Correlation between copy number variation genes (focal events) and molecular subtypes
Sarcoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1B56HF6
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1B56HF6
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 58 focal events and 8 molecular subtypes across 150 patients, 76 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1p32.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • amp_1q24.3 cnv correlated to 'CN_CNMF'.

  • amp_5p15.33 cnv correlated to 'CN_CNMF'.

  • amp_6p21.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • amp_6q24.3 cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_12q15 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_17p11.2 cnv correlated to 'CN_CNMF'.

  • amp_17q24.3 cnv correlated to 'METHLYATION_CNMF'.

  • amp_19p13.2 cnv correlated to 'CN_CNMF'.

  • amp_19q12 cnv correlated to 'CN_CNMF'.

  • amp_21q21.1 cnv correlated to 'CN_CNMF'.

  • amp_xp21.1 cnv correlated to 'CN_CNMF'.

  • del_1p36.32 cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_1q44 cnv correlated to 'CN_CNMF'.

  • del_2p25.3 cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_2q37.3 cnv correlated to 'CN_CNMF'.

  • del_2q37.3 cnv correlated to 'CN_CNMF'.

  • del_3p21.31 cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • del_4q35.1 cnv correlated to 'CN_CNMF'.

  • del_6q14.1 cnv correlated to 'CN_CNMF'.

  • del_9p24.3 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • del_9p21.3 cnv correlated to 'CN_CNMF'.

  • del_10q23.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_11p15.5 cnv correlated to 'CN_CNMF'.

  • del_11q24.3 cnv correlated to 'CN_CNMF'.

  • del_12p13.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_13q14.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_16q12.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_17p13.1 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_17q11.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_19p13.3 cnv correlated to 'METHLYATION_CNMF'.

  • del_22q13.31 cnv correlated to 'CN_CNMF'.

  • del_xq21.1 cnv correlated to 'METHLYATION_CNMF'.

