Correlation between copy number variation genes (focal events) and molecular subtypes
Esophageal Carcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1TT4PPJ
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/C1TT4PPJ
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 75 focal events and 8 molecular subtypes across 126 patients, 44 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_3q26.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_11q13.3 cnv correlated to 'CN_CNMF'.

  • amp_12p13.33 cnv correlated to 'CN_CNMF'.

  • del_2q22.1 cnv correlated to 'METHLYATION_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • del_3p25.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_3p14.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_3p14.2 cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_8p23.2 cnv correlated to 'CN_CNMF'.

  • del_9p21.3 cnv correlated to 'CN_CNMF'.

  • del_10p11.21 cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • del_11q24.3 cnv correlated to 'CN_CNMF'.

  • del_16q23.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_17p11.2 cnv correlated to 'MIRSEQ_CNMF'.

  • del_22q11.1 cnv correlated to 'METHLYATION_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 75 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, 44 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 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 3q26 2 90 (71%) 36 1e-05
(0.006) 		1e-05
(0.006) 		0.00422
(1.00) 		0.00024
(0.135) 		1e-05
(0.006) 		1e-05
(0.006) 		1e-05
(0.006) 		1e-05
(0.006)
del 3p25 3 77 (61%) 49 2e-05
(0.0117) 		1e-05
(0.006) 		0.0684
(1.00) 		0.0151
(1.00) 		2e-05
(0.0117) 		0.00012
(0.0682) 		3e-05
(0.0174) 		3e-05
(0.0174)
del 3p14 3 89 (71%) 37 1e-05
(0.006) 		5e-05
(0.0288) 		0.0194
(1.00) 		0.00367
(1.00) 		1e-05
(0.006) 		2e-05
(0.0117) 		2e-05
(0.0117) 		2e-05
(0.0117)
del 16q23 1 53 (42%) 73 1e-05
(0.006) 		1e-05
(0.006) 		0.00125
(0.681) 		0.0062
(1.00) 		1e-05
(0.006) 		1e-05
(0.006) 		1e-05
(0.006) 		1e-05
(0.006)
del 3p14 2 89 (71%) 37 1e-05
(0.006) 		0.0011
(0.601) 		0.308
(1.00) 		0.115
(1.00) 		8e-05
(0.0457) 		6e-05
(0.0344) 		0.00011
(0.0626) 		0.0001
(0.057)
del 10p11 21 32 (25%) 94 0.00039
(0.218) 		0.00062
(0.343) 		0.11
(1.00) 		0.0148
(1.00) 		0.00012
(0.0682) 		0.00179
(0.961) 		6e-05
(0.0344) 		0.00099
(0.543)
del 22q11 1 50 (40%) 76 0.00846
(1.00) 		0.00015
(0.0847) 		0.0149
(1.00) 		0.0884
(1.00) 		0.00084
(0.462) 		0.021
(1.00) 		0.00026
(0.146) 		0.00029
(0.162)
del 2q22 1 46 (37%) 80 0.0104
