Correlation between copy number variations of arm-level result and molecular subtypes
Head and Neck Squamous Cell Carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1D21WVT
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1D21WVT
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.

Summary

Testing the association between copy number variation 82 arm-level events and 10 molecular subtypes across 522 patients, 339 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

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

  • 3p gain cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 3q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 4p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 5p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 5q gain cnv correlated to 'CN_CNMF'.

  • 6p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 6q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • 7q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 8p gain cnv correlated to 'CN_CNMF'.

  • 8q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

  • 9q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 10p gain cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 10q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • 11p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 11q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

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

  • 13q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 16p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

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

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

  • 18p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 18q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

  • 19q gain cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 20p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 21q gain cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 22q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • xp gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • xq gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 1p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 1q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 3p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 3q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

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

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

  • 5p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 5q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 6p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 6q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 7p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 8p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 8q loss cnv correlated to 'CN_CNMF'.

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

  • 9q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 10p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 10q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

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

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

  • 12p loss cnv correlated to 'METHLYATION_CNMF'.

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

  • 13q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 14q loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 15q loss cnv correlated to 'CN_CNMF'.

  • 16p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

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

  • 17p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

  • 18p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 18q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 19p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 19q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 20p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 20q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 22q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • xp loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • xq loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 339 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
14q gain 151 (29%) 371 1e-05
(9.65e-05) 		1e-05
(9.65e-05) 		0.195
(0.324) 		0.0952
(0.193) 		0.00997
(0.0339) 		1e-05
(9.65e-05) 		0.00643
(0.0234) 		0.00037
(0.00202) 		1e-05
(9.65e-05) 		0.00037
(0.00202)
16q loss 81 (16%) 441 0.00217
(0.00941) 		1e-05
(9.65e-05) 		0.517
(0.663) 		0.243
(0.386) 		1e-05
(9.65e-05) 		1e-05
(9.65e-05) 		0.00776
(0.0275) 		0.0088
(0.0308) 		1e-05
(9.65e-05) 		0.00274
(0.0115)
1q gain 121 (23%) 401 1e-05
(9.65e-05) 		1e-05
(9.65e-05) 		0.979
(0.994) 		0.771
(0.852) 		7e-05
(0.000478) 		0.00067
(0.00337) 		0.00026
(0.00152) 		0.0003
(0.00168) 		0.0121
(0.04) 		0.0971
(0.194)
2p gain 97 (19%) 425 1e-05
(9.65e-05) 		1e-05
(9.65e-05) 		0.86
(0.911) 		0.439
(0.585) 		0.0342
(0.0901) 		1e-05
(9.65e-05) 		0.0211
(0.0616) 		0.0197
(0.0583) 		0.0022
(0.00949) 		0.0901
(0.189)
9p gain 102 (20%) 420 1e-05
(9.65e-05) 		1e-05
(9.65e-05) 		0.131
(0.242) 		0.0933
(0.192) 		0.004
(0.0156) 		0.0007
(0.0035) 		0.00759
(0.0272) 		0.00895
(0.031) 		0.00013
(0.00082) 		0.156
(0.276)
20q gain 201 (39%) 321 1e-05
(9.65e-05) 		1e-05
(9.65e-05) 		0.262
(0.407) 		0.872
(0.92) 		0.0303
(0.0818) 		0.0001
(0.000651) 		0.0628
(0.146) 		0.00424
(0.0164) 		0.0356
(0.0932) 		0.0114
(0.0381)
18q loss 211 (40%) 311 1e-05
(9.65e-05) 		1e-05
(9.65e-05) 		0.909
(0.94) 		0.33
(0.479) 		0.00091
(0.00434) 		1e-05
(9.65e-05) 		0.00091
(0.00434) 		3e-05
(0.000232) 		5e-05
(0.000363) 		0.0535
(0.128)
19p loss 98 (19%) 424 1e-05
(9.65e-05) 		6e-05
(0.000417) 		0.332
(0.48) 		0.713
(0.819) 		0.0542
(0.13) 		0.00882
(0.0308) 		0.0215
(0.0621) 		0.00406
(0.0158) 		0.011
(0.0367) 		0.0372
(0.0964)
20q loss 28 (5%) 494 0.00027
(0.00157) 		0.00466
(0.0178) 		0.945
(0.967) 		0.755
(0.844) 		0.0123
(0.0402) 		0.0191
(0.057) 		0.0685
(0.154) 		0.0484
(0.118) 		0.0191
(0.057) 		0.03
(0.0812)
xq loss 83 (16%) 439 1e-05
(9.65e-05) 		1e-05
(9.65e-05) 		0.011
(0.0367) 		0.00041
(0.00216) 		0.032
(0.0858) 		0.00606
(0.0225) 		0.00032
(0.00179) 		0.0972
(0.194) 		0.294
(0.447) 		0.426
(0.572)
12p gain 148 (28%) 374 1e-05
(9.65e-05) 		1e-05
(9.65e-05) 		0.548
(0.688) 		0.823
(0.882) 		0.0136
(0.0429) 		9e-05
(0.000595) 		0.0125
(0.0405) 		0.0964
(0.194) 		0.0379
(0.0979) 		0.522
(0.666)
13q gain 57 (11%) 465 1e-05
(9.65e-05) 		0.00259
(0.0109) 		0.595
(0.735) 		0.734
(0.832) 		0.00102
(0.00475) 		0.00575
(0.0215) 		0.124
(0.233) 		0.239
(0.384) 		0.0266
(0.0743) 		0.0152
(0.0468)
18q gain 53 (10%) 469 0.0015
(0.0068) 		2e-05
(0.000171) 		0.13
(0.242) 		0.0881
(0.185) 		0.0003
(0.00168) 		0.00017
(0.00105) 		2e-05
(0.000171) 		0.141
(0.257) 		5e-05
(0.000363) 		0.0633
(0.146)
3p loss 297 (57%) 225 1e-05
(9.65e-05) 		1e-05
(9.65e-05) 		0.749
(0.84) 		0.679
(0.791) 		0.0299
(0.0812) 		1e-05
(9.65e-05) 		0.0993
(0.197) 		0.00076
(0.00373) 		8e-05
(0.000538) 		0.238
(0.383)
4p loss 194 (37%) 328 1e-05
(9.65e-05) 		1e-05
(9.65e-05) 		0.428
(0.573) 		0.547
(0.688) 		0.00017
(0.00105) 		1e-05
(9.65e-05) 		0.182
(0.307) 		0.0282
(0.0779) 		0.00056
(0.00291) 		0.0653
(0.148)
8p loss 187 (36%) 335 1e-05
(9.65e-05) 		1e-05
(9.65e-05) 		0.478
(0.627) 		0.678
(0.791) 		0.151
(0.271) 		2e-05
(0.000171) 		0.142
(0.257) 		0.00297
(0.0122) 		0.00014
(0.000876) 		3e-05
(0.000232)
14q loss 58 (11%) 464 0.0631
(0.146) 		0.00287
(0.0119) 		0.413
(0.559) 		0.526
(0.67) 		4e-05
(0.000304) 		0.00155
(0.00695) 		0.00058
(0.00297) 		0.312
(0.465) 		3e-05
(0.000232) 		0.0123
(0.0402)
21q loss 184 (35%) 338 1e-05
(9.65e-05) 		1e-05
(9.65e-05) 		0.817
(0.881) 		0.983
(0.996) 		0.0124
(0.0402) 		2e-05
(0.000171) 		0.301
(0.454) 		0.00038
(0.00205) 		0.00062
(0.00316) 		0.231
(0.373)
22q loss 75 (14%) 447 0.00011
(0.000705) 		0.00305
(0.0125) 		0.874
(0.92) 		0.654
(0.778) 		0.00234
(0.00999) 		0.327
(0.477) 		0.00137
(0.00624) 		0.516
(0.663) 		0.0175
(0.0526) 		0.0475
(0.116)
2q gain 74 (14%) 448 1e-05
(9.65e-05) 		1e-05
(9.65e-05) 		0.599
(0.737) 		0.73
(0.832) 		0.06
(0.141) 		1e-05
(9.65e-05) 		0.104
(0.203) 		0.102
(0.2) 		0.0164
(0.0503) 		0.0397
(0.101)
3q gain 254 (49%) 268 0.00012
(0.000763) 		1e-05
(9.65e-05) 		0.351
(0.5) 		0.283
(0.434) 		0.00029
(0.00165) 		0.153
(0.271) 		0.00886
(0.0308) 		0.803
(0.871) 		0.0212
(0.0616) 		0.0966
(0.194)
7q gain 129 (25%) 393 1e-05
(9.65e-05) 		1e-05
(9.65e-05) 		0.362
(0.512) 		0.633
(0.758) 		0.542
(0.682) 		0.00038
(0.00205) 		0.0133
(0.0422) 		0.00018
(0.0011) 		0.326
(0.477) 		0.499
(0.65)
8q gain 310 (59%) 212 5e-05
(0.000363) 		3e-05
(0.000232) 		0.19
(0.317) 		0.886
(0.927) 		0.0723
(0.16) 		2e-05
(0.000171) 		0.173
(0.297) 		0.0105
(0.0357) 		0.0402
(0.102) 		0.0698
(0.155)
11p gain 66 (13%) 456 8e-05
(0.000538) 		1e-05
(9.65e-05) 		0.802
(0.871) 		0.409
(0.556) 		0.106
(0.206) 		0.147
(0.265) 		0.0453
(0.112) 		0.264
(0.408) 		0.00336
(0.0134) 		0.00883
(0.0308)
15q gain 72 (14%) 450 9e-05
(0.000595) 		0.00644
(0.0234) 		0.843
(0.897) 		0.586
(0.726) 		0.0957
(0.193) 		0.035
(0.092) 		0.885
(0.927) 		0.0058
(0.0216) 		0.036
(0.094) 		0.521
(0.666)
17p gain 67 (13%) 455 1e-05
(9.65e-05) 		0.0001
(0.000651) 		0.0924
(0.192) 		0.902
(0.938) 		0.0021
(0.0092) 		0.00326
(0.0132) 		0.0556
(0.132) 		0.0463
(0.114) 		0.248
(0.391) 		0.167
(0.288)
18p gain 123 (24%) 399 1e-05
(9.65e-05) 		1e-05
(9.65e-05) 		0.721
(0.826) 		0.319
(0.471) 		0.349
(0.498) 		5e-05
(0.000363) 		0.247
(0.391) 		0.0151
(0.0467) 		0.00082
(0.004) 		0.167
(0.288)
19p gain 56 (11%) 466 0.0135
(0.0427) 		2e-05
(0.000171) 		0.193
(0.322) 		0.765
(0.849) 		0.0202
(0.0593) 		0.0152
(0.0468) 		0.00039
(0.00209) 		0.0513
(0.123) 		0.402
(0.55) 		0.183
(0.308)
20p gain 190 (36%) 332 1e-05
(9.65e-05) 		6e-05
(0.000417) 		0.967
(0.984) 		0.733
(0.832) 		0.0509
(0.123) 		0.00455
(0.0175) 		0.0951
(0.193) 		0.0123
(0.0402) 		0.509
(0.657) 		0.0391
