Correlation between copy number variations of arm-level result and molecular subtypes
Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1X065WF
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 80 arm-level events and 12 molecular subtypes across 524 patients, 377 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 1q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

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

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

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

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

  • 4p gain cnv correlated to 'CN_CNMF'.

  • 5p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • 7p gain cnv correlated to 'CN_CNMF'.

  • 7q gain cnv correlated to 'CN_CNMF'.

  • 8p gain cnv correlated to 'CN_CNMF'.

  • 8q gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF', and 'MRNASEQ_CNMF'.

  • 10p gain cnv correlated to 'CN_CNMF'.

  • 10q gain cnv correlated to 'CN_CNMF'.

  • 11p gain cnv correlated to 'CN_CNMF'.

  • 11q gain cnv correlated to 'CN_CNMF'.

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

  • 12q gain cnv correlated to 'CN_CNMF'.

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

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

  • 16p gain cnv correlated to 'CN_CNMF'.

  • 17p gain cnv correlated to 'CN_CNMF'.

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

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

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

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

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

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

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

  • 21q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • xq gain cnv correlated to 'CN_CNMF'.

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

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

  • 2q loss cnv correlated to 'CN_CNMF'.

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

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

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

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

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

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

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

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

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

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

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

  • 8q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

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

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

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

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

  • 12p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 12q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

  • 15q loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

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

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

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

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

  • 20p loss cnv correlated to 'CN_CNMF'.

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

  • 22q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 377 significant findings detected.