(1.00) 		0.00021
(0.118) 		0.395
(1.00) 		0.3
(1.00) 		0.00072
(0.397) 		0.0015
(0.81) 		0.00012
(0.0682) 		0.00133
(0.722)
amp 11q13 3 75 (60%) 51 5e-05
(0.0288) 		0.0183
(1.00) 		0.177
(1.00) 		0.124
(1.00) 		0.00334
(1.00) 		0.0134
(1.00) 		0.0317
(1.00) 		0.0105
(1.00)
amp 12p13 33 53 (42%) 73 3e-05
(0.0174) 		0.017
(1.00) 		0.0374
(1.00) 		0.0441
(1.00) 		0.0534
(1.00) 		0.0305
(1.00) 		0.0546
(1.00) 		0.0368
(1.00)
del 8p23 2 57 (45%) 69 0.0002
(0.113) 		0.1
(1.00) 		0.0427
(1.00) 		0.265
(1.00) 		0.00987
(1.00) 		0.235
(1.00) 		0.122
(1.00) 		0.122
(1.00)
del 9p21 3 98 (78%) 28 0.00039
(0.218) 		0.322
(1.00) 		0.0453
(1.00) 		0.0209
(1.00) 		0.0245
(1.00) 		0.0727
(1.00) 		0.0983
(1.00) 		0.0352
(1.00)
del 11q24 3 56 (44%) 70 0.00022
(0.124) 		0.15
(1.00) 		0.673
(1.00) 		0.396
(1.00) 		0.0676
(1.00) 		0.123
(1.00) 		0.163
(1.00) 		0.1
(1.00)
del 17p11 2 57 (45%) 69 0.0871
(1.00) 		0.00471
(1.00) 		0.0152
(1.00) 		0.0384
(1.00) 		7e-05
(0.04) 		0.00287
(1.00) 		0.00131
(0.713) 		0.00063
(0.348)
amp 1p34 2 26 (21%) 100 0.505
(1.00) 		0.325
(1.00) 		0.811
(1.00) 		0.509
(1.00) 		0.384
(1.00) 		0.159
(1.00) 		0.265
(1.00) 		0.205
(1.00)
amp 1q21 3 65 (52%) 61 0.0007
(0.386) 		0.0321
(1.00) 		1
(1.00) 		0.754
(1.00) 		0.102
(1.00) 		0.109
(1.00) 		0.0146
(1.00) 		0.223
(1.00)
amp 2q14 2 41 (33%) 85 0.583
(1.00) 		0.368
(1.00) 		0.613
(1.00) 		0.907
(1.00) 		0.538
(1.00) 		0.507
(1.00) 		0.499
(1.00) 		0.669
(1.00)
amp 5p15 33 73 (58%) 53 0.00055
(0.306) 		0.0748
(1.00) 		0.0517
(1.00) 		0.0705
(1.00) 		0.00714
(1.00) 		0.0145
(1.00) 		0.00343
(1.00) 		0.00593
(1.00)
amp 6p21 1 43 (34%) 83 0.0105
(1.00) 		0.316
(1.00) 		0.288
(1.00) 		0.731
(1.00) 		0.0315
(1.00) 		0.0227
(1.00) 		0.0123
(1.00) 		0.0296
(1.00)
amp 6q23 3 27 (21%) 99 0.0342
(1.00) 		0.178
(1.00) 		0.00796
(1.00) 		0.0316
(1.00) 		0.154
(1.00) 		0.188
(1.00) 		0.111
(1.00) 		0.0957
(1.00)
amp 7p22 3 85 (67%) 41 0.0898
(1.00) 		0.368
(1.00) 		0.00101
(0.552) 		0.0186
(1.00) 		0.00182
(0.976) 		0.685
(1.00) 		0.0157
(1.00) 		0.272
(1.00)
amp 7p11 2 83 (66%) 43 0.148
(1.00) 		0.309
(1.00) 		0.0416
(1.00) 		0.227
(1.00) 		0.0195
(1.00) 		0.58
(1.00) 		0.0247
(1.00) 		0.325
(1.00)
amp 7q21 2 79 (63%) 47 0.0787
(1.00) 		0.0825
(1.00) 		0.982
(1.00) 		1
(1.00) 		0.188
(1.00) 		0.688
(1.00) 		0.0901
(1.00) 		0.386
(1.00)
amp 8p11 23 49 (39%) 77 0.00885
(1.00) 		0.232
(1.00) 		0.287
(1.00) 		0.235
(1.00) 		0.52
(1.00) 		0.175
(1.00) 		0.245
(1.00) 		0.0146
(1.00)
amp 8p11 21 58 (46%) 68 0.00188
(1.00) 		0.507