(0.1)
22q gain 112 (21%) 410 1e-05
(9.65e-05) 		1e-05
(9.65e-05) 		0.506
(0.656) 		0.515
(0.663) 		0.156
(0.276) 		0.00028
(0.00161) 		0.00042
(0.00219) 		0.079
(0.17) 		0.0139
(0.0435) 		0.53
(0.674)
1p loss 58 (11%) 464 1e-05
(9.65e-05) 		1e-05
(9.65e-05) 		0.314
(0.466) 		0.166
(0.288) 		0.00171
(0.00758) 		1e-05
(9.65e-05) 		0.402
(0.55) 		0.0861
(0.182) 		0.261
(0.406) 		0.0201
(0.0593)
4q loss 151 (29%) 371 1e-05
(9.65e-05) 		1e-05
(9.65e-05) 		0.613
(0.748) 		0.224
(0.364) 		0.00904
(0.031) 		2e-05
(0.000171) 		0.26
(0.406) 		0.0925
(0.192) 		0.0297
(0.0811) 		0.162
(0.283)
5q loss 164 (31%) 358 1e-05
(9.65e-05) 		1e-05
(9.65e-05) 		0.326
(0.477) 		0.774
(0.852) 		0.345
(0.493) 		1e-05
(9.65e-05) 		0.387
(0.536) 		0.00011
(0.000705) 		0.00023
(0.00136) 		0.0776
(0.169)
9p loss 186 (36%) 336 1e-05
(9.65e-05) 		1e-05
(9.65e-05) 		0.0825
(0.175) 		0.116
(0.222) 		0.295
(0.447) 		1e-05
(9.65e-05) 		0.0575
(0.136) 		6e-05
(0.000417) 		1e-05
(9.65e-05) 		0.602
(0.738)
9q loss 87 (17%) 435 1e-05
(9.65e-05) 		1e-05
(9.65e-05) 		0.467
(0.616) 		0.971
(0.986) 		0.372
(0.521) 		0.0138
(0.0433) 		0.425
(0.571) 		0.00314
(0.0127) 		0.0132
(0.0422) 		0.312
(0.465)
13q loss 167 (32%) 355 1e-05
(9.65e-05) 		1e-05
(9.65e-05) 		0.173
(0.297) 		0.827
(0.886) 		0.00028
(0.00161) 		0.00515
(0.0196) 		0.0397
(0.101) 		0.19
(0.317) 		0.108
(0.21) 		0.201
(0.33)
19q loss 86 (16%) 436 1e-05
(9.65e-05) 		3e-05
(0.000232) 		0.183
(0.308) 		0.517
(0.663) 		0.342
(0.493) 		0.00771
(0.0275) 		0.152
(0.271) 		0.0324
(0.0863) 		0.169
(0.291) 		0.0408
(0.103)
xp loss 134 (26%) 388 1e-05
(9.65e-05) 		1e-05
(9.65e-05) 		0.218
(0.356) 		0.0134
(0.0426) 		0.103
(0.203) 		0.0432
(0.108) 		0.0211
(0.0616) 		0.441
(0.586) 		0.0785
(0.17) 		0.602
(0.738)
3p gain 81 (16%) 441 0.196
(0.326) 		0.00023
(0.00136) 		0.343
(0.493) 		0.754
(0.844) 		0.0126
(0.0405) 		0.0371
(0.0963) 		0.128
(0.239) 		0.157
(0.277) 		0.114
(0.219) 		0.0293
(0.0806)
7p gain 183 (35%) 339 1e-05
(9.65e-05) 		1e-05
(9.65e-05) 		1
(1.00) 		0.505
(0.656) 		0.148
(0.265) 		1e-05
(9.65e-05) 		0.688
(0.793) 		1e-05
(9.65e-05) 		0.125
(0.234) 		0.535
(0.679)
9q gain 139 (27%) 383 1e-05
(9.65e-05) 		0.00307
(0.0125) 		0.106
(0.206) 		0.256
(0.401) 		0.393
(0.543) 		0.00097
(0.00457) 		0.4
(0.55) 		0.0498
(0.12) 		0.298
(0.452) 		0.438
(0.585)
10p gain 40 (8%) 482 0.0759
(0.165) 		4e-05
(0.000304) 		0.135
(0.25) 		0.0657
(0.148) 		0.0977
(0.194) 		0.00074
(0.00366) 		0.0445
(0.111) 		0.0169
(0.0514) 		0.56
(0.701) 		0.368
(0.516)
11q gain 71 (14%) 451 3e-05
(0.000232) 		3e-05
(0.000232) 		0.657
(0.778) 		0.582
(0.722) 		0.124
(0.233) 		0.0789
(0.17) 		0.278
(0.427) 		0.0174
(0.0526) 		0.0175
(0.0527) 		0.0622
(0.145)
16p gain 107 (20%) 415 1e-05
(9.65e-05) 		1e-05
(9.65e-05) 		0.648
(0.772) 		0.179
(0.305) 		0.401
(0.55) 		0.0141
(0.0439) 		0.868
(0.918) 		3e-05
(0.000232) 		0.479
(0.627) 		0.539
(0.682)
16q gain 107 (20%) 415 1e-05
(9.65e-05) 		1e-05
(9.65e-05) 		0.802
(0.871) 		0.815
(0.881) 		0.179
(0.305) 		0.00694
(0.0251) 		0.289
(0.441) 		6e-05
(0.000417) 		0.0882
(0.185) 		0.197
(0.326)
17q gain 87 (17%) 435 1e-05
(9.65e-05) 		0.00057
(0.00294) 		0.684
(0.793) 		0.677
(0.791) 		0.0886
(0.186) 		0.00133
(0.00609) 		0.418
(0.563) 		0.00365
(0.0144) 		0.0629
(0.146) 		0.0993
(0.197)
xq gain 95 (18%) 427 3e-05
(0.000232) 		5e-05
(0.000363) 		0.885
(0.927) 		1
(1.00) 		0.58
(0.722) 		0.0192
(0.057) 		0.131
(0.242) 		0.515
(0.663) 		0.0249
(0.0699) 		0.138
(0.252)
1q loss 39 (7%) 483 0.0169
(0.0514) 		0.139
(0.255) 		1
(1.00) 		0.491
(0.642) 		0.0268
(0.0745) 		0.00287
(0.0119) 		0.0946
(0.193) 		0.00086
(0.00415) 		0.411
(0.557) 		0.508
(0.657)
5p loss 51 (10%) 471 2e-05
(0.000171) 		2e-05
(0.000171) 		0.82
(0.881) 		0.382
(0.531) 		0.567
(0.709) 		0.0121
(0.04) 		0.408
(0.555) 		0.256
(0.401) 		0.0917
(0.191) 		0.0245
(0.069)
11p loss 141 (27%) 381 1e-05
(9.65e-05) 		0.0002
(0.00121) 		0.853
(0.907) 		0.331
(0.48) 		0.00097
(0.00457) 		0.16
(0.281) 		0.0038
(0.0149) 		0.121
(0.23) 		0.0958
(0.193) 		0.232
(0.374)
11q loss 172 (33%) 350 1e-05
(9.65e-05) 		2e-05
(0.000171) 		0.747
(0.84) 		0.0798
(0.171) 		0.00037
(0.00202) 		0.00281
(0.0118) 		0.109
(0.211) 		0.43
(0.575) 		0.152
(0.271) 		0.506
(0.656)
18p loss 104 (20%) 418 0.00154
(0.00694) 		3e-05
(0.000232) 		0.6
(0.737) 		0.328
(0.477) 		0.314
(0.466) 		0.00362
(0.0143) 		0.62
(0.752) 		0.0124
(0.0402) 		0.225
(0.365) 		0.582
(0.722)
1p gain 70 (13%) 452 7e-05
(0.000478) 		0.00967
(0.033) 		0.414
(0.56) 		0.628
(0.756) 		0.944
(0.967) 		0.73
(0.832) 		0.688
(0.793) 		0.00538
(0.0203) 		0.117
(0.223) 		0.875
(0.92)
5p gain 201 (39%) 321 1e-05
(9.65e-05) 		0.00221
(0.00949) 		0.399
(0.55) 		0.834
(0.892) 		0.0911
(0.19) 		0.921
(0.949) 		0.575
(0.717) 		0.0324
(0.0863) 		0.837
(0.894) 		0.659
(0.778)
6q gain 63 (12%) 459 0.00202
(0.00891) 		0.0308
(0.0829) 		0.326
(0.477) 		0.0742
(0.163) 		0.1
(0.198) 		0.0417
(0.105) 		0.24
(0.384) 		0.913
(0.943) 		0.0652
(0.148) 		0.299
(0.453)
12q gain 89 (17%) 433 2e-05
(0.000171) 		0.00108
(0.005) 		0.549
(0.689) 		0.181
(0.307) 		0.0547
(0.13) 		0.00803
(0.0284) 		0.661
(0.78) 		0.78
(0.856) 		0.448
(0.595) 		0.787
(0.86)
19q gain 78 (15%) 444 0.374
(0.522) 		0.00041
(0.00216) 		0.624
(0.753) 		0.784
(0.858) 		0.0595
(0.14) 		0.0443
(0.111) 		0.00064
(0.00324) 		0.0806
(0.173) 		0.498
(0.65) 		0.0655
(0.148)
21q gain 35 (7%) 487 0.064
(0.147) 		0.0406
(0.103) 		0.664
(0.781) 		0.131
(0.242) 		0.00564
(0.0212) 		0.0753
(0.165) 		0.0954
(0.193) 		0.252
(0.397) 		0.00611
(0.0225) 		0.772
(0.852)
2p loss 33 (6%) 489 0.0279
(0.0772) 		0.0061
(0.0225) 		0.316
(0.468) 		0.0446
(0.111) 		0.0612
(0.143) 		0.0634
(0.146) 		0.0574
(0.136) 		0.673
(0.79) 		0.199
(0.329) 		0.368
(0.516)
6q loss 68 (13%) 454 0.0453
(0.112) 		0.00345
(0.0137) 		0.738
(0.835) 		0.122
(0.231) 		0.726
(0.83) 		0.755
(0.844) 		0.761
(0.847) 		0.375
(0.522) 		0.766
(0.849) 		0.0214
(0.0619)
7p loss 29 (6%) 493 0.0296
(0.0811) 		0.00627
(0.023) 		0.915
(0.943) 		0.626
(0.754) 		0.363
(0.513) 		0.0824
(0.175) 		0.257
(0.401) 		0.763
(0.847) 		0.0216
(0.0621) 		0.775
(0.852)
10p loss 156 (30%) 366 1e-05
(9.65e-05) 		0.00334
(0.0134) 		0.718
(0.823) 		0.231
(0.373) 		0.0662
(0.149) 		0.0657
(0.148) 		0.0654
(0.148) 		0.0929
(0.192) 		0.023
(0.0653) 		0.24
(0.384)
10q loss 113 (22%) 409 1e-05
(9.65e-05) 		0.00071
(0.00353) 		0.362
(0.512) 		0.302
(0.454) 		0.0692
(0.155) 		0.104
(0.203) 		0.0299
(0.0812) 		0.145
(0.262) 		0.123
(0.231) 		0.166
(0.288)
16p loss 63 (12%) 459 6e-05
(0.000417) 		0.011
(0.0367) 		0.14
(0.256) 		0.0811
(0.173) 		0.00169
(0.00753) 		0.194
(0.323) 		0.658
(0.778) 		0.631
(0.757) 		0.179
(0.305) 		0.896
(0.934)
20p loss 47 (9%) 475 1e-05
(9.65e-05) 		0.0265
(0.0741) 		1
(1.00) 		0.775
(0.852) 		0.262
(0.407) 		0.0943
(0.193) 		0.324
(0.476) 		0.0222
(0.0637) 		0.116
(0.222) 		0.0945
(0.193)
4p gain 41 (8%) 481 0.0229
(0.0652) 		0.00211
(0.0092) 		0.821
(0.882) 		0.356
(0.505) 		0.144
(0.26) 		0.673
(0.79) 		0.0731
(0.161) 		0.644
(0.768) 		0.731
(0.832) 		0.327
(0.477)
6p gain 83 (16%) 439 0.00019
(0.00115) 		0.00246
(0.0105) 		0.241
(0.384) 		0.741
(0.836) 		0.686
(0.793) 		0.219
(0.358) 		0.605
(0.74) 		0.071
(0.158) 		0.323
(0.476) 		0.662
(0.78)
10q gain 34 (7%) 488 0.00468
(0.0178) 		0.242
(0.385) 		0.157
(0.277) 		0.404
(0.551) 		0.359
(0.509) 		0.142
(0.257) 		0.877
(0.92) 		0.0365
(0.095) 		0.216
(0.354) 		0.614
(0.748)
xp gain 53 (10%) 469 0.033
(0.0873) 		0.0326
(0.0865) 		0.468
(0.617) 		0.376
(0.523) 		0.616
(0.749) 		0.539
(0.682) 		0.696
(0.8) 		0.631
(0.757) 		0.302
(0.454) 		1
(1.00)
3q loss 61 (12%) 461 0.00901
(0.031) 		0.228
(0.37) 		0.624
(0.753) 		0.758
(0.845) 		0.628
(0.756) 		0.264
(0.408) 		1
(1.00) 		0.00749
(0.0269) 		0.365
(0.514) 		0.947
(0.967)
6p loss 68 (13%) 454 0.00041
(0.00216) 		0.00084
(0.00408) 		0.0721
(0.16) 		0.128
(0.239) 		0.0639
(0.147) 		0.12
(0.228) 		0.31
(0.463) 		0.682
(0.793) 		0.74
(0.836) 		0.0748
(0.164)
12q loss 33 (6%) 489 0.0455
(0.112) 		0.00121
(0.00557) 		0.541
(0.682) 		0.0958
(0.193) 		0.408
(0.555) 		0.964
(0.982) 		1
(1.00) 		0.19
(0.317) 		0.301
(0.454) 		0.216
(0.354)
17p loss 107 (20%) 415 0.00023
(0.00136) 		0.00102
(0.00475) 		0.936
(0.962) 		0.758
(0.845) 		0.695
(0.8) 		0.162
(0.284) 		0.395
(0.546) 		0.11
(0.212) 		0.345
(0.493) 		0.858
(0.91)
17q loss 34 (7%) 488 0.0127
(0.0406) 		0.111
(0.213) 		0.242
(0.385) 		0.506
(0.656) 		0.455
(0.602) 		0.0393
(0.101) 		0.742
(0.836) 		0.95
(0.969) 		0.873
(0.92) 		0.541
(0.682)
5q gain 68 (13%) 454 0.0491
(0.119) 		0.591
(0.731) 		0.336
(0.485) 		0.889
(0.929) 		0.818
(0.881) 		0.624
(0.753) 		0.679
(0.791) 		0.449
(0.596) 		0.858
(0.91) 		0.312
(0.465)
8p gain 155 (30%) 367 0.0225
(0.0644) 		0.247
(0.391) 		0.807
(0.872) 		0.641
(0.766) 		0.792
(0.864) 		0.904
(0.939) 		0.597
(0.736) 		0.788
(0.86) 		0.454
(0.601) 		0.136
(0.25)
8q loss 30 (6%) 492 0.0243
(0.0688) 		0.288
(0.44) 		0.319
(0.471) 		0.874
(0.92) 		0.783
(0.858) 		0.658
(0.778) 		0.373
(0.522) 		0.416
(0.561) 		0.651
(0.774) 		0.264
(0.408)
12p loss 37 (7%) 485 0.729
(0.832) 		0.0487
(0.118) 		0.616
(0.749) 		0.109
(0.211) 		0.909
(0.94) 		0.166
(0.288) 		0.819
(0.881) 		0.804
(0.871) 		0.339
(0.489) 		0.284
(0.436)
15q loss 103 (20%) 419 1e-05
(9.65e-05) 		0.168
(0.29) 		1
(1.00) 		0.347
(0.495) 		0.0843
(0.179) 		0.136
(0.25) 		0.608
(0.743) 		0.275
(0.424) 		0.0789
(0.17) 		0.94
(0.965)
4q gain 37 (7%) 485 0.902
(0.938) 		0.199
(0.329) 		1
(1.00) 		0.767
(0.849) 		0.839
(0.894) 		0.478
(0.627) 		1
(1.00) 		0.909
(0.94) 		0.684
(0.793) 		0.737
(0.835)
2q loss 46 (9%) 476 0.476
(0.627) 		0.216
(0.354) 		0.947
(0.967) 		0.676
(0.791) 		0.527
(0.67) 		0.902
(0.938) 		0.154
(0.274) 		0.687
(0.793) 		0.403
(0.55) 		0.167
(0.288)
7q loss 40 (8%) 482 0.367
(0.516) 		0.304
(0.456) 		0.574
(0.716) 		1
(1.00) 		0.181
(0.307) 		0.8
(0.871) 		0.102
(0.201) 		0.936
(0.962) 		0.748
(0.84) 		0.287
(0.438)
'1p gain' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00048

