) 		0.00401
(0.0334) 		0.754
(0.846) 		0.939
(0.953) 		0.00999
(0.0606) 		0.314
(0.515) 		0.806
(0.874) 		0.753
(0.846) 		0.616
(0.753) 		0.768
(0.849)
amp 20q13 33 187 (51%) 179 1e-05
(0.00025) 		0.00148
(0.0154) 		0.828
(0.884) 		0.989
(0.989) 		0.00584
(0.0434) 		0.0756
(0.236) 		0.181
(0.387) 		0.589
(0.733) 		0.795
(0.868) 		0.367
(0.561)
del 1p36 31 81 (22%) 285 0.0377
(0.151) 		2e-05
(0.000423) 		0.579
(0.724) 		0.209
(0.426) 		0.0332
(0.144) 		0.0895
(0.254) 		0.0641
(0.216) 		0.0595
(0.208) 		0.403
(0.596) 		0.857
(0.896)
del 6q22 31 215 (59%) 151 1e-05
(0.00025) 		0.00482
(0.0373) 		0.959
(0.966) 		0.445
(0.633) 		0.0003
(0.00471) 		0.165
(0.369) 		0.479
(0.654) 		0.533
(0.698) 		0.467
(0.647) 		0.267
(0.474)
del 9p23 249 (68%) 117 3e-05
(0.000611) 		0.103
(0.272) 		0.455
(0.638) 		0.612
(0.752) 		0.00874
(0.0577) 		0.158
(0.364) 		0.035
(0.144) 		0.169
(0.374) 		0.825
(0.883) 		0.153
(0.359)
del 10q21 1 217 (59%) 149 1e-05
(0.00025) 		0.466
(0.647) 		0.715
(0.819) 		0.148
(0.349) 		0.0133
(0.0749) 		0.0317
(0.14) 		0.0606
(0.211) 		0.25
(0.463) 		0.225
(0.441) 		0.761
(0.847)
del 10q26 3 236 (64%) 130 1e-05
(0.00025) 		0.393
(0.587) 		0.833
(0.886) 		0.309
(0.51) 		0.0002
(0.0035) 		0.00444
(0.0358) 		0.079
(0.242) 		0.513
(0.686) 		0.185
(0.391) 		0.394
(0.587)
del 16q12 1 117 (32%) 249 0.26
(0.468) 		0.306
(0.509) 		0.0217
(0.104) 		0.68
(0.796) 		0.0387
(0.154) 		0.0709
(0.23) 		0.186
(0.391) 		0.0217
(0.104) 		0.267
(0.474) 		0.059
(0.208)
amp 4q12 65 (18%) 301 0.00277
(0.025) 		0.223
(0.439) 		0.0823
(0.243) 		0.539
(0.699) 		0.757
(0.846) 		0.103
(0.272) 		0.0634
(0.215) 		0.0276
(0.127) 		0.279
(0.483) 		0.503
(0.677)
amp 7p22 1 208 (57%) 158 1e-05
(0.00025) 		0.814
(0.878) 		0.628
(0.759) 		0.214
(0.431) 		0.0238
(0.11) 		0.131
(0.315) 		0.075
(0.236) 		0.408
(0.602) 		0.913
(0.932) 		0.475
(0.651)
amp 12q14 1 58 (16%) 308 0.00285
(0.0253) 		0.332
(0.534) 		0.871
(0.905) 		0.285
(0.49) 		0.0461
(0.173) 		0.485
(0.657) 		0.768
(0.849) 		0.216
(0.431) 		0.171
(0.376) 		0.644
(0.771)
amp 19p13 2 69 (19%) 297 0.00091
(0.0109) 		0.0934
(0.257) 		0.442
(0.633) 		0.959
(0.966) 		0.00254
(0.0233) 		0.137
(0.325) 		0.95
(0.961) 		0.29
(0.495) 		0.129
(0.312) 		0.738
(0.84)
amp 22q13 2 151 (41%) 215 7e-05
(0.00137) 		0.0419
(0.161) 		0.974
(0.978) 		0.715
(0.819) 		0.234
(0.453) 		0.133
(0.32) 		0.807
(0.874) 		0.0856
(0.248) 		0.261
(0.468) 		0.317
(0.519)
del 4q34 3 110 (30%) 256 0.268
(0.474) 		0.0659
(0.217) 		0.515
(0.687) 		0.551
(0.703) 		0.0766
(0.238) 		0.011
(0.0635) 		0.678
(0.796) 		0.00935
(0.0597) 		0.124
(0.303) 		0.173
(0.378)
del 8p23 3 89 (24%) 277 0.00908
(0.0588) 		0.107
(0.278) 		0.203
(0.418) 		0.16
(0.366) 		0.0394
(0.155) 		0.278
(0.483) 		0.374
(0.566) 		0.253
(0.463) 		0.0858
(0.248) 		0.0816
(0.243)
del 11p15 5 114 (31%) 252 0.0198
(0.0975) 		0.0503
(0.182) 		0.618
(0.753) 		0.712
(0.819) 		0.535
(0.698) 		0.255
(0.465) 		0.482
(0.656) 		0.247
(0.463) 		0.0288
(0.131) 		0.338
(0.537)
del 12q23 3 92 (25%) 274 0.0137
(0.0761) 		0.0361
(0.146) 		0.965
(0.971) 		0.819
(0.879) 		0.302
(0.506) 		0.368
(0.561) 		0.301
(0.506) 		0.245
(0.463) 		0.47
(0.648) 		0.455
(0.638)
del 13q34 85 (23%) 281 0.951
(0.961) 		0.0105
(0.0616) 		0.066
(0.217) 		0.74
(0.84) 		0.817
(0.879) 		0.00733
(0.0516) 		0.642
(0.771) 		0.0974
(0.261) 		0.292
(0.495) 		0.697
(0.811)
del 16p13 3 62 (17%) 304 0.561
(0.706) 		0.0907
(0.255) 		0.0121
(0.0693) 		0.336
(0.537) 		0.161
(0.366) 		0.108
(0.28) 		0.366
(0.561) 		0.33
(0.532) 		0.0454
(0.171) 		0.091
(0.255)
del 17p13 3 135 (37%) 231 0.252
(0.463) 		0.00034
(0.00505) 		0.366
(0.561) 		0.636
(0.768) 		0.0918
(0.255) 		0.0183
(0.0923) 		0.85
(0.892) 		0.359
(0.557) 		0.387
(0.583) 		0.215
(0.431)
amp 1p12 121 (33%) 245 0.0354
(0.144) 		0.911
(0.932) 		0.708
(0.816) 		0.883
(0.913) 		0.371
(0.563) 		0.251
(0.463) 		0.62
(0.753) 		0.525
(0.693) 		0.777
(0.855) 		0.612
(0.752)
amp 7q34 224 (61%) 142 2e-05
(0.000423) 		0.479
(0.654) 		0.234
(0.453) 		0.939
(0.953) 		0.157
(0.364) 		0.252
(0.463) 		0.0974
(0.261) 		0.258
(0.467) 		0.082
(0.243) 		0.418
(0.611)
amp 15q26 2 119 (33%) 247 0.00042
(0.00608) 		0.204
(0.418) 		0.939
(0.953) 		0.81
(0.875) 		0.159
(0.366) 		0.455
(0.638) 		0.805
(0.874) 		0.237
(0.457) 		0.163
(0.367) 		0.442
(0.633)
del 4p16 3 91 (25%) 275 0.544
(0.701) 		0.111
(0.284) 		0.649
(0.775) 		0.705
(0.815) 		0.176
(0.381) 		0.0173
(0.0907) 		0.666
(0.788) 		0.253
(0.463) 		0.432
(0.622) 		0.981
(0.983)
del 5q12 1 97 (27%) 269 0.233
(0.453) 		0.221
(0.438) 		0.39
(0.585) 		0.115
(0.289) 		0.494
(0.667) 		0.0344
(0.144) 		0.302
(0.506) 		0.522
(0.693) 		0.34
(0.538) 		0.653
(0.775)
del 5q31 3 131 (36%) 235 0.274
(0.479) 		0.00249
(0.0232) 		0.616
(0.753) 		0.306
(0.509) 		0.736
(0.84) 		0.176
(0.381) 		0.832
(0.886) 		0.638
(0.768) 		0.39
(0.585) 		0.475
(0.651)
amp 3p13 103 (28%) 263 0.122
(0.301) 		0.534
(0.698) 		0.065
(0.217) 		0.052
(0.186) 		0.601
(0.744) 		0.294
(0.497) 		0.484
(0.657) 		0.671
(0.792) 		0.841
(0.887) 		0.872
(0.905)
amp 6q12 80 (22%) 286 0.55
(0.703) 		0.561
(0.706) 		0.528
(0.693) 		0.0815
(0.243) 		0.456
(0.638) 		0.0695
(0.228) 		0.214
(0.431) 		0.169
(0.374) 		0.347
(0.546) 		0.106
(0.278)
amp 11q13 3 69 (19%) 297 0.128
(0.31) 		0.0863
(0.249) 		0.907
(0.929) 		0.838
(0.886) 		0.283
(0.487) 		0.446
(0.634) 		0.157
(0.364) 		0.109
(0.282) 		0.557
(0.706) 		0.249
(0.463)
amp 12q15 59 (16%) 307 0.0729
(0.233) 		0.228
(0.446) 		0.607
(0.748) 		0.427
(0.618) 		0.0965
(0.261) 		0.184
(0.391) 		0.658
(0.78) 		0.291
(0.495) 		0.366
(0.561) 		0.314
(0.515)
del 3p25 1 71 (19%) 295 0.174
(0.378) 		0.238
(0.457) 		0.427
(0.618) 		0.216
(0.431) 		0.528
(0.693) 		0.751
(0.846) 		0.353
(0.551) 		0.398
(0.592) 		0.324
(0.525) 		0.169
(0.374)
del 3q13 31 62 (17%) 304 0.163
(0.367) 		0.0926
(0.256) 		0.411
(0.603) 		0.115
(0.289) 		0.0522
(0.186) 		0.555
(0.705) 		0.253
(0.463) 		0.279
(0.483) 		0.0777
(0.239) 		0.55
(0.703)
del 5p15 31 79 (22%) 287 0.651
(0.775) 		0.376
(0.568) 		0.545
(0.701) 		0.541
(0.699) 		0.819
(0.879) 		0.071
(0.23) 		0.678
(0.796) 		0.363
(0.561) 		0.0893
(0.254) 		0.905
(0.929)
del 15q21 1 91 (25%) 275 0.0778
(0.239) 		0.103
(0.272) 		0.541
(0.699) 		0.338
(0.537) 		0.5
(0.675) 		0.291
(0.495) 		0.864
(0.902) 		0.518
(0.69) 		0.115
(0.289) 		0.846
(0.889)
'amp_1p12' versus 'CN_CNMF'

