Correlation between copy number variations of arm-level result and molecular subtypes
Colon Adenocarcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1BG2N69
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/C1BG2N69
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 81 arm-level events and 12 molecular subtypes across 450 patients, 301 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 1q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

  • 2q gain cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 3p gain cnv correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.

  • 3q gain cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 4q gain cnv correlated to 'MRNASEQ_CNMF'.

  • 5p gain cnv correlated to 'CN_CNMF'.

  • 5q gain cnv correlated to 'CN_CNMF'.

  • 6p gain cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 6q gain cnv correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.

  • 7p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 7q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 8p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

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

  • 9p gain cnv correlated to 'CN_CNMF'.

  • 9q gain cnv correlated to 'CN_CNMF'.

  • 10p gain cnv correlated to 'CN_CNMF'.

  • 10q gain cnv correlated to 'METHLYATION_CNMF'.

  • 11p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 11q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 12p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

  • 13q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 15q gain cnv correlated to 'RPPA_CNMF' and 'RPPA_CHIERARCHICAL'.

  • 16p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 16q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 17q gain cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

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

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

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

  • 19q gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 20p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 20q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 21q gain cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.

  • xp gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • xq gain cnv correlated to 'MRNA_CNMF',  'CN_CNMF', and 'RPPA_CNMF'.

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

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

  • 4p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • 6p loss cnv correlated to 'MIRSEQ_MATURE_CNMF'.

  • 7q loss cnv correlated to 'CN_CNMF'.

  • 8p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 8q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 10p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 10q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 11p loss cnv correlated to 'CN_CNMF'.

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

  • 12p loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 12q loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 13q loss cnv correlated to 'METHLYATION_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • 14q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 15q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 17p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 17q loss cnv correlated to 'CN_CNMF'.

  • 18p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 18q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 19p loss cnv correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 19q loss cnv correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 21q loss cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 22q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • xp loss cnv correlated to 'MRNA_CNMF',  'CN_CNMF', and 'RPPA_CNMF'.