Clinical
Features
MRNA
CNMF
MRNA
CHIERARCHICAL
CN
CNMF
METHLYATION
CNMF
RPPA
CNMF
RPPA
CHIERARCHICAL
MRNASEQ
CNMF
MRNASEQ
CHIERARCHICAL
MIRSEQ
CNMF
MIRSEQ
CHIERARCHICAL
MIRSEQ
MATURE
CNMF
MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
8p loss 75 (14%) 449 0.00791
(1.00)
0.00011
(0.0595)
1e-05
(0.00892)
1e-05
(0.00892)
0.034
(1.00)
0.0255
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
5e-05
(0.028)
9q loss 117 (22%) 407 3e-05
(0.017)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
0.0003
(0.156)
0.7
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
0.00185
(0.866)
0.00462
(1.00)
15q loss 106 (20%) 418 0.00062
(0.316)
2e-05
(0.0118)
1e-05
(0.00892)
1e-05
(0.00892)
0.00082
(0.407)
0.487
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
5p gain 49 (9%) 475 0.901
(1.00)
0.219
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
0.0592
(1.00)
0.428
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
2e-05
(0.0118)
0.00016
(0.0856)
18p gain 68 (13%) 456 0.334
(1.00)
0.241
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
0.0127
(1.00)
0.163
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
2e-05
(0.0118)
4p loss 100 (19%) 424 0.00372
(1.00)
0.00137
(0.651)
1e-05
(0.00892)
1e-05
(0.00892)
0.00109
(0.529)
0.186
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
3e-05
(0.017)
2e-05
(0.0118)
4q loss 99 (19%) 425 0.152
(1.00)
0.00524
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
0.0138
(1.00)
0.188
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
2e-05
(0.0118)
11q loss 68 (13%) 456 1e-05
(0.00892)
1e-05
(0.00892)
0.851
(1.00)
0.79
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
0.0003
(0.156)
0.00044
(0.227)
16p loss 94 (18%) 430 0.00182
(0.854)
0.0077
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
0.0934
(1.00)
0.318
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
0.0001
(0.0542)
0.00028
(0.147)
16q loss 135 (26%) 389 0.00086
(0.426)
0.00156
(0.735)
1e-05
(0.00892)
1e-05
(0.00892)
0.343
(1.00)
0.973
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
2e-05
(0.0118)
6e-05
(0.0332)
19p loss 57 (11%) 467 1e-05
(0.00892)
1e-05
(0.00892)
0.0817
(1.00)
0.216
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
3e-05
(0.017)
0.00015
(0.0804)
21q loss 53 (10%) 471 0.00765
(1.00)
0.00497
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
0.128
(1.00)
0.328
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
0.00028
(0.147)
xq loss 69 (13%) 455 0.00785
(1.00)
0.00498
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
0.00017
(0.0904)
0.214
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
0.00071
(0.356)
2e-05
(0.0118)
2p gain 92 (18%) 432 0.855
(1.00)
0.37
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
0.0574
(1.00)
0.24
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
0.00021
(0.111)
0.00107
(0.52)
2q gain 75 (14%) 449 0.341
(1.00)
0.601
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
0.0634
(1.00)
0.134
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
0.00027
(0.142)
0.00262
(1.00)
18q gain 41 (8%) 483 0.253
(1.00)
0.0448
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
0.278
(1.00)
0.095
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
5e-05
(0.028)
0.00466
(1.00)
20p gain 107 (20%) 417 0.00818
(1.00)
0.0499
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
0.163
(1.00)
0.741
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
8e-05
(0.0438)
0.00105
(0.511)
20q gain 125 (24%) 399 0.00212
(0.982)
0.00723
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
0.0325
(1.00)
0.67
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
0.00021
(0.111)
0.00336
(1.00)
22q gain 31 (6%) 493 1e-05