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
1P GAIN MUTATED 25 30 11 4
1P GAIN WILD-TYPE 130 105 178 39

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

'1p gain' versus 'METHLYATION_CNMF'

P value = 0.00967 (Fisher's exact test), Q value = 0.033

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
1P GAIN MUTATED 5 14 22 13 8 5 3
1P GAIN WILD-TYPE 79 65 74 79 70 70 15

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

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00538 (Fisher's exact test), Q value = 0.02

Table S3.  Gene #1: '1p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
1P GAIN MUTATED 26 29 15
1P GAIN WILD-TYPE 164 113 171

Figure S3.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S4.  Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
1Q GAIN MUTATED 36 57 21 7
1Q GAIN WILD-TYPE 119 78 168 36

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

'1q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S5.  Gene #2: '1q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
1Q GAIN MUTATED 7 27 25 38 15 5 4
1Q GAIN WILD-TYPE 77 52 71 54 63 70 14

Figure S5.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00048

Table S6.  Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
1Q GAIN MUTATED 25 70 25
1Q GAIN WILD-TYPE 116 142 136

Figure S6.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00067 (Fisher's exact test), Q value = 0.0034

Table S7.  Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
1Q GAIN MUTATED 31 40 35 14
1Q GAIN WILD-TYPE 145 63 135 51

Figure S7.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0015

Table S8.  Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
1Q GAIN MUTATED 70 22 29
1Q GAIN WILD-TYPE 151 130 116

Figure S8.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.0017

Table S9.  Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
1Q GAIN MUTATED 36 51 34
1Q GAIN WILD-TYPE 154 91 152

Figure S9.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.04

Table S10.  Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
1Q GAIN MUTATED 22 22 33 26 9
1Q GAIN WILD-TYPE 50 118 65 90 38

Figure S10.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S11.  Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
2P GAIN MUTATED 34 51 9 3
2P GAIN WILD-TYPE 121 84 180 40

Figure S11.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S12.  Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
2P GAIN MUTATED 5 30 18 35 3 5 1
2P GAIN WILD-TYPE 79 49 78 57 75 70 17

Figure S12.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.0342 (Fisher's exact test), Q value = 0.09

Table S13.  Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
2P GAIN MUTATED 30 47 20
2P GAIN WILD-TYPE 111 165 141

Figure S13.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S14.  Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
2P GAIN MUTATED 34 36 24 3
2P GAIN WILD-TYPE 142 67 146 62

Figure S14.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CNMF'

P value = 0.0211 (Fisher's exact test), Q value = 0.062

Table S15.  Gene #3: '2p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
2P GAIN MUTATED 51 18 27
2P GAIN WILD-TYPE 170 134 118

Figure S15.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0197 (Fisher's exact test), Q value = 0.058

Table S16.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
2P GAIN MUTATED 33 37 26
2P GAIN WILD-TYPE 157 105 160

Figure S16.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0022 (Fisher's exact test), Q value = 0.0095

Table S17.  Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
2P GAIN MUTATED 17 19 27 24 2
2P GAIN WILD-TYPE 55 121 71 92 45

Figure S17.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S18.  Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
2Q GAIN MUTATED 22 43 7 2
2Q GAIN WILD-TYPE 133 92 182 41

Figure S18.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S19.  Gene #4: '2q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
2Q GAIN MUTATED 3 25 15 26 1 2 2
2Q GAIN WILD-TYPE 81 54 81 66 77 73 16

Figure S19.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S20.  Gene #4: '2q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
2Q GAIN MUTATED 30 28 15 1
2Q GAIN WILD-TYPE 146 75 155 64

Figure S20.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0164 (Fisher's exact test), Q value = 0.05

Table S21.  Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
2Q GAIN MUTATED 15 17 19 16 1
2Q GAIN WILD-TYPE 57 123 79 100 46

Figure S21.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0397 (Fisher's exact test), Q value = 0.1

Table S22.  Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
2Q GAIN MUTATED 29 30 9
2Q GAIN WILD-TYPE 111 214 80

Figure S22.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p gain' versus 'METHLYATION_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0014

Table S23.  Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
3P GAIN MUTATED 13 11 11 15 26 4 1
3P GAIN WILD-TYPE 71 68 85 77 52 71 17

Figure S23.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 0.0126 (Fisher's exact test), Q value = 0.04

Table S24.  Gene #5: '3p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
3P GAIN MUTATED 18 45 17
3P GAIN WILD-TYPE 123 167 144

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

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0371 (Fisher's exact test), Q value = 0.096

Table S25.  Gene #5: '3p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
3P GAIN MUTATED 21 16 25 18
3P GAIN WILD-TYPE 155 87 145 47

Figure S25.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0293 (Fisher's exact test), Q value = 0.081

Table S26.  Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
3P GAIN MUTATED 21 44 6
3P GAIN WILD-TYPE 119 200 83

Figure S26.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00076

Table S27.  Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
3Q GAIN MUTATED 82 82 67 23
3Q GAIN WILD-TYPE 73 53 122 20

Figure S27.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S28.  Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
3Q GAIN MUTATED 32 46 51 54 46 15 10
3Q GAIN WILD-TYPE 52 33 45 38 32 60 8

Figure S28.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.0017

Table S29.  Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
3Q GAIN MUTATED 73 120 58
3Q GAIN WILD-TYPE 68 92 103

Figure S29.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 0.00886 (Fisher's exact test), Q value = 0.031

Table S30.  Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
3Q GAIN MUTATED 123 60 70
3Q GAIN WILD-TYPE 98 92 75

Figure S30.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0212 (Fisher's exact test), Q value = 0.062

Table S31.  Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
3Q GAIN MUTATED 40 51 54 51 23
3Q GAIN WILD-TYPE 32 89 44 65 24

Figure S31.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4p gain' versus 'CN_CNMF'

P value = 0.0229 (Fisher's exact test), Q value = 0.065

Table S32.  Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
4P GAIN MUTATED 21 8 9 3
4P GAIN WILD-TYPE 134 127 180 40

Figure S32.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

'4p gain' versus 'METHLYATION_CNMF'

P value = 0.00211 (Fisher's exact test), Q value = 0.0092

Table S33.  Gene #7: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
4P GAIN MUTATED 2 7 18 7 4 2 1
4P GAIN WILD-TYPE 82 72 78 85 74 73 17

Figure S33.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S34.  Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
5P GAIN MUTATED 80 67 39 15
5P GAIN WILD-TYPE 75 68 150 28

Figure S34.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.00221 (Fisher's exact test), Q value = 0.0095

Table S35.  Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
5P GAIN MUTATED 25 34 46 41 29 16 10
5P GAIN WILD-TYPE 59 45 50 51 49 59 8

Figure S35.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0324 (Fisher's exact test), Q value = 0.086

Table S36.  Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
5P GAIN MUTATED 72 66 60
5P GAIN WILD-TYPE 118 76 126

Figure S36.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 0.0491 (Fisher's exact test), Q value = 0.12

Table S37.  Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
5Q GAIN MUTATED 25 20 15 8
5Q GAIN WILD-TYPE 130 115 174 35

Figure S37.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0012

Table S38.  Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
6P GAIN MUTATED 35 24 14 10
6P GAIN WILD-TYPE 120 111 175 33

