Correlation between copy number variations of arm-level result and molecular subtypes
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C18G8JSB
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/C18G8JSB
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 74 arm-level events and 10 molecular subtypes across 288 patients, 376 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

  • 2p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 2q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.

  • 3p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 3q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

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

  • 7q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 8p gain cnv correlated to 'METHLYATION_CNMF'.

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

  • 9p gain cnv correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 10p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

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

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

  • 12p gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 12q gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 14q gain cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 15q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 16p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 17p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 18p gain cnv correlated to 'CN_CNMF'.

  • 18q gain cnv correlated to 'CN_CNMF'.

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

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

  • 20p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 22q gain cnv correlated to 'CN_CNMF'.

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

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

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

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

  • 2p loss cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

  • 2q loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

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

  • 3q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

  • 5p loss cnv correlated to 'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • 8p loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 8q loss cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 9p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 10q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 11p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • 15q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

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

  • 19p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 19q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 21q loss cnv correlated to 'CN_CNMF'.

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

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

  • xq loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_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 74 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 376 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
7p gain 172 (60%) 116 1e-05
(6.98e-05) 		1e-05
(6.98e-05) 		0.00616
(0.0181) 		1e-05
(6.98e-05) 		1e-05
(6.98e-05) 		1e-05
(6.98e-05) 		0.0495
(0.098) 		1e-05
(6.98e-05) 		0.00015
(0.00076) 		1e-05
(6.98e-05)
17p gain 174 (60%) 114 1e-05
(6.98e-05) 		1e-05
(6.98e-05) 		0.00302
(0.0102) 		3e-05
(0.00018) 		1e-05
(6.98e-05) 		1e-05
(6.98e-05) 		0.00394
(0.0126) 		1e-05
(6.98e-05) 		1e-05
(6.98e-05) 		1e-05
(6.98e-05)
17q gain 191 (66%) 97 1e-05
(6.98e-05) 		1e-05
(6.98e-05) 		0.0305
(0.0663) 		1e-05
(6.98e-05) 		1e-05
(6.98e-05) 		1e-05
(6.98e-05) 		0.0349
(0.0744) 		4e-05
(0.000235) 		0.00013
(0.000673) 		2e-05
(0.000131)
7q gain 173 (60%) 115 1e-05
(6.98e-05) 		1e-05
(6.98e-05) 		0.0131
(0.0325) 		1e-05
(6.98e-05) 		1e-05
(6.98e-05) 		1e-05
(6.98e-05) 		0.0699
(0.131) 		1e-05
(6.98e-05) 		0.00014
(0.000714) 		3e-05
(0.00018)
16p gain 153 (53%) 135 1e-05
(6.98e-05) 		0.0114
(0.0293) 		0.647
(0.751) 		0.014
(0.0342) 		1e-05
(6.98e-05) 		4e-05
(0.000235) 		0.00068
(0.00284) 		2e-05
(0.000131) 		0.00926
(0.0252) 		0.00016
(0.000795)
16q gain 148 (51%) 140 1e-05
(6.98e-05) 		0.00664
(0.019) 		0.753
(0.839) 		0.0213
(0.0486) 		1e-05
(6.98e-05) 		9e-05
(0.00049) 		3e-05
(0.00018) 		1e-05
(6.98e-05) 		0.00279
(0.00955) 		3e-05
(0.00018)
20q gain 101 (35%) 187 0.00018
(0.000871) 		0.0204
(0.0468) 		0.0355
(0.0754) 		0.0099
(0.0263) 		0.0114
(0.0293) 		0.0499
(0.0982) 		0.0189
(0.0445) 		0.006
(0.0178) 		0.339
(0.459) 		0.0434
(0.0889)
xp gain 87 (30%) 201 1e-05
(6.98e-05) 		1e-05
(6.98e-05) 		0.335
(0.457) 		0.0182
(0.0433) 		1e-05
(6.98e-05) 		4e-05
(0.000235) 		0.00849
(0.0233) 		1e-05
(6.98e-05) 		0.00216
(0.00776) 		0.00065
(0.00273)
xq gain 91 (32%) 197 1e-05
(6.98e-05) 		3e-05
(0.00018) 		0.329
(0.45) 		0.031
(0.0673) 		1e-05
(6.98e-05) 		3e-05
(0.00018) 		0.00991
(0.0263) 		1e-05
(6.98e-05) 		0.0103
(0.0271) 		0.00376
(0.0122)
13q loss 24 (8%) 264 1e-05
(6.98e-05) 		8e-05
(0.000442) 		0.532
(0.644) 		1e-05
(6.98e-05) 		1e-05
(6.98e-05) 		1e-05
(6.98e-05) 		0.0427
(0.0878) 		0.00745
(0.0206) 		0.00379
(0.0122) 		2e-05
(0.000131)
3p gain 74 (26%) 214 1e-05
(6.98e-05) 		0.002
(0.00733) 		0.193
(0.299) 		0.00019
(0.000901) 		1e-05
(6.98e-05) 		0.00218
(0.00779) 		0.0397
(0.0827) 		0.0001
(0.00054) 		0.0911
(0.163) 		0.0144
(0.0353)
3q gain 94 (33%) 194 1e-05
(6.98e-05) 		0.0047
(0.0147) 		0.222
(0.335) 		0.00963
(0.0259) 		1e-05
(6.98e-05) 		0.00379
(0.0122) 		0.0102
(0.0269) 		0.00017
(0.000833) 		0.521
(0.634) 		0.0131
(0.0325)
20p gain 99 (34%) 189 3e-05
(0.00018) 		0.0202
(0.0466) 		0.0245
(0.0551) 		0.00563
(0.017) 		0.00487
(0.0151) 		0.0223
(0.0505) 		0.0116
(0.0295) 		0.00322
(0.0106) 		0.179
(0.283) 		0.0605
(0.115)
3p loss 22 (8%) 266 1e-05
(6.98e-05) 		1e-05
(6.98e-05) 		0.664
(0.762) 		0.00211
(0.00762) 		1e-05
(6.98e-05) 		2e-05
(0.000131) 		0.43
(0.548) 		0.0265
(0.0587) 		0.0474
(0.0951) 		0.016
(0.0388)
9p loss 33 (11%) 255 1e-05
(6.98e-05) 		1e-05
(6.98e-05) 		0.653
(0.757) 		0.0016
(0.00607) 		1e-05
(6.98e-05) 		1e-05
(6.98e-05) 		0.00595
(0.0178) 		0.254
(0.371) 		0.00569
(0.0171) 		0.00077
(0.00315)
9q loss 34 (12%) 254 1e-05
(6.98e-05) 		1e-05
(6.98e-05) 		0.194
(0.3) 		0.00174
(0.00654) 		1e-05
(6.98e-05) 		1e-05
(6.98e-05) 		0.00434
(0.0138) 		0.136
(0.224) 		0.00095
(0.00376) 		0.00019
(0.000901)
14q loss 47 (16%) 241 1e-05
(6.98e-05) 		0.00021
(0.000965) 		0.0157
(0.0383) 		7e-05
(0.000395) 		1e-05
(6.98e-05) 		1e-05
(6.98e-05) 		0.207
(0.316) 		0.774
(0.857) 		0.00449
(0.0141) 		0.00647
(0.0188)
18p loss 42 (15%) 246 1e-05
(6.98e-05) 		1e-05
(6.98e-05) 		0.0541
(0.104) 		0.00053
(0.00224) 		1e-05
(6.98e-05) 		1e-05
(6.98e-05) 		0.234
(0.348) 		0.00085
(0.00342) 		0.0197
(0.0458) 		0.00079
(0.00321)
18q loss 45 (16%) 243 1e-05
(6.98e-05) 		1e-05
(6.98e-05) 		0.133
(0.222) 		1e-05
(6.98e-05) 		1e-05
(6.98e-05) 		1e-05
(6.98e-05) 		0.126
(0.211) 		0.0007
(0.00291) 		0.0066
(0.019) 		0.00027
(0.00121)
1q gain 17 (6%) 271 1e-05
(6.98e-05) 		1e-05
(6.98e-05) 		0.93
(0.975) 		0.0856
(0.156) 		3e-05
(0.00018) 		0.00017
(0.000833) 		0.52
(0.634) 		0.00043
(0.00183) 		0.00656
(0.019) 		0.0113
(0.0292)
4p loss 25 (9%) 263 1e-05
(6.98e-05) 		1e-05
(6.98e-05) 		0.424
(0.542) 		0.00013
(0.000673) 		1e-05
(6.98e-05) 		1e-05
(6.98e-05) 		0.261
(0.379) 		0.109
(0.186) 		0.00586
(0.0176) 		1e-05
(6.98e-05)
4q loss 26 (9%) 262 1e-05
(6.98e-05) 		1e-05
(6.98e-05) 		0.581
(0.692) 		0.00035
(0.00151) 		1e-05
(6.98e-05) 		2e-05
(0.000131) 		0.382
(0.501) 		0.172
(0.275) 		0.00672
(0.0192) 		1e-05
(6.98e-05)
5p loss 8 (3%) 280 0.17
(0.271) 		0.0488
(0.0968) 		0.437
(0.557) 		0.00953
(0.0257) 		0.03
(0.0654) 		0.00033
(0.00144) 		0.072
(0.134) 		0.0396
(0.0827) 		0.0126
(0.0319) 		0.00012
(0.00063)
5q loss 8 (3%) 280 0.169
(0.271) 		0.0487
(0.0968) 		0.87
(0.933) 		0.0101
(0.0268) 		0.0298
(0.0653) 		0.00025
(0.00113) 		0.0709
(0.132) 		0.0404
(0.0839) 		0.0122
(0.031) 		1e-05
(6.98e-05)
10p loss 16 (6%) 272 1e-05
(6.98e-05) 		0.00016
(0.000795) 		0.501
(0.617) 		0.025
(0.056) 		0.00033
(0.00144) 		0.003
(0.0101) 		0.399
(0.52) 		0.915
(0.967) 		0.0197
(0.0458) 		0.00663
(0.019)
10q loss 17 (6%) 271 1e-05
(6.98e-05) 		0.00019
(0.000901) 		0.413
(0.532) 		0.00483
(0.0151) 		0.00021
(0.000965) 		0.00208
(0.00755) 		0.0844
(0.154) 		0.863
(0.93) 		0.00183
(0.0068) 		0.00116
(0.00454)
11q loss 21 (7%) 267 1e-05
(6.98e-05) 		6e-05
(0.000344) 		0.32
(0.44) 		0.0295
(0.065) 		0.00014
(0.000714) 		0.00236
(0.00824) 		0.656
(0.76) 		0.101
(0.176) 		0.037
(0.0777) 		0.0389
(0.0815)
xp loss 34 (12%) 254 1e-05
(6.98e-05) 		1e-05
(6.98e-05) 		0.598
(0.709) 		0.00194
(0.00714) 		1e-05
(6.98e-05) 		8e-05
(0.000442) 		0.307
(0.429) 		0.226
(0.338) 		0.0183
(0.0433) 		0.00728
(0.0203)
xq loss 30 (10%) 258 1e-05
(6.98e-05) 		2e-05
(0.000131) 		0.659
(0.762) 		0.0106
(0.0277) 		1e-05
(6.98e-05) 		9e-05
(0.00049) 		0.266
(0.385) 		0.447
(0.568) 		0.0499
(0.0982) 		0.0214
(0.0486)
1p gain 9 (3%) 279 3e-05
(0.00018) 		3e-05