P value = 0.0354 (Fisher's exact test), Q value = 0.14

Table S1.  Gene #1: 'amp_1p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
AMP PEAK 1(1P12) MUTATED 43 37 41
AMP PEAK 1(1P12) WILD-TYPE 58 102 85

Figure S1.  Get High-res Image Gene #1: 'amp_1p12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S2.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
AMP PEAK 2(1Q21.3) MUTATED 92 51 60
AMP PEAK 2(1Q21.3) WILD-TYPE 9 88 66

Figure S2.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q21.3' versus 'MRNASEQ_CNMF'

P value = 0.00393 (Fisher's exact test), Q value = 0.033

Table S3.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
AMP PEAK 2(1Q21.3) MUTATED 87 44 72
AMP PEAK 2(1Q21.3) WILD-TYPE 50 60 53

Figure S3.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q21.3' versus 'MIRSEQ_CNMF'

P value = 0.0228 (Fisher's exact test), Q value = 0.11

Table S4.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 102 79 114 8
AMP PEAK 2(1Q21.3) MUTATED 32 55 35 69 2
AMP PEAK 2(1Q21.3) WILD-TYPE 15 47 44 45 6

Figure S4.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_1q44' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S5.  Gene #3: 'amp_1q44' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
AMP PEAK 3(1Q44) MUTATED 90 50 61
AMP PEAK 3(1Q44) WILD-TYPE 11 89 65

Figure S5.  Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q44' versus 'METHLYATION_CNMF'

P value = 0.00882 (Fisher's exact test), Q value = 0.058

Table S6.  Gene #3: 'amp_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
AMP PEAK 3(1Q44) MUTATED 74 66 61
AMP PEAK 3(1Q44) WILD-TYPE 55 78 32

Figure S6.  Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q44' versus 'MRNASEQ_CNMF'

P value = 0.00872 (Fisher's exact test), Q value = 0.058

Table S7.  Gene #3: 'amp_1q44' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
AMP PEAK 3(1Q44) MUTATED 83 44 74
AMP PEAK 3(1Q44) WILD-TYPE 54 60 51

Figure S7.  Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q44' versus 'MIRSEQ_CNMF'

P value = 0.00437 (Fisher's exact test), Q value = 0.036

Table S8.  Gene #3: 'amp_1q44' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 102 79 114 8
AMP PEAK 3(1Q44) MUTATED 34 52 33 70 3
AMP PEAK 3(1Q44) WILD-TYPE 13 50 46 44 5

Figure S8.  Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_1q44' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0062 (Fisher's exact test), Q value = 0.045

Table S9.  Gene #3: 'amp_1q44' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 147 74 38
AMP PEAK 3(1Q44) MUTATED 49 83 31 29
AMP PEAK 3(1Q44) WILD-TYPE 42 64 43 9

Figure S9.  Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_1q44' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0199 (Fisher's exact test), Q value = 0.098

Table S10.  Gene #3: 'amp_1q44' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 105 139
AMP PEAK 3(1Q44) MUTATED 41 57 88
AMP PEAK 3(1Q44) WILD-TYPE 51 48 51

Figure S10.  Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_1q44' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00221 (Fisher's exact test), Q value = 0.022

Table S11.  Gene #3: 'amp_1q44' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 137 30
AMP PEAK 3(1Q44) MUTATED 93 68 25
AMP PEAK 3(1Q44) WILD-TYPE 76 69 5

Figure S11.  Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4q12' versus 'CN_CNMF'

P value = 0.00277 (Fisher's exact test), Q value = 0.025

Table S12.  Gene #5: 'amp_4q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
AMP PEAK 5(4Q12) MUTATED 22 13 30
AMP PEAK 5(4Q12) WILD-TYPE 79 126 96

Figure S12.  Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_4q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0276 (Fisher's exact test), Q value = 0.13

Table S13.  Gene #5: 'amp_4q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 147 74 38
AMP PEAK 5(4Q12) MUTATED 14 38 8 5
AMP PEAK 5(4Q12) WILD-TYPE 77 109 66 33