  • xq loss cnv correlated to 'MRNA_CNMF',  'CN_CNMF', and 'RPPA_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 81 arm-level events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 301 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		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 Fisher's exact test Fisher's exact test
20q gain 321 (71%) 129 1e-05
(0.000116) 		1e-05
(0.000116) 		1e-05
(0.000116) 		1e-05
(0.000116) 		0.00723
(0.0332) 		1e-05
(0.000116) 		1e-05
(0.000116) 		1e-05
(0.000116) 		0.795
(0.94) 		0.00118
(0.00712) 		0.894
(0.993) 		0.00628
(0.0298)
7p gain 246 (55%) 204 0.00619
(0.0296) 		1e-05
(0.000116) 		1e-05
(0.000116) 		1e-05
(0.000116) 		0.0309
(0.11) 		0.00183
(0.0104) 		3e-05
(0.00031) 		1e-05
(0.000116) 		0.537
(0.779) 		0.481
(0.73) 		0.96
(1.00) 		0.0181
(0.0721)
18p loss 254 (56%) 196 1e-05
(0.000116) 		1e-05
(0.000116) 		1e-05
(0.000116) 		1e-05
(0.000116) 		0.318
(0.578) 		0.00288
(0.0154) 		1e-05
(0.000116) 		1e-05
(0.000116) 		0.99
(1.00) 		0.0186
(0.0735) 		0.465
(0.713) 		0.00061
(0.00398)
18q loss 271 (60%) 179 1e-05
(0.000116) 		1e-05
(0.000116) 		1e-05
(0.000116) 		1e-05
(0.000116) 		0.395
(0.651) 		0.0112
(0.0489) 		1e-05
(0.000116) 		1e-05
(0.000116) 		0.746
(0.913) 		0.0127
(0.0539) 		0.26
(0.504) 		0.00044
(0.00306)
7q gain 223 (50%) 227 0.00383
(0.0197) 		2e-05
(0.000218) 		1e-05
(0.000116) 		0.00108
(0.00664) 		0.0613
(0.183) 		0.00461
(0.0233) 		0.00103
(0.00638) 		1e-05
(0.000116) 		0.47
(0.718) 		0.654
(0.852) 		0.817
(0.948) 		0.00959
(0.0424)
11q gain 51 (11%) 399 0.00019
(0.00151) 		1e-05
(0.000116) 		1e-05
(0.000116) 		0.00121
(0.00722) 		0.381
(0.643) 		0.077
(0.211) 		6e-05
(0.00055) 		1e-05
(0.000116) 		0.628
(0.837) 		0.00603
(0.029) 		1
(1.00) 		0.0329
(0.115)
4p loss 138 (31%) 312 0.00011
(0.000955) 		0.00121
(0.00722) 		1e-05
(0.000116) 		0.00063
(0.00403) 		0.92
(0.999) 		0.0318
(0.112) 		1e-05
(0.000116) 		1e-05
(0.000116) 		0.463
(0.711) 		0.38
(0.643) 		0.0599
(0.181) 		0.0246
(0.0913)
8p loss 142 (32%) 308 0.0156
(0.0647) 		0.0009
(0.00568) 		1e-05
(0.000116) 		0.00111
(0.00679) 		0.662
(0.856) 		0.0313
(0.111) 		7e-05
(0.000619) 		1e-05
(0.000116) 		0.625
(0.835) 		0.132
(0.319) 		0.808
(0.945) 		0.0218
(0.0832)
14q loss 139 (31%) 311 1e-05
(0.000116) 		6e-05
(0.00055) 		1e-05
(0.000116) 		1e-05
(0.000116) 		0.0705
(0.2) 		0.0621
(0.185) 		1e-05
(0.000116) 		1e-05
(0.000116) 		0.298
(0.555) 		0.0214
(0.0823) 		0.0813
(0.22) 		0.00543
(0.0265)
17p loss 236 (52%) 214 1e-05
(0.000116) 		1e-05
(0.000116) 		1e-05
(0.000116) 		1e-05
(0.000116) 		0.183
(0.398) 		0.0066
(0.031) 		1e-05
(0.000116) 		1e-05
(0.000116) 		0.804
(0.945) 		0.065
(0.189) 		0.608
(0.829) 		0.00118
(0.00712)
11p gain 53 (12%) 397 0.00063
(0.00403) 		5e-05
(0.000486) 		1e-05
(0.000116) 		0.00023
(0.00175) 		0.293
(0.549) 		0.21
(0.43) 		0.00039
(0.00281) 		1e-05
(0.000116) 		0.895
(0.993) 		0.00248
(0.0135) 		0.926
(1.00) 		0.087
(0.231)
20p gain 243 (54%) 207 0.00293
(0.0155) 		3e-05
(0.00031) 		1e-05
(0.000116) 		0.00021
(0.00165) 		0.0303
(0.108) 		0.438
(0.692) 		0.00026
(0.00196) 		1e-05
(0.000116) 		0.702
(0.88) 		0.0701
(0.199) 		0.147
(0.342) 		0.244
(0.478)
22q loss 146 (32%) 304 0.00045
(0.00306) 		0.00045
(0.00306) 		1e-05
(0.000116) 		0.0275
(0.0994) 		0.195
(0.41) 		0.00622
(0.0296) 		4e-05
(0.000397) 		1e-05
(0.000116) 		0.183
(0.398) 		0.399
(0.657) 		0.613
(0.829) 		0.448
(0.699)
2p gain 82 (18%) 368 0.0716
(0.201) 		0.0218
(0.0832) 		0.00462
(0.0233) 		0.00744
(0.0338) 		0.322
(0.58) 		0.736
(0.907) 		7e-05
(0.000619) 		0.00346
(0.018) 		0.408
(0.662) 		0.0152
(0.0637) 		0.899
(0.993) 		0.805
(0.945)
8q gain 227 (50%) 223 0.883
(0.988) 		0.0201
(0.0787) 		1e-05
(0.000116) 		0.0121
(0.0516) 		0.307
(0.562) 		0.107
(0.271) 		0.0023
(0.0128) 		0.00047
(0.00317) 		0.655
(0.852) 		0.0143
(0.0601) 		0.408
(0.662) 		0.0738
(0.204)
13q gain 256 (57%) 194 0.00015
(0.00125) 		1e-05
(0.000116) 		1e-05
(0.000116) 		1e-05
(0.000116) 		0.32
(0.58) 		0.203
(0.421) 		1e-05
(0.000116) 		1e-05
(0.000116) 		0.441
(0.694) 		0.794
(0.94) 		0.139
(0.331) 		0.165
(0.373)
16p gain 107 (24%) 343 6e-05
(0.00055) 		1e-05
(0.000116) 		1e-05
(0.000116) 		0.105
(0.268) 		0.0435
(0.143) 		0.108
(0.273) 		0.00219
(0.0122) 		1e-05
(0.000116) 		0.574
(0.801) 		0.189
(0.403) 		0.903
(0.994) 		0.139
(0.331)
17q gain 81 (18%) 369 0.068
(0.195) 		0.041
(0.138) 		1e-05
(0.000116) 		0.00023
(0.00175) 		0.635
(0.84) 		0.142
(0.336) 		1e-05
(0.000116) 		0.00059
(0.00387) 		0.00914
(0.0411) 		0.0646
(0.189) 		0.519
(0.762) 		0.703
(0.88)
1p loss 95 (21%) 355 0.0287
(0.103) 		0.191
(0.406) 		1e-05
(0.000116) 		0.00079
(0.00502) 		0.931
(1.00) 		0.192
(0.409) 		0.00013
(0.0011) 		4e-05
(0.000397) 		0.88
(0.988) 		0.0208
(0.0808) 		0.852
(0.966) 		0.573
(0.801)
4q loss 127 (28%) 323 0.00011
(0.000955) 		0.00937
(0.042) 		1e-05
(0.000116) 		0.00045
(0.00306) 		0.717
(0.895) 		0.391
(0.65) 		1e-05
(0.000116) 		1e-05
(0.000116) 		0.219
(0.442) 		0.288
(0.543) 		0.254
(0.495) 		0.205
(0.423)
10p loss 69 (15%) 381 0.021
(0.0812) 		0.0252
(0.0926) 		1e-05
(0.000116) 		6e-05
(0.00055) 		0.644
(0.845) 		0.409
(0.662) 		4e-05
(0.000397) 		0.00017
(0.00139) 		0.499
(0.744) 		0.232
(0.464) 		0.502
(0.747) 		0.0913
(0.239)
10q loss 73 (16%) 377 0.0245
(0.0912) 		0.0407
(0.138) 		1e-05
(0.000116) 		1e-05
(0.000116) 		0.412
(0.664) 		0.206
(0.423) 		1e-05
(0.000116) 		1e-05
(0.000116) 		0.612
(0.829) 		0.393
(0.65) 		0.0712
(0.201) 		0.449
(0.699)
12p loss 47 (10%) 403 0.0624
(0.185) 		0.00709
(0.0329) 		1e-05
(0.000116) 		0.00728
(0.0332) 		0.369
(0.633) 		0.908
(0.998) 		0.00095
(0.00592) 		7e-05
(0.000619) 		0.882
(0.988) 		0.413
(0.664) 		0.445
(0.696) 		0.0214
(0.0823)
12q loss 49 (11%) 401 0.11
(0.277) 		0.0071
(0.0329) 		1e-05
(0.000116) 		0.0108
(0.0472) 		0.556
(0.792) 		0.744
(0.913) 		0.00039
(0.00281) 		0.00014
(0.00117) 		0.953
(1.00) 		0.682
(0.868) 		0.915
(0.998) 		0.0223
(0.0841)
15q loss 157 (35%) 293 0.00165
(0.00943) 		0.00149
(0.00862) 		1e-05
(0.000116) 		0.00021
(0.00165) 		0.217
(0.44) 		0.384
(0.646) 		1e-05
(0.000116) 		1e-05
(0.000116) 		0.902
(0.994) 		0.84
(0.962) 		0.141
(0.334) 		0.0669
(0.194)
20p loss 44 (10%) 406 0.0908
(0.239) 		0.00063
(0.00403) 		7e-05
(0.000619) 		0.00556
(0.027) 		0.418
(0.672) 		0.2
(0.418) 		0.0181
(0.0721) 		0.0104
(0.0457) 		0.83
(0.955) 		0.046
(0.15) 		0.484
(0.73) 		0.624
(0.835)
2q gain 78 (17%) 372 0.072
(0.202) 		0.022
(0.0836) 		0.00131
(0.00772) 		0.0118
(0.0509) 		0.334
(0.594) 		0.826
(0.955) 		0.00043
(0.00306) 		0.0013
(0.0077) 		0.494
(0.74) 		0.0737
(0.204) 		1
(1.00) 		0.56
(0.792)
6p gain 85 (19%) 365 0.213
(0.435) 		2e-05
(0.000218) 		1e-05
(0.000116) 		0.0421
(0.14) 		0.175
(0.389) 		0.382
(0.644) 		0.0428
(0.142) 		0.0182
(0.0721) 		0.549
(0.787) 		0.936
(1.00) 		0.265
(0.509) 		0.163
(0.372)
16q gain 105 (23%) 345 6e-05
(0.00055) 		2e-05
(0.000218) 		1e-05
(0.000116) 		0.157
(0.361) 		0.0573
(0.177) 		0.113
(0.283) 		0.00268
(0.0145) 		1e-05
(0.000116) 		0.804
(0.945) 		0.181
(0.397) 		1
(1.00) 		0.178
(0.394)
19q gain 84 (19%) 366 0.292
(0.548) 		0.193
(0.41) 		0.00251
(0.0136) 		0.367
(0.631) 		0.0134
(0.0565) 		0.126
(0.308) 		0.495
(0.74) 		0.00013
(0.0011) 		0.165
(0.373) 		0.723
(0.896) 		0.0407
(0.138) 		0.0005
(0.00333)
11q loss 63 (14%) 387 0.0417
(0.14) 		0.0153
(0.0637) 		0.00351
(0.0181) 		0.0244
(0.0912) 		0.542
(0.782) 		0.897
(0.993) 		0.239
(0.471) 		0.00238
(0.0131) 		0.84
(0.962) 		0.68
(0.868) 		0.779
(0.932) 		0.837
(0.961)
3q gain 65 (14%) 385 0.0928
(0.242) 		0.00023
(0.00175) 		1e-05
(0.000116) 		0.0468
(0.152) 		0.695
(0.878) 		0.232
(0.464) 		0.233
(0.464) 		0.027
(0.0984) 		0.671
(0.861) 		0.634
(0.84) 		0.79
(0.936) 		0.0577
(0.177)
18p gain 22 (5%) 428 0.0909
(0.239) 		0.671
(0.861) 		3e-05
(0.00031) 		0.00149
(0.00862) 		0.334
(0.594) 		0.94
(1.00) 		0.0331
(0.115) 		5e-05
(0.000486) 		0.267
(0.512) 		0.177
(0.393) 		0.912
(0.998) 		0.483
(0.73)
18q gain 13 (3%) 437 0.142
(0.336) 		1
(1.00) 		0.00459
(0.0233) 		0.0113
(0.0489) 		0.524
(0.764) 		0.911
(0.998) 		0.0181
(0.0721) 		2e-05
(0.000218) 		0.558
(0.792) 		0.185
(0.399) 		0.448
(0.699) 		0.195
(0.41)
19p gain 74 (16%) 376 0.351
(0.612) 		0.272
(0.518) 		4e-05
(0.000397) 		0.0494
(0.16) 		0.104
(0.265) 		0.152
(0.352) 		0.393
(0.65) 		0.00012
(0.00103) 		0.0907
(0.239) 		0.335
(0.594) 		0.18
(0.397) 		0.019
(0.0748)
1q loss 56 (12%) 394 0.411
(0.664) 		0.695
(0.878) 		2e-05
(0.000218) 		0.051
(0.163) 		0.892
(0.993) 		0.596
(0.819) 		0.00203
(0.0114) 		0.00515
(0.0254) 		0.645
(0.845) 		0.00532
(0.0261) 		0.173
(0.386) 		0.818
(0.948)
5q loss 78 (17%) 372 0.164
(0.373) 		0.305
(0.562) 		3e-05
(0.00031) 		0.0242
(0.0909) 		0.814
(0.948) 		0.419
(0.673) 		0.00019
(0.00151) 		0.00032
(0.00237) 		0.903
(0.994) 		0.7
(0.88) 		0.756
(0.92) 		0.351
(0.612)
9p loss 54 (12%) 396 0.567
(0.797) 		0.0636
(0.187) 		0.00044
(0.00306) 		0.00044
(0.00306) 		1
(1.00) 		0.216
(0.439) 		6e-05
(0.00055) 		0.00045
(0.00306) 		0.37
(0.633) 		0.281
(0.532) 		0.412
(0.664) 		0.317
(0.578)
9q loss 53 (12%) 397 0.118
(0.294) 		0.0603
(0.181) 		0.00017
(0.00139) 		3e-05
(0.00031) 		0.872
(0.983) 		0.158
(0.362) 		0.00018
(0.00146) 		0.00137
(0.00802) 		0.54
(0.781) 		0.187
(0.403) 		0.223
(0.447) 		0.371
(0.633)
19p loss 40 (9%) 410 1
(1.00) 		0.343
(0.604) 		0.0502
(0.162) 		0.578
(0.804) 		0.377
(0.641) 		0.685
(0.87) 		0.00334
(0.0175) 		0.0222
(0.0839) 		0.0419
(0.14) 		0.00462
(0.0233) 		0.652
(0.852) 		0.63
(0.839)
21q loss 124 (28%) 326 0.00954
(0.0424) 		0.0857
(0.229) 		1e-05
(0.000116) 		0.0673
(0.194) 		0.965
(1.00) 		0.326
(0.583) 		1e-05
(0.000116) 		0.00955
(0.0424) 		0.458
(0.706) 		0.0514
(0.164) 		0.815
(0.948) 		0.376
(0.641)
1q gain 80 (18%) 370 0.87
(0.982) 		0.696
(0.878) 		0.0113
(0.0489) 		0.0169
(0.069) 		0.13
(0.316) 		0.323
(0.58) 		0.487
(0.733) 		0.0945
(0.245) 		0.731
(0.903) 		0.134
(0.324) 		0.0456
(0.149) 		0.469
(0.718)
xp gain 67 (15%) 383 0.0991
(0.254) 		0.238
(0.471) 		0.00053
(0.0035) 		0.091
(0.239) 		0.00726
(0.0332) 		0.261
(0.505) 		0.777
(0.932) 		0.0814
(0.22) 		0.79
(0.936) 		0.967
(1.00) 		0.0429
(0.142) 		0.0594
(0.18)
xq gain 76 (17%) 374 0.0431
(0.142) 		0.238
(0.471) 		0.00031
(0.00232) 		0.312
(0.569) 		0.00514
(0.0254) 		0.284
(0.537) 		0.803
(0.945) 		0.579
(0.804) 		0.434
(0.69) 		0.958
(1.00) 		0.324
(0.582) 		0.269
(0.513)
5p loss 59 (13%) 391 0.659
(0.853) 		0.854
(0.966) 		0.00035
(0.00256) 		0.0206
(0.0804) 		0.737
(0.907) 		0.766
(0.928) 		0.0734
(0.204) 		0.00091
(0.00571) 		0.751
(0.919) 		0.671
(0.861) 		0.299
(0.555) 		0.4
(0.657)
19q loss 35 (8%) 415 0.732
(0.903) 		0.706
(0.883) 		0.069
(0.197) 		0.803
(0.945) 		0.361
(0.623) 		0.299
(0.555) 		0.0047
(0.0235) 		0.0174
(0.0703) 		0.296
(0.554) 		0.0497
(0.16) 		0.321
(0.58) 		0.463
(0.711)
xp loss 65 (14%) 385 0.0294
(0.105) 		0.239
(0.471) 		0.0172
(0.0697) 		0.523
(0.764) 		0.0122
(0.0519) 		0.165
(0.373) 		0.56
(0.792) 		0.521
(0.763) 		0.0636
(0.187) 		0.437
(0.692) 		0.633
(0.84) 		0.184
(0.398)
xq loss 54 (12%) 396 0.0158
(0.0651) 		0.25
(0.488) 		0.00296
(0.0156) 		0.1
(0.256) 		0.0526
(0.167) 		0.0172
(0.0697) 		0.189
(0.403) 		0.201
(0.418) 		0.0701
(0.199) 		0.657
(0.853) 		0.483
(0.73) 		0.0673
(0.194)
1p gain 35 (8%) 415 0.64
(0.843) 		0.443
(0.695) 		0.0303
(0.108) 		0.0982
(0.253) 		0.111
(0.279) 		0.647
(0.846) 		0.776
(0.932) 		0.0325
(0.114) 		0.388
(0.648) 		0.144
(0.339) 		0.256
(0.498) 		0.148
(0.344)
3p gain 45 (10%) 405 0.139
(0.331) 		0.00709
(0.0329) 		1e-05
(0.000116) 		0.0739
(0.204) 		0.321
(0.58) 		0.098
(0.253) 		0.776
(0.932) 		0.354
(0.614) 		0.688
(0.872) 		0.851
(0.966) 		0.724
(0.896) 		0.392
(0.65)
6q gain 77 (17%) 373 0.184
(0.399) 		1e-05
(0.000116) 		1e-05
(0.000116) 		0.0578
(0.177) 		0.456
(0.706) 		0.051
(0.163) 		0.281
(0.532) 		0.172
(0.384) 		0.503
(0.747) 		0.916
(0.998) 		0.614
(0.829) 		0.162
(0.372)
8p gain 132 (29%) 318 0.974
(1.00) 		0.965
(1.00) 		0.00022
(0.00171) 		0.938
(1.00) 		0.322
(0.58) 		0.611
(0.829) 		0.025
(0.0923) 		0.055
(0.173) 		0.572
(0.801) 		0.185
(0.4) 		0.881
(0.988) 		0.917
(0.998)
12p gain 93 (21%) 357 0.178
(0.394) 		1
(1.00) 		0.00575
(0.0278) 		0.0164
(0.0675) 		0.681
(0.868) 		0.634
(0.84) 		0.937
(1.00) 		0.654
(0.852) 		0.428
(0.683) 		0.547
(0.787) 		0.346
(0.607) 		0.963
(1.00)
12q gain 87 (19%) 363 0.195
(0.41) 		0.897
(0.993) 		0.00476
(0.0237) 		0.0029
(0.0154) 		0.563
(0.794) 		0.597
(0.819) 		0.776
(0.932) 		0.621
(0.835) 		0.198
(0.415) 		0.183
(0.398) 		0.51
(0.751) 		0.717
(0.895)
15q gain 12 (3%) 438 1
(1.00) 		0.81
(0.945) 		0.494
(0.74) 		0.816
(0.948) 		0.0332
(0.115) 		0.0156
(0.0647) 		0.979
(1.00) 		0.851
(0.966) 		0.923
(1.00) 		0.769
(0.929)
21q gain 24 (5%) 426 0.035
(0.12) 		0.297
(0.555) 		0.00158
(0.00909) 		0.089
(0.236) 		0.342
(0.602) 		0.571
(0.8) 		0.645
(0.845) 		0.0966
(0.25) 		0.222
(0.447) 		0.265
(0.509)
8q loss 25 (6%) 425 0.807
(0.945) 		0.404
(0.662) 		0.00234
(0.0129) 		0.664
(0.857) 		0.602
(0.824) 		0.385
(0.646) 		0.358
(0.62) 		0.505
(0.747) 		0.388
(0.648) 		0.745
(0.913) 		0.407
(0.662) 		0.00193
(0.0109)
13q loss 12 (3%) 438 0.874
(0.983) 		0.438
(0.692) 		0.247
(0.482) 		0.0412
(0.139) 		0.231
(0.463) 		0.0575
(0.177) 		0.455
(0.706) 		0.919
(0.999) 		0.597
(0.819) 		0.107
(0.271) 		0.0348
(0.12) 		0.806
(0.945)
4q gain 17 (4%) 433 0.127
(0.309) 		0.122
(0.301) 		0.152
(0.352) 		0.931
(1.00) 		0.142
(0.336) 		0.132
(0.319) 		0.0335
(0.116) 		0.548
(0.787) 		0.147
(0.342) 		0.136
(0.326)
5p gain 69 (15%) 381 0.354
(0.614) 		0.122
(0.301) 		0.0252
(0.0926) 		0.729
(0.901) 		0.298
(0.555) 		0.909
(0.998) 		0.119
(0.296) 		0.0761
(0.209) 		0.85
(0.966) 		0.445
(0.696) 		0.724
(0.896) 		0.555
(0.792)
5q gain 44 (10%) 406 0.874
(0.983) 		0.773
(0.932) 		0.00631
(0.0298) 		0.591
(0.817) 		0.594
(0.819) 		0.848
(0.966) 		0.205
(0.423) 		0.0725
(0.203) 		0.508
(0.75) 		0.0943
(0.245) 		1
(1.00) 		0.854
(0.966)
9p gain 81 (18%) 369 0.194
(0.41) 		0.137
(0.329) 		0.00049
(0.00328) 		0.776
(0.932) 		0.0823
(0.222) 		0.682
(0.868) 		0.93
(1.00) 		0.675
(0.864) 		0.876
(0.984) 		0.925
(1.00) 		0.0712
(0.201) 		0.145
(0.34)
9q gain 71 (16%) 379 0.166
(0.373) 		0.205
(0.423) 		0.026
(0.095) 		0.585
(0.811) 		0.0546
(0.172) 		0.623
(0.835) 		0.965
(1.00) 		0.938
(1.00) 		0.354
(0.614) 		0.39
(0.649) 		0.308
(0.562) 		0.535
(0.777)
10p gain 37 (8%) 413 0.597
(0.819) 		1
(1.00) 		0.00284
(0.0153) 		0.458
(0.706) 		0.968
(1.00) 		0.567
(0.797) 		0.379
(0.643) 		0.34
(0.601) 		0.428
(0.683) 		0.721
(0.896) 		0.932
(1.00) 		0.35
(0.611)
10q gain 23 (5%) 427 0.172
(0.384) 		0.441
(0.694) 		0.0552
(0.173) 		0.037
(0.126) 		0.183
(0.398) 		0.885
(0.989) 		0.78
(0.932) 		0.588
(0.814) 		0.756
(0.92) 		0.864
(0.976) 		0.887
(0.989) 		0.244
(0.478)
6p loss 34 (8%) 416 1
(1.00) 		0.456
(0.706) 		0.371
(0.633) 		0.844
(0.965) 		0.432
(0.689) 		0.815
(0.948) 		0.302
(0.558) 		0.966
(1.00) 		0.615
(0.829) 		0.785
(0.936) 		0.0273
(0.0992) 		0.0823
(0.222)
7q loss 4 (1%) 446 0.0381
(0.13) 		0.0656
(0.19) 		0.672
(0.861) 		0.723
(0.896) 		0.56
(0.792) 		0.627
(0.837)
11p loss 52 (12%) 398 0.223
(0.447) 		0.194
(0.41) 		0.00853
(0.0386) 		0.081
(0.22) 		0.756
(0.92) 		0.935
(1.00) 		0.0799
(0.218) 		0.0859
(0.229) 		0.853
(0.966) 		0.206
(0.423) 		0.639
(0.843) 		0.766
(0.928)
17q loss 66 (15%) 384 0.263
(0.507) 		0.38
(0.643) 		0.00034
(0.0025) 		0.455
(0.706) 		0.896
(0.993) 		0.561
(0.793) 		0.165
(0.373) 		0.0567
(0.176) 		0.33
(0.589) 		0.268
(0.513) 		0.702
(0.88) 		0.164
(0.373)
4p gain 12 (3%) 438 0.0753
(0.207) 		0.155
(0.357) 		0.06
(0.181) 		0.436
(0.692) 		0.106
(0.269) 		0.658
(0.853) 		0.608
(0.829) 		0.578
(0.804)
14q gain 35 (8%) 415 0.34
(0.602) 		0.634
(0.84) 		0.505
(0.747) 		0.526
(0.765) 		0.8
(0.945) 		0.666
(0.859) 		0.488
(0.733) 		0.574
(0.801) 		0.672
(0.861) 		0.181
(0.397) 		0.238
(0.471) 		0.342
(0.602)
17p gain 29 (6%) 421 0.841
(0.962) 		0.567
(0.797) 		0.426
(0.682) 		0.44
(0.694) 		0.553
(0.79) 		0.916
(0.998) 		0.364
(0.628) 		0.115
(0.287) 		0.383
(0.646) 		0.76
(0.923) 		0.547
(0.787) 		0.459
(0.706)
22q gain 13 (3%) 437 1
(1.00) 		0.789
(0.936) 		0.058
(0.177) 		0.0526
(0.167) 		0.515
(0.757) 		0.79
(0.936) 		0.0573
(0.177) 		0.216
(0.439) 		0.924
(1.00) 		0.644
(0.845) 		0.83
(0.955) 		0.482
(0.73)
2p loss 6 (1%) 444 0.898
(0.993) 		0.81
(0.945) 		0.281
(0.532) 		1
(1.00) 		0.975
(1.00) 		0.131
(0.319) 		0.124
(0.305) 		0.64
(0.843) 		0.477
(0.728)
2q loss 7 (2%) 443 1
(1.00) 		0.504
(0.747) 		0.613
(0.829) 		0.56
(0.792) 		0.767
(0.928) 		0.397
(0.654) 		0.0612
(0.183) 		0.387
(0.648) 		0.243
(0.478)
3p loss 55 (12%) 395 0.781
(0.932) 		0.487
(0.733) 		0.0849
(0.227) 		0.208
(0.426) 		0.3
(0.555) 		0.994
(1.00) 		0.0626
(0.185) 		0.0557
(0.174) 		0.613
(0.829) 		0.603
(0.825) 		0.306
(0.562) 		0.659
(0.853)
3q loss 34 (8%) 416 0.827
(0.955) 		1
(1.00) 		0.77
(0.929) 		0.405
(0.662) 		0.541
(0.782) 		0.928
(1.00) 		0.0839
(0.225) 		0.201
(0.418) 		0.262
(0.507) 		0.931
(1.00) 		0.894
(0.993) 		0.125
(0.308)
6q loss 46 (10%) 404 0.821
(0.95) 		1
(1.00) 		0.539
(0.78) 		0.788
(0.936) 		0.33
(0.589) 		0.523
(0.764) 		0.279
(0.531) 		0.723
(0.896) 		0.611
(0.829) 		0.963
(1.00) 		0.0607
(0.182) 		0.0648
(0.189)
16p loss 31 (7%) 419 0.405
(0.662) 		0.688
(0.872) 		0.909
(0.998) 		0.592
(0.817) 		0.746
(0.913) 		0.482
(0.73) 		0.172
(0.384) 		0.2
(0.418) 		0.506
(0.747) 		0.48
(0.73) 		0.625
(0.835) 		1
(1.00)
16q loss 29 (6%) 421 0.408
(0.662) 		0.689
(0.872) 		0.348
(0.609) 		0.849
(0.966) 		0.916
(0.998) 		0.495
(0.74) 		0.147
(0.342) 		0.308
(0.562) 		0.52
(0.762) 		0.754
(0.92) 		0.621
(0.835) 		1
(1.00)
20q loss 4 (1%) 446 0.828
(0.955) 		0.0559
(0.174) 		0.697
(0.878) 		0.188
(0.403) 		0.55
(0.787) 		0.389
(0.649) 		0.305
(0.562)
'1p gain' versus 'CN_CNMF'