(0.00018) 		0.61
(0.72) 		0.0534
(0.104) 		0.00313
(0.0104) 		0.00334
(0.011) 		0.477
(0.593) 		0.0832
(0.153) 		0.0486
(0.0968) 		0.0288
(0.0637)
11p loss 18 (6%) 270 1e-05
(6.98e-05) 		0.00073
(0.00302) 		0.93
(0.975) 		0.308
(0.43) 		6e-05
(0.000344) 		0.0028
(0.00955) 		0.296
(0.421) 		0.061
(0.116) 		0.0197
(0.0458) 		0.0069
(0.0196)
15q loss 31 (11%) 257 1e-05
(6.98e-05) 		0.00235
(0.00824) 		0.0886
(0.16) 		0.00162
(0.00612) 		0.00011
(0.000581) 		1e-05
(6.98e-05) 		0.0918
(0.163) 		0.637
(0.742) 		0.0649
(0.122) 		0.00268
(0.00922)
17p loss 12 (4%) 276 0.00423
(0.0135) 		0.00031
(0.00137) 		0.545
(0.655) 		0.249
(0.365) 		1e-05
(6.98e-05) 		0.00021
(0.000965) 		0.536
(0.647) 		0.267
(0.386) 		0.00609
(0.018) 		0.00121
(0.00471)
22q loss 60 (21%) 228 1e-05
(6.98e-05) 		1e-05
(6.98e-05) 		0.697
(0.789) 		0.00104
(0.00409) 		1e-05
(6.98e-05) 		1e-05
(6.98e-05) 		0.983
(1.00) 		0.453
(0.571) 		0.054
(0.104) 		0.0108
(0.0279)
11q gain 10 (3%) 278 1e-05
(6.98e-05) 		0.00311
(0.0104) 		0.759
(0.844) 		0.016
(0.0388) 		0.0214
(0.0486) 		0.00373
(0.0122) 		0.849
(0.921) 		1
(1.00) 		0.818
(0.896) 		0.226
(0.338)
6p loss 21 (7%) 267 1e-05
(6.98e-05) 		0.0449
(0.0912) 		0.62
(0.728) 		0.159
(0.257) 		0.00617
(0.0181) 		0.00026
(0.00117) 		0.0196
(0.0458) 		0.0502
(0.0985) 		0.47
(0.586) 		0.111
(0.189)
16p loss 4 (1%) 284 0.0423
(0.0873) 		0.0338
(0.0728) 		1
(1.00) 		0.564
(0.675) 		0.0439
(0.0897) 		0.00686
(0.0195) 		0.84
(0.912) 		0.206
(0.316) 		0.116
(0.196) 		0.0127
(0.0321)
16q loss 7 (2%) 281 0.00037
(0.00159) 		0.00725
(0.0203) 		1
(1.00) 		0.27
(0.39) 		0.00221
(0.00786) 		0.0129
(0.0322) 		0.403
(0.522) 		0.235
(0.35) 		0.0324
(0.0702) 		0.0524
(0.102)
19p loss 17 (6%) 271 8e-05
(0.000442) 		0.00235
(0.00824) 		0.917
(0.967) 		0.0342
(0.0732) 		0.00552
(0.0167) 		0.00629
(0.0184) 		0.224
(0.337) 		0.105
(0.181) 		0.0884
(0.159) 		0.0581
(0.111)
19q loss 16 (6%) 272 1e-05
(6.98e-05) 		0.00488
(0.0151) 		0.621
(0.728) 		0.00944
(0.0256) 		0.00499
(0.0154) 		0.0226
(0.051) 		0.402
(0.522) 		0.15
(0.246) 		0.09
(0.161) 		0.277
(0.398)
5p gain 33 (11%) 255 1e-05
(6.98e-05) 		0.00716
(0.0201) 		0.67
(0.769) 		0.329
(0.45) 		0.0184
(0.0435) 		0.00011
(0.000581) 		0.571
(0.681) 		0.116
(0.196) 		0.31
(0.432) 		0.251
(0.367)
5q gain 31 (11%) 257 1e-05
(6.98e-05) 		0.00092
(0.00366) 		0.53
(0.642) 		0.166
(0.268) 		0.00507
(0.0156) 		7e-05
(0.000395) 		0.316
(0.439) 		0.153
(0.249) 		0.452
(0.571) 		0.373
(0.491)
8q gain 25 (9%) 263 0.126
(0.212) 		0.00011
(0.000581) 		0.195
(0.302) 		0.385
(0.505) 		0.0129
(0.0322) 		0.0447
(0.0912) 		0.152
(0.247) 		0.111
(0.189) 		0.046
(0.0929) 		0.134
(0.223)
11p gain 11 (4%) 277 0.00031
(0.00137) 		0.02
(0.0462) 		0.907
(0.963) 		0.0104
(0.0272) 		0.188
(0.294) 		0.00033
(0.00144) 		0.929
(0.975) 		0.95
(0.99) 		0.819
(0.896) 		0.224
(0.337)
12p gain 112 (39%) 176 0.00551
(0.0167) 		0.302
(0.424) 		0.0259
(0.0577) 		0.32
(0.44) 		0.00021
(0.000965) 		0.115
(0.195) 		0.0917
(0.163) 		0.0167
(0.04) 		0.663
(0.762) 		0.0688
(0.129)
12q gain 112 (39%) 176 0.00518
(0.0158) 		0.3
(0.423) 		0.0262
(0.0583) 		0.322
(0.442) 		0.00016
(0.000795) 		0.115
(0.195) 		0.0899
(0.161) 		0.0169
(0.0404) 		0.664
(0.762) 		0.0706
(0.132)
1p loss 30 (10%) 258 1e-05
(6.98e-05) 		0.0298
(0.0653) 		0.415
(0.533) 		0.378
(0.497) 		5e-05
(0.000291) 		0.00081
(0.00328) 		0.351
(0.47) 		0.177
(0.28) 		0.837
(0.912) 		0.0863
(0.157)
3q loss 7 (2%) 281 1e-05
(6.98e-05) 		0.00184
(0.00681) 		0.629
(0.735) 		0.0571
(0.11) 		0.0213
(0.0486) 		0.00297
(0.0101) 		0.4
(0.521) 		0.838
(0.912) 		0.391
(0.512) 		0.355
(0.475)
6q loss 26 (9%) 262 1e-05
(6.98e-05) 		0.0023
(0.00814) 		0.912
(0.967) 		0.0613
(0.116) 		0.00018
(0.000871) 		2e-05
(0.000131) 		0.305
(0.427) 		0.276
(0.397) 		0.0993
(0.174) 		0.0943
(0.166)
8q loss 9 (3%) 279 0.00239
(0.0083) 		0.382
(0.501) 		0.63
(0.736) 		0.0465
(0.0936) 		0.0125
(0.0317) 		0.0009
(0.0036) 		0.914
(0.967) 		0.784
(0.866) 		0.683
(0.78) 		0.553
(0.665)
2q gain 47 (16%) 241 1e-05
(6.98e-05) 		0.00745
(0.0206) 		1
(1.00) 		0.00696
(0.0197) 		0.602
(0.713) 		0.737
(0.825) 		0.218
(0.331) 		0.0514
(0.101) 		0.42
(0.537) 		0.405
(0.524)
6p gain 10 (3%) 278 0.048
(0.096) 		0.00367
(0.012) 		0.0717
(0.134) 		0.188
(0.294) 		0.00201
(0.00733) 		0.0627
(0.119) 		0.169
(0.271) 		0.25
(0.367) 		0.104
(0.18) 		0.0581
(0.111)
6q gain 8 (3%) 280 0.0227
(0.0511) 		0.00183
(0.0068) 		0.481
(0.597) 		0.173
(0.276) 		0.013
(0.0324) 		0.131
(0.218) 		0.226
(0.338) 		0.644
(0.75) 		0.126
(0.212) 		0.0862
(0.157)
14q gain 3 (1%) 285 0.243
(0.358) 		0.0167
(0.04) 		0.454
(0.571) 		0.852
(0.922) 		0.491
(0.607) 		0.0358
(0.076) 		1
(1.00) 		0.37
(0.49) 		0.299
(0.423) 		0.0136
(0.0335)
19p gain 4 (1%) 284 0.0015
(0.00575) 		0.692
(0.786) 		0.282
(0.403) 		0.107
(0.184) 		0.046
(0.0929) 		0.0411
(0.0851) 		1
(1.00) 		0.478
(0.593) 		1
(1.00) 		0.337
(0.458)
19q gain 4 (1%) 284 0.00135
(0.0052) 		0.689
(0.784) 		0.283
(0.404) 		0.107
(0.184) 		0.0456
(0.0924) 		0.0406
(0.0842) 		1
(1.00) 		0.477
(0.593) 		1
(1.00) 		0.338
(0.458)
8p loss 16 (6%) 272 0.00156
(0.00595) 		0.32
(0.44) 		0.238
(0.353) 		0.699
(0.789) 		0.00445
(0.0141) 		0.00965
(0.0259) 		0.901
(0.958) 		0.758
(0.843) 		0.371
(0.49) 		0.312
(0.434)
2p gain 42 (15%) 246 1e-05
(6.98e-05) 		0.0074
(0.0206) 		0.825
(0.902) 		0.0524
(0.102) 		0.135
(0.223) 		0.901
(0.958) 		0.12
(0.202) 		0.0725
(0.134) 		0.788
(0.869) 		0.168
(0.27)
9p gain 3 (1%) 285 0.874
(0.936) 		0.0998
(0.175) 		0.036
(0.076) 		0.413
(0.532) 		0.37
(0.49) 		0.3
(0.423) 		0.0134
(0.033)
10p gain 9 (3%) 279 0.00077
(0.00315) 		0.0329
(0.071) 		1
(1.00) 		0.342
(0.46) 		0.092
(0.163) 		0.359
(0.478) 		0.145
(0.237) 		0.682
(0.779) 		0.893
(0.952) 		0.187
(0.294)
10q gain 9 (3%) 279 0.00124
(0.0048) 		0.0339
(0.0728) 		1
(1.00) 		0.341
(0.46) 		0.0907
(0.162) 		0.357
(0.477) 		0.141
(0.233) 		0.684
(0.78) 		0.893
(0.952) 		0.188
(0.294)
15q gain 5 (2%) 283 0.00021
(0.000965) 		0.0198
(0.0458) 		0.203
(0.311) 		0.188
(0.294) 		0.219
(0.331) 		0.263
(0.382) 		0.453
(0.571) 		0.767
(0.851)
1q loss 21 (7%) 267 0.00023
(0.00105) 		0.724
(0.813) 		0.943
(0.987) 		0.259
(0.378) 		0.056
(0.108) 		0.00755
(0.0208) 		0.297
(0.421) 		0.0845
(0.154) 		0.57
(0.681) 		0.197
(0.304)
2p loss 5 (2%) 283 0.28
(0.401) 		0.00979
(0.0262) 		0.174
(0.276) 		0.616
(0.725) 		0.0162
(0.0391) 		0.0754
(0.14) 		0.241
(0.356) 		0.868
(0.932)
8p gain 20 (7%) 268 0.749
(0.836) 		0.0104
(0.0272) 		0.134
(0.223) 		0.289
(0.411) 		0.0989
(0.174) 		0.0822
(0.151) 		0.456
(0.573) 		0.539
(0.649) 		0.406
(0.524) 		0.242
(0.358)
18p gain 12 (4%) 276 0.00258
(0.00892) 		0.201
(0.309) 		0.592
(0.703) 		0.966
(1.00) 		0.559
(0.67) 		0.483
(0.597) 		0.191
(0.297) 		0.513
(0.629) 		0.466
(0.582) 		0.606
(0.716)
18q gain 9 (3%) 279 0.00306
(0.0102) 		0.0929
(0.164) 		0.341
(0.46) 		0.852
(0.922) 		0.578
(0.688) 		0.159
(0.257) 		0.4
(0.521) 		0.447
(0.568) 		0.32
(0.44) 		0.0821
(0.151)
22q gain 5 (2%) 283 0.00873
(0.0238) 		0.729
(0.817) 		1
(1.00) 		0.363
(0.482) 		0.863
(0.93) 		0.716
(0.805) 		0.453
(0.571) 		0.301
(0.423) 		0.868
(0.932) 		1
(1.00)
2q loss 3 (1%) 285 0.661
(0.762) 		0.106
(0.183) 		0.102
(0.177) 		0.0367
(0.0774) 		0.529
(0.642) 		1
(1.00)
21q loss 43 (15%) 245 0.00042
(0.0018) 		0.458
(0.574) 		0.199
(0.306) 		0.359
(0.478) 		0.187
(0.294) 		0.417
(0.535) 		0.627
(0.734) 		0.219
(0.331) 		0.809
(0.89) 		0.0869
(0.157)
4p gain 10 (3%) 278 0.244
(0.36) 		0.811
(0.89) 		0.699
(0.789) 		0.341
(0.46) 		0.327
(0.448) 		0.686
(0.781) 		0.617
(0.725) 		0.922
(0.97) 		0.836
(0.912) 		0.95
(0.99)
4q gain 9 (3%) 279 0.517
(0.633) 		0.811
(0.89) 		0.698
(0.789) 		0.342
(0.46) 		0.53
(0.642) 		0.739
(0.826) 		0.278
(0.398) 		0.856
(0.925) 		0.493
(0.609) 		1
(1.00)
13q gain 28 (10%) 260 0.223
(0.336) 		0.964
(1.00) 		0.916
(0.967) 		0.967
(1.00) 		0.184
(0.29) 		0.775
(0.858) 		0.879
(0.94) 		0.464
(0.581) 		0.32
(0.44) 		0.521
(0.634)
21q gain 19 (7%) 269 0.516
(0.632) 		0.153
(0.248) 		0.678
(0.776) 		0.704
(0.793) 		0.111
(0.189) 		0.95
(0.99) 		0.147
(0.241) 		0.218
(0.331) 		0.508
(0.625) 		0.142
(0.233)
'1p gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00018

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
1P GAIN MUTATED 1 0 0 8
1P GAIN WILD-TYPE 113 76 46 44

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

'1p gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00018

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
1P GAIN MUTATED 1 8 0
1P GAIN WILD-TYPE 81 63 119

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

'1p gain' versus 'MRNASEQ_CNMF'

P value = 0.00313 (Fisher's exact test), Q value = 0.01

Table S3.  Gene #1: '1p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
1P GAIN MUTATED 0 0 1 8
1P GAIN WILD-TYPE 34 96 65 84

Figure S3.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00334 (Fisher's exact test), Q value = 0.011

Table S4.  Gene #1: '1p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
1P GAIN MUTATED 5 0 4
1P GAIN WILD-TYPE 113 123 43

Figure S4.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0486 (Fisher's exact test), Q value = 0.097

