Correlation between copy number variation genes (focal events) and molecular subtypes
Sarcoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
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/C13F4NKG
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 66 focal events and 8 molecular subtypes across 257 patients, 178 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1p32.1 cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_1q21.3 cnv correlated to 'CN_CNMF'.

  • amp_1q24.3 cnv correlated to 'CN_CNMF'.

  • amp_2p11.2 cnv correlated to 'CN_CNMF'.

  • amp_3p12.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_4q12 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_5p15.33 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • amp_6p21.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_6q25.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_7q31.2 cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  '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_13q34 cnv correlated to 'CN_CNMF'.

  • amp_15q26.3 cnv correlated to 'CN_CNMF'.

  • amp_17p12 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_17p11.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • amp_19p13.2 cnv correlated to 'CN_CNMF'.

  • amp_19q12 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

  • amp_21q21.1 cnv correlated to 'CN_CNMF'.

  • amp_xp21.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • amp_xq21.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

  • del_1q44 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_2p25.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_2q37.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • del_2q37.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • del_3p21.31 cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_3q29 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_4q35.1 cnv correlated to 'CN_CNMF'.

  • del_6p25.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • del_7q36.3 cnv correlated to 'CN_CNMF'.

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

  • del_9p21.3 cnv correlated to 'MIRSEQ_MATURE_CNMF'.

  • del_9q34.3 cnv correlated to 'CN_CNMF'.

  • del_10p15.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

  • del_10q26.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_11q24.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_12p13.1 cnv correlated to 'CN_CNMF'.

  • del_12q12 cnv correlated to 'CN_CNMF'.

  • del_12q24.33 cnv correlated to 'CN_CNMF'.

  • del_13q14.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_14q24.1 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • del_16q11.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_17p13.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_17q11.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_17q25.3 cnv correlated to 'CN_CNMF'.

  • del_18q23 cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_19p13.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • del_19q13.43 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_21q11.2 cnv correlated to 'CN_CNMF'.

  • del_22q13.32 cnv correlated to 'CN_CNMF'.