P value = 0.0303 (Fisher's exact test), Q value = 0.11

Table S1.  Gene #1: '1p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
1P GAIN MUTATED 9 20 6
1P GAIN WILD-TYPE 193 150 72

Figure S1.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #3: 'CN_CNMF'

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0325 (Fisher's exact test), Q value = 0.11

Table S2.  Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
1P GAIN MUTATED 6 14 2 12 1
1P GAIN WILD-TYPE 73 94 94 117 35

Figure S2.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'CN_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.049

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
1Q GAIN MUTATED 26 42 12
1Q GAIN WILD-TYPE 176 128 66

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

'1q gain' versus 'METHLYATION_CNMF'

P value = 0.0169 (Fisher's exact test), Q value = 0.069

Table S4.  Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
1Q GAIN MUTATED 32 14 9
1Q GAIN WILD-TYPE 88 83 67

Figure S4.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0456 (Fisher's exact test), Q value = 0.15

Table S5.  Gene #2: '1q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 32 24
1Q GAIN MUTATED 1 7 6
1Q GAIN WILD-TYPE 28 25 18

Figure S5.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0218 (Fisher's exact test), Q value = 0.083

Table S6.  Gene #3: '2p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
2P GAIN MUTATED 2 10 9
2P GAIN WILD-TYPE 40 62 23

Figure S6.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 0.00462 (Fisher's exact test), Q value = 0.023

Table S7.  Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
2P GAIN MUTATED 26 44 12
2P GAIN WILD-TYPE 176 126 66

Figure S7.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'

'2p gain' versus 'METHLYATION_CNMF'

P value = 0.00744 (Fisher's exact test), Q value = 0.034

Table S8.  Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
2P GAIN MUTATED 35 12 13
2P GAIN WILD-TYPE 85 85 63

