Correlation between copy number variations of arm-level result and molecular subtypes
Lung Squamous Cell Carcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1C53JX2
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/C1C53JX2
Overview
Introduction

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

Summary

Testing the association between copy number variation 82 arm-level events and 12 molecular subtypes across 501 patients, 389 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

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

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

  • 4p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 4q gain cnv correlated to 'CN_CNMF'.

  • 5p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • 5q gain cnv correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 7p gain cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

  • 8p gain cnv correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

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

  • 9q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 10q gain cnv correlated to 'RPPA_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 11p gain cnv correlated to 'RPPA_CHIERARCHICAL' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 11q gain cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.

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

  • 12q gain cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 14q gain cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • 16p gain cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

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

  • 17p gain cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 18p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 19p gain cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 19q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

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

  • 20q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

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

  • xp gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

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

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

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

  • 2p loss cnv correlated to 'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 2q loss cnv correlated to 'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • 5p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

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

  • 6q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 7p loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • 7q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 8q loss cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 9p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 9q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 10p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • 12p loss cnv correlated to 'MRNA_CNMF' and 'MRNA_CHIERARCHICAL'.

  • 12q loss cnv correlated to 'RPPA_CNMF'.

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

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

  • 15q loss cnv correlated to 'RPPA_CHIERARCHICAL' and 'MIRSEQ_CNMF'.

  • 16p loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • 16q loss cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • 19q loss cnv correlated to 'CN_CNMF'.