  • del_xq27.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 58 focal events and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 76 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
amp 12q15 58 (39%) 92 3.94e-17
(1.83e-14) 		8.67e-10
(3.94e-07) 		5.17e-10
(2.36e-07) 		3.47e-13
(1.6e-10) 		2.88e-10
(1.32e-07) 		1.03e-11
(4.77e-09) 		5.53e-11
(2.55e-08) 		1.03e-11
(4.77e-09)
amp 6q24 3 47 (31%) 103 0.00291
(1.00) 		2.06e-05
(0.00883) 		0.000218
(0.0882) 		9.54e-06
(0.00413) 		2.36e-05
(0.01) 		2.74e-05
(0.0117) 		1.11e-05
(0.00481) 		0.000142
(0.058)
del 1p36 32 46 (31%) 104 0.0281
(1.00) 		1.35e-06
(0.000597) 		2.77e-05
(0.0117) 		4.56e-06
(0.00199) 		2e-06
(0.000878) 		3.48e-09
(1.58e-06) 		6.19e-07
(0.000277) 		3.48e-09
(1.58e-06)
del 10q23 31 84 (56%) 66 6.14e-10
(2.8e-07) 		3.5e-10
(1.6e-07) 		3.76e-09
(1.7e-06) 		3.3e-07
(0.000148) 		0.00176
(0.642) 		0.000606
(0.237) 		0.00148
(0.549) 		0.000606
(0.237)
del 2p25 3 52 (35%) 98 0.00207
(0.738) 		2.29e-05
(0.00978) 		0.000317
(0.127) 		4.79e-06
(0.00208) 		0.00176
(0.642) 		8.81e-05
(0.0363) 		0.00283
(0.983) 		8.81e-05
(0.0363)
del 13q14 2 106 (71%) 44 6.33e-07
(0.000282) 		7.15e-07
(0.000318) 		2.08e-05
(0.00892) 		4.37e-06
(0.0019) 		0.0138
(1.00) 		0.0141
(1.00) 		0.00805
(1.00) 		0.0141
(1.00)
del 17p13 1 71 (47%) 79 0.00044
(0.174) 		0.000961
(0.369) 		3.34e-05
(0.0141) 		0.000263
(0.106) 		0.0684
(1.00) 		0.0518
(1.00) 		0.0303
(1.00) 		0.0518
(1.00)
del xq27 1 74 (49%) 76 0.000611
(0.238) 		0.000303
(0.122) 		0.0403
(1.00) 		0.00051
(0.201) 		0.00607
(1.00) 		0.00115
(0.438) 		0.00553
(1.00) 		0.00115
(0.438)
amp 1p32 1 55 (37%) 95 1.32e-06
(0.000584) 		9.87e-07
(0.000438) 		0.887
(1.00) 		0.219
(1.00) 		0.017
(1.00) 		0.00269
(0.941) 		0.0596
(1.00) 		0.00834
(1.00)
amp 6p21 1 36 (24%) 114 4.82e-05
(0.0202) 		7.31e-05
(0.0304) 		0.0015
(0.554) 		0.00129
(0.482) 		0.0177
(1.00) 		0.0015
(0.554) 		0.00825
(1.00) 		0.00643
(1.00)
del 3p21 31 33 (22%) 117 0.012
(1.00) 		0.00019
(0.0773) 		0.00194
(0.695) 		0.000343
(0.136) 		0.0089
(1.00) 		0.0152
(1.00) 		0.00505
(1.00) 		0.00409
(1.00)
del 9p24 3 58 (39%) 92 0.000266
(0.107) 		0.0283
(1.00) 		0.172
(1.00) 		0.00114
(0.435) 		0.00289
(1.00) 		0.000341
(0.136) 		0.0021
(0.746) 		0.00113
(0.433)
del 12p13 1 52 (35%) 98 5.89e-05
(0.0245) 		7.32e-05
(0.0304) 		0.281
(1.00) 		0.269
(1.00) 		0.0468
(1.00) 		0.0315
(1.00) 		0.0819
(1.00) 		0.0315
(1.00)
del 16q12 1 83 (55%) 67 4.93e-05
(0.0206) 		0.000406
(0.161) 		0.0457
(1.00) 		0.00556
(1.00) 		0.0472
(1.00) 		0.00586
(1.00) 		0.0399
(1.00) 		0.00586
(1.00)
del 17q11 2 45 (30%) 105 3.5e-06
(0.00153) 		0.00012
(0.0494) 		0.139
(1.00) 		0.179
(1.00) 		0.00234
(0.828) 		0.000696
(0.269) 		0.00127
(0.475) 		0.0027
(0.943)
amp 1q24 3 65 (43%) 85 5.84e-05
(0.0243) 		0.00482
(1.00) 		0.747
(1.00) 		0.28
(1.00) 		0.268
(1.00) 		0.154
(1.00) 		0.142
(1.00) 		0.305
(1.00)
amp 5p15 33 67 (45%) 83 0.000629
(0.245) 		0.0258
(1.00) 		0.237
(1.00) 		0.386
(1.00) 		0.273
(1.00) 		0.113
(1.00) 		0.178
(1.00) 		0.212
(1.00)
amp 17p11 2 60 (40%) 90 1.73e-07
(7.77e-05) 		0.0174
(1.00) 		0.456
(1.00) 		0.319
(1.00) 		1
(1.00) 		1
(1.00) 		0.841
(1.00) 		1
(1.00)
amp 17q24 3 45 (30%) 105 0.085
(1.00) 		0.000162
(0.0658) 		0.00505
(1.00) 		0.5
(1.00) 		0.0353
(1.00) 		0.00121
(0.456) 		0.0671
(1.00) 		0.00358
(1.00)
amp 19p13 2 60 (40%) 90 4.12e-05
(0.0174) 		0.527
(1.00) 		1
(1.00) 		0.428
(1.00) 		0.659
(1.00) 		0.562
(1.00) 		0.892
(1.00) 		0.562
(1.00)
amp 19q12 53 (35%) 97 1.09e-06
(0.000482) 		0.00143
(0.532) 		0.777
(1.00) 		0.0638
(1.00) 		0.391
(1.00) 		0.228
(1.00) 		0.539
(1.00) 		0.228
(1.00)
amp 21q21 1 48 (32%) 102 4.36e-05
(0.0184) 		0.000889
(0.342) 		0.763
(1.00) 		0.271
(1.00) 		0.191
(1.00) 		0.268
(1.00) 		0.164
(1.00) 		0.268
(1.00)
amp xp21 1 52 (35%) 98 2.3e-06
(0.00101) 		0.0273
(1.00) 		1
(1.00) 		0.451
(1.00) 		0.913
(1.00) 		0.788
(1.00) 		0.882
(1.00) 		1
(1.00)
del 1q44 47 (31%) 103 1.19e-05
(0.00513) 		0.00786
(1.00) 		0.42
(1.00) 		0.0625
(1.00) 		0.077
(1.00) 		0.0658
(1.00) 		0.129
(1.00) 		0.183
(1.00)
del 2q37 3 63 (42%) 87 2.62e-08
(1.18e-05) 		0.0278
(1.00) 		0.0664
(1.00) 		0.467
(1.00) 		0.705
(1.00) 		0.751
(1.00) 		0.639
(1.00) 		0.751
(1.00)
del 2q37 3 65 (43%) 85 1.21e-08
(5.44e-06) 		0.0083
(1.00) 		0.0134
(1.00) 		0.216
(1.00) 		0.872
(1.00) 		1
(1.00) 		0.859
(1.00) 		1
(1.00)
del 4q35 1 56 (37%) 94 1.3e-05
(0.00561) 		0.207
(1.00) 		0.057
(1.00) 		0.766
(1.00) 		0.729
(1.00) 		0.675
(1.00) 		0.611
(1.00) 		0.675
(1.00)
del 6q14 1 43 (29%) 107 0.000574
(0.226) 		0.0389