(0.00892)
1e-05
(0.00892)
0.372
(1.00)
0.186
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
0.0161
(1.00)
5q loss 72 (14%) 452 0.013
(1.00)
0.00974
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
0.00129
(0.618)
0.00223
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
2e-05
(0.0118)
0.00068
(0.343)
9p loss 99 (19%) 425 0.001
(0.488)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
0.00406
(1.00)
0.565
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
0.00571
(1.00)
0.033
(1.00)
14q loss 56 (11%) 468 0.00185
(0.866)
0.00056
(0.287)
1e-05
(0.00892)
1e-05
(0.00892)
0.0253
(1.00)
0.075
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
2e-05
(0.0118)
0.00123
(0.59)
17p loss 122 (23%) 402 0.0035
(1.00)
0.00016
(0.0856)
1e-05
(0.00892)
1e-05
(0.00892)
0.00372
(1.00)
0.371
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
0.00065
(0.328)
0.00746
(1.00)
17q loss 88 (17%) 436 0.00215
(0.993)
2e-05
(0.0118)
1e-05
(0.00892)
1e-05
(0.00892)
0.109
(1.00)
0.919
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
0.0123
(1.00)
0.00524
(1.00)
3q gain 78 (15%) 446 0.618
(1.00)
0.25
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
0.105
(1.00)
0.161
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
0.0005
(0.257)
0.00228
(1.00)
6p gain 76 (15%) 448 0.212
(1.00)
0.663
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
0.0994
(1.00)
0.834
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
0.0186
(1.00)
0.0629
(1.00)
13q gain 28 (5%) 496 0.137
(1.00)
0.00635
(1.00)
1e-05
(0.00892)
0.00016
(0.0856)
0.252
(1.00)
0.0113
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
0.0405
(1.00)
0.0847
(1.00)
19p gain 50 (10%) 474 0.0412
(1.00)
0.0302
(1.00)
1e-05
(0.00892)
0.00024
(0.126)
0.908
(1.00)
0.0731
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
2e-05
(0.0118)
0.0623
(1.00)
0.354
(1.00)
19q gain 55 (10%) 469 1e-05
(0.00892)
1e-05
(0.00892)
0.487
(1.00)
0.0439
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
0.00745
(1.00)
0.0802
(1.00)
1p loss 22 (4%) 502 1e-05
(0.00892)
1e-05
(0.00892)
0.787
(1.00)
0.362
(1.00)
5e-05
(0.028)
1e-05
(0.00892)
7e-05
(0.0384)
6e-05
(0.0332)
0.0262
(1.00)
0.0308
(1.00)
1q loss 13 (2%) 511 9e-05
(0.049)
2e-05
(0.0118)
3e-05
(0.017)
7e-05
(0.0384)
5e-05
(0.028)
0.00011
(0.0595)
0.0443
(1.00)
0.0708
(1.00)
3p loss 50 (10%) 474 0.0386
(1.00)
0.0007
(0.351)
1e-05
(0.00892)
1e-05
(0.00892)
0.0217
(1.00)
0.125
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
0.00472
(1.00)
0.00315
(1.00)
3q loss 30 (6%) 494 0.0396
(1.00)
0.00064
(0.324)
1e-05
(0.00892)
0.00011
(0.0595)
0.0656
(1.00)
0.264
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
0.114
(1.00)
0.236
(1.00)
5p loss 54 (10%) 470 0.15
(1.00)
0.114
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
0.00662
(1.00)
0.216
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
0.00262
(1.00)
0.00719
(1.00)
7q loss 41 (8%) 483 1e-05
(0.00892)
1e-05
(0.00892)
0.0469
(1.00)
0.015
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
0.00344
(1.00)
0.00752
(1.00)
8q loss 25 (5%) 499 1e-05
(0.00892)
1e-05
(0.00892)
0.329
(1.00)
0.838
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
0.00202
(0.939)
0.00729
(1.00)
10p loss 40 (8%) 484 0.039
(1.00)
0.0303
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
0.0565
(1.00)
0.185
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
0.00541
(1.00)
0.0274
(1.00)
10q loss 39 (7%) 485 0.137
(1.00)
0.166
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
0.0541
(1.00)
0.169
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
2e-05
(0.0118)
2e-05
(0.0118)
0.0334
(1.00)
0.0568
(1.00)
11p loss 72 (14%) 452 1e-05
(0.00892)
1e-05
(0.00892)