(1.00) 		0.252
(1.00) 		0.0865
(1.00) 		0.582
(1.00) 		0.767
(1.00) 		0.485
(1.00) 		0.189
(1.00)
amp 8q24 21 99 (79%) 27 0.00093
(0.511) 		0.0244
(1.00) 		0.173
(1.00) 		0.232
(1.00) 		0.00355
(1.00) 		0.0135
(1.00) 		0.0343
(1.00) 		0.0014
(0.757)
amp 9p13 3 27 (21%) 99 0.556
(1.00) 		0.114
(1.00) 		0.328
(1.00) 		0.262
(1.00) 		0.714
(1.00) 		0.169
(1.00) 		0.825
(1.00) 		0.886
(1.00)
amp 10p11 21 34 (27%) 92 0.581
(1.00) 		0.0171
(1.00) 		0.94
(1.00) 		0.849
(1.00) 		0.434
(1.00) 		0.823
(1.00) 		0.516
(1.00) 		0.576
(1.00)
amp 11p13 37 (29%) 89 0.939
(1.00) 		0.935
(1.00) 		0.245
(1.00) 		0.27
(1.00) 		0.538
(1.00) 		0.604
(1.00) 		0.761
(1.00) 		0.786
(1.00)
amp 12p12 1 59 (47%) 67 0.00057
(0.316) 		0.19
(1.00) 		0.358
(1.00) 		0.119
(1.00) 		0.14
(1.00) 		0.0838
(1.00) 		0.137
(1.00) 		0.0746
(1.00)
amp 13q22 1 41 (33%) 85 0.122
(1.00) 		0.173
(1.00) 		0.306
(1.00) 		0.0712
(1.00) 		0.00445
(1.00) 		0.0726
(1.00) 		0.00797
(1.00) 		0.0202
(1.00)
amp 15q26 3 42 (33%) 84 0.127
(1.00) 		0.0129
(1.00) 		0.307
(1.00) 		0.249
(1.00) 		0.00502
(1.00) 		0.0269
(1.00) 		0.006
(1.00) 		0.00222
(1.00)
amp 17q12 46 (37%) 80 0.00413
(1.00) 		0.268
(1.00) 		0.356
(1.00) 		0.278
(1.00) 		0.032
(1.00) 		0.352
(1.00) 		0.117
(1.00) 		0.125
(1.00)
amp 18p11 32 45 (36%) 81 0.00844
(1.00) 		0.311
(1.00) 		0.818
(1.00) 		0.812
(1.00) 		0.117
(1.00) 		0.675
(1.00) 		0.454
(1.00) 		0.52
(1.00)
amp 18q11 2 33 (26%) 93 0.0628
(1.00) 		0.013
(1.00) 		0.362
(1.00) 		0.0333
(1.00) 		0.00583
(1.00) 		0.00334
(1.00) 		0.0413
(1.00) 		0.00205
(1.00)
amp 19p13 2 22 (17%) 104 0.0596
(1.00) 		0.215
(1.00) 		0.221
(1.00) 		0.414
(1.00) 		0.174
(1.00) 		0.462
(1.00) 		0.0589
(1.00) 		0.601
(1.00)
amp 19q12 32 (25%) 94 0.00849
(1.00) 		0.19
(1.00) 		0.432
(1.00) 		0.336
(1.00) 		0.0419
(1.00) 		0.0887
(1.00) 		0.0739
(1.00) 		0.0428
(1.00)
del 1p36 13 43 (34%) 83 0.0598
(1.00) 		0.0356
(1.00) 		0.108
(1.00) 		0.0512
(1.00) 		0.0822
(1.00) 		0.0875
(1.00) 		0.0101
(1.00) 		0.25
(1.00)
del 1p13 2 44 (35%) 82 0.00771
(1.00) 		0.391
(1.00) 		0.259
(1.00) 		0.357
(1.00) 		0.959
(1.00) 		0.115
(1.00) 		0.702
(1.00) 		0.838
(1.00)
del 1q44 15 (12%) 111 0.734
(1.00) 		0.674
(1.00) 		0.262
(1.00) 		0.298
(1.00) 		0.827
(1.00) 		0.662
(1.00) 		0.461
(1.00) 		0.342
(1.00)
del 2q33 3 25 (20%) 101 0.846
(1.00) 		0.109
(1.00) 		0.265
(1.00) 		0.358
(1.00) 		0.0996
(1.00) 		0.056
(1.00) 		0.177
(1.00) 		0.0551
(1.00)
del 3q11 1 18 (14%) 108 0.95
(1.00) 		1
(1.00) 		0.462
(1.00) 		0.138
(1.00) 		0.923
(1.00) 		0.908