Figure S38.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 0.00246 (Fisher's exact test), Q value = 0.01

Table S39.  Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
6P GAIN MUTATED 7 20 24 15 6 8 3
6P GAIN WILD-TYPE 77 59 72 77 72 67 15

Figure S39.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q gain' versus 'CN_CNMF'

P value = 0.00202 (Fisher's exact test), Q value = 0.0089

Table S40.  Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
6Q GAIN MUTATED 26 17 11 9
6Q GAIN WILD-TYPE 129 118 178 34

Figure S40.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 0.0308 (Fisher's exact test), Q value = 0.083

Table S41.  Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
6Q GAIN MUTATED 6 12 19 12 3 9 2
6Q GAIN WILD-TYPE 78 67 77 80 75 66 16

Figure S41.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0417 (Fisher's exact test), Q value = 0.11

Table S42.  Gene #12: '6q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
6Q GAIN MUTATED 20 13 27 2
6Q GAIN WILD-TYPE 156 90 143 63

Figure S42.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S43.  Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
7P GAIN MUTATED 69 64 34 16
7P GAIN WILD-TYPE 86 71 155 27

Figure S43.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S44.  Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
7P GAIN MUTATED 22 34 42 51 5 22 7
7P GAIN WILD-TYPE 62 45 54 41 73 53 11

Figure S44.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S45.  Gene #13: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
7P GAIN MUTATED 60 47 68 5
7P GAIN WILD-TYPE 116 56 102 60

Figure S45.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S46.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
7P GAIN MUTATED 67 70 43
7P GAIN WILD-TYPE 123 72 143

Figure S46.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S47.  Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
7Q GAIN MUTATED 36 58 21 14
7Q GAIN WILD-TYPE 119 77 168 29

Figure S47.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S48.  Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
7Q GAIN MUTATED 10 27 25 46 5 12 4
7Q GAIN WILD-TYPE 74 52 71 46 73 63 14

Figure S48.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.002

Table S49.  Gene #14: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
7Q GAIN MUTATED 38 38 45 6
7Q GAIN WILD-TYPE 138 65 125 59

Figure S49.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 0.0133 (Fisher's exact test), Q value = 0.042

Table S50.  Gene #14: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
7Q GAIN MUTATED 69 29 30
7Q GAIN WILD-TYPE 152 123 115

Figure S50.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.0011

Table S51.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
7Q GAIN MUTATED 46 52 30
7Q GAIN WILD-TYPE 144 90 156

Figure S51.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 0.0225 (Fisher's exact test), Q value = 0.064

Table S52.  Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
8P GAIN MUTATED 41 51 46 17
8P GAIN WILD-TYPE 114 84 143 26

Figure S52.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00036

Table S53.  Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
8Q GAIN MUTATED 108 82 88 32
8Q GAIN WILD-TYPE 47 53 101 11

Figure S53.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00023

Table S54.  Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
8Q GAIN MUTATED 57 42 73 55 30 39 14
8Q GAIN WILD-TYPE 27 37 23 37 48 36 4

Figure S54.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00017

Table S55.  Gene #16: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
8Q GAIN MUTATED 117 55 111 23
8Q GAIN WILD-TYPE 59 48 59 42

Figure S55.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0105 (Fisher's exact test), Q value = 0.036

Table S56.  Gene #16: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
8Q GAIN MUTATED 127 85 96
8Q GAIN WILD-TYPE 63 57 90

Figure S56.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0402 (Fisher's exact test), Q value = 0.1

Table S57.  Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
8Q GAIN MUTATED 45 91 52 74 20
8Q GAIN WILD-TYPE 27 49 46 42 27

Figure S57.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S58.  Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
9P GAIN MUTATED 19 17 31 35
9P GAIN WILD-TYPE 136 118 158 8

Figure S58.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S59.  Gene #17: '9p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
9P GAIN MUTATED 12 6 16 18 13 34 3
9P GAIN WILD-TYPE 72 73 80 74 65 41 15

Figure S59.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p gain' versus 'MRNASEQ_CNMF'

P value = 0.004 (Fisher's exact test), Q value = 0.016

Table S60.  Gene #17: '9p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
9P GAIN MUTATED 25 29 44
9P GAIN WILD-TYPE 116 183 117

Figure S60.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-04 (Fisher's exact test), Q value = 0.0035

Table S61.  Gene #17: '9p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
9P GAIN MUTATED 31 16 47 4
9P GAIN WILD-TYPE 145 87 123 61

Figure S61.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_CNMF'

P value = 0.00759 (Fisher's exact test), Q value = 0.027

Table S62.  Gene #17: '9p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
9P GAIN MUTATED 34 43 25
9P GAIN WILD-TYPE 187 109 120

Figure S62.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00895 (Fisher's exact test), Q value = 0.031

Table S63.  Gene #17: '9p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
9P GAIN MUTATED 38 17 47
9P GAIN WILD-TYPE 152 125 139

Figure S63.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00082

Table S64.  Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
9P GAIN MUTATED 8 43 9 29 8
9P GAIN WILD-TYPE 64 97 89 87 39

Figure S64.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S65.  Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
9Q GAIN MUTATED 30 36 37 36
9Q GAIN WILD-TYPE 125 99 152 7

Figure S65.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'9q gain' versus 'METHLYATION_CNMF'

P value = 0.00307 (Fisher's exact test), Q value = 0.013

Table S66.  Gene #18: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
9Q GAIN MUTATED 17 17 24 24 17 36 4
9Q GAIN WILD-TYPE 67 62 72 68 61 39 14

Figure S66.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00097 (Fisher's exact test), Q value = 0.0046

Table S67.  Gene #18: '9q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
9Q GAIN MUTATED 44 25 60 7
9Q GAIN WILD-TYPE 132 78 110 58

Figure S67.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0498 (Fisher's exact test), Q value = 0.12

Table S68.  Gene #18: '9q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
9Q GAIN MUTATED 52 28 59
9Q GAIN WILD-TYPE 138 114 127

Figure S68.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10p gain' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 3e-04

Table S69.  Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
10P GAIN MUTATED 2 18 3 7 5 2 3
10P GAIN WILD-TYPE 82 61 93 85 73 73 15

Figure S69.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00074 (Fisher's exact test), Q value = 0.0037

Table S70.  Gene #19: '10p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
10P GAIN MUTATED 8 19 10 3
10P GAIN WILD-TYPE 168 84 160 62

Figure S70.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_CNMF'

P value = 0.0445 (Fisher's exact test), Q value = 0.11

Table S71.  Gene #19: '10p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
10P GAIN MUTATED 23 11 5
10P GAIN WILD-TYPE 198 141 140

Figure S71.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0169 (Fisher's exact test), Q value = 0.051

Table S72.  Gene #19: '10p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
10P GAIN MUTATED 8 18 13
10P GAIN WILD-TYPE 182 124 173

Figure S72.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 0.00468 (Fisher's exact test), Q value = 0.018

Table S73.  Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
10Q GAIN MUTATED 11 14 4 5
10Q GAIN WILD-TYPE 144 121 185 38

Figure S73.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

'10q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0365 (Fisher's exact test), Q value = 0.095

Table S74.  Gene #20: '10q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
10Q GAIN MUTATED 14 14 6
10Q GAIN WILD-TYPE 176 128 180

Figure S74.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11p gain' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00054

Table S75.  Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
11P GAIN MUTATED 34 10 14 8
11P GAIN WILD-TYPE 121 125 175 35

Figure S75.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S76.  Gene #21: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
11P GAIN MUTATED 3 4 26 13 5 11 4
11P GAIN WILD-TYPE 81 75 70 79 73 64 14

Figure S76.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p gain' versus 'MIRSEQ_CNMF'

P value = 0.0453 (Fisher's exact test), Q value = 0.11

Table S77.  Gene #21: '11p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
11P GAIN MUTATED 20 27 17
11P GAIN WILD-TYPE 201 125 128

Figure S77.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00336 (Fisher's exact test), Q value = 0.013

Table S78.  Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
11P GAIN MUTATED 4 27 6 19 3
11P GAIN WILD-TYPE 68 113 92 97 44

Figure S78.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00883 (Fisher's exact test), Q value = 0.031

Table S79.  Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
11P GAIN MUTATED 12 27 20
11P GAIN WILD-TYPE 128 217 69

Figure S79.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00023

Table S80.  Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
11Q GAIN MUTATED 37 16 13 5
11Q GAIN WILD-TYPE 118 119 176 38

Figure S80.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00023

Table S81.  Gene #22: '11q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
11Q GAIN MUTATED 4 12 24 14 2 10 5
11Q GAIN WILD-TYPE 80 67 72 78 76 65 13

Figure S81.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0174 (Fisher's exact test), Q value = 0.053

Table S82.  Gene #22: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
11Q GAIN MUTATED 28 26 15
11Q GAIN WILD-TYPE 162 116 171

Figure S82.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0175 (Fisher's exact test), Q value = 0.053

Table S83.  Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
11Q GAIN MUTATED 6 25 9 22 2
11Q GAIN WILD-TYPE 66 115 89 94 45

Figure S83.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S84.  Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
12P GAIN MUTATED 53 61 20 14
12P GAIN WILD-TYPE 102 74 169 29

Figure S84.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S85.  Gene #23: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
12P GAIN MUTATED 12 34 28 43 18 10 3
12P GAIN WILD-TYPE 72 45 68 49 60 65 15

Figure S85.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 0.0136 (Fisher's exact test), Q value = 0.043

Table S86.  Gene #23: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
12P GAIN MUTATED 39 74 34
12P GAIN WILD-TYPE 102 138 127

Figure S86.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 6e-04

Table S87.  Gene #23: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
12P GAIN MUTATED 50 48 35 14
12P GAIN WILD-TYPE 126 55 135 51

Figure S87.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 0.0125 (Fisher's exact test), Q value = 0.04

Table S88.  Gene #23: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
12P GAIN MUTATED 76 31 40
12P GAIN WILD-TYPE 145 121 105

Figure S88.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0379 (Fisher's exact test), Q value = 0.098

Table S89.  Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
12P GAIN MUTATED 23 37 39 27 9
12P GAIN WILD-TYPE 49 103 59 89 38

Figure S89.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00017

Table S90.  Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
12Q GAIN MUTATED 29 35 13 12
12Q GAIN WILD-TYPE 126 100 176 31

Figure S90.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 0.00108 (Fisher's exact test), Q value = 0.005

Table S91.  Gene #24: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
12Q GAIN MUTATED 5 22 20 20 14 6 2
12Q GAIN WILD-TYPE 79 57 76 72 64 69 16

Figure S91.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00803 (Fisher's exact test), Q value = 0.028

Table S92.  Gene #24: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
12Q GAIN MUTATED 29 29 20 10
12Q GAIN WILD-TYPE 147 74 150 55

Figure S92.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S93.  Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
13Q GAIN MUTATED 35 12 8 2
13Q GAIN WILD-TYPE 120 123 181 41

Figure S93.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 0.00259 (Fisher's exact test), Q value = 0.011

Table S94.  Gene #25: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
13Q GAIN MUTATED 5 11 17 10 4 4 6
13Q GAIN WILD-TYPE 79 68 79 82 74 71 12

Figure S94.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 0.00102 (Fisher's exact test), Q value = 0.0048

Table S95.  Gene #25: '13q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
13Q GAIN MUTATED 22 11 23
13Q GAIN WILD-TYPE 119 201 138

Figure S95.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00575 (Fisher's exact test), Q value = 0.022

Table S96.  Gene #25: '13q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
13Q GAIN MUTATED 28 12 15 1
13Q GAIN WILD-TYPE 148 91 155 64

Figure S96.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0266 (Fisher's exact test), Q value = 0.074

Table S97.  Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
13Q GAIN MUTATED 6 18 4 18 2
13Q GAIN WILD-TYPE 66 122 94 98 45