(1.00) 		0.42
(1.00) 		0.749
(1.00) 		0.23
(1.00) 		0.237
(1.00) 		0.282
(1.00) 		0.159
(1.00)
del 9p21 3 63 (42%) 87 0.0004
(0.159) 		0.00866
(1.00) 		0.328
(1.00) 		0.00398
(1.00) 		0.0102
(1.00) 		0.00363
(1.00) 		0.00164
(0.598) 		0.00943
(1.00)
del 11p15 5 67 (45%) 83 4.79e-05
(0.0201) 		0.00121
(0.455) 		0.298
(1.00) 		0.222
(1.00) 		0.852
(1.00) 		0.896
(1.00) 		0.771
(1.00) 		1
(1.00)
del 11q24 3 65 (43%) 85 2.43e-06
(0.00106) 		0.00305
(1.00) 		0.359
(1.00) 		0.0129
(1.00) 		0.00346
(1.00) 		0.00532
(1.00) 		0.00719
(1.00) 		0.0144
(1.00)
del 19p13 3 45 (30%) 105 0.00141
(0.525) 		7.93e-05
(0.0328) 		0.00736
(1.00) 		0.0216
(1.00) 		0.0213
(1.00) 		0.031
(1.00) 		0.0149
(1.00) 		0.031
(1.00)
del 22q13 31 53 (35%) 97 0.00033
(0.132) 		0.0221
(1.00) 		0.00225
(0.795) 		0.388
(1.00) 		0.491
(1.00) 		0.324
(1.00) 		0.545
(1.00) 		0.324
(1.00)
del xq21 1 72 (48%) 78 0.106
(1.00) 		0.00013
(0.0534) 		0.0137
(1.00) 		0.00316
(1.00) 		0.00921
(1.00) 		0.00181
(0.653) 		0.0109
(1.00) 		0.00181
(0.653)
amp 3p11 2 36 (24%) 114 0.0104
(1.00) 		0.0983
(1.00) 		0.627
(1.00) 		1
(1.00) 		0.608
(1.00) 		0.407
(1.00) 		0.268
(1.00) 		0.692
(1.00)
amp 7q31 1 44 (29%) 106 0.000825
(0.318) 		0.0379
(1.00) 		0.494
(1.00) 		0.0578
(1.00) 		0.0707
(1.00) 		0.0405
(1.00) 		0.0154
(1.00) 		0.115
(1.00)
amp 8q21 12 54 (36%) 96 0.0199
(1.00) 		0.0323
(1.00) 		0.852
(1.00) 		0.577
(1.00) 		0.807
(1.00) 		0.873
(1.00) 		0.843
(1.00) 		0.873
(1.00)
amp 11q22 2 25 (17%) 125 0.226
(1.00) 		0.098
(1.00) 		0.0485
(1.00) 		0.0499
(1.00) 		0.0578
(1.00) 		0.0649
(1.00) 		0.0762
(1.00) 		0.0649
(1.00)
amp 12p13 32 28 (19%) 122 0.291
(1.00) 		0.594
(1.00) 		0.302
(1.00) 		0.0785
(1.00) 		0.086
(1.00) 		0.284
(1.00) 		0.122
(1.00) 		0.129
(1.00)
amp 13q34 28 (19%) 122 0.00158
(0.581) 		0.00162
(0.593) 		0.212
(1.00) 		0.391
(1.00) 		0.736
(1.00) 		1
(1.00) 		0.843
(1.00) 		0.789
(1.00)
amp 20q13 33 62 (41%) 88 0.00136
(0.506) 		0.0086
(1.00) 		0.253
(1.00) 		0.00877
(1.00) 		0.0103
(1.00) 		0.0736
(1.00) 		0.0112
(1.00) 		0.0302
(1.00)
amp xq21 2 24 (16%) 126 0.00394
(1.00) 		0.0179
(1.00) 		0.191
(1.00) 		0.616
(1.00) 		0.349
(1.00) 		0.334
(1.00) 		0.382
(1.00) 		0.334
(1.00)
del 1p32 3 26 (17%) 124 0.315
(1.00) 		0.145
(1.00) 		0.048
(1.00) 		1
(1.00) 		0.752
(1.00) 		0.04
(1.00) 		0.757
(1.00) 		0.04
(1.00)
del 3q29 35 (23%) 115 0.00592
(1.00) 		0.00237
(0.835) 		0.0551
(1.00) 		0.161
(1.00) 		0.28
(1.00) 		0.214
(1.00) 		0.326
(1.00) 		0.214
(1.00)
del 6p25 1 52 (35%) 98 0.376
(1.00) 		0.0448
(1.00) 		0.0421
(1.00) 		0.0106
(1.00) 		0.107
(1.00) 		0.233
(1.00) 		0.117
(1.00) 		0.233
(1.00)
del 7q36 3 38 (25%) 112 0.00119
(0.451) 		0.209
(1.00) 		0.821
(1.00) 		0.611
(1.00) 		0.397
(1.00) 		0.43
(1.00) 		0.782
(1.00) 		0.43
(1.00)
del 8p23 3 44 (29%) 106 0.0822
(1.00) 		0.00212
(0.751) 		0.188
(1.00) 		0.0988
(1.00) 		0.00487
(1.00) 		0.00503
(1.00) 		0.00268
(0.939) 		0.00179
(0.647)
del 9q34 3 42 (28%) 108 0.00436
(1.00) 		0.0976
(1.00) 		0.00509
(1.00) 		0.156
(1.00) 		0.176
(1.00) 		0.101
(1.00) 		0.134
(1.00) 		0.101
(1.00)
del 10p15 3 76 (51%) 74 0.00809
(1.00) 		0.00069
(0.268) 		0.0463
(1.00) 		0.138
(1.00) 		0.959
(1.00) 		0.62
(1.00) 		0.863
(1.00) 		0.62
(1.00)
del 12q12 29 (19%) 121 0.0999
(1.00) 		0.0642
(1.00) 		0.203
(1.00) 		0.585
(1.00) 		0.478
(1.00) 		1
(1.00) 		0.514
(1.00) 		1
(1.00)
del 14q24 1 51 (34%) 99 0.68
(1.00) 		0.0105
(1.00) 		0.00104
(0.398) 		0.268
(1.00) 		0.566
(1.00) 		0.156
(1.00) 		0.534
(1.00) 		0.275
(1.00)
del 15q11 2 30 (20%) 120 0.453
(1.00) 		0.206
(1.00) 		0.0752
(1.00) 		0.135
(1.00) 		0.112
(1.00) 		0.108
(1.00) 		0.0611
(1.00) 		0.108
(1.00)
del 17q25 3 40 (27%) 110 0.00515
(1.00) 		0.0573
(1.00) 		0.335
(1.00) 		0.078
(1.00) 		0.357
(1.00) 		0.192
(1.00) 		0.273
(1.00) 		0.317
(1.00)
del 18q23 50 (33%) 100 0.0593
(1.00) 		0.0312
(1.00) 		0.632
(1.00) 		0.137
(1.00) 		0.0409
(1.00) 		0.291
(1.00) 		0.0514
(1.00) 		0.429
(1.00)
del 19q13 43 63 (42%) 87 0.00601
(1.00) 		0.00443
(1.00) 		0.166
(1.00) 		0.0769
(1.00) 		0.0533
(1.00) 		0.0815
(1.00) 		0.104
(1.00) 		0.0815
(1.00)
del 21q11 2 28 (19%) 122 0.383
(1.00) 		0.257
(1.00) 		0.565
(1.00) 		0.297
(1.00) 		0.055
(1.00) 		0.153
(1.00) 		0.137
(1.00) 		0.153
(1.00)
del 21q22 3 39 (26%) 111 0.052
(1.00) 		0.05
(1.00) 		0.875
(1.00) 		0.269
(1.00) 		0.552
(1.00) 		0.804
(1.00) 		0.442
(1.00) 		0.804
(1.00)
del xp22 32 47 (31%) 103 0.0979
(1.00) 		0.00196
(0.702) 		0.0171
(1.00) 		0.0219
(1.00) 		0.0594
(1.00) 		0.0254
(1.00) 		0.0312
(1.00) 		0.0254
(1.00)
'amp_1p32.1' versus 'CN_CNMF'