  • del_xp21.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_xq21.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_xq22.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 66 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, 178 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 12q15 94 (37%) 163 1e-05
(0.00528)
1e-05
(0.00528)
1e-05
(0.00528)
1e-05
(0.00528)
1e-05
(0.00528)
1e-05
(0.00528)
1e-05
(0.00528)
1e-05
(0.00528)
del 1p36 32 69 (27%) 188 1e-05
(0.00528)
1e-05
(0.00528)
1e-05
(0.00528)
1e-05
(0.00528)
1e-05
(0.00528)
1e-05
(0.00528)
1e-05
(0.00528)
0.00021
(0.0817)
del 10q23 31 138 (54%) 119 1e-05
(0.00528)
1e-05
(0.00528)
1e-05
(0.00528)
1e-05
(0.00528)
1e-05
(0.00528)
1e-05
(0.00528)
0.00042
(0.156)
0.00041
(0.153)
del 10q26 3 132 (51%) 125 1e-05
(0.00528)
1e-05
(0.00528)
1e-05
(0.00528)
1e-05
(0.00528)
0.00014
(0.0557)
2e-05
(0.00876)
8e-05
(0.0331)
0.00029
(0.11)
del 13q14 2 180 (70%) 77 1e-05
(0.00528)
1e-05
(0.00528)
1e-05
(0.00528)
1e-05
(0.00528)
1e-05
(0.00528)
1e-05
(0.00528)
0.00024
(0.0922)
0.00022
(0.0851)
del 16q11 2 130 (51%) 127 1e-05
(0.00528)
7e-05
(0.0293)
0.00027
(0.103)
0.00068
(0.239)
0.00303
(0.936)
0.0003
(0.114)
2e-05
(0.00876)
4e-05
(0.0171)
del 17p13 1 129 (50%) 128 1e-05
(0.00528)
1e-05
(0.00528)
1e-05
(0.00528)
4e-05
(0.0171)
3e-05
(0.013)
4e-05
(0.0171)
3e-05
(0.013)
0.00077
(0.266)
amp 6q25 1 75 (29%) 182 0.00023
(0.0885)
1e-05
(0.00528)
1e-05
(0.00528)
1e-05
(0.00528)
0.0006
(0.213)
0.0001
(0.0407)
0.00396
(1.00)
0.00812
(1.00)
del 2p25 3 94 (37%) 163 1e-05
(0.00528)
3e-05
(0.013)
1e-05
(0.00528)
0.00097
(0.328)
0.00033
(0.125)
1e-05
(0.00528)
0.00021
(0.0817)
0.00074
(0.258)
del xq21 1 114 (44%) 143 1e-05
(0.00528)
1e-05
(0.00528)
0.00033
(0.125)
0.00017
(0.067)
0.00019
(0.0741)
0.00049
(0.179)
0.0255
(1.00)
0.0303
(1.00)
del xq22 3 123 (48%) 134 1e-05
(0.00528)
1e-05
(0.00528)
1e-05
(0.00528)
2e-05
(0.00876)
0.00048
(0.176)
9e-05
(0.0371)
0.017
(1.00)
0.0338
(1.00)
del 3p21 31 65 (25%) 192 0.0101
(1.00)
1e-05
(0.00528)
1e-05
(0.00528)
1e-05
(0.00528)
0.00017
(0.067)
0.00798
(1.00)
0.00186
(0.601)
1e-05
(0.00528)
del 16q23 1 134 (52%) 123 1e-05
(0.00528)
0.00044
(0.162)
0.00118
(0.393)
0.00354
(1.00)
0.00511
(1.00)
0.00014
(0.0557)
1e-05
(0.00528)
7e-05
(0.0293)
amp 3p12 1 69 (27%) 188 0.00017
(0.067)
0.00059
(0.211)
7e-05
(0.0293)
9e-05
(0.0371)
0.506
(1.00)
0.00339
(1.00)
0.00121
(0.402)
0.00237
(0.751)
amp 4q12 78 (30%) 179 0.00036
(0.135)
0.00012
(0.0482)
1e-05
(0.00528)
0.00051
(0.185)
0.0556
(1.00)
0.0134
(1.00)
0.0474
(1.00)
0.0195
(1.00)
amp 6p21 1 60 (23%) 197 3e-05
(0.013)
1e-05
(0.00528)
0.00045
(0.165)
0.00012
(0.0482)
0.0183
(1.00)
0.0112
(1.00)
0.289
(1.00)
0.0419
(1.00)
amp 7q31 2 77 (30%) 180 0.00656
(1.00)
9e-05
(0.0371)
0.0001
(0.0407)
0.00188
(0.605)
0.00148
(0.487)
0.0457
(1.00)
5e-05
(0.0212)
0.00041
(0.153)
amp 20q13 33 98 (38%) 159 1e-05
(0.00528)
6e-05
(0.0253)
6e-05
(0.0253)
0.00117
(0.391)
0.0288
(1.00)
0.0006
(0.213)
0.0135
(1.00)
0.012
(1.00)
del 1q44 80 (31%) 177 5e-05
(0.0212)
1e-05
(0.00528)
3e-05
(0.013)
6e-05
(0.0253)
0.0163
(1.00)
0.00703
(1.00)
0.138
(1.00)
0.00554
(1.00)
del 17q11 2 81 (32%) 176 0.0001
(0.0407)
1e-05
(0.00528)
2e-05
(0.00876)
0.00013
(0.052)
0.0091
(1.00)
0.122
(1.00)
0.012
(1.00)
0.0162
(1.00)
amp 1p32 1 94 (37%) 163 0.00083
(0.284)
1e-05
(0.00528)
1e-05
(0.00528)
1e-05
(0.00528)
0.00914
(1.00)
0.00473
(1.00)
0.211
(1.00)
0.00073
(0.255)
amp 17p12 102 (40%) 155 1e-05
(0.00528)
1e-05
(0.00528)
0.00795
(1.00)
0.0001
(0.0407)
0.373
(1.00)
0.00195
(0.622)
0.0466
(1.00)
0.00977
(1.00)
del 6p25 3 81 (32%) 176 1e-05
(0.00528)
0.00059
(0.211)
0.00014
(0.0557)
0.00132
(0.437)
0.0144
(1.00)
0.0257
(1.00)
0.0359
(1.00)
0.272
(1.00)
del 8p23 3 81 (32%) 176 3e-05
(0.013)
1e-05
(0.00528)
0.00059
(0.211)
0.0022
(0.7)
0.00746
(1.00)
0.00419
(1.00)
0.00928
(1.00)
0.00106
(0.356)
del 18q23 86 (33%) 171 0.0017
(0.554)
0.00017
(0.067)
1e-05
(0.00528)
0.00349
(1.00)
0.01
(1.00)
0.146
(1.00)
0.133
(1.00)
0.00035
(0.132)
amp 5p15 33 119 (46%) 138 1e-05
(0.00528)
0.0129
(1.00)
0.0271
(1.00)
0.0005
(0.182)
0.343
(1.00)
0.0134
(1.00)
0.688
(1.00)
0.747
(1.00)
amp 17p11 2 104 (40%) 153 1e-05
(0.00528)
1e-05
(0.00528)
0.00526
(1.00)
0.00441
(1.00)
0.778
(1.00)
0.00188
(0.605)
0.0852
(1.00)
0.00578
(1.00)
amp 19q12 93 (36%) 164 1e-05
(0.00528)
7e-05
(0.0293)
0.0317
(1.00)
0.00581
(1.00)
0.693
(1.00)
0.00931
(1.00)
0.769
(1.00)
0.0264
(1.00)
amp xp21 2 97 (38%) 160 1e-05
(0.00528)
0.00027
(0.103)
0.116
(1.00)
0.00688
(1.00)
0.925
(1.00)
0.0405
(1.00)
0.304
(1.00)
0.0109
(1.00)
amp xq21 1 46 (18%) 211 0.00013
(0.052)
0.00051
(0.185)
0.0396
(1.00)
0.0237
(1.00)
0.109
(1.00)
0.405
(1.00)
0.589
(1.00)
0.586
(1.00)
del 2q37 3 108 (42%) 149 1e-05
(0.00528)
0.006
(1.00)
0.0183
(1.00)
0.00039
(0.146)
0.204
(1.00)
0.00632
(1.00)
0.0548
(1.00)
0.0492
(1.00)
del 2q37 3 110 (43%) 147 1e-05
(0.00528)
0.00098
(0.33)
0.00811
(1.00)
0.0005
(0.182)
0.631
(1.00)
0.0246
(1.00)
0.477
(1.00)
0.156
(1.00)
del 3q29 54 (21%) 203 0.00067
(0.236)
0.00022
(0.0851)
0.198
(1.00)
0.0839
(1.00)
0.301
(1.00)
0.0384
(1.00)
0.215
(1.00)
0.071
(1.00)
del 10p15 3 128 (50%) 129 1e-05
(0.00528)
1e-05
(0.00528)
0.364
(1.00)
0.00901
(1.00)
0.284
(1.00)
0.0195
(1.00)
0.727
(1.00)
0.566
(1.00)
del 11p15 5 110 (43%) 147 1e-05
(0.00528)
0.00054
(0.194)
0.487
(1.00)
0.145
(1.00)
0.477
(1.00)
0.318
(1.00)
0.737
(1.00)
0.758
(1.00)
del 11q24 2 123 (48%) 134 1e-05
(0.00528)
1e-05
(0.00528)
0.00243
(0.768)
0.00134
(0.442)
0.0545
(1.00)
0.0407
(1.00)
0.376
(1.00)
0.0329
(1.00)
del 14q24 1 80 (31%) 177 1e-05
(0.00528)
0.00078
(0.268)
0.235
(1.00)
1e-05
(0.00528)
0.108
(1.00)
0.00446
(1.00)
0.162
(1.00)
0.0257
(1.00)
del 19p13 3 70 (27%) 187 9e-05
(0.0371)
0.00181
(0.588)
0.0001
(0.0407)
0.00453
(1.00)
0.0183
(1.00)
0.00396
(1.00)
0.00114
(0.382)
0.0192
(1.00)
del 19q13 43 106 (41%) 151 1e-05
(0.00528)
0.00038
(0.142)
0.39
(1.00)
0.276
(1.00)
0.385
(1.00)
0.0333
(1.00)
0.435
(1.00)
0.00767
(1.00)
del xp21 1 55 (21%) 202 0.00043
(0.159)
0.00061
(0.215)
0.0101
(1.00)
0.0249
(1.00)
0.00858
(1.00)
0.1
(1.00)
0.32
(1.00)
0.109
(1.00)
amp 1q21 3 104 (40%) 153 1e-05
(0.00528)
0.00799
(1.00)
0.174
(1.00)
0.0919
(1.00)
0.554
(1.00)
0.132
(1.00)
0.0624
(1.00)
0.248
(1.00)
amp 1q24 3 102 (40%) 155 1e-05
(0.00528)
0.00504
(1.00)
0.0474
(1.00)
0.213
(1.00)
0.888
(1.00)
0.135
(1.00)
0.616
(1.00)
0.491
(1.00)
amp 2p11 2 64 (25%) 193 0.00054
(0.194)
0.00876
(1.00)
0.917
(1.00)
0.877
(1.00)
1
(1.00)
0.316
(1.00)
0.767
(1.00)
1
(1.00)
amp 13q34 54 (21%) 203 0.00014
(0.0557)
0.0107
(1.00)
0.219
(1.00)
0.0333
(1.00)
0.512
(1.00)
0.141
(1.00)
0.803
(1.00)
0.00977
(1.00)
amp 15q26 3 84 (33%) 173 1e-05
(0.00528)
0.00422
(1.00)
0.849
(1.00)
0.278
(1.00)
0.812
(1.00)
0.184
(1.00)
0.878
(1.00)
0.697
(1.00)
amp 19p13 2 107 (42%) 150 1e-05
(0.00528)
0.0186
(1.00)
0.0835
(1.00)
0.0493
(1.00)
0.76
(1.00)
0.267
(1.00)
0.946
(1.00)
0.0811
(1.00)
amp 21q21 1 73 (28%) 184 1e-05
(0.00528)
0.00079
(0.271)
0.0852
(1.00)
0.248
(1.00)
0.397
(1.00)
0.141
(1.00)
0.603
(1.00)
0.374
(1.00)
del 4q35 1 94 (37%) 163 1e-05
(0.00528)
0.00194
(0.621)
0.0897
(1.00)
0.0444
(1.00)
0.859
(1.00)
0.108
(1.00)
1
(1.00)
0.551
(1.00)
del 7q36 3 71 (28%) 186 2e-05
(0.00876)
0.0622
(1.00)
0.0174
(1.00)
0.157
(1.00)
0.108
(1.00)
0.00554
(1.00)
0.086
(1.00)
0.514
(1.00)
del 9p21 3 114 (44%) 143 0.0332
(1.00)
0.111
(1.00)
0.00074
(0.258)
0.00582
(1.00)
0.0251
(1.00)
0.557
(1.00)
7e-05
(0.0293)
0.0016
(0.525)
del 9q34 3 61 (24%) 196 1e-05
(0.00528)
0.00246
(0.775)
0.0254
(1.00)
0.132
(1.00)
0.00268
(0.836)
0.00271
(0.843)
0.105
(1.00)
0.0408
(1.00)
del 12p13 1 87 (34%) 170 1e-05
(0.00528)
0.00084
(0.286)
0.0313
(1.00)
0.00535
(1.00)
0.227
(1.00)
0.0337
(1.00)
0.33
(1.00)
0.33
(1.00)
del 12q12 56 (22%) 201 9e-05
(0.0371)
0.00874
(1.00)
0.0953
(1.00)
0.0158
(1.00)
0.0446
(1.00)
0.0304
(1.00)
0.108
(1.00)
0.395
(1.00)
del 12q24 33 69 (27%) 188 8e-05
(0.0331)
0.00167
(0.546)
0.725
(1.00)
0.0171
(1.00)
0.242
(1.00)
0.125
(1.00)
0.159
(1.00)
0.464
(1.00)
del 17q25 3 67 (26%) 190 1e-05
(0.00528)
0.00742
(1.00)
0.196
(1.00)
0.359
(1.00)
0.608
(1.00)
0.00782
(1.00)
0.207
(1.00)
0.104
(1.00)
del 21q11 2 51 (20%) 206 0.00044
(0.162)
0.22
(1.00)
0.0361
(1.00)
0.282
(1.00)
0.00246
(0.775)
0.955
(1.00)
0.0681
(1.00)
0.288
(1.00)
del 22q13 32 83 (32%) 174 1e-05
(0.00528)
0.0629
(1.00)
0.845
(1.00)
0.0356
(1.00)
0.287
(1.00)
0.44
(1.00)
0.946
(1.00)
0.534
(1.00)
amp 8p11 22 81 (32%) 176 0.00092
(0.313)
0.0835
(1.00)
0.00291
(0.902)
0.0362
(1.00)
0.151
(1.00)
0.0103
(1.00)
0.421
(1.00)
0.164
(1.00)
amp 8q24 21 83 (32%) 174 0.00782
(1.00)
0.0431
(1.00)
0.0338
(1.00)
0.238
(1.00)
0.539
(1.00)
0.291
(1.00)
0.174
(1.00)
0.348
(1.00)
amp 11q22 2 36 (14%) 221 0.0269
(1.00)
0.0285
(1.00)
0.0129
(1.00)
0.0532
(1.00)
0.316
(1.00)
0.00428
(1.00)
0.651
(1.00)
0.0549
(1.00)
amp 17q24 3 79 (31%) 178 0.00096
(0.325)
0.00248
(0.776)
0.0691
(1.00)
0.00477
(1.00)
0.106
(1.00)
0.153
(1.00)
0.066
(1.00)
0.256
(1.00)
del 3q13 31 51 (20%) 206 0.00665
(1.00)
0.00183
(0.593)
0.0115
(1.00)
0.0109
(1.00)
0.0177
(1.00)
0.0186
(1.00)
0.0216
(1.00)
0.0306
(1.00)
del 5p15 33 33 (13%) 224 0.243
(1.00)
0.0868
(1.00)
0.00077
(0.266)
0.00075
(0.26)
0.132
(1.00)
0.611
(1.00)
0.0495
(1.00)
0.0552
(1.00)
del 6q14 1 78 (30%) 179 0.00824
(1.00)
0.00443
(1.00)
0.231
(1.00)
0.565
(1.00)
0.453
(1.00)
0.591
(1.00)
0.0368
(1.00)
0.967
(1.00)
del 9p24 3 100 (39%) 157 0.215
(1.00)
0.732
(1.00)
0.0234
(1.00)
0.438
(1.00)
0.198
(1.00)
0.913
(1.00)
0.0671
(1.00)
0.803
(1.00)
del 21q22 3 66 (26%) 191 0.00474
(1.00)
0.0082
(1.00)
0.0208
(1.00)
0.0654
(1.00)
0.436
(1.00)
0.0572
(1.00)
0.431
(1.00)
0.48
(1.00)
'amp_1p32.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S1.  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 42 41 57 32 18 43 5
AMP PEAK 1(1P32.1) MUTATED 15 14 12 3 3 35 3
AMP PEAK 1(1P32.1) WILD-TYPE 27 27 45 29 15 8 2