Table S5.  Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 81 71
1P GAIN MUTATED 1 1 6
1P GAIN WILD-TYPE 68 80 65

Figure S5.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0288 (Fisher's exact test), Q value = 0.064

Table S6.  Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
1P GAIN MUTATED 2 3 3 0
1P GAIN WILD-TYPE 96 74 13 30

Figure S6.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
1Q GAIN MUTATED 4 1 0 12
1Q GAIN WILD-TYPE 110 75 46 40

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

'1q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
1Q GAIN MUTATED 3 13 0
1Q GAIN WILD-TYPE 79 58 119

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

'1q gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00018

Table S9.  Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
1Q GAIN MUTATED 0 0 3 14
1Q GAIN WILD-TYPE 34 96 63 78

Figure S9.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00083

Table S10.  Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
1Q GAIN MUTATED 12 0 5
1Q GAIN WILD-TYPE 106 123 42

Figure S10.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.0018

Table S11.  Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 66 81 86
1Q GAIN MUTATED 8 0 1 8
1Q GAIN WILD-TYPE 47 66 80 78

Figure S11.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00656 (Fisher's exact test), Q value = 0.019

Table S12.  Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 81 71
1Q GAIN MUTATED 4 1 10
1Q GAIN WILD-TYPE 65 80 61

Figure S12.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.029

Table S13.  Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
1Q GAIN MUTATED 4 7 4 0
1Q GAIN WILD-TYPE 94 70 12 30

Figure S13.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S14.  Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
2P GAIN MUTATED 1 3 14 24
2P GAIN WILD-TYPE 113 73 32 28

Figure S14.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p gain' versus 'METHLYATION_CNMF'

P value = 0.0074 (Fisher's exact test), Q value = 0.021

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
2P GAIN MUTATED 4 14 21
2P GAIN WILD-TYPE 78 57 98

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

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S16.  Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
2Q GAIN MUTATED 1 4 15 27
2Q GAIN WILD-TYPE 113 72 31 25

Figure S16.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 0.00745 (Fisher's exact test), Q value = 0.021

Table S17.  Gene #4: '2q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
2Q GAIN MUTATED 5 15 24
2Q GAIN WILD-TYPE 77 56 95

Figure S17.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00696 (Fisher's exact test), Q value = 0.02

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 22 41 35 26 39 26
2Q GAIN MUTATED 6 3 6 6 10 2 2
2Q GAIN WILD-TYPE 11 19 35 29 16 37 24

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

'3p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S19.  Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
3P GAIN MUTATED 11 8 45 10
3P GAIN WILD-TYPE 103 68 1 42

Figure S19.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

'3p gain' versus 'METHLYATION_CNMF'

P value = 0.002 (Fisher's exact test), Q value = 0.0073

Table S20.  Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
3P GAIN MUTATED 20 8 40
3P GAIN WILD-TYPE 62 63 79

Figure S20.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 9e-04

Table S21.  Gene #5: '3p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 22 41 35 26 39 26
3P GAIN MUTATED 11 9 12 7 1 7 4
3P GAIN WILD-TYPE 6 13 29 28 25 32 22

Figure S21.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S22.  Gene #5: '3p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
3P GAIN MUTATED 13 30 25 6
3P GAIN WILD-TYPE 21 66 41 86

Figure S22.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00218 (Fisher's exact test), Q value = 0.0078

Table S23.  Gene #5: '3p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
3P GAIN MUTATED 26 43 5
3P GAIN WILD-TYPE 92 80 42

Figure S23.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_CNMF'

P value = 0.0397 (Fisher's exact test), Q value = 0.083

Table S24.  Gene #5: '3p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 103 96
3P GAIN MUTATED 26 32 16
3P GAIN WILD-TYPE 63 71 80

Figure S24.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00054

Table S25.  Gene #5: '3p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 66 81 86
3P GAIN MUTATED 10 18 35 11
3P GAIN WILD-TYPE 45 48 46 75

Figure S25.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0144 (Fisher's exact test), Q value = 0.035

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
3P GAIN MUTATED 31 9 3 7
3P GAIN WILD-TYPE 67 68 13 23

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

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
3Q GAIN MUTATED 20 14 45 15
3Q GAIN WILD-TYPE 94 62 1 37

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

'3q gain' versus 'METHLYATION_CNMF'

P value = 0.0047 (Fisher's exact test), Q value = 0.015

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
3Q GAIN MUTATED 24 14 50
3Q GAIN WILD-TYPE 58 57 69

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

'3q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00963 (Fisher's exact test), Q value = 0.026

Table S29.  Gene #6: '3q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 22 41 35 26 39 26
3Q GAIN MUTATED 12 9 15 9 5 9 6
3Q GAIN WILD-TYPE 5 13 26 26 21 30 20

Figure S29.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S30.  Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
3Q GAIN MUTATED 18 35 31 10
3Q GAIN WILD-TYPE 16 61 35 82

Figure S30.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00379 (Fisher's exact test), Q value = 0.012

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
3Q GAIN MUTATED 34 52 8
3Q GAIN WILD-TYPE 84 71 39

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

'3q gain' versus 'MIRSEQ_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.027

Table S32.  Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 103 96
3Q GAIN MUTATED 38 35 21
3Q GAIN WILD-TYPE 51 68 75

Figure S32.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00083

Table S33.  Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 66 81 86
3Q GAIN MUTATED 18 19 41 16
3Q GAIN WILD-TYPE 37 47 40 70

Figure S33.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0131 (Fisher's exact test), Q value = 0.032

Table S34.  Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
3Q GAIN MUTATED 41 17 3 6
3Q GAIN WILD-TYPE 57 60 13 24

Figure S34.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S35.  Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
5P GAIN MUTATED 13 3 0 17
5P GAIN WILD-TYPE 101 73 46 35

Figure S35.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.00716 (Fisher's exact test), Q value = 0.02

Table S36.  Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
5P GAIN MUTATED 10 14 6
5P GAIN WILD-TYPE 72 57 113

Figure S36.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 0.0184 (Fisher's exact test), Q value = 0.044

Table S37.  Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
5P GAIN MUTATED 4 5 6 18
5P GAIN WILD-TYPE 30 91 60 74

Figure S37.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00058

Table S38.  Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
5P GAIN MUTATED 23 4 6
5P GAIN WILD-TYPE 95 119 41

Figure S38.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S39.  Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
5Q GAIN MUTATED 14 1 0 16
5Q GAIN WILD-TYPE 100 75 46 36

Figure S39.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 0.00092 (Fisher's exact test), Q value = 0.0037

Table S40.  Gene #10: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
5Q GAIN MUTATED 10 14 4
5Q GAIN WILD-TYPE 72 57 115

Figure S40.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.00507 (Fisher's exact test), Q value = 0.016

Table S41.  Gene #10: '5q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
5Q GAIN MUTATED 4 3 7 17
5Q GAIN WILD-TYPE 30 93 59 75

Figure S41.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 4e-04

Table S42.  Gene #10: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
5Q GAIN MUTATED 23 3 5
5Q GAIN WILD-TYPE 95 120 42

Figure S42.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 0.048 (Fisher's exact test), Q value = 0.096

Table S43.  Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
6P GAIN MUTATED 4 1 0 5
6P GAIN WILD-TYPE 110 75 46 47

Figure S43.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 0.00367 (Fisher's exact test), Q value = 0.012

Table S44.  Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
6P GAIN MUTATED 1 7 1
6P GAIN WILD-TYPE 81 64 118

Figure S44.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 0.00201 (Fisher's exact test), Q value = 0.0073

Table S45.  Gene #11: '6p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
6P GAIN MUTATED 0 1 0 9
6P GAIN WILD-TYPE 34 95 66 83

Figure S45.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6q gain' versus 'CN_CNMF'

P value = 0.0227 (Fisher's exact test), Q value = 0.051

Table S46.  Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
6Q GAIN MUTATED 2 1 0 5
6Q GAIN WILD-TYPE 112 75 46 47

Figure S46.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 0.00183 (Fisher's exact test), Q value = 0.0068

Table S47.  Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
6Q GAIN MUTATED 0 6 1
6Q GAIN WILD-TYPE 82 65 118

Figure S47.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q gain' versus 'MRNASEQ_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.032

Table S48.  Gene #12: '6q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
6Q GAIN MUTATED 0 1 0 7
6Q GAIN WILD-TYPE 34 95 66 85

Figure S48.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S49.  Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
7P GAIN MUTATED 32 73 43 24
7P GAIN WILD-TYPE 82 3 3 28

Figure S49.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S50.  Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
7P GAIN MUTATED 38 23 101
7P GAIN WILD-TYPE 44 48 18

Figure S50.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 0.00616 (Fisher's exact test), Q value = 0.018

Table S51.  Gene #13: '7p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 86 47
7P GAIN MUTATED 45 61 20
7P GAIN WILD-TYPE 28 25 27

Figure S51.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'7p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S52.  Gene #13: '7p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 22 41 35 26 39 26
7P GAIN MUTATED 14 17 39 15 10 18 13
7P GAIN WILD-TYPE 3 5 2 20 16 21 13

Figure S52.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S53.  Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
7P GAIN MUTATED 29 82 39 22
7P GAIN WILD-TYPE 5 14 27 70

Figure S53.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S54.  Gene #13: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
7P GAIN MUTATED 53 103 16
7P GAIN WILD-TYPE 65 20 31

Figure S54.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.0495 (Fisher's exact test), Q value = 0.098

Table S55.  Gene #13: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 103 96
7P GAIN MUTATED 45 70 57
7P GAIN WILD-TYPE 44 33 39

Figure S55.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S56.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 66 81 86
7P GAIN MUTATED 21 39 67 45
7P GAIN WILD-TYPE 34 27 14 41

Figure S56.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00076

Table S57.  Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 81 71
7P GAIN MUTATED 32 62 34
7P GAIN WILD-TYPE 37 19 37

Figure S57.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S58.  Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
7P GAIN MUTATED 65 33 4 26
7P GAIN WILD-TYPE 33 44 12 4

Figure S58.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S59.  Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
7Q GAIN MUTATED 32 73 43 25
7Q GAIN WILD-TYPE 82 3 3 27

Figure S59.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S60.  Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
7Q GAIN MUTATED 38 24 101
7Q GAIN WILD-TYPE 44 47 18

Figure S60.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'RPPA_CNMF'

P value = 0.0131 (Fisher's exact test), Q value = 0.032

Table S61.  Gene #14: '7q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 86 47
7Q GAIN MUTATED 45 61 21
7Q GAIN WILD-TYPE 28 25 26

Figure S61.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'7q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S62.  Gene #14: '7q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 22 41 35 26 39 26
7Q GAIN MUTATED 14 17 39 15 11 18 13
7Q GAIN WILD-TYPE 3 5 2 20 15 21 13

Figure S62.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S63.  Gene #14: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
7Q GAIN MUTATED 29 82 39 23
7Q GAIN WILD-TYPE 5 14 27 69

Figure S63.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S64.  Gene #14: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
7Q GAIN MUTATED 54 103 16
7Q GAIN WILD-TYPE 64 20 31

Figure S64.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S65.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 66 81 86
7Q GAIN MUTATED 22 39 67 45
7Q GAIN WILD-TYPE 33 27 14 41

Figure S65.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00071

Table S66.  Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 81 71
7Q GAIN MUTATED 33 62 34
7Q GAIN WILD-TYPE 36 19 37

Figure S66.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00018

Table S67.  Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
7Q GAIN MUTATED 65 34 4 26
7Q GAIN WILD-TYPE 33 43 12 4

Figure S67.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.027

Table S68.  Gene #15: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
8P GAIN MUTATED 3 11 5
8P GAIN WILD-TYPE 79 60 114

Figure S68.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00058

Table S69.  Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
8Q GAIN MUTATED 2 15 6
8Q GAIN WILD-TYPE 80 56 113

Figure S69.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.032

Table S70.  Gene #16: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
8Q GAIN MUTATED 0 6 4 15
8Q GAIN WILD-TYPE 34 90 62 77

Figure S70.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0447 (Fisher's exact test), Q value = 0.091

Table S71.  Gene #16: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
8Q GAIN MUTATED 14 5 6
8Q GAIN WILD-TYPE 104 118 41

Figure S71.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.046 (Fisher's exact test), Q value = 0.093

Table S72.  Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 81 71
8Q GAIN MUTATED 4 7 13
8Q GAIN WILD-TYPE 65 74 58

Figure S72.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.036 (Fisher's exact test), Q value = 0.076

Table S73.  Gene #17: '9p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
9P GAIN MUTATED 1 0 2
9P GAIN WILD-TYPE 117 123 45

Figure S73.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0134 (Fisher's exact test), Q value = 0.033

Table S74.  Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
9P GAIN MUTATED 0 1 2 0
9P GAIN WILD-TYPE 98 76 14 30

Figure S74.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.0031

Table S75.  Gene #18: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
10P GAIN MUTATED 0 2 1 6
10P GAIN WILD-TYPE 114 74 45 46

Figure S75.  Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 0.0329 (Fisher's exact test), Q value = 0.071

Table S76.  Gene #18: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
10P GAIN MUTATED 1 5 1
10P GAIN WILD-TYPE 81 66 118

Figure S76.  Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q gain' versus 'CN_CNMF'