P value = 1.32e-06 (Fisher's exact test), Q value = 0.00058

Table S1.  Gene #1: 'amp_1p32.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 55 54
AMP PEAK 1(1P32.1) MUTATED 15 33 7
AMP PEAK 1(1P32.1) WILD-TYPE 26 22 47

Figure S1.  Get High-res Image Gene #1: 'amp_1p32.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1p32.1' versus 'METHLYATION_CNMF'

P value = 9.87e-07 (Chi-square test), Q value = 0.00044

Table S2.  Gene #1: 'amp_1p32.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 30 28 15 21 18 35 3
AMP PEAK 1(1P32.1) MUTATED 9 11 3 19 1 10 2
AMP PEAK 1(1P32.1) WILD-TYPE 21 17 12 2 17 25 1

Figure S2.  Get High-res Image Gene #1: 'amp_1p32.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q24.3' versus 'CN_CNMF'

P value = 5.84e-05 (Fisher's exact test), Q value = 0.024

Table S3.  Gene #2: 'amp_1q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 55 54
AMP PEAK 2(1Q24.3) MUTATED 21 33 11
AMP PEAK 2(1Q24.3) WILD-TYPE 20 22 43

Figure S3.  Get High-res Image Gene #2: 'amp_1q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'CN_CNMF'

P value = 0.000629 (Fisher's exact test), Q value = 0.24

Table S4.  Gene #4: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 55 54
AMP PEAK 4(5P15.33) MUTATED 23 31 13
AMP PEAK 4(5P15.33) WILD-TYPE 18 24 41

Figure S4.  Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p21.1' versus 'CN_CNMF'

P value = 4.82e-05 (Fisher's exact test), Q value = 0.02

Table S5.  Gene #5: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 55 54
AMP PEAK 5(6P21.1) MUTATED 11 22 3
AMP PEAK 5(6P21.1) WILD-TYPE 30 33 51

Figure S5.  Get High-res Image Gene #5: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p21.1' versus 'METHLYATION_CNMF'

P value = 7.31e-05 (Chi-square test), Q value = 0.03

Table S6.  Gene #5: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 30 28 15 21 18 35 3
AMP PEAK 5(6P21.1) MUTATED 5 12 5 10 0 2 2
AMP PEAK 5(6P21.1) WILD-TYPE 25 16 10 11 18 33 1

Figure S6.  Get High-res Image Gene #5: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q24.3' versus 'METHLYATION_CNMF'

P value = 2.06e-05 (Chi-square test), Q value = 0.0088

Table S7.  Gene #6: 'amp_6q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 30 28 15 21 18 35 3
AMP PEAK 6(6Q24.3) MUTATED 13 18 3 8 1 3 1
AMP PEAK 6(6Q24.3) WILD-TYPE 17 10 12 13 17 32 2

Figure S7.  Get High-res Image Gene #6: 'amp_6q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q24.3' versus 'MRNASEQ_CNMF'

P value = 0.000218 (Fisher's exact test), Q value = 0.088

Table S8.  Gene #6: 'amp_6q24.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 30 32
AMP PEAK 6(6Q24.3) MUTATED 21 6 3
AMP PEAK 6(6Q24.3) WILD-TYPE 20 24 29

Figure S8.  Get High-res Image Gene #6: 'amp_6q24.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_6q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.54e-06 (Fisher's exact test), Q value = 0.0041

Table S9.  Gene #6: 'amp_6q24.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 53 4
AMP PEAK 6(6Q24.3) MUTATED 4 26 0
AMP PEAK 6(6Q24.3) WILD-TYPE 42 27 4

Figure S9.  Get High-res Image Gene #6: 'amp_6q24.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_6q24.3' versus 'MIRSEQ_CNMF'

P value = 2.36e-05 (Fisher's exact test), Q value = 0.01

Table S10.  Gene #6: 'amp_6q24.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 63 22
AMP PEAK 6(6Q24.3) MUTATED 8 27 12
AMP PEAK 6(6Q24.3) WILD-TYPE 56 36 10

Figure S10.  Get High-res Image Gene #6: 'amp_6q24.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_6q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.74e-05 (Fisher's exact test), Q value = 0.012

Table S11.  Gene #6: 'amp_6q24.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 2 65
AMP PEAK 6(6Q24.3) MUTATED 38 0 9
AMP PEAK 6(6Q24.3) WILD-TYPE 44 2 56

Figure S11.  Get High-res Image Gene #6: 'amp_6q24.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_6q24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.11e-05 (Fisher's exact test), Q value = 0.0048

Table S12.  Gene #6: 'amp_6q24.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 65 22
AMP PEAK 6(6Q24.3) MUTATED 7 28 12
AMP PEAK 6(6Q24.3) WILD-TYPE 55 37 10

Figure S12.  Get High-res Image Gene #6: 'amp_6q24.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_6q24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000142 (Fisher's exact test), Q value = 0.058

Table S13.  Gene #6: 'amp_6q24.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 2 65 82
AMP PEAK 6(6Q24.3) MUTATED 0 10 37
AMP PEAK 6(6Q24.3) WILD-TYPE 2 55 45

Figure S13.  Get High-res Image Gene #6: 'amp_6q24.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q15' versus 'CN_CNMF'

P value = 3.94e-17 (Fisher's exact test), Q value = 1.8e-14

Table S14.  Gene #11: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 55 54
AMP PEAK 11(12Q15) MUTATED 38 13 7
AMP PEAK 11(12Q15) WILD-TYPE 3 42 47

Figure S14.  Get High-res Image Gene #11: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

P value = 8.67e-10 (Chi-square test), Q value = 3.9e-07

Table S15.  Gene #11: 'amp_12q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 30 28 15 21 18 35 3
AMP PEAK 11(12Q15) MUTATED 20 20 9 6 1 1 1
AMP PEAK 11(12Q15) WILD-TYPE 10 8 6 15 17 34 2