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

  • 20q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

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

  • 22q loss cnv correlated to 'MRNA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 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, 389 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
9q gain 92 (18%) 409 0.0047
(0.0197) 		0.0005
(0.00364) 		1e-05
(0.000147) 		1e-05
(0.000147) 		0.0579
(0.139) 		0.0277
(0.0801) 		1e-05
(0.000147) 		1e-05
(0.000147) 		0.00021
(0.00175) 		6e-05
(0.000621) 		0.00096
(0.0058) 		0.00162
(0.00843)
9q loss 245 (49%) 256 1e-05
(0.000147) 		1e-05
(0.000147) 		1e-05
(0.000147) 		1e-05
(0.000147) 		0.172
(0.293) 		0.0135
(0.0466) 		1e-05
(0.000147) 		1e-05
(0.000147) 		1e-05
(0.000147) 		1e-05
(0.000147) 		0.00408
(0.018) 		0.0001
(0.000974)
7q gain 221 (44%) 280 0.00335
(0.0152) 		0.00034
(0.00263) 		1e-05
(0.000147) 		1e-05
(0.000147) 		0.904
(0.944) 		0.226
(0.357) 		1e-05
(0.000147) 		1e-05
(0.000147) 		0.00046
(0.00343) 		0.00017
(0.00153) 		0.00117
(0.00669) 		0.00069
(0.00444)
12p gain 229 (46%) 272 0.0182
(0.0586) 		0.0328
(0.0911) 		1e-05
(0.000147) 		0.00561
(0.0226) 		0.22
(0.35) 		0.802
(0.871) 		3e-05
(0.000356) 		0.00216
(0.0106) 		0.0295
(0.0836) 		0.00983
(0.0357) 		0.0235
(0.0719) 		0.0015
(0.00807)
17q gain 158 (32%) 343 0.00156
(0.00825) 		0.00054
(0.0038) 		1e-05
(0.000147) 		1e-05
(0.000147) 		0.42
(0.552) 		0.977
(0.988) 		1e-05
(0.000147) 		1e-05
(0.000147) 		0.00048
(0.00355) 		0.0113
(0.04) 		0.00053
(0.00378) 		3e-05
(0.000356)
1p loss 152 (30%) 349 4e-05
(0.000452) 		3e-05
(0.000356) 		1e-05
(0.000147) 		1e-05
(0.000147) 		0.885
(0.934) 		0.171
(0.292) 		1e-05
(0.000147) 		1e-05
(0.000147) 		0.00137
(0.00762) 		1e-05
(0.000147) 		0.00081
(0.00508) 		0.00037
(0.00284)
4q loss 298 (59%) 203 0.00235
(0.0113) 		0.00103
(0.006) 		1e-05
(0.000147) 		1e-05
(0.000147) 		0.293
(0.434) 		0.548
(0.666) 		2e-05
(0.00027) 		0.00027
(0.00218) 		0.00286
(0.0133) 		0.0303
(0.0852) 		0.00064
(0.00428) 		4e-05
(0.000452)
10q loss 229 (46%) 272 0.00093
(0.00568) 		0.00017
(0.00153) 		4e-05
(0.000452) 		1e-05
(0.000147) 		0.0954
(0.199) 		0.0797
(0.175) 		1e-05
(0.000147) 		1e-05
(0.000147) 		0.00055
(0.00384) 		1e-05
(0.000147) 		0.0149
(0.0502) 		0.00729
(0.0279)
2p gain 223 (45%) 278 0.104
(0.209) 		0.0244
(0.0735) 		1e-05
(0.000147) 		2e-05
(0.00027) 		0.419
(0.552) 		0.757
(0.837) 		1e-05
(0.000147) 		1e-05
(0.000147) 		0.00741
(0.0282) 		0.0308
(0.0862) 		0.00297
(0.0137) 		5e-05
(0.000541)
9p gain 62 (12%) 439 0.088
(0.189) 		0.0213
(0.0668) 		6e-05
(0.000621) 		5e-05
(0.000541) 		0.175
(0.297) 		0.0479
(0.122) 		1e-05
(0.000147) 		1e-05
(0.000147) 		0.0137
(0.047) 		0.0496
(0.125) 		0.00098
(0.00583) 		0.0742
(0.167)
4p loss 315 (63%) 186 0.00132
(0.00738) 		0.00011
(0.00105) 		1e-05
(0.000147) 		1e-05
(0.000147) 		0.211
(0.339) 		0.373
(0.514) 		1e-05
(0.000147) 		1e-05
(0.000147) 		0.00065
(0.00432) 		0.0547
(0.134) 		1e-05
(0.000147) 		1e-05
(0.000147)
9p loss 310 (62%) 191 0.00717
(0.0276) 		0.00119
(0.00677) 		1e-05
(0.000147) 		0.0237
(0.0722) 		0.206
(0.333) 		0.0769
(0.17) 		1e-05
(0.000147) 		2e-05
(0.00027) 		0.044
(0.113) 		0.00033
(0.00258) 		0.434
(0.564) 		0.028
(0.0805)
14q loss 166 (33%) 335 0.0001
(0.000974) 		0.00029
(0.00232) 		0.0181
(0.0585) 		0.0925
(0.196) 		0.054
(0.133) 		0.153
(0.269) 		1e-05
(0.000147) 		1e-05
(0.000147) 		0.00018
(0.00158) 		1e-05
(0.000147) 		0.00267
(0.0126) 		0.00218
(0.0106)
1q gain 203 (41%) 298 0.682
(0.785) 		0.549
(0.666) 		1e-05
(0.000147) 		0.00045
(0.00338) 		0.495
(0.618) 		0.455
(0.584) 		0.00378
(0.0169) 		0.00061
(0.00411) 		0.00108
(0.00625) 		0.00435
(0.0189) 		0.0432
(0.112) 		0.0395
(0.104)
7p gain 243 (49%) 258 0.0603
(0.143) 		0.0124
(0.0432) 		3e-05
(0.000356) 		0.00014
(0.0013) 		0.57
(0.685) 		0.66
(0.768) 		8e-05
(0.000803) 		1e-05
(0.000147) 		0.0007
(0.00447) 		0.00027
(0.00218) 		0.013
(0.045) 		0.083
(0.181)
18p gain 150 (30%) 351 0.00796
(0.0301) 		0.00114
(0.00656) 		1e-05
(0.000147) 		1e-05
(0.000147) 		0.488
(0.611) 		0.715
(0.804) 		0.00099
(0.00583) 		1e-05
(0.000147) 		0.0165
(0.054) 		0.283
(0.422) 		0.0867
(0.187) 		0.00052
(0.00376)
18q gain 104 (21%) 397 0.0164
(0.054) 		0.0143
(0.0488) 		1e-05
(0.000147) 		0.00139
(0.00768) 		0.52
(0.641) 		0.338
(0.482) 		0.00076
(0.00479) 		0.00025
(0.00205) 		0.0576
(0.139) 		0.0329
(0.0912) 		0.259
(0.396) 		0.00217
(0.0106)
19p gain 111 (22%) 390 0.0464
(0.119) 		0.123
(0.234) 		1e-05
(0.000147) 		0.00018
(0.00158) 		0.0229
(0.0706) 		0.0673
(0.156) 		0.00015
(0.00138) 		0.00221
(0.0107) 		0.13
(0.242) 		0.00159
(0.00837) 		0.0689
(0.158) 		0.00539
(0.022)
10p loss 214 (43%) 287 0.204
(0.33) 		0.218
(0.348) 		4e-05
(0.000452) 		1e-05
(0.000147) 		0.396
(0.534) 		0.159
(0.277) 		3e-05
(0.000356) 		6e-05
(0.000621) 		0.00038
(0.0029) 		1e-05
(0.000147) 		0.0475
(0.121) 		0.00437
(0.0189)
17q loss 94 (19%) 407 0.0102
(0.0367) 		0.00498
(0.0207) 		0.00058
(0.00396) 		0.00161
(0.00843) 		0.662
(0.768) 		0.969
(0.983) 		0.00019
(0.00164) 		1e-05
(0.000147) 		0.0768
(0.17) 		0.00908
(0.0333) 		0.694
(0.794) 		0.0434
(0.112)
xp loss 146 (29%) 355 0.228
(0.357) 		0.508
(0.632) 		3e-05
(0.000356) 		1e-05
(0.000147) 		0.347
(0.491) 		0.479
(0.604) 		0.00254
(0.012) 		0.0192
(0.0614) 		0.0118
(0.0418) 		0.00152
(0.00808) 		0.0005
(0.00364) 		1e-05
(0.000147)
8q gain 257 (51%) 244 0.0484
(0.123) 		0.0367
(0.0987) 		0.0221
(0.0688) 		0.00631
(0.0248) 		0.265
(0.402) 		0.753
(0.836) 		0.00633
(0.0248) 		0.0003
(0.00238) 		0.0652
(0.153) 		0.00471
(0.0197) 		0.413
(0.548) 		0.459
(0.587)
12q gain 153 (31%) 348 0.0239
(0.0725) 		0.308
(0.453) 		1e-05
(0.000147) 		0.00633
(0.0248) 		0.534
(0.653) 		0.614
(0.728) 		0.00334
(0.0152) 		0.00097
(0.00582) 		0.118
(0.228) 		0.13
(0.242) 		0.00952
(0.0347) 		8e-05
(0.000803)
17p gain 68 (14%) 433 0.00406
(0.018) 		0.101
(0.204) 		1e-05
(0.000147) 		0.0018
(0.00918) 		0.839
(0.9) 		0.14
(0.254) 		0.00067
(0.0044) 		0.00095
(0.00577) 		0.0166
(0.054) 		0.0955
(0.199) 		0.0503
(0.127) 		0.00734
(0.028)
17p loss 291 (58%) 210 0.00468
(0.0197) 		0.172
(0.293) 		6e-05
(0.000621) 		0.0113
(0.0401) 		0.435
(0.565) 		0.00631
(0.0248) 		0.00169
(0.00875) 		0.00128
(0.0072) 		0.0947
(0.199) 		0.00073
(0.00463) 		0.133
(0.243) 		0.0929
(0.196)
21q loss 265 (53%) 236 0.9
(0.941) 		0.322
(0.465) 		1e-05
(0.000147) 		0.00543
(0.0221) 		0.524
(0.645) 		0.45
(0.579) 		0.0602
(0.143) 		0.0384
(0.102) 		0.0158
(0.0524) 		0.00059
(0.004) 		0.0243
(0.0732) 		0.0126
(0.0437)
xq loss 112 (22%) 389 0.076
(0.17) 		0.364
(0.505) 		1e-05
(0.000147) 		0.00013
(0.00122) 		0.651
(0.762) 		0.815
(0.881) 		0.00808
(0.0304) 		0.981
(0.989) 		0.00842
(0.0314) 		0.0147
(0.0498) 		0.0046
(0.0197) 		2e-05
(0.00027)
2q gain 140 (28%) 361 0.472
(0.599) 		0.36
(0.501) 		0.00045
(0.00338) 		0.0405
(0.106) 		0.453
(0.581) 		0.647
(0.758) 		0.00146
(0.00794) 		0.0213
(0.0668) 		0.145
(0.259) 		0.27
(0.406) 		0.00239
(0.0114) 		0.0123
(0.0429)
4p gain 32 (6%) 469 0.562
(0.678) 		0.203
(0.33) 		0.00021
(0.00175) 		0.0809
(0.177) 		0.578
(0.694) 		0.41
(0.547) 		0.0298
(0.0841) 		0.00641
(0.025) 		0.00533
(0.0219) 		0.309
(0.453) 		0.0122
(0.0428) 		0.0153
(0.0512)
15q gain 105 (21%) 396 0.838
(0.899) 		0.427
(0.559) 		0.00086
(0.00536) 		0.00126
(0.00713) 		0.221
(0.35) 		0.659
(0.767) 		0.0015
(0.00807) 		0.011
(0.0395) 		0.108
(0.215) 		0.0356
(0.0964) 		0.086
(0.186) 		0.00214
(0.0106)
22q gain 221 (44%) 280 0.00827
(0.0309) 		0.0287
(0.0821) 		0.00453
(0.0196) 		0.034
(0.0933) 		0.966
(0.982) 		0.0675
(0.156) 		0.00056
(0.00388) 		0.00013
(0.00122) 		0.802
(0.871) 		0.109
(0.217) 		0.99
(0.996) 		0.755
(0.837)
5q loss 291 (58%) 210 0.131
(0.243) 		0.0545
(0.134) 		0.00018
(0.00158) 		0.00239
(0.0114) 		0.267
(0.404) 		0.126
(0.236) 		0.006
(0.0241) 		0.00033
(0.00258) 		0.133
(0.243) 		0.0198
(0.0626) 		0.0141
(0.0483) 		0.0945
(0.199)
6p loss 112 (22%) 389 0.0349
(0.095) 		0.0144
(0.0488) 		0.00392
(0.0175) 		0.00011
(0.00105) 		0.151
(0.266) 		0.145
(0.259) 		3e-05
(0.000356) 		3e-05
(0.000356) 		0.196
(0.32) 		0.163
(0.282) 		0.178
(0.3) 		0.404
(0.541)
6q loss 113 (23%) 388 0.00469
(0.0197) 		0.00103
(0.006) 		0.0254
(0.0754) 		0.00277
(0.013) 		0.701
(0.797) 		0.396
(0.534) 		0.00179
(0.00918) 		0.0238
(0.0722) 		0.553
(0.67) 		0.756
(0.837) 		0.116
(0.225) 		0.344
(0.488)
xq gain 83 (17%) 418 0.162
(0.281) 		0.0335
(0.0925) 		1e-05
(0.000147) 		0.00348
(0.0157) 		0.697
(0.796) 		0.605
(0.722) 		0.00693
(0.0267) 		0.00865
(0.0321) 		0.0589
(0.141) 		0.294
(0.434) 		0.365
(0.506) 		0.276
(0.413)
5p loss 78 (16%) 423 0.825
(0.889) 		0.933
(0.959) 		0.00435
(0.0189) 		0.00422
(0.0185) 		0.431
(0.564) 		0.0336
(0.0925) 		0.229
(0.357) 		0.284
(0.424) 		0.0384
(0.102) 		0.372
(0.513) 		0.0155
(0.0516) 		0.0938
(0.198)
19p loss 167 (33%) 334 0.0384
(0.102) 		0.0534
(0.132) 		3e-05
(0.000356) 		0.544
(0.664) 		0.891
(0.937) 		0.319
(0.462) 		0.0437
(0.113) 		0.0194
(0.0617) 		0.101
(0.205) 		0.00019
(0.00164) 		0.837
(0.899) 		0.162
(0.281)
20q loss 46 (9%) 455 0.0551
(0.134) 		0.0752
(0.169) 		0.00203
(0.0102) 		0.0235
(0.0719) 		0.436
(0.566) 		0.427
(0.559) 		2e-05
(0.00027) 		0.00144
(0.00787) 		0.01
(0.0362) 		0.0999
(0.203) 		0.464
(0.591) 		0.266
(0.403)
6q gain 94 (19%) 407 0.0682
(0.157) 		0.121
(0.232) 		0.00151
(0.00808) 		0.392
(0.533) 		0.876
(0.928) 		0.963
(0.98) 		0.0165
(0.054) 		0.0162
(0.0535) 		0.801
(0.871) 		0.179
(0.301) 		0.462
(0.59) 		0.0395
(0.104)
20p gain 261 (52%) 240 0.0196
(0.0624) 		0.0221
(0.0688) 		1e-05
(0.000147) 		0.00068
(0.0044) 		0.888
(0.935) 		0.311
(0.454) 		0.228
(0.357) 		0.142
(0.257) 		0.0764
(0.17) 		0.718
(0.806) 		0.636
(0.747) 		0.927
(0.956)
2p loss 21 (4%) 480 0.13
(0.242) 		0.188
(0.313) 		0.374
(0.515) 		0.103
(0.208) 		0.14
(0.254) 		0.1
(0.203) 		0.451
(0.58) 		0.0292
(0.0832) 		0.00659
(0.0255) 		0.529
(0.649) 		0.0376
(0.101) 		0.00057
(0.00392)
7q loss 51 (10%) 450 0.161
(0.28) 		0.0899
(0.192) 		0.00285
(0.0133) 		0.124
(0.235) 		0.83
(0.894) 		0.0629
(0.149) 		7e-05
(0.000717) 		2e-05
(0.00027) 		0.107
(0.214) 		0.0336
(0.0925) 		0.809
(0.877) 		0.403
(0.541)
16q loss 182 (36%) 319 0.777
(0.852) 		0.125
(0.235) 		0.0174
(0.0564) 		0.17
(0.292) 		0.132
(0.243) 		0.851
(0.909) 		0.0525
(0.131) 		0.0543
(0.134) 		0.00022
(0.00182) 		0.394
(0.533) 		0.00215
(0.0106) 		0.00183
(0.00928)
22q loss 98 (20%) 403 0.00907
(0.0333) 		0.1
(0.203) 		0.17
(0.292) 		0.0664
(0.155) 		0.253
(0.388) 		0.0577
(0.139) 		9e-05
(0.000895) 		1e-05
(0.000147) 		0.788
(0.862) 		0.009
(0.0333) 		0.193
(0.318) 		0.199
(0.324)
6p gain 109 (22%) 392 0.0552
(0.134) 		0.182
(0.305) 		0.00068
(0.0044) 		0.788
(0.862) 		0.935
(0.96) 		0.19
(0.314) 		0.0018
(0.00918) 		0.00647
(0.0252) 		0.951
(0.972) 		0.338
(0.482) 		0.173
(0.293) 		0.154
(0.27)
8p gain 129 (26%) 372 0.404
(0.541) 		0.552
(0.67) 		0.406
(0.542) 		0.0992
(0.203) 		0.255
(0.39) 		0.952
(0.972) 		0.0366
(0.0986) 		0.0251
(0.0746) 		0.392
(0.533) 		0.0152
(0.0508) 		0.854
(0.91) 		0.863
(0.917)
14q gain 129 (26%) 372 0.142
(0.257) 		0.0223
(0.0691) 		0.0403
(0.106) 		0.0976
(0.202) 		0.254
(0.389) 		0.328
(0.471) 		0.184
(0.307) 		0.00482
(0.0201) 		0.0731
(0.165) 		0.167
(0.287) 		0.571
(0.686) 		0.907
(0.945)
19q gain 159 (32%) 342 0.115
(0.224) 		0.179
(0.301) 		5e-05
(0.000541) 		0.0272
(0.0791) 		0.228
(0.357) 		0.118
(0.228) 		0.0221
(0.0688) 		0.507
(0.631) 		0.943
(0.966) 		0.418
(0.552) 		0.363
(0.505) 		0.146
(0.26)
xp gain 65 (13%) 436 0.215
(0.344) 		0.135
(0.248) 		5e-05
(0.000541) 		0.165
(0.284) 		0.772
(0.849) 		0.227
(0.357) 		0.00467
(0.0197) 		0.193
(0.318) 		0.00809
(0.0304) 		0.202
(0.328) 		0.696
(0.796) 		0.308
(0.453)
1q loss 60 (12%) 441 0.555
(0.671) 		0.671
(0.776) 		0.00229
(0.011) 		0.0892
(0.191) 		0.959
(0.978) 		0.61
(0.726) 		0.0347
(0.095) 		0.0269
(0.0791) 		0.249
(0.383) 		0.0846
(0.183) 		0.227
(0.357) 		0.529
(0.649)
2q loss 42 (8%) 459 0.707
(0.797) 		1
(1.00) 		0.274
(0.411) 		0.194
(0.318) 		0.881
(0.931) 		0.143
(0.257) 		0.0649
(0.153) 		0.0256
(0.0758) 		3e-05
(0.000356) 		0.193
(0.318) 		0.124
(0.235) 		0.00142
(0.00781)
3p loss 309 (62%) 192 0.368
(0.51) 		0.051
(0.128) 		0.13
(0.242) 		0.00209
(0.0104) 		0.931
(0.958) 		0.103
(0.208) 		0.396
(0.534) 		0.384
(0.526) 		0.272
(0.409) 		0.00021
(0.00175) 		0.0311
(0.0867) 		0.112
(0.22)
8p loss 244 (49%) 257 0.923
(0.954) 		0.959
(0.978) 		0.00533
(0.0219) 		0.00093
(0.00568) 		0.103
(0.208) 		0.441
(0.57) 		0.114
(0.223) 		0.085
(0.184) 		0.391
(0.533) 		0.015
(0.0502) 		0.189
(0.313) 		0.623
(0.735)
11p loss 171 (34%) 330 0.254
(0.389) 		0.251
(0.387) 		0.00609
(0.0244) 		0.00463
(0.0197) 		0.14
(0.255) 		0.00325
(0.0149) 		0.122
(0.234) 		0.627
(0.739) 		0.0556
(0.135) 		0.584
(0.699) 		0.476
(0.604) 		0.0647
(0.153)
13q loss 311 (62%) 190 0.617
(0.731) 		0.709
(0.798) 		0.0775
(0.171) 		0.0409
(0.107) 		0.705
(0.797) 		0.369
(0.51) 		0.274
(0.411) 		0.706
(0.797) 		0.0769
(0.17) 		0.108
(0.215) 		0.00067
(0.0044) 		0.0251
(0.0746)
20p loss 42 (8%) 459 0.143
(0.257) 		0.14
(0.255) 		0.0248
(0.0743) 		0.0032
(0.0147) 		0.112
(0.22) 		0.146
(0.26) 		0.201
(0.327) 		0.0311
(0.0867) 		0.44
(0.569) 		0.0642
(0.152) 		0.962
(0.98) 		0.337
(0.481)
3q gain 316 (63%) 185 0.599
(0.715) 		0.737
(0.823) 		0.0132
(0.0457) 		0.292
(0.433) 		1
(1.00) 		0.112
(0.22) 		0.308
(0.453) 		0.311
(0.454) 		0.449
(0.579) 		0.0271
(0.0791) 		0.688
(0.791) 		0.187
(0.311)
5p gain 309 (62%) 192 0.775
(0.852) 		0.853
(0.91) 		0.0297
(0.084) 		0.165
(0.284) 		0.311
(0.454) 		0.228
(0.357) 		0.318
(0.462) 		0.479
(0.604) 		0.232
(0.36) 		0.0544
(0.134) 		0.0404
(0.106) 		0.13
(0.242)
5q gain 93 (19%) 408 0.235
(0.365) 		0.208
(0.336) 		0.376
(0.517) 		0.177
(0.299) 		0.713
(0.802) 		0.149
(0.263) 		0.316
(0.459) 		0.0184
(0.0589) 		0.52
(0.641) 		0.279
(0.418) 		0.115
(0.225) 		0.0363
(0.0981)
10p gain 79 (16%) 422 0.322
(0.465) 		0.703
(0.797) 		0.109
(0.217) 		0.0949
(0.199) 		0.0653
(0.153) 		0.0846
(0.183) 		0.0701
(0.16) 		0.0534
(0.132) 		0.0453
(0.116) 		0.00054
(0.0038) 		0.899
(0.941) 		0.182
(0.306)
10q gain 45 (9%) 456 0.113
(0.221) 		0.141
(0.255) 		0.0516
(0.129) 		0.384
(0.526) 		0.0274
(0.0797) 		0.209
(0.336) 		0.06
(0.143) 		0.0111
(0.0398) 		0.411
(0.547) 		0.132
(0.243) 		0.765
(0.844) 		0.353
(0.495)
11p gain 74 (15%) 427 0.677
(0.781) 		0.477
(0.604) 		0.0589
(0.141) 		0.433
(0.564) 		0.246
(0.38) 		0.0101
(0.0363) 		0.655
(0.764) 		0.923
(0.954) 		0.131
(0.243) 		0.0747
(0.168) 		0.185
(0.309) 		0.0385
(0.102)
11q gain 91 (18%) 410 0.018
(0.0582) 		0.212
(0.34) 		0.00087
(0.00538) 		0.545
(0.664) 		0.394
(0.533) 		0.0526
(0.131) 		0.246
(0.381) 		0.065
(0.153) 		0.144
(0.259) 		0.111
(0.22) 		0.646
(0.757) 		0.072
(0.164)
16q gain 87 (17%) 414 0.918
(0.952) 		0.935
(0.96) 		0.0246
(0.0738) 		0.332
(0.475) 		0.692
(0.793) 		0.438
(0.567) 		0.16
(0.279) 		0.652
(0.762) 		0.213
(0.341) 		0.0271
(0.0791) 		0.418
(0.552) 		0.426
(0.558)
20q gain 251 (50%) 250 0.674
(0.779) 		0.316
(0.459) 		0.00053
(0.00378) 		0.433
(0.564) 		0.559
(0.675) 		0.583
(0.699) 		0.31
(0.454) 		0.116
(0.226) 		0.0957
(0.199) 		0.0291
(0.083) 		0.843
(0.902) 		0.348
(0.491)
7p loss 58 (12%) 443 0.394
(0.533) 		1
(1.00) 		0.00021
(0.00175) 		0.483
(0.607) 		0.481
(0.606) 		0.123
(0.234) 		0.399
(0.537) 		0.092
(0.195) 		0.0912
(0.194) 		0.00561
(0.0226) 		0.927
(0.956) 		0.296
(0.437)
8q loss 48 (10%) 453 0.349
(0.492) 		0.356
(0.498) 		0.394
(0.533) 		0.0349
(0.095) 		0.0713
(0.162) 		0.877
(0.928) 		0.265
(0.402) 		0.0419
(0.109) 		0.0993
(0.203) 		0.123
(0.234) 		0.261
(0.397) 		0.908
(0.945)
11q loss 141 (28%) 360 0.988
(0.995) 		0.758
(0.837) 		0.0063
(0.0248) 		0.00099
(0.00583) 		0.54
(0.66) 		0.867
(0.92) 		0.124
(0.235) 		0.707
(0.797) 		0.0683
(0.157) 		0.236
(0.366) 		0.42
(0.552) 		0.0954
(0.199)
12p loss 39 (8%) 462 0.0233
(0.0716) 		0.00512
(0.0212) 		0.261
(0.397) 		0.517
(0.639) 		0.099
(0.203) 		0.885
(0.934) 		0.981
(0.989) 		0.111
(0.22) 		0.186
(0.31) 		0.0832
(0.182) 		0.0676
(0.156) 		0.189
(0.314)
15q loss 142 (28%) 359 0.72
(0.807) 		0.745
(0.831) 		0.121
(0.232) 		0.128
(0.24) 		0.324
(0.467) 		0.00197
(0.00994) 		0.0898
(0.192) 		0.285
(0.424) 		0.0277
(0.0801) 		0.159
(0.277) 		0.53
(0.65) 		0.411
(0.547)
16p loss 163 (33%) 338 0.979
(0.989) 		0.705
(0.797) 		0.00356
(0.016) 		0.211
(0.339) 		0.12
(0.231) 		0.269
(0.406) 		0.327
(0.471) 		0.443
(0.571) 		0.201
(0.327) 		0.835
(0.898) 		0.0267
(0.0787) 		0.084
(0.183)
4q gain 23 (5%) 478 0.741
(0.826) 		0.731
(0.817) 		0.00918
(0.0336) 		0.511
(0.635) 		0.876
(0.928) 		0.172
(0.293) 		0.842
(0.902) 		0.89
(0.937) 		0.0963
(0.2) 		0.353
(0.495) 		0.148
(0.263) 		0.193
(0.318)
16p gain 86 (17%) 415 0.356
(0.498) 		0.553
(0.67) 		0.116
(0.226) 		0.359
(0.501) 		0.613
(0.728) 		0.781
(0.856) 		0.686
(0.789) 		0.769
(0.847) 		0.482
(0.606) 		0.0207
(0.0653) 		0.476
(0.604) 		0.29
(0.431)
12q loss 48 (10%) 453 0.364
(0.505) 		0.142
(0.257) 		0.813
(0.88) 		0.673
(0.778) 		0.0282
(0.0808) 		0.753
(0.836) 		0.703
(0.797) 		0.791
(0.864) 		0.806
(0.874) 		0.118
(0.228) 		0.543
(0.663) 		0.148
(0.262)
19q loss 112 (22%) 389 0.614
(0.728) 		0.511
(0.635) 		0.0414
(0.108) 		0.0994
(0.203) 		0.343
(0.487) 		0.693
(0.794) 		0.821
(0.885) 		0.339
(0.482) 		0.479
(0.604) 		0.12
(0.231) 		0.458
(0.586) 		0.568
(0.684)
1p gain 89 (18%) 412 0.132
(0.243) 		0.153
(0.269) 		0.748
(0.832) 		0.729
(0.816) 		0.491
(0.615) 		0.916
(0.952) 		0.801
(0.871) 		0.433
(0.564) 		0.352
(0.495) 		0.747
(0.831) 		0.351
(0.494) 		0.328
(0.471)
3p gain 109 (22%) 392 0.977
(0.988) 		0.852
(0.909) 		0.22
(0.35) 		0.0991
(0.203) 		1
(1.00) 		0.251
(0.387) 		0.313
(0.457) 		0.149
(0.263) 		0.921
(0.954) 		0.689
(0.792) 		0.972
(0.985) 		0.497
(0.62)
13q gain 39 (8%) 462 0.699
(0.797) 		0.662
(0.768) 		0.799
(0.871) 		1
(1.00) 		0.415
(0.549) 		0.662
(0.768) 		0.513
(0.635) 		0.707
(0.797) 		0.227
(0.357) 		0.591
(0.706) 		0.895
(0.939) 		0.914
(0.951)
21q gain 57 (11%) 444 0.893
(0.938) 		0.815
(0.881) 		0.967
(0.982) 		0.0664
(0.155) 		0.378
(0.518) 		1
(1.00) 		0.409
(0.547) 		0.776
(0.852) 		0.513
(0.635) 		0.466
(0.593) 		0.221
(0.35) 		0.525
(0.646)
3q loss 69 (14%) 432 0.945
(0.967) 		0.927
(0.956) 		0.496
(0.619) 		0.898
(0.941) 		0.632
(0.743) 		0.412
(0.547) 		0.905
(0.944) 		0.319
(0.462) 		0.609
(0.725) 		0.239
(0.37) 		0.163
(0.281) 		0.344
(0.488)
18p loss 140 (28%) 361 0.856
(0.911) 		0.653
(0.762) 		0.0921
(0.195) 		0.0579
(0.139) 		0.627
(0.739) 		0.919
(0.952) 		0.196
(0.32) 		0.0733
(0.166) 		0.416
(0.55) 		0.0777
(0.171) 		0.0684
(0.157) 		0.622
(0.735)
18q loss 189 (38%) 312 0.223
(0.353) 		0.332
(0.475) 		0.0527
(0.131) 		0.394
(0.533) 		0.704
(0.797) 		0.388
(0.53) 		0.486
(0.61) 		0.146
(0.26) 		0.0726
(0.165) 		0.125
(0.235) 		0.0792
(0.174) 		0.619
(0.732)
'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S1.  Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
1Q GAIN MUTATED 65 92 46
1Q GAIN WILD-TYPE 117 74 107