Figure S13.  Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S14.  Gene #6: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
AMP PEAK 6(5P15.33) MUTATED 31 24 55
AMP PEAK 6(5P15.33) WILD-TYPE 70 115 71

Figure S14.  Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CNMF'

P value = 0.00546 (Fisher's exact test), Q value = 0.041

Table S15.  Gene #6: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 102 79 114 8
AMP PEAK 6(5P15.33) MUTATED 18 17 24 41 4
AMP PEAK 6(5P15.33) WILD-TYPE 29 85 55 73 4

Figure S15.  Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0235 (Fisher's exact test), Q value = 0.11

Table S16.  Gene #6: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 137 30
AMP PEAK 6(5P15.33) MUTATED 58 30 12
AMP PEAK 6(5P15.33) WILD-TYPE 111 107 18

Figure S16.  Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5q35.3' versus 'CN_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0035

Table S17.  Gene #7: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
AMP PEAK 7(5Q35.3) MUTATED 21 9 29
AMP PEAK 7(5Q35.3) WILD-TYPE 80 130 97

Figure S17.  Get High-res Image Gene #7: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5q35.3' versus 'METHLYATION_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0049

Table S18.  Gene #7: 'amp_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
AMP PEAK 7(5Q35.3) MUTATED 19 13 27
AMP PEAK 7(5Q35.3) WILD-TYPE 110 131 66

Figure S18.  Get High-res Image Gene #7: 'amp_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5q35.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0327 (Fisher's exact test), Q value = 0.14

Table S19.  Gene #7: 'amp_5q35.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 58 35 49
AMP PEAK 7(5Q35.3) MUTATED 3 4 7 13
AMP PEAK 7(5Q35.3) WILD-TYPE 24 54 28 36

Figure S19.  Get High-res Image Gene #7: 'amp_5q35.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_5q35.3' versus 'MRNASEQ_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.078

Table S20.  Gene #7: 'amp_5q35.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
AMP PEAK 7(5Q35.3) MUTATED 26 8 25
AMP PEAK 7(5Q35.3) WILD-TYPE 111 96 100

Figure S20.  Get High-res Image Gene #7: 'amp_5q35.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6p24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S21.  Gene #8: 'amp_6p24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
AMP PEAK 8(6P24.3) MUTATED 78 57 75
AMP PEAK 8(6P24.3) WILD-TYPE 23 82 51

Figure S21.  Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p24.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S22.  Gene #8: 'amp_6p24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
AMP PEAK 8(6P24.3) MUTATED 79 61 70
AMP PEAK 8(6P24.3) WILD-TYPE 50 83 23

Figure S22.  Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p24.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0159 (Fisher's exact test), Q value = 0.087

Table S23.  Gene #8: 'amp_6p24.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 58 35 49
AMP PEAK 8(6P24.3) MUTATED 12 38 13 32
AMP PEAK 8(6P24.3) WILD-TYPE 15 20 22 17

Figure S23.  Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_6p24.3' versus 'MRNASEQ_CNMF'

P value = 0.0349 (Fisher's exact test), Q value = 0.14

Table S24.  Gene #8: 'amp_6p24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
AMP PEAK 8(6P24.3) MUTATED 87 49 74
AMP PEAK 8(6P24.3) WILD-TYPE 50 55 51

Figure S24.  Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6p24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00812 (Fisher's exact test), Q value = 0.055

Table S25.  Gene #8: 'amp_6p24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
AMP PEAK 8(6P24.3) MUTATED 71 65 42 32
AMP PEAK 8(6P24.3) WILD-TYPE 36 40 54 26

Figure S25.  Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6p24.3' versus 'MIRSEQ_CNMF'

P value = 0.00083 (Fisher's exact test), Q value = 0.01

Table S26.  Gene #8: 'amp_6p24.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 102 79 114 8
AMP PEAK 8(6P24.3) MUTATED 29 51 40 80 1
AMP PEAK 8(6P24.3) WILD-TYPE 18 51 39 34 7

Figure S26.  Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_6p24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0174 (Fisher's exact test), Q value = 0.091

Table S27.  Gene #8: 'amp_6p24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 147 74 38
AMP PEAK 8(6P24.3) MUTATED 59 90 31 21
AMP PEAK 8(6P24.3) WILD-TYPE 32 57 43 17

Figure S27.  Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6p24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.01

Table S28.  Gene #8: 'amp_6p24.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 105 139
AMP PEAK 8(6P24.3) MUTATED 44 52 96
AMP PEAK 8(6P24.3) WILD-TYPE 48 53 43

Figure S28.  Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_6p24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00187 (Fisher's exact test), Q value = 0.019

Table S29.  Gene #8: 'amp_6p24.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 137 30
AMP PEAK 8(6P24.3) MUTATED 112 63 17
AMP PEAK 8(6P24.3) WILD-TYPE 57 74 13

Figure S29.  Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7p22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S30.  Gene #10: 'amp_7p22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
AMP PEAK 10(7P22.1) MUTATED 62 55 91
AMP PEAK 10(7P22.1) WILD-TYPE 39 84 35

Figure S30.  Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p22.1' versus 'MRNASEQ_CNMF'

P value = 0.0238 (Fisher's exact test), Q value = 0.11

Table S31.  Gene #10: 'amp_7p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
AMP PEAK 10(7P22.1) MUTATED 73 52 83
AMP PEAK 10(7P22.1) WILD-TYPE 64 52 42

Figure S31.  Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7q34' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00042

Table S32.  Gene #11: 'amp_7q34' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
AMP PEAK 11(7Q34) MUTATED 64 66 94
AMP PEAK 11(7Q34) WILD-TYPE 37 73 32

Figure S32.  Get High-res Image Gene #11: 'amp_7q34' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S33.  Gene #12: 'amp_8q11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
AMP PEAK 12(8Q11.21) MUTATED 35 39 89
AMP PEAK 12(8Q11.21) WILD-TYPE 66 100 37

Figure S33.  Get High-res Image Gene #12: 'amp_8q11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q11.21' versus 'METHLYATION_CNMF'

P value = 0.00145 (Fisher's exact test), Q value = 0.015

Table S34.  Gene #12: 'amp_8q11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
AMP PEAK 12(8Q11.21) MUTATED 47 60 56
AMP PEAK 12(8Q11.21) WILD-TYPE 82 84 37

Figure S34.  Get High-res Image Gene #12: 'amp_8q11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q11.21' versus 'MRNASEQ_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 0.092

Table S35.  Gene #12: 'amp_8q11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
AMP PEAK 12(8Q11.21) MUTATED 57 38 68
AMP PEAK 12(8Q11.21) WILD-TYPE 80 66 57

Figure S35.  Get High-res Image Gene #12: 'amp_8q11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_8q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0105 (Fisher's exact test), Q value = 0.062

Table S36.  Gene #12: 'amp_8q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
AMP PEAK 12(8Q11.21) MUTATED 56 43 48 16
AMP PEAK 12(8Q11.21) WILD-TYPE 51 62 48 42

Figure S36.  Get High-res Image Gene #12: 'amp_8q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S37.  Gene #13: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
AMP PEAK 13(8Q24.21) MUTATED 47 48 96
AMP PEAK 13(8Q24.21) WILD-TYPE 54 91 30

Figure S37.  Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 0.00401 (Fisher's exact test), Q value = 0.033

Table S38.  Gene #13: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
AMP PEAK 13(8Q24.21) MUTATED 58 71 62
AMP PEAK 13(8Q24.21) WILD-TYPE 71 73 31

Figure S38.  Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 0.00999 (Fisher's exact test), Q value = 0.061