Figure S1.  Get High-res Image Gene #1: 'amp_1p32.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1p32.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S2.  Gene #1: 'amp_1p32.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 68 76 63 46
AMP PEAK 1(1P32.1) MUTATED 25 16 45 8
AMP PEAK 1(1P32.1) WILD-TYPE 43 60 18 38

Figure S2.  Get High-res Image Gene #1: 'amp_1p32.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_1p32.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S3.  Gene #1: 'amp_1p32.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 22 49 28 59 29 19
AMP PEAK 1(1P32.1) MUTATED 19 8 10 7 43 6 1
AMP PEAK 1(1P32.1) WILD-TYPE 28 14 39 21 16 23 18

Figure S3.  Get High-res Image Gene #1: 'amp_1p32.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S4.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
AMP PEAK 2(1Q21.3) MUTATED 15 6 17 15 18 32 1
AMP PEAK 2(1Q21.3) WILD-TYPE 11 52 26 36 16 12 0

Figure S4.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S5.  Gene #3: 'amp_1q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
AMP PEAK 3(1Q24.3) MUTATED 13 11 20 12 14 31 1
AMP PEAK 3(1Q24.3) WILD-TYPE 13 47 23 39 20 13 0

Figure S5.  Get High-res Image Gene #3: 'amp_1q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2p11.2' versus 'CN_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.19

Table S6.  Gene #4: 'amp_2p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
AMP PEAK 4(2P11.2) MUTATED 3 5 15 12 16 13 0
AMP PEAK 4(2P11.2) WILD-TYPE 23 53 28 39 18 31 1

Figure S6.  Get High-res Image Gene #4: 'amp_2p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3p12.1' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.067

Table S7.  Gene #5: 'amp_3p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
AMP PEAK 5(3P12.1) MUTATED 11 9 9 6 14 20 0
AMP PEAK 5(3P12.1) WILD-TYPE 15 49 34 45 20 24 1

Figure S7.  Get High-res Image Gene #5: 'amp_3p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3p12.1' versus 'METHLYATION_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 0.21

Table S8.  Gene #5: 'amp_3p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
AMP PEAK 5(3P12.1) MUTATED 14 11 15 1 1 18 0
AMP PEAK 5(3P12.1) WILD-TYPE 28 30 42 31 17 25 5

Figure S8.  Get High-res Image Gene #5: 'amp_3p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3p12.1' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.029

Table S9.  Gene #5: 'amp_3p12.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 68 76 63 46
AMP PEAK 5(3P12.1) MUTATED 21 16 28 3
AMP PEAK 5(3P12.1) WILD-TYPE 47 60 35 43

Figure S9.  Get High-res Image Gene #5: 'amp_3p12.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_3p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.037

Table S10.  Gene #5: 'amp_3p12.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 22 49 28 59 29 19
AMP PEAK 5(3P12.1) MUTATED 18 7 12 2 25 4 0
AMP PEAK 5(3P12.1) WILD-TYPE 29 15 37 26 34 25 19

Figure S10.  Get High-res Image Gene #5: 'amp_3p12.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_4q12' versus 'CN_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.14

Table S11.  Gene #6: 'amp_4q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
AMP PEAK 6(4Q12) MUTATED 8 7 12 13 16 22 0
AMP PEAK 6(4Q12) WILD-TYPE 18 51 31 38 18 22 1

Figure S11.  Get High-res Image Gene #6: 'amp_4q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_4q12' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.048

Table S12.  Gene #6: 'amp_4q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
AMP PEAK 6(4Q12) MUTATED 16 12 11 5 1 23 3
AMP PEAK 6(4Q12) WILD-TYPE 26 29 46 27 17 20 2

Figure S12.  Get High-res Image Gene #6: 'amp_4q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_4q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S13.  Gene #6: 'amp_4q12' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 68 76 63 46
AMP PEAK 6(4Q12) MUTATED 26 14 32 6
AMP PEAK 6(4Q12) WILD-TYPE 42 62 31 40

Figure S13.  Get High-res Image Gene #6: 'amp_4q12' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_4q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.18

Table S14.  Gene #6: 'amp_4q12' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 22 49 28 59 29 19
AMP PEAK 6(4Q12) MUTATED 19 8 7 8 28 7 1
AMP PEAK 6(4Q12) WILD-TYPE 28 14 42 20 31 22 18

Figure S14.  Get High-res Image Gene #6: 'amp_4q12' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S15.  Gene #7: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
AMP PEAK 7(5P15.33) MUTATED 26 14 23 21 14 21 0
AMP PEAK 7(5P15.33) WILD-TYPE 0 44 20 30 20 23 1

Figure S15.  Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-04 (Fisher's exact test), Q value = 0.18

Table S16.  Gene #7: 'amp_5p15.33' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 22 49 28 59 29 19
AMP PEAK 7(5P15.33) MUTATED 33 8 23 9 32 6 7
AMP PEAK 7(5P15.33) WILD-TYPE 14 14 26 19 27 23 12

Figure S16.  Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.013

Table S17.  Gene #8: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
AMP PEAK 8(6P21.1) MUTATED 10 5 14 4 8 19 0
AMP PEAK 8(6P21.1) WILD-TYPE 16 53 29 47 26 25 1

Figure S17.  Get High-res Image Gene #8: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p21.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S18.  Gene #8: '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 42 41 57 32 18 43 5
AMP PEAK 8(6P21.1) MUTATED 20 5 5 5 0 17 3
AMP PEAK 8(6P21.1) WILD-TYPE 22 36 52 27 18 26 2

Figure S18.  Get High-res Image Gene #8: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.17

Table S19.  Gene #8: 'amp_6p21.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 68 76 63 46
AMP PEAK 8(6P21.1) MUTATED 25 7 19 9
AMP PEAK 8(6P21.1) WILD-TYPE 43 69 44 37

Figure S19.  Get High-res Image Gene #8: 'amp_6p21.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.048

Table S20.  Gene #8: 'amp_6p21.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 22 49 28 59 29 19
AMP PEAK 8(6P21.1) MUTATED 21 3 3 6 20 4 3
AMP PEAK 8(6P21.1) WILD-TYPE 26 19 46 22 39 25 16

Figure S20.  Get High-res Image Gene #8: 'amp_6p21.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_6q25.1' versus 'CN_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.089

Table S21.  Gene #9: 'amp_6q25.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
AMP PEAK 9(6Q25.1) MUTATED 10 11 23 6 10 15 0
AMP PEAK 9(6Q25.1) WILD-TYPE 16 47 20 45 24 29 1

Figure S21.  Get High-res Image Gene #9: 'amp_6q25.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q25.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S22.  Gene #9: 'amp_6q25.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
AMP PEAK 9(6Q25.1) MUTATED 27 15 7 3 1 16 1
AMP PEAK 9(6Q25.1) WILD-TYPE 15 26 50 29 17 27 4

Figure S22.  Get High-res Image Gene #9: 'amp_6q25.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q25.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S23.  Gene #9: 'amp_6q25.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 68 76 63 46
AMP PEAK 9(6Q25.1) MUTATED 38 8 20 8
AMP PEAK 9(6Q25.1) WILD-TYPE 30 68 43 38

Figure S23.  Get High-res Image Gene #9: 'amp_6q25.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_6q25.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S24.  Gene #9: 'amp_6q25.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 22 49 28 59 29 19
AMP PEAK 9(6Q25.1) MUTATED 26 13 5 8 17 3 2
AMP PEAK 9(6Q25.1) WILD-TYPE 21 9 44 20 42 26 17

Figure S24.  Get High-res Image Gene #9: 'amp_6q25.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_6q25.1' versus 'MIRSEQ_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.21

Table S25.  Gene #9: 'amp_6q25.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 47 99
AMP PEAK 9(6Q25.1) MUTATED 43 16 16
AMP PEAK 9(6Q25.1) WILD-TYPE 66 31 83

Figure S25.  Get High-res Image Gene #9: 'amp_6q25.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_6q25.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.041

Table S26.  Gene #9: 'amp_6q25.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
AMP PEAK 9(6Q25.1) MUTATED 37 14 22 2
AMP PEAK 9(6Q25.1) WILD-TYPE 45 23 92 20

Figure S26.  Get High-res Image Gene #9: 'amp_6q25.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.037

Table S27.  Gene #10: 'amp_7q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
AMP PEAK 10(7Q31.2) MUTATED 21 13 8 6 1 17 3
AMP PEAK 10(7Q31.2) WILD-TYPE 21 28 49 26 17 26 2

Figure S27.  Get High-res Image Gene #10: 'amp_7q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.041

Table S28.  Gene #10: 'amp_7q31.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 68 76 63 46
AMP PEAK 10(7Q31.2) MUTATED 28 10 27 12
AMP PEAK 10(7Q31.2) WILD-TYPE 40 66 36 34

Figure S28.  Get High-res Image Gene #10: 'amp_7q31.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.021