Figure S1.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1q gain' versus 'METHLYATION_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.0034

Table S2.  Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
1Q GAIN MUTATED 46 64 31
1Q GAIN WILD-TYPE 106 58 62

Figure S2.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 0.00378 (Fisher's exact test), Q value = 0.017

Table S3.  Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
1Q GAIN MUTATED 38 80 59 26
1Q GAIN WILD-TYPE 75 72 95 53

Figure S3.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00061 (Fisher's exact test), Q value = 0.0041

Table S4.  Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
1Q GAIN MUTATED 54 94 55
1Q GAIN WILD-TYPE 124 95 76

Figure S4.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CNMF'

P value = 0.00108 (Fisher's exact test), Q value = 0.0063

Table S5.  Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
1Q GAIN MUTATED 53 57 35 35 9
1Q GAIN WILD-TYPE 68 77 86 27 28

Figure S5.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00435 (Fisher's exact test), Q value = 0.019

Table S6.  Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
1Q GAIN MUTATED 49 50 66 24
1Q GAIN WILD-TYPE 40 68 133 45

Figure S6.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0432 (Fisher's exact test), Q value = 0.11

Table S7.  Gene #2: '1q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
1Q GAIN MUTATED 24 52 50
1Q GAIN WILD-TYPE 65 77 66

Figure S7.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0395 (Fisher's exact test), Q value = 0.1

Table S8.  Gene #2: '1q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
1Q GAIN MUTATED 11 68 47
1Q GAIN WILD-TYPE 28 83 97

Figure S8.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0244 (Fisher's exact test), Q value = 0.074

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
2P GAIN MUTATED 19 31 15
2P GAIN WILD-TYPE 28 25 36

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

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
2P GAIN MUTATED 53 108 62
2P GAIN WILD-TYPE 129 58 91

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00027

Table S11.  Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
2P GAIN MUTATED 53 80 36
2P GAIN WILD-TYPE 99 42 57

Figure S11.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S12.  Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
2P GAIN MUTATED 36 94 67 24
2P GAIN WILD-TYPE 77 58 87 55

Figure S12.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S13.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
2P GAIN MUTATED 62 111 48
2P GAIN WILD-TYPE 116 78 83

Figure S13.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CNMF'

P value = 0.00741 (Fisher's exact test), Q value = 0.028

Table S14.  Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
2P GAIN MUTATED 52 77 42 27 16
2P GAIN WILD-TYPE 69 57 79 35 21

Figure S14.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0308 (Fisher's exact test), Q value = 0.086

Table S15.  Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
2P GAIN MUTATED 44 50 99 21
2P GAIN WILD-TYPE 45 68 100 48

Figure S15.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00297 (Fisher's exact test), Q value = 0.014

Table S16.  Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
2P GAIN MUTATED 28 62 64
2P GAIN WILD-TYPE 61 67 52

Figure S16.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00054

Table S17.  Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
2P GAIN MUTATED 17 90 47
2P GAIN WILD-TYPE 22 61 97

Figure S17.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.0034

Table S18.  Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
2Q GAIN MUTATED 36 64 40
2Q GAIN WILD-TYPE 146 102 113

Figure S18.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 0.0405 (Fisher's exact test), Q value = 0.11

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
2Q GAIN MUTATED 37 46 24
2Q GAIN WILD-TYPE 115 76 69

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

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.00146 (Fisher's exact test), Q value = 0.0079

Table S20.  Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
2Q GAIN MUTATED 24 56 46 12
2Q GAIN WILD-TYPE 89 96 108 67

Figure S20.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0213 (Fisher's exact test), Q value = 0.067

Table S21.  Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
2Q GAIN MUTATED 38 65 35
2Q GAIN WILD-TYPE 140 124 96

Figure S21.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00239 (Fisher's exact test), Q value = 0.011

Table S22.  Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
2Q GAIN MUTATED 13 44 38
2Q GAIN WILD-TYPE 76 85 78

Figure S22.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0123 (Fisher's exact test), Q value = 0.043

Table S23.  Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
2Q GAIN MUTATED 7 55 33
2Q GAIN WILD-TYPE 32 96 111

Figure S23.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 0.0132 (Fisher's exact test), Q value = 0.046

Table S24.  Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
3Q GAIN MUTATED 103 103 110
3Q GAIN WILD-TYPE 79 63 43

Figure S24.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0271 (Fisher's exact test), Q value = 0.079

Table S25.  Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
3Q GAIN MUTATED 55 75 136 33
3Q GAIN WILD-TYPE 34 43 63 36

Figure S25.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0018

Table S26.  Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
4P GAIN MUTATED 9 3 20
4P GAIN WILD-TYPE 173 163 133

Figure S26.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 0.0298 (Fisher's exact test), Q value = 0.084

Table S27.  Gene #7: '4p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
4P GAIN MUTATED 5 4 16 6
4P GAIN WILD-TYPE 108 148 138 73

Figure S27.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00641 (Fisher's exact test), Q value = 0.025

Table S28.  Gene #7: '4p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
4P GAIN MUTATED 15 4 12
4P GAIN WILD-TYPE 163 185 119

Figure S28.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_CNMF'

P value = 0.00533 (Fisher's exact test), Q value = 0.022

Table S29.  Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
4P GAIN MUTATED 10 2 12 1 4
4P GAIN WILD-TYPE 111 132 109 61 33

Figure S29.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.043

Table S30.  Gene #7: '4p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
4P GAIN MUTATED 8 8 1
4P GAIN WILD-TYPE 81 121 115

Figure S30.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0153 (Fisher's exact test), Q value = 0.051

Table S31.  Gene #7: '4p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
4P GAIN MUTATED 5 3 9
4P GAIN WILD-TYPE 34 148 135

Figure S31.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q gain' versus 'CN_CNMF'

P value = 0.00918 (Fisher's exact test), Q value = 0.034

Table S32.  Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
4Q GAIN MUTATED 4 5 14
4Q GAIN WILD-TYPE 178 161 139

Figure S32.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 0.0297 (Fisher's exact test), Q value = 0.084

Table S33.  Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
5P GAIN MUTATED 102 100 107
5P GAIN WILD-TYPE 80 66 46

Figure S33.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0404 (Fisher's exact test), Q value = 0.11

Table S34.  Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
5P GAIN MUTATED 57 89 62
5P GAIN WILD-TYPE 32 40 54

Figure S34.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0184 (Fisher's exact test), Q value = 0.059

Table S35.  Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
5Q GAIN MUTATED 44 25 24
5Q GAIN WILD-TYPE 134 164 107

Figure S35.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0363 (Fisher's exact test), Q value = 0.098

Table S36.  Gene #10: '5q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
5Q GAIN MUTATED 14 30 24
5Q GAIN WILD-TYPE 25 121 120

Figure S36.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 0.00068 (Fisher's exact test), Q value = 0.0044

Table S37.  Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
6P GAIN MUTATED 27 33 49
6P GAIN WILD-TYPE 155 133 104

Figure S37.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 0.0018 (Fisher's exact test), Q value = 0.0092

Table S38.  Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
6P GAIN MUTATED 15 27 49 17
6P GAIN WILD-TYPE 98 125 105 62

Figure S38.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00647 (Fisher's exact test), Q value = 0.025

Table S39.  Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
6P GAIN MUTATED 36 31 41
6P GAIN WILD-TYPE 142 158 90

Figure S39.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 0.00151 (Fisher's exact test), Q value = 0.0081

Table S40.  Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
6Q GAIN MUTATED 22 30 42
6Q GAIN WILD-TYPE 160 136 111

Figure S40.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'MRNASEQ_CNMF'

P value = 0.0165 (Fisher's exact test), Q value = 0.054

Table S41.  Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
6Q GAIN MUTATED 17 21 42 14
6Q GAIN WILD-TYPE 96 131 112 65