P value = 0.00124 (Fisher's exact test), Q value = 0.0048

Table S77.  Gene #19: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
10Q GAIN MUTATED 0 2 1 6
10Q GAIN WILD-TYPE 114 74 45 46

Figure S77.  Get High-res Image Gene #19: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

'10q gain' versus 'METHLYATION_CNMF'

P value = 0.0339 (Fisher's exact test), Q value = 0.073

Table S78.  Gene #19: '10q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
10Q GAIN MUTATED 1 5 1
10Q GAIN WILD-TYPE 81 66 118

Figure S78.  Get High-res Image Gene #19: '10q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0014

Table S79.  Gene #20: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
11P GAIN MUTATED 2 1 0 8
11P GAIN WILD-TYPE 112 75 46 44

Figure S79.  Get High-res Image Gene #20: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 0.02 (Fisher's exact test), Q value = 0.046

Table S80.  Gene #20: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
11P GAIN MUTATED 3 6 1
11P GAIN WILD-TYPE 79 65 118

Figure S80.  Get High-res Image Gene #20: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 0.027

Table S81.  Gene #20: '11p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 22 41 35 26 39 26
11P GAIN MUTATED 0 0 0 3 2 0 4
11P GAIN WILD-TYPE 17 22 41 32 24 39 22

Figure S81.  Get High-res Image Gene #20: '11p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.0014

Table S82.  Gene #20: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
11P GAIN MUTATED 5 0 6
11P GAIN WILD-TYPE 113 123 41

Figure S82.  Get High-res Image Gene #20: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S83.  Gene #21: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
11Q GAIN MUTATED 1 0 0 9
11Q GAIN WILD-TYPE 113 76 46 43

Figure S83.  Get High-res Image Gene #21: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 0.00311 (Fisher's exact test), Q value = 0.01

Table S84.  Gene #21: '11q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
11Q GAIN MUTATED 1 7 1
11Q GAIN WILD-TYPE 81 64 118

Figure S84.  Get High-res Image Gene #21: '11q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.016 (Fisher's exact test), Q value = 0.039

Table S85.  Gene #21: '11q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 22 41 35 26 39 26
11Q GAIN MUTATED 0 0 0 3 3 0 3
11Q GAIN WILD-TYPE 17 22 41 32 23 39 23

Figure S85.  Get High-res Image Gene #21: '11q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 0.0214 (Fisher's exact test), Q value = 0.049

Table S86.  Gene #21: '11q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
11Q GAIN MUTATED 0 1 1 8
11Q GAIN WILD-TYPE 34 95 65 84

Figure S86.  Get High-res Image Gene #21: '11q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00373 (Fisher's exact test), Q value = 0.012

Table S87.  Gene #21: '11q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
11Q GAIN MUTATED 6 0 4
11Q GAIN WILD-TYPE 112 123 43

Figure S87.  Get High-res Image Gene #21: '11q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 0.00551 (Fisher's exact test), Q value = 0.017

Table S88.  Gene #22: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
12P GAIN MUTATED 31 33 25 23
12P GAIN WILD-TYPE 83 43 21 29

Figure S88.  Get High-res Image Gene #22: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'RPPA_CNMF'

P value = 0.0259 (Fisher's exact test), Q value = 0.058

Table S89.  Gene #22: '12p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 86 47
12P GAIN MUTATED 37 30 13
12P GAIN WILD-TYPE 36 56 34

Figure S89.  Get High-res Image Gene #22: '12p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00097

Table S90.  Gene #22: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
12P GAIN MUTATED 21 40 30 21
12P GAIN WILD-TYPE 13 56 36 71

Figure S90.  Get High-res Image Gene #22: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0167 (Fisher's exact test), Q value = 0.04

Table S91.  Gene #22: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 66 81 86
12P GAIN MUTATED 26 24 39 23
12P GAIN WILD-TYPE 29 42 42 63

Figure S91.  Get High-res Image Gene #22: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 0.00518 (Fisher's exact test), Q value = 0.016

Table S92.  Gene #23: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
12Q GAIN MUTATED 31 33 25 23
12Q GAIN WILD-TYPE 83 43 21 29

Figure S92.  Get High-res Image Gene #23: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'RPPA_CNMF'

P value = 0.0262 (Fisher's exact test), Q value = 0.058

Table S93.  Gene #23: '12q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 86 47
12Q GAIN MUTATED 37 30 13
12Q GAIN WILD-TYPE 36 56 34

Figure S93.  Get High-res Image Gene #23: '12q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00079

Table S94.  Gene #23: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
12Q GAIN MUTATED 21 40 30 21
12Q GAIN WILD-TYPE 13 56 36 71

Figure S94.  Get High-res Image Gene #23: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0169 (Fisher's exact test), Q value = 0.04

Table S95.  Gene #23: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 66 81 86
12Q GAIN MUTATED 26 24 39 23
12Q GAIN WILD-TYPE 29 42 42 63

Figure S95.  Get High-res Image Gene #23: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'METHLYATION_CNMF'

P value = 0.0167 (Fisher's exact test), Q value = 0.04

Table S96.  Gene #25: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
14Q GAIN MUTATED 0 3 0
14Q GAIN WILD-TYPE 82 68 119

Figure S96.  Get High-res Image Gene #25: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0358 (Fisher's exact test), Q value = 0.076

Table S97.  Gene #25: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
14Q GAIN MUTATED 1 0 2
14Q GAIN WILD-TYPE 117 123 45

Figure S97.  Get High-res Image Gene #25: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0136 (Fisher's exact test), Q value = 0.034

Table S98.  Gene #25: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
14Q GAIN MUTATED 0 1 2 0
14Q GAIN WILD-TYPE 98 76 14 30

Figure S98.  Get High-res Image Gene #25: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q gain' versus 'CN_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00097

Table S99.  Gene #26: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
15Q GAIN MUTATED 0 0 0 5
15Q GAIN WILD-TYPE 114 76 46 47

Figure S99.  Get High-res Image Gene #26: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

'15q gain' versus 'METHLYATION_CNMF'

P value = 0.0198 (Fisher's exact test), Q value = 0.046

Table S100.  Gene #26: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
15Q GAIN MUTATED 0 4 1
15Q GAIN WILD-TYPE 82 67 118

Figure S100.  Get High-res Image Gene #26: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S101.  Gene #27: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
16P GAIN MUTATED 49 36 46 22
16P GAIN WILD-TYPE 65 40 0 30

Figure S101.  Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.029

Table S102.  Gene #27: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
16P GAIN MUTATED 37 33 76
16P GAIN WILD-TYPE 45 38 43

Figure S102.  Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.014 (Fisher's exact test), Q value = 0.034

Table S103.  Gene #27: '16p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 22 41 35 26 39 26
16P GAIN MUTATED 13 14 23 16 8 26 10
16P GAIN WILD-TYPE 4 8 18 19 18 13 16

Figure S103.  Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S104.  Gene #27: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
16P GAIN MUTATED 18 57 50 28
16P GAIN WILD-TYPE 16 39 16 64

Figure S104.  Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00023

Table S105.  Gene #27: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
16P GAIN MUTATED 68 74 11
16P GAIN WILD-TYPE 50 49 36

Figure S105.  Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 0.00068 (Fisher's exact test), Q value = 0.0028

Table S106.  Gene #27: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 103 96
16P GAIN MUTATED 51 66 36
16P GAIN WILD-TYPE 38 37 60

Figure S106.  Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S107.  Gene #27: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 66 81 86
16P GAIN MUTATED 24 39 61 29
16P GAIN WILD-TYPE 31 27 20 57

Figure S107.  Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00926 (Fisher's exact test), Q value = 0.025

Table S108.  Gene #27: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 81 71
16P GAIN MUTATED 41 47 26
16P GAIN WILD-TYPE 28 34 45

Figure S108.  Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00079

Table S109.  Gene #27: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
16P GAIN MUTATED 67 30 5 12
16P GAIN WILD-TYPE 31 47 11 18

Figure S109.  Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S110.  Gene #28: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
16Q GAIN MUTATED 49 35 46 18
16Q GAIN WILD-TYPE 65 41 0 34

Figure S110.  Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 0.00664 (Fisher's exact test), Q value = 0.019

Table S111.  Gene #28: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
16Q GAIN MUTATED 37 30 75
16Q GAIN WILD-TYPE 45 41 44

Figure S111.  Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0213 (Fisher's exact test), Q value = 0.049

Table S112.  Gene #28: '16q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 22 41 35 26 39 26
16Q GAIN MUTATED 13 14 23 17 8 24 9
16Q GAIN WILD-TYPE 4 8 18 18 18 15 17

Figure S112.  Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S113.  Gene #28: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
16Q GAIN MUTATED 18 56 50 24
16Q GAIN WILD-TYPE 16 40 16 68

Figure S113.  Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00049

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
16Q GAIN MUTATED 64 73 11
16Q GAIN WILD-TYPE 54 50 36

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

'16q gain' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00018

Table S115.  Gene #28: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 103 96
16Q GAIN MUTATED 49 67 32
16Q GAIN WILD-TYPE 40 36 64

Figure S115.  Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S116.  Gene #28: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 66 81 86
16Q GAIN MUTATED 19 40 61 28
16Q GAIN WILD-TYPE 36 26 20 58

Figure S116.  Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00279 (Fisher's exact test), Q value = 0.0095

Table S117.  Gene #28: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 81 71
16Q GAIN MUTATED 40 46 23
16Q GAIN WILD-TYPE 29 35 48

Figure S117.  Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00018

Table S118.  Gene #28: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
16Q GAIN MUTATED 67 26 5 11
16Q GAIN WILD-TYPE 31 51 11 19

Figure S118.  Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S119.  Gene #29: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
17P GAIN MUTATED 29 75 45 25
17P GAIN WILD-TYPE 85 1 1 27

Figure S119.  Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S120.  Gene #29: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
17P GAIN MUTATED 37 22 105
17P GAIN WILD-TYPE 45 49 14

Figure S120.  Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'RPPA_CNMF'

P value = 0.00302 (Fisher's exact test), Q value = 0.01

Table S121.  Gene #29: '17p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 86 47
17P GAIN MUTATED 48 60 19
17P GAIN WILD-TYPE 25 26 28

Figure S121.  Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'17p gain' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00018

Table S122.  Gene #29: '17p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 22 41 35 26 39 26
17P GAIN MUTATED 14 17 37 18 9 17 15
17P GAIN WILD-TYPE 3 5 4 17 17 22 11

Figure S122.  Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S123.  Gene #29: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
17P GAIN MUTATED 23 87 41 23
17P GAIN WILD-TYPE 11 9 25 69

Figure S123.  Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S124.  Gene #29: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
17P GAIN MUTATED 55 108 11
17P GAIN WILD-TYPE 63 15 36

Figure S124.  Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CNMF'

P value = 0.00394 (Fisher's exact test), Q value = 0.013

Table S125.  Gene #29: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 103 96
17P GAIN MUTATED 45 75 54
17P GAIN WILD-TYPE 44 28 42

Figure S125.  Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S126.  Gene #29: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 66 81 86
17P GAIN MUTATED 20 40 67 47
17P GAIN WILD-TYPE 35 26 14 39

Figure S126.  Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S127.  Gene #29: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 81 71
17P GAIN MUTATED 32 66 30
17P GAIN WILD-TYPE 37 15 41

Figure S127.  Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S128.  Gene #29: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
17P GAIN MUTATED 67 30 4 27
17P GAIN WILD-TYPE 31 47 12 3

Figure S128.  Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S129.  Gene #30: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
17Q GAIN MUTATED 38 75 45 33
17Q GAIN WILD-TYPE 76 1 1 19

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

'17q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S130.  Gene #30: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
17Q GAIN MUTATED 42 33 105
17Q GAIN WILD-TYPE 40 38 14

Figure S130.  Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'RPPA_CNMF'

P value = 0.0305 (Fisher's exact test), Q value = 0.066

Table S131.  Gene #30: '17q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 86 47
17Q GAIN MUTATED 53 62 24
17Q GAIN WILD-TYPE 20 24 23

Figure S131.  Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'17q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S132.  Gene #30: '17q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 22 41 35 26 39 26
17Q GAIN MUTATED 15 20 37 20 11 20 16
17Q GAIN WILD-TYPE 2 2 4 15 15 19 10

Figure S132.  Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S133.  Gene #30: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
17Q GAIN MUTATED 24 87 44 36
17Q GAIN WILD-TYPE 10 9 22 56

Figure S133.  Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S134.  Gene #30: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
17Q GAIN MUTATED 68 108 15
17Q GAIN WILD-TYPE 50 15 32

Figure S134.  Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 0.0349 (Fisher's exact test), Q value = 0.074

Table S135.  Gene #30: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 103 96
17Q GAIN MUTATED 53 78 60
17Q GAIN WILD-TYPE 36 25 36

Figure S135.  Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00023

Table S136.  Gene #30: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 66 81 86
17Q GAIN MUTATED 26 45 69 51
17Q GAIN WILD-TYPE 29 21 12 35

Figure S136.  Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00067

Table S137.  Gene #30: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 81 71
17Q GAIN MUTATED 38 66 38
17Q GAIN WILD-TYPE 31 15 33