Table S39.  Gene #13: 'amp_8q24.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
AMP PEAK 13(8Q24.21) MUTATED 71 43 77
AMP PEAK 13(8Q24.21) WILD-TYPE 66 61 48

Figure S39.  Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_12q14.1' versus 'CN_CNMF'

P value = 0.00285 (Fisher's exact test), Q value = 0.025

Table S40.  Gene #15: 'amp_12q14.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
AMP PEAK 15(12Q14.1) MUTATED 16 12 30
AMP PEAK 15(12Q14.1) WILD-TYPE 85 127 96

Figure S40.  Get High-res Image Gene #15: 'amp_12q14.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q14.1' versus 'MRNASEQ_CNMF'

P value = 0.0461 (Fisher's exact test), Q value = 0.17

Table S41.  Gene #15: 'amp_12q14.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
AMP PEAK 15(12Q14.1) MUTATED 25 9 24
AMP PEAK 15(12Q14.1) WILD-TYPE 112 95 101

Figure S41.  Get High-res Image Gene #15: 'amp_12q14.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_13q31.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S42.  Gene #17: 'amp_13q31.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
AMP PEAK 17(13Q31.3) MUTATED 34 19 51
AMP PEAK 17(13Q31.3) WILD-TYPE 67 120 75

Figure S42.  Get High-res Image Gene #17: 'amp_13q31.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q31.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S43.  Gene #17: 'amp_13q31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
AMP PEAK 17(13Q31.3) MUTATED 37 23 44
AMP PEAK 17(13Q31.3) WILD-TYPE 92 121 49

Figure S43.  Get High-res Image Gene #17: 'amp_13q31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q31.3' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0035

Table S44.  Gene #17: 'amp_13q31.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
AMP PEAK 17(13Q31.3) MUTATED 31 21 52
AMP PEAK 17(13Q31.3) WILD-TYPE 106 83 73

Figure S44.  Get High-res Image Gene #17: 'amp_13q31.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_13q31.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00121 (Fisher's exact test), Q value = 0.013

Table S45.  Gene #17: 'amp_13q31.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
AMP PEAK 17(13Q31.3) MUTATED 35 31 33 5
AMP PEAK 17(13Q31.3) WILD-TYPE 72 74 63 53

Figure S45.  Get High-res Image Gene #17: 'amp_13q31.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_15q26.2' versus 'CN_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.0061

Table S46.  Gene #18: 'amp_15q26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
AMP PEAK 18(15Q26.2) MUTATED 30 32 57
AMP PEAK 18(15Q26.2) WILD-TYPE 71 107 69

Figure S46.  Get High-res Image Gene #18: 'amp_15q26.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q25.3' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0031

Table S47.  Gene #19: 'amp_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
AMP PEAK 19(17Q25.3) MUTATED 50 33 39
AMP PEAK 19(17Q25.3) WILD-TYPE 51 106 87

Figure S47.  Get High-res Image Gene #19: 'amp_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q25.3' versus 'METHLYATION_CNMF'

P value = 0.0409 (Fisher's exact test), Q value = 0.16

Table S48.  Gene #19: 'amp_17q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
AMP PEAK 19(17Q25.3) MUTATED 43 39 40
AMP PEAK 19(17Q25.3) WILD-TYPE 86 105 53

Figure S48.  Get High-res Image Gene #19: 'amp_17q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q25.3' versus 'RPPA_CNMF'

P value = 0.0296 (Fisher's exact test), Q value = 0.13

Table S49.  Gene #19: 'amp_17q25.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 58 26 38
AMP PEAK 19(17Q25.3) MUTATED 11 24 15 16
AMP PEAK 19(17Q25.3) WILD-TYPE 36 34 11 22

Figure S49.  Get High-res Image Gene #19: 'amp_17q25.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_17q25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00729 (Fisher's exact test), Q value = 0.052

Table S50.  Gene #19: 'amp_17q25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
AMP PEAK 19(17Q25.3) MUTATED 32 40 22 28
AMP PEAK 19(17Q25.3) WILD-TYPE 75 65 74 30

Figure S50.  Get High-res Image Gene #19: 'amp_17q25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.2' versus 'CN_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.011

Table S51.  Gene #20: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
AMP PEAK 20(19P13.2) MUTATED 16 16 37
AMP PEAK 20(19P13.2) WILD-TYPE 85 123 89

Figure S51.  Get High-res Image Gene #20: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19p13.2' versus 'MRNASEQ_CNMF'

P value = 0.00254 (Fisher's exact test), Q value = 0.023

Table S52.  Gene #20: 'amp_19p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
AMP PEAK 20(19P13.2) MUTATED 25 10 34
AMP PEAK 20(19P13.2) WILD-TYPE 112 94 91

Figure S52.  Get High-res Image Gene #20: 'amp_19p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_20q13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S53.  Gene #21: 'amp_20q13.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
AMP PEAK 21(20Q13.33) MUTATED 64 41 82
AMP PEAK 21(20Q13.33) WILD-TYPE 37 98 44

Figure S53.  Get High-res Image Gene #21: 'amp_20q13.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.33' versus 'METHLYATION_CNMF'

P value = 0.00148 (Fisher's exact test), Q value = 0.015

Table S54.  Gene #21: 'amp_20q13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
AMP PEAK 21(20Q13.33) MUTATED 63 62 62
AMP PEAK 21(20Q13.33) WILD-TYPE 66 82 31

Figure S54.  Get High-res Image Gene #21: 'amp_20q13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CNMF'

P value = 0.00584 (Fisher's exact test), Q value = 0.043

Table S55.  Gene #21: 'amp_20q13.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
AMP PEAK 21(20Q13.33) MUTATED 65 44 78
AMP PEAK 21(20Q13.33) WILD-TYPE 72 60 47

Figure S55.  Get High-res Image Gene #21: 'amp_20q13.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_22q13.2' versus 'CN_CNMF'

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

Table S56.  Gene #22: 'amp_22q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
AMP PEAK 22(22Q13.2) MUTATED 54 37 60
AMP PEAK 22(22Q13.2) WILD-TYPE 47 102 66

Figure S56.  Get High-res Image Gene #22: 'amp_22q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_22q13.2' versus 'METHLYATION_CNMF'

P value = 0.0419 (Fisher's exact test), Q value = 0.16

Table S57.  Gene #22: 'amp_22q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
AMP PEAK 22(22Q13.2) MUTATED 58 48 45
AMP PEAK 22(22Q13.2) WILD-TYPE 71 96 48

Figure S57.  Get High-res Image Gene #22: 'amp_22q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.31' versus 'CN_CNMF'

P value = 0.0377 (Fisher's exact test), Q value = 0.15

Table S58.  Gene #23: 'del_1p36.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
DEL PEAK 1(1P36.31) MUTATED 30 22 29
DEL PEAK 1(1P36.31) WILD-TYPE 71 117 97

Figure S58.  Get High-res Image Gene #23: 'del_1p36.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.31' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00042

Table S59.  Gene #23: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
DEL PEAK 1(1P36.31) MUTATED 20 22 39
DEL PEAK 1(1P36.31) WILD-TYPE 109 122 54

Figure S59.  Get High-res Image Gene #23: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.31' versus 'MRNASEQ_CNMF'

P value = 0.0332 (Fisher's exact test), Q value = 0.14

Table S60.  Gene #23: 'del_1p36.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
DEL PEAK 1(1P36.31) MUTATED 30 15 36
DEL PEAK 1(1P36.31) WILD-TYPE 107 89 89