Figure S41.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0162 (Fisher's exact test), Q value = 0.053

Table S42.  Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
6Q GAIN MUTATED 35 25 34
6Q GAIN WILD-TYPE 143 164 97

Figure S42.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0395 (Fisher's exact test), Q value = 0.1

Table S43.  Gene #12: '6q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
6Q GAIN MUTATED 9 37 19
6Q GAIN WILD-TYPE 30 114 125

Figure S43.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0124 (Fisher's exact test), Q value = 0.043

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
7P GAIN MUTATED 25 38 20
7P GAIN WILD-TYPE 22 18 31

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

'7p gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00036

Table S45.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
7P GAIN MUTATED 73 105 65
7P GAIN WILD-TYPE 109 61 88

Figure S45.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.0013

Table S46.  Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
7P GAIN MUTATED 55 75 43
7P GAIN WILD-TYPE 97 47 50

Figure S46.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 8e-04

Table S47.  Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
7P GAIN MUTATED 50 96 68 27
7P GAIN WILD-TYPE 63 56 86 52

Figure S47.  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 = 0.00015

Table S48.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
7P GAIN MUTATED 68 121 52
7P GAIN WILD-TYPE 110 68 79

Figure S48.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 7e-04 (Fisher's exact test), Q value = 0.0045

Table S49.  Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
7P GAIN MUTATED 66 81 42 31 15
7P GAIN WILD-TYPE 55 53 79 31 22

Figure S49.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.0022

Table S50.  Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
7P GAIN MUTATED 61 60 85 29
7P GAIN WILD-TYPE 28 58 114 40

Figure S50.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.045

Table S51.  Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
7P GAIN MUTATED 36 53 67
7P GAIN WILD-TYPE 53 76 49

Figure S51.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MRNA_CNMF'

P value = 0.00335 (Fisher's exact test), Q value = 0.015

Table S52.  Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
7Q GAIN MUTATED 21 35 9 11
7Q GAIN WILD-TYPE 21 17 23 17

Figure S52.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'7q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.0026

Table S53.  Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
7Q GAIN MUTATED 23 38 15
7Q GAIN WILD-TYPE 24 18 36

Figure S53.  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 = 0.00015

Table S54.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
7Q GAIN MUTATED 52 109 60
7Q GAIN WILD-TYPE 130 57 93

Figure S54.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S55.  Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
7Q GAIN MUTATED 43 75 37
7Q GAIN WILD-TYPE 109 47 56

Figure S55.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S56.  Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
7Q GAIN MUTATED 43 100 48 28
7Q GAIN WILD-TYPE 70 52 106 51

Figure S56.  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 = 0.00015

Table S57.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
7Q GAIN MUTATED 56 123 40
7Q GAIN WILD-TYPE 122 66 91

Figure S57.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0034

Table S58.  Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
7Q GAIN MUTATED 59 73 37 33 12
7Q GAIN WILD-TYPE 62 61 84 29 25

Figure S58.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.0015

Table S59.  Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
7Q GAIN MUTATED 59 48 81 26
7Q GAIN WILD-TYPE 30 70 118 43

Figure S59.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00117 (Fisher's exact test), Q value = 0.0067

Table S60.  Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
7Q GAIN MUTATED 26 51 63
7Q GAIN WILD-TYPE 63 78 53

Figure S60.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00069 (Fisher's exact test), Q value = 0.0044

Table S61.  Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
7Q GAIN MUTATED 9 79 52
7Q GAIN WILD-TYPE 30 72 92

Figure S61.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.0366 (Fisher's exact test), Q value = 0.099

Table S62.  Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
8P GAIN MUTATED 27 28 49 24
8P GAIN WILD-TYPE 86 124 105 55

Figure S62.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0251 (Fisher's exact test), Q value = 0.075

Table S63.  Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
8P GAIN MUTATED 55 36 37
8P GAIN WILD-TYPE 123 153 94

Figure S63.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0152 (Fisher's exact test), Q value = 0.051

Table S64.  Gene #15: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
8P GAIN MUTATED 16 22 63 21
8P GAIN WILD-TYPE 73 96 136 48

Figure S64.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MRNA_CNMF'

P value = 0.0484 (Fisher's exact test), Q value = 0.12

Table S65.  Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
8Q GAIN MUTATED 26 18 16 16
8Q GAIN WILD-TYPE 16 34 16 12

Figure S65.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'8q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0367 (Fisher's exact test), Q value = 0.099

Table S66.  Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
8Q GAIN MUTATED 27 20 29
8Q GAIN WILD-TYPE 20 36 22

Figure S66.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 0.0221 (Fisher's exact test), Q value = 0.069

Table S67.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
8Q GAIN MUTATED 93 73 91
8Q GAIN WILD-TYPE 89 93 62

Figure S67.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.00631 (Fisher's exact test), Q value = 0.025

Table S68.  Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
8Q GAIN MUTATED 86 49 55
8Q GAIN WILD-TYPE 66 73 38

Figure S68.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 0.00633 (Fisher's exact test), Q value = 0.025

Table S69.  Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
8Q GAIN MUTATED 61 61 92 41
8Q GAIN WILD-TYPE 52 91 62 38

Figure S69.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.0024

Table S70.  Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
8Q GAIN MUTATED 106 75 74
8Q GAIN WILD-TYPE 72 114 57

Figure S70.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00471 (Fisher's exact test), Q value = 0.02

Table S71.  Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
8Q GAIN MUTATED 33 53 115 39
8Q GAIN WILD-TYPE 56 65 84 30

Figure S71.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0213 (Fisher's exact test), Q value = 0.067

Table S72.  Gene #17: '9p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
9P GAIN MUTATED 1 9 9
9P GAIN WILD-TYPE 46 47 42

Figure S72.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00062

Table S73.  Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
9P GAIN MUTATED 21 34 7
9P GAIN WILD-TYPE 161 132 146

Figure S73.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00054

Table S74.  Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
9P GAIN MUTATED 11 30 7
9P GAIN WILD-TYPE 141 92 86

Figure S74.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0479 (Fisher's exact test), Q value = 0.12

Table S75.  Gene #17: '9p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 41 52 47
9P GAIN MUTATED 10 1 3 4
9P GAIN WILD-TYPE 44 40 49 43

Figure S75.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S76.  Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
9P GAIN MUTATED 3 36 15 8
9P GAIN WILD-TYPE 110 116 139 71

Figure S76.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S77.  Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
9P GAIN MUTATED 6 39 17
9P GAIN WILD-TYPE 172 150 114

Figure S77.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.047

Table S78.  Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
9P GAIN MUTATED 17 22 8 12 1
9P GAIN WILD-TYPE 104 112 113 50 36

Figure S78.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0496 (Fisher's exact test), Q value = 0.13

Table S79.  Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
9P GAIN MUTATED 16 19 16 9
9P GAIN WILD-TYPE 73 99 183 60

Figure S79.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00098 (Fisher's exact test), Q value = 0.0058

Table S80.  Gene #17: '9p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
9P GAIN MUTATED 2 18 20
9P GAIN WILD-TYPE 87 111 96

Figure S80.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q gain' versus 'MRNA_CNMF'

P value = 0.0047 (Fisher's exact test), Q value = 0.02

Table S81.  Gene #18: '9q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
9Q GAIN MUTATED 2 17 5 7
9Q GAIN WILD-TYPE 40 35 27 21

Figure S81.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q gain' versus 'MRNA_CHIERARCHICAL'

P value = 5e-04 (Fisher's exact test), Q value = 0.0036

Table S82.  Gene #18: '9q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
9Q GAIN MUTATED 2 19 10
9Q GAIN WILD-TYPE 45 37 41

Figure S82.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S83.  Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
9Q GAIN MUTATED 23 61 8
9Q GAIN WILD-TYPE 159 105 145

Figure S83.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

'9q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S84.  Gene #18: '9q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
9Q GAIN MUTATED 12 46 9
9Q GAIN WILD-TYPE 140 76 84

Figure S84.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0277 (Fisher's exact test), Q value = 0.08

Table S85.  Gene #18: '9q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 41 52 47
9Q GAIN MUTATED 14 5 3 9
9Q GAIN WILD-TYPE 40 36 49 38

Figure S85.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S86.  Gene #18: '9q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
9Q GAIN MUTATED 5 60 21 6
9Q GAIN WILD-TYPE 108 92 133 73

Figure S86.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S87.  Gene #18: '9q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
9Q GAIN MUTATED 6 65 21
9Q GAIN WILD-TYPE 172 124 110

Figure S87.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0018

Table S88.  Gene #18: '9q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
9Q GAIN MUTATED 24 31 9 20 4
9Q GAIN WILD-TYPE 97 103 112 42 33

Figure S88.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00062

Table S89.  Gene #18: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
9Q GAIN MUTATED 30 26 24 8
9Q GAIN WILD-TYPE 59 92 175 61

Figure S89.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00096 (Fisher's exact test), Q value = 0.0058

Table S90.  Gene #18: '9q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
9Q GAIN MUTATED 5 26 27
9Q GAIN WILD-TYPE 84 103 89

Figure S90.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00162 (Fisher's exact test), Q value = 0.0084

Table S91.  Gene #18: '9q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
9Q GAIN MUTATED 2 38 18
9Q GAIN WILD-TYPE 37 113 126

Figure S91.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_CNMF'

P value = 0.0453 (Fisher's exact test), Q value = 0.12

Table S92.  Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
10P GAIN MUTATED 17 28 21 3 5
10P GAIN WILD-TYPE 104 106 100 59 32

Figure S92.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00054 (Fisher's exact test), Q value = 0.0038

Table S93.  Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
10P GAIN MUTATED 3 18 42 11
10P GAIN WILD-TYPE 86 100 157 58

Figure S93.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q gain' versus 'RPPA_CNMF'

P value = 0.0274 (Fisher's exact test), Q value = 0.08

Table S94.  Gene #20: '10q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 73 61
10Q GAIN MUTATED 5 14 3
10Q GAIN WILD-TYPE 55 59 58

Figure S94.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'10q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0111 (Fisher's exact test), Q value = 0.04

Table S95.  Gene #20: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
10Q GAIN MUTATED 16 9 19
10Q GAIN WILD-TYPE 162 180 112

Figure S95.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0101 (Fisher's exact test), Q value = 0.036

Table S96.  Gene #21: '11p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 41 52 47
11P GAIN MUTATED 9 2 8 15
11P GAIN WILD-TYPE 45 39 44 32

Figure S96.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0385 (Fisher's exact test), Q value = 0.1

Table S97.  Gene #21: '11p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
11P GAIN MUTATED 4 30 14
11P GAIN WILD-TYPE 35 121 130

Figure S97.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q gain' versus 'MRNA_CNMF'

P value = 0.018 (Fisher's exact test), Q value = 0.058

Table S98.  Gene #22: '11q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
11Q GAIN MUTATED 12 7 2 9
11Q GAIN WILD-TYPE 30 45 30 19

Figure S98.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.0054

Table S99.  Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
11Q GAIN MUTATED 20 30 41
11Q GAIN WILD-TYPE 162 136 112

Figure S99.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'MRNA_CNMF'

P value = 0.0182 (Fisher's exact test), Q value = 0.059

Table S100.  Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
12P GAIN MUTATED 11 30 13 14
12P GAIN WILD-TYPE 31 22 19 14

Figure S100.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'12p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0328 (Fisher's exact test), Q value = 0.091

Table S101.  Gene #23: '12p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
12P GAIN MUTATED 15 32 21
12P GAIN WILD-TYPE 32 24 30

Figure S101.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S102.  Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
12P GAIN MUTATED 49 100 80
12P GAIN WILD-TYPE 133 66 73

Figure S102.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 0.00561 (Fisher's exact test), Q value = 0.023

Table S103.  Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
12P GAIN MUTATED 57 67 50
12P GAIN WILD-TYPE 95 55 43

Figure S103.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00036

Table S104.  Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
12P GAIN MUTATED 36 86 79 26
12P GAIN WILD-TYPE 77 66 75 53

Figure S104.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00216 (Fisher's exact test), Q value = 0.011

Table S105.  Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
12P GAIN MUTATED 63 100 64
12P GAIN WILD-TYPE 115 89 67

Figure S105.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 0.0295 (Fisher's exact test), Q value = 0.084

Table S106.  Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
12P GAIN MUTATED 53 77 46 27 16
12P GAIN WILD-TYPE 68 57 75 35 21

Figure S106.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00983 (Fisher's exact test), Q value = 0.036

Table S107.  Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
12P GAIN MUTATED 51 54 93 21
12P GAIN WILD-TYPE 38 64 106 48

Figure S107.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0235 (Fisher's exact test), Q value = 0.072

Table S108.  Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
12P GAIN MUTATED 30 65 59
12P GAIN WILD-TYPE 59 64 57

Figure S108.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0015 (Fisher's exact test), Q value = 0.0081

Table S109.  Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
12P GAIN MUTATED 14 86 54
12P GAIN WILD-TYPE 25 65 90

Figure S109.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'MRNA_CNMF'

P value = 0.0239 (Fisher's exact test), Q value = 0.073

Table S110.  Gene #24: '12q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
12Q GAIN MUTATED 8 20 10 15
12Q GAIN WILD-TYPE 34 32 22 13

Figure S110.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S111.  Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
12Q GAIN MUTATED 33 75 45
12Q GAIN WILD-TYPE 149 91 108

Figure S111.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 0.00633 (Fisher's exact test), Q value = 0.025