(1.00) 		0.595
(1.00) 		0.924
(1.00)
del 3q26 31 11 (9%) 115 0.0683
(1.00) 		0.0189
(1.00) 		0.0676
(1.00) 		0.0966
(1.00) 		0.0148
(1.00) 		0.0122
(1.00) 		0.00692
(1.00) 		0.00165
(0.889)
del 4p15 2 68 (54%) 58 0.0135
(1.00) 		0.226
(1.00) 		0.176
(1.00) 		0.375
(1.00) 		0.00784
(1.00) 		0.594
(1.00) 		0.00435
(1.00) 		0.0906
(1.00)
del 4q21 23 60 (48%) 66 0.00379
(1.00) 		0.18
(1.00) 		0.0519
(1.00) 		0.521
(1.00) 		0.08
(1.00) 		0.509
(1.00) 		0.0173
(1.00) 		0.0627
(1.00)
del 4q22 1 67 (53%) 59 0.00353
(1.00) 		0.519
(1.00) 		0.0325
(1.00) 		0.484
(1.00) 		0.0585
(1.00) 		0.637
(1.00) 		0.0395
(1.00) 		0.174
(1.00)
del 4q31 3 65 (52%) 61 0.0144
(1.00) 		0.0495
(1.00) 		0.188
(1.00) 		0.592
(1.00) 		0.0132
(1.00) 		0.194
(1.00) 		0.0117
(1.00) 		0.0503
(1.00)
del 5q11 2 72 (57%) 54 0.0633
(1.00) 		0.00518
(1.00) 		0.716
(1.00) 		0.655
(1.00) 		0.00905
(1.00) 		0.0422
(1.00) 		0.222
(1.00) 		0.139
(1.00)
del 5q15 72 (57%) 54 0.0764
(1.00) 		0.0513
(1.00) 		0.915
(1.00) 		1
(1.00) 		0.00552
(1.00) 		0.0766
(1.00) 		0.249
(1.00) 		0.21
(1.00)
del 6p25 3 45 (36%) 81 0.0582
(1.00) 		0.172
(1.00) 		0.675
(1.00) 		0.586
(1.00) 		0.198
(1.00) 		0.00886
(1.00) 		0.278
(1.00) 		0.135
(1.00)
del 6q16 3 40 (32%) 86 0.208
(1.00) 		0.635
(1.00) 		0.372
(1.00) 		0.405
(1.00) 		0.227
(1.00) 		0.412
(1.00) 		0.455
(1.00) 		0.698
(1.00)
del 6q26 36 (29%) 90 0.112
(1.00) 		0.482
(1.00) 		0.0708
(1.00) 		0.145
(1.00) 		0.0981
(1.00) 		0.263
(1.00) 		0.203
(1.00) 		0.433
(1.00)
del 7q31 1 34 (27%) 92 0.562
(1.00) 		0.108
(1.00) 		0.319
(1.00) 		0.847
(1.00) 		0.437
(1.00) 		0.562
(1.00) 		0.269
(1.00) 		0.404
(1.00)
del 7q36 2 41 (33%) 85 0.634
(1.00) 		0.332
(1.00) 		0.146
(1.00) 		1
(1.00) 		0.288
(1.00) 		0.473
(1.00) 		0.193
(1.00) 		0.956
(1.00)
del 10p15 1 35 (28%) 91 0.094
(1.00) 		0.396
(1.00) 		0.536
(1.00) 		0.229
(1.00) 		0.312
(1.00) 		0.0555
(1.00) 		0.164
(1.00) 		0.167
(1.00)
del 10q22 3 39 (31%) 87 0.0241
(1.00) 		0.0167
(1.00) 		0.208
(1.00) 		0.124
(1.00) 		0.0603
(1.00) 		0.0253
(1.00) 		0.0731
(1.00) 		0.0734
(1.00)
del 10q23 31 47 (37%) 79 0.174
(1.00) 		0.118
(1.00) 		0.539
(1.00) 		0.509
(1.00) 		0.477
(1.00) 		0.248
(1.00) 		0.362
(1.00) 		0.626
(1.00)
del 11p15 4 54 (43%) 72 0.121
(1.00) 		0.278
(1.00) 		0.0645
(1.00) 		0.0459
(1.00) 		0.887
(1.00) 		0.235
(1.00) 		0.717
(1.00) 		0.437
(1.00)
del 12q21 2 29 (23%) 97 0.743
(1.00) 		0.191
(1.00) 		0.208
(1.00) 		0.164
(1.00) 		0.225
(1.00) 		0.18
(1.00) 		0.33
(1.00) 		0.227
(1.00)
del 13q12 11 56 (44%) 70 0.00509