Table S29.  Gene #10: 'amp_7q31.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 64 45
AMP PEAK 10(7Q31.2) MUTATED 24 11 26
AMP PEAK 10(7Q31.2) WILD-TYPE 61 53 19

Figure S29.  Get High-res Image Gene #10: 'amp_7q31.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.15

Table S30.  Gene #10: 'amp_7q31.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 32 37 23 12 23 21 22
AMP PEAK 10(7Q31.2) MUTATED 11 12 5 12 1 3 12 5
AMP PEAK 10(7Q31.2) WILD-TYPE 13 20 32 11 11 20 9 17

Figure S30.  Get High-res Image Gene #10: 'amp_7q31.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q15' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S31.  Gene #14: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
AMP PEAK 14(12Q15) MUTATED 9 19 41 11 7 7 0
AMP PEAK 14(12Q15) WILD-TYPE 17 39 2 40 27 37 1

Figure S31.  Get High-res Image Gene #14: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S32.  Gene #14: 'amp_12q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
AMP PEAK 14(12Q15) MUTATED 27 25 1 13 2 14 2
AMP PEAK 14(12Q15) WILD-TYPE 15 16 56 19 16 29 3

Figure S32.  Get High-res Image Gene #14: 'amp_12q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12q15' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S33.  Gene #14: 'amp_12q15' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 68 76 63 46
AMP PEAK 14(12Q15) MUTATED 43 2 26 23
AMP PEAK 14(12Q15) WILD-TYPE 25 74 37 23

Figure S33.  Get High-res Image Gene #14: 'amp_12q15' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_12q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S34.  Gene #14: 'amp_12q15' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 22 49 28 59 29 19
AMP PEAK 14(12Q15) MUTATED 30 13 1 19 24 1 6
AMP PEAK 14(12Q15) WILD-TYPE 17 9 48 9 35 28 13

Figure S34.  Get High-res Image Gene #14: 'amp_12q15' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S35.  Gene #14: 'amp_12q15' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 47 99
AMP PEAK 14(12Q15) MUTATED 58 23 11
AMP PEAK 14(12Q15) WILD-TYPE 51 24 88

Figure S35.  Get High-res Image Gene #14: 'amp_12q15' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_12q15' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S36.  Gene #14: 'amp_12q15' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
AMP PEAK 14(12Q15) MUTATED 50 19 16 7
AMP PEAK 14(12Q15) WILD-TYPE 32 18 98 15

Figure S36.  Get High-res Image Gene #14: 'amp_12q15' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S37.  Gene #14: 'amp_12q15' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 64 45
AMP PEAK 14(12Q15) MUTATED 48 7 20
AMP PEAK 14(12Q15) WILD-TYPE 37 57 25

Figure S37.  Get High-res Image Gene #14: 'amp_12q15' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_12q15' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S38.  Gene #14: 'amp_12q15' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 32 37 23 12 23 21 22
AMP PEAK 14(12Q15) MUTATED 8 27 0 10 1 10 10 9
AMP PEAK 14(12Q15) WILD-TYPE 16 5 37 13 11 13 11 13

Figure S38.  Get High-res Image Gene #14: 'amp_12q15' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q34' versus 'CN_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.056

Table S39.  Gene #15: 'amp_13q34' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
AMP PEAK 15(13Q34) MUTATED 7 4 5 8 11 19 0
AMP PEAK 15(13Q34) WILD-TYPE 19 54 38 43 23 25 1

Figure S39.  Get High-res Image Gene #15: 'amp_13q34' versus Molecular Subtype #1: 'CN_CNMF'

'amp_15q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S40.  Gene #16: 'amp_15q26.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
AMP PEAK 16(15Q26.3) MUTATED 17 0 18 20 18 11 0
AMP PEAK 16(15Q26.3) WILD-TYPE 9 58 25 31 16 33 1

Figure S40.  Get High-res Image Gene #16: 'amp_15q26.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S41.  Gene #17: 'amp_17p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
AMP PEAK 17(17P12) MUTATED 10 4 12 21 34 20 1
AMP PEAK 17(17P12) WILD-TYPE 16 54 31 30 0 24 0

Figure S41.  Get High-res Image Gene #17: 'amp_17p12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17p12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S42.  Gene #17: 'amp_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
AMP PEAK 17(17P12) MUTATED 19 8 32 6 2 27 1
AMP PEAK 17(17P12) WILD-TYPE 23 33 25 26 16 16 4

Figure S42.  Get High-res Image Gene #17: 'amp_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.041

Table S43.  Gene #17: 'amp_17p12' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 22 49 28 59 29 19
AMP PEAK 17(17P12) MUTATED 24 2 26 10 27 11 1
AMP PEAK 17(17P12) WILD-TYPE 23 20 23 18 32 18 18

Figure S43.  Get High-res Image Gene #17: 'amp_17p12' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_17p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S44.  Gene #18: 'amp_17p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
AMP PEAK 18(17P11.2) MUTATED 12 4 11 21 33 22 1
AMP PEAK 18(17P11.2) WILD-TYPE 14 54 32 30 1 22 0

Figure S44.  Get High-res Image Gene #18: 'amp_17p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17p11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S45.  Gene #18: 'amp_17p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
AMP PEAK 18(17P11.2) MUTATED 20 7 30 7 1 30 1
AMP PEAK 18(17P11.2) WILD-TYPE 22 34 27 25 17 13 4

Figure S45.  Get High-res Image Gene #18: 'amp_17p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S46.  Gene #20: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
AMP PEAK 20(19P13.2) MUTATED 17 6 25 21 15 23 0
AMP PEAK 20(19P13.2) WILD-TYPE 9 52 18 30 19 21 1

Figure S46.  Get High-res Image Gene #20: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S47.  Gene #21: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
AMP PEAK 21(19Q12) MUTATED 17 2 20 7 21 26 0
AMP PEAK 21(19Q12) WILD-TYPE 9 56 23 44 13 18 1

Figure S47.  Get High-res Image Gene #21: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.029

Table S48.  Gene #21: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
AMP PEAK 21(19Q12) MUTATED 23 10 15 8 2 25 2
AMP PEAK 21(19Q12) WILD-TYPE 19 31 42 24 16 18 3

Figure S48.  Get High-res Image Gene #21: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S49.  Gene #22: 'amp_20q13.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
AMP PEAK 22(20Q13.33) MUTATED 18 6 22 19 15 18 0
AMP PEAK 22(20Q13.33) WILD-TYPE 8 52 21 32 19 26 1

Figure S49.  Get High-res Image Gene #22: 'amp_20q13.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.33' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.025

Table S50.  Gene #22: 'amp_20q13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
AMP PEAK 22(20Q13.33) MUTATED 25 12 13 10 3 27 1
AMP PEAK 22(20Q13.33) WILD-TYPE 17 29 44 22 15 16 4

Figure S50.  Get High-res Image Gene #22: 'amp_20q13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.025

Table S51.  Gene #22: 'amp_20q13.33' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 68 76 63 46
AMP PEAK 22(20Q13.33) MUTATED 29 16 37 15
AMP PEAK 22(20Q13.33) WILD-TYPE 39 60 26 31

Figure S51.  Get High-res Image Gene #22: 'amp_20q13.33' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_20q13.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-04 (Fisher's exact test), Q value = 0.21

Table S52.  Gene #22: 'amp_20q13.33' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
AMP PEAK 22(20Q13.33) MUTATED 43 15 38 2
AMP PEAK 22(20Q13.33) WILD-TYPE 39 22 76 20

Figure S52.  Get High-res Image Gene #22: 'amp_20q13.33' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_21q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S53.  Gene #23: 'amp_21q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
AMP PEAK 23(21Q21.1) MUTATED 19 7 12 5 16 14 0
AMP PEAK 23(21Q21.1) WILD-TYPE 7 51 31 46 18 30 1

Figure S53.  Get High-res Image Gene #23: 'amp_21q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xp21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S54.  Gene #24: 'amp_xp21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
AMP PEAK 24(XP21.2) MUTATED 14 7 20 9 27 20 0
AMP PEAK 24(XP21.2) WILD-TYPE 12 51 23 42 7 24 1

Figure S54.  Get High-res Image Gene #24: 'amp_xp21.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xp21.2' versus 'METHLYATION_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.1

Table S55.  Gene #24: 'amp_xp21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
AMP PEAK 24(XP21.2) MUTATED 26 10 23 7 2 19 3
AMP PEAK 24(XP21.2) WILD-TYPE 16 31 34 25 16 24 2

Figure S55.  Get High-res Image Gene #24: 'amp_xp21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_xq21.1' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.052

Table S56.  Gene #25: 'amp_xq21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
AMP PEAK 25(XQ21.1) MUTATED 10 3 16 5 5 7 0
AMP PEAK 25(XQ21.1) WILD-TYPE 16 55 27 46 29 37 1

Figure S56.  Get High-res Image Gene #25: 'amp_xq21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq21.1' versus 'METHLYATION_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.18

Table S57.  Gene #25: 'amp_xq21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
AMP PEAK 25(XQ21.1) MUTATED 15 4 4 6 1 11 3
AMP PEAK 25(XQ21.1) WILD-TYPE 27 37 53 26 17 32 2

Figure S57.  Get High-res Image Gene #25: 'amp_xq21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S58.  Gene #26: 'del_1p36.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
DEL PEAK 1(1P36.32) MUTATED 7 3 5 30 12 11 1
DEL PEAK 1(1P36.32) WILD-TYPE 19 55 38 21 22 33 0