0.299
(1.00)
0.333
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
0.00057
(0.291)
0.00206
(0.956)
12p loss 42 (8%) 482 0.136
(1.00)
0.167
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
0.0418
(1.00)
0.0381
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
0.00136
(0.647)
0.00719
(1.00)
12q loss 34 (6%) 490 1e-05
(0.00892)
1e-05
(0.00892)
0.102
(1.00)
0.0155
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
6e-05
(0.0332)
1e-05
(0.00892)
0.00069
(0.347)
0.00452
(1.00)
13q loss 89 (17%) 435 0.903
(1.00)
0.194
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
0.0247
(1.00)
0.499
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
0.0483
(1.00)
0.0453
(1.00)
18q loss 65 (12%) 459 0.537
(1.00)
0.513
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
0.53
(1.00)
1
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
0.00315
(1.00)
0.00513
(1.00)
19q loss 53 (10%) 471 0.254
(1.00)
0.0179
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
0.196
(1.00)
0.696
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
2e-05
(0.0118)
0.00088
(0.434)
0.00875
(1.00)
22q loss 105 (20%) 419 0.00226
(1.00)
0.00718
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
0.0402
(1.00)
0.28
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
0.0208
(1.00)
0.0442
(1.00)
1p gain 46 (9%) 478 0.535
(1.00)
0.218
(1.00)
1e-05
(0.00892)
0.0012
(0.578)
0.0447
(1.00)
0.263
(1.00)
2e-05
(0.0118)
2e-05
(0.0118)
1e-05
(0.00892)
1e-05
(0.00892)
0.00151
(0.714)
0.00749
(1.00)
17q gain 28 (5%) 496 1e-05
(0.00892)
2e-05
(0.0118)
0.0415
(1.00)
1
(1.00)
0.00014
(0.0752)
1e-05
(0.00892)
8e-05
(0.0438)
0.00089
(0.436)
0.0626
(1.00)
0.213
(1.00)
21q gain 36 (7%) 488 1e-05
(0.00892)
0.00137
(0.651)
0.375
(1.00)
0.838
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
0.221
(1.00)
0.244
(1.00)
6q loss 24 (5%) 500 0.38
(1.00)
0.0299
(1.00)
1e-05
(0.00892)
5e-05
(0.028)
0.48
(1.00)
0.802
(1.00)
2e-05
(0.0118)
1e-05
(0.00892)
0.00406
(1.00)
3e-05
(0.017)
0.111
(1.00)
0.0495
(1.00)
7p loss 43 (8%) 481 0.0393
(1.00)
0.194
(1.00)
1e-05
(0.00892)
0.00062
(0.316)
0.0384
(1.00)
0.55
(1.00)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
1e-05
(0.00892)
0.128
(1.00)
0.526
(1.00)
18p loss 52 (10%) 472 1e-05
(0.00892)
1e-05
(0.00892)
0.474
(1.00)
0.567
(1.00)
1e-05
(0.00892)
0.00531
(1.00)
0.00013
(0.0699)
0.00029
(0.151)
0.00491
(1.00)
0.00834
(1.00)
12p gain 66 (13%) 458 0.385
(1.00)
0.689
(1.00)
1e-05
(0.00892)
3e-05
(0.017)
0.915
(1.00)
0.97
(1.00)
2e-05
(0.0118)
8e-05
(0.0438)
0.00073
(0.364)
0.00059
(0.301)
0.00154
(0.727)
0.0475
(1.00)
14q gain 36 (7%) 488 1
(1.00)
0.843
(1.00)
1e-05
(0.00892)
0.00097
(0.474)
0.0855
(1.00)
0.693
(1.00)
1e-05
(0.00892)
6e-05
(0.0332)
0.00119
(0.576)
9e-05
(0.049)
0.308
(1.00)
0.624
(1.00)
1q gain 178 (34%) 346 0.179
(1.00)
0.0102
(1.00)
0.00019
(0.101)
0.18
(1.00)
0.0925
(1.00)
0.0154
(1.00)
0.00023
(0.121)
0.00383
(1.00)
1e-05
(0.00892)
0.0464
(1.00)
0.961
(1.00)
0.271
(1.00)
6q gain 61 (12%) 463 0.209
(1.00)
0.662
(1.00)
1e-05
(0.00892)
0.00078
(0.388)
0.0523
(1.00)
0.757
(1.00)
1e-05
(0.00892)
0.0013
(0.621)
0.00087
(0.43)
0.00034
(0.176)
0.41
(1.00)
0.485
(1.00)
8q gain 152 (29%) 372 0.0109
(1.00)
0.03
(1.00)
1e-05
(0.00892)
0.145
(1.00)
0.00018
(0.0956)
0.0222
(1.00)
2e-05
(0.0118)
0.00188
(0.876)
0.00088
(0.434)
0.00445
(1.00)
0.135
(1.00)
0.335
(1.00)
3p gain 45 (9%) 479 1e-05
(0.00892)
0.0177
(1.00)
0.301
(1.00)
0.946
(1.00)
6e-05
(0.0332)
0.0204
(1.00)
0.0039
(1.00)
0.00769
(1.00)
0.0443
(1.00)
0.189
(1.00)
5q gain 19 (4%) 505 1e-05
(0.00892)
0.0599
(1.00)
0.368
(1.00)
0.292
(1.00)
0.00028
(0.147)
0.00122
(0.587)
0.0024
(1.00)
0.00609
(1.00)
0.0323
(1.00)
0.00343