Figure S8.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00062

Table S9.  Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
2P GAIN MUTATED 39 9 16 18
2P GAIN WILD-TYPE 82 98 74 112

Figure S9.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00346 (Fisher's exact test), Q value = 0.018

Table S10.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
2P GAIN MUTATED 16 30 12 23 1
2P GAIN WILD-TYPE 63 78 84 106 35

Figure S10.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0152 (Fisher's exact test), Q value = 0.064

Table S11.  Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 50 77 135
2P GAIN MUTATED 20 9 23 17
2P GAIN WILD-TYPE 115 41 54 118

Figure S11.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.022 (Fisher's exact test), Q value = 0.084

Table S12.  Gene #4: '2q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
2Q GAIN MUTATED 2 10 9
2Q GAIN WILD-TYPE 40 62 23

Figure S12.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 0.00131 (Fisher's exact test), Q value = 0.0077

Table S13.  Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
2Q GAIN MUTATED 22 43 13
2Q GAIN WILD-TYPE 180 127 65

Figure S13.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.051

Table S14.  Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
2Q GAIN MUTATED 33 12 11
2Q GAIN WILD-TYPE 87 85 65

Figure S14.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.0031

Table S15.  Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
2Q GAIN MUTATED 36 10 14 18
2Q GAIN WILD-TYPE 85 97 76 112

Figure S15.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0013 (Fisher's exact test), Q value = 0.0077

Table S16.  Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
2Q GAIN MUTATED 16 29 9 23 1
2Q GAIN WILD-TYPE 63 79 87 106 35

Figure S16.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00709 (Fisher's exact test), Q value = 0.033

Table S17.  Gene #5: '3p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
3P GAIN MUTATED 2 4 8
3P GAIN WILD-TYPE 40 68 24

Figure S17.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S18.  Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
3P GAIN MUTATED 9 32 4
3P GAIN WILD-TYPE 193 138 74

Figure S18.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

'3q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.0017

Table S19.  Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
3Q GAIN MUTATED 2 6 12
3Q GAIN WILD-TYPE 40 66 20

Figure S19.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S20.  Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
3Q GAIN MUTATED 10 46 9
3Q GAIN WILD-TYPE 192 124 69

Figure S20.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 0.0468 (Fisher's exact test), Q value = 0.15

Table S21.  Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
3Q GAIN MUTATED 25 14 6
3Q GAIN WILD-TYPE 95 83 70

Figure S21.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.027 (Fisher's exact test), Q value = 0.098

Table S22.  Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
3Q GAIN MUTATED 16 19 8 21 1
3Q GAIN WILD-TYPE 63 89 88 108 35

Figure S22.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 0.0335 (Fisher's exact test), Q value = 0.12

Table S23.  Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
4Q GAIN MUTATED 8 0 4 5
4Q GAIN WILD-TYPE 113 107 86 125

Figure S23.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 0.0252 (Fisher's exact test), Q value = 0.093

Table S24.  Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
5P GAIN MUTATED 21 34 14
5P GAIN WILD-TYPE 181 136 64

Figure S24.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'CN_CNMF'

P value = 0.00631 (Fisher's exact test), Q value = 0.03

Table S25.  Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
5Q GAIN MUTATED 11 26 7
5Q GAIN WILD-TYPE 191 144 71

Figure S25.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

'6p gain' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00022

Table S26.  Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
6P GAIN MUTATED 5 7 16
6P GAIN WILD-TYPE 37 65 16

Figure S26.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S27.  Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
6P GAIN MUTATED 16 57 12
6P GAIN WILD-TYPE 186 113 66

Figure S27.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 0.0421 (Fisher's exact test), Q value = 0.14

Table S28.  Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
6P GAIN MUTATED 31 14 10
6P GAIN WILD-TYPE 89 83 66

Figure S28.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 0.0428 (Fisher's exact test), Q value = 0.14

Table S29.  Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
6P GAIN MUTATED 24 11 19 31
6P GAIN WILD-TYPE 97 96 71 99

Figure S29.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0182 (Fisher's exact test), Q value = 0.072

Table S30.  Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
6P GAIN MUTATED 20 21 9 31 4
6P GAIN WILD-TYPE 59 87 87 98 32

Figure S30.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S31.  Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
6Q GAIN MUTATED 5 4 14
6Q GAIN WILD-TYPE 37 68 18

Figure S31.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S32.  Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
6Q GAIN MUTATED 15 50 12
6Q GAIN WILD-TYPE 187 120 66

Figure S32.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'MRNA_CNMF'

P value = 0.00619 (Fisher's exact test), Q value = 0.03

Table S33.  Gene #13: '7p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
7P GAIN MUTATED 11 39 10 9
7P GAIN WILD-TYPE 24 22 19 12

Figure S33.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'7p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S34.  Gene #13: '7p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
7P GAIN MUTATED 10 33 26
7P GAIN WILD-TYPE 32 39 6

Figure S34.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S35.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
7P GAIN MUTATED 66 127 53
7P GAIN WILD-TYPE 136 43 25

Figure S35.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S36.  Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
7P GAIN MUTATED 90 45 37
7P GAIN WILD-TYPE 30 52 39

Figure S36.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 0.0309 (Fisher's exact test), Q value = 0.11

Table S37.  Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 144 125
7P GAIN MUTATED 55 74 58
7P GAIN WILD-TYPE 30 70 67

Figure S37.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00183 (Fisher's exact test), Q value = 0.01

Table S38.  Gene #13: '7p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 42 86 22 20 26
7P GAIN MUTATED 37 11 20 16 27 38 9 11 18
7P GAIN WILD-TYPE 14 22 15 23 15 48 13 9 8

Figure S38.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00031

Table S39.  Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
7P GAIN MUTATED 86 43 50 66
7P GAIN WILD-TYPE 35 64 40 64

Figure S39.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S40.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
7P GAIN MUTATED 58 71 33 75 8
7P GAIN WILD-TYPE 21 37 63 54 28

Figure S40.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0181 (Fisher's exact test), Q value = 0.072

Table S41.  Gene #13: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 22 17 24 10
7P GAIN MUTATED 12 15 11 11 6
7P GAIN WILD-TYPE 0 7 6 13 4

Figure S41.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'MRNA_CNMF'

P value = 0.00383 (Fisher's exact test), Q value = 0.02

Table S42.  Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
7Q GAIN MUTATED 7 34 9 9
7Q GAIN WILD-TYPE 28 27 20 12

Figure S42.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'7q gain' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00022

Table S43.  Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
7Q GAIN MUTATED 8 27 24
7Q GAIN WILD-TYPE 34 45 8

Figure S43.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S44.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
7Q GAIN MUTATED 65 111 47
7Q GAIN WILD-TYPE 137 59 31

Figure S44.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 0.00108 (Fisher's exact test), Q value = 0.0066

Table S45.  Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
7Q GAIN MUTATED 80 42 36
7Q GAIN WILD-TYPE 40 55 40

Figure S45.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00461 (Fisher's exact test), Q value = 0.023

Table S46.  Gene #14: '7q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 42 86 22 20 26
7Q GAIN MUTATED 34 8 17 17 21 35 9 10 18
7Q GAIN WILD-TYPE 17 25 18 22 21 51 13 10 8

Figure S46.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 0.00103 (Fisher's exact test), Q value = 0.0064

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
7Q GAIN MUTATED 76 40 47 59
7Q GAIN WILD-TYPE 45 67 43 71

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

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S48.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
7Q GAIN MUTATED 54 64 32 67 5
7Q GAIN WILD-TYPE 25 44 64 62 31

Figure S48.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00959 (Fisher's exact test), Q value = 0.042

Table S49.  Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 22 17 24 10
7Q GAIN MUTATED 12 13 8 11 7
7Q GAIN WILD-TYPE 0 9 9 13 3

Figure S49.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0017

Table S50.  Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
8P GAIN MUTATED 47 47 38
8P GAIN WILD-TYPE 155 123 40

Figure S50.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.025 (Fisher's exact test), Q value = 0.092

Table S51.  Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
8P GAIN MUTATED 40 33 32 25
8P GAIN WILD-TYPE 81 74 58 105

Figure S51.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0201 (Fisher's exact test), Q value = 0.079

Table S52.  Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
8Q GAIN MUTATED 14 31 21
8Q GAIN WILD-TYPE 28 41 11

Figure S52.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S53.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
8Q GAIN MUTATED 66 90 71
8Q GAIN WILD-TYPE 136 80 7

Figure S53.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.052

Table S54.  Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
8Q GAIN MUTATED 77 43 39
8Q GAIN WILD-TYPE 43 54 37

Figure S54.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 0.0023 (Fisher's exact test), Q value = 0.013

Table S55.  Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
8Q GAIN MUTATED 73 41 52 59
8Q GAIN WILD-TYPE 48 66 38 71

Figure S55.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.0032

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
8Q GAIN MUTATED 48 61 40 68 8
8Q GAIN WILD-TYPE 31 47 56 61 28

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

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0143 (Fisher's exact test), Q value = 0.06

Table S57.  Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 50 77 135
8Q GAIN MUTATED 60 32 47 61
8Q GAIN WILD-TYPE 75 18 30 74

Figure S57.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0033

Table S58.  Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
9P GAIN MUTATED 28 46 7
9P GAIN WILD-TYPE 174 124 71

Figure S58.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

'9q gain' versus 'CN_CNMF'

P value = 0.026 (Fisher's exact test), Q value = 0.095

Table S59.  Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
9Q GAIN MUTATED 26 37 8
9Q GAIN WILD-TYPE 176 133 70

Figure S59.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 0.00284 (Fisher's exact test), Q value = 0.015

Table S60.  Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
10P GAIN MUTATED 9 24 4
10P GAIN WILD-TYPE 193 146 74

Figure S60.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10q gain' versus 'METHLYATION_CNMF'

P value = 0.037 (Fisher's exact test), Q value = 0.13

Table S61.  Gene #20: '10q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
10Q GAIN MUTATED 5 11 2
10Q GAIN WILD-TYPE 115 86 74

Figure S61.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p gain' versus 'MRNA_CNMF'

P value = 0.00063 (Fisher's exact test), Q value = 0.004

Table S62.  Gene #21: '11p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
11P GAIN MUTATED 1 9 0 7
11P GAIN WILD-TYPE 34 52 29 14

Figure S62.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'11p gain' versus 'MRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00049

Table S63.  Gene #21: '11p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
11P GAIN MUTATED 1 5 11
11P GAIN WILD-TYPE 41 67 21

Figure S63.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S64.  Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
11P GAIN MUTATED 6 38 9
11P GAIN WILD-TYPE 196 132 69

Figure S64.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0017

Table S65.  Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
11P GAIN MUTATED 25 3 8
11P GAIN WILD-TYPE 95 94 68

Figure S65.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p gain' versus 'MRNASEQ_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.0028

Table S66.  Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
11P GAIN MUTATED 24 3 9 17
11P GAIN WILD-TYPE 97 104 81 113

Figure S66.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S67.  Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
11P GAIN MUTATED 14 17 0 22 0
11P GAIN WILD-TYPE 65 91 96 107 36

Figure S67.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00248 (Fisher's exact test), Q value = 0.014