Figure S60.  Get High-res Image Gene #23: 'del_1p36.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p22.1' versus 'CN_CNMF'

P value = 0.00096 (Fisher's exact test), Q value = 0.011

Table S61.  Gene #24: 'del_1p22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
DEL PEAK 2(1P22.1) MUTATED 32 22 43
DEL PEAK 2(1P22.1) WILD-TYPE 69 117 83

Figure S61.  Get High-res Image Gene #24: 'del_1p22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S62.  Gene #24: 'del_1p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
DEL PEAK 2(1P22.1) MUTATED 22 31 44
DEL PEAK 2(1P22.1) WILD-TYPE 107 113 49

Figure S62.  Get High-res Image Gene #24: 'del_1p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p22.1' versus 'MRNASEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0036

Table S63.  Gene #24: 'del_1p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
DEL PEAK 2(1P22.1) MUTATED 36 14 47
DEL PEAK 2(1P22.1) WILD-TYPE 101 90 78

Figure S63.  Get High-res Image Gene #24: 'del_1p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.023 (Fisher's exact test), Q value = 0.11

Table S64.  Gene #24: 'del_1p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
DEL PEAK 2(1P22.1) MUTATED 26 22 37 12
DEL PEAK 2(1P22.1) WILD-TYPE 81 83 59 46

Figure S64.  Get High-res Image Gene #24: 'del_1p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0195 (Fisher's exact test), Q value = 0.097

Table S65.  Gene #25: 'del_2q37.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 58 35 49
DEL PEAK 3(2Q37.3) MUTATED 4 11 8 21
DEL PEAK 3(2Q37.3) WILD-TYPE 23 47 27 28

Figure S65.  Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 0.00494 (Fisher's exact test), Q value = 0.038

Table S66.  Gene #25: 'del_2q37.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
DEL PEAK 3(2Q37.3) MUTATED 48 19 26
DEL PEAK 3(2Q37.3) WILD-TYPE 89 85 99

Figure S66.  Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0177 (Fisher's exact test), Q value = 0.091

Table S67.  Gene #25: 'del_2q37.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
DEL PEAK 3(2Q37.3) MUTATED 37 28 15 13
DEL PEAK 3(2Q37.3) WILD-TYPE 70 77 81 45

Figure S67.  Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_CNMF'

P value = 0.0305 (Fisher's exact test), Q value = 0.14

Table S68.  Gene #25: 'del_2q37.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 102 79 114 8
DEL PEAK 3(2Q37.3) MUTATED 11 21 15 42 2
DEL PEAK 3(2Q37.3) WILD-TYPE 36 81 64 72 6

Figure S68.  Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q37.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0101 (Fisher's exact test), Q value = 0.061

Table S69.  Gene #25: 'del_2q37.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 147 74 38
DEL PEAK 3(2Q37.3) MUTATED 22 50 10 9
DEL PEAK 3(2Q37.3) WILD-TYPE 69 97 64 29

Figure S69.  Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0173 (Fisher's exact test), Q value = 0.091

Table S70.  Gene #28: 'del_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
DEL PEAK 6(4P16.3) MUTATED 33 16 30 12
DEL PEAK 6(4P16.3) WILD-TYPE 74 89 66 46

Figure S70.  Get High-res Image Gene #28: 'del_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.011 (Fisher's exact test), Q value = 0.064

Table S71.  Gene #29: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
DEL PEAK 7(4Q34.3) MUTATED 27 26 42 15
DEL PEAK 7(4Q34.3) WILD-TYPE 80 79 54 43

Figure S71.  Get High-res Image Gene #29: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00935 (Fisher's exact test), Q value = 0.06

Table S72.  Gene #29: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 147 74 38
DEL PEAK 7(4Q34.3) MUTATED 29 32 31 15
DEL PEAK 7(4Q34.3) WILD-TYPE 62 115 43 23

Figure S72.  Get High-res Image Gene #29: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0344 (Fisher's exact test), Q value = 0.14

Table S73.  Gene #31: 'del_5q12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
DEL PEAK 9(5Q12.1) MUTATED 32 17 30 18
DEL PEAK 9(5Q12.1) WILD-TYPE 75 88 66 40

Figure S73.  Get High-res Image Gene #31: 'del_5q12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q31.3' versus 'METHLYATION_CNMF'

P value = 0.00249 (Fisher's exact test), Q value = 0.023

Table S74.  Gene #32: 'del_5q31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
DEL PEAK 10(5Q31.3) MUTATED 58 52 21
DEL PEAK 10(5Q31.3) WILD-TYPE 71 92 72

Figure S74.  Get High-res Image Gene #32: 'del_5q31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q22.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S75.  Gene #33: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
DEL PEAK 11(6Q22.31) MUTATED 81 47 87
DEL PEAK 11(6Q22.31) WILD-TYPE 20 92 39

Figure S75.  Get High-res Image Gene #33: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q22.31' versus 'METHLYATION_CNMF'

P value = 0.00482 (Fisher's exact test), Q value = 0.037

Table S76.  Gene #33: 'del_6q22.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
DEL PEAK 11(6Q22.31) MUTATED 87 70 58
DEL PEAK 11(6Q22.31) WILD-TYPE 42 74 35

Figure S76.  Get High-res Image Gene #33: 'del_6q22.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q22.31' versus 'MRNASEQ_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0047

Table S77.  Gene #33: 'del_6q22.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
DEL PEAK 11(6Q22.31) MUTATED 87 44 84
DEL PEAK 11(6Q22.31) WILD-TYPE 50 60 41

Figure S77.  Get High-res Image Gene #33: 'del_6q22.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q26' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S78.  Gene #34: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
DEL PEAK 12(6Q26) MUTATED 82 50 89
DEL PEAK 12(6Q26) WILD-TYPE 19 89 37

Figure S78.  Get High-res Image Gene #34: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 0.00981 (Fisher's exact test), Q value = 0.061

Table S79.  Gene #34: 'del_6q26' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
DEL PEAK 12(6Q26) MUTATED 87 73 61
DEL PEAK 12(6Q26) WILD-TYPE 42 71 32

Figure S79.  Get High-res Image Gene #34: 'del_6q26' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.0017

Table S80.  Gene #34: 'del_6q26' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
DEL PEAK 12(6Q26) MUTATED 90 45 86
DEL PEAK 12(6Q26) WILD-TYPE 47 59 39

Figure S80.  Get High-res Image Gene #34: 'del_6q26' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0487 (Fisher's exact test), Q value = 0.18

Table S81.  Gene #34: 'del_6q26' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
DEL PEAK 12(6Q26) MUTATED 72 52 62 35
DEL PEAK 12(6Q26) WILD-TYPE 35 53 34 23

Figure S81.  Get High-res Image Gene #34: 'del_6q26' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.3' versus 'CN_CNMF'

P value = 0.00908 (Fisher's exact test), Q value = 0.059

Table S82.  Gene #35: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
DEL PEAK 13(8P23.3) MUTATED 35 24 30
DEL PEAK 13(8P23.3) WILD-TYPE 66 115 96

Figure S82.  Get High-res Image Gene #35: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.3' versus 'MRNASEQ_CNMF'

P value = 0.0394 (Fisher's exact test), Q value = 0.15

Table S83.  Gene #35: 'del_8p23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
DEL PEAK 13(8P23.3) MUTATED 38 16 35
DEL PEAK 13(8P23.3) WILD-TYPE 99 88 90

Figure S83.  Get High-res Image Gene #35: 'del_8p23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p23' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00061