(1.00)
6p loss 17 (3%) 507 0.38
(1.00)
0.03
(1.00)
1e-05
(0.00892)
0.00223
(1.00)
0.363
(1.00)
1
(1.00)
0.00062
(0.316)
1e-05
(0.00892)
0.0639
(1.00)
0.00356
(1.00)
0.189
(1.00)
0.204
(1.00)
4p gain 13 (2%) 511 5e-05
(0.028)
0.913
(1.00)
0.372
(1.00)
0.0371
(1.00)
0.0013
(0.621)
0.0197
(1.00)
0.00723
(1.00)
0.0114
(1.00)
0.164
(1.00)
0.436
(1.00)
7p gain 64 (12%) 460 0.855
(1.00)
0.905
(1.00)
1e-05
(0.00892)
0.00072
(0.359)
0.847
(1.00)
0.864
(1.00)
0.0242
(1.00)
0.0967
(1.00)
0.0199
(1.00)
0.386
(1.00)
0.269
(1.00)
0.411
(1.00)
7q gain 62 (12%) 462 0.854
(1.00)
0.906
(1.00)
1e-05
(0.00892)
0.00056
(0.287)
0.854
(1.00)
0.531
(1.00)
0.157
(1.00)
0.205
(1.00)
0.14
(1.00)
0.586
(1.00)
0.741
(1.00)
0.98
(1.00)
8p gain 116 (22%) 408 0.355
(1.00)
0.407
(1.00)
1e-05
(0.00892)
0.921
(1.00)
0.0208
(1.00)
0.216
(1.00)
0.164
(1.00)
0.66
(1.00)
0.204
(1.00)
0.113
(1.00)
0.61
(1.00)
0.314
(1.00)
10p gain 116 (22%) 408 0.00746
(1.00)
0.0891
(1.00)
1e-05
(0.00892)
0.839
(1.00)
0.194
(1.00)
0.816
(1.00)
0.101
(1.00)
0.21
(1.00)
0.619
(1.00)
0.0077
(1.00)
0.173
(1.00)
0.0475
(1.00)
10q gain 109 (21%) 415 0.00505
(1.00)
0.0889
(1.00)
1e-05
(0.00892)
0.757
(1.00)
0.121
(1.00)
0.659
(1.00)
0.177
(1.00)
0.326
(1.00)
0.441
(1.00)
0.00283
(1.00)
0.18
(1.00)
0.0887
(1.00)
11p gain 22 (4%) 502 0.0382
(1.00)
0.195
(1.00)
1e-05
(0.00892)
0.0765
(1.00)
0.0553
(1.00)
0.113
(1.00)
0.0042
(1.00)
0.00734
(1.00)
0.00476
(1.00)
0.0532
(1.00)
0.209
(1.00)
0.802
(1.00)
11q gain 19 (4%) 505 1e-05
(0.00892)
0.113
(1.00)
0.181
(1.00)
0.0119
(1.00)
0.0285
(1.00)
0.137
(1.00)
0.0732
(1.00)
0.326
(1.00)
0.689
(1.00)
0.94
(1.00)
12q gain 52 (10%) 472 0.387
(1.00)
0.69
(1.00)
1e-05
(0.00892)
0.00443
(1.00)
0.962
(1.00)
0.981
(1.00)
0.0016
(0.752)
0.00893
(1.00)
0.0311
(1.00)
0.0716
(1.00)
0.0664
(1.00)
0.446
(1.00)
16p gain 25 (5%) 499 1e-05
(0.00892)
0.00629
(1.00)
0.178
(1.00)
0.632
(1.00)
0.117
(1.00)
0.179
(1.00)
0.0123
(1.00)
0.0479
(1.00)
0.731
(1.00)
0.877
(1.00)
17p gain 12 (2%) 512 0.00043
(0.222)
0.16
(1.00)
0.225
(1.00)
1
(1.00)
0.0976
(1.00)
0.00309
(1.00)
0.0829
(1.00)
0.0847
(1.00)
0.713
(1.00)
0.303
(1.00)
xq gain 63 (12%) 461 0.703
(1.00)
0.928
(1.00)
1e-05
(0.00892)
0.502
(1.00)
0.871
(1.00)
0.337
(1.00)
0.549
(1.00)
0.342
(1.00)
0.528
(1.00)
0.876
(1.00)
0.171
(1.00)
0.517
(1.00)
2q loss 16 (3%) 508 1e-05
(0.00892)
0.155
(1.00)
0.00071
(0.356)
0.105
(1.00)
0.0376
(1.00)
0.0758
(1.00)
0.829
(1.00)
0.576
(1.00)
20p loss 18 (3%) 506 5e-05
(0.028)
0.323
(1.00)
0.466
(1.00)
0.665
(1.00)
0.0272
(1.00)
0.00384
(1.00)
0.0687
(1.00)
0.0921
(1.00)
0.519
(1.00)
0.659
(1.00)
4q gain 8 (2%) 516 0.00386
(1.00)
0.619
(1.00)
0.0308
(1.00)
0.145
(1.00)
0.27
(1.00)
0.126
(1.00)
0.549
(1.00)
0.423
(1.00)
9p gain 22 (4%) 502 0.00051
(0.262)
0.00279
(1.00)
0.095
(1.00)
0.325
(1.00)
0.00446
(1.00)
0.0682
(1.00)
0.00409
(1.00)
0.0244
(1.00)
0.352
(1.00)
0.533
(1.00)
9q gain 9 (2%) 515 0.0991
(1.00)
0.149
(1.00)
0.364
(1.00)
0.697
(1.00)
0.173
(1.00)
0.684
(1.00)
0.335
(1.00)
0.547
(1.00)
15q gain 11 (2%) 513 0.00519
(1.00)
0.915
(1.00)
0.691
(1.00)
0.506
(1.00)
0.465
(1.00)
0.792
(1.00)
0.57
(1.00)
0.579
(1.00)
16q gain 9 (2%) 515 0.0217
(1.00)
0.0916
(1.00)
0.947
(1.00)
0.842
(1.00)
0.171
(1.00)
0.27
(1.00)
0.173
(1.00)
0.445
(1.00)
0.767
(1.00)
0.127
(1.00)
2p loss 10 (2%) 514 0.00088
(0.434)
0.38
(1.00)
0.00733
(1.00)
0.143
(1.00)
0.614
(1.00)
0.684
(1.00)
0.91
(1.00)
1
(1.00)
20q loss 9 (2%) 515 0.00119
(0.576)
0.0882
(1.00)
0.642
(1.00)
1
(1.00)
0.0369
(1.00)
0.00294
(1.00)
0.297
(1.00)
0.116
(1.00)
0.281
(1.00)
0.181
(1.00)
'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
1P GAIN MUTATED 6 5 34 1 0
1P GAIN WILD-TYPE 299 43 120 11 5