Figure S137.  Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S138.  Gene #30: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
17Q GAIN MUTATED 70 40 5 27
17Q GAIN WILD-TYPE 28 37 11 3

Figure S138.  Get High-res Image Gene #30: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 0.00258 (Fisher's exact test), Q value = 0.0089

Table S139.  Gene #31: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
18P GAIN MUTATED 0 4 5 3
18P GAIN WILD-TYPE 114 72 41 49

Figure S139.  Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18q gain' versus 'CN_CNMF'

P value = 0.00306 (Fisher's exact test), Q value = 0.01

Table S140.  Gene #32: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
18Q GAIN MUTATED 0 3 5 1
18Q GAIN WILD-TYPE 114 73 41 51

Figure S140.  Get High-res Image Gene #32: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 0.0015 (Fisher's exact test), Q value = 0.0058

Table S141.  Gene #33: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
19P GAIN MUTATED 0 0 0 4
19P GAIN WILD-TYPE 114 76 46 48

Figure S141.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 0.046 (Fisher's exact test), Q value = 0.093

Table S142.  Gene #33: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
19P GAIN MUTATED 0 0 0 4
19P GAIN WILD-TYPE 34 96 66 88

Figure S142.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0411 (Fisher's exact test), Q value = 0.085

Table S143.  Gene #33: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
19P GAIN MUTATED 2 0 2
19P GAIN WILD-TYPE 116 123 45

Figure S143.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 0.00135 (Fisher's exact test), Q value = 0.0052

Table S144.  Gene #34: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
19Q GAIN MUTATED 0 0 0 4
19Q GAIN WILD-TYPE 114 76 46 48

Figure S144.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 0.0456 (Fisher's exact test), Q value = 0.092

Table S145.  Gene #34: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
19Q GAIN MUTATED 0 0 0 4
19Q GAIN WILD-TYPE 34 96 66 88

Figure S145.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0406 (Fisher's exact test), Q value = 0.084

Table S146.  Gene #34: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
19Q GAIN MUTATED 2 0 2
19Q GAIN WILD-TYPE 116 123 45

Figure S146.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00018

Table S147.  Gene #35: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
20P GAIN MUTATED 21 31 24 23
20P GAIN WILD-TYPE 93 45 22 29

Figure S147.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.0202 (Fisher's exact test), Q value = 0.047

Table S148.  Gene #35: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
20P GAIN MUTATED 19 23 50
20P GAIN WILD-TYPE 63 48 69

Figure S148.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'RPPA_CNMF'

P value = 0.0245 (Fisher's exact test), Q value = 0.055

Table S149.  Gene #35: '20p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 86 47
20P GAIN MUTATED 22 36 9
20P GAIN WILD-TYPE 51 50 38

Figure S149.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'20p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00563 (Fisher's exact test), Q value = 0.017

Table S150.  Gene #35: '20p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 22 41 35 26 39 26
20P GAIN MUTATED 8 6 22 12 7 5 7
20P GAIN WILD-TYPE 9 16 19 23 19 34 19

Figure S150.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 0.00487 (Fisher's exact test), Q value = 0.015

Table S151.  Gene #35: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
20P GAIN MUTATED 9 46 22 22
20P GAIN WILD-TYPE 25 50 44 70

Figure S151.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0223 (Fisher's exact test), Q value = 0.05

Table S152.  Gene #35: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
20P GAIN MUTATED 35 53 11
20P GAIN WILD-TYPE 83 70 36

Figure S152.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 0.0116 (Fisher's exact test), Q value = 0.03

Table S153.  Gene #35: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 103 96
20P GAIN MUTATED 24 47 28
20P GAIN WILD-TYPE 65 56 68

Figure S153.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00322 (Fisher's exact test), Q value = 0.011

Table S154.  Gene #35: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 66 81 86
20P GAIN MUTATED 13 21 41 24
20P GAIN WILD-TYPE 42 45 40 62

Figure S154.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00087

Table S155.  Gene #36: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
20Q GAIN MUTATED 23 32 23 23
20Q GAIN WILD-TYPE 91 44 23 29

Figure S155.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 0.0204 (Fisher's exact test), Q value = 0.047

Table S156.  Gene #36: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
20Q GAIN MUTATED 19 24 50
20Q GAIN WILD-TYPE 63 47 69

Figure S156.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 0.0355 (Fisher's exact test), Q value = 0.075

Table S157.  Gene #36: '20q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 86 47
20Q GAIN MUTATED 23 35 9
20Q GAIN WILD-TYPE 50 51 38

Figure S157.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0099 (Fisher's exact test), Q value = 0.026

Table S158.  Gene #36: '20q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 22 41 35 26 39 26
20Q GAIN MUTATED 7 6 22 12 8 5 7
20Q GAIN WILD-TYPE 10 16 19 23 18 34 19

Figure S158.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.029

Table S159.  Gene #36: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
20Q GAIN MUTATED 9 46 22 24
20Q GAIN WILD-TYPE 25 50 44 68

Figure S159.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0499 (Fisher's exact test), Q value = 0.098

Table S160.  Gene #36: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
20Q GAIN MUTATED 35 53 13
20Q GAIN WILD-TYPE 83 70 34

Figure S160.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 0.0189 (Fisher's exact test), Q value = 0.044

Table S161.  Gene #36: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 103 96
20Q GAIN MUTATED 24 47 30
20Q GAIN WILD-TYPE 65 56 66

Figure S161.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.006 (Fisher's exact test), Q value = 0.018

Table S162.  Gene #36: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 66 81 86
20Q GAIN MUTATED 13 21 41 26
20Q GAIN WILD-TYPE 42 45 40 60

Figure S162.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0434 (Fisher's exact test), Q value = 0.089

Table S163.  Gene #36: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
20Q GAIN MUTATED 38 17 7 13
20Q GAIN WILD-TYPE 60 60 9 17

Figure S163.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 0.00873 (Fisher's exact test), Q value = 0.024

Table S164.  Gene #38: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
22Q GAIN MUTATED 0 0 2 3
22Q GAIN WILD-TYPE 114 76 44 49

Figure S164.  Get High-res Image Gene #38: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

'xp gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S165.  Gene #39: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
XP GAIN MUTATED 6 30 39 12
XP GAIN WILD-TYPE 108 46 7 40

Figure S165.  Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

'xp gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S166.  Gene #39: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
XP GAIN MUTATED 14 12 54
XP GAIN WILD-TYPE 68 59 65

Figure S166.  Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0182 (Fisher's exact test), Q value = 0.043

Table S167.  Gene #39: 'xp gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 22 41 35 26 39 26
XP GAIN MUTATED 8 10 17 9 3 8 5
XP GAIN WILD-TYPE 9 12 24 26 23 31 21

Figure S167.  Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'xp gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S168.  Gene #39: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
XP GAIN MUTATED 8 45 28 6
XP GAIN WILD-TYPE 26 51 38 86

Figure S168.  Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00023

Table S169.  Gene #39: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
XP GAIN MUTATED 27 55 5
XP GAIN WILD-TYPE 91 68 42

Figure S169.  Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_CNMF'

P value = 0.00849 (Fisher's exact test), Q value = 0.023

Table S170.  Gene #39: 'xp gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 103 96
XP GAIN MUTATED 25 42 20
XP GAIN WILD-TYPE 64 61 76

Figure S170.  Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xp gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S171.  Gene #39: 'xp gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 66 81 86
XP GAIN MUTATED 7 21 43 16
XP GAIN WILD-TYPE 48 45 38 70

Figure S171.  Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00216 (Fisher's exact test), Q value = 0.0078

Table S172.  Gene #39: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 81 71
XP GAIN MUTATED 20 30 9
XP GAIN WILD-TYPE 49 51 62

Figure S172.  Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xp gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00065 (Fisher's exact test), Q value = 0.0027

Table S173.  Gene #39: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
XP GAIN MUTATED 36 9 3 11
XP GAIN WILD-TYPE 62 68 13 19

Figure S173.  Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S174.  Gene #40: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
XQ GAIN MUTATED 7 31 39 14
XQ GAIN WILD-TYPE 107 45 7 38

Figure S174.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00018

Table S175.  Gene #40: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
XQ GAIN MUTATED 14 14 55
XQ GAIN WILD-TYPE 68 57 64

Figure S175.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.031 (Fisher's exact test), Q value = 0.067

Table S176.  Gene #40: 'xq gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 22 41 35 26 39 26
XQ GAIN MUTATED 8 10 17 9 3 8 7
XQ GAIN WILD-TYPE 9 12 24 26 23 31 19

Figure S176.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S177.  Gene #40: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
XQ GAIN MUTATED 8 46 28 9
XQ GAIN WILD-TYPE 26 50 38 83

Figure S177.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00018

Table S178.  Gene #40: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
XQ GAIN MUTATED 29 56 6
XQ GAIN WILD-TYPE 89 67 41

Figure S178.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_CNMF'

P value = 0.00991 (Fisher's exact test), Q value = 0.026

Table S179.  Gene #40: 'xq gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 103 96
XQ GAIN MUTATED 27 43 21
XQ GAIN WILD-TYPE 62 60 75

Figure S179.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xq gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S180.  Gene #40: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 66 81 86
XQ GAIN MUTATED 8 23 43 17
XQ GAIN WILD-TYPE 47 43 38 69

Figure S180.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.027

Table S181.  Gene #40: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 81 71
XQ GAIN MUTATED 20 30 11
XQ GAIN WILD-TYPE 49 51 60

Figure S181.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00376 (Fisher's exact test), Q value = 0.012

Table S182.  Gene #40: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
XQ GAIN MUTATED 36 11 3 11
XQ GAIN WILD-TYPE 62 66 13 19

Figure S182.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S183.  Gene #41: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
1P LOSS MUTATED 13 0 2 15
1P LOSS WILD-TYPE 101 76 44 37

Figure S183.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 0.0298 (Fisher's exact test), Q value = 0.065

Table S184.  Gene #41: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
1P LOSS MUTATED 9 13 7
1P LOSS WILD-TYPE 73 58 112

Figure S184.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00029

Table S185.  Gene #41: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
1P LOSS MUTATED 0 4 5 21
1P LOSS WILD-TYPE 34 92 61 71

Figure S185.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00081 (Fisher's exact test), Q value = 0.0033

Table S186.  Gene #41: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
1P LOSS MUTATED 12 6 12
1P LOSS WILD-TYPE 106 117 35

Figure S186.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0011

Table S187.  Gene #42: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
1Q LOSS MUTATED 9 0 2 10
1Q LOSS WILD-TYPE 105 76 44 42

Figure S187.  Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00755 (Fisher's exact test), Q value = 0.021

Table S188.  Gene #42: '1q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
1Q LOSS MUTATED 6 6 9
1Q LOSS WILD-TYPE 112 117 38

Figure S188.  Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'METHLYATION_CNMF'

P value = 0.00979 (Fisher's exact test), Q value = 0.026

Table S189.  Gene #43: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
2P LOSS MUTATED 1 4 0
2P LOSS WILD-TYPE 81 67 119

Figure S189.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.039

Table S190.  Gene #43: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
2P LOSS MUTATED 0 0 0 5
2P LOSS WILD-TYPE 34 96 66 87

Figure S190.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0367 (Fisher's exact test), Q value = 0.077

Table S191.  Gene #44: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
2Q LOSS MUTATED 1 0 2
2Q LOSS WILD-TYPE 117 123 45

Figure S191.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S192.  Gene #45: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
3P LOSS MUTATED 5 0 0 17
3P LOSS WILD-TYPE 109 76 46 35

Figure S192.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S193.  Gene #45: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
3P LOSS MUTATED 5 15 1
3P LOSS WILD-TYPE 77 56 118

Figure S193.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00211 (Fisher's exact test), Q value = 0.0076

Table S194.  Gene #45: '3p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 22 41 35 26 39 26
3P LOSS MUTATED 0 3 0 3 6 1 5
3P LOSS WILD-TYPE 17 19 41 32 20 38 21

Figure S194.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S195.  Gene #45: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
3P LOSS MUTATED 0 0 4 18
3P LOSS WILD-TYPE 34 96 62 74

Figure S195.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S196.  Gene #45: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
3P LOSS MUTATED 18 0 4
3P LOSS WILD-TYPE 100 123 43

Figure S196.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0265 (Fisher's exact test), Q value = 0.059

Table S197.  Gene #45: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 66 81 86
3P LOSS MUTATED 7 5 1 9
3P LOSS WILD-TYPE 48 61 80 77

Figure S197.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0474 (Fisher's exact test), Q value = 0.095

Table S198.  Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 81 71
3P LOSS MUTATED 9 3 10
3P LOSS WILD-TYPE 60 78 61

Figure S198.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.016 (Fisher's exact test), Q value = 0.039

Table S199.  Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
3P LOSS MUTATED 7 14 1 0
3P LOSS WILD-TYPE 91 63 15 30

Figure S199.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S200.  Gene #46: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
3Q LOSS MUTATED 0 0 0 7
3Q LOSS WILD-TYPE 114 76 46 45

Figure S200.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 0.00184 (Fisher's exact test), Q value = 0.0068