Table S112.  Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
12Q GAIN MUTATED 32 47 29
12Q GAIN WILD-TYPE 120 75 64

Figure S112.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 0.00334 (Fisher's exact test), Q value = 0.015

Table S113.  Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
12Q GAIN MUTATED 22 61 47 21
12Q GAIN WILD-TYPE 91 91 107 58

Figure S113.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00097 (Fisher's exact test), Q value = 0.0058

Table S114.  Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
12Q GAIN MUTATED 36 66 49
12Q GAIN WILD-TYPE 142 123 82

Figure S114.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00952 (Fisher's exact test), Q value = 0.035

Table S115.  Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
12Q GAIN MUTATED 16 34 43
12Q GAIN WILD-TYPE 73 95 73

Figure S115.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 8e-04

Table S116.  Gene #24: '12q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
12Q GAIN MUTATED 3 58 32
12Q GAIN WILD-TYPE 36 93 112

Figure S116.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0223 (Fisher's exact test), Q value = 0.069

Table S117.  Gene #26: '14q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
14Q GAIN MUTATED 19 11 9
14Q GAIN WILD-TYPE 28 45 42

Figure S117.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 0.0403 (Fisher's exact test), Q value = 0.11

Table S118.  Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
14Q GAIN MUTATED 37 42 50
14Q GAIN WILD-TYPE 145 124 103

Figure S118.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00482 (Fisher's exact test), Q value = 0.02

Table S119.  Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
14Q GAIN MUTATED 60 46 23
14Q GAIN WILD-TYPE 118 143 108

Figure S119.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q gain' versus 'CN_CNMF'

P value = 0.00086 (Fisher's exact test), Q value = 0.0054

Table S120.  Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
15Q GAIN MUTATED 24 49 32
15Q GAIN WILD-TYPE 158 117 121

Figure S120.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

'15q gain' versus 'METHLYATION_CNMF'

P value = 0.00126 (Fisher's exact test), Q value = 0.0071

Table S121.  Gene #27: '15q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
15Q GAIN MUTATED 20 38 17
15Q GAIN WILD-TYPE 132 84 76

Figure S121.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q gain' versus 'MRNASEQ_CNMF'

P value = 0.0015 (Fisher's exact test), Q value = 0.0081

Table S122.  Gene #27: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
15Q GAIN MUTATED 14 47 26 16
15Q GAIN WILD-TYPE 99 105 128 63

Figure S122.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.011 (Fisher's exact test), Q value = 0.04

Table S123.  Gene #27: '15q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
15Q GAIN MUTATED 32 52 19
15Q GAIN WILD-TYPE 146 137 112

Figure S123.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0356 (Fisher's exact test), Q value = 0.096

Table S124.  Gene #27: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
15Q GAIN MUTATED 28 22 41 9
15Q GAIN WILD-TYPE 61 96 158 60

Figure S124.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00214 (Fisher's exact test), Q value = 0.011

Table S125.  Gene #27: '15q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
15Q GAIN MUTATED 6 43 18
15Q GAIN WILD-TYPE 33 108 126

Figure S125.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0207 (Fisher's exact test), Q value = 0.065

Table S126.  Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
16P GAIN MUTATED 13 23 41 4
16P GAIN WILD-TYPE 76 95 158 65

Figure S126.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 0.0246 (Fisher's exact test), Q value = 0.074

Table S127.  Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
16Q GAIN MUTATED 21 32 34
16Q GAIN WILD-TYPE 161 134 119

Figure S127.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0271 (Fisher's exact test), Q value = 0.079

Table S128.  Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
16Q GAIN MUTATED 15 25 38 4
16Q GAIN WILD-TYPE 74 93 161 65

Figure S128.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'MRNA_CNMF'

P value = 0.00406 (Fisher's exact test), Q value = 0.018

Table S129.  Gene #30: '17p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
17P GAIN MUTATED 1 11 1 6
17P GAIN WILD-TYPE 41 41 31 22

Figure S129.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S130.  Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
17P GAIN MUTATED 11 41 16
17P GAIN WILD-TYPE 171 125 137

Figure S130.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 0.0018 (Fisher's exact test), Q value = 0.0092

Table S131.  Gene #30: '17p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
17P GAIN MUTATED 14 30 11
17P GAIN WILD-TYPE 138 92 82

Figure S131.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0044

Table S132.  Gene #30: '17p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
17P GAIN MUTATED 9 36 16 7
17P GAIN WILD-TYPE 104 116 138 72

Figure S132.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00095 (Fisher's exact test), Q value = 0.0058

Table S133.  Gene #30: '17p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
17P GAIN MUTATED 12 38 18
17P GAIN WILD-TYPE 166 151 113

Figure S133.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.054

Table S134.  Gene #30: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
17P GAIN MUTATED 12 25 8 12 6
17P GAIN WILD-TYPE 109 109 113 50 31

Figure S134.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00734 (Fisher's exact test), Q value = 0.028

Table S135.  Gene #30: '17p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
17P GAIN MUTATED 2 31 14
17P GAIN WILD-TYPE 37 120 130

Figure S135.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q gain' versus 'MRNA_CNMF'

P value = 0.00156 (Fisher's exact test), Q value = 0.0083

Table S136.  Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
17Q GAIN MUTATED 7 27 7 9
17Q GAIN WILD-TYPE 35 25 25 19

Figure S136.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00054 (Fisher's exact test), Q value = 0.0038

Table S137.  Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
17Q GAIN MUTATED 12 29 9
17Q GAIN WILD-TYPE 35 27 42

Figure S137.  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 = 0.00015

Table S138.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
17Q GAIN MUTATED 32 91 35
17Q GAIN WILD-TYPE 150 75 118

Figure S138.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S139.  Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
17Q GAIN MUTATED 31 61 25
17Q GAIN WILD-TYPE 121 61 68

Figure S139.  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 = 0.00015

Table S140.  Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
17Q GAIN MUTATED 19 76 44 18
17Q GAIN WILD-TYPE 94 76 110 61

Figure S140.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S141.  Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
17Q GAIN MUTATED 32 88 37
17Q GAIN WILD-TYPE 146 101 94

Figure S141.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.0036

Table S142.  Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
17Q GAIN MUTATED 38 55 20 21 13
17Q GAIN WILD-TYPE 83 79 101 41 24

Figure S142.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.04

Table S143.  Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
17Q GAIN MUTATED 40 34 58 15
17Q GAIN WILD-TYPE 49 84 141 54

Figure S143.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.0038

Table S144.  Gene #31: '17q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
17Q GAIN MUTATED 14 44 46
17Q GAIN WILD-TYPE 75 85 70

Figure S144.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00036

Table S145.  Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
17Q GAIN MUTATED 8 66 30
17Q GAIN WILD-TYPE 31 85 114

Figure S145.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'MRNA_CNMF'

P value = 0.00796 (Fisher's exact test), Q value = 0.03

Table S146.  Gene #32: '18p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
18P GAIN MUTATED 6 24 9 7
18P GAIN WILD-TYPE 36 28 23 21

Figure S146.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00114 (Fisher's exact test), Q value = 0.0066

Table S147.  Gene #32: '18p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
18P GAIN MUTATED 9 27 10
18P GAIN WILD-TYPE 38 29 41

Figure S147.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S148.  Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
18P GAIN MUTATED 33 76 41
18P GAIN WILD-TYPE 149 90 112

Figure S148.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S149.  Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
18P GAIN MUTATED 26 55 31
18P GAIN WILD-TYPE 126 67 62

Figure S149.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 0.00099 (Fisher's exact test), Q value = 0.0058

Table S150.  Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
18P GAIN MUTATED 27 64 42 16
18P GAIN WILD-TYPE 86 88 112 63

Figure S150.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S151.  Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
18P GAIN MUTATED 35 81 33
18P GAIN WILD-TYPE 143 108 98

Figure S151.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_CNMF'

P value = 0.0165 (Fisher's exact test), Q value = 0.054

Table S152.  Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
18P GAIN MUTATED 31 51 25 21 14
18P GAIN WILD-TYPE 90 83 96 41 23

Figure S152.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.0038

Table S153.  Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
18P GAIN MUTATED 7 61 31
18P GAIN WILD-TYPE 32 90 113

Figure S153.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'MRNA_CNMF'

P value = 0.0164 (Fisher's exact test), Q value = 0.054

Table S154.  Gene #33: '18q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
18Q GAIN MUTATED 5 20 5 7
18Q GAIN WILD-TYPE 37 32 27 21

Figure S154.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0143 (Fisher's exact test), Q value = 0.049

Table S155.  Gene #33: '18q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
18Q GAIN MUTATED 7 21 9
18Q GAIN WILD-TYPE 40 35 42

Figure S155.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S156.  Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
18Q GAIN MUTATED 23 57 24
18Q GAIN WILD-TYPE 159 109 129

Figure S156.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 0.00139 (Fisher's exact test), Q value = 0.0077

Table S157.  Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
18Q GAIN MUTATED 19 37 18
18Q GAIN WILD-TYPE 133 85 75

Figure S157.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.0048

Table S158.  Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
18Q GAIN MUTATED 16 46 32 8
18Q GAIN WILD-TYPE 97 106 122 71

Figure S158.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.002

Table S159.  Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
18Q GAIN MUTATED 22 56 24
18Q GAIN WILD-TYPE 156 133 107

Figure S159.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0329 (Fisher's exact test), Q value = 0.091

Table S160.  Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
18Q GAIN MUTATED 26 20 45 8
18Q GAIN WILD-TYPE 63 98 154 61

Figure S160.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00217 (Fisher's exact test), Q value = 0.011

Table S161.  Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
18Q GAIN MUTATED 4 41 18
18Q GAIN WILD-TYPE 35 110 126

Figure S161.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p gain' versus 'MRNA_CNMF'

P value = 0.0464 (Fisher's exact test), Q value = 0.12

Table S162.  Gene #34: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
19P GAIN MUTATED 7 16 2 5
19P GAIN WILD-TYPE 35 36 30 23

Figure S162.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S163.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
19P GAIN MUTATED 30 65 16
19P GAIN WILD-TYPE 152 101 137

Figure S163.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0016

Table S164.  Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
19P GAIN MUTATED 24 45 18
19P GAIN WILD-TYPE 128 77 75

Figure S164.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p gain' versus 'RPPA_CNMF'

P value = 0.0229 (Fisher's exact test), Q value = 0.071

Table S165.  Gene #34: '19p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 73 61
19P GAIN MUTATED 19 10 18
19P GAIN WILD-TYPE 41 63 43

Figure S165.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0014

Table S166.  Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
19P GAIN MUTATED 18 52 31 9
19P GAIN WILD-TYPE 95 100 123 70

Figure S166.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00221 (Fisher's exact test), Q value = 0.011

Table S167.  Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
19P GAIN MUTATED 27 57 26
19P GAIN WILD-TYPE 151 132 105

Figure S167.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00159 (Fisher's exact test), Q value = 0.0084

Table S168.  Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
19P GAIN MUTATED 34 28 34 13
19P GAIN WILD-TYPE 55 90 165 56

Figure S168.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00539 (Fisher's exact test), Q value = 0.022

Table S169.  Gene #34: '19p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
19P GAIN MUTATED 4 46 26
19P GAIN WILD-TYPE 35 105 118

Figure S169.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00054

Table S170.  Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
19Q GAIN MUTATED 42 74 43
19Q GAIN WILD-TYPE 140 92 110

Figure S170.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 0.0272 (Fisher's exact test), Q value = 0.079

Table S171.  Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
19Q GAIN MUTATED 48 51 23
19Q GAIN WILD-TYPE 104 71 70

Figure S171.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 0.0221 (Fisher's exact test), Q value = 0.069

Table S172.  Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
19Q GAIN MUTATED 27 58 53 18
19Q GAIN WILD-TYPE 86 94 101 61

Figure S172.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNA_CNMF'

P value = 0.0196 (Fisher's exact test), Q value = 0.062

Table S173.  Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
20P GAIN MUTATED 23 32 9 12
20P GAIN WILD-TYPE 19 20 23 16

Figure S173.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0221 (Fisher's exact test), Q value = 0.069

Table S174.  Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
20P GAIN MUTATED 27 32 17
20P GAIN WILD-TYPE 20 24 34

Figure S174.  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 = 0.00015

Table S175.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
20P GAIN MUTATED 68 107 86
20P GAIN WILD-TYPE 114 59 67

Figure S175.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.00068 (Fisher's exact test), Q value = 0.0044

Table S176.  Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
20P GAIN MUTATED 71 82 42
20P GAIN WILD-TYPE 81 40 51

Figure S176.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.0038

Table S177.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
20Q GAIN MUTATED 72 86 93
20Q GAIN WILD-TYPE 110 80 60

Figure S177.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0291 (Fisher's exact test), Q value = 0.083

Table S178.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
20Q GAIN MUTATED 35 53 113 36
20Q GAIN WILD-TYPE 54 65 86 33

Figure S178.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'MRNA_CNMF'

P value = 0.00827 (Fisher's exact test), Q value = 0.031

Table S179.  Gene #39: '22q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
22Q GAIN MUTATED 21 31 10 7
22Q GAIN WILD-TYPE 21 21 22 21

Figure S179.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0287 (Fisher's exact test), Q value = 0.082

Table S180.  Gene #39: '22q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
22Q GAIN MUTATED 21 32 16
22Q GAIN WILD-TYPE 26 24 35

Figure S180.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 0.00453 (Fisher's exact test), Q value = 0.02

Table S181.  Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
22Q GAIN MUTATED 63 85 73
22Q GAIN WILD-TYPE 119 81 80