Figure S15.  Get High-res Image Gene #11: 'amp_12q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12q15' versus 'MRNASEQ_CNMF'

P value = 5.17e-10 (Fisher's exact test), Q value = 2.4e-07

Table S16.  Gene #11: 'amp_12q15' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 30 32
AMP PEAK 11(12Q15) MUTATED 30 9 1
AMP PEAK 11(12Q15) WILD-TYPE 11 21 31

Figure S16.  Get High-res Image Gene #11: 'amp_12q15' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_12q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.47e-13 (Fisher's exact test), Q value = 1.6e-10

Table S17.  Gene #11: 'amp_12q15' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 53 4
AMP PEAK 11(12Q15) MUTATED 2 38 0
AMP PEAK 11(12Q15) WILD-TYPE 44 15 4

Figure S17.  Get High-res Image Gene #11: 'amp_12q15' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_CNMF'

P value = 2.88e-10 (Fisher's exact test), Q value = 1.3e-07

Table S18.  Gene #11: 'amp_12q15' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 63 22
AMP PEAK 11(12Q15) MUTATED 6 38 13
AMP PEAK 11(12Q15) WILD-TYPE 58 25 9

Figure S18.  Get High-res Image Gene #11: 'amp_12q15' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_12q15' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.03e-11 (Fisher's exact test), Q value = 4.8e-09

Table S19.  Gene #11: 'amp_12q15' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 2 65
AMP PEAK 11(12Q15) MUTATED 51 0 6
AMP PEAK 11(12Q15) WILD-TYPE 31 2 59

Figure S19.  Get High-res Image Gene #11: 'amp_12q15' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.53e-11 (Fisher's exact test), Q value = 2.5e-08

Table S20.  Gene #11: 'amp_12q15' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 65 22
AMP PEAK 11(12Q15) MUTATED 5 41 11
AMP PEAK 11(12Q15) WILD-TYPE 57 24 11

Figure S20.  Get High-res Image Gene #11: 'amp_12q15' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_12q15' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.03e-11 (Fisher's exact test), Q value = 4.8e-09

Table S21.  Gene #11: 'amp_12q15' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 2 65 82
AMP PEAK 11(12Q15) MUTATED 0 6 51
AMP PEAK 11(12Q15) WILD-TYPE 2 59 31

Figure S21.  Get High-res Image Gene #11: 'amp_12q15' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17p11.2' versus 'CN_CNMF'

P value = 1.73e-07 (Fisher's exact test), Q value = 7.8e-05

Table S22.  Gene #13: 'amp_17p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 55 54
AMP PEAK 13(17P11.2) MUTATED 8 38 14
AMP PEAK 13(17P11.2) WILD-TYPE 33 17 40

Figure S22.  Get High-res Image Gene #13: 'amp_17p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q24.3' versus 'METHLYATION_CNMF'

P value = 0.000162 (Chi-square test), Q value = 0.066

Table S23.  Gene #14: 'amp_17q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 30 28 15 21 18 35 3
AMP PEAK 14(17Q24.3) MUTATED 6 13 8 9 3 3 3
AMP PEAK 14(17Q24.3) WILD-TYPE 24 15 7 12 15 32 0

Figure S23.  Get High-res Image Gene #14: 'amp_17q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19p13.2' versus 'CN_CNMF'

P value = 4.12e-05 (Fisher's exact test), Q value = 0.017

Table S24.  Gene #15: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 55 54
AMP PEAK 15(19P13.2) MUTATED 17 33 10
AMP PEAK 15(19P13.2) WILD-TYPE 24 22 44

Figure S24.  Get High-res Image Gene #15: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q12' versus 'CN_CNMF'

P value = 1.09e-06 (Fisher's exact test), Q value = 0.00048

Table S25.  Gene #16: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 55 54
AMP PEAK 16(19Q12) MUTATED 13 33 7
AMP PEAK 16(19Q12) WILD-TYPE 28 22 47

Figure S25.  Get High-res Image Gene #16: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_21q21.1' versus 'CN_CNMF'

P value = 4.36e-05 (Fisher's exact test), Q value = 0.018

Table S26.  Gene #18: 'amp_21q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 55 54
AMP PEAK 18(21Q21.1) MUTATED 9 30 9
AMP PEAK 18(21Q21.1) WILD-TYPE 32 25 45

Figure S26.  Get High-res Image Gene #18: 'amp_21q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xp21.1' versus 'CN_CNMF'

P value = 2.3e-06 (Fisher's exact test), Q value = 0.001

Table S27.  Gene #19: 'amp_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 55 54
AMP PEAK 19(XP21.1) MUTATED 11 33 8
AMP PEAK 19(XP21.1) WILD-TYPE 30 22 46

Figure S27.  Get High-res Image Gene #19: 'amp_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.32' versus 'METHLYATION_CNMF'

P value = 1.35e-06 (Chi-square test), Q value = 6e-04

Table S28.  Gene #21: 'del_1p36.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 30 28 15 21 18 35 3
DEL PEAK 1(1P36.32) MUTATED 0 6 5 3 8 22 2
DEL PEAK 1(1P36.32) WILD-TYPE 30 22 10 18 10 13 1

Figure S28.  Get High-res Image Gene #21: 'del_1p36.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.32' versus 'MRNASEQ_CNMF'

P value = 2.77e-05 (Fisher's exact test), Q value = 0.012

Table S29.  Gene #21: 'del_1p36.32' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 30 32
DEL PEAK 1(1P36.32) MUTATED 5 15 19
DEL PEAK 1(1P36.32) WILD-TYPE 36 15 13

Figure S29.  Get High-res Image Gene #21: 'del_1p36.32' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_1p36.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.56e-06 (Fisher's exact test), Q value = 0.002