Figure S58.  Get High-res Image Gene #26: 'del_1p36.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S59.  Gene #26: '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 42 41 57 32 18 43 5
DEL PEAK 1(1P36.32) MUTATED 8 1 36 8 6 5 3
DEL PEAK 1(1P36.32) WILD-TYPE 34 40 21 24 12 38 2

Figure S59.  Get High-res Image Gene #26: 'del_1p36.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S60.  Gene #26: 'del_1p36.32' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 68 76 63 46
DEL PEAK 1(1P36.32) MUTATED 9 44 7 8
DEL PEAK 1(1P36.32) WILD-TYPE 59 32 56 38

Figure S60.  Get High-res Image Gene #26: 'del_1p36.32' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_1p36.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S61.  Gene #26: 'del_1p36.32' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 22 49 28 59 29 19
DEL PEAK 1(1P36.32) MUTATED 8 1 30 3 6 15 5
DEL PEAK 1(1P36.32) WILD-TYPE 39 21 19 25 53 14 14

Figure S61.  Get High-res Image Gene #26: 'del_1p36.32' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.32' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S62.  Gene #26: 'del_1p36.32' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 47 99
DEL PEAK 1(1P36.32) MUTATED 14 6 49
DEL PEAK 1(1P36.32) WILD-TYPE 95 41 50

Figure S62.  Get High-res Image Gene #26: 'del_1p36.32' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_1p36.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S63.  Gene #26: 'del_1p36.32' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
DEL PEAK 1(1P36.32) MUTATED 11 3 51 4
DEL PEAK 1(1P36.32) WILD-TYPE 71 34 63 18

Figure S63.  Get High-res Image Gene #26: 'del_1p36.32' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S64.  Gene #26: 'del_1p36.32' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 64 45
DEL PEAK 1(1P36.32) MUTATED 14 31 4
DEL PEAK 1(1P36.32) WILD-TYPE 71 33 41

Figure S64.  Get High-res Image Gene #26: 'del_1p36.32' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_1p36.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.082

Table S65.  Gene #26: 'del_1p36.32' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 32 37 23 12 23 21 22
DEL PEAK 1(1P36.32) MUTATED 4 5 18 4 8 2 3 5
DEL PEAK 1(1P36.32) WILD-TYPE 20 27 19 19 4 21 18 17

Figure S65.  Get High-res Image Gene #26: 'del_1p36.32' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1q44' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.021

Table S66.  Gene #27: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
DEL PEAK 2(1Q44) MUTATED 9 5 18 12 16 20 0
DEL PEAK 2(1Q44) WILD-TYPE 17 53 25 39 18 24 1

Figure S66.  Get High-res Image Gene #27: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

'del_1q44' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S67.  Gene #27: 'del_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
DEL PEAK 2(1Q44) MUTATED 23 10 10 3 2 22 2
DEL PEAK 2(1Q44) WILD-TYPE 19 31 47 29 16 21 3

Figure S67.  Get High-res Image Gene #27: 'del_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1q44' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.013

Table S68.  Gene #27: 'del_1q44' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 68 76 63 46
DEL PEAK 2(1Q44) MUTATED 32 13 27 8
DEL PEAK 2(1Q44) WILD-TYPE 36 63 36 38

Figure S68.  Get High-res Image Gene #27: 'del_1q44' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_1q44' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.025

Table S69.  Gene #27: 'del_1q44' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 22 49 28 59 29 19
DEL PEAK 2(1Q44) MUTATED 27 6 10 8 24 3 2
DEL PEAK 2(1Q44) WILD-TYPE 20 16 39 20 35 26 17

Figure S69.  Get High-res Image Gene #27: 'del_1q44' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_2p25.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S70.  Gene #28: 'del_2p25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
DEL PEAK 3(2P25.3) MUTATED 16 5 9 20 21 23 0
DEL PEAK 3(2P25.3) WILD-TYPE 10 53 34 31 13 21 1

Figure S70.  Get High-res Image Gene #28: 'del_2p25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2p25.3' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.013

Table S71.  Gene #28: '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 42 41 57 32 18 43 5
DEL PEAK 3(2P25.3) MUTATED 18 7 33 3 6 15 3
DEL PEAK 3(2P25.3) WILD-TYPE 24 34 24 29 12 28 2

Figure S71.  Get High-res Image Gene #28: 'del_2p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2p25.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S72.  Gene #28: 'del_2p25.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 68 76 63 46
DEL PEAK 3(2P25.3) MUTATED 26 42 21 4
DEL PEAK 3(2P25.3) WILD-TYPE 42 34 42 42

Figure S72.  Get High-res Image Gene #28: 'del_2p25.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_2p25.3' versus 'MIRSEQ_CNMF'

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

Table S73.  Gene #28: 'del_2p25.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 47 99
DEL PEAK 3(2P25.3) MUTATED 25 20 48
DEL PEAK 3(2P25.3) WILD-TYPE 84 27 51

Figure S73.  Get High-res Image Gene #28: 'del_2p25.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_2p25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S74.  Gene #28: 'del_2p25.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
DEL PEAK 3(2P25.3) MUTATED 27 10 56 0
DEL PEAK 3(2P25.3) WILD-TYPE 55 27 58 22

Figure S74.  Get High-res Image Gene #28: 'del_2p25.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_2p25.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.082

Table S75.  Gene #28: 'del_2p25.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 64 45
DEL PEAK 3(2P25.3) MUTATED 19 35 19
DEL PEAK 3(2P25.3) WILD-TYPE 66 29 26

Figure S75.  Get High-res Image Gene #28: 'del_2p25.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_2q37.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S76.  Gene #29: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
DEL PEAK 4(2Q37.3) MUTATED 16 8 12 10 22 39 1
DEL PEAK 4(2Q37.3) WILD-TYPE 10 50 31 41 12 5 0

Figure S76.  Get High-res Image Gene #29: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.15

Table S77.  Gene #29: 'del_2q37.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 22 49 28 59 29 19
DEL PEAK 4(2Q37.3) MUTATED 27 6 16 9 27 19 2
DEL PEAK 4(2Q37.3) WILD-TYPE 20 16 33 19 32 10 17

Figure S77.  Get High-res Image Gene #29: 'del_2q37.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S78.  Gene #30: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
DEL PEAK 5(2Q37.3) MUTATED 16 7 14 11 22 39 1
DEL PEAK 5(2Q37.3) WILD-TYPE 10 51 29 40 12 5 0

Figure S78.  Get High-res Image Gene #30: 'del_2q37.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-04 (Fisher's exact test), Q value = 0.18

Table S79.  Gene #30: 'del_2q37.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 22 49 28 59 29 19
DEL PEAK 5(2Q37.3) MUTATED 29 6 16 9 26 19 3
DEL PEAK 5(2Q37.3) WILD-TYPE 18 16 33 19 33 10 16

Figure S79.  Get High-res Image Gene #30: 'del_2q37.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3p21.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S80.  Gene #31: '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 42 41 57 32 18 43 5
DEL PEAK 6(3P21.31) MUTATED 21 5 2 10 2 13 1
DEL PEAK 6(3P21.31) WILD-TYPE 21 36 55 22 16 30 4

Figure S80.  Get High-res Image Gene #31: 'del_3p21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p21.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S81.  Gene #31: 'del_3p21.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 68 76 63 46
DEL PEAK 6(3P21.31) MUTATED 28 4 15 18
DEL PEAK 6(3P21.31) WILD-TYPE 40 72 48 28

Figure S81.  Get High-res Image Gene #31: 'del_3p21.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3p21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S82.  Gene #31: 'del_3p21.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 22 49 28 59 29 19
DEL PEAK 6(3P21.31) MUTATED 23 5 2 9 13 3 10
DEL PEAK 6(3P21.31) WILD-TYPE 24 17 47 19 46 26 9

Figure S82.  Get High-res Image Gene #31: 'del_3p21.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3p21.31' versus 'MIRSEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.067

Table S83.  Gene #31: 'del_3p21.31' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 47 99
DEL PEAK 6(3P21.31) MUTATED 39 14 12
DEL PEAK 6(3P21.31) WILD-TYPE 70 33 87

Figure S83.  Get High-res Image Gene #31: 'del_3p21.31' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3p21.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S84.  Gene #31: 'del_3p21.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 32 37 23 12 23 21 22
DEL PEAK 6(3P21.31) MUTATED 12 14 0 8 2 4 5 10
DEL PEAK 6(3P21.31) WILD-TYPE 12 18 37 15 10 19 16 12

Figure S84.  Get High-res Image Gene #31: 'del_3p21.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q29' versus 'CN_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.24

Table S85.  Gene #33: 'del_3q29' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
DEL PEAK 8(3Q29) MUTATED 4 4 19 8 8 11 0
DEL PEAK 8(3Q29) WILD-TYPE 22 54 24 43 26 33 1

Figure S85.  Get High-res Image Gene #33: 'del_3q29' versus Molecular Subtype #1: 'CN_CNMF'

'del_3q29' versus 'METHLYATION_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.085

Table S86.  Gene #33: 'del_3q29' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
DEL PEAK 8(3Q29) MUTATED 14 3 10 5 0 12 4
DEL PEAK 8(3Q29) WILD-TYPE 28 38 47 27 18 31 1

Figure S86.  Get High-res Image Gene #33: 'del_3q29' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q35.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S87.  Gene #34: 'del_4q35.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
DEL PEAK 9(4Q35.1) MUTATED 16 10 13 11 19 24 1
DEL PEAK 9(4Q35.1) WILD-TYPE 10 48 30 40 15 20 0