Table S84.  Gene #36: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
DEL PEAK 14(9P23) MUTATED 63 80 106
DEL PEAK 14(9P23) WILD-TYPE 38 59 20

Figure S84.  Get High-res Image Gene #36: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 0.00874 (Fisher's exact test), Q value = 0.058

Table S85.  Gene #36: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
DEL PEAK 14(9P23) MUTATED 93 60 96
DEL PEAK 14(9P23) WILD-TYPE 44 44 29

Figure S85.  Get High-res Image Gene #36: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CNMF'

P value = 0.035 (Fisher's exact test), Q value = 0.14

Table S86.  Gene #36: 'del_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 102 79 114 8
DEL PEAK 14(9P23) MUTATED 28 75 46 79 8
DEL PEAK 14(9P23) WILD-TYPE 19 27 33 35 0

Figure S86.  Get High-res Image Gene #36: 'del_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S87.  Gene #37: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
DEL PEAK 15(9P21.3) MUTATED 77 86 115
DEL PEAK 15(9P21.3) WILD-TYPE 24 53 11

Figure S87.  Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 0.00792 (Fisher's exact test), Q value = 0.054

Table S88.  Gene #37: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
DEL PEAK 15(9P21.3) MUTATED 107 97 74
DEL PEAK 15(9P21.3) WILD-TYPE 22 47 19

Figure S88.  Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00042

Table S89.  Gene #37: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
DEL PEAK 15(9P21.3) MUTATED 102 65 111
DEL PEAK 15(9P21.3) WILD-TYPE 35 39 14

Figure S89.  Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00741 (Fisher's exact test), Q value = 0.052

Table S90.  Gene #37: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
DEL PEAK 15(9P21.3) MUTATED 83 75 83 37
DEL PEAK 15(9P21.3) WILD-TYPE 24 30 13 21

Figure S90.  Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 0.034 (Fisher's exact test), Q value = 0.14

Table S91.  Gene #37: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 102 79 114 8
DEL PEAK 15(9P21.3) MUTATED 34 84 51 87 8
DEL PEAK 15(9P21.3) WILD-TYPE 13 18 28 27 0

Figure S91.  Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10p15.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S92.  Gene #38: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
DEL PEAK 16(10P15.3) MUTATED 54 48 97
DEL PEAK 16(10P15.3) WILD-TYPE 47 91 29

Figure S92.  Get High-res Image Gene #38: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 0.0448 (Fisher's exact test), Q value = 0.17

Table S93.  Gene #38: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
DEL PEAK 16(10P15.3) MUTATED 70 69 60
DEL PEAK 16(10P15.3) WILD-TYPE 59 75 33

Figure S93.  Get High-res Image Gene #38: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p15.3' versus 'MRNASEQ_CNMF'

P value = 0.00064 (Fisher's exact test), Q value = 0.0086

Table S94.  Gene #38: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
DEL PEAK 16(10P15.3) MUTATED 66 48 85
DEL PEAK 16(10P15.3) WILD-TYPE 71 56 40

Figure S94.  Get High-res Image Gene #38: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00094 (Fisher's exact test), Q value = 0.011

Table S95.  Gene #38: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
DEL PEAK 16(10P15.3) MUTATED 57 50 68 24
DEL PEAK 16(10P15.3) WILD-TYPE 50 55 28 34

Figure S95.  Get High-res Image Gene #38: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S96.  Gene #39: 'del_10q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
DEL PEAK 17(10Q21.1) MUTATED 48 61 108
DEL PEAK 17(10Q21.1) WILD-TYPE 53 78 18

Figure S96.  Get High-res Image Gene #39: 'del_10q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q21.1' versus 'MRNASEQ_CNMF'

P value = 0.0133 (Fisher's exact test), Q value = 0.075

Table S97.  Gene #39: 'del_10q21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
DEL PEAK 17(10Q21.1) MUTATED 75 55 87
DEL PEAK 17(10Q21.1) WILD-TYPE 62 49 38

Figure S97.  Get High-res Image Gene #39: 'del_10q21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0317 (Fisher's exact test), Q value = 0.14

Table S98.  Gene #39: 'del_10q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
DEL PEAK 17(10Q21.1) MUTATED 59 58 69 31
DEL PEAK 17(10Q21.1) WILD-TYPE 48 47 27 27

Figure S98.  Get High-res Image Gene #39: 'del_10q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S99.  Gene #40: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
DEL PEAK 18(10Q23.31) MUTATED 53 66 111
DEL PEAK 18(10Q23.31) WILD-TYPE 48 73 15

Figure S99.  Get High-res Image Gene #40: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 0.00394 (Fisher's exact test), Q value = 0.033

Table S100.  Gene #40: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
DEL PEAK 18(10Q23.31) MUTATED 79 58 93
DEL PEAK 18(10Q23.31) WILD-TYPE 58 46 32

Figure S100.  Get High-res Image Gene #40: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0172 (Fisher's exact test), Q value = 0.091

Table S101.  Gene #40: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
DEL PEAK 18(10Q23.31) MUTATED 63 60 73 34
DEL PEAK 18(10Q23.31) WILD-TYPE 44 45 23 24

Figure S101.  Get High-res Image Gene #40: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 0.0299 (Fisher's exact test), Q value = 0.13

Table S102.  Gene #40: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 102 79 114 8
DEL PEAK 18(10Q23.31) MUTATED 30 64 41 78 8
DEL PEAK 18(10Q23.31) WILD-TYPE 17 38 38 36 0

Figure S102.  Get High-res Image Gene #40: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S103.  Gene #41: 'del_10q26.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
DEL PEAK 19(10Q26.3) MUTATED 51 71 114
DEL PEAK 19(10Q26.3) WILD-TYPE 50 68 12

Figure S103.  Get High-res Image Gene #41: 'del_10q26.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q26.3' versus 'MRNASEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0035

Table S104.  Gene #41: 'del_10q26.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
DEL PEAK 19(10Q26.3) MUTATED 78 60 98
DEL PEAK 19(10Q26.3) WILD-TYPE 59 44 27

Figure S104.  Get High-res Image Gene #41: 'del_10q26.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00444 (Fisher's exact test), Q value = 0.036

Table S105.  Gene #41: 'del_10q26.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
DEL PEAK 19(10Q26.3) MUTATED 63 64 76 33
DEL PEAK 19(10Q26.3) WILD-TYPE 44 41 20 25

Figure S105.  Get High-res Image Gene #41: 'del_10q26.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 0.0198 (Fisher's exact test), Q value = 0.098

Table S106.  Gene #42: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
DEL PEAK 20(11P15.5) MUTATED 41 33 40
DEL PEAK 20(11P15.5) WILD-TYPE 60 106 86

Figure S106.  Get High-res Image Gene #42: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.5' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0288 (Fisher's exact test), Q value = 0.13

Table S107.  Gene #42: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 105 139
DEL PEAK 20(11P15.5) MUTATED 23 28 55
DEL PEAK 20(11P15.5) WILD-TYPE 69 77 84

Figure S107.  Get High-res Image Gene #42: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S108.  Gene #43: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
DEL PEAK 21(11Q23.3) MUTATED 77 63 62
DEL PEAK 21(11Q23.3) WILD-TYPE 24 76 64

Figure S108.  Get High-res Image Gene #43: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q23.3' versus 'MRNASEQ_CNMF'

P value = 0.043 (Fisher's exact test), Q value = 0.16

Table S109.  Gene #43: 'del_11q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
DEL PEAK 21(11Q23.3) MUTATED 87 51 64
DEL PEAK 21(11Q23.3) WILD-TYPE 50 53 61