Table S30.  Gene #21: 'del_1p36.32' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 53 4
DEL PEAK 1(1P36.32) MUTATED 29 10 0
DEL PEAK 1(1P36.32) WILD-TYPE 17 43 4

Figure S30.  Get High-res Image Gene #21: 'del_1p36.32' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.32' versus 'MIRSEQ_CNMF'

P value = 2e-06 (Fisher's exact test), Q value = 0.00088

Table S31.  Gene #21: 'del_1p36.32' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 63 22
DEL PEAK 1(1P36.32) MUTATED 34 9 3
DEL PEAK 1(1P36.32) WILD-TYPE 30 54 19

Figure S31.  Get High-res Image Gene #21: 'del_1p36.32' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_1p36.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.48e-09 (Fisher's exact test), Q value = 1.6e-06

Table S32.  Gene #21: 'del_1p36.32' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 2 65
DEL PEAK 1(1P36.32) MUTATED 9 2 35
DEL PEAK 1(1P36.32) WILD-TYPE 73 0 30

Figure S32.  Get High-res Image Gene #21: 'del_1p36.32' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.19e-07 (Fisher's exact test), Q value = 0.00028

Table S33.  Gene #21: 'del_1p36.32' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 62 65 22
DEL PEAK 1(1P36.32) MUTATED 34 9 3
DEL PEAK 1(1P36.32) WILD-TYPE 28 56 19

Figure S33.  Get High-res Image Gene #21: 'del_1p36.32' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_1p36.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.48e-09 (Fisher's exact test), Q value = 1.6e-06

Table S34.  Gene #21: 'del_1p36.32' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 2 65 82
DEL PEAK 1(1P36.32) MUTATED 2 35 9
DEL PEAK 1(1P36.32) WILD-TYPE 0 30 73

Figure S34.  Get High-res Image Gene #21: 'del_1p36.32' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1q44' versus 'CN_CNMF'

P value = 1.19e-05 (Fisher's exact test), Q value = 0.0051

Table S35.  Gene #23: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 55 54
DEL PEAK 3(1Q44) MUTATED 15 27 5
DEL PEAK 3(1Q44) WILD-TYPE 26 28 49

Figure S35.  Get High-res Image Gene #23: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

'del_2p25.3' versus 'METHLYATION_CNMF'

P value = 2.29e-05 (Chi-square test), Q value = 0.0098

Table S36.  Gene #24: 'del_2p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 30 28 15 21 18 35 3
DEL PEAK 4(2P25.3) MUTATED 3 10 1 7 6 22 3
DEL PEAK 4(2P25.3) WILD-TYPE 27 18 14 14 12 13 0

Figure S36.  Get High-res Image Gene #24: 'del_2p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2p25.3' versus 'MRNASEQ_CNMF'

P value = 0.000317 (Fisher's exact test), Q value = 0.13

Table S37.  Gene #24: 'del_2p25.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 30 32
DEL PEAK 4(2P25.3) MUTATED 6 10 19
DEL PEAK 4(2P25.3) WILD-TYPE 35 20 13

Figure S37.  Get High-res Image Gene #24: 'del_2p25.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_2p25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.79e-06 (Fisher's exact test), Q value = 0.0021

Table S38.  Gene #24: 'del_2p25.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 53 4
DEL PEAK 4(2P25.3) MUTATED 27 8 0
DEL PEAK 4(2P25.3) WILD-TYPE 19 45 4

Figure S38.  Get High-res Image Gene #24: 'del_2p25.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_2p25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.81e-05 (Fisher's exact test), Q value = 0.036

Table S39.  Gene #24: 'del_2p25.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 2 65
DEL PEAK 4(2P25.3) MUTATED 17 0 34
DEL PEAK 4(2P25.3) WILD-TYPE 65 2 31

Figure S39.  Get High-res Image Gene #24: 'del_2p25.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_2p25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.81e-05 (Fisher's exact test), Q value = 0.036

Table S40.  Gene #24: 'del_2p25.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 2 65 82
DEL PEAK 4(2P25.3) MUTATED 0 34 17
DEL PEAK 4(2P25.3) WILD-TYPE 2 31 65

Figure S40.  Get High-res Image Gene #24: 'del_2p25.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q37.3' versus 'CN_CNMF'

P value = 2.62e-08 (Fisher's exact test), Q value = 1.2e-05

Table S41.  Gene #25: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 55 54
DEL PEAK 5(2Q37.3) MUTATED 12 40 11
DEL PEAK 5(2Q37.3) WILD-TYPE 29 15 43

Figure S41.  Get High-res Image Gene #25: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.3' versus 'CN_CNMF'

P value = 1.21e-08 (Fisher's exact test), Q value = 5.4e-06

Table S42.  Gene #26: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 55 54
DEL PEAK 6(2Q37.3) MUTATED 13 41 11
DEL PEAK 6(2Q37.3) WILD-TYPE 28 14 43

Figure S42.  Get High-res Image Gene #26: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p21.31' versus 'METHLYATION_CNMF'

P value = 0.00019 (Chi-square test), Q value = 0.077

Table S43.  Gene #27: 'del_3p21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 30 28 15 21 18 35 3
DEL PEAK 7(3P21.31) MUTATED 4 14 5 7 2 1 0
DEL PEAK 7(3P21.31) WILD-TYPE 26 14 10 14 16 34 3

Figure S43.  Get High-res Image Gene #27: 'del_3p21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000343 (Fisher's exact test), Q value = 0.14

Table S44.  Gene #27: 'del_3p21.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 53 4
DEL PEAK 7(3P21.31) MUTATED 3 20 0
DEL PEAK 7(3P21.31) WILD-TYPE 43 33 4

Figure S44.  Get High-res Image Gene #27: 'del_3p21.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_4q35.1' versus 'CN_CNMF'

P value = 1.3e-05 (Fisher's exact test), Q value = 0.0056

Table S45.  Gene #29: 'del_4q35.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 55 54
DEL PEAK 9(4Q35.1) MUTATED 14 33 9
DEL PEAK 9(4Q35.1) WILD-TYPE 27 22 45