Figure S87.  Get High-res Image Gene #34: 'del_4q35.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p25.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S88.  Gene #36: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
DEL PEAK 11(6P25.3) MUTATED 4 6 10 27 18 16 0
DEL PEAK 11(6P25.3) WILD-TYPE 22 52 33 24 16 28 1

Figure S88.  Get High-res Image Gene #36: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p25.3' versus 'METHLYATION_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 0.21

Table S89.  Gene #36: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
DEL PEAK 11(6P25.3) MUTATED 10 7 31 6 4 17 2
DEL PEAK 11(6P25.3) WILD-TYPE 32 34 26 26 14 26 3

Figure S89.  Get High-res Image Gene #36: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6p25.3' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.056

Table S90.  Gene #36: 'del_6p25.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 68 76 63 46
DEL PEAK 11(6P25.3) MUTATED 12 37 21 8
DEL PEAK 11(6P25.3) WILD-TYPE 56 39 42 38

Figure S90.  Get High-res Image Gene #36: 'del_6p25.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_7q36.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0088

Table S91.  Gene #38: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
DEL PEAK 13(7Q36.3) MUTATED 9 5 11 11 9 26 0
DEL PEAK 13(7Q36.3) WILD-TYPE 17 53 32 40 25 18 1

Figure S91.  Get High-res Image Gene #38: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.3' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.013

Table S92.  Gene #39: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
DEL PEAK 14(8P23.3) MUTATED 5 8 23 10 14 21 0
DEL PEAK 14(8P23.3) WILD-TYPE 21 50 20 41 20 23 1

Figure S92.  Get High-res Image Gene #39: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S93.  Gene #39: 'del_8p23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
DEL PEAK 14(8P23.3) MUTATED 22 6 6 10 2 23 3
DEL PEAK 14(8P23.3) WILD-TYPE 20 35 51 22 16 20 2

Figure S93.  Get High-res Image Gene #39: 'del_8p23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p23.3' versus 'MRNASEQ_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 0.21

Table S94.  Gene #39: 'del_8p23.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 68 76 63 46
DEL PEAK 14(8P23.3) MUTATED 30 12 26 12
DEL PEAK 14(8P23.3) WILD-TYPE 38 64 37 34

Figure S94.  Get High-res Image Gene #39: 'del_8p23.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.029

Table S95.  Gene #41: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 64 45
DEL PEAK 16(9P21.3) MUTATED 41 19 32
DEL PEAK 16(9P21.3) WILD-TYPE 44 45 13

Figure S95.  Get High-res Image Gene #41: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_9q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S96.  Gene #42: 'del_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
DEL PEAK 17(9Q34.3) MUTATED 8 3 7 10 15 17 1
DEL PEAK 17(9Q34.3) WILD-TYPE 18 55 36 41 19 27 0

Figure S96.  Get High-res Image Gene #42: 'del_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p15.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S97.  Gene #43: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
DEL PEAK 18(10P15.3) MUTATED 14 10 20 34 25 25 0
DEL PEAK 18(10P15.3) WILD-TYPE 12 48 23 17 9 19 1

Figure S97.  Get High-res Image Gene #43: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S98.  Gene #43: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
DEL PEAK 18(10P15.3) MUTATED 28 9 38 14 4 23 3
DEL PEAK 18(10P15.3) WILD-TYPE 14 32 19 18 14 20 2

Figure S98.  Get High-res Image Gene #43: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S99.  Gene #44: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
DEL PEAK 19(10Q23.31) MUTATED 16 8 12 42 26 33 1
DEL PEAK 19(10Q23.31) WILD-TYPE 10 50 31 9 8 11 0

Figure S99.  Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S100.  Gene #44: '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 42 41 57 32 18 43 5
DEL PEAK 19(10Q23.31) MUTATED 26 6 50 8 6 29 4
DEL PEAK 19(10Q23.31) WILD-TYPE 16 35 7 24 12 14 1

Figure S100.  Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S101.  Gene #44: 'del_10q23.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 68 76 63 46
DEL PEAK 19(10Q23.31) MUTATED 29 60 36 12
DEL PEAK 19(10Q23.31) WILD-TYPE 39 16 27 34

Figure S101.  Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S102.  Gene #44: 'del_10q23.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 22 49 28 59 29 19
DEL PEAK 19(10Q23.31) MUTATED 25 7 46 7 33 15 4
DEL PEAK 19(10Q23.31) WILD-TYPE 22 15 3 21 26 14 15

Figure S102.  Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S103.  Gene #44: 'del_10q23.31' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 47 99
DEL PEAK 19(10Q23.31) MUTATED 42 26 69
DEL PEAK 19(10Q23.31) WILD-TYPE 67 21 30

Figure S103.  Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S104.  Gene #44: 'del_10q23.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
DEL PEAK 19(10Q23.31) MUTATED 38 14 81 4
DEL PEAK 19(10Q23.31) WILD-TYPE 44 23 33 18

Figure S104.  Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.16

Table S105.  Gene #44: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 64 45
DEL PEAK 19(10Q23.31) MUTATED 35 47 24
DEL PEAK 19(10Q23.31) WILD-TYPE 50 17 21

Figure S105.  Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.15

Table S106.  Gene #44: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 32 37 23 12 23 21 22
DEL PEAK 19(10Q23.31) MUTATED 15 12 30 13 8 14 9 5
DEL PEAK 19(10Q23.31) WILD-TYPE 9 20 7 10 4 9 12 17

Figure S106.  Get High-res Image Gene #44: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S107.  Gene #45: 'del_10q26.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
DEL PEAK 20(10Q26.3) MUTATED 14 8 11 42 24 32 1
DEL PEAK 20(10Q26.3) WILD-TYPE 12 50 32 9 10 12 0

Figure S107.  Get High-res Image Gene #45: 'del_10q26.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q26.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S108.  Gene #45: 'del_10q26.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
DEL PEAK 20(10Q26.3) MUTATED 23 7 47 6 7 31 4
DEL PEAK 20(10Q26.3) WILD-TYPE 19 34 10 26 11 12 1

Figure S108.  Get High-res Image Gene #45: 'del_10q26.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q26.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S109.  Gene #45: 'del_10q26.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 68 76 63 46
DEL PEAK 20(10Q26.3) MUTATED 24 56 39 11
DEL PEAK 20(10Q26.3) WILD-TYPE 44 20 24 35

Figure S109.  Get High-res Image Gene #45: 'del_10q26.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_10q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S110.  Gene #45: 'del_10q26.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 22 49 28 59 29 19
DEL PEAK 20(10Q26.3) MUTATED 21 7 41 6 35 16 4
DEL PEAK 20(10Q26.3) WILD-TYPE 26 15 8 22 24 13 15

Figure S110.  Get High-res Image Gene #45: 'del_10q26.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.056

Table S111.  Gene #45: 'del_10q26.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 47 99
DEL PEAK 20(10Q26.3) MUTATED 39 27 64
DEL PEAK 20(10Q26.3) WILD-TYPE 70 20 35

Figure S111.  Get High-res Image Gene #45: 'del_10q26.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_10q26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0088

Table S112.  Gene #45: 'del_10q26.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
DEL PEAK 20(10Q26.3) MUTATED 37 14 76 3
DEL PEAK 20(10Q26.3) WILD-TYPE 45 23 38 19

Figure S112.  Get High-res Image Gene #45: 'del_10q26.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.033

Table S113.  Gene #45: 'del_10q26.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 64 45
DEL PEAK 20(10Q26.3) MUTATED 32 47 24
DEL PEAK 20(10Q26.3) WILD-TYPE 53 17 21

Figure S113.  Get High-res Image Gene #45: 'del_10q26.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_10q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.11

Table S114.  Gene #45: 'del_10q26.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 32 37 23 12 23 21 22
DEL PEAK 20(10Q26.3) MUTATED 14 10 29 12 9 14 10 5
DEL PEAK 20(10Q26.3) WILD-TYPE 10 22 8 11 3 9 11 17

Figure S114.  Get High-res Image Gene #45: 'del_10q26.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S115.  Gene #46: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
DEL PEAK 21(11P15.5) MUTATED 14 3 27 21 20 25 0
DEL PEAK 21(11P15.5) WILD-TYPE 12 55 16 30 14 19 1

Figure S115.  Get High-res Image Gene #46: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.19

Table S116.  Gene #46: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
DEL PEAK 21(11P15.5) MUTATED 25 9 29 9 3 21 3
DEL PEAK 21(11P15.5) WILD-TYPE 17 32 28 23 15 22 2

Figure S116.  Get High-res Image Gene #46: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q24.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S117.  Gene #47: 'del_11q24.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
DEL PEAK 22(11Q24.2) MUTATED 12 8 32 16 20 35 0
DEL PEAK 22(11Q24.2) WILD-TYPE 14 50 11 35 14 9 1

Figure S117.  Get High-res Image Gene #47: 'del_11q24.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q24.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S118.  Gene #47: 'del_11q24.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
DEL PEAK 22(11Q24.2) MUTATED 35 12 23 10 2 27 4
DEL PEAK 22(11Q24.2) WILD-TYPE 7 29 34 22 16 16 1

Figure S118.  Get High-res Image Gene #47: 'del_11q24.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S119.  Gene #48: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
DEL PEAK 23(12P13.1) MUTATED 17 9 18 6 17 20 0
DEL PEAK 23(12P13.1) WILD-TYPE 9 49 25 45 17 24 1