Figure S181.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 0.034 (Fisher's exact test), Q value = 0.093

Table S182.  Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
22Q GAIN MUTATED 56 64 42
22Q GAIN WILD-TYPE 96 58 51

Figure S182.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.0039

Table S183.  Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
22Q GAIN MUTATED 50 86 52 31
22Q GAIN WILD-TYPE 63 66 102 48

Figure S183.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.0012

Table S184.  Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
22Q GAIN MUTATED 84 98 37
22Q GAIN WILD-TYPE 94 91 94

Figure S184.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xp gain' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00054

Table S185.  Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
XP GAIN MUTATED 9 28 28
XP GAIN WILD-TYPE 173 138 125

Figure S185.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

'xp gain' versus 'MRNASEQ_CNMF'

P value = 0.00467 (Fisher's exact test), Q value = 0.02

Table S186.  Gene #40: 'xp gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
XP GAIN MUTATED 10 25 27 3
XP GAIN WILD-TYPE 103 127 127 76

Figure S186.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xp gain' versus 'MIRSEQ_CNMF'

P value = 0.00809 (Fisher's exact test), Q value = 0.03

Table S187.  Gene #40: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
XP GAIN MUTATED 11 29 9 6 5
XP GAIN WILD-TYPE 110 105 112 56 32

Figure S187.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0335 (Fisher's exact test), Q value = 0.092

Table S188.  Gene #41: 'xq gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
XQ GAIN MUTATED 10 15 4
XQ GAIN WILD-TYPE 37 41 47

Figure S188.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S189.  Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
XQ GAIN MUTATED 14 45 24
XQ GAIN WILD-TYPE 168 121 129

Figure S189.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 0.00348 (Fisher's exact test), Q value = 0.016

Table S190.  Gene #41: 'xq gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
XQ GAIN MUTATED 15 30 12
XQ GAIN WILD-TYPE 137 92 81

Figure S190.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 0.00693 (Fisher's exact test), Q value = 0.027

Table S191.  Gene #41: 'xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
XQ GAIN MUTATED 14 38 24 7
XQ GAIN WILD-TYPE 99 114 130 72

Figure S191.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00865 (Fisher's exact test), Q value = 0.032

Table S192.  Gene #41: 'xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
XQ GAIN MUTATED 21 44 18
XQ GAIN WILD-TYPE 157 145 113

Figure S192.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00045

Table S193.  Gene #42: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
1P LOSS MUTATED 8 29 8 3
1P LOSS WILD-TYPE 34 23 24 25

Figure S193.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00036

Table S194.  Gene #42: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
1P LOSS MUTATED 8 31 9
1P LOSS WILD-TYPE 39 25 42

Figure S194.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S195.  Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
1P LOSS MUTATED 31 97 24
1P LOSS WILD-TYPE 151 69 129

Figure S195.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S196.  Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
1P LOSS MUTATED 23 64 22
1P LOSS WILD-TYPE 129 58 71

Figure S196.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S197.  Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
1P LOSS MUTATED 19 83 31 18
1P LOSS WILD-TYPE 94 69 123 61

Figure S197.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S198.  Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
1P LOSS MUTATED 28 98 25
1P LOSS WILD-TYPE 150 91 106

Figure S198.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 0.00137 (Fisher's exact test), Q value = 0.0076

Table S199.  Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
1P LOSS MUTATED 36 48 22 28 9
1P LOSS WILD-TYPE 85 86 99 34 28

Figure S199.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S200.  Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
1P LOSS MUTATED 49 32 52 10
1P LOSS WILD-TYPE 40 86 147 59

Figure S200.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00081 (Fisher's exact test), Q value = 0.0051

Table S201.  Gene #42: '1p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
1P LOSS MUTATED 16 33 48
1P LOSS WILD-TYPE 73 96 68

Figure S201.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.0028

Table S202.  Gene #42: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
1P LOSS MUTATED 6 60 31
1P LOSS WILD-TYPE 33 91 113

Figure S202.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 0.00229 (Fisher's exact test), Q value = 0.011

Table S203.  Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
1Q LOSS MUTATED 11 30 19
1Q LOSS WILD-TYPE 171 136 134

Figure S203.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 0.0347 (Fisher's exact test), Q value = 0.095

Table S204.  Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
1Q LOSS MUTATED 9 27 18 5
1Q LOSS WILD-TYPE 104 125 136 74

Figure S204.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0269 (Fisher's exact test), Q value = 0.079

Table S205.  Gene #43: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
1Q LOSS MUTATED 16 32 11
1Q LOSS WILD-TYPE 162 157 120

Figure S205.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0292 (Fisher's exact test), Q value = 0.083

Table S206.  Gene #44: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
2P LOSS MUTATED 4 6 11
2P LOSS WILD-TYPE 174 183 120

Figure S206.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 0.00659 (Fisher's exact test), Q value = 0.026

Table S207.  Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
2P LOSS MUTATED 9 9 0 1 1
2P LOSS WILD-TYPE 112 125 121 61 36

Figure S207.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0376 (Fisher's exact test), Q value = 0.1

Table S208.  Gene #44: '2p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
2P LOSS MUTATED 1 2 8
2P LOSS WILD-TYPE 88 127 108

Figure S208.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00057 (Fisher's exact test), Q value = 0.0039

Table S209.  Gene #44: '2p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
2P LOSS MUTATED 0 11 0
2P LOSS WILD-TYPE 39 140 144

Figure S209.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0256 (Fisher's exact test), Q value = 0.076

Table S210.  Gene #45: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
2Q LOSS MUTATED 8 17 17
2Q LOSS WILD-TYPE 170 172 114

Figure S210.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00036

Table S211.  Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
2Q LOSS MUTATED 15 18 0 5 3
2Q LOSS WILD-TYPE 106 116 121 57 34

Figure S211.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00142 (Fisher's exact test), Q value = 0.0078

Table S212.  Gene #45: '2q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
2Q LOSS MUTATED 2 21 4
2Q LOSS WILD-TYPE 37 130 140

Figure S212.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p loss' versus 'METHLYATION_CNMF'

P value = 0.00209 (Fisher's exact test), Q value = 0.01

Table S213.  Gene #46: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
3P LOSS MUTATED 79 75 69
3P LOSS WILD-TYPE 73 47 24

Figure S213.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.0018

Table S214.  Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
3P LOSS MUTATED 62 79 123 26
3P LOSS WILD-TYPE 27 39 76 43

Figure S214.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0311 (Fisher's exact test), Q value = 0.087

Table S215.  Gene #46: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
3P LOSS MUTATED 44 81 78
3P LOSS WILD-TYPE 45 48 38

Figure S215.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MRNA_CNMF'

P value = 0.00132 (Fisher's exact test), Q value = 0.0074

Table S216.  Gene #48: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
4P LOSS MUTATED 30 40 12 15
4P LOSS WILD-TYPE 12 12 20 13

Figure S216.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.0011

Table S217.  Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
4P LOSS MUTATED 33 44 20
4P LOSS WILD-TYPE 14 12 31

Figure S217.  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 = 0.00015

Table S218.  Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
4P LOSS MUTATED 85 139 91
4P LOSS WILD-TYPE 97 27 62

Figure S218.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S219.  Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
4P LOSS MUTATED 70 99 61
4P LOSS WILD-TYPE 82 23 32

Figure S219.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S220.  Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
4P LOSS MUTATED 74 119 81 40
4P LOSS WILD-TYPE 39 33 73 39

Figure S220.  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 = 0.00015

Table S221.  Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
4P LOSS MUTATED 98 150 66
4P LOSS WILD-TYPE 80 39 65

Figure S221.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.0043

Table S222.  Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
4P LOSS MUTATED 80 100 59 41 21
4P LOSS WILD-TYPE 41 34 62 21 16

Figure S222.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S223.  Gene #48: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
4P LOSS MUTATED 39 79 92
4P LOSS WILD-TYPE 50 50 24

Figure S223.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S224.  Gene #48: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
4P LOSS MUTATED 17 118 75
4P LOSS WILD-TYPE 22 33 69

Figure S224.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'MRNA_CNMF'

P value = 0.00235 (Fisher's exact test), Q value = 0.011

Table S225.  Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
4Q LOSS MUTATED 26 38 10 17
4Q LOSS WILD-TYPE 16 14 22 11

Figure S225.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00103 (Fisher's exact test), Q value = 0.006

Table S226.  Gene #49: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
4Q LOSS MUTATED 30 41 20
4Q LOSS WILD-TYPE 17 15 31

Figure S226.  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 = 0.00015

Table S227.  Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
4Q LOSS MUTATED 86 132 80
4Q LOSS WILD-TYPE 96 34 73

Figure S227.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S228.  Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
4Q LOSS MUTATED 73 94 53
4Q LOSS WILD-TYPE 79 28 40

Figure S228.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00027

Table S229.  Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
4Q LOSS MUTATED 64 114 85 34
4Q LOSS WILD-TYPE 49 38 69 45

Figure S229.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.0022

Table S230.  Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
4Q LOSS MUTATED 96 134 67
4Q LOSS WILD-TYPE 82 55 64

Figure S230.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 0.00286 (Fisher's exact test), Q value = 0.013

Table S231.  Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
4Q LOSS MUTATED 76 89 54 42 23
4Q LOSS WILD-TYPE 45 45 67 20 14

Figure S231.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0303 (Fisher's exact test), Q value = 0.085

Table S232.  Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
4Q LOSS MUTATED 63 68 120 33
4Q LOSS WILD-TYPE 26 50 79 36

Figure S232.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00064 (Fisher's exact test), Q value = 0.0043

Table S233.  Gene #49: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
4Q LOSS MUTATED 45 69 85
4Q LOSS WILD-TYPE 44 60 31

Figure S233.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00045

Table S234.  Gene #49: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
4Q LOSS MUTATED 22 110 67
4Q LOSS WILD-TYPE 17 41 77

Figure S234.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 0.00435 (Fisher's exact test), Q value = 0.019

Table S235.  Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
5P LOSS MUTATED 16 31 31
5P LOSS WILD-TYPE 166 135 122

Figure S235.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 0.00422 (Fisher's exact test), Q value = 0.019

Table S236.  Gene #50: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
5P LOSS MUTATED 11 20 20
5P LOSS WILD-TYPE 141 102 73

Figure S236.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0336 (Fisher's exact test), Q value = 0.092

Table S237.  Gene #50: '5p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 41 52 47
5P LOSS MUTATED 4 9 7 13
5P LOSS WILD-TYPE 50 32 45 34

Figure S237.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CNMF'

P value = 0.0384 (Fisher's exact test), Q value = 0.1

Table S238.  Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
5P LOSS MUTATED 20 26 9 13 5
5P LOSS WILD-TYPE 101 108 112 49 32

Figure S238.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0155 (Fisher's exact test), Q value = 0.052

Table S239.  Gene #50: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
5P LOSS MUTATED 8 15 26
5P LOSS WILD-TYPE 81 114 90

Figure S239.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0016

Table S240.  Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
5Q LOSS MUTATED 84 109 98
5Q LOSS WILD-TYPE 98 57 55

Figure S240.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 0.00239 (Fisher's exact test), Q value = 0.011

Table S241.  Gene #51: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
5Q LOSS MUTATED 71 82 55
5Q LOSS WILD-TYPE 81 40 38

Figure S241.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 0.006 (Fisher's exact test), Q value = 0.024

Table S242.  Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
5Q LOSS MUTATED 62 105 83 38
5Q LOSS WILD-TYPE 51 47 71 41

Figure S242.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.0026

Table S243.  Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
5Q LOSS MUTATED 90 131 67
5Q LOSS WILD-TYPE 88 58 64

Figure S243.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0198 (Fisher's exact test), Q value = 0.063

Table S244.  Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
5Q LOSS MUTATED 55 70 122 28
5Q LOSS WILD-TYPE 34 48 77 41

Figure S244.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.048

Table S245.  Gene #51: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
5Q LOSS MUTATED 39 82 68
5Q LOSS WILD-TYPE 50 47 48

Figure S245.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6p loss' versus 'MRNA_CNMF'

P value = 0.0349 (Fisher's exact test), Q value = 0.095

Table S246.  Gene #52: '6p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
6P LOSS MUTATED 6 18 5 3
6P LOSS WILD-TYPE 36 34 27 25

Figure S246.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'6p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0144 (Fisher's exact test), Q value = 0.049

Table S247.  Gene #52: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
6P LOSS MUTATED 6 19 7
6P LOSS WILD-TYPE 41 37 44

Figure S247.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 0.00392 (Fisher's exact test), Q value = 0.017

Table S248.  Gene #52: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
6P LOSS MUTATED 33 52 27
6P LOSS WILD-TYPE 149 114 126

Figure S248.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.0011

Table S249.  Gene #52: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
6P LOSS MUTATED 24 45 16
6P LOSS WILD-TYPE 128 77 77

Figure S249.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00036

Table S250.  Gene #52: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
6P LOSS MUTATED 20 56 21 14
6P LOSS WILD-TYPE 93 96 133 65

Figure S250.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00036

Table S251.  Gene #52: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
6P LOSS MUTATED 29 65 17
6P LOSS WILD-TYPE 149 124 114

Figure S251.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MRNA_CNMF'

P value = 0.00469 (Fisher's exact test), Q value = 0.02

Table S252.  Gene #53: '6q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
6Q LOSS MUTATED 6 21 4 4
6Q LOSS WILD-TYPE 36 31 28 24

Figure S252.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'6q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00103 (Fisher's exact test), Q value = 0.006