Figure S45.  Get High-res Image Gene #29: 'del_4q35.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q14.1' versus 'CN_CNMF'

P value = 0.000574 (Fisher's exact test), Q value = 0.23

Table S46.  Gene #31: 'del_6q14.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 55 54
DEL PEAK 11(6Q14.1) MUTATED 9 26 8
DEL PEAK 11(6Q14.1) WILD-TYPE 32 29 46

Figure S46.  Get High-res Image Gene #31: 'del_6q14.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p24.3' versus 'CN_CNMF'

P value = 0.000266 (Fisher's exact test), Q value = 0.11

Table S47.  Gene #34: 'del_9p24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 55 54
DEL PEAK 14(9P24.3) MUTATED 25 22 11
DEL PEAK 14(9P24.3) WILD-TYPE 16 33 43

Figure S47.  Get High-res Image Gene #34: 'del_9p24.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000341 (Fisher's exact test), Q value = 0.14

Table S48.  Gene #34: 'del_9p24.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 2 65
DEL PEAK 14(9P24.3) MUTATED 41 2 15
DEL PEAK 14(9P24.3) WILD-TYPE 41 0 50

Figure S48.  Get High-res Image Gene #34: 'del_9p24.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.16

Table S49.  Gene #35: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 55 54
DEL PEAK 15(9P21.3) MUTATED 25 26 12
DEL PEAK 15(9P21.3) WILD-TYPE 16 29 42

Figure S49.  Get High-res Image Gene #35: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'CN_CNMF'

P value = 6.14e-10 (Fisher's exact test), Q value = 2.8e-07

Table S50.  Gene #38: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 55 54
DEL PEAK 18(10Q23.31) MUTATED 7 45 32
DEL PEAK 18(10Q23.31) WILD-TYPE 34 10 22

Figure S50.  Get High-res Image Gene #38: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 3.5e-10 (Chi-square test), Q value = 1.6e-07

Table S51.  Gene #38: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 30 28 15 21 18 35 3
DEL PEAK 18(10Q23.31) MUTATED 5 12 5 18 8 33 3
DEL PEAK 18(10Q23.31) WILD-TYPE 25 16 10 3 10 2 0

Figure S51.  Get High-res Image Gene #38: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 3.76e-09 (Fisher's exact test), Q value = 1.7e-06

Table S52.  Gene #38: 'del_10q23.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 30 32
DEL PEAK 18(10Q23.31) MUTATED 10 17 30
DEL PEAK 18(10Q23.31) WILD-TYPE 31 13 2

Figure S52.  Get High-res Image Gene #38: 'del_10q23.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.3e-07 (Fisher's exact test), Q value = 0.00015

Table S53.  Gene #38: 'del_10q23.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 53 4
DEL PEAK 18(10Q23.31) MUTATED 38 19 0
DEL PEAK 18(10Q23.31) WILD-TYPE 8 34 4

Figure S53.  Get High-res Image Gene #38: 'del_10q23.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000606 (Fisher's exact test), Q value = 0.24

Table S54.  Gene #38: 'del_10q23.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 2 65
DEL PEAK 18(10Q23.31) MUTATED 35 2 46
DEL PEAK 18(10Q23.31) WILD-TYPE 47 0 19

Figure S54.  Get High-res Image Gene #38: 'del_10q23.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000606 (Fisher's exact test), Q value = 0.24

Table S55.  Gene #38: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 2 65 82
DEL PEAK 18(10Q23.31) MUTATED 2 46 35
DEL PEAK 18(10Q23.31) WILD-TYPE 0 19 47

Figure S55.  Get High-res Image Gene #38: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 4.79e-05 (Fisher's exact test), Q value = 0.02

Table S56.  Gene #39: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 55 54
DEL PEAK 19(11P15.5) MUTATED 20 35 12
DEL PEAK 19(11P15.5) WILD-TYPE 21 20 42

Figure S56.  Get High-res Image Gene #39: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q24.3' versus 'CN_CNMF'

P value = 2.43e-06 (Fisher's exact test), Q value = 0.0011

Table S57.  Gene #40: 'del_11q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 55 54
DEL PEAK 20(11Q24.3) MUTATED 24 32 9
DEL PEAK 20(11Q24.3) WILD-TYPE 17 23 45

Figure S57.  Get High-res Image Gene #40: 'del_11q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p13.1' versus 'CN_CNMF'

P value = 5.89e-05 (Fisher's exact test), Q value = 0.025

Table S58.  Gene #41: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 55 54
DEL PEAK 21(12P13.1) MUTATED 14 30 8
DEL PEAK 21(12P13.1) WILD-TYPE 27 25 46

Figure S58.  Get High-res Image Gene #41: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p13.1' versus 'METHLYATION_CNMF'

P value = 7.32e-05 (Chi-square test), Q value = 0.03

Table S59.  Gene #41: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 30 28 15 21 18 35 3
DEL PEAK 21(12P13.1) MUTATED 4 18 2 13 4 10 1
DEL PEAK 21(12P13.1) WILD-TYPE 26 10 13 8 14 25 2

Figure S59.  Get High-res Image Gene #41: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q14.2' versus 'CN_CNMF'

P value = 6.33e-07 (Fisher's exact test), Q value = 0.00028

Table S60.  Gene #43: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 55 54
DEL PEAK 23(13Q14.2) MUTATED 21 52 33
DEL PEAK 23(13Q14.2) WILD-TYPE 20 3 21

Figure S60.  Get High-res Image Gene #43: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 7.15e-07 (Chi-square test), Q value = 0.00032

Table S61.  Gene #43: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 30 28 15 21 18 35 3
DEL PEAK 23(13Q14.2) MUTATED 11 21 7 19 11 34 3
DEL PEAK 23(13Q14.2) WILD-TYPE 19 7 8 2 7 1 0

Figure S61.  Get High-res Image Gene #43: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 2.08e-05 (Fisher's exact test), Q value = 0.0089