Table S201.  Gene #46: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
3Q LOSS MUTATED 0 6 1
3Q LOSS WILD-TYPE 82 65 118

Figure S201.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 0.0213 (Fisher's exact test), Q value = 0.049

Table S202.  Gene #46: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
3Q LOSS MUTATED 0 0 1 6
3Q LOSS WILD-TYPE 34 96 65 86

Figure S202.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00297 (Fisher's exact test), Q value = 0.01

Table S203.  Gene #46: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
3Q LOSS MUTATED 3 0 4
3Q LOSS WILD-TYPE 115 123 43

Figure S203.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S204.  Gene #47: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
4P LOSS MUTATED 6 0 0 19
4P LOSS WILD-TYPE 108 76 46 33

Figure S204.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S205.  Gene #47: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
4P LOSS MUTATED 5 18 1
4P LOSS WILD-TYPE 77 53 118

Figure S205.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00067

Table S206.  Gene #47: '4p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 22 41 35 26 39 26
4P LOSS MUTATED 0 2 0 4 7 1 7
4P LOSS WILD-TYPE 17 20 41 31 19 38 19

Figure S206.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S207.  Gene #47: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
4P LOSS MUTATED 0 0 1 24
4P LOSS WILD-TYPE 34 96 65 68

Figure S207.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S208.  Gene #47: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
4P LOSS MUTATED 12 1 12
4P LOSS WILD-TYPE 106 122 35

Figure S208.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00586 (Fisher's exact test), Q value = 0.018

Table S209.  Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 81 71
4P LOSS MUTATED 5 2 12
4P LOSS WILD-TYPE 64 79 59

Figure S209.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S210.  Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
4P LOSS MUTATED 4 7 8 0
4P LOSS WILD-TYPE 94 70 8 30

Figure S210.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S211.  Gene #48: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
4Q LOSS MUTATED 6 0 0 20
4Q LOSS WILD-TYPE 108 76 46 32

Figure S211.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S212.  Gene #48: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
4Q LOSS MUTATED 5 19 1
4Q LOSS WILD-TYPE 77 52 118

Figure S212.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.0015

Table S213.  Gene #48: '4q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 22 41 35 26 39 26
4Q LOSS MUTATED 0 2 0 5 6 1 7
4Q LOSS WILD-TYPE 17 20 41 30 20 38 19

Figure S213.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S214.  Gene #48: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
4Q LOSS MUTATED 0 0 1 25
4Q LOSS WILD-TYPE 34 96 65 67

Figure S214.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S215.  Gene #48: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
4Q LOSS MUTATED 14 1 11
4Q LOSS WILD-TYPE 104 122 36

Figure S215.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00672 (Fisher's exact test), Q value = 0.019

Table S216.  Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 81 71
4Q LOSS MUTATED 6 2 12
4Q LOSS WILD-TYPE 63 79 59

Figure S216.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S217.  Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
4Q LOSS MUTATED 4 9 7 0
4Q LOSS WILD-TYPE 94 68 9 30

Figure S217.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'METHLYATION_CNMF'

P value = 0.0488 (Fisher's exact test), Q value = 0.097

Table S218.  Gene #49: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
5P LOSS MUTATED 2 5 1
5P LOSS WILD-TYPE 80 66 118

Figure S218.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00953 (Fisher's exact test), Q value = 0.026

Table S219.  Gene #49: '5p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 22 41 35 26 39 26
5P LOSS MUTATED 0 0 0 1 4 0 1
5P LOSS WILD-TYPE 17 22 41 34 22 39 25

Figure S219.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 0.03 (Fisher's exact test), Q value = 0.065

Table S220.  Gene #49: '5p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
5P LOSS MUTATED 1 0 1 6
5P LOSS WILD-TYPE 33 96 65 86

Figure S220.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.0014

Table S221.  Gene #49: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
5P LOSS MUTATED 1 1 6
5P LOSS WILD-TYPE 117 122 41

Figure S221.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0396 (Fisher's exact test), Q value = 0.083

Table S222.  Gene #49: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 66 81 86
5P LOSS MUTATED 1 1 0 6
5P LOSS WILD-TYPE 54 65 81 80

Figure S222.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0126 (Fisher's exact test), Q value = 0.032

Table S223.  Gene #49: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 81 71
5P LOSS MUTATED 2 0 6
5P LOSS WILD-TYPE 67 81 65

Figure S223.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00063

Table S224.  Gene #49: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
5P LOSS MUTATED 2 1 5 0
5P LOSS WILD-TYPE 96 76 11 30

Figure S224.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'METHLYATION_CNMF'

P value = 0.0487 (Fisher's exact test), Q value = 0.097

Table S225.  Gene #50: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
5Q LOSS MUTATED 2 5 1
5Q LOSS WILD-TYPE 80 66 118

Figure S225.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0101 (Fisher's exact test), Q value = 0.027

Table S226.  Gene #50: '5q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 22 41 35 26 39 26
5Q LOSS MUTATED 0 0 0 1 4 0 1
5Q LOSS WILD-TYPE 17 22 41 34 22 39 25

Figure S226.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 0.0298 (Fisher's exact test), Q value = 0.065

Table S227.  Gene #50: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
5Q LOSS MUTATED 1 0 1 6
5Q LOSS WILD-TYPE 33 96 65 86

Figure S227.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.0011

Table S228.  Gene #50: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
5Q LOSS MUTATED 1 1 6
5Q LOSS WILD-TYPE 117 122 41

Figure S228.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0404 (Fisher's exact test), Q value = 0.084

Table S229.  Gene #50: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 66 81 86
5Q LOSS MUTATED 1 1 0 6
5Q LOSS WILD-TYPE 54 65 81 80

Figure S229.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.031

Table S230.  Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 81 71
5Q LOSS MUTATED 2 0 6
5Q LOSS WILD-TYPE 67 81 65

Figure S230.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S231.  Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
5Q LOSS MUTATED 2 0 6 0
5Q LOSS WILD-TYPE 96 77 10 30

Figure S231.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S232.  Gene #51: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
6P LOSS MUTATED 6 0 1 14
6P LOSS WILD-TYPE 108 76 45 38

Figure S232.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.0449 (Fisher's exact test), Q value = 0.091

Table S233.  Gene #51: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
6P LOSS MUTATED 5 10 5
6P LOSS WILD-TYPE 77 61 114

Figure S233.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 0.00617 (Fisher's exact test), Q value = 0.018

Table S234.  Gene #51: '6p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
6P LOSS MUTATED 0 4 3 14
6P LOSS WILD-TYPE 34 92 63 78

Figure S234.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.0012

Table S235.  Gene #51: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
6P LOSS MUTATED 6 4 11
6P LOSS WILD-TYPE 112 119 36

Figure S235.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CNMF'

P value = 0.0196 (Fisher's exact test), Q value = 0.046

Table S236.  Gene #51: '6p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 103 96
6P LOSS MUTATED 2 13 6
6P LOSS WILD-TYPE 87 90 90

Figure S236.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S237.  Gene #52: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
6Q LOSS MUTATED 7 0 1 18
6Q LOSS WILD-TYPE 107 76 45 34

Figure S237.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.0023 (Fisher's exact test), Q value = 0.0081

Table S238.  Gene #52: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
6Q LOSS MUTATED 8 13 4
6Q LOSS WILD-TYPE 74 58 115

Figure S238.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00087

Table S239.  Gene #52: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
6Q LOSS MUTATED 0 3 5 18
6Q LOSS WILD-TYPE 34 93 61 74

Figure S239.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S240.  Gene #52: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
6Q LOSS MUTATED 11 3 12
6Q LOSS WILD-TYPE 107 120 35

Figure S240.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 0.00156 (Fisher's exact test), Q value = 0.006

Table S241.  Gene #53: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
8P LOSS MUTATED 5 2 0 9
8P LOSS WILD-TYPE 109 74 46 43

Figure S241.  Get High-res Image Gene #53: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 0.00445 (Fisher's exact test), Q value = 0.014

Table S242.  Gene #53: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
8P LOSS MUTATED 1 2 1 12
8P LOSS WILD-TYPE 33 94 65 80

Figure S242.  Get High-res Image Gene #53: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00965 (Fisher's exact test), Q value = 0.026

Table S243.  Gene #53: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
8P LOSS MUTATED 6 3 7
8P LOSS WILD-TYPE 112 120 40

Figure S243.  Get High-res Image Gene #53: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 0.00239 (Fisher's exact test), Q value = 0.0083

Table S244.  Gene #54: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
8Q LOSS MUTATED 3 0 0 6
8Q LOSS WILD-TYPE 111 76 46 46

Figure S244.  Get High-res Image Gene #54: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0465 (Fisher's exact test), Q value = 0.094

Table S245.  Gene #54: '8q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 22 41 35 26 39 26
8Q LOSS MUTATED 0 0 0 3 0 0 2
8Q LOSS WILD-TYPE 17 22 41 32 26 39 24

Figure S245.  Get High-res Image Gene #54: '8q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 0.0125 (Fisher's exact test), Q value = 0.032

Table S246.  Gene #54: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
8Q LOSS MUTATED 1 0 1 7
8Q LOSS WILD-TYPE 33 96 65 85

Figure S246.  Get High-res Image Gene #54: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-04 (Fisher's exact test), Q value = 0.0036

Table S247.  Gene #54: '8q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
8Q LOSS MUTATED 2 1 6
8Q LOSS WILD-TYPE 116 122 41

Figure S247.  Get High-res Image Gene #54: '8q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S248.  Gene #55: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
9P LOSS MUTATED 9 0 1 23
9P LOSS WILD-TYPE 105 76 45 29

Figure S248.  Get High-res Image Gene #55: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S249.  Gene #55: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
9P LOSS MUTATED 11 18 1
9P LOSS WILD-TYPE 71 53 118

Figure S249.  Get High-res Image Gene #55: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0016 (Fisher's exact test), Q value = 0.0061

Table S250.  Gene #55: '9p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 22 41 35 26 39 26
9P LOSS MUTATED 0 3 0 6 6 3 7
9P LOSS WILD-TYPE 17 19 41 29 20 36 19

Figure S250.  Get High-res Image Gene #55: '9p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S251.  Gene #55: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
9P LOSS MUTATED 1 0 3 29
9P LOSS WILD-TYPE 33 96 63 63

Figure S251.  Get High-res Image Gene #55: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S252.  Gene #55: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
9P LOSS MUTATED 19 0 14
9P LOSS WILD-TYPE 99 123 33

Figure S252.  Get High-res Image Gene #55: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 0.00595 (Fisher's exact test), Q value = 0.018

Table S253.  Gene #55: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 103 96
9P LOSS MUTATED 3 14 16
9P LOSS WILD-TYPE 86 89 80

Figure S253.  Get High-res Image Gene #55: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00569 (Fisher's exact test), Q value = 0.017

Table S254.  Gene #55: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 81 71
9P LOSS MUTATED 8 4 16
9P LOSS WILD-TYPE 61 77 55

Figure S254.  Get High-res Image Gene #55: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00077 (Fisher's exact test), Q value = 0.0031

Table S255.  Gene #55: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
9P LOSS MUTATED 7 17 4 0
9P LOSS WILD-TYPE 91 60 12 30

Figure S255.  Get High-res Image Gene #55: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S256.  Gene #56: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
9Q LOSS MUTATED 11 1 1 21
9Q LOSS WILD-TYPE 103 75 45 31

Figure S256.  Get High-res Image Gene #56: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S257.  Gene #56: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
9Q LOSS MUTATED 12 18 1
9Q LOSS WILD-TYPE 70 53 118

Figure S257.  Get High-res Image Gene #56: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00174 (Fisher's exact test), Q value = 0.0065

Table S258.  Gene #56: '9q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 22 41 35 26 39 26
9Q LOSS MUTATED 0 3 0 6 5 4 8
9Q LOSS WILD-TYPE 17 19 41 29 21 35 18

Figure S258.  Get High-res Image Gene #56: '9q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S259.  Gene #56: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
9Q LOSS MUTATED 1 0 3 30
9Q LOSS WILD-TYPE 33 96 63 62

Figure S259.  Get High-res Image Gene #56: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S260.  Gene #56: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
9Q LOSS MUTATED 17 0 17
9Q LOSS WILD-TYPE 101 123 30

Figure S260.  Get High-res Image Gene #56: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 0.00434 (Fisher's exact test), Q value = 0.014

Table S261.  Gene #56: '9q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 103 96
9Q LOSS MUTATED 3 14 17
9Q LOSS WILD-TYPE 86 89 79

Figure S261.  Get High-res Image Gene #56: '9q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00095 (Fisher's exact test), Q value = 0.0038

Table S262.  Gene #56: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 81 71
9Q LOSS MUTATED 8 4 18
9Q LOSS WILD-TYPE 61 77 53

Figure S262.  Get High-res Image Gene #56: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 9e-04

Table S263.  Gene #56: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
9Q LOSS MUTATED 8 15 7 0
9Q LOSS WILD-TYPE 90 62 9 30

Figure S263.  Get High-res Image Gene #56: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S264.  Gene #57: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
10P LOSS MUTATED 3 0 0 13
10P LOSS WILD-TYPE 111 76 46 39