(1.00) 		0.0229
(1.00) 		0.0227
(1.00) 		0.0617
(1.00) 		0.00507
(1.00) 		0.0129
(1.00) 		0.0178
(1.00) 		0.00955
(1.00)
del 13q14 2 59 (47%) 67 0.0106
(1.00) 		0.00525
(1.00) 		0.0262
(1.00) 		0.0432
(1.00) 		0.00982
(1.00) 		0.0306
(1.00) 		0.0288
(1.00) 		0.0275
(1.00)
del 13q21 2 51 (40%) 75 0.0422
(1.00) 		0.111
(1.00) 		0.34
(1.00) 		0.458
(1.00) 		0.0727
(1.00) 		0.149
(1.00) 		0.201
(1.00) 		0.123
(1.00)
del 14q31 1 44 (35%) 82 0.00363
(1.00) 		0.00325
(1.00) 		0.0208
(1.00) 		0.0147
(1.00) 		0.014
(1.00) 		0.00405
(1.00) 		0.00487
(1.00) 		0.00631
(1.00)
del 15q11 2 41 (33%) 85 0.414
(1.00) 		0.305
(1.00) 		0.801
(1.00) 		0.899
(1.00) 		0.514
(1.00) 		0.324
(1.00) 		0.317
(1.00) 		0.174
(1.00)
del 17q25 3 28 (22%) 98 0.796
(1.00) 		0.612
(1.00) 		0.166
(1.00) 		1
(1.00) 		0.215
(1.00) 		0.775
(1.00) 		0.232
(1.00) 		0.796
(1.00)
del 18q12 2 71 (56%) 55 0.507
(1.00) 		0.0748
(1.00) 		0.114
(1.00) 		0.151
(1.00) 		0.138
(1.00) 		0.105
(1.00) 		0.0746
(1.00) 		0.146
(1.00)
del 18q21 2 77 (61%) 49 0.677
(1.00) 		0.0241
(1.00) 		0.296
(1.00) 		0.36
(1.00) 		0.062
(1.00) 		0.197
(1.00) 		0.0583
(1.00) 		0.152
(1.00)
del 19p13 3 56 (44%) 70 0.0133
(1.00) 		0.598
(1.00) 		0.747
(1.00) 		0.745
(1.00) 		0.0725
(1.00) 		0.0955
(1.00) 		0.0716
(1.00) 		0.253
(1.00)
del 19q13 31 36 (29%) 90 0.0531
(1.00) 		0.0602
(1.00) 		0.333
(1.00) 		0.122
(1.00) 		0.101
(1.00) 		0.074
(1.00) 		0.12
(1.00) 		0.0533
(1.00)
del 20p12 1 23 (18%) 103 0.393
(1.00) 		0.629
(1.00) 		0.58
(1.00) 		0.162
(1.00) 		0.293
(1.00) 		0.0738
(1.00) 		0.471
(1.00) 		0.135
(1.00)
del 21q11 2 75 (60%) 51 0.28
(1.00) 		0.0953
(1.00) 		0.316
(1.00) 		0.247
(1.00) 		0.0475
(1.00) 		0.16
(1.00) 		0.101
(1.00) 		0.0827
(1.00)
del 21q22 12 73 (58%) 53 0.428
(1.00) 		0.0173
(1.00) 		0.0159
(1.00) 		0.00526
(1.00) 		0.0202
(1.00) 		0.151
(1.00) 		0.00933
(1.00) 		0.0233
(1.00)
del xp21 1 50 (40%) 76 0.0132
(1.00) 		0.0557
(1.00) 		0.0481
(1.00) 		0.382
(1.00) 		0.0839
(1.00) 		0.0692
(1.00) 		0.0387
(1.00) 		0.0553
(1.00)
del xp11 3 52 (41%) 74 0.0248
(1.00) 		0.116
(1.00) 		0.0588
(1.00) 		0.0904
(1.00) 		0.00136
(0.737) 		0.00177
(0.952) 		0.0034
(1.00) 		0.00239
(1.00)
del xq21 33 26 (21%) 100 0.671
(1.00) 		0.273
(1.00) 		0.534
(1.00) 		0.125
(1.00) 		0.126
(1.00) 		0.103
(1.00) 		0.264
(1.00) 		0.207
(1.00)
'amp_3q26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S1.  Gene #4: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 52 32
AMP PEAK 4(3Q26.2) MUTATED 15 52 23
AMP PEAK 4(3Q26.2) WILD-TYPE 27 0 9