Table S253.  Gene #53: '6q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
6Q LOSS MUTATED 8 22 5
6Q LOSS WILD-TYPE 39 34 46

Figure S253.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 0.0254 (Fisher's exact test), Q value = 0.075

Table S254.  Gene #53: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
6Q LOSS MUTATED 32 49 32
6Q LOSS WILD-TYPE 150 117 121

Figure S254.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.00277 (Fisher's exact test), Q value = 0.013

Table S255.  Gene #53: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
6Q LOSS MUTATED 27 42 17
6Q LOSS WILD-TYPE 125 80 76

Figure S255.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 0.00179 (Fisher's exact test), Q value = 0.0092

Table S256.  Gene #53: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
6Q LOSS MUTATED 20 51 25 16
6Q LOSS WILD-TYPE 93 101 129 63

Figure S256.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0238 (Fisher's exact test), Q value = 0.072

Table S257.  Gene #53: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
6Q LOSS MUTATED 34 55 23
6Q LOSS WILD-TYPE 144 134 108

Figure S257.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p loss' versus 'CN_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0018

Table S258.  Gene #54: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
7P LOSS MUTATED 10 17 31
7P LOSS WILD-TYPE 172 149 122

Figure S258.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

'7p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00561 (Fisher's exact test), Q value = 0.023

Table S259.  Gene #54: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
7P LOSS MUTATED 4 10 34 5
7P LOSS WILD-TYPE 85 108 165 64

Figure S259.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q loss' versus 'CN_CNMF'

P value = 0.00285 (Fisher's exact test), Q value = 0.013

Table S260.  Gene #55: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
7Q LOSS MUTATED 18 8 25
7Q LOSS WILD-TYPE 164 158 128

Figure S260.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

'7q loss' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00072

Table S261.  Gene #55: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
7Q LOSS MUTATED 10 5 30 6
7Q LOSS WILD-TYPE 103 147 124 73

Figure S261.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00027

Table S262.  Gene #55: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
7Q LOSS MUTATED 17 7 27
7Q LOSS WILD-TYPE 161 182 104

Figure S262.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0336 (Fisher's exact test), Q value = 0.092

Table S263.  Gene #55: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
7Q LOSS MUTATED 3 14 26 4
7Q LOSS WILD-TYPE 86 104 173 65

Figure S263.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 0.00533 (Fisher's exact test), Q value = 0.022

Table S264.  Gene #56: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
8P LOSS MUTATED 72 85 87
8P LOSS WILD-TYPE 110 81 66

Figure S264.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 0.00093 (Fisher's exact test), Q value = 0.0057

Table S265.  Gene #56: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
8P LOSS MUTATED 60 76 47
8P LOSS WILD-TYPE 92 46 46

Figure S265.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.015 (Fisher's exact test), Q value = 0.05

Table S266.  Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
8P LOSS MUTATED 48 69 91 25
8P LOSS WILD-TYPE 41 49 108 44

Figure S266.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q loss' versus 'METHLYATION_CNMF'

P value = 0.0349 (Fisher's exact test), Q value = 0.095

Table S267.  Gene #57: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
8Q LOSS MUTATED 11 21 9
8Q LOSS WILD-TYPE 141 101 84

Figure S267.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0419 (Fisher's exact test), Q value = 0.11

Table S268.  Gene #57: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
8Q LOSS MUTATED 10 25 13
8Q LOSS WILD-TYPE 168 164 118

Figure S268.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MRNA_CNMF'

P value = 0.00717 (Fisher's exact test), Q value = 0.028

Table S269.  Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
9P LOSS MUTATED 35 27 19 15
9P LOSS WILD-TYPE 7 25 13 13

Figure S269.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00119 (Fisher's exact test), Q value = 0.0068

Table S270.  Gene #58: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
9P LOSS MUTATED 39 28 29
9P LOSS WILD-TYPE 8 28 22

Figure S270.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S271.  Gene #58: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
9P LOSS MUTATED 99 90 121
9P LOSS WILD-TYPE 83 76 32

Figure S271.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 0.0237 (Fisher's exact test), Q value = 0.072

Table S272.  Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
9P LOSS MUTATED 90 68 68
9P LOSS WILD-TYPE 62 54 25

Figure S272.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S273.  Gene #58: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
9P LOSS MUTATED 89 74 104 40
9P LOSS WILD-TYPE 24 78 50 39

Figure S273.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00027

Table S274.  Gene #58: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
9P LOSS MUTATED 133 96 78
9P LOSS WILD-TYPE 45 93 53

Figure S274.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 0.044 (Fisher's exact test), Q value = 0.11

Table S275.  Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
9P LOSS MUTATED 74 84 74 31 30
9P LOSS WILD-TYPE 47 50 47 31 7

Figure S275.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.0026

Table S276.  Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
9P LOSS MUTATED 44 75 141 33
9P LOSS WILD-TYPE 45 43 58 36

Figure S276.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.028 (Fisher's exact test), Q value = 0.08

Table S277.  Gene #58: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
9P LOSS MUTATED 31 94 81
9P LOSS WILD-TYPE 8 57 63

Figure S277.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S278.  Gene #59: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
9Q LOSS MUTATED 29 11 21 13
9Q LOSS WILD-TYPE 13 41 11 15

Figure S278.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S279.  Gene #59: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
9Q LOSS MUTATED 32 12 30
9Q LOSS WILD-TYPE 15 44 21

Figure S279.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S280.  Gene #59: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
9Q LOSS MUTATED 89 44 112
9Q LOSS WILD-TYPE 93 122 41

Figure S280.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S281.  Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
9Q LOSS MUTATED 87 31 62
9Q LOSS WILD-TYPE 65 91 31

Figure S281.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0135 (Fisher's exact test), Q value = 0.047

Table S282.  Gene #59: '9q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 41 52 47
9Q LOSS MUTATED 20 19 34 18
9Q LOSS WILD-TYPE 34 22 18 29

Figure S282.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S283.  Gene #59: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
9Q LOSS MUTATED 78 28 95 42
9Q LOSS WILD-TYPE 35 124 59 37

Figure S283.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S284.  Gene #59: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
9Q LOSS MUTATED 127 42 74
9Q LOSS WILD-TYPE 51 147 57

Figure S284.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S285.  Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
9Q LOSS MUTATED 57 59 72 14 29
9Q LOSS WILD-TYPE 64 75 49 48 8

Figure S285.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S286.  Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
9Q LOSS MUTATED 18 54 128 31
9Q LOSS WILD-TYPE 71 64 71 38

Figure S286.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00408 (Fisher's exact test), Q value = 0.018

Table S287.  Gene #59: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
9Q LOSS MUTATED 56 64 46
9Q LOSS WILD-TYPE 33 65 70

Figure S287.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00097

Table S288.  Gene #59: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
9Q LOSS MUTATED 31 63 72
9Q LOSS WILD-TYPE 8 88 72

Figure S288.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00045

Table S289.  Gene #60: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
10P LOSS MUTATED 55 90 69
10P LOSS WILD-TYPE 127 76 84

Figure S289.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S290.  Gene #60: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
10P LOSS MUTATED 41 79 34
10P LOSS WILD-TYPE 111 43 59

Figure S290.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00036

Table S291.  Gene #60: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
10P LOSS MUTATED 39 91 56 27
10P LOSS WILD-TYPE 74 61 98 52

Figure S291.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00062

Table S292.  Gene #60: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
10P LOSS MUTATED 67 104 42
10P LOSS WILD-TYPE 111 85 89

Figure S292.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0029

Table S293.  Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
10P LOSS MUTATED 52 61 35 39 17
10P LOSS WILD-TYPE 69 73 86 23 20

Figure S293.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S294.  Gene #60: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
10P LOSS MUTATED 58 41 90 15
10P LOSS WILD-TYPE 31 77 109 54

Figure S294.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0475 (Fisher's exact test), Q value = 0.12

Table S295.  Gene #60: '10p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
10P LOSS MUTATED 30 50 58
10P LOSS WILD-TYPE 59 79 58

Figure S295.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00437 (Fisher's exact test), Q value = 0.019

Table S296.  Gene #60: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
10P LOSS MUTATED 18 75 45
10P LOSS WILD-TYPE 21 76 99

Figure S296.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'MRNA_CNMF'

P value = 0.00093 (Fisher's exact test), Q value = 0.0057

Table S297.  Gene #61: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
10Q LOSS MUTATED 13 34 11 8
10Q LOSS WILD-TYPE 29 18 21 20

Figure S297.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.0015

Table S298.  Gene #61: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
10Q LOSS MUTATED 12 36 18
10Q LOSS WILD-TYPE 35 20 33

Figure S298.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00045

Table S299.  Gene #61: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
10Q LOSS MUTATED 62 99 68
10Q LOSS WILD-TYPE 120 67 85

Figure S299.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S300.  Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
10Q LOSS MUTATED 48 81 41
10Q LOSS WILD-TYPE 104 41 52

Figure S300.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S301.  Gene #61: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
10Q LOSS MUTATED 44 102 56 26
10Q LOSS WILD-TYPE 69 50 98 53

Figure S301.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S302.  Gene #61: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
10Q LOSS MUTATED 69 119 40
10Q LOSS WILD-TYPE 109 70 91

Figure S302.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.0038

Table S303.  Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
10Q LOSS MUTATED 48 72 41 39 18
10Q LOSS WILD-TYPE 73 62 80 23 19

Figure S303.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S304.  Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
10Q LOSS MUTATED 61 43 96 18
10Q LOSS WILD-TYPE 28 75 103 51

Figure S304.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0149 (Fisher's exact test), Q value = 0.05

Table S305.  Gene #61: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
10Q LOSS MUTATED 31 59 64
10Q LOSS WILD-TYPE 58 70 52

Figure S305.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00729 (Fisher's exact test), Q value = 0.028

Table S306.  Gene #61: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
10Q LOSS MUTATED 18 83 53
10Q LOSS WILD-TYPE 21 68 91

Figure S306.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 0.00609 (Fisher's exact test), Q value = 0.024

Table S307.  Gene #62: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
11P LOSS MUTATED 48 57 66
11P LOSS WILD-TYPE 134 109 87

Figure S307.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 0.00463 (Fisher's exact test), Q value = 0.02

Table S308.  Gene #62: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
11P LOSS MUTATED 37 44 41
11P LOSS WILD-TYPE 115 78 52

Figure S308.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00325 (Fisher's exact test), Q value = 0.015

Table S309.  Gene #62: '11p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 41 52 47
11P LOSS MUTATED 21 9 26 9
11P LOSS WILD-TYPE 33 32 26 38

Figure S309.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 0.0063 (Fisher's exact test), Q value = 0.025

Table S310.  Gene #63: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
11Q LOSS MUTATED 36 55 50
11Q LOSS WILD-TYPE 146 111 103

Figure S310.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 0.00099 (Fisher's exact test), Q value = 0.0058

Table S311.  Gene #63: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
11Q LOSS MUTATED 29 41 37
11Q LOSS WILD-TYPE 123 81 56

Figure S311.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p loss' versus 'MRNA_CNMF'

P value = 0.0233 (Fisher's exact test), Q value = 0.072

Table S312.  Gene #64: '12p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
12P LOSS MUTATED 0 3 3 5
12P LOSS WILD-TYPE 42 49 29 23

Figure S312.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'12p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00512 (Fisher's exact test), Q value = 0.021

Table S313.  Gene #64: '12p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
12P LOSS MUTATED 0 3 8
12P LOSS WILD-TYPE 47 53 43

Figure S313.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12q loss' versus 'RPPA_CNMF'

P value = 0.0282 (Fisher's exact test), Q value = 0.081

Table S314.  Gene #65: '12q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 73 61
12Q LOSS MUTATED 3 2 9
12Q LOSS WILD-TYPE 57 71 52

Figure S314.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.0409 (Fisher's exact test), Q value = 0.11

Table S315.  Gene #66: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
13Q LOSS MUTATED 81 81 62
13Q LOSS WILD-TYPE 71 41 31

Figure S315.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0044

Table S316.  Gene #66: '13q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
13Q LOSS MUTATED 42 79 85
13Q LOSS WILD-TYPE 47 50 31

Figure S316.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0251 (Fisher's exact test), Q value = 0.075

Table S317.  Gene #66: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
13Q LOSS MUTATED 21 105 80
13Q LOSS WILD-TYPE 18 46 64

Figure S317.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'MRNA_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00097

Table S318.  Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
14Q LOSS MUTATED 2 20 12 12
14Q LOSS WILD-TYPE 40 32 20 16

Figure S318.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.0023

Table S319.  Gene #67: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
14Q LOSS MUTATED 4 22 20
14Q LOSS WILD-TYPE 43 34 31

Figure S319.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 0.059

Table S320.  Gene #67: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
14Q LOSS MUTATED 55 69 42
14Q LOSS WILD-TYPE 127 97 111

Figure S320.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S321.  Gene #67: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
14Q LOSS MUTATED 16 63 69 16
14Q LOSS WILD-TYPE 97 89 85 63

Figure S321.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S322.  Gene #67: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
14Q LOSS MUTATED 28 75 61
14Q LOSS WILD-TYPE 150 114 70

Figure S322.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0016

Table S323.  Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
14Q LOSS MUTATED 34 44 28 35 15
14Q LOSS WILD-TYPE 87 90 93 27 22

Figure S323.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S324.  Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
14Q LOSS MUTATED 51 34 58 13
14Q LOSS WILD-TYPE 38 84 141 56

Figure S324.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00267 (Fisher's exact test), Q value = 0.013