Figure S97.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'13q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0152 (Fisher's exact test), Q value = 0.047

Table S98.  Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
13Q GAIN MUTATED 23 17 8
13Q GAIN WILD-TYPE 117 227 81

Figure S98.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S99.  Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
14Q GAIN MUTATED 73 42 19 17
14Q GAIN WILD-TYPE 82 93 170 26

Figure S99.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S100.  Gene #26: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
14Q GAIN MUTATED 21 26 40 35 4 19 6
14Q GAIN WILD-TYPE 63 53 56 57 74 56 12

Figure S100.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.00997 (Fisher's exact test), Q value = 0.034

Table S101.  Gene #26: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
14Q GAIN MUTATED 50 46 52
14Q GAIN WILD-TYPE 91 166 109

Figure S101.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S102.  Gene #26: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
14Q GAIN MUTATED 59 36 51 2
14Q GAIN WILD-TYPE 117 67 119 63

Figure S102.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 0.00643 (Fisher's exact test), Q value = 0.023

Table S103.  Gene #26: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
14Q GAIN MUTATED 50 45 55
14Q GAIN WILD-TYPE 171 107 90

Figure S103.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.002

Table S104.  Gene #26: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
14Q GAIN MUTATED 69 46 35
14Q GAIN WILD-TYPE 121 96 151

Figure S104.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S105.  Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
14Q GAIN MUTATED 22 52 18 45 4
14Q GAIN WILD-TYPE 50 88 80 71 43

Figure S105.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.002

Table S106.  Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
14Q GAIN MUTATED 50 54 37
14Q GAIN WILD-TYPE 90 190 52

Figure S106.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q gain' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 6e-04

Table S107.  Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
15Q GAIN MUTATED 29 28 11 4
15Q GAIN WILD-TYPE 126 107 178 39

Figure S107.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

'15q gain' versus 'METHLYATION_CNMF'

P value = 0.00644 (Fisher's exact test), Q value = 0.023

Table S108.  Gene #27: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
15Q GAIN MUTATED 6 15 20 13 3 12 3
15Q GAIN WILD-TYPE 78 64 76 79 75 63 15

Figure S108.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.035 (Fisher's exact test), Q value = 0.092

Table S109.  Gene #27: '15q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
15Q GAIN MUTATED 21 19 28 3
15Q GAIN WILD-TYPE 155 84 142 62

Figure S109.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0058 (Fisher's exact test), Q value = 0.022

Table S110.  Gene #27: '15q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
15Q GAIN MUTATED 23 31 18
15Q GAIN WILD-TYPE 167 111 168

Figure S110.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.036 (Fisher's exact test), Q value = 0.094

Table S111.  Gene #27: '15q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
15Q GAIN MUTATED 7 18 13 25 2
15Q GAIN WILD-TYPE 65 122 85 91 45

Figure S111.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S112.  Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
16P GAIN MUTATED 52 34 14 7
16P GAIN WILD-TYPE 103 101 175 36

Figure S112.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S113.  Gene #28: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
16P GAIN MUTATED 13 32 29 18 7 3 5
16P GAIN WILD-TYPE 71 47 67 74 71 72 13

Figure S113.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0141 (Fisher's exact test), Q value = 0.044

Table S114.  Gene #28: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
16P GAIN MUTATED 39 28 34 5
16P GAIN WILD-TYPE 137 75 136 60

Figure S114.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00023

Table S115.  Gene #28: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
16P GAIN MUTATED 42 44 20
16P GAIN WILD-TYPE 148 98 166

Figure S115.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S116.  Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
16Q GAIN MUTATED 56 32 14 5
16Q GAIN WILD-TYPE 99 103 175 38

Figure S116.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S117.  Gene #29: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
16Q GAIN MUTATED 13 26 32 20 7 5 4
16Q GAIN WILD-TYPE 71 53 64 72 71 70 14

Figure S117.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00694 (Fisher's exact test), Q value = 0.025

Table S118.  Gene #29: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
16Q GAIN MUTATED 44 23 34 4
16Q GAIN WILD-TYPE 132 80 136 61

Figure S118.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00042

Table S119.  Gene #29: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
16Q GAIN MUTATED 48 39 19
16Q GAIN WILD-TYPE 142 103 167

Figure S119.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S120.  Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
17P GAIN MUTATED 21 33 7 6
17P GAIN WILD-TYPE 134 102 182 37

Figure S120.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00065

Table S121.  Gene #30: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
17P GAIN MUTATED 7 13 13 26 3 4 1
17P GAIN WILD-TYPE 77 66 83 66 75 71 17

Figure S121.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 0.0021 (Fisher's exact test), Q value = 0.0092

Table S122.  Gene #30: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
17P GAIN MUTATED 23 34 9
17P GAIN WILD-TYPE 118 178 152

Figure S122.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00326 (Fisher's exact test), Q value = 0.013

Table S123.  Gene #30: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
17P GAIN MUTATED 25 23 14 4
17P GAIN WILD-TYPE 151 80 156 61

Figure S123.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0463 (Fisher's exact test), Q value = 0.11

Table S124.  Gene #30: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
17P GAIN MUTATED 31 19 15
17P GAIN WILD-TYPE 159 123 171

Figure S124.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S125.  Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
17Q GAIN MUTATED 24 41 13 9
17Q GAIN WILD-TYPE 131 94 176 34

Figure S125.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.0029

Table S126.  Gene #31: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
17Q GAIN MUTATED 9 21 19 24 6 6 2
17Q GAIN WILD-TYPE 75 58 77 68 72 69 16

Figure S126.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00133 (Fisher's exact test), Q value = 0.0061

Table S127.  Gene #31: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
17Q GAIN MUTATED 27 31 21 7
17Q GAIN WILD-TYPE 149 72 149 58

Figure S127.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00365 (Fisher's exact test), Q value = 0.014

Table S128.  Gene #31: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
17Q GAIN MUTATED 33 34 19
17Q GAIN WILD-TYPE 157 108 167

Figure S128.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S129.  Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
18P GAIN MUTATED 49 48 18 8
18P GAIN WILD-TYPE 106 87 171 35

Figure S129.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S130.  Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
18P GAIN MUTATED 7 35 25 27 18 8 3
18P GAIN WILD-TYPE 77 44 71 65 60 67 15

Figure S130.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00036

Table S131.  Gene #32: '18p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
18P GAIN MUTATED 38 42 27 14
18P GAIN WILD-TYPE 138 61 143 51

Figure S131.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0151 (Fisher's exact test), Q value = 0.047

Table S132.  Gene #32: '18p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
18P GAIN MUTATED 42 46 35
18P GAIN WILD-TYPE 148 96 151

Figure S132.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00082 (Fisher's exact test), Q value = 0.004

Table S133.  Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
18P GAIN MUTATED 19 24 37 25 5
18P GAIN WILD-TYPE 53 116 61 91 42

Figure S133.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18q gain' versus 'CN_CNMF'

P value = 0.0015 (Fisher's exact test), Q value = 0.0068

Table S134.  Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
18Q GAIN MUTATED 7 25 17 4
18Q GAIN WILD-TYPE 148 110 172 39

Figure S134.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00017

Table S135.  Gene #33: '18q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
18Q GAIN MUTATED 1 14 5 11 18 3 1
18Q GAIN WILD-TYPE 83 65 91 81 60 72 17

Figure S135.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0017

Table S136.  Gene #33: '18q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
18Q GAIN MUTATED 13 34 6
18Q GAIN WILD-TYPE 128 178 155

Figure S136.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.001

Table S137.  Gene #33: '18q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
18Q GAIN MUTATED 12 18 9 14
18Q GAIN WILD-TYPE 164 85 161 51

Figure S137.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00017

Table S138.  Gene #33: '18q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
18Q GAIN MUTATED 37 4 12
18Q GAIN WILD-TYPE 184 148 133

Figure S138.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00036

Table S139.  Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
18Q GAIN MUTATED 8 4 21 7 6
18Q GAIN WILD-TYPE 64 136 77 109 41

Figure S139.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.043

Table S140.  Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
19P GAIN MUTATED 12 24 14 6
19P GAIN WILD-TYPE 143 111 175 37

Figure S140.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00017

Table S141.  Gene #34: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
19P GAIN MUTATED 2 7 5 21 17 3 1
19P GAIN WILD-TYPE 82 72 91 71 61 72 17

Figure S141.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 0.0202 (Fisher's exact test), Q value = 0.059

Table S142.  Gene #34: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
19P GAIN MUTATED 11 32 11
19P GAIN WILD-TYPE 130 180 150

Figure S142.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0152 (Fisher's exact test), Q value = 0.047

Table S143.  Gene #34: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
19P GAIN MUTATED 12 16 14 12
19P GAIN WILD-TYPE 164 87 156 53

Figure S143.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.0021

Table S144.  Gene #34: '19p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
19P GAIN MUTATED 38 10 8
19P GAIN WILD-TYPE 183 142 137

Figure S144.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.0022

Table S145.  Gene #35: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
19Q GAIN MUTATED 4 12 11 23 20 6 2
19Q GAIN WILD-TYPE 80 67 85 69 58 69 16

Figure S145.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0443 (Fisher's exact test), Q value = 0.11

Table S146.  Gene #35: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
19Q GAIN MUTATED 18 22 23 13
19Q GAIN WILD-TYPE 158 81 147 52

Figure S146.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 0.00064 (Fisher's exact test), Q value = 0.0032

Table S147.  Gene #35: '19q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
19Q GAIN MUTATED 49 15 14
19Q GAIN WILD-TYPE 172 137 131

Figure S147.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S148.  Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
20P GAIN MUTATED 80 49 44 17
20P GAIN WILD-TYPE 75 86 145 26

Figure S148.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00042

Table S149.  Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
20P GAIN MUTATED 26 27 54 40 19 17 7
20P GAIN WILD-TYPE 58 52 42 52 59 58 11

Figure S149.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00455 (Fisher's exact test), Q value = 0.018

Table S150.  Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
20P GAIN MUTATED 78 34 61 13
20P GAIN WILD-TYPE 98 69 109 52

Figure S150.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0123 (Fisher's exact test), Q value = 0.04

Table S151.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
20P GAIN MUTATED 83 53 54
20P GAIN WILD-TYPE 107 89 132

Figure S151.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0391 (Fisher's exact test), Q value = 0.1

Table S152.  Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
20P GAIN MUTATED 59 75 37
20P GAIN WILD-TYPE 81 169 52

Figure S152.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S153.  Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
20Q GAIN MUTATED 88 54 41 18
20Q GAIN WILD-TYPE 67 81 148 25

Figure S153.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S154.  Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
20Q GAIN MUTATED 27 35 54 41 15 20 9
20Q GAIN WILD-TYPE 57 44 42 51 63 55 9

Figure S154.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 0.0303 (Fisher's exact test), Q value = 0.082

Table S155.  Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
20Q GAIN MUTATED 67 72 58
20Q GAIN WILD-TYPE 74 140 103

Figure S155.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00065

Table S156.  Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
20Q GAIN MUTATED 83 39 64 11
20Q GAIN WILD-TYPE 93 64 106 54

Figure S156.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00424 (Fisher's exact test), Q value = 0.016

Table S157.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
20Q GAIN MUTATED 89 55 56
20Q GAIN WILD-TYPE 101 87 130

Figure S157.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0356 (Fisher's exact test), Q value = 0.093

Table S158.  Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
20Q GAIN MUTATED 27 62 37 48 9
20Q GAIN WILD-TYPE 45 78 61 68 38

Figure S158.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0114 (Fisher's exact test), Q value = 0.038

Table S159.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
20Q GAIN MUTATED 66 79 38
20Q GAIN WILD-TYPE 74 165 51

Figure S159.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'METHLYATION_CNMF'