Figure S1.  Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S2.  Gene #4: 'amp_3q26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 25 60
AMP PEAK 4(3Q26.2) MUTATED 19 15 56
AMP PEAK 4(3Q26.2) WILD-TYPE 22 10 4

Figure S2.  Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.13

Table S3.  Gene #4: 'amp_3q26.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 20 27 8
AMP PEAK 4(3Q26.2) MUTATED 15 18 13 7
AMP PEAK 4(3Q26.2) WILD-TYPE 0 2 14 1

Figure S3.  Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S4.  Gene #4: 'amp_3q26.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 68 10
AMP PEAK 4(3Q26.2) MUTATED 22 62 5
AMP PEAK 4(3Q26.2) WILD-TYPE 25 6 5

Figure S4.  Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_3q26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S5.  Gene #4: 'amp_3q26.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 15 43 31
AMP PEAK 4(3Q26.2) MUTATED 17 5 41 26
AMP PEAK 4(3Q26.2) WILD-TYPE 19 10 2 5

Figure S5.  Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S6.  Gene #4: 'amp_3q26.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 64 16
AMP PEAK 4(3Q26.2) MUTATED 21 59 9
AMP PEAK 4(3Q26.2) WILD-TYPE 24 5 7

Figure S6.  Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S7.  Gene #4: 'amp_3q26.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 10 75
AMP PEAK 4(3Q26.2) MUTATED 19 3 67
AMP PEAK 4(3Q26.2) WILD-TYPE 21 7 8

Figure S7.  Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q13.3' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.029

Table S8.  Gene #17: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 52 32
AMP PEAK 17(11Q13.3) MUTATED 19 43 13
AMP PEAK 17(11Q13.3) WILD-TYPE 23 9 19

Figure S8.  Get High-res Image Gene #17: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12p13.33' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S9.  Gene #18: 'amp_12p13.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 52 32
AMP PEAK 18(12P13.33) MUTATED 7 32 14
AMP PEAK 18(12P13.33) WILD-TYPE 35 20 18

Figure S9.  Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.12

Table S10.  Gene #30: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 25 60
DEL PEAK 4(2Q22.1) MUTATED 7 6 33
DEL PEAK 4(2Q22.1) WILD-TYPE 34 19 27

Figure S10.  Get High-res Image Gene #30: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.068

Table S11.  Gene #30: 'del_2q22.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 64 16
DEL PEAK 4(2Q22.1) MUTATED 9 35 2
DEL PEAK 4(2Q22.1) WILD-TYPE 36 29 14

Figure S11.  Get High-res Image Gene #30: 'del_2q22.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_3p25.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S12.  Gene #32: 'del_3p25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 52 32
DEL PEAK 6(3P25.3) MUTATED 19 44 14
DEL PEAK 6(3P25.3) WILD-TYPE 23 8 18

Figure S12.  Get High-res Image Gene #32: 'del_3p25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p25.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S13.  Gene #32: 'del_3p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 25 60
DEL PEAK 6(3P25.3) MUTATED 15 13 49
DEL PEAK 6(3P25.3) WILD-TYPE 26 12 11

Figure S13.  Get High-res Image Gene #32: 'del_3p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p25.3' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S14.  Gene #32: 'del_3p25.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 68 10
DEL PEAK 6(3P25.3) MUTATED 19 54 4
DEL PEAK 6(3P25.3) WILD-TYPE 28 14 6

Figure S14.  Get High-res Image Gene #32: 'del_3p25.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3p25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.068

Table S15.  Gene #32: 'del_3p25.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 15 43 31
DEL PEAK 6(3P25.3) MUTATED 14 5 34 24
DEL PEAK 6(3P25.3) WILD-TYPE 22 10 9 7

Figure S15.  Get High-res Image Gene #32: 'del_3p25.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3p25.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S16.  Gene #32: 'del_3p25.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 64 16
DEL PEAK 6(3P25.3) MUTATED 18 52 7
DEL PEAK 6(3P25.3) WILD-TYPE 27 12 9