Table S325.  Gene #67: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
14Q LOSS MUTATED 18 52 46
14Q LOSS WILD-TYPE 71 77 70

Figure S325.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00218 (Fisher's exact test), Q value = 0.011

Table S326.  Gene #67: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
14Q LOSS MUTATED 6 65 45
14Q LOSS WILD-TYPE 33 86 99

Figure S326.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00197 (Fisher's exact test), Q value = 0.0099

Table S327.  Gene #68: '15q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 41 52 47
15Q LOSS MUTATED 21 3 18 12
15Q LOSS WILD-TYPE 33 38 34 35

Figure S327.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 0.0277 (Fisher's exact test), Q value = 0.08

Table S328.  Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
15Q LOSS MUTATED 39 45 25 11 13
15Q LOSS WILD-TYPE 82 89 96 51 24

Figure S328.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p loss' versus 'CN_CNMF'

P value = 0.00356 (Fisher's exact test), Q value = 0.016

Table S329.  Gene #69: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
16P LOSS MUTATED 43 59 61
16P LOSS WILD-TYPE 139 107 92

Figure S329.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0267 (Fisher's exact test), Q value = 0.079

Table S330.  Gene #69: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
16P LOSS MUTATED 21 44 48
16P LOSS WILD-TYPE 68 85 68

Figure S330.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 0.056

Table S331.  Gene #70: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
16Q LOSS MUTATED 52 71 59
16Q LOSS WILD-TYPE 130 95 94

Figure S331.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0018

Table S332.  Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
16Q LOSS MUTATED 39 53 32 24 25
16Q LOSS WILD-TYPE 82 81 89 38 12

Figure S332.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00215 (Fisher's exact test), Q value = 0.011

Table S333.  Gene #70: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
16Q LOSS MUTATED 20 51 52
16Q LOSS WILD-TYPE 69 78 64

Figure S333.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00183 (Fisher's exact test), Q value = 0.0093

Table S334.  Gene #70: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
16Q LOSS MUTATED 9 71 43
16Q LOSS WILD-TYPE 30 80 101

Figure S334.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'MRNA_CNMF'

P value = 0.00468 (Fisher's exact test), Q value = 0.02

Table S335.  Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
17P LOSS MUTATED 33 26 22 12
17P LOSS WILD-TYPE 9 26 10 16

Figure S335.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00062

Table S336.  Gene #71: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
17P LOSS MUTATED 93 87 111
17P LOSS WILD-TYPE 89 79 42

Figure S336.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.04

Table S337.  Gene #71: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
17P LOSS MUTATED 81 60 64
17P LOSS WILD-TYPE 71 62 29

Figure S337.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00631 (Fisher's exact test), Q value = 0.025

Table S338.  Gene #71: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 41 52 47
17P LOSS MUTATED 41 19 26 23
17P LOSS WILD-TYPE 13 22 26 24

Figure S338.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 0.00169 (Fisher's exact test), Q value = 0.0088

Table S339.  Gene #71: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
17P LOSS MUTATED 76 70 99 45
17P LOSS WILD-TYPE 37 82 55 34

Figure S339.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00128 (Fisher's exact test), Q value = 0.0072

Table S340.  Gene #71: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
17P LOSS MUTATED 121 93 76
17P LOSS WILD-TYPE 57 96 55

Figure S340.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00073 (Fisher's exact test), Q value = 0.0046

Table S341.  Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
17P LOSS MUTATED 41 76 131 31
17P LOSS WILD-TYPE 48 42 68 38

Figure S341.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MRNA_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.037

Table S342.  Gene #72: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
17Q LOSS MUTATED 13 3 7 4
17Q LOSS WILD-TYPE 29 49 25 24

Figure S342.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00498 (Fisher's exact test), Q value = 0.021

Table S343.  Gene #72: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
17Q LOSS MUTATED 13 3 11
17Q LOSS WILD-TYPE 34 53 40

Figure S343.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.004

Table S344.  Gene #72: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
17Q LOSS MUTATED 41 16 37
17Q LOSS WILD-TYPE 141 150 116

Figure S344.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 0.00161 (Fisher's exact test), Q value = 0.0084

Table S345.  Gene #72: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
17Q LOSS MUTATED 37 11 22
17Q LOSS WILD-TYPE 115 111 71

Figure S345.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0016

Table S346.  Gene #72: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
17Q LOSS MUTATED 32 13 31 18
17Q LOSS WILD-TYPE 81 139 123 61

Figure S346.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S347.  Gene #72: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
17Q LOSS MUTATED 55 17 22
17Q LOSS WILD-TYPE 123 172 109

Figure S347.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00908 (Fisher's exact test), Q value = 0.033

Table S348.  Gene #72: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
17Q LOSS MUTATED 8 19 46 18
17Q LOSS WILD-TYPE 81 99 153 51

Figure S348.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0434 (Fisher's exact test), Q value = 0.11

Table S349.  Gene #72: '17q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
17Q LOSS MUTATED 10 21 35
17Q LOSS WILD-TYPE 29 130 109

Figure S349.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'MRNA_CNMF'

P value = 0.0384 (Fisher's exact test), Q value = 0.1

Table S350.  Gene #75: '19p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
19P LOSS MUTATED 11 13 15 14
19P LOSS WILD-TYPE 31 39 17 14

Figure S350.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'19p loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00036

Table S351.  Gene #75: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
19P LOSS MUTATED 47 47 73
19P LOSS WILD-TYPE 135 119 80

Figure S351.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 0.0437 (Fisher's exact test), Q value = 0.11

Table S352.  Gene #75: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
19P LOSS MUTATED 38 38 58 32
19P LOSS WILD-TYPE 75 114 96 47

Figure S352.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0194 (Fisher's exact test), Q value = 0.062

Table S353.  Gene #75: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
19P LOSS MUTATED 62 50 54
19P LOSS WILD-TYPE 116 139 77

Figure S353.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.0016

Table S354.  Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
19P LOSS MUTATED 17 39 84 15
19P LOSS WILD-TYPE 72 79 115 54

Figure S354.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 0.0414 (Fisher's exact test), Q value = 0.11

Table S355.  Gene #76: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
19Q LOSS MUTATED 30 40 42
19Q LOSS WILD-TYPE 152 126 111

Figure S355.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'20p loss' versus 'CN_CNMF'

P value = 0.0248 (Fisher's exact test), Q value = 0.074

Table S356.  Gene #77: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
20P LOSS MUTATED 16 7 19
20P LOSS WILD-TYPE 166 159 134

Figure S356.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'20p loss' versus 'METHLYATION_CNMF'

P value = 0.0032 (Fisher's exact test), Q value = 0.015

Table S357.  Gene #77: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
20P LOSS MUTATED 10 4 15
20P LOSS WILD-TYPE 142 118 78

Figure S357.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0311 (Fisher's exact test), Q value = 0.087

Table S358.  Gene #77: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
20P LOSS MUTATED 16 9 17
20P LOSS WILD-TYPE 162 180 114

Figure S358.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q loss' versus 'CN_CNMF'

P value = 0.00203 (Fisher's exact test), Q value = 0.01

Table S359.  Gene #78: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
20Q LOSS MUTATED 13 26 7
20Q LOSS WILD-TYPE 169 140 146

Figure S359.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'

'20q loss' versus 'METHLYATION_CNMF'

P value = 0.0235 (Fisher's exact test), Q value = 0.072

Table S360.  Gene #78: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
20Q LOSS MUTATED 8 18 7
20Q LOSS WILD-TYPE 144 104 86

Figure S360.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00027

Table S361.  Gene #78: '20q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
20Q LOSS MUTATED 3 28 12 3
20Q LOSS WILD-TYPE 110 124 142 76

Figure S361.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00144 (Fisher's exact test), Q value = 0.0079

Table S362.  Gene #78: '20q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
20Q LOSS MUTATED 9 29 8
20Q LOSS WILD-TYPE 169 160 123

Figure S362.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q loss' versus 'MIRSEQ_CNMF'

P value = 0.01 (Fisher's exact test), Q value = 0.036

Table S363.  Gene #78: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
20Q LOSS MUTATED 14 19 3 7 3
20Q LOSS WILD-TYPE 107 115 118 55 34

Figure S363.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S364.  Gene #79: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
21Q LOSS MUTATED 69 106 90
21Q LOSS WILD-TYPE 113 60 63

Figure S364.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 0.00543 (Fisher's exact test), Q value = 0.022

Table S365.  Gene #79: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
21Q LOSS MUTATED 65 76 47
21Q LOSS WILD-TYPE 87 46 46

Figure S365.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0384 (Fisher's exact test), Q value = 0.1

Table S366.  Gene #79: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
21Q LOSS MUTATED 86 114 64
21Q LOSS WILD-TYPE 92 75 67

Figure S366.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 0.0158 (Fisher's exact test), Q value = 0.052

Table S367.  Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
21Q LOSS MUTATED 72 74 50 32 25
21Q LOSS WILD-TYPE 49 60 71 30 12

Figure S367.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00059 (Fisher's exact test), Q value = 0.004

Table S368.  Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
21Q LOSS MUTATED 51 64 117 21
21Q LOSS WILD-TYPE 38 54 82 48

Figure S368.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0243 (Fisher's exact test), Q value = 0.073

Table S369.  Gene #79: '21q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
21Q LOSS MUTATED 36 63 69
21Q LOSS WILD-TYPE 53 66 47

Figure S369.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0126 (Fisher's exact test), Q value = 0.044

Table S370.  Gene #79: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
21Q LOSS MUTATED 22 87 59
21Q LOSS WILD-TYPE 17 64 85

Figure S370.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'MRNA_CNMF'

P value = 0.00907 (Fisher's exact test), Q value = 0.033

Table S371.  Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
22Q LOSS MUTATED 7 7 6 13
22Q LOSS WILD-TYPE 35 45 26 15

Figure S371.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00089

Table S372.  Gene #80: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
22Q LOSS MUTATED 22 15 47 14
22Q LOSS WILD-TYPE 91 137 107 65

Figure S372.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S373.  Gene #80: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
22Q LOSS MUTATED 26 24 48
22Q LOSS WILD-TYPE 152 165 83

Figure S373.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.009 (Fisher's exact test), Q value = 0.033

Table S374.  Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
22Q LOSS MUTATED 10 31 41 7
22Q LOSS WILD-TYPE 79 87 158 62

Figure S374.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xp loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00036

Table S375.  Gene #81: 'xp loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
XP LOSS MUTATED 30 63 53
XP LOSS WILD-TYPE 152 103 100

Figure S375.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #3: 'CN_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S376.  Gene #81: 'xp loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
XP LOSS MUTATED 22 50 33
XP LOSS WILD-TYPE 130 72 60

Figure S376.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xp loss' versus 'MRNASEQ_CNMF'

P value = 0.00254 (Fisher's exact test), Q value = 0.012

Table S377.  Gene #81: 'xp loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
XP LOSS MUTATED 33 58 41 12
XP LOSS WILD-TYPE 80 94 113 67

Figure S377.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0192 (Fisher's exact test), Q value = 0.061

Table S378.  Gene #81: 'xp loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
XP LOSS MUTATED 47 68 29
XP LOSS WILD-TYPE 131 121 102

Figure S378.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.042

Table S379.  Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
XP LOSS MUTATED 40 46 21 22 12
XP LOSS WILD-TYPE 81 88 100 40 25

Figure S379.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xp loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00152 (Fisher's exact test), Q value = 0.0081

Table S380.  Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
XP LOSS MUTATED 35 40 57 9
XP LOSS WILD-TYPE 54 78 142 60

Figure S380.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0036

Table S381.  Gene #81: 'xp loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
XP LOSS MUTATED 12 39 43
XP LOSS WILD-TYPE 77 90 73

Figure S381.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xp loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S382.  Gene #81: 'xp loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
XP LOSS MUTATED 9 63 22
XP LOSS WILD-TYPE 30 88 122

Figure S382.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S383.  Gene #82: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
XQ LOSS MUTATED 20 40 52
XQ LOSS WILD-TYPE 162 126 101

Figure S383.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.0012

Table S384.  Gene #82: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 152 122 93
XQ LOSS MUTATED 18 32 32
XQ LOSS WILD-TYPE 134 90 61

Figure S384.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 0.00808 (Fisher's exact test), Q value = 0.03

Table S385.  Gene #82: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
XQ LOSS MUTATED 26 36 42 7
XQ LOSS WILD-TYPE 87 116 112 72

Figure S385.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 0.00842 (Fisher's exact test), Q value = 0.031

Table S386.  Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
XQ LOSS MUTATED 30 40 15 12 11
XQ LOSS WILD-TYPE 91 94 106 50 26

Figure S386.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0147 (Fisher's exact test), Q value = 0.05

Table S387.  Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
XQ LOSS MUTATED 22 28 52 6
XQ LOSS WILD-TYPE 67 90 147 63

Figure S387.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0046 (Fisher's exact test), Q value = 0.02

Table S388.  Gene #82: 'xq loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
XQ LOSS MUTATED 10 29 35
XQ LOSS WILD-TYPE 79 100 81

Figure S388.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00027

Table S389.  Gene #82: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
XQ LOSS MUTATED 8 51 15
XQ LOSS WILD-TYPE 31 100 129

Figure S389.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_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/LUSC-TP/15093662/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LUSC-TP/15114194/LUSC-TP.transferedmergedcluster.txt

  • Number of patients = 501

  • Number of significantly arm-level cnvs = 82

  • 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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