Figure S264.  Get High-res Image Gene #57: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00079

Table S265.  Gene #57: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
10P LOSS MUTATED 1 11 2
10P LOSS WILD-TYPE 81 60 117

Figure S265.  Get High-res Image Gene #57: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.025 (Fisher's exact test), Q value = 0.056

Table S266.  Gene #57: '10p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 22 41 35 26 39 26
10P LOSS MUTATED 1 0 0 3 3 0 3
10P LOSS WILD-TYPE 16 22 41 32 23 39 23

Figure S266.  Get High-res Image Gene #57: '10p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0014

Table S267.  Gene #57: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
10P LOSS MUTATED 0 1 2 13
10P LOSS WILD-TYPE 34 95 64 79

Figure S267.  Get High-res Image Gene #57: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.003 (Fisher's exact test), Q value = 0.01

Table S268.  Gene #57: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
10P LOSS MUTATED 10 1 5
10P LOSS WILD-TYPE 108 122 42

Figure S268.  Get High-res Image Gene #57: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0197 (Fisher's exact test), Q value = 0.046

Table S269.  Gene #57: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 81 71
10P LOSS MUTATED 2 1 8
10P LOSS WILD-TYPE 67 80 63

Figure S269.  Get High-res Image Gene #57: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00663 (Fisher's exact test), Q value = 0.019

Table S270.  Gene #57: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
10P LOSS MUTATED 1 9 1 0
10P LOSS WILD-TYPE 97 68 15 30

Figure S270.  Get High-res Image Gene #57: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S271.  Gene #58: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
10Q LOSS MUTATED 3 0 0 14
10Q LOSS WILD-TYPE 111 76 46 38

Figure S271.  Get High-res Image Gene #58: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 9e-04

Table S272.  Gene #58: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
10Q LOSS MUTATED 2 12 2
10Q LOSS WILD-TYPE 80 59 117

Figure S272.  Get High-res Image Gene #58: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00483 (Fisher's exact test), Q value = 0.015

Table S273.  Gene #58: '10q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 22 41 35 26 39 26
10Q LOSS MUTATED 1 0 0 3 4 0 4
10Q LOSS WILD-TYPE 16 22 41 32 22 39 22

Figure S273.  Get High-res Image Gene #58: '10q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00097

Table S274.  Gene #58: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
10Q LOSS MUTATED 0 1 2 14
10Q LOSS WILD-TYPE 34 95 64 78

Figure S274.  Get High-res Image Gene #58: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00208 (Fisher's exact test), Q value = 0.0075

Table S275.  Gene #58: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
10Q LOSS MUTATED 12 1 4
10Q LOSS WILD-TYPE 106 122 43

Figure S275.  Get High-res Image Gene #58: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00183 (Fisher's exact test), Q value = 0.0068

Table S276.  Gene #58: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 81 71
10Q LOSS MUTATED 2 1 10
10Q LOSS WILD-TYPE 67 80 61

Figure S276.  Get High-res Image Gene #58: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00116 (Fisher's exact test), Q value = 0.0045

Table S277.  Gene #58: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
10Q LOSS MUTATED 1 11 1 0
10Q LOSS WILD-TYPE 97 66 15 30

Figure S277.  Get High-res Image Gene #58: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S278.  Gene #59: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
11P LOSS MUTATED 5 1 0 12
11P LOSS WILD-TYPE 109 75 46 40

Figure S278.  Get High-res Image Gene #59: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.003

Table S279.  Gene #59: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
11P LOSS MUTATED 4 11 2
11P LOSS WILD-TYPE 78 60 117

Figure S279.  Get High-res Image Gene #59: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00034

Table S280.  Gene #59: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
11P LOSS MUTATED 0 1 2 15
11P LOSS WILD-TYPE 34 95 64 77

Figure S280.  Get High-res Image Gene #59: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0028 (Fisher's exact test), Q value = 0.0095

Table S281.  Gene #59: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
11P LOSS MUTATED 9 2 7
11P LOSS WILD-TYPE 109 121 40

Figure S281.  Get High-res Image Gene #59: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0197 (Fisher's exact test), Q value = 0.046

Table S282.  Gene #59: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 81 71
11P LOSS MUTATED 4 2 10
11P LOSS WILD-TYPE 65 79 61

Figure S282.  Get High-res Image Gene #59: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0069 (Fisher's exact test), Q value = 0.02

Table S283.  Gene #59: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
11P LOSS MUTATED 3 10 3 0
11P LOSS WILD-TYPE 95 67 13 30

Figure S283.  Get High-res Image Gene #59: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S284.  Gene #60: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
11Q LOSS MUTATED 5 0 0 16
11Q LOSS WILD-TYPE 109 76 46 36

Figure S284.  Get High-res Image Gene #60: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00034

Table S285.  Gene #60: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
11Q LOSS MUTATED 5 14 2
11Q LOSS WILD-TYPE 77 57 117

Figure S285.  Get High-res Image Gene #60: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0295 (Fisher's exact test), Q value = 0.065

Table S286.  Gene #60: '11q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 22 41 35 26 39 26
11Q LOSS MUTATED 1 2 0 2 4 3 6
11Q LOSS WILD-TYPE 16 20 41 33 22 36 20

Figure S286.  Get High-res Image Gene #60: '11q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00071

Table S287.  Gene #60: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
11Q LOSS MUTATED 1 1 3 16
11Q LOSS WILD-TYPE 33 95 63 76

Figure S287.  Get High-res Image Gene #60: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00236 (Fisher's exact test), Q value = 0.0082

Table S288.  Gene #60: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
11Q LOSS MUTATED 13 2 6
11Q LOSS WILD-TYPE 105 121 41

Figure S288.  Get High-res Image Gene #60: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.037 (Fisher's exact test), Q value = 0.078

Table S289.  Gene #60: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 81 71
11Q LOSS MUTATED 5 3 11
11Q LOSS WILD-TYPE 64 78 60

Figure S289.  Get High-res Image Gene #60: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0389 (Fisher's exact test), Q value = 0.082

Table S290.  Gene #60: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
11Q LOSS MUTATED 6 12 1 0
11Q LOSS WILD-TYPE 92 65 15 30

Figure S290.  Get High-res Image Gene #60: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S291.  Gene #61: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
13Q LOSS MUTATED 6 0 1 17
13Q LOSS WILD-TYPE 108 76 45 35

Figure S291.  Get High-res Image Gene #61: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00044

Table S292.  Gene #61: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
13Q LOSS MUTATED 5 15 3
13Q LOSS WILD-TYPE 77 56 116

Figure S292.  Get High-res Image Gene #61: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S293.  Gene #61: '13q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 22 41 35 26 39 26
13Q LOSS MUTATED 2 2 0 2 10 1 4
13Q LOSS WILD-TYPE 15 20 41 33 16 38 22

Figure S293.  Get High-res Image Gene #61: '13q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S294.  Gene #61: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
13Q LOSS MUTATED 0 2 0 22
13Q LOSS WILD-TYPE 34 94 66 70

Figure S294.  Get High-res Image Gene #61: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S295.  Gene #61: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
13Q LOSS MUTATED 8 2 14
13Q LOSS WILD-TYPE 110 121 33

Figure S295.  Get High-res Image Gene #61: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 0.0427 (Fisher's exact test), Q value = 0.088

Table S296.  Gene #61: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 103 96
13Q LOSS MUTATED 3 8 13
13Q LOSS WILD-TYPE 86 95 83

Figure S296.  Get High-res Image Gene #61: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00745 (Fisher's exact test), Q value = 0.021

Table S297.  Gene #61: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 66 81 86
13Q LOSS MUTATED 0 4 7 13
13Q LOSS WILD-TYPE 55 62 74 73

Figure S297.  Get High-res Image Gene #61: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00379 (Fisher's exact test), Q value = 0.012

Table S298.  Gene #61: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 81 71
13Q LOSS MUTATED 3 3 13
13Q LOSS WILD-TYPE 66 78 58

Figure S298.  Get High-res Image Gene #61: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S299.  Gene #61: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
13Q LOSS MUTATED 4 8 7 0
13Q LOSS WILD-TYPE 94 69 9 30

Figure S299.  Get High-res Image Gene #61: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S300.  Gene #62: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
14Q LOSS MUTATED 18 0 1 28
14Q LOSS WILD-TYPE 96 76 45 24

Figure S300.  Get High-res Image Gene #62: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00097

Table S301.  Gene #62: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
14Q LOSS MUTATED 18 18 7
14Q LOSS WILD-TYPE 64 53 112

Figure S301.  Get High-res Image Gene #62: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.038

Table S302.  Gene #62: '14q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 86 47
14Q LOSS MUTATED 19 10 4
14Q LOSS WILD-TYPE 54 76 43

Figure S302.  Get High-res Image Gene #62: '14q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'14q loss' versus 'RPPA_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 4e-04

Table S303.  Gene #62: '14q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 22 41 35 26 39 26
14Q LOSS MUTATED 3 4 1 6 9 1 9
14Q LOSS WILD-TYPE 14 18 40 29 17 38 17

Figure S303.  Get High-res Image Gene #62: '14q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S304.  Gene #62: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
14Q LOSS MUTATED 3 4 9 31
14Q LOSS WILD-TYPE 31 92 57 61

Figure S304.  Get High-res Image Gene #62: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S305.  Gene #62: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
14Q LOSS MUTATED 22 6 19
14Q LOSS WILD-TYPE 96 117 28

Figure S305.  Get High-res Image Gene #62: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00449 (Fisher's exact test), Q value = 0.014

Table S306.  Gene #62: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 81 71
14Q LOSS MUTATED 9 7 20
14Q LOSS WILD-TYPE 60 74 51

Figure S306.  Get High-res Image Gene #62: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00647 (Fisher's exact test), Q value = 0.019

Table S307.  Gene #62: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
14Q LOSS MUTATED 11 20 4 1
14Q LOSS WILD-TYPE 87 57 12 29

Figure S307.  Get High-res Image Gene #62: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S308.  Gene #63: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
15Q LOSS MUTATED 11 0 3 17
15Q LOSS WILD-TYPE 103 76 43 35

Figure S308.  Get High-res Image Gene #63: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.00235 (Fisher's exact test), Q value = 0.0082

Table S309.  Gene #63: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
15Q LOSS MUTATED 11 14 5
15Q LOSS WILD-TYPE 71 57 114

Figure S309.  Get High-res Image Gene #63: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00162 (Fisher's exact test), Q value = 0.0061

Table S310.  Gene #63: '15q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 22 41 35 26 39 26
15Q LOSS MUTATED 2 1 0 5 6 3 8
15Q LOSS WILD-TYPE 15 21 41 30 20 36 18

Figure S310.  Get High-res Image Gene #63: '15q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00058

Table S311.  Gene #63: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
15Q LOSS MUTATED 1 3 6 21
15Q LOSS WILD-TYPE 33 93 60 71

Figure S311.  Get High-res Image Gene #63: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S312.  Gene #63: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
15Q LOSS MUTATED 12 4 15
15Q LOSS WILD-TYPE 106 119 32

Figure S312.  Get High-res Image Gene #63: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00268 (Fisher's exact test), Q value = 0.0092

Table S313.  Gene #63: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
15Q LOSS MUTATED 9 10 6 0
15Q LOSS WILD-TYPE 89 67 10 30

Figure S313.  Get High-res Image Gene #63: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 0.0423 (Fisher's exact test), Q value = 0.087

Table S314.  Gene #64: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
16P LOSS MUTATED 1 0 0 3
16P LOSS WILD-TYPE 113 76 46 49

Figure S314.  Get High-res Image Gene #64: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 0.0338 (Fisher's exact test), Q value = 0.073

Table S315.  Gene #64: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
16P LOSS MUTATED 1 3 0
16P LOSS WILD-TYPE 81 68 119

Figure S315.  Get High-res Image Gene #64: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 0.0439 (Fisher's exact test), Q value = 0.09

Table S316.  Gene #64: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
16P LOSS MUTATED 0 0 0 4
16P LOSS WILD-TYPE 34 96 66 88

Figure S316.  Get High-res Image Gene #64: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00686 (Fisher's exact test), Q value = 0.02

Table S317.  Gene #64: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
16P LOSS MUTATED 1 0 3
16P LOSS WILD-TYPE 117 123 44

Figure S317.  Get High-res Image Gene #64: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0127 (Fisher's exact test), Q value = 0.032

Table S318.  Gene #64: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
16P LOSS MUTATED 0 2 2 0
16P LOSS WILD-TYPE 98 75 14 30

Figure S318.  Get High-res Image Gene #64: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0016

Table S319.  Gene #65: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
16Q LOSS MUTATED 1 0 0 6
16Q LOSS WILD-TYPE 113 76 46 46

Figure S319.  Get High-res Image Gene #65: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 0.00725 (Fisher's exact test), Q value = 0.02

Table S320.  Gene #65: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
16Q LOSS MUTATED 2 5 0
16Q LOSS WILD-TYPE 80 66 119

Figure S320.  Get High-res Image Gene #65: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 0.00221 (Fisher's exact test), Q value = 0.0079

Table S321.  Gene #65: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
16Q LOSS MUTATED 0 0 0 7
16Q LOSS WILD-TYPE 34 96 66 85