Table S68.  Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 50 77 135
11P GAIN MUTATED 7 8 17 15
11P GAIN WILD-TYPE 128 42 60 120

Figure S68.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'MRNA_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0015

Table S69.  Gene #22: '11q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
11Q GAIN MUTATED 1 9 0 8
11Q GAIN WILD-TYPE 34 52 29 13

Figure S69.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S70.  Gene #22: '11q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
11Q GAIN MUTATED 1 4 13
11Q GAIN WILD-TYPE 41 68 19

Figure S70.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S71.  Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
11Q GAIN MUTATED 3 37 11
11Q GAIN WILD-TYPE 199 133 67

Figure S71.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 0.00121 (Fisher's exact test), Q value = 0.0072

Table S72.  Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
11Q GAIN MUTATED 23 4 6
11Q GAIN WILD-TYPE 97 93 70

Figure S72.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00055

Table S73.  Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
11Q GAIN MUTATED 25 2 8 16
11Q GAIN WILD-TYPE 96 105 82 114

Figure S73.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S74.  Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
11Q GAIN MUTATED 13 18 0 20 0
11Q GAIN WILD-TYPE 66 90 96 109 36

Figure S74.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00603 (Fisher's exact test), Q value = 0.029

Table S75.  Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 50 77 135
11Q GAIN MUTATED 7 7 16 15
11Q GAIN WILD-TYPE 128 43 61 120

Figure S75.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0329 (Fisher's exact test), Q value = 0.11

Table S76.  Gene #22: '11q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 22 17 24 10
11Q GAIN MUTATED 3 5 1 0 2
11Q GAIN WILD-TYPE 9 17 16 24 8

Figure S76.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 0.00575 (Fisher's exact test), Q value = 0.028

Table S77.  Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
12P GAIN MUTATED 51 22 20
12P GAIN WILD-TYPE 151 148 58

Figure S77.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 0.0164 (Fisher's exact test), Q value = 0.067

Table S78.  Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
12P GAIN MUTATED 15 27 16
12P GAIN WILD-TYPE 105 70 60

Figure S78.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 0.00476 (Fisher's exact test), Q value = 0.024

Table S79.  Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
12Q GAIN MUTATED 48 20 19
12Q GAIN WILD-TYPE 154 150 59

Figure S79.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 0.0029 (Fisher's exact test), Q value = 0.015

Table S80.  Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
12Q GAIN MUTATED 12 27 13
12Q GAIN WILD-TYPE 108 70 63

Figure S80.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q gain' versus 'MRNA_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0012

Table S81.  Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
13Q GAIN MUTATED 14 46 10 15
13Q GAIN WILD-TYPE 21 15 19 6

Figure S81.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S82.  Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
13Q GAIN MUTATED 12 46 27
13Q GAIN WILD-TYPE 30 26 5

Figure S82.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S83.  Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
13Q GAIN MUTATED 64 147 45
13Q GAIN WILD-TYPE 138 23 33

Figure S83.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S84.  Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
13Q GAIN MUTATED 90 43 35
13Q GAIN WILD-TYPE 30 54 41

Figure S84.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S85.  Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
13Q GAIN MUTATED 86 36 50 82
13Q GAIN WILD-TYPE 35 71 40 48

Figure S85.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S86.  Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
13Q GAIN MUTATED 62 71 26 87 8
13Q GAIN WILD-TYPE 17 37 70 42 28

Figure S86.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q gain' versus 'RPPA_CNMF'

P value = 0.0332 (Fisher's exact test), Q value = 0.12

Table S87.  Gene #27: '15q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 144 125
15Q GAIN MUTATED 4 5 0
15Q GAIN WILD-TYPE 81 139 125

Figure S87.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'15q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0156 (Fisher's exact test), Q value = 0.065

Table S88.  Gene #27: '15q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 42 86 22 20 26
15Q GAIN MUTATED 2 0 0 2 0 0 2 2 1
15Q GAIN WILD-TYPE 49 33 35 37 42 86 20 18 25

Figure S88.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16p gain' versus 'MRNA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00055

Table S89.  Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
16P GAIN MUTATED 5 21 2 13
16P GAIN WILD-TYPE 30 40 27 8

Figure S89.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S90.  Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
16P GAIN MUTATED 4 16 21
16P GAIN WILD-TYPE 38 56 11

Figure S90.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S91.  Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
16P GAIN MUTATED 15 79 13
16P GAIN WILD-TYPE 187 91 65

Figure S91.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'16p gain' versus 'RPPA_CNMF'

P value = 0.0435 (Fisher's exact test), Q value = 0.14

Table S92.  Gene #28: '16p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 144 125
16P GAIN MUTATED 27 25 27
16P GAIN WILD-TYPE 58 119 98

Figure S92.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.00219 (Fisher's exact test), Q value = 0.012

Table S93.  Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
16P GAIN MUTATED 34 14 17 42
16P GAIN WILD-TYPE 87 93 73 88

Figure S93.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S94.  Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
16P GAIN MUTATED 25 22 10 50 0
16P GAIN WILD-TYPE 54 86 86 79 36

Figure S94.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MRNA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00055

Table S95.  Gene #29: '16q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
16Q GAIN MUTATED 4 19 2 13
16Q GAIN WILD-TYPE 31 42 27 8

Figure S95.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16q gain' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00022

Table S96.  Gene #29: '16q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
16Q GAIN MUTATED 3 16 19
16Q GAIN WILD-TYPE 39 56 13

Figure S96.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S97.  Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
16Q GAIN MUTATED 14 78 13
16Q GAIN WILD-TYPE 188 92 65

Figure S97.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 0.00268 (Fisher's exact test), Q value = 0.014

Table S98.  Gene #29: '16q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
16Q GAIN MUTATED 35 14 16 40
16Q GAIN WILD-TYPE 86 93 74 90

Figure S98.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S99.  Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
16Q GAIN MUTATED 25 23 10 47 0
16Q GAIN WILD-TYPE 54 85 86 82 36

Figure S99.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.041 (Fisher's exact test), Q value = 0.14

Table S100.  Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
17Q GAIN MUTATED 3 10 9
17Q GAIN WILD-TYPE 39 62 23

Figure S100.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S101.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
17Q GAIN MUTATED 18 46 17
17Q GAIN WILD-TYPE 184 124 61

Figure S101.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0017

Table S102.  Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
17Q GAIN MUTATED 38 15 7
17Q GAIN WILD-TYPE 82 82 69

Figure S102.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S103.  Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
17Q GAIN MUTATED 43 10 10 18
17Q GAIN WILD-TYPE 78 97 80 112

Figure S103.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00059 (Fisher's exact test), Q value = 0.0039

Table S104.  Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
17Q GAIN MUTATED 17 31 7 23 3
17Q GAIN WILD-TYPE 62 77 89 106 33

Figure S104.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 0.00914 (Fisher's exact test), Q value = 0.041

Table S105.  Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 65 172
17Q GAIN MUTATED 40 6 26
17Q GAIN WILD-TYPE 120 59 146

Figure S105.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00031

Table S106.  Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
18P GAIN MUTATED 14 0 8
18P GAIN WILD-TYPE 188 170 70

Figure S106.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 0.00149 (Fisher's exact test), Q value = 0.0086

Table S107.  Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
18P GAIN MUTATED 1 11 4
18P GAIN WILD-TYPE 119 86 72

Figure S107.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 0.0331 (Fisher's exact test), Q value = 0.12

Table S108.  Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
18P GAIN MUTATED 2 10 6 4
18P GAIN WILD-TYPE 119 97 84 126

Figure S108.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00049

Table S109.  Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
18P GAIN MUTATED 2 2 13 1 4
18P GAIN WILD-TYPE 77 106 83 128 32

Figure S109.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 0.00459 (Fisher's exact test), Q value = 0.023

Table S110.  Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
18Q GAIN MUTATED 10 0 3
18Q GAIN WILD-TYPE 192 170 75

Figure S110.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.049

Table S111.  Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
18Q GAIN MUTATED 0 6 3
18Q GAIN WILD-TYPE 120 91 73

Figure S111.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 0.072

Table S112.  Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
18Q GAIN MUTATED 0 4 6 3
18Q GAIN WILD-TYPE 121 103 84 127

Figure S112.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00022

Table S113.  Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
18Q GAIN MUTATED 1 0 8 0 4
18Q GAIN WILD-TYPE 78 108 88 129 32

Figure S113.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

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

Table S114.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
19P GAIN MUTATED 16 43 15
19P GAIN WILD-TYPE 186 127 63

Figure S114.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 0.0494 (Fisher's exact test), Q value = 0.16

Table S115.  Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
19P GAIN MUTATED 31 17 9
19P GAIN WILD-TYPE 89 80 67

Figure S115.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.001

Table S116.  Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
19P GAIN MUTATED 26 18 9 20 1
19P GAIN WILD-TYPE 53 90 87 109 35

Figure S116.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.019 (Fisher's exact test), Q value = 0.075

Table S117.  Gene #34: '19p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 22 17 24 10
19P GAIN MUTATED 3 9 2 1 1
19P GAIN WILD-TYPE 9 13 15 23 9

Figure S117.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 0.00251 (Fisher's exact test), Q value = 0.014

Table S118.  Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
19Q GAIN MUTATED 25 45 14
19Q GAIN WILD-TYPE 177 125 64

Figure S118.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'RPPA_CNMF'

P value = 0.0134 (Fisher's exact test), Q value = 0.057

Table S119.  Gene #35: '19q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 144 125
19Q GAIN MUTATED 23 32 15
19Q GAIN WILD-TYPE 62 112 110

Figure S119.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.0011

Table S120.  Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
19Q GAIN MUTATED 28 20 12 23 1
19Q GAIN WILD-TYPE 51 88 84 106 35

Figure S120.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0407 (Fisher's exact test), Q value = 0.14

Table S121.  Gene #35: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 32 24
19Q GAIN MUTATED 4 11 2
19Q GAIN WILD-TYPE 25 21 22

Figure S121.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-04 (Fisher's exact test), Q value = 0.0033

Table S122.  Gene #35: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 22 17 24 10
19Q GAIN MUTATED 4 10 2 0 1
19Q GAIN WILD-TYPE 8 12 15 24 9

Figure S122.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p gain' versus 'MRNA_CNMF'

P value = 0.00293 (Fisher's exact test), Q value = 0.015

Table S123.  Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
20P GAIN MUTATED 12 41 14 16
20P GAIN WILD-TYPE 23 20 15 5

Figure S123.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00031

Table S124.  Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
20P GAIN MUTATED 11 51 21
20P GAIN WILD-TYPE 31 21 11

Figure S124.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S125.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
20P GAIN MUTATED 75 125 43
20P GAIN WILD-TYPE 127 45 35

Figure S125.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0016

Table S126.  Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
20P GAIN MUTATED 81 41 35
20P GAIN WILD-TYPE 39 56 41

Figure S126.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'RPPA_CNMF'

P value = 0.0303 (Fisher's exact test), Q value = 0.11

Table S127.  Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 144 125
20P GAIN MUTATED 51 78 53
20P GAIN WILD-TYPE 34 66 72

Figure S127.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.002

Table S128.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
20P GAIN MUTATED 79 41 44 77
20P GAIN WILD-TYPE 42 66 46 53