Figure S16.  Get High-res Image Gene #32: 'del_3p25.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_3p25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S17.  Gene #32: 'del_3p25.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 10 75
DEL PEAK 6(3P25.3) MUTATED 15 4 58
DEL PEAK 6(3P25.3) WILD-TYPE 25 6 17

Figure S17.  Get High-res Image Gene #32: 'del_3p25.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p14.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S18.  Gene #33: 'del_3p14.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 52 32
DEL PEAK 7(3P14.3) MUTATED 22 50 17
DEL PEAK 7(3P14.3) WILD-TYPE 20 2 15

Figure S18.  Get High-res Image Gene #33: 'del_3p14.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p14.3' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.029

Table S19.  Gene #33: 'del_3p14.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 25 60
DEL PEAK 7(3P14.3) MUTATED 19 18 52
DEL PEAK 7(3P14.3) WILD-TYPE 22 7 8

Figure S19.  Get High-res Image Gene #33: 'del_3p14.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p14.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S20.  Gene #33: 'del_3p14.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 68 10
DEL PEAK 7(3P14.3) MUTATED 23 60 6
DEL PEAK 7(3P14.3) WILD-TYPE 24 8 4

Figure S20.  Get High-res Image Gene #33: 'del_3p14.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3p14.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S21.  Gene #33: 'del_3p14.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 15 43 31
DEL PEAK 7(3P14.3) MUTATED 18 6 39 26
DEL PEAK 7(3P14.3) WILD-TYPE 18 9 4 5

Figure S21.  Get High-res Image Gene #33: 'del_3p14.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S22.  Gene #33: 'del_3p14.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 64 16
DEL PEAK 7(3P14.3) MUTATED 22 57 10
DEL PEAK 7(3P14.3) WILD-TYPE 23 7 6

Figure S22.  Get High-res Image Gene #33: 'del_3p14.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_3p14.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S23.  Gene #33: 'del_3p14.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 10 75
DEL PEAK 7(3P14.3) MUTATED 19 5 65
DEL PEAK 7(3P14.3) WILD-TYPE 21 5 10

Figure S23.  Get High-res Image Gene #33: 'del_3p14.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S24.  Gene #34: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 52 32
DEL PEAK 8(3P14.2) MUTATED 21 49 19
DEL PEAK 8(3P14.2) WILD-TYPE 21 3 13

Figure S24.  Get High-res Image Gene #34: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p14.2' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.046

Table S25.  Gene #34: 'del_3p14.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 68 10
DEL PEAK 8(3P14.2) MUTATED 25 59 5
DEL PEAK 8(3P14.2) WILD-TYPE 22 9 5

Figure S25.  Get High-res Image Gene #34: 'del_3p14.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3p14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.034

Table S26.  Gene #34: 'del_3p14.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 15 43 31
DEL PEAK 8(3P14.2) MUTATED 19 6 38 26
DEL PEAK 8(3P14.2) WILD-TYPE 17 9 5 5

Figure S26.  Get High-res Image Gene #34: 'del_3p14.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.063

Table S27.  Gene #34: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 64 16
DEL PEAK 8(3P14.2) MUTATED 24 56 9
DEL PEAK 8(3P14.2) WILD-TYPE 21 8 7

Figure S27.  Get High-res Image Gene #34: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_3p14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.057

Table S28.  Gene #34: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 10 75
DEL PEAK 8(3P14.2) MUTATED 21 4 64
DEL PEAK 8(3P14.2) WILD-TYPE 19 6 11

Figure S28.  Get High-res Image Gene #34: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.11

Table S29.  Gene #48: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 52 32
DEL PEAK 22(8P23.2) MUTATED 9 32 16
DEL PEAK 22(8P23.2) WILD-TYPE 33 20 16

Figure S29.  Get High-res Image Gene #48: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.22

Table S30.  Gene #49: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 52 32
DEL PEAK 23(9P21.3) MUTATED 28 49 21
DEL PEAK 23(9P21.3) WILD-TYPE 14 3 11

Figure S30.  Get High-res Image Gene #49: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p11.21' versus 'CN_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.22