Table S62.  Gene #43: 'del_13q14.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 30 32
DEL PEAK 23(13Q14.2) MUTATED 19 24 30
DEL PEAK 23(13Q14.2) WILD-TYPE 22 6 2

Figure S62.  Get High-res Image Gene #43: 'del_13q14.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.37e-06 (Fisher's exact test), Q value = 0.0019

Table S63.  Gene #43: 'del_13q14.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 53 4
DEL PEAK 23(13Q14.2) MUTATED 42 31 0
DEL PEAK 23(13Q14.2) WILD-TYPE 4 22 4

Figure S63.  Get High-res Image Gene #43: 'del_13q14.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_16q12.1' versus 'CN_CNMF'

P value = 4.93e-05 (Fisher's exact test), Q value = 0.021

Table S64.  Gene #46: 'del_16q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 55 54
DEL PEAK 26(16Q12.1) MUTATED 13 42 28
DEL PEAK 26(16Q12.1) WILD-TYPE 28 13 26

Figure S64.  Get High-res Image Gene #46: 'del_16q12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q12.1' versus 'METHLYATION_CNMF'

P value = 0.000406 (Chi-square test), Q value = 0.16

Table S65.  Gene #46: 'del_16q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 30 28 15 21 18 35 3
DEL PEAK 26(16Q12.1) MUTATED 6 17 6 15 11 26 2
DEL PEAK 26(16Q12.1) WILD-TYPE 24 11 9 6 7 9 1

Figure S65.  Get High-res Image Gene #46: 'del_16q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p13.1' versus 'CN_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.17

Table S66.  Gene #47: 'del_17p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 55 54
DEL PEAK 27(17P13.1) MUTATED 9 33 29
DEL PEAK 27(17P13.1) WILD-TYPE 32 22 25

Figure S66.  Get High-res Image Gene #47: 'del_17p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.1' versus 'MRNASEQ_CNMF'

P value = 3.34e-05 (Fisher's exact test), Q value = 0.014

Table S67.  Gene #47: 'del_17p13.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 30 32
DEL PEAK 27(17P13.1) MUTATED 8 13 23
DEL PEAK 27(17P13.1) WILD-TYPE 33 17 9

Figure S67.  Get High-res Image Gene #47: 'del_17p13.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_17p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000263 (Fisher's exact test), Q value = 0.11

Table S68.  Gene #47: 'del_17p13.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 53 4
DEL PEAK 27(17P13.1) MUTATED 29 15 0
DEL PEAK 27(17P13.1) WILD-TYPE 17 38 4

Figure S68.  Get High-res Image Gene #47: 'del_17p13.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_17q11.2' versus 'CN_CNMF'

P value = 3.5e-06 (Fisher's exact test), Q value = 0.0015

Table S69.  Gene #48: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 55 54
DEL PEAK 28(17Q11.2) MUTATED 14 27 4
DEL PEAK 28(17Q11.2) WILD-TYPE 27 28 50

Figure S69.  Get High-res Image Gene #48: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q11.2' versus 'METHLYATION_CNMF'

P value = 0.00012 (Chi-square test), Q value = 0.049

Table S70.  Gene #48: 'del_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 30 28 15 21 18 35 3
DEL PEAK 28(17Q11.2) MUTATED 5 15 7 11 0 6 1
DEL PEAK 28(17Q11.2) WILD-TYPE 25 13 8 10 18 29 2

Figure S70.  Get High-res Image Gene #48: 'del_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 7.93e-05 (Chi-square test), Q value = 0.033

Table S71.  Gene #51: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 30 28 15 21 18 35 3
DEL PEAK 31(19P13.3) MUTATED 1 4 5 11 6 15 3
DEL PEAK 31(19P13.3) WILD-TYPE 29 24 10 10 12 20 0

Figure S71.  Get High-res Image Gene #51: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.31' versus 'CN_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.13

Table S72.  Gene #55: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 55 54
DEL PEAK 35(22Q13.31) MUTATED 15 29 9
DEL PEAK 35(22Q13.31) WILD-TYPE 26 26 45

Figure S72.  Get High-res Image Gene #55: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq21.1' versus 'METHLYATION_CNMF'

P value = 0.00013 (Chi-square test), Q value = 0.053

Table S73.  Gene #57: 'del_xq21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 30 28 15 21 18 35 3
DEL PEAK 37(XQ21.1) MUTATED 5 15 6 10 9 27 0
DEL PEAK 37(XQ21.1) WILD-TYPE 25 13 9 11 9 8 3

Figure S73.  Get High-res Image Gene #57: 'del_xq21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq27.1' versus 'CN_CNMF'

P value = 0.000611 (Fisher's exact test), Q value = 0.24

Table S74.  Gene #58: 'del_xq27.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 55 54
DEL PEAK 38(XQ27.1) MUTATED 13 38 23
DEL PEAK 38(XQ27.1) WILD-TYPE 28 17 31

Figure S74.  Get High-res Image Gene #58: 'del_xq27.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq27.1' versus 'METHLYATION_CNMF'

P value = 0.000303 (Chi-square test), Q value = 0.12

Table S75.  Gene #58: 'del_xq27.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 30 28 15 21 18 35 3
DEL PEAK 38(XQ27.1) MUTATED 7 13 4 11 9 27 3
DEL PEAK 38(XQ27.1) WILD-TYPE 23 15 11 10 9 8 0

Figure S75.  Get High-res Image Gene #58: 'del_xq27.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq27.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.2

Table S76.  Gene #58: 'del_xq27.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 53 4
DEL PEAK 38(XQ27.1) MUTATED 33 22 0
DEL PEAK 38(XQ27.1) WILD-TYPE 13 31 4

Figure S76.  Get High-res Image Gene #58: 'del_xq27.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

  • Molecular subtype file = SARC-TP.transferedmergedcluster.txt

  • Number of patients = 150

  • Number of significantly focal cnvs = 58

  • Number of molecular subtypes = 8

  • 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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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