Figure S109.  Get High-res Image Gene #43: 'del_11q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.0065

Table S110.  Gene #43: 'del_11q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
DEL PEAK 21(11Q23.3) MUTATED 62 49 46 45
DEL PEAK 21(11Q23.3) WILD-TYPE 45 56 50 13

Figure S110.  Get High-res Image Gene #43: 'del_11q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0337 (Fisher's exact test), Q value = 0.14

Table S111.  Gene #43: 'del_11q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 147 74 38
DEL PEAK 21(11Q23.3) MUTATED 58 87 31 21
DEL PEAK 21(11Q23.3) WILD-TYPE 33 60 43 17

Figure S111.  Get High-res Image Gene #43: 'del_11q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11q23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00986 (Fisher's exact test), Q value = 0.061

Table S112.  Gene #43: 'del_11q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 105 139
DEL PEAK 21(11Q23.3) MUTATED 49 50 92
DEL PEAK 21(11Q23.3) WILD-TYPE 43 55 47

Figure S112.  Get High-res Image Gene #43: 'del_11q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_12q23.3' versus 'CN_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.076

Table S113.  Gene #44: 'del_12q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
DEL PEAK 22(12Q23.3) MUTATED 23 26 43
DEL PEAK 22(12Q23.3) WILD-TYPE 78 113 83

Figure S113.  Get High-res Image Gene #44: 'del_12q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q23.3' versus 'METHLYATION_CNMF'

P value = 0.0361 (Fisher's exact test), Q value = 0.15

Table S114.  Gene #44: 'del_12q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
DEL PEAK 22(12Q23.3) MUTATED 40 26 26
DEL PEAK 22(12Q23.3) WILD-TYPE 89 118 67

Figure S114.  Get High-res Image Gene #44: 'del_12q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q34' versus 'METHLYATION_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.062

Table S115.  Gene #45: 'del_13q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
DEL PEAK 23(13Q34) MUTATED 28 44 13
DEL PEAK 23(13Q34) WILD-TYPE 101 100 80

Figure S115.  Get High-res Image Gene #45: 'del_13q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00733 (Fisher's exact test), Q value = 0.052

Table S116.  Gene #45: 'del_13q34' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
DEL PEAK 23(13Q34) MUTATED 21 16 26 22
DEL PEAK 23(13Q34) WILD-TYPE 86 89 70 36

Figure S116.  Get High-res Image Gene #45: 'del_13q34' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q23.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00042

Table S117.  Gene #46: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
DEL PEAK 24(14Q23.3) MUTATED 30 29 61
DEL PEAK 24(14Q23.3) WILD-TYPE 71 110 65

Figure S117.  Get High-res Image Gene #46: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q23.3' versus 'MRNASEQ_CNMF'

P value = 0.00592 (Fisher's exact test), Q value = 0.043

Table S118.  Gene #46: 'del_14q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
DEL PEAK 24(14Q23.3) MUTATED 32 36 52
DEL PEAK 24(14Q23.3) WILD-TYPE 105 68 73

Figure S118.  Get High-res Image Gene #46: 'del_14q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0354 (Fisher's exact test), Q value = 0.14

Table S119.  Gene #46: 'del_14q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
DEL PEAK 24(14Q23.3) MUTATED 32 35 41 12
DEL PEAK 24(14Q23.3) WILD-TYPE 75 70 55 46

Figure S119.  Get High-res Image Gene #46: 'del_14q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q23.3' versus 'MIRSEQ_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 0.0081

Table S120.  Gene #46: 'del_14q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 102 79 114 8
DEL PEAK 24(14Q23.3) MUTATED 17 39 24 24 7
DEL PEAK 24(14Q23.3) WILD-TYPE 30 63 55 90 1

Figure S120.  Get High-res Image Gene #46: 'del_14q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_14q23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0388 (Fisher's exact test), Q value = 0.15

Table S121.  Gene #46: 'del_14q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 137 30
DEL PEAK 24(14Q23.3) MUTATED 43 53 11
DEL PEAK 24(14Q23.3) WILD-TYPE 126 84 19

Figure S121.  Get High-res Image Gene #46: 'del_14q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q32.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S122.  Gene #47: 'del_14q32.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
DEL PEAK 25(14Q32.31) MUTATED 28 27 62
DEL PEAK 25(14Q32.31) WILD-TYPE 73 112 64

Figure S122.  Get High-res Image Gene #47: 'del_14q32.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q32.31' versus 'MRNASEQ_CNMF'

P value = 0.00449 (Fisher's exact test), Q value = 0.036

Table S123.  Gene #47: 'del_14q32.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
DEL PEAK 25(14Q32.31) MUTATED 31 34 52
DEL PEAK 25(14Q32.31) WILD-TYPE 106 70 73

Figure S123.  Get High-res Image Gene #47: 'del_14q32.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q32.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0344 (Fisher's exact test), Q value = 0.14

Table S124.  Gene #47: 'del_14q32.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
DEL PEAK 25(14Q32.31) MUTATED 32 32 41 12
DEL PEAK 25(14Q32.31) WILD-TYPE 75 73 55 46

Figure S124.  Get High-res Image Gene #47: 'del_14q32.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q32.31' versus 'MIRSEQ_CNMF'

P value = 0.00372 (Fisher's exact test), Q value = 0.032

Table S125.  Gene #47: 'del_14q32.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 102 79 114 8
DEL PEAK 25(14Q32.31) MUTATED 16 34 25 26 7
DEL PEAK 25(14Q32.31) WILD-TYPE 31 68 54 88 1

Figure S125.  Get High-res Image Gene #47: 'del_14q32.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_15q13.3' versus 'CN_CNMF'

P value = 0.0496 (Fisher's exact test), Q value = 0.18

Table S126.  Gene #48: 'del_15q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
DEL PEAK 26(15Q13.3) MUTATED 31 24 29
DEL PEAK 26(15Q13.3) WILD-TYPE 70 115 97

Figure S126.  Get High-res Image Gene #48: 'del_15q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q13.3' versus 'METHLYATION_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.061

Table S127.  Gene #48: 'del_15q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
DEL PEAK 26(15Q13.3) MUTATED 33 22 29
DEL PEAK 26(15Q13.3) WILD-TYPE 96 122 64

Figure S127.  Get High-res Image Gene #48: 'del_15q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0175 (Fisher's exact test), Q value = 0.091

Table S128.  Gene #48: 'del_15q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
DEL PEAK 26(15Q13.3) MUTATED 35 21 21 7
DEL PEAK 26(15Q13.3) WILD-TYPE 72 84 75 51

Figure S128.  Get High-res Image Gene #48: 'del_15q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.087

Table S129.  Gene #48: 'del_15q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 105 139
DEL PEAK 26(15Q13.3) MUTATED 12 30 37
DEL PEAK 26(15Q13.3) WILD-TYPE 80 75 102

Figure S129.  Get High-res Image Gene #48: 'del_15q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16p13.3' versus 'RPPA_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.069

Table S130.  Gene #50: 'del_16p13.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 58 26 38
DEL PEAK 28(16P13.3) MUTATED 9 16 0 8
DEL PEAK 28(16P13.3) WILD-TYPE 38 42 26 30

Figure S130.  Get High-res Image Gene #50: 'del_16p13.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_16p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0454 (Fisher's exact test), Q value = 0.17

Table S131.  Gene #50: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 105 139
DEL PEAK 28(16P13.3) MUTATED 18 11 31
DEL PEAK 28(16P13.3) WILD-TYPE 74 94 108