P value = 0.0406 (Fisher's exact test), Q value = 0.1

Table S160.  Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
21Q GAIN MUTATED 4 10 3 9 7 1 1
21Q GAIN WILD-TYPE 80 69 93 83 71 74 17

Figure S160.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 0.00564 (Fisher's exact test), Q value = 0.021

Table S161.  Gene #38: '21q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
21Q GAIN MUTATED 8 23 4
21Q GAIN WILD-TYPE 133 189 157

Figure S161.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'21q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00611 (Fisher's exact test), Q value = 0.022

Table S162.  Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
21Q GAIN MUTATED 6 4 14 4 2
21Q GAIN WILD-TYPE 66 136 84 112 45

Figure S162.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S163.  Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
22Q GAIN MUTATED 34 52 20 6
22Q GAIN WILD-TYPE 121 83 169 37

Figure S163.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S164.  Gene #39: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
22Q GAIN MUTATED 15 22 24 43 5 1 2
22Q GAIN WILD-TYPE 69 57 72 49 73 74 16

Figure S164.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.0016

Table S165.  Gene #39: '22q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
22Q GAIN MUTATED 38 37 30 6
22Q GAIN WILD-TYPE 138 66 140 59

Figure S165.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.0022

Table S166.  Gene #39: '22q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
22Q GAIN MUTATED 60 17 35
22Q GAIN WILD-TYPE 161 135 110

Figure S166.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0139 (Fisher's exact test), Q value = 0.043

Table S167.  Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
22Q GAIN MUTATED 19 22 23 33 4
22Q GAIN WILD-TYPE 53 118 75 83 43

Figure S167.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xp gain' versus 'CN_CNMF'

P value = 0.033 (Fisher's exact test), Q value = 0.087

Table S168.  Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
XP GAIN MUTATED 20 18 10 5
XP GAIN WILD-TYPE 135 117 179 38

Figure S168.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

'xp gain' versus 'METHLYATION_CNMF'

P value = 0.0326 (Fisher's exact test), Q value = 0.087

Table S169.  Gene #40: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
XP GAIN MUTATED 2 8 15 14 8 5 1
XP GAIN WILD-TYPE 82 71 81 78 70 70 17

Figure S169.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00023

Table S170.  Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
XQ GAIN MUTATED 41 30 15 9
XQ GAIN WILD-TYPE 114 105 174 34

Figure S170.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00036

Table S171.  Gene #41: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
XQ GAIN MUTATED 5 15 30 24 9 8 4
XQ GAIN WILD-TYPE 79 64 66 68 69 67 14

Figure S171.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0192 (Fisher's exact test), Q value = 0.057

Table S172.  Gene #41: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
XQ GAIN MUTATED 39 22 30 4
XQ GAIN WILD-TYPE 137 81 140 61

Figure S172.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0249 (Fisher's exact test), Q value = 0.07

Table S173.  Gene #41: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
XQ GAIN MUTATED 12 27 19 23 1
XQ GAIN WILD-TYPE 60 113 79 93 46

Figure S173.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S174.  Gene #42: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
1P LOSS MUTATED 18 30 7 3
1P LOSS WILD-TYPE 137 105 182 40

Figure S174.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S175.  Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
1P LOSS MUTATED 6 7 8 30 2 4 1
1P LOSS WILD-TYPE 78 72 88 62 76 71 17

Figure S175.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 0.00171 (Fisher's exact test), Q value = 0.0076

Table S176.  Gene #42: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
1P LOSS MUTATED 22 28 7
1P LOSS WILD-TYPE 119 184 154

Figure S176.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S177.  Gene #42: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
1P LOSS MUTATED 26 23 6 2
1P LOSS WILD-TYPE 150 80 164 63

Figure S177.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0201 (Fisher's exact test), Q value = 0.059

Table S178.  Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
1P LOSS MUTATED 20 28 3
1P LOSS WILD-TYPE 120 216 86

Figure S178.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 0.0169 (Fisher's exact test), Q value = 0.051

Table S179.  Gene #43: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
1Q LOSS MUTATED 18 11 6 4
1Q LOSS WILD-TYPE 137 124 183 39

Figure S179.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 0.0268 (Fisher's exact test), Q value = 0.075

Table S180.  Gene #43: '1q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
1Q LOSS MUTATED 17 9 12
1Q LOSS WILD-TYPE 124 203 149

Figure S180.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00287 (Fisher's exact test), Q value = 0.012

Table S181.  Gene #43: '1q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
1Q LOSS MUTATED 22 9 6 1
1Q LOSS WILD-TYPE 154 94 164 64

Figure S181.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00086 (Fisher's exact test), Q value = 0.0041

Table S182.  Gene #43: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
1Q LOSS MUTATED 22 12 4
1Q LOSS WILD-TYPE 168 130 182

Figure S182.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 0.0279 (Fisher's exact test), Q value = 0.077

Table S183.  Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
2P LOSS MUTATED 15 9 5 4
2P LOSS WILD-TYPE 140 126 184 39

Figure S183.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 0.0061 (Fisher's exact test), Q value = 0.022

Table S184.  Gene #44: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
2P LOSS MUTATED 2 1 15 5 5 4 1
2P LOSS WILD-TYPE 82 78 81 87 73 71 17

Figure S184.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0446 (Fisher's exact test), Q value = 0.11

Table S185.  Gene #44: '2p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 82 48
2P LOSS MUTATED 7 1 4
2P LOSS WILD-TYPE 69 81 44

Figure S185.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S186.  Gene #46: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
3P LOSS MUTATED 123 102 45 27
3P LOSS WILD-TYPE 32 33 144 16

Figure S186.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S187.  Gene #46: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
3P LOSS MUTATED 36 60 73 70 15 27 16
3P LOSS WILD-TYPE 48 19 23 22 63 48 2

Figure S187.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 0.0299 (Fisher's exact test), Q value = 0.081

Table S188.  Gene #46: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
3P LOSS MUTATED 93 110 90
3P LOSS WILD-TYPE 48 102 71

Figure S188.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S189.  Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
3P LOSS MUTATED 114 77 86 16
3P LOSS WILD-TYPE 62 26 84 49

Figure S189.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00076 (Fisher's exact test), Q value = 0.0037

Table S190.  Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
3P LOSS MUTATED 120 89 85
3P LOSS WILD-TYPE 70 53 101

Figure S190.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00054

Table S191.  Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
3P LOSS MUTATED 48 77 61 70 12
3P LOSS WILD-TYPE 24 63 37 46 35

Figure S191.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3q loss' versus 'CN_CNMF'

P value = 0.00901 (Fisher's exact test), Q value = 0.031

Table S192.  Gene #47: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
3Q LOSS MUTATED 25 20 11 5
3Q LOSS WILD-TYPE 130 115 178 38

Figure S192.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00749 (Fisher's exact test), Q value = 0.027

Table S193.  Gene #47: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
3Q LOSS MUTATED 21 26 13
3Q LOSS WILD-TYPE 169 116 173

Figure S193.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S194.  Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
4P LOSS MUTATED 67 89 24 14
4P LOSS WILD-TYPE 88 46 165 29

Figure S194.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S195.  Gene #48: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
4P LOSS MUTATED 17 43 29 61 21 12 11
4P LOSS WILD-TYPE 67 36 67 31 57 63 7

Figure S195.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.001

Table S196.  Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
4P LOSS MUTATED 59 93 39
4P LOSS WILD-TYPE 82 119 122

Figure S196.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S197.  Gene #48: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
4P LOSS MUTATED 72 58 43 18
4P LOSS WILD-TYPE 104 45 127 47

Figure S197.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0282 (Fisher's exact test), Q value = 0.078

Table S198.  Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
4P LOSS MUTATED 71 64 57
4P LOSS WILD-TYPE 119 78 129

Figure S198.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.0029

Table S199.  Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
4P LOSS MUTATED 36 39 44 44 9
4P LOSS WILD-TYPE 36 101 54 72 38

Figure S199.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S200.  Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
4Q LOSS MUTATED 51 70 17 13
4Q LOSS WILD-TYPE 104 65 172 30

Figure S200.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S201.  Gene #49: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
4Q LOSS MUTATED 14 32 27 48 15 11 4
4Q LOSS WILD-TYPE 70 47 69 44 63 64 14

Figure S201.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 0.00904 (Fisher's exact test), Q value = 0.031

Table S202.  Gene #49: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
4Q LOSS MUTATED 45 71 32
4Q LOSS WILD-TYPE 96 141 129

Figure S202.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00017

Table S203.  Gene #49: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
4Q LOSS MUTATED 58 46 31 13
4Q LOSS WILD-TYPE 118 57 139 52

Figure S203.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0297 (Fisher's exact test), Q value = 0.081

Table S204.  Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
4Q LOSS MUTATED 24 30 34 41 9
4Q LOSS WILD-TYPE 48 110 64 75 38

Figure S204.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00017

Table S205.  Gene #50: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
5P LOSS MUTATED 18 22 4 7
5P LOSS WILD-TYPE 137 113 185 36

Figure S205.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00017

Table S206.  Gene #50: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
5P LOSS MUTATED 1 15 14 16 2 2 1
5P LOSS WILD-TYPE 83 64 82 76 76 73 17

Figure S206.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0121 (Fisher's exact test), Q value = 0.04

Table S207.  Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
5P LOSS MUTATED 21 17 10 3
5P LOSS WILD-TYPE 155 86 160 62

Figure S207.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0245 (Fisher's exact test), Q value = 0.069

Table S208.  Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
5P LOSS MUTATED 22 17 8
5P LOSS WILD-TYPE 118 227 81

Figure S208.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S209.  Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
5Q LOSS MUTATED 62 76 16 10
5Q LOSS WILD-TYPE 93 59 173 33

Figure S209.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S210.  Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
5Q LOSS MUTATED 14 46 41 45 6 4 8
5Q LOSS WILD-TYPE 70 33 55 47 72 71 10

Figure S210.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S211.  Gene #51: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
5Q LOSS MUTATED 63 59 31 10
5Q LOSS WILD-TYPE 113 44 139 55

Figure S211.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 7e-04

Table S212.  Gene #51: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
5Q LOSS MUTATED 67 57 38
5Q LOSS WILD-TYPE 123 85 148

Figure S212.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0014

Table S213.  Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
5Q LOSS MUTATED 21 45 44 33 4
5Q LOSS WILD-TYPE 51 95 54 83 43

Figure S213.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6p loss' versus 'CN_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.0022

Table S214.  Gene #52: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
6P LOSS MUTATED 21 30 12 5
6P LOSS WILD-TYPE 134 105 177 38

Figure S214.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.00084 (Fisher's exact test), Q value = 0.0041

Table S215.  Gene #52: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
6P LOSS MUTATED 4 9 14 24 11 4 2
6P LOSS WILD-TYPE 80 70 82 68 67 71 16

Figure S215.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 0.0453 (Fisher's exact test), Q value = 0.11

Table S216.  Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
6Q LOSS MUTATED 18 26 17 7
6Q LOSS WILD-TYPE 137 109 172 36

Figure S216.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.00345 (Fisher's exact test), Q value = 0.014

Table S217.  Gene #53: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
6Q LOSS MUTATED 3 12 10 17 15 6 5
6Q LOSS WILD-TYPE 81 67 86 75 63 69 13

Figure S217.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0214 (Fisher's exact test), Q value = 0.062

Table S218.  Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
6Q LOSS MUTATED 18 37 4
6Q LOSS WILD-TYPE 122 207 85

Figure S218.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p loss' versus 'CN_CNMF'

P value = 0.0296 (Fisher's exact test), Q value = 0.081

Table S219.  Gene #54: '7p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
7P LOSS MUTATED 6 12 6 5
7P LOSS WILD-TYPE 149 123 183 38

Figure S219.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #1: 'CN_CNMF'

'7p loss' versus 'METHLYATION_CNMF'