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

'1p gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S2.  Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
1P GAIN MUTATED 36 5 5
1P GAIN WILD-TYPE 188 145 140

Figure S2.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
1P GAIN MUTATED 29 11 6
1P GAIN WILD-TYPE 134 202 137

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

'1p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S4.  Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
1P GAIN MUTATED 10 33 2
1P GAIN WILD-TYPE 131 186 153

Figure S4.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S5.  Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
1P GAIN MUTATED 1 29 2 13
1P GAIN WILD-TYPE 54 133 114 169

Figure S5.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1q gain' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.1

Table S6.  Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
1Q GAIN MUTATED 91 26 50 6 5
1Q GAIN WILD-TYPE 214 22 104 6 0

Figure S6.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.12

Table S7.  Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
1Q GAIN MUTATED 70 70 36
1Q GAIN WILD-TYPE 154 80 109

Figure S7.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S8.  Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
1Q GAIN MUTATED 72 66 39
1Q GAIN WILD-TYPE 69 153 116

Figure S8.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
2P GAIN MUTATED 9 24 56 2 1
2P GAIN WILD-TYPE 296 24 98 10 4

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S10.  Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
2P GAIN MUTATED 50 9 11
2P GAIN WILD-TYPE 108 77 155

Figure S10.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S11.  Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
2P GAIN MUTATED 66 16 9
2P GAIN WILD-TYPE 158 134 136

Figure S11.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S12.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
2P GAIN MUTATED 57 25 9
2P GAIN WILD-TYPE 106 188 134

Figure S12.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S13.  Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
2P GAIN MUTATED 16 64 11
2P GAIN WILD-TYPE 125 155 144

Figure S13.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S14.  Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
2P GAIN MUTATED 8 54 9 20
2P GAIN WILD-TYPE 47 108 107 162

Figure S14.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.11

Table S15.  Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 177 94
2P GAIN MUTATED 8 42 18
2P GAIN WILD-TYPE 113 135 76

Figure S15.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S16.  Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
2Q GAIN MUTATED 6 22 45 1 1
2Q GAIN WILD-TYPE 299 26 109 11 4

Figure S16.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
2Q GAIN MUTATED 43 7 10
2Q GAIN WILD-TYPE 115 79 156

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

'2q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S18.  Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
2Q GAIN MUTATED 54 13 7
2Q GAIN WILD-TYPE 170 137 138

Figure S18.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S19.  Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
2Q GAIN MUTATED 47 19 8
2Q GAIN WILD-TYPE 116 194 135

Figure S19.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S20.  Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
2Q GAIN MUTATED 14 53 8
2Q GAIN WILD-TYPE 127 166 147

Figure S20.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S21.  Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
2Q GAIN MUTATED 6 45 7 17
2Q GAIN WILD-TYPE 49 117 109 165

Figure S21.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.14

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 177 94
2Q GAIN MUTATED 6 37 15
2Q GAIN WILD-TYPE 115 140 79

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

'3p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
3P GAIN MUTATED 2 7 25 9 2
3P GAIN WILD-TYPE 303 41 129 3 3