Figure S119.  Get High-res Image Gene #48: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q12' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.037

Table S120.  Gene #49: 'del_12q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
DEL PEAK 24(12Q12) MUTATED 9 3 7 9 14 13 1
DEL PEAK 24(12Q12) WILD-TYPE 17 55 36 42 20 31 0

Figure S120.  Get High-res Image Gene #49: 'del_12q12' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q24.33' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.033

Table S121.  Gene #50: 'del_12q24.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
DEL PEAK 25(12Q24.33) MUTATED 14 7 10 8 15 14 1
DEL PEAK 25(12Q24.33) WILD-TYPE 12 51 33 43 19 30 0

Figure S121.  Get High-res Image Gene #50: 'del_12q24.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S122.  Gene #51: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
DEL PEAK 26(13Q14.2) MUTATED 21 13 27 47 31 40 1
DEL PEAK 26(13Q14.2) WILD-TYPE 5 45 16 4 3 4 0

Figure S122.  Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S123.  Gene #51: '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 42 41 57 32 18 43 5
DEL PEAK 26(13Q14.2) MUTATED 34 18 55 12 9 34 5
DEL PEAK 26(13Q14.2) WILD-TYPE 8 23 2 20 9 9 0

Figure S123.  Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S124.  Gene #51: 'del_13q14.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 68 76 63 46
DEL PEAK 26(13Q14.2) MUTATED 41 68 50 19
DEL PEAK 26(13Q14.2) WILD-TYPE 27 8 13 27

Figure S124.  Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S125.  Gene #51: 'del_13q14.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 22 49 28 59 29 19
DEL PEAK 26(13Q14.2) MUTATED 34 11 47 13 44 22 7
DEL PEAK 26(13Q14.2) WILD-TYPE 13 11 2 15 15 7 12

Figure S125.  Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S126.  Gene #51: 'del_13q14.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 47 99
DEL PEAK 26(13Q14.2) MUTATED 61 32 85
DEL PEAK 26(13Q14.2) WILD-TYPE 48 15 14

Figure S126.  Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S127.  Gene #51: 'del_13q14.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
DEL PEAK 26(13Q14.2) MUTATED 54 20 97 7
DEL PEAK 26(13Q14.2) WILD-TYPE 28 17 17 15

Figure S127.  Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.092

Table S128.  Gene #51: 'del_13q14.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 64 45
DEL PEAK 26(13Q14.2) MUTATED 50 56 35
DEL PEAK 26(13Q14.2) WILD-TYPE 35 8 10

Figure S128.  Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_13q14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.085

Table S129.  Gene #51: 'del_13q14.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 32 37 23 12 23 21 22
DEL PEAK 26(13Q14.2) MUTATED 17 21 36 19 8 16 15 9
DEL PEAK 26(13Q14.2) WILD-TYPE 7 11 1 4 4 7 6 13

Figure S129.  Get High-res Image Gene #51: 'del_13q14.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S130.  Gene #52: 'del_14q24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
DEL PEAK 27(14Q24.1) MUTATED 7 4 19 18 5 26 1
DEL PEAK 27(14Q24.1) WILD-TYPE 19 54 24 33 29 18 0

Figure S130.  Get High-res Image Gene #52: 'del_14q24.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S131.  Gene #52: 'del_14q24.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 22 49 28 59 29 19
DEL PEAK 27(14Q24.1) MUTATED 21 5 9 9 13 21 2
DEL PEAK 27(14Q24.1) WILD-TYPE 26 17 40 19 46 8 17

Figure S131.  Get High-res Image Gene #52: 'del_14q24.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_16q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S132.  Gene #53: 'del_16q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
DEL PEAK 28(16Q11.2) MUTATED 14 10 18 33 28 26 1
DEL PEAK 28(16Q11.2) WILD-TYPE 12 48 25 18 6 18 0

Figure S132.  Get High-res Image Gene #53: 'del_16q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q11.2' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.029

Table S133.  Gene #53: 'del_16q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
DEL PEAK 28(16Q11.2) MUTATED 23 11 40 9 9 28 2
DEL PEAK 28(16Q11.2) WILD-TYPE 19 30 17 23 9 15 3

Figure S133.  Get High-res Image Gene #53: 'del_16q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.1

Table S134.  Gene #53: 'del_16q11.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 68 76 63 46
DEL PEAK 28(16Q11.2) MUTATED 28 50 37 14
DEL PEAK 28(16Q11.2) WILD-TYPE 40 26 26 32

Figure S134.  Get High-res Image Gene #53: 'del_16q11.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_16q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00068 (Fisher's exact test), Q value = 0.24

Table S135.  Gene #53: 'del_16q11.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 22 49 28 59 29 19
DEL PEAK 28(16Q11.2) MUTATED 24 8 34 7 34 17 5
DEL PEAK 28(16Q11.2) WILD-TYPE 23 14 15 21 25 12 14

Figure S135.  Get High-res Image Gene #53: 'del_16q11.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_16q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.11

Table S136.  Gene #53: 'del_16q11.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
DEL PEAK 28(16Q11.2) MUTATED 38 11 73 7
DEL PEAK 28(16Q11.2) WILD-TYPE 44 26 41 15

Figure S136.  Get High-res Image Gene #53: 'del_16q11.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_16q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0088

Table S137.  Gene #53: 'del_16q11.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 64 45
DEL PEAK 28(16Q11.2) MUTATED 31 47 29
DEL PEAK 28(16Q11.2) WILD-TYPE 54 17 16

Figure S137.  Get High-res Image Gene #53: 'del_16q11.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_16q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.017

Table S138.  Gene #53: 'del_16q11.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 32 37 23 12 23 21 22
DEL PEAK 28(16Q11.2) MUTATED 12 10 31 14 8 13 14 5
DEL PEAK 28(16Q11.2) WILD-TYPE 12 22 6 9 4 10 7 17

Figure S138.  Get High-res Image Gene #53: 'del_16q11.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S139.  Gene #54: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
DEL PEAK 29(16Q23.1) MUTATED 14 11 19 33 27 29 1
DEL PEAK 29(16Q23.1) WILD-TYPE 12 47 24 18 7 15 0

Figure S139.  Get High-res Image Gene #54: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.16

Table S140.  Gene #54: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
DEL PEAK 29(16Q23.1) MUTATED 26 13 40 10 9 27 2
DEL PEAK 29(16Q23.1) WILD-TYPE 16 28 17 22 9 16 3

Figure S140.  Get High-res Image Gene #54: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.056

Table S141.  Gene #54: 'del_16q23.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
DEL PEAK 29(16Q23.1) MUTATED 40 12 75 6
DEL PEAK 29(16Q23.1) WILD-TYPE 42 25 39 16

Figure S141.  Get High-res Image Gene #54: '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 = 0.0053

Table S142.  Gene #54: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 64 45
DEL PEAK 29(16Q23.1) MUTATED 31 47 31
DEL PEAK 29(16Q23.1) WILD-TYPE 54 17 14

Figure S142.  Get High-res Image Gene #54: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.029

Table S143.  Gene #54: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 32 37 23 12 23 21 22
DEL PEAK 29(16Q23.1) MUTATED 14 10 30 15 9 10 15 6
DEL PEAK 29(16Q23.1) WILD-TYPE 10 22 7 8 3 13 6 16

Figure S143.  Get High-res Image Gene #54: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S144.  Gene #55: 'del_17p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
DEL PEAK 30(17P13.1) MUTATED 9 9 13 45 23 29 1
DEL PEAK 30(17P13.1) WILD-TYPE 17 49 30 6 11 15 0

Figure S144.  Get High-res Image Gene #55: 'del_17p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S145.  Gene #55: 'del_17p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
DEL PEAK 30(17P13.1) MUTATED 15 13 46 12 8 22 2
DEL PEAK 30(17P13.1) WILD-TYPE 27 28 11 20 10 21 3

Figure S145.  Get High-res Image Gene #55: 'del_17p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S146.  Gene #55: 'del_17p13.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 68 76 63 46
DEL PEAK 30(17P13.1) MUTATED 23 54 35 15
DEL PEAK 30(17P13.1) WILD-TYPE 45 22 28 31

Figure S146.  Get High-res Image Gene #55: 'del_17p13.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_17p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.017

Table S147.  Gene #55: 'del_17p13.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 22 49 28 59 29 19
DEL PEAK 30(17P13.1) MUTATED 18 9 40 7 29 14 10
DEL PEAK 30(17P13.1) WILD-TYPE 29 13 9 21 30 15 9

Figure S147.  Get High-res Image Gene #55: 'del_17p13.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.1' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.013

Table S148.  Gene #55: 'del_17p13.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 47 99
DEL PEAK 30(17P13.1) MUTATED 37 26 64
DEL PEAK 30(17P13.1) WILD-TYPE 72 21 35

Figure S148.  Get High-res Image Gene #55: 'del_17p13.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_17p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.017

Table S149.  Gene #55: 'del_17p13.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
DEL PEAK 30(17P13.1) MUTATED 30 16 75 6
DEL PEAK 30(17P13.1) WILD-TYPE 52 21 39 16

Figure S149.  Get High-res Image Gene #55: 'del_17p13.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_17p13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.013

Table S150.  Gene #55: 'del_17p13.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 64 45
DEL PEAK 30(17P13.1) MUTATED 27 44 29
DEL PEAK 30(17P13.1) WILD-TYPE 58 20 16