P value = 0.00627 (Fisher's exact test), Q value = 0.023

Table S220.  Gene #54: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
7P LOSS MUTATED 1 7 5 7 9 0 0
7P LOSS WILD-TYPE 83 72 91 85 69 75 18

Figure S220.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0216 (Fisher's exact test), Q value = 0.062

Table S221.  Gene #54: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
7P LOSS MUTATED 0 8 11 5 3
7P LOSS WILD-TYPE 72 132 87 111 44

Figure S221.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S222.  Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
8P LOSS MUTATED 87 46 36 18
8P LOSS WILD-TYPE 68 89 153 25

Figure S222.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S223.  Gene #56: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
8P LOSS MUTATED 29 27 52 39 10 25 5
8P LOSS WILD-TYPE 55 52 44 53 68 50 13

Figure S223.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00017

Table S224.  Gene #56: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
8P LOSS MUTATED 72 39 66 6
8P LOSS WILD-TYPE 104 64 104 59

Figure S224.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00297 (Fisher's exact test), Q value = 0.012

Table S225.  Gene #56: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
8P LOSS MUTATED 83 53 50
8P LOSS WILD-TYPE 107 89 136

Figure S225.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00088

Table S226.  Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
8P LOSS MUTATED 30 60 28 48 5
8P LOSS WILD-TYPE 42 80 70 68 42

Figure S226.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00023

Table S227.  Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
8P LOSS MUTATED 63 65 43
8P LOSS WILD-TYPE 77 179 46

Figure S227.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 0.0243 (Fisher's exact test), Q value = 0.069

Table S228.  Gene #57: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
8Q LOSS MUTATED 13 9 4 4
8Q LOSS WILD-TYPE 142 126 185 39

Figure S228.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S229.  Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
9P LOSS MUTATED 79 81 25 1
9P LOSS WILD-TYPE 76 54 164 42

Figure S229.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S230.  Gene #58: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
9P LOSS MUTATED 20 51 37 52 9 8 9
9P LOSS WILD-TYPE 64 28 59 40 69 67 9

Figure S230.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S231.  Gene #58: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
9P LOSS MUTATED 61 57 54 12
9P LOSS WILD-TYPE 115 46 116 53

Figure S231.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00042

Table S232.  Gene #58: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
9P LOSS MUTATED 64 72 48
9P LOSS WILD-TYPE 126 70 138

Figure S232.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S233.  Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
9P LOSS MUTATED 32 40 53 34 7
9P LOSS WILD-TYPE 40 100 45 82 40

Figure S233.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S234.  Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
9Q LOSS MUTATED 41 32 13 1
9Q LOSS WILD-TYPE 114 103 176 42

Figure S234.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S235.  Gene #59: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
9Q LOSS MUTATED 5 26 17 26 4 4 5
9Q LOSS WILD-TYPE 79 53 79 66 74 71 13

Figure S235.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0138 (Fisher's exact test), Q value = 0.043

Table S236.  Gene #59: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
9Q LOSS MUTATED 32 25 25 4
9Q LOSS WILD-TYPE 144 78 145 61

Figure S236.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00314 (Fisher's exact test), Q value = 0.013

Table S237.  Gene #59: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
9Q LOSS MUTATED 33 34 19
9Q LOSS WILD-TYPE 157 108 167

Figure S237.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0132 (Fisher's exact test), Q value = 0.042

Table S238.  Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
9Q LOSS MUTATED 19 19 20 21 2
9Q LOSS WILD-TYPE 53 121 78 95 45

Figure S238.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S239.  Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
10P LOSS MUTATED 68 46 27 15
10P LOSS WILD-TYPE 87 89 162 28

Figure S239.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.00334 (Fisher's exact test), Q value = 0.013

Table S240.  Gene #60: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
10P LOSS MUTATED 16 24 39 35 14 21 7
10P LOSS WILD-TYPE 68 55 57 57 64 54 11

Figure S240.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.023 (Fisher's exact test), Q value = 0.065

Table S241.  Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
10P LOSS MUTATED 25 40 23 47 9
10P LOSS WILD-TYPE 47 100 75 69 38

Figure S241.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S242.  Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
10Q LOSS MUTATED 40 47 19 7
10Q LOSS WILD-TYPE 115 88 170 36

Figure S242.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.0035

Table S243.  Gene #61: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
10Q LOSS MUTATED 8 19 26 31 13 10 6
10Q LOSS WILD-TYPE 76 60 70 61 65 65 12

Figure S243.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 0.0299 (Fisher's exact test), Q value = 0.081

Table S244.  Gene #61: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
10Q LOSS MUTATED 57 22 31
10Q LOSS WILD-TYPE 164 130 114

Figure S244.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S245.  Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
11P LOSS MUTATED 38 71 26 6
11P LOSS WILD-TYPE 117 64 163 37

Figure S245.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0012

Table S246.  Gene #62: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
11P LOSS MUTATED 22 27 21 38 21 7 5
11P LOSS WILD-TYPE 62 52 75 54 57 68 13

Figure S246.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 0.00097 (Fisher's exact test), Q value = 0.0046

Table S247.  Gene #62: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
11P LOSS MUTATED 38 73 28
11P LOSS WILD-TYPE 103 139 133

Figure S247.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 0.0038 (Fisher's exact test), Q value = 0.015

Table S248.  Gene #62: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
11P LOSS MUTATED 76 29 36
11P LOSS WILD-TYPE 145 123 109

Figure S248.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S249.  Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
11Q LOSS MUTATED 43 71 44 14
11Q LOSS WILD-TYPE 112 64 145 29

Figure S249.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00017

Table S250.  Gene #63: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
11Q LOSS MUTATED 21 23 29 39 44 11 5
11Q LOSS WILD-TYPE 63 56 67 53 34 64 13

Figure S250.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.002

Table S251.  Gene #63: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
11Q LOSS MUTATED 45 88 36
11Q LOSS WILD-TYPE 96 124 125

Figure S251.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00281 (Fisher's exact test), Q value = 0.012

Table S252.  Gene #63: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
11Q LOSS MUTATED 52 30 52 35
11Q LOSS WILD-TYPE 124 73 118 30

Figure S252.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'METHLYATION_CNMF'

P value = 0.0487 (Fisher's exact test), Q value = 0.12

Table S253.  Gene #64: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
12P LOSS MUTATED 2 4 8 7 9 3 4
12P LOSS WILD-TYPE 82 75 88 85 69 72 14

Figure S253.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q loss' versus 'CN_CNMF'

P value = 0.0455 (Fisher's exact test), Q value = 0.11

Table S254.  Gene #65: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
12Q LOSS MUTATED 14 12 6 1
12Q LOSS WILD-TYPE 141 123 183 42

Figure S254.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 0.00121 (Fisher's exact test), Q value = 0.0056

Table S255.  Gene #65: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
12Q LOSS MUTATED 1 5 7 12 5 0 3
12Q LOSS WILD-TYPE 83 74 89 80 73 75 15

Figure S255.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S256.  Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
13Q LOSS MUTATED 37 79 36 15
13Q LOSS WILD-TYPE 118 56 153 28

Figure S256.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S257.  Gene #66: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
13Q LOSS MUTATED 18 37 30 43 25 13 1
13Q LOSS WILD-TYPE 66 42 66 49 53 62 17

Figure S257.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0016

Table S258.  Gene #66: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
13Q LOSS MUTATED 45 86 34
13Q LOSS WILD-TYPE 96 126 127

Figure S258.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00515 (Fisher's exact test), Q value = 0.02

Table S259.  Gene #66: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
13Q LOSS MUTATED 56 47 42 20
13Q LOSS WILD-TYPE 120 56 128 45

Figure S259.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 0.0397 (Fisher's exact test), Q value = 0.1

Table S260.  Gene #66: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
13Q LOSS MUTATED 84 40 42
13Q LOSS WILD-TYPE 137 112 103

Figure S260.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 0.00287 (Fisher's exact test), Q value = 0.012

Table S261.  Gene #67: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
14Q LOSS MUTATED 3 13 7 15 15 4 1
14Q LOSS WILD-TYPE 81 66 89 77 63 71 17

Figure S261.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 3e-04

Table S262.  Gene #67: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
14Q LOSS MUTATED 13 38 6
14Q LOSS WILD-TYPE 128 174 155

Figure S262.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00155 (Fisher's exact test), Q value = 0.0069

Table S263.  Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
14Q LOSS MUTATED 16 17 10 14
14Q LOSS WILD-TYPE 160 86 160 51

Figure S263.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.003

Table S264.  Gene #67: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
14Q LOSS MUTATED 38 8 11
14Q LOSS WILD-TYPE 183 144 134

Figure S264.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00023

Table S265.  Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
14Q LOSS MUTATED 8 6 24 8 9
14Q LOSS WILD-TYPE 64 134 74 108 38

Figure S265.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0123 (Fisher's exact test), Q value = 0.04

Table S266.  Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
14Q LOSS MUTATED 17 35 3
14Q LOSS WILD-TYPE 123 209 86

Figure S266.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S267.  Gene #68: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
15Q LOSS MUTATED 43 26 17 17
15Q LOSS WILD-TYPE 112 109 172 26

Figure S267.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16p loss' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00042

Table S268.  Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
16P LOSS MUTATED 17 28 9 9
16P LOSS WILD-TYPE 138 107 180 34

Figure S268.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.037

Table S269.  Gene #69: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
16P LOSS MUTATED 7 8 9 22 10 4 3
16P LOSS WILD-TYPE 77 71 87 70 68 71 15

Figure S269.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 0.00169 (Fisher's exact test), Q value = 0.0075

Table S270.  Gene #69: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
16P LOSS MUTATED 20 34 8
16P LOSS WILD-TYPE 121 178 153

Figure S270.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 0.00217 (Fisher's exact test), Q value = 0.0094

Table S271.  Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
16Q LOSS MUTATED 14 32 25 10
16Q LOSS WILD-TYPE 141 103 164 33

Figure S271.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S272.  Gene #70: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
16Q LOSS MUTATED 5 12 4 26 27 4 3
16Q LOSS WILD-TYPE 79 67 92 66 51 71 15

Figure S272.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S273.  Gene #70: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
16Q LOSS MUTATED 15 59 7
16Q LOSS WILD-TYPE 126 153 154

Figure S273.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S274.  Gene #70: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
16Q LOSS MUTATED 18 25 12 26
16Q LOSS WILD-TYPE 158 78 158 39

Figure S274.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 0.00776 (Fisher's exact test), Q value = 0.028

Table S275.  Gene #70: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
16Q LOSS MUTATED 47 18 15
16Q LOSS WILD-TYPE 174 134 130

Figure S275.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0088 (Fisher's exact test), Q value = 0.031

Table S276.  Gene #70: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
16Q LOSS MUTATED 19 21 40
16Q LOSS WILD-TYPE 171 121 146

Figure S276.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S277.  Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
16Q LOSS MUTATED 9 11 32 9 10
16Q LOSS WILD-TYPE 63 129 66 107 37

Figure S277.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00274 (Fisher's exact test), Q value = 0.012

Table S278.  Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
16Q LOSS MUTATED 14 50 7
16Q LOSS WILD-TYPE 126 194 82

Figure S278.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0014

Table S279.  Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
17P LOSS MUTATED 41 37 20 9
17P LOSS WILD-TYPE 114 98 169 34

Figure S279.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.00102 (Fisher's exact test), Q value = 0.0048

Table S280.  Gene #71: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
17P LOSS MUTATED 8 26 22 22 17 7 5
17P LOSS WILD-TYPE 76 53 74 70 61 68 13

Figure S280.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q loss' versus 'CN_CNMF'

P value = 0.0127 (Fisher's exact test), Q value = 0.041

Table S281.  Gene #72: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
17Q LOSS MUTATED 13 10 5 6
17Q LOSS WILD-TYPE 142 125 184 37