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

'3p gain' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.033

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
3P GAIN MUTATED 32 3 9
3P GAIN WILD-TYPE 192 147 136

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

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
3Q GAIN MUTATED 5 9 52 10 2
3Q GAIN WILD-TYPE 300 39 102 2 3

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

'3q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S26.  Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
3Q GAIN MUTATED 49 9 10
3Q GAIN WILD-TYPE 109 77 156

Figure S26.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S27.  Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
3Q GAIN MUTATED 62 5 10
3Q GAIN WILD-TYPE 162 145 135

Figure S27.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S28.  Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
3Q GAIN MUTATED 51 18 8
3Q GAIN WILD-TYPE 112 195 135

Figure S28.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S29.  Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
3Q GAIN MUTATED 8 61 9
3Q GAIN WILD-TYPE 133 158 146

Figure S29.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S30.  Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
3Q GAIN MUTATED 0 50 9 19
3Q GAIN WILD-TYPE 55 112 107 163

Figure S30.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.028

Table S31.  Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
4P GAIN MUTATED 0 1 12 0 0
4P GAIN WILD-TYPE 305 47 142 12 5

Figure S31.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S32.  Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
5P GAIN MUTATED 3 5 40 0 1
5P GAIN WILD-TYPE 302 43 114 12 4

Figure S32.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S33.  Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
5P GAIN MUTATED 32 4 5
5P GAIN WILD-TYPE 126 82 161

Figure S33.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S34.  Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
5P GAIN MUTATED 43 5 1
5P GAIN WILD-TYPE 181 145 144

Figure S34.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S35.  Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
5P GAIN MUTATED 37 10 2
5P GAIN WILD-TYPE 126 203 141

Figure S35.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
5P GAIN MUTATED 9 38 1
5P GAIN WILD-TYPE 132 181 154

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

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S37.  Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
5P GAIN MUTATED 4 37 0 7
5P GAIN WILD-TYPE 51 125 116 175

Figure S37.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S38.  Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 177 94
5P GAIN MUTATED 2 30 7
5P GAIN WILD-TYPE 119 147 87

Figure S38.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.086

Table S39.  Gene #9: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 108 113
5P GAIN MUTATED 28 2 9
5P GAIN WILD-TYPE 143 106 104

Figure S39.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S40.  Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
5Q GAIN MUTATED 1 3 14 0 1
5Q GAIN WILD-TYPE 304 45 140 12 4

Figure S40.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.15

Table S41.  Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
5Q GAIN MUTATED 16 3 0
5Q GAIN WILD-TYPE 208 147 145

Figure S41.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S42.  Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
6P GAIN MUTATED 6 5 57 7 1
6P GAIN WILD-TYPE 299 43 97 5 4

Figure S42.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S43.  Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
6P GAIN MUTATED 46 12 10
6P GAIN WILD-TYPE 112 74 156

Figure S43.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S44.  Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
6P GAIN MUTATED 57 5 14
6P GAIN WILD-TYPE 167 145 131

Figure S44.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S45.  Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
6P GAIN MUTATED 45 18 13
6P GAIN WILD-TYPE 118 195 130

Figure S45.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S46.  Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
6P GAIN MUTATED 10 55 11
6P GAIN WILD-TYPE 131 164 144

Figure S46.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S47.  Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
6P GAIN MUTATED 1 46 10 19
6P GAIN WILD-TYPE 54 116 106 163

Figure S47.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S48.  Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
6Q GAIN MUTATED 5 5 43 7 1
6Q GAIN WILD-TYPE 300 43 111 5 4

Figure S48.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S49.  Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
6Q GAIN MUTATED 42 5 14
6Q GAIN WILD-TYPE 182 145 131

Figure S49.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.18

Table S50.  Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
6Q GAIN MUTATED 1 33 10 17
6Q GAIN WILD-TYPE 54 129 106 165

Figure S50.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
7P GAIN MUTATED 8 24 27 4 1
7P GAIN WILD-TYPE 297 24 127 8 4

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

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S52.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
7Q GAIN MUTATED 11 24 22 4 1
7Q GAIN WILD-TYPE 294 24 132 8 4

Figure S52.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S53.  Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
8P GAIN MUTATED 39 22 41 12 2
8P GAIN WILD-TYPE 266 26 113 0 3