Figure S321.  Get High-res Image Gene #65: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0129 (Fisher's exact test), Q value = 0.032

Table S322.  Gene #65: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
16Q LOSS MUTATED 4 0 3
16Q LOSS WILD-TYPE 114 123 44

Figure S322.  Get High-res Image Gene #65: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0324 (Fisher's exact test), Q value = 0.07

Table S323.  Gene #65: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 81 71
16Q LOSS MUTATED 2 0 5
16Q LOSS WILD-TYPE 67 81 66

Figure S323.  Get High-res Image Gene #65: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 0.00423 (Fisher's exact test), Q value = 0.013

Table S324.  Gene #66: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
17P LOSS MUTATED 6 0 0 6
17P LOSS WILD-TYPE 108 76 46 46

Figure S324.  Get High-res Image Gene #66: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0014

Table S325.  Gene #66: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
17P LOSS MUTATED 3 8 0
17P LOSS WILD-TYPE 79 63 119

Figure S325.  Get High-res Image Gene #66: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S326.  Gene #66: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
17P LOSS MUTATED 0 0 0 12
17P LOSS WILD-TYPE 34 96 66 80

Figure S326.  Get High-res Image Gene #66: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.00097

Table S327.  Gene #66: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
17P LOSS MUTATED 6 0 6
17P LOSS WILD-TYPE 112 123 41

Figure S327.  Get High-res Image Gene #66: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00609 (Fisher's exact test), Q value = 0.018

Table S328.  Gene #66: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 81 71
17P LOSS MUTATED 3 0 7
17P LOSS WILD-TYPE 66 81 64

Figure S328.  Get High-res Image Gene #66: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00121 (Fisher's exact test), Q value = 0.0047

Table S329.  Gene #66: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
17P LOSS MUTATED 1 5 4 0
17P LOSS WILD-TYPE 97 72 12 30

Figure S329.  Get High-res Image Gene #66: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S330.  Gene #67: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
18P LOSS MUTATED 17 5 1 19
18P LOSS WILD-TYPE 97 71 45 33

Figure S330.  Get High-res Image Gene #67: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S331.  Gene #67: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
18P LOSS MUTATED 11 23 6
18P LOSS WILD-TYPE 71 48 113

Figure S331.  Get High-res Image Gene #67: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00053 (Fisher's exact test), Q value = 0.0022

Table S332.  Gene #67: '18p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 22 41 35 26 39 26
18P LOSS MUTATED 1 4 0 3 9 7 7
18P LOSS WILD-TYPE 16 18 41 32 17 32 19

Figure S332.  Get High-res Image Gene #67: '18p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S333.  Gene #67: '18p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
18P LOSS MUTATED 2 2 7 31
18P LOSS WILD-TYPE 32 94 59 61

Figure S333.  Get High-res Image Gene #67: '18p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S334.  Gene #67: '18p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
18P LOSS MUTATED 24 3 15
18P LOSS WILD-TYPE 94 120 32

Figure S334.  Get High-res Image Gene #67: '18p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00085 (Fisher's exact test), Q value = 0.0034

Table S335.  Gene #67: '18p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 66 81 86
18P LOSS MUTATED 6 13 3 20
18P LOSS WILD-TYPE 49 53 78 66

Figure S335.  Get High-res Image Gene #67: '18p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0197 (Fisher's exact test), Q value = 0.046

Table S336.  Gene #67: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 81 71
18P LOSS MUTATED 10 8 19
18P LOSS WILD-TYPE 59 73 52

Figure S336.  Get High-res Image Gene #67: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00079 (Fisher's exact test), Q value = 0.0032

Table S337.  Gene #67: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
18P LOSS MUTATED 12 16 8 1
18P LOSS WILD-TYPE 86 61 8 29

Figure S337.  Get High-res Image Gene #67: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S338.  Gene #68: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
18Q LOSS MUTATED 18 4 1 22
18Q LOSS WILD-TYPE 96 72 45 30

Figure S338.  Get High-res Image Gene #68: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S339.  Gene #68: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
18Q LOSS MUTATED 12 26 5
18Q LOSS WILD-TYPE 70 45 114

Figure S339.  Get High-res Image Gene #68: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S340.  Gene #68: '18q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 22 41 35 26 39 26
18Q LOSS MUTATED 1 4 0 3 11 7 8
18Q LOSS WILD-TYPE 16 18 41 32 15 32 18

Figure S340.  Get High-res Image Gene #68: '18q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S341.  Gene #68: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
18Q LOSS MUTATED 2 1 7 35
18Q LOSS WILD-TYPE 32 95 59 57

Figure S341.  Get High-res Image Gene #68: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S342.  Gene #68: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
18Q LOSS MUTATED 28 3 14
18Q LOSS WILD-TYPE 90 120 33

Figure S342.  Get High-res Image Gene #68: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-04 (Fisher's exact test), Q value = 0.0029

Table S343.  Gene #68: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 66 81 86
18Q LOSS MUTATED 8 13 3 21
18Q LOSS WILD-TYPE 47 53 78 65

Figure S343.  Get High-res Image Gene #68: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0066 (Fisher's exact test), Q value = 0.019

Table S344.  Gene #68: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 81 71
18Q LOSS MUTATED 11 8 21
18Q LOSS WILD-TYPE 58 73 50

Figure S344.  Get High-res Image Gene #68: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.0012

Table S345.  Gene #68: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
18Q LOSS MUTATED 12 19 8 1
18Q LOSS WILD-TYPE 86 58 8 29

Figure S345.  Get High-res Image Gene #68: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00044

Table S346.  Gene #69: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
19P LOSS MUTATED 3 2 1 11
19P LOSS WILD-TYPE 111 74 45 41

Figure S346.  Get High-res Image Gene #69: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 0.00235 (Fisher's exact test), Q value = 0.0082

Table S347.  Gene #69: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
19P LOSS MUTATED 3 11 3
19P LOSS WILD-TYPE 79 60 116

Figure S347.  Get High-res Image Gene #69: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0342 (Fisher's exact test), Q value = 0.073

Table S348.  Gene #69: '19p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 22 41 35 26 39 26
19P LOSS MUTATED 1 1 0 3 4 0 1
19P LOSS WILD-TYPE 16 21 41 32 22 39 25

Figure S348.  Get High-res Image Gene #69: '19p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 0.00552 (Fisher's exact test), Q value = 0.017

Table S349.  Gene #69: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
19P LOSS MUTATED 0 1 6 10
19P LOSS WILD-TYPE 34 95 60 82

Figure S349.  Get High-res Image Gene #69: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00629 (Fisher's exact test), Q value = 0.018

Table S350.  Gene #69: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
19P LOSS MUTATED 13 2 2
19P LOSS WILD-TYPE 105 121 45

Figure S350.  Get High-res Image Gene #69: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S351.  Gene #70: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
19Q LOSS MUTATED 1 2 1 12
19Q LOSS WILD-TYPE 113 74 45 40

Figure S351.  Get High-res Image Gene #70: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 0.00488 (Fisher's exact test), Q value = 0.015

Table S352.  Gene #70: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
19Q LOSS MUTATED 3 10 3
19Q LOSS WILD-TYPE 79 61 116

Figure S352.  Get High-res Image Gene #70: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00944 (Fisher's exact test), Q value = 0.026

Table S353.  Gene #70: '19q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 22 41 35 26 39 26
19Q LOSS MUTATED 1 2 0 2 5 0 1
19Q LOSS WILD-TYPE 16 20 41 33 21 39 25

Figure S353.  Get High-res Image Gene #70: '19q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 0.00499 (Fisher's exact test), Q value = 0.015

Table S354.  Gene #70: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
19Q LOSS MUTATED 0 1 4 11
19Q LOSS WILD-TYPE 34 95 62 81

Figure S354.  Get High-res Image Gene #70: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0226 (Fisher's exact test), Q value = 0.051

Table S355.  Gene #70: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
19Q LOSS MUTATED 11 2 3
19Q LOSS WILD-TYPE 107 121 44

Figure S355.  Get High-res Image Gene #70: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.0018

Table S356.  Gene #71: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
21Q LOSS MUTATED 12 6 7 18
21Q LOSS WILD-TYPE 102 70 39 34

Figure S356.  Get High-res Image Gene #71: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S357.  Gene #72: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
22Q LOSS MUTATED 22 5 2 31
22Q LOSS WILD-TYPE 92 71 44 21

Figure S357.  Get High-res Image Gene #72: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S358.  Gene #72: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
22Q LOSS MUTATED 13 34 10
22Q LOSS WILD-TYPE 69 37 109

Figure S358.  Get High-res Image Gene #72: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00104 (Fisher's exact test), Q value = 0.0041

Table S359.  Gene #72: '22q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 22 41 35 26 39 26
22Q LOSS MUTATED 1 3 2 10 12 9 8
22Q LOSS WILD-TYPE 16 19 39 25 14 30 18

Figure S359.  Get High-res Image Gene #72: '22q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S360.  Gene #72: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
22Q LOSS MUTATED 0 6 12 42
22Q LOSS WILD-TYPE 34 90 54 50

Figure S360.  Get High-res Image Gene #72: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S361.  Gene #72: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
22Q LOSS MUTATED 35 8 17
22Q LOSS WILD-TYPE 83 115 30

Figure S361.  Get High-res Image Gene #72: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0108 (Fisher's exact test), Q value = 0.028

Table S362.  Gene #72: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
22Q LOSS MUTATED 21 21 6 1
22Q LOSS WILD-TYPE 77 56 10 29

Figure S362.  Get High-res Image Gene #72: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S363.  Gene #73: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
XP LOSS MUTATED 10 2 2 20
XP LOSS WILD-TYPE 104 74 44 32

Figure S363.  Get High-res Image Gene #73: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S364.  Gene #73: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
XP LOSS MUTATED 8 19 4
XP LOSS WILD-TYPE 74 52 115

Figure S364.  Get High-res Image Gene #73: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00194 (Fisher's exact test), Q value = 0.0071

Table S365.  Gene #73: 'xp loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 22 41 35 26 39 26
XP LOSS MUTATED 0 1 2 4 7 1 7
XP LOSS WILD-TYPE 17 21 39 31 19 38 19

Figure S365.  Get High-res Image Gene #73: 'xp loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'xp loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S366.  Gene #73: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
XP LOSS MUTATED 0 3 4 27
XP LOSS WILD-TYPE 34 93 62 65

Figure S366.  Get High-res Image Gene #73: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00044

Table S367.  Gene #73: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
XP LOSS MUTATED 19 4 11
XP LOSS WILD-TYPE 99 119 36

Figure S367.  Get High-res Image Gene #73: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0183 (Fisher's exact test), Q value = 0.043

Table S368.  Gene #73: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 81 71
XP LOSS MUTATED 8 4 14
XP LOSS WILD-TYPE 61 77 57

Figure S368.  Get High-res Image Gene #73: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xp loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00728 (Fisher's exact test), Q value = 0.02

Table S369.  Gene #73: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
XP LOSS MUTATED 6 16 3 1
XP LOSS WILD-TYPE 92 61 13 29

Figure S369.  Get High-res Image Gene #73: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S370.  Gene #74: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
XQ LOSS MUTATED 9 1 2 18
XQ LOSS WILD-TYPE 105 75 44 34

Figure S370.  Get High-res Image Gene #74: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S371.  Gene #74: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 82 71 119
XQ LOSS MUTATED 8 17 3
XQ LOSS WILD-TYPE 74 54 116

Figure S371.  Get High-res Image Gene #74: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0106 (Fisher's exact test), Q value = 0.028

Table S372.  Gene #74: 'xq loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 22 41 35 26 39 26
XQ LOSS MUTATED 0 1 2 4 7 1 5
XQ LOSS WILD-TYPE 17 21 39 31 19 38 21

Figure S372.  Get High-res Image Gene #74: 'xq loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 7e-05

Table S373.  Gene #74: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 96 66 92
XQ LOSS MUTATED 0 2 4 24
XQ LOSS WILD-TYPE 34 94 62 68

Figure S373.  Get High-res Image Gene #74: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00049

Table S374.  Gene #74: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 123 47
XQ LOSS MUTATED 17 3 10
XQ LOSS WILD-TYPE 101 120 37

Figure S374.  Get High-res Image Gene #74: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0499 (Fisher's exact test), Q value = 0.098

Table S375.  Gene #74: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 81 71
XQ LOSS MUTATED 8 4 12
XQ LOSS WILD-TYPE 61 77 59

Figure S375.  Get High-res Image Gene #74: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0214 (Fisher's exact test), Q value = 0.049

Table S376.  Gene #74: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
XQ LOSS MUTATED 6 14 3 1
XQ LOSS WILD-TYPE 92 63 13 29

Figure S376.  Get High-res Image Gene #74: 'xq loss' versus Molecular Subtype #10: '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/KIRP-TP/15087099/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIRP-TP/15098835/KIRP-TP.transferedmergedcluster.txt

  • Number of patients = 288

  • Number of significantly arm-level cnvs = 74

  • Number of molecular subtypes = 10

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

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

Download Results

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

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