Figure S128.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S129.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
20P GAIN MUTATED 47 71 30 87 6
20P GAIN WILD-TYPE 32 37 66 42 30

Figure S129.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S130.  Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
20Q GAIN MUTATED 13 58 15 18
20Q GAIN WILD-TYPE 22 3 14 3

Figure S130.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S131.  Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
20Q GAIN MUTATED 12 61 31
20Q GAIN WILD-TYPE 30 11 1

Figure S131.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S132.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
20Q GAIN MUTATED 88 168 65
20Q GAIN WILD-TYPE 114 2 13

Figure S132.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S133.  Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
20Q GAIN MUTATED 117 49 45
20Q GAIN WILD-TYPE 3 48 31

Figure S133.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 0.00723 (Fisher's exact test), Q value = 0.033

Table S134.  Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 144 125
20Q GAIN MUTATED 67 106 75
20Q GAIN WILD-TYPE 18 38 50

Figure S134.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S135.  Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 42 86 22 20 26
20Q GAIN MUTATED 46 20 29 25 31 47 11 16 23
20Q GAIN WILD-TYPE 5 13 6 14 11 39 11 4 3

Figure S135.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S136.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
20Q GAIN MUTATED 116 46 64 93
20Q GAIN WILD-TYPE 5 61 26 37

Figure S136.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S137.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
20Q GAIN MUTATED 73 95 34 111 6
20Q GAIN WILD-TYPE 6 13 62 18 30

Figure S137.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00118 (Fisher's exact test), Q value = 0.0071

Table S138.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 50 77 135
20Q GAIN MUTATED 92 36 68 87
20Q GAIN WILD-TYPE 43 14 9 48

Figure S138.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00628 (Fisher's exact test), Q value = 0.03

Table S139.  Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 22 17 24 10
20Q GAIN MUTATED 12 20 13 13 9
20Q GAIN WILD-TYPE 0 2 4 11 1

Figure S139.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'MRNA_CNMF'

P value = 0.035 (Fisher's exact test), Q value = 0.12

Table S140.  Gene #38: '21q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
21Q GAIN MUTATED 0 2 0 3
21Q GAIN WILD-TYPE 35 59 29 18

Figure S140.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q gain' versus 'CN_CNMF'

P value = 0.00158 (Fisher's exact test), Q value = 0.0091

Table S141.  Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
21Q GAIN MUTATED 3 14 7
21Q GAIN WILD-TYPE 199 156 71

Figure S141.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'xp gain' versus 'CN_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.0035

Table S142.  Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
XP GAIN MUTATED 16 33 18
XP GAIN WILD-TYPE 186 137 60

Figure S142.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

'xp gain' versus 'RPPA_CNMF'

P value = 0.00726 (Fisher's exact test), Q value = 0.033

Table S143.  Gene #40: 'xp gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 144 125
XP GAIN MUTATED 14 33 11
XP GAIN WILD-TYPE 71 111 114

Figure S143.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'xp gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0429 (Fisher's exact test), Q value = 0.14

Table S144.  Gene #40: 'xp gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 32 24
XP GAIN MUTATED 1 8 5
XP GAIN WILD-TYPE 28 24 19

Figure S144.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'MRNA_CNMF'

P value = 0.0431 (Fisher's exact test), Q value = 0.14

Table S145.  Gene #41: 'xq gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
XQ GAIN MUTATED 2 9 9 2
XQ GAIN WILD-TYPE 33 52 20 19

Figure S145.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0023

Table S146.  Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
XQ GAIN MUTATED 21 31 24
XQ GAIN WILD-TYPE 181 139 54

Figure S146.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'xq gain' versus 'RPPA_CNMF'

P value = 0.00514 (Fisher's exact test), Q value = 0.025

Table S147.  Gene #41: 'xq gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 144 125
XQ GAIN MUTATED 17 35 12
XQ GAIN WILD-TYPE 68 109 113

Figure S147.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'1p loss' versus 'MRNA_CNMF'

P value = 0.0287 (Fisher's exact test), Q value = 0.1

Table S148.  Gene #42: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
1P LOSS MUTATED 7 18 1 4
1P LOSS WILD-TYPE 28 43 28 17

Figure S148.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S149.  Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
1P LOSS MUTATED 22 64 9
1P LOSS WILD-TYPE 180 106 69

Figure S149.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 0.00079 (Fisher's exact test), Q value = 0.005

Table S150.  Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
1P LOSS MUTATED 39 12 12
1P LOSS WILD-TYPE 81 85 64

Figure S150.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.0011

Table S151.  Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
1P LOSS MUTATED 38 8 20 28
1P LOSS WILD-TYPE 83 99 70 102

Figure S151.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S152.  Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
1P LOSS MUTATED 29 23 8 31 3
1P LOSS WILD-TYPE 50 85 88 98 33

Figure S152.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0208 (Fisher's exact test), Q value = 0.081

Table S153.  Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 50 77 135
1P LOSS MUTATED 27 9 26 21
1P LOSS WILD-TYPE 108 41 51 114

Figure S153.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00022

Table S154.  Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
1Q LOSS MUTATED 11 37 8
1Q LOSS WILD-TYPE 191 133 70

Figure S154.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 0.00203 (Fisher's exact test), Q value = 0.011

Table S155.  Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
1Q LOSS MUTATED 23 4 14 14
1Q LOSS WILD-TYPE 98 103 76 116

Figure S155.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00515 (Fisher's exact test), Q value = 0.025

Table S156.  Gene #43: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
1Q LOSS MUTATED 17 15 4 17 2
1Q LOSS WILD-TYPE 62 93 92 112 34

Figure S156.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00532 (Fisher's exact test), Q value = 0.026

Table S157.  Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 50 77 135
1Q LOSS MUTATED 14 7 18 9
1Q LOSS WILD-TYPE 121 43 59 126

Figure S157.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MRNA_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00095

Table S158.  Gene #48: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
4P LOSS MUTATED 8 28 1 9
4P LOSS WILD-TYPE 27 33 28 12

Figure S158.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00121 (Fisher's exact test), Q value = 0.0072

Table S159.  Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
4P LOSS MUTATED 7 21 18
4P LOSS WILD-TYPE 35 51 14

Figure S159.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S160.  Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
4P LOSS MUTATED 31 88 19
4P LOSS WILD-TYPE 171 82 59

Figure S160.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 0.00063 (Fisher's exact test), Q value = 0.004

Table S161.  Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
4P LOSS MUTATED 51 19 19
4P LOSS WILD-TYPE 69 78 57

Figure S161.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0318 (Fisher's exact test), Q value = 0.11

Table S162.  Gene #48: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 42 86 22 20 26
4P LOSS MUTATED 16 7 13 13 17 17 7 1 10
4P LOSS WILD-TYPE 35 26 22 26 25 69 15 19 16

Figure S162.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S163.  Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
4P LOSS MUTATED 56 12 28 41
4P LOSS WILD-TYPE 65 95 62 89

Figure S163.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S164.  Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
4P LOSS MUTATED 35 41 8 50 3
4P LOSS WILD-TYPE 44 67 88 79 33

Figure S164.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0246 (Fisher's exact test), Q value = 0.091

Table S165.  Gene #48: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 22 17 24 10
4P LOSS MUTATED 8 6 4 4 5
4P LOSS WILD-TYPE 4 16 13 20 5

Figure S165.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'MRNA_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00095

Table S166.  Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
4Q LOSS MUTATED 7 26 1 9
4Q LOSS WILD-TYPE 28 35 28 12

Figure S166.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00937 (Fisher's exact test), Q value = 0.042

Table S167.  Gene #49: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
4Q LOSS MUTATED 6 22 15
4Q LOSS WILD-TYPE 36 50 17

Figure S167.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S168.  Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
4Q LOSS MUTATED 26 85 16
4Q LOSS WILD-TYPE 176 85 62

Figure S168.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.0031

Table S169.  Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
4Q LOSS MUTATED 47 15 19
4Q LOSS WILD-TYPE 73 82 57

Figure S169.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S170.  Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
4Q LOSS MUTATED 51 12 23 40
4Q LOSS WILD-TYPE 70 95 67 90

Figure S170.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S171.  Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
4Q LOSS MUTATED 33 38 6 46 3
4Q LOSS WILD-TYPE 46 70 90 83 33

Figure S171.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0026

Table S172.  Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
5P LOSS MUTATED 13 34 12
5P LOSS WILD-TYPE 189 136 66

Figure S172.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 0.0206 (Fisher's exact test), Q value = 0.08

Table S173.  Gene #50: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
5P LOSS MUTATED 24 7 9
5P LOSS WILD-TYPE 96 90 67

Figure S173.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00091 (Fisher's exact test), Q value = 0.0057

Table S174.  Gene #50: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
5P LOSS MUTATED 12 21 2 20 4
5P LOSS WILD-TYPE 67 87 94 109 32

Figure S174.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00031

Table S175.  Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
5Q LOSS MUTATED 16 44 18
5Q LOSS WILD-TYPE 186 126 60

Figure S175.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 0.0242 (Fisher's exact test), Q value = 0.091

Table S176.  Gene #51: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
5Q LOSS MUTATED 29 10 16
5Q LOSS WILD-TYPE 91 87 60

Figure S176.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0015

Table S177.  Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
5Q LOSS MUTATED 32 6 19 21
5Q LOSS WILD-TYPE 89 101 71 109

Figure S177.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.0024

Table S178.  Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
5Q LOSS MUTATED 20 26 5 24 3
5Q LOSS WILD-TYPE 59 82 91 105 33

Figure S178.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0273 (Fisher's exact test), Q value = 0.099

Table S179.  Gene #52: '6p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 32 24
6P LOSS MUTATED 6 2 0
6P LOSS WILD-TYPE 23 30 24

Figure S179.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q loss' versus 'CN_CNMF'

P value = 0.0381 (Fisher's exact test), Q value = 0.13

Table S180.  Gene #54: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
7Q LOSS MUTATED 0 4 0
7Q LOSS WILD-TYPE 202 166 78

Figure S180.  Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'MRNA_CNMF'

P value = 0.0156 (Fisher's exact test), Q value = 0.065

Table S181.  Gene #55: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
8P LOSS MUTATED 7 27 5 9
8P LOSS WILD-TYPE 28 34 24 12

Figure S181.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'8p loss' versus 'MRNA_CHIERARCHICAL'

P value = 9e-04 (Fisher's exact test), Q value = 0.0057

Table S182.  Gene #55: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
8P LOSS MUTATED 5 27 16
8P LOSS WILD-TYPE 37 45 16

Figure S182.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S183.  Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
8P LOSS MUTATED 25 80 37
8P LOSS WILD-TYPE 177 90 41

Figure S183.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.0068

Table S184.  Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
8P LOSS MUTATED 52 20 21
8P LOSS WILD-TYPE 68 77 55

Figure S184.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0313 (Fisher's exact test), Q value = 0.11

Table S185.  Gene #55: '8p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 42 86 22 20 26
8P LOSS MUTATED 25 6 13 11 14 18 4 6 9
8P LOSS WILD-TYPE 26 27 22 28 28 68 18 14 17

Figure S185.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00062

Table S186.  Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
8P LOSS MUTATED 50 16 28 48
8P LOSS WILD-TYPE 71 91 62 82