Figure S150.  Get High-res Image Gene #55: 'del_17p13.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_17q11.2' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.041

Table S151.  Gene #56: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
DEL PEAK 31(17Q11.2) MUTATED 13 7 19 10 15 17 0
DEL PEAK 31(17Q11.2) WILD-TYPE 13 51 24 41 19 27 1

Figure S151.  Get High-res Image Gene #56: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S152.  Gene #56: '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 42 41 57 32 18 43 5
DEL PEAK 31(17Q11.2) MUTATED 22 8 9 9 0 23 2
DEL PEAK 31(17Q11.2) WILD-TYPE 20 33 48 23 18 20 3

Figure S152.  Get High-res Image Gene #56: 'del_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q11.2' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0088

Table S153.  Gene #56: 'del_17q11.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 68 76 63 46
DEL PEAK 31(17Q11.2) MUTATED 30 10 29 12
DEL PEAK 31(17Q11.2) WILD-TYPE 38 66 34 34

Figure S153.  Get High-res Image Gene #56: 'del_17q11.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_17q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.052

Table S154.  Gene #56: 'del_17q11.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 22 49 28 59 29 19
DEL PEAK 31(17Q11.2) MUTATED 24 7 7 7 26 3 7
DEL PEAK 31(17Q11.2) WILD-TYPE 23 15 42 21 33 26 12

Figure S154.  Get High-res Image Gene #56: 'del_17q11.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_17q25.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S155.  Gene #57: 'del_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
DEL PEAK 32(17Q25.3) MUTATED 13 5 13 6 17 12 1
DEL PEAK 32(17Q25.3) WILD-TYPE 13 53 30 45 17 32 0

Figure S155.  Get High-res Image Gene #57: 'del_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q23' versus 'METHLYATION_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.067

Table S156.  Gene #58: 'del_18q23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
DEL PEAK 33(18Q23) MUTATED 14 13 14 6 3 28 1
DEL PEAK 33(18Q23) WILD-TYPE 28 28 43 26 15 15 4

Figure S156.  Get High-res Image Gene #58: 'del_18q23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S157.  Gene #58: 'del_18q23' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 68 76 63 46
DEL PEAK 33(18Q23) MUTATED 21 17 37 10
DEL PEAK 33(18Q23) WILD-TYPE 47 59 26 36

Figure S157.  Get High-res Image Gene #58: 'del_18q23' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_18q23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.13

Table S158.  Gene #58: 'del_18q23' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 32 37 23 12 23 21 22
DEL PEAK 33(18Q23) MUTATED 6 8 9 11 2 14 15 5
DEL PEAK 33(18Q23) WILD-TYPE 18 24 28 12 10 9 6 17

Figure S158.  Get High-res Image Gene #58: 'del_18q23' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.037

Table S159.  Gene #59: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
DEL PEAK 34(19P13.3) MUTATED 9 5 8 16 17 14 1
DEL PEAK 34(19P13.3) WILD-TYPE 17 53 35 35 17 30 0

Figure S159.  Get High-res Image Gene #59: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.041

Table S160.  Gene #59: 'del_19p13.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 68 76 63 46
DEL PEAK 34(19P13.3) MUTATED 9 31 23 7
DEL PEAK 34(19P13.3) WILD-TYPE 59 45 40 39

Figure S160.  Get High-res Image Gene #59: 'del_19p13.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_19q13.43' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S161.  Gene #60: 'del_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
DEL PEAK 35(19Q13.43) MUTATED 12 3 21 30 15 25 0
DEL PEAK 35(19Q13.43) WILD-TYPE 14 55 22 21 19 19 1

Figure S161.  Get High-res Image Gene #60: 'del_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

'del_19q13.43' versus 'METHLYATION_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.14

Table S162.  Gene #60: 'del_19q13.43' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
DEL PEAK 35(19Q13.43) MUTATED 23 6 30 8 7 20 3
DEL PEAK 35(19Q13.43) WILD-TYPE 19 35 27 24 11 23 2

Figure S162.  Get High-res Image Gene #60: 'del_19q13.43' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q11.2' versus 'CN_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.16

Table S163.  Gene #61: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
DEL PEAK 36(21Q11.2) MUTATED 2 3 7 17 7 15 0
DEL PEAK 36(21Q11.2) WILD-TYPE 24 55 36 34 27 29 1

Figure S163.  Get High-res Image Gene #61: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S164.  Gene #63: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
DEL PEAK 38(22Q13.32) MUTATED 9 8 9 9 18 29 1
DEL PEAK 38(22Q13.32) WILD-TYPE 17 50 34 42 16 15 0

Figure S164.  Get High-res Image Gene #63: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp21.1' versus 'CN_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.16

Table S165.  Gene #64: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
DEL PEAK 39(XP21.1) MUTATED 5 5 6 19 4 15 1
DEL PEAK 39(XP21.1) WILD-TYPE 21 53 37 32 30 29 0

Figure S165.  Get High-res Image Gene #64: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp21.1' versus 'METHLYATION_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.22

Table S166.  Gene #64: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
DEL PEAK 39(XP21.1) MUTATED 5 1 19 7 7 10 2
DEL PEAK 39(XP21.1) WILD-TYPE 37 40 38 25 11 33 3

Figure S166.  Get High-res Image Gene #64: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S167.  Gene #65: 'del_xq21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
DEL PEAK 40(XQ21.1) MUTATED 14 5 16 30 23 25 1
DEL PEAK 40(XQ21.1) WILD-TYPE 12 53 27 21 11 19 0

Figure S167.  Get High-res Image Gene #65: 'del_xq21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq21.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S168.  Gene #65: '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 42 41 57 32 18 43 5
DEL PEAK 40(XQ21.1) MUTATED 20 7 41 11 8 15 2
DEL PEAK 40(XQ21.1) WILD-TYPE 22 34 16 21 10 28 3

Figure S168.  Get High-res Image Gene #65: 'del_xq21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq21.1' versus 'MRNASEQ_CNMF'

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

Table S169.  Gene #65: 'del_xq21.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 68 76 63 46
DEL PEAK 40(XQ21.1) MUTATED 25 50 22 16
DEL PEAK 40(XQ21.1) WILD-TYPE 43 26 41 30

Figure S169.  Get High-res Image Gene #65: 'del_xq21.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_xq21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.067

Table S170.  Gene #65: 'del_xq21.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 22 49 28 59 29 19
DEL PEAK 40(XQ21.1) MUTATED 19 6 36 13 19 15 5
DEL PEAK 40(XQ21.1) WILD-TYPE 28 16 13 15 40 14 14

Figure S170.  Get High-res Image Gene #65: 'del_xq21.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_xq21.1' versus 'MIRSEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.074

Table S171.  Gene #65: 'del_xq21.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 47 99
DEL PEAK 40(XQ21.1) MUTATED 36 17 60
DEL PEAK 40(XQ21.1) WILD-TYPE 73 30 39

Figure S171.  Get High-res Image Gene #65: 'del_xq21.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_xq21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.18

Table S172.  Gene #65: 'del_xq21.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
DEL PEAK 40(XQ21.1) MUTATED 28 12 67 6
DEL PEAK 40(XQ21.1) WILD-TYPE 54 25 47 16

Figure S172.  Get High-res Image Gene #65: 'del_xq21.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_xq22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S173.  Gene #66: 'del_xq22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 26 58 43 51 34 44 1
DEL PEAK 41(XQ22.3) MUTATED 14 7 17 31 24 29 1
DEL PEAK 41(XQ22.3) WILD-TYPE 12 51 26 20 10 15 0

Figure S173.  Get High-res Image Gene #66: 'del_xq22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq22.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S174.  Gene #66: 'del_xq22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 41 57 32 18 43 5
DEL PEAK 41(XQ22.3) MUTATED 23 7 42 8 9 19 4
DEL PEAK 41(XQ22.3) WILD-TYPE 19 34 15 24 9 24 1

Figure S174.  Get High-res Image Gene #66: 'del_xq22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq22.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0053

Table S175.  Gene #66: 'del_xq22.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 68 76 63 46
DEL PEAK 41(XQ22.3) MUTATED 33 54 22 13
DEL PEAK 41(XQ22.3) WILD-TYPE 35 22 41 33

Figure S175.  Get High-res Image Gene #66: 'del_xq22.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_xq22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0088

Table S176.  Gene #66: 'del_xq22.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 47 22 49 28 59 29 19
DEL PEAK 41(XQ22.3) MUTATED 27 5 35 11 21 19 4
DEL PEAK 41(XQ22.3) WILD-TYPE 20 17 14 17 38 10 15

Figure S176.  Get High-res Image Gene #66: 'del_xq22.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_xq22.3' versus 'MIRSEQ_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.18

Table S177.  Gene #66: 'del_xq22.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 47 99
DEL PEAK 41(XQ22.3) MUTATED 40 19 62
DEL PEAK 41(XQ22.3) WILD-TYPE 69 28 37

Figure S177.  Get High-res Image Gene #66: 'del_xq22.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_xq22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.037

Table S178.  Gene #66: 'del_xq22.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 82 37 114 22
DEL PEAK 41(XQ22.3) MUTATED 32 10 72 7
DEL PEAK 41(XQ22.3) WILD-TYPE 50 27 42 15

Figure S178.  Get High-res Image Gene #66: 'del_xq22.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

Methods & Data
Input
  • Copy number data file = transformed.cor.cli.txt

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

  • Number of patients = 257

  • Number of significantly focal cnvs = 66

  • 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)