Figure S131.  Get High-res Image Gene #50: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16q12.1' versus 'RPPA_CNMF'

P value = 0.0217 (Fisher's exact test), Q value = 0.1

Table S132.  Gene #51: 'del_16q12.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 58 26 38
DEL PEAK 29(16Q12.1) MUTATED 15 24 3 17
DEL PEAK 29(16Q12.1) WILD-TYPE 32 34 23 21

Figure S132.  Get High-res Image Gene #51: 'del_16q12.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_16q12.1' versus 'MRNASEQ_CNMF'

P value = 0.0387 (Fisher's exact test), Q value = 0.15

Table S133.  Gene #51: 'del_16q12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
DEL PEAK 29(16Q12.1) MUTATED 55 29 33
DEL PEAK 29(16Q12.1) WILD-TYPE 82 75 92

Figure S133.  Get High-res Image Gene #51: 'del_16q12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0217 (Fisher's exact test), Q value = 0.1

Table S134.  Gene #51: 'del_16q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 147 74 38
DEL PEAK 29(16Q12.1) MUTATED 39 48 17 8
DEL PEAK 29(16Q12.1) WILD-TYPE 52 99 57 30

Figure S134.  Get High-res Image Gene #51: 'del_16q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16q24.3' versus 'MRNASEQ_CNMF'

P value = 0.00945 (Fisher's exact test), Q value = 0.06

Table S135.  Gene #52: 'del_16q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
DEL PEAK 30(16Q24.3) MUTATED 63 35 35
DEL PEAK 30(16Q24.3) WILD-TYPE 74 69 90

Figure S135.  Get High-res Image Gene #52: 'del_16q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0024 (Fisher's exact test), Q value = 0.023

Table S136.  Gene #52: 'del_16q24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
DEL PEAK 30(16Q24.3) MUTATED 41 36 24 32
DEL PEAK 30(16Q24.3) WILD-TYPE 66 69 72 26

Figure S136.  Get High-res Image Gene #52: 'del_16q24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 0.073

Table S137.  Gene #52: 'del_16q24.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 105 139
DEL PEAK 30(16Q24.3) MUTATED 40 26 54
DEL PEAK 30(16Q24.3) WILD-TYPE 52 79 85

Figure S137.  Get High-res Image Gene #52: 'del_16q24.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16q24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0413 (Fisher's exact test), Q value = 0.16

Table S138.  Gene #52: 'del_16q24.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 137 30
DEL PEAK 30(16Q24.3) MUTATED 71 42 7
DEL PEAK 30(16Q24.3) WILD-TYPE 98 95 23

Figure S138.  Get High-res Image Gene #52: 'del_16q24.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p13.3' versus 'METHLYATION_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0051

Table S139.  Gene #53: 'del_17p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
DEL PEAK 31(17P13.3) MUTATED 59 57 19
DEL PEAK 31(17P13.3) WILD-TYPE 70 87 74

Figure S139.  Get High-res Image Gene #53: 'del_17p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0183 (Fisher's exact test), Q value = 0.092

Table S140.  Gene #53: 'del_17p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
DEL PEAK 31(17P13.3) MUTATED 44 33 28 30
DEL PEAK 31(17P13.3) WILD-TYPE 63 72 68 28

Figure S140.  Get High-res Image Gene #53: 'del_17p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 0.0215 (Fisher's exact test), Q value = 0.1

Table S141.  Gene #54: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
DEL PEAK 32(19P13.3) MUTATED 39 31 34
DEL PEAK 32(19P13.3) WILD-TYPE 62 108 92

Figure S141.  Get High-res Image Gene #54: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'RPPA_CNMF'

P value = 0.00236 (Fisher's exact test), Q value = 0.023

Table S142.  Gene #54: 'del_19p13.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 58 26 38
DEL PEAK 32(19P13.3) MUTATED 15 12 16 9
DEL PEAK 32(19P13.3) WILD-TYPE 32 46 10 29

Figure S142.  Get High-res Image Gene #54: 'del_19p13.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 0.00079 (Fisher's exact test), Q value = 0.01

Table S143.  Gene #54: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
DEL PEAK 32(19P13.3) MUTATED 55 22 27
DEL PEAK 32(19P13.3) WILD-TYPE 82 82 98

Figure S143.  Get High-res Image Gene #54: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00124 (Fisher's exact test), Q value = 0.013

Table S144.  Gene #54: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
DEL PEAK 32(19P13.3) MUTATED 37 21 20 26
DEL PEAK 32(19P13.3) WILD-TYPE 70 84 76 32

Figure S144.  Get High-res Image Gene #54: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xp21.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S145.  Gene #55: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 144 93
DEL PEAK 33(XP21.1) MUTATED 47 16 24
DEL PEAK 33(XP21.1) WILD-TYPE 82 128 69

Figure S145.  Get High-res Image Gene #55: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp21.1' versus 'RPPA_CNMF'

P value = 0.0469 (Fisher's exact test), Q value = 0.17

Table S146.  Gene #55: 'del_xp21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 58 26 38
DEL PEAK 33(XP21.1) MUTATED 4 17 7 8
DEL PEAK 33(XP21.1) WILD-TYPE 43 41 19 30

Figure S146.  Get High-res Image Gene #55: 'del_xp21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_xp21.1' versus 'MRNASEQ_CNMF'

P value = 0.00463 (Fisher's exact test), Q value = 0.036

Table S147.  Gene #55: 'del_xp21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 104 125
DEL PEAK 33(XP21.1) MUTATED 39 13 35
DEL PEAK 33(XP21.1) WILD-TYPE 98 91 90

Figure S147.  Get High-res Image Gene #55: 'del_xp21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xp21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00219 (Fisher's exact test), Q value = 0.022

Table S148.  Gene #55: 'del_xp21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 105 96 58
DEL PEAK 33(XP21.1) MUTATED 36 13 26 12
DEL PEAK 33(XP21.1) WILD-TYPE 71 92 70 46

Figure S148.  Get High-res Image Gene #55: 'del_xp21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_CNMF'

P value = 0.00086 (Fisher's exact test), Q value = 0.011

Table S149.  Gene #55: 'del_xp21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 102 79 114 8
DEL PEAK 33(XP21.1) MUTATED 7 16 15 41 4
DEL PEAK 33(XP21.1) WILD-TYPE 40 86 64 73 4

Figure S149.  Get High-res Image Gene #55: 'del_xp21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xp21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.048 (Fisher's exact test), Q value = 0.18

Table S150.  Gene #55: 'del_xp21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 147 74 38
DEL PEAK 33(XP21.1) MUTATED 23 43 13 4
DEL PEAK 33(XP21.1) WILD-TYPE 68 104 61 34

Figure S150.  Get High-res Image Gene #55: 'del_xp21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00106 (Fisher's exact test), Q value = 0.012

Table S151.  Gene #55: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 105 139
DEL PEAK 33(XP21.1) MUTATED 17 15 46
DEL PEAK 33(XP21.1) WILD-TYPE 75 90 93

Figure S151.  Get High-res Image Gene #55: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

Methods & Data
Input

  • Copy number data file = all_lesions.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/SKCM-TM/15098585/transformed.cor.cli.txt

  • Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/SKCM-TM/15111349/SKCM-TM.transferedmergedcluster.txt

  • Number of patients = 366

  • Number of significantly focal cnvs = 55

  • Number of molecular subtypes = 10

  • Exclude genes that fewer than K tumors have alterations, 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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