Table S31.  Gene #51: 'del_10p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 52 32
DEL PEAK 25(10P11.21) MUTATED 5 23 4
DEL PEAK 25(10P11.21) WILD-TYPE 37 29 28

Figure S31.  Get High-res Image Gene #51: 'del_10p11.21' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p11.21' versus 'MIRSEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.068

Table S32.  Gene #51: 'del_10p11.21' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 68 10
DEL PEAK 25(10P11.21) MUTATED 3 26 2
DEL PEAK 25(10P11.21) WILD-TYPE 44 42 8

Figure S32.  Get High-res Image Gene #51: 'del_10p11.21' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_10p11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.034

Table S33.  Gene #51: 'del_10p11.21' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 64 16
DEL PEAK 25(10P11.21) MUTATED 3 26 2
DEL PEAK 25(10P11.21) WILD-TYPE 42 38 14

Figure S33.  Get High-res Image Gene #51: 'del_10p11.21' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_11q24.3' versus 'CN_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.12

Table S34.  Gene #55: 'del_11q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 52 32
DEL PEAK 29(11Q24.3) MUTATED 10 34 12
DEL PEAK 29(11Q24.3) WILD-TYPE 32 18 20

Figure S34.  Get High-res Image Gene #55: 'del_11q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S35.  Gene #62: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 52 32
DEL PEAK 36(16Q23.1) MUTATED 18 10 25
DEL PEAK 36(16Q23.1) WILD-TYPE 24 42 7

Figure S35.  Get High-res Image Gene #62: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S36.  Gene #62: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 25 60
DEL PEAK 36(16Q23.1) MUTATED 31 8 14
DEL PEAK 36(16Q23.1) WILD-TYPE 10 17 46

Figure S36.  Get High-res Image Gene #62: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S37.  Gene #62: 'del_16q23.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 68 10
DEL PEAK 36(16Q23.1) MUTATED 34 17 1
DEL PEAK 36(16Q23.1) WILD-TYPE 13 51 9

Figure S37.  Get High-res Image Gene #62: 'del_16q23.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_16q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S38.  Gene #62: 'del_16q23.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 15 43 31
DEL PEAK 36(16Q23.1) MUTATED 27 8 8 9
DEL PEAK 36(16Q23.1) WILD-TYPE 9 7 35 22

Figure S38.  Get High-res Image Gene #62: 'del_16q23.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S39.  Gene #62: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 64 16
DEL PEAK 36(16Q23.1) MUTATED 34 16 2
DEL PEAK 36(16Q23.1) WILD-TYPE 11 48 14

Figure S39.  Get High-res Image Gene #62: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.006

Table S40.  Gene #62: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 10 75
DEL PEAK 36(16Q23.1) MUTATED 31 4 17
DEL PEAK 36(16Q23.1) WILD-TYPE 9 6 58

Figure S40.  Get High-res Image Gene #62: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p11.2' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.04

Table S41.  Gene #63: 'del_17p11.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 68 10
DEL PEAK 37(17P11.2) MUTATED 32 24 1
DEL PEAK 37(17P11.2) WILD-TYPE 15 44 9

Figure S41.  Get High-res Image Gene #63: 'del_17p11.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_22q11.1' versus 'METHLYATION_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.085

Table S42.  Gene #72: 'del_22q11.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 25 60
DEL PEAK 46(22Q11.1) MUTATED 27 8 15
DEL PEAK 46(22Q11.1) WILD-TYPE 14 17 45

Figure S42.  Get High-res Image Gene #72: 'del_22q11.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q11.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.15

Table S43.  Gene #72: 'del_22q11.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 64 16
DEL PEAK 46(22Q11.1) MUTATED 28 20 2
DEL PEAK 46(22Q11.1) WILD-TYPE 17 44 14

Figure S43.  Get High-res Image Gene #72: 'del_22q11.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_22q11.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.16

Table S44.  Gene #72: 'del_22q11.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 10 75
DEL PEAK 46(22Q11.1) MUTATED 26 2 22
DEL PEAK 46(22Q11.1) WILD-TYPE 14 8 53

Figure S44.  Get High-res Image Gene #72: 'del_22q11.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

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

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

  • Number of patients = 126

  • Number of significantly focal cnvs = 75

  • 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

Q value calculation

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

Download Results

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

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