Figure S186.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S187.  Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
8P LOSS MUTATED 37 35 13 54 3
8P LOSS WILD-TYPE 42 73 83 75 33

Figure S187.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0218 (Fisher's exact test), Q value = 0.083

Table S188.  Gene #55: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 22 17 24 10
8P LOSS MUTATED 8 9 6 3 3
8P LOSS WILD-TYPE 4 13 11 21 7

Figure S188.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 0.00234 (Fisher's exact test), Q value = 0.013

Table S189.  Gene #56: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
8Q LOSS MUTATED 5 18 2
8Q LOSS WILD-TYPE 197 152 76

Figure S189.  Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00193 (Fisher's exact test), Q value = 0.011

Table S190.  Gene #56: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 22 17 24 10
8Q LOSS MUTATED 6 1 1 2 0
8Q LOSS WILD-TYPE 6 21 16 22 10

Figure S190.  Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.0031

Table S191.  Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
9P LOSS MUTATED 12 32 10
9P LOSS WILD-TYPE 190 138 68

Figure S191.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.0031

Table S192.  Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
9P LOSS MUTATED 26 4 9
9P LOSS WILD-TYPE 94 93 67

Figure S192.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00055

Table S193.  Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
9P LOSS MUTATED 26 3 13 12
9P LOSS WILD-TYPE 95 104 77 118

Figure S193.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0031

Table S194.  Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
9P LOSS MUTATED 16 18 4 16 0
9P LOSS WILD-TYPE 63 90 92 113 36

Figure S194.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0014

Table S195.  Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
9Q LOSS MUTATED 11 33 9
9Q LOSS WILD-TYPE 191 137 69

Figure S195.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00031

Table S196.  Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
9Q LOSS MUTATED 27 2 9
9Q LOSS WILD-TYPE 93 95 67

Figure S196.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0015

Table S197.  Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
9Q LOSS MUTATED 24 3 14 12
9Q LOSS WILD-TYPE 97 104 76 118

Figure S197.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00137 (Fisher's exact test), Q value = 0.008

Table S198.  Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
9Q LOSS MUTATED 18 15 4 15 1
9Q LOSS WILD-TYPE 61 93 92 114 35

Figure S198.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MRNA_CNMF'

P value = 0.021 (Fisher's exact test), Q value = 0.081

Table S199.  Gene #59: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
10P LOSS MUTATED 2 11 0 4
10P LOSS WILD-TYPE 33 50 29 17

Figure S199.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0252 (Fisher's exact test), Q value = 0.093

Table S200.  Gene #59: '10p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
10P LOSS MUTATED 1 9 7
10P LOSS WILD-TYPE 41 63 25

Figure S200.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S201.  Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
10P LOSS MUTATED 11 44 14
10P LOSS WILD-TYPE 191 126 64

Figure S201.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00055

Table S202.  Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
10P LOSS MUTATED 35 6 10
10P LOSS WILD-TYPE 85 91 66

Figure S202.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

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

Table S203.  Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
10P LOSS MUTATED 32 5 14 17
10P LOSS WILD-TYPE 89 102 76 113

Figure S203.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.0014

Table S204.  Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
10P LOSS MUTATED 22 18 7 21 0
10P LOSS WILD-TYPE 57 90 89 108 36

Figure S204.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MRNA_CNMF'

P value = 0.0245 (Fisher's exact test), Q value = 0.091

Table S205.  Gene #60: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
10Q LOSS MUTATED 3 12 0 4
10Q LOSS WILD-TYPE 32 49 29 17

Figure S205.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0407 (Fisher's exact test), Q value = 0.14

Table S206.  Gene #60: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
10Q LOSS MUTATED 2 9 8
10Q LOSS WILD-TYPE 40 63 24

Figure S206.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S207.  Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
10Q LOSS MUTATED 10 48 15
10Q LOSS WILD-TYPE 192 122 63

Figure S207.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S208.  Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
10Q LOSS MUTATED 37 6 10
10Q LOSS WILD-TYPE 83 91 66

Figure S208.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S209.  Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
10Q LOSS MUTATED 34 4 15 19
10Q LOSS WILD-TYPE 87 103 75 111

Figure S209.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S210.  Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
10Q LOSS MUTATED 24 19 5 24 0
10Q LOSS WILD-TYPE 55 89 91 105 36

Figure S210.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 0.00853 (Fisher's exact test), Q value = 0.039

Table S211.  Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
11P LOSS MUTATED 17 30 5
11P LOSS WILD-TYPE 185 140 73

Figure S211.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'MRNA_CNMF'

P value = 0.0417 (Fisher's exact test), Q value = 0.14

Table S212.  Gene #62: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
11Q LOSS MUTATED 2 13 1 4
11Q LOSS WILD-TYPE 33 48 28 17

Figure S212.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0153 (Fisher's exact test), Q value = 0.064

Table S213.  Gene #62: '11q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
11Q LOSS MUTATED 1 15 4
11Q LOSS WILD-TYPE 41 57 28

Figure S213.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 0.00351 (Fisher's exact test), Q value = 0.018

Table S214.  Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
11Q LOSS MUTATED 20 36 7
11Q LOSS WILD-TYPE 182 134 71

Figure S214.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 0.0244 (Fisher's exact test), Q value = 0.091

Table S215.  Gene #62: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
11Q LOSS MUTATED 24 7 11
11Q LOSS WILD-TYPE 96 90 65

Figure S215.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00238 (Fisher's exact test), Q value = 0.013

Table S216.  Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
11Q LOSS MUTATED 16 16 7 24 0
11Q LOSS WILD-TYPE 63 92 89 105 36

Figure S216.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00709 (Fisher's exact test), Q value = 0.033

Table S217.  Gene #63: '12p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
12P LOSS MUTATED 0 8 6
12P LOSS WILD-TYPE 42 64 26

Figure S217.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S218.  Gene #63: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
12P LOSS MUTATED 2 37 8
12P LOSS WILD-TYPE 200 133 70

Figure S218.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 0.00728 (Fisher's exact test), Q value = 0.033

Table S219.  Gene #63: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
12P LOSS MUTATED 22 6 5
12P LOSS WILD-TYPE 98 91 71

Figure S219.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 0.00095 (Fisher's exact test), Q value = 0.0059

Table S220.  Gene #63: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
12P LOSS MUTATED 20 2 9 16
12P LOSS WILD-TYPE 101 105 81 114

Figure S220.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00062

Table S221.  Gene #63: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
12P LOSS MUTATED 15 13 1 18 0
12P LOSS WILD-TYPE 64 95 95 111 36

Figure S221.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0214 (Fisher's exact test), Q value = 0.082

Table S222.  Gene #63: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 22 17 24 10
12P LOSS MUTATED 4 3 1 0 2
12P LOSS WILD-TYPE 8 19 16 24 8

Figure S222.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0071 (Fisher's exact test), Q value = 0.033

Table S223.  Gene #64: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
12Q LOSS MUTATED 0 7 6
12Q LOSS WILD-TYPE 42 65 26

Figure S223.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S224.  Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
12Q LOSS MUTATED 5 36 8
12Q LOSS WILD-TYPE 197 134 70

Figure S224.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.047

Table S225.  Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
12Q LOSS MUTATED 23 6 7
12Q LOSS WILD-TYPE 97 91 69

Figure S225.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q loss' versus 'MRNASEQ_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.0028

Table S226.  Gene #64: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
12Q LOSS MUTATED 22 2 9 16
12Q LOSS WILD-TYPE 99 105 81 114

Figure S226.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.0012

Table S227.  Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
12Q LOSS MUTATED 15 14 2 18 0
12Q LOSS WILD-TYPE 64 94 94 111 36

Figure S227.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0223 (Fisher's exact test), Q value = 0.084

Table S228.  Gene #64: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 22 17 24 10
12Q LOSS MUTATED 4 3 1 0 2
12Q LOSS WILD-TYPE 8 19 16 24 8

Figure S228.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.0412 (Fisher's exact test), Q value = 0.14

Table S229.  Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
13Q LOSS MUTATED 5 0 4
13Q LOSS WILD-TYPE 115 97 72

Figure S229.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0348 (Fisher's exact test), Q value = 0.12

Table S230.  Gene #65: '13q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 32 24
13Q LOSS MUTATED 0 4 0
13Q LOSS WILD-TYPE 29 28 24

Figure S230.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S231.  Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
14Q LOSS MUTATED 5 33 2 10
14Q LOSS WILD-TYPE 30 28 27 11

Figure S231.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00055

Table S232.  Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
14Q LOSS MUTATED 4 29 17
14Q LOSS WILD-TYPE 38 43 15

Figure S232.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S233.  Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
14Q LOSS MUTATED 23 103 13
14Q LOSS WILD-TYPE 179 67 65

Figure S233.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S234.  Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
14Q LOSS MUTATED 57 14 16
14Q LOSS WILD-TYPE 63 83 60

Figure S234.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S235.  Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
14Q LOSS MUTATED 60 9 22 48
14Q LOSS WILD-TYPE 61 98 68 82

Figure S235.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S236.  Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
14Q LOSS MUTATED 33 45 4 55 2
14Q LOSS WILD-TYPE 46 63 92 74 34

Figure S236.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0214 (Fisher's exact test), Q value = 0.082

Table S237.  Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 50 77 135
14Q LOSS MUTATED 40 8 32 39
14Q LOSS WILD-TYPE 95 42 45 96

Figure S237.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00543 (Fisher's exact test), Q value = 0.027

Table S238.  Gene #66: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 22 17 24 10
14Q LOSS MUTATED 4 8 5 3 8
14Q LOSS WILD-TYPE 8 14 12 21 2

Figure S238.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'MRNA_CNMF'

P value = 0.00165 (Fisher's exact test), Q value = 0.0094

Table S239.  Gene #67: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
15Q LOSS MUTATED 8 30 4 10
15Q LOSS WILD-TYPE 27 31 25 11

Figure S239.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00149 (Fisher's exact test), Q value = 0.0086

Table S240.  Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
15Q LOSS MUTATED 7 27 18
15Q LOSS WILD-TYPE 35 45 14

Figure S240.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S241.  Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
15Q LOSS MUTATED 28 107 22
15Q LOSS WILD-TYPE 174 63 56

Figure S241.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0016

Table S242.  Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
15Q LOSS MUTATED 59 22 23
15Q LOSS WILD-TYPE 61 75 53

Figure S242.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S243.  Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
15Q LOSS MUTATED 59 14 32 51
15Q LOSS WILD-TYPE 62 93 58 79

Figure S243.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S244.  Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
15Q LOSS MUTATED 40 45 10 57 4
15Q LOSS WILD-TYPE 39 63 86 72 32

Figure S244.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S245.  Gene #70: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
17P LOSS MUTATED 9 46 8 15
17P LOSS WILD-TYPE 26 15 21 6

Figure S245.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S246.  Gene #70: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
17P LOSS MUTATED 8 46 24
17P LOSS WILD-TYPE 34 26 8

Figure S246.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S247.  Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
17P LOSS MUTATED 48 135 53
17P LOSS WILD-TYPE 154 35 25

Figure S247.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S248.  Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
17P LOSS MUTATED 94 32 28
17P LOSS WILD-TYPE 26 65 48

Figure S248.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0066 (Fisher's exact test), Q value = 0.031