Figure S281.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0393 (Fisher's exact test), Q value = 0.1

Table S282.  Gene #72: '17q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
17Q LOSS MUTATED 15 1 13 4
17Q LOSS WILD-TYPE 161 102 157 61

Figure S282.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 0.00154 (Fisher's exact test), Q value = 0.0069

Table S283.  Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
18P LOSS MUTATED 43 26 23 12
18P LOSS WILD-TYPE 112 109 166 31

Figure S283.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00023

Table S284.  Gene #73: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
18P LOSS MUTATED 18 15 23 30 2 11 5
18P LOSS WILD-TYPE 66 64 73 62 76 64 13

Figure S284.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00362 (Fisher's exact test), Q value = 0.014

Table S285.  Gene #73: '18p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
18P LOSS MUTATED 37 22 40 3
18P LOSS WILD-TYPE 139 81 130 62

Figure S285.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0124 (Fisher's exact test), Q value = 0.04

Table S286.  Gene #73: '18p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
18P LOSS MUTATED 42 35 24
18P LOSS WILD-TYPE 148 107 162

Figure S286.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S287.  Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
18Q LOSS MUTATED 106 51 33 21
18Q LOSS WILD-TYPE 49 84 156 22

Figure S287.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S288.  Gene #74: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
18Q LOSS MUTATED 35 40 56 47 2 22 9
18Q LOSS WILD-TYPE 49 39 40 45 76 53 9

Figure S288.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.0043

Table S289.  Gene #74: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
18Q LOSS MUTATED 71 66 70
18Q LOSS WILD-TYPE 70 146 91

Figure S289.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S290.  Gene #74: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
18Q LOSS MUTATED 85 47 72 3
18Q LOSS WILD-TYPE 91 56 98 62

Figure S290.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.0043

Table S291.  Gene #74: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
18Q LOSS MUTATED 70 65 74
18Q LOSS WILD-TYPE 151 87 71

Figure S291.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00023

Table S292.  Gene #74: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
18Q LOSS MUTATED 93 65 51
18Q LOSS WILD-TYPE 97 77 135

Figure S292.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00036

Table S293.  Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
18Q LOSS MUTATED 29 65 31 59 7
18Q LOSS WILD-TYPE 43 75 67 57 40

Figure S293.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S294.  Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
19P LOSS MUTATED 48 26 16 8
19P LOSS WILD-TYPE 107 109 173 35

Figure S294.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00042

Table S295.  Gene #75: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
19P LOSS MUTATED 8 13 33 23 7 10 4
19P LOSS WILD-TYPE 76 66 63 69 71 65 14

Figure S295.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00882 (Fisher's exact test), Q value = 0.031

Table S296.  Gene #75: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
19P LOSS MUTATED 43 19 30 4
19P LOSS WILD-TYPE 133 84 140 61

Figure S296.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 0.0215 (Fisher's exact test), Q value = 0.062

Table S297.  Gene #75: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
19P LOSS MUTATED 33 25 38
19P LOSS WILD-TYPE 188 127 107

Figure S297.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00406 (Fisher's exact test), Q value = 0.016

Table S298.  Gene #75: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
19P LOSS MUTATED 45 30 21
19P LOSS WILD-TYPE 145 112 165

Figure S298.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.037

Table S299.  Gene #75: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
19P LOSS MUTATED 13 29 11 30 3
19P LOSS WILD-TYPE 59 111 87 86 44

Figure S299.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0372 (Fisher's exact test), Q value = 0.096

Table S300.  Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
19P LOSS MUTATED 30 34 22
19P LOSS WILD-TYPE 110 210 67

Figure S300.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S301.  Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
19Q LOSS MUTATED 37 32 9 8
19Q LOSS WILD-TYPE 118 103 180 35

Figure S301.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00023

Table S302.  Gene #76: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
19Q LOSS MUTATED 6 13 27 26 5 7 2
19Q LOSS WILD-TYPE 78 66 69 66 73 68 16

Figure S302.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00771 (Fisher's exact test), Q value = 0.027

Table S303.  Gene #76: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
19Q LOSS MUTATED 36 21 24 3
19Q LOSS WILD-TYPE 140 82 146 62

Figure S303.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0324 (Fisher's exact test), Q value = 0.086

Table S304.  Gene #76: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
19Q LOSS MUTATED 38 26 20
19Q LOSS WILD-TYPE 152 116 166

Figure S304.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0408 (Fisher's exact test), Q value = 0.1

Table S305.  Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
19Q LOSS MUTATED 21 32 22
19Q LOSS WILD-TYPE 119 212 67

Figure S305.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S306.  Gene #77: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
20P LOSS MUTATED 14 27 5 1
20P LOSS WILD-TYPE 141 108 184 42

Figure S306.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

'20p loss' versus 'METHLYATION_CNMF'

P value = 0.0265 (Fisher's exact test), Q value = 0.074

Table S307.  Gene #77: '20p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
20P LOSS MUTATED 3 10 8 16 6 4 0
20P LOSS WILD-TYPE 81 69 88 76 72 71 18

Figure S307.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0222 (Fisher's exact test), Q value = 0.064

Table S308.  Gene #77: '20p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
20P LOSS MUTATED 10 20 16
20P LOSS WILD-TYPE 180 122 170

Figure S308.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q loss' versus 'CN_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0016

Table S309.  Gene #78: '20q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
20Q LOSS MUTATED 3 17 8 0
20Q LOSS WILD-TYPE 152 118 181 43

Figure S309.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #1: 'CN_CNMF'

'20q loss' versus 'METHLYATION_CNMF'

P value = 0.00466 (Fisher's exact test), Q value = 0.018

Table S310.  Gene #78: '20q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
20Q LOSS MUTATED 0 6 2 10 7 2 1
20Q LOSS WILD-TYPE 84 73 94 82 71 73 17

Figure S310.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q loss' versus 'MRNASEQ_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.04

Table S311.  Gene #78: '20q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
20Q LOSS MUTATED 3 19 6
20Q LOSS WILD-TYPE 138 193 155

Figure S311.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0191 (Fisher's exact test), Q value = 0.057

Table S312.  Gene #78: '20q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
20Q LOSS MUTATED 4 9 8 7
20Q LOSS WILD-TYPE 172 94 162 58

Figure S312.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0484 (Fisher's exact test), Q value = 0.12

Table S313.  Gene #78: '20q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
20Q LOSS MUTATED 5 12 11
20Q LOSS WILD-TYPE 185 130 175

Figure S313.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0191 (Fisher's exact test), Q value = 0.057

Table S314.  Gene #78: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
20Q LOSS MUTATED 3 2 11 6 3
20Q LOSS WILD-TYPE 69 138 87 110 44

Figure S314.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.03 (Fisher's exact test), Q value = 0.081

Table S315.  Gene #78: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
20Q LOSS MUTATED 5 19 1
20Q LOSS WILD-TYPE 135 225 88

Figure S315.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S316.  Gene #79: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
21Q LOSS MUTATED 77 66 23 18
21Q LOSS WILD-TYPE 78 69 166 25

Figure S316.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S317.  Gene #79: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
21Q LOSS MUTATED 22 29 50 47 9 19 8
21Q LOSS WILD-TYPE 62 50 46 45 69 56 10

Figure S317.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.04

Table S318.  Gene #79: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
21Q LOSS MUTATED 63 62 57
21Q LOSS WILD-TYPE 78 150 104

Figure S318.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00017

Table S319.  Gene #79: '21q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
21Q LOSS MUTATED 80 41 52 9
21Q LOSS WILD-TYPE 96 62 118 56

Figure S319.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.002

Table S320.  Gene #79: '21q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
21Q LOSS MUTATED 79 59 45
21Q LOSS WILD-TYPE 111 83 141

Figure S320.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.0032

Table S321.  Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
21Q LOSS MUTATED 33 56 30 49 6
21Q LOSS WILD-TYPE 39 84 68 67 41

Figure S321.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 7e-04

Table S322.  Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
22Q LOSS MUTATED 34 17 13 11
22Q LOSS WILD-TYPE 121 118 176 32

Figure S322.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 0.00305 (Fisher's exact test), Q value = 0.013

Table S323.  Gene #80: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
22Q LOSS MUTATED 6 8 26 10 10 10 5
22Q LOSS WILD-TYPE 78 71 70 82 68 65 13

Figure S323.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 0.00234 (Fisher's exact test), Q value = 0.01

Table S324.  Gene #80: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
22Q LOSS MUTATED 19 19 35
22Q LOSS WILD-TYPE 122 193 126

Figure S324.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 0.00137 (Fisher's exact test), Q value = 0.0062

Table S325.  Gene #80: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
22Q LOSS MUTATED 22 35 16
22Q LOSS WILD-TYPE 199 117 129

Figure S325.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0175 (Fisher's exact test), Q value = 0.053

Table S326.  Gene #80: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
22Q LOSS MUTATED 8 32 9 12 5
22Q LOSS WILD-TYPE 64 108 89 104 42

Figure S326.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0475 (Fisher's exact test), Q value = 0.12

Table S327.  Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
22Q LOSS MUTATED 17 29 20
22Q LOSS WILD-TYPE 123 215 69

Figure S327.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S328.  Gene #81: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
XP LOSS MUTATED 55 50 23 6
XP LOSS WILD-TYPE 100 85 166 37

Figure S328.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S329.  Gene #81: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
XP LOSS MUTATED 15 21 29 44 13 6 6
XP LOSS WILD-TYPE 69 58 67 48 65 69 12

Figure S329.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0134 (Fisher's exact test), Q value = 0.043

Table S330.  Gene #81: 'xp loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 82 48
XP LOSS MUTATED 16 31 8
XP LOSS WILD-TYPE 60 51 40

Figure S330.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0432 (Fisher's exact test), Q value = 0.11

Table S331.  Gene #81: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
XP LOSS MUTATED 51 34 32 16
XP LOSS WILD-TYPE 125 69 138 49

Figure S331.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_CNMF'

P value = 0.0211 (Fisher's exact test), Q value = 0.062

Table S332.  Gene #81: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
XP LOSS MUTATED 67 27 37
XP LOSS WILD-TYPE 154 125 108

Figure S332.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S333.  Gene #82: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
XQ LOSS MUTATED 33 35 14 1
XQ LOSS WILD-TYPE 122 100 175 42

Figure S333.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.6e-05

Table S334.  Gene #82: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
XQ LOSS MUTATED 6 14 17 29 12 2 3
XQ LOSS WILD-TYPE 78 65 79 63 66 73 15

Figure S334.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'RPPA_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.037

Table S335.  Gene #82: 'xq loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 64 78
XQ LOSS MUTATED 10 3 17
XQ LOSS WILD-TYPE 54 61 61

Figure S335.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'xq loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.0022

Table S336.  Gene #82: 'xq loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 82 48
XQ LOSS MUTATED 5 22 3
XQ LOSS WILD-TYPE 71 60 45

Figure S336.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 0.032 (Fisher's exact test), Q value = 0.086

Table S337.  Gene #82: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 212 161
XQ LOSS MUTATED 19 44 18
XQ LOSS WILD-TYPE 122 168 143

Figure S337.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00606 (Fisher's exact test), Q value = 0.022

Table S338.  Gene #82: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 103 170 65
XQ LOSS MUTATED 23 25 18 15
XQ LOSS WILD-TYPE 153 78 152 50

Figure S338.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0018

Table S339.  Gene #82: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
XQ LOSS MUTATED 51 16 14
XQ LOSS WILD-TYPE 170 136 131

Figure S339.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

Methods & Data
Input

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

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/HNSC-TP/20144080/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/HNSC-TP/20125733/HNSC-TP.transferedmergedcluster.txt

  • Number of patients = 522

  • Number of significantly arm-level cnvs = 82

  • Number of molecular subtypes = 10

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

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

Download Results

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

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