Table S249.  Gene #70: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 42 86 22 20 26
17P LOSS MUTATED 33 12 24 21 20 34 8 10 18
17P LOSS WILD-TYPE 18 21 11 18 22 52 14 10 8

Figure S249.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S250.  Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
17P LOSS MUTATED 91 26 46 72
17P LOSS WILD-TYPE 30 81 44 58

Figure S250.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S251.  Gene #70: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
17P LOSS MUTATED 53 73 19 86 4
17P LOSS WILD-TYPE 26 35 77 43 32

Figure S251.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00118 (Fisher's exact test), Q value = 0.0071

Table S252.  Gene #70: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 22 17 24 10
17P LOSS MUTATED 8 17 11 8 10
17P LOSS WILD-TYPE 4 5 6 16 0

Figure S252.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0025

Table S253.  Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
17Q LOSS MUTATED 16 38 12
17Q LOSS WILD-TYPE 186 132 66

Figure S253.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S254.  Gene #72: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
18P LOSS MUTATED 7 51 6 16
18P LOSS WILD-TYPE 28 10 23 5

Figure S254.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S255.  Gene #72: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
18P LOSS MUTATED 6 46 28
18P LOSS WILD-TYPE 36 26 4

Figure S255.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S256.  Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
18P LOSS MUTATED 50 157 47
18P LOSS WILD-TYPE 152 13 31

Figure S256.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S257.  Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
18P LOSS MUTATED 110 30 31
18P LOSS WILD-TYPE 10 67 45

Figure S257.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00288 (Fisher's exact test), Q value = 0.015

Table S258.  Gene #72: '18p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 42 86 22 20 26
18P LOSS MUTATED 32 18 23 21 25 35 8 11 22
18P LOSS WILD-TYPE 19 15 12 18 17 51 14 9 4

Figure S258.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S259.  Gene #72: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
18P LOSS MUTATED 107 25 48 73
18P LOSS WILD-TYPE 14 82 42 57

Figure S259.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S260.  Gene #72: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
18P LOSS MUTATED 62 83 15 91 2
18P LOSS WILD-TYPE 17 25 81 38 34

Figure S260.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0186 (Fisher's exact test), Q value = 0.073

Table S261.  Gene #72: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 50 77 135
18P LOSS MUTATED 71 25 55 70
18P LOSS WILD-TYPE 64 25 22 65

Figure S261.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00061 (Fisher's exact test), Q value = 0.004

Table S262.  Gene #72: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 22 17 24 10
18P LOSS MUTATED 10 15 12 6 9
18P LOSS WILD-TYPE 2 7 5 18 1

Figure S262.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S263.  Gene #73: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
18Q LOSS MUTATED 8 52 7 16
18Q LOSS WILD-TYPE 27 9 22 5

Figure S263.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S264.  Gene #73: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
18Q LOSS MUTATED 7 48 28
18Q LOSS WILD-TYPE 35 24 4

Figure S264.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S265.  Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
18Q LOSS MUTATED 57 157 57
18Q LOSS WILD-TYPE 145 13 21

Figure S265.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S266.  Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
18Q LOSS MUTATED 111 38 35
18Q LOSS WILD-TYPE 9 59 41

Figure S266.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0112 (Fisher's exact test), Q value = 0.049

Table S267.  Gene #73: '18q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 42 86 22 20 26
18Q LOSS MUTATED 35 18 24 23 26 38 9 13 21
18Q LOSS WILD-TYPE 16 15 11 16 16 48 13 7 5

Figure S267.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S268.  Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
18Q LOSS MUTATED 107 31 54 78
18Q LOSS WILD-TYPE 14 76 36 52

Figure S268.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S269.  Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
18Q LOSS MUTATED 67 86 21 94 2
18Q LOSS WILD-TYPE 12 22 75 35 34

Figure S269.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0127 (Fisher's exact test), Q value = 0.054

Table S270.  Gene #73: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 50 77 135
18Q LOSS MUTATED 79 28 58 72
18Q LOSS WILD-TYPE 56 22 19 63

Figure S270.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.0031

Table S271.  Gene #73: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 22 17 24 10
18Q LOSS MUTATED 10 17 12 8 10
18Q LOSS WILD-TYPE 2 5 5 16 0

Figure S271.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 0.00334 (Fisher's exact test), Q value = 0.017

Table S272.  Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
19P LOSS MUTATED 20 4 4 12
19P LOSS WILD-TYPE 101 103 86 118

Figure S272.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0222 (Fisher's exact test), Q value = 0.084

Table S273.  Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
19P LOSS MUTATED 4 15 3 16 2
19P LOSS WILD-TYPE 75 93 93 113 34

Figure S273.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 0.0419 (Fisher's exact test), Q value = 0.14

Table S274.  Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 65 172
19P LOSS MUTATED 15 1 19
19P LOSS WILD-TYPE 145 64 153

Figure S274.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00462 (Fisher's exact test), Q value = 0.023

Table S275.  Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 50 77 135
19P LOSS MUTATED 9 0 13 13
19P LOSS WILD-TYPE 126 50 64 122

Figure S275.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 0.0047 (Fisher's exact test), Q value = 0.024

Table S276.  Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
19Q LOSS MUTATED 17 3 3 12
19Q LOSS WILD-TYPE 104 104 87 118

Figure S276.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0174 (Fisher's exact test), Q value = 0.07

Table S277.  Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
19Q LOSS MUTATED 2 12 3 16 2
19Q LOSS WILD-TYPE 77 96 93 113 34

Figure S277.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0497 (Fisher's exact test), Q value = 0.16

Table S278.  Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 50 77 135
19Q LOSS MUTATED 7 1 11 11
19Q LOSS WILD-TYPE 128 49 66 124

Figure S278.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00063 (Fisher's exact test), Q value = 0.004

Table S279.  Gene #76: '20p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
20P LOSS MUTATED 0 5 8
20P LOSS WILD-TYPE 42 67 24

Figure S279.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00062

Table S280.  Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
20P LOSS MUTATED 7 23 14
20P LOSS WILD-TYPE 195 147 64

Figure S280.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'20p loss' versus 'METHLYATION_CNMF'

P value = 0.00556 (Fisher's exact test), Q value = 0.027

Table S281.  Gene #76: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
20P LOSS MUTATED 20 4 5
20P LOSS WILD-TYPE 100 93 71

Figure S281.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p loss' versus 'MRNASEQ_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 0.072

Table S282.  Gene #76: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
20P LOSS MUTATED 19 4 10 11
20P LOSS WILD-TYPE 102 103 80 119

Figure S282.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 0.046

Table S283.  Gene #76: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
20P LOSS MUTATED 14 12 3 14 1
20P LOSS WILD-TYPE 65 96 93 115 35

Figure S283.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.046 (Fisher's exact test), Q value = 0.15

Table S284.  Gene #76: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 50 77 135
20P LOSS MUTATED 10 10 9 9
20P LOSS WILD-TYPE 125 40 68 126

Figure S284.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'MRNA_CNMF'

P value = 0.00954 (Fisher's exact test), Q value = 0.042

Table S285.  Gene #78: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
21Q LOSS MUTATED 7 25 3 4
21Q LOSS WILD-TYPE 28 36 26 17

Figure S285.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S286.  Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
21Q LOSS MUTATED 37 74 13
21Q LOSS WILD-TYPE 165 96 65

Figure S286.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S287.  Gene #78: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
21Q LOSS MUTATED 55 15 21 32
21Q LOSS WILD-TYPE 66 92 69 98

Figure S287.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00955 (Fisher's exact test), Q value = 0.042

Table S288.  Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
21Q LOSS MUTATED 29 33 18 39 4
21Q LOSS WILD-TYPE 50 75 78 90 32

Figure S288.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MRNA_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.0031

Table S289.  Gene #79: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
22Q LOSS MUTATED 7 32 4 9
22Q LOSS WILD-TYPE 28 29 25 12

Figure S289.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0031

Table S290.  Gene #79: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 72 32
22Q LOSS MUTATED 5 33 14
22Q LOSS WILD-TYPE 37 39 18

Figure S290.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S291.  Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
22Q LOSS MUTATED 37 94 15
22Q LOSS WILD-TYPE 165 76 63

Figure S291.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 0.0275 (Fisher's exact test), Q value = 0.099

Table S292.  Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 97 76
22Q LOSS MUTATED 44 20 26
22Q LOSS WILD-TYPE 76 77 50

Figure S292.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00622 (Fisher's exact test), Q value = 0.03

Table S293.  Gene #79: '22q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 42 86 22 20 26
22Q LOSS MUTATED 17 6 22 8 13 22 7 6 7
22Q LOSS WILD-TYPE 34 27 13 31 29 64 15 14 19

Figure S293.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'22q loss' versus 'MRNASEQ_CNMF'

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

Table S294.  Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 107 90 130
22Q LOSS MUTATED 52 16 28 49
22Q LOSS WILD-TYPE 69 91 62 81

Figure S294.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S295.  Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 79 108 96 129 36
22Q LOSS MUTATED 35 41 10 57 2
22Q LOSS WILD-TYPE 44 67 86 72 34

Figure S295.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MRNA_CNMF'

P value = 0.0294 (Fisher's exact test), Q value = 0.11

Table S296.  Gene #80: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
XP LOSS MUTATED 4 15 3 0
XP LOSS WILD-TYPE 31 46 26 21

Figure S296.  Get High-res Image Gene #80: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'xp loss' versus 'CN_CNMF'

P value = 0.0172 (Fisher's exact test), Q value = 0.07

Table S297.  Gene #80: 'xp loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
XP LOSS MUTATED 19 33 13
XP LOSS WILD-TYPE 183 137 65

Figure S297.  Get High-res Image Gene #80: 'xp loss' versus Molecular Subtype #3: 'CN_CNMF'

'xp loss' versus 'RPPA_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.052

Table S298.  Gene #80: 'xp loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 144 125
XP LOSS MUTATED 9 30 11
XP LOSS WILD-TYPE 76 114 114

Figure S298.  Get High-res Image Gene #80: 'xp loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'xq loss' versus 'MRNA_CNMF'

P value = 0.0158 (Fisher's exact test), Q value = 0.065

Table S299.  Gene #81: 'xq loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
XQ LOSS MUTATED 4 15 2 0
XQ LOSS WILD-TYPE 31 46 27 21

Figure S299.  Get High-res Image Gene #81: 'xq loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 0.00296 (Fisher's exact test), Q value = 0.016

Table S300.  Gene #81: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 170 78
XQ LOSS MUTATED 15 32 7
XQ LOSS WILD-TYPE 187 138 71

Figure S300.  Get High-res Image Gene #81: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

'xq loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0172 (Fisher's exact test), Q value = 0.07

Table S301.  Gene #81: 'xq loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 51 33 35 39 42 86 22 20 26
XQ LOSS MUTATED 8 1 11 5 4 5 2 3 2
XQ LOSS WILD-TYPE 43 32 24 34 38 81 20 17 24

Figure S301.  Get High-res Image Gene #81: 'xq loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

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/COAD-TP/19780706/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/COAD-TP/20125559/COAD-TP.transferedmergedcluster.txt

  • Number of patients = 450

  • Number of significantly arm-level cnvs = 81

  • Number of molecular subtypes = 12

  • 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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