Figure S53.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S54.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
8Q GAIN MUTATED 41 26 70 12 3
8Q GAIN WILD-TYPE 264 22 84 0 2

Figure S54.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'RPPA_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.096

Table S55.  Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
8Q GAIN MUTATED 9 12 7 2 2 13
8Q GAIN WILD-TYPE 32 25 32 10 39 11

Figure S55.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S56.  Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
8Q GAIN MUTATED 90 29 33
8Q GAIN WILD-TYPE 134 121 112

Figure S56.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S57.  Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
10P GAIN MUTATED 47 24 37 6 2
10P GAIN WILD-TYPE 258 24 117 6 3

Figure S57.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S58.  Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
10Q GAIN MUTATED 46 23 33 5 2
10Q GAIN WILD-TYPE 259 25 121 7 3

Figure S58.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S59.  Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
11P GAIN MUTATED 0 6 15 1 0
11P GAIN WILD-TYPE 305 42 139 11 5

Figure S59.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S60.  Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
11Q GAIN MUTATED 0 6 12 1 0
11Q GAIN WILD-TYPE 305 42 142 11 5

Figure S60.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S61.  Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
12P GAIN MUTATED 11 14 37 1 3
12P GAIN WILD-TYPE 294 34 117 11 2

Figure S61.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S62.  Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
12P GAIN MUTATED 31 14 7
12P GAIN WILD-TYPE 127 72 159

Figure S62.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S63.  Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
12P GAIN MUTATED 47 9 9
12P GAIN WILD-TYPE 177 141 136

Figure S63.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.044

Table S64.  Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
12P GAIN MUTATED 36 20 9
12P GAIN WILD-TYPE 127 193 134

Figure S64.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S65.  Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
12Q GAIN MUTATED 11 13 24 1 3
12Q GAIN WILD-TYPE 294 35 130 11 2

Figure S65.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S66.  Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
13Q GAIN MUTATED 1 0 25 1 1
13Q GAIN WILD-TYPE 304 48 129 11 4

Figure S66.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.086

Table S67.  Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
13Q GAIN MUTATED 16 7 1
13Q GAIN WILD-TYPE 142 79 165

Figure S67.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S68.  Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
13Q GAIN MUTATED 25 1 2
13Q GAIN WILD-TYPE 199 149 143

Figure S68.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S69.  Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
13Q GAIN MUTATED 25 1 2
13Q GAIN WILD-TYPE 138 212 141

Figure S69.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S70.  Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
13Q GAIN MUTATED 0 26 2
13Q GAIN WILD-TYPE 141 193 153

Figure S70.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S71.  Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
13Q GAIN MUTATED 0 24 2 2
13Q GAIN WILD-TYPE 55 138 114 180

Figure S71.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S72.  Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
14Q GAIN MUTATED 4 6 24 2 0
14Q GAIN WILD-TYPE 301 42 130 10 5

Figure S72.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S73.  Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
14Q GAIN MUTATED 28 1 6
14Q GAIN WILD-TYPE 196 149 139

Figure S73.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.033

Table S74.  Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
14Q GAIN MUTATED 23 6 6
14Q GAIN WILD-TYPE 140 207 137

Figure S74.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.049

Table S75.  Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
14Q GAIN MUTATED 0 23 7 6
14Q GAIN WILD-TYPE 55 139 109 176

Figure S75.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S76.  Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
16P GAIN MUTATED 1 5 18 1 0
16P GAIN WILD-TYPE 304 43 136 11 5

Figure S76.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.22

Table S77.  Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
17P GAIN MUTATED 1 1 8 1 1
17P GAIN WILD-TYPE 304 47 146 11 4

Figure S77.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S78.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
17Q GAIN MUTATED 1 3 22 1 1
17Q GAIN WILD-TYPE 304 45 132 11 4

Figure S78.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S79.  Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
17Q GAIN MUTATED 21 2 2
17Q GAIN WILD-TYPE 137 84 164

Figure S79.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.075

Table S80.  Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
17Q GAIN MUTATED 23 2 3
17Q GAIN WILD-TYPE 201 148 142

Figure S80.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S81.  Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
17Q GAIN MUTATED 22 4 2
17Q GAIN WILD-TYPE 141 209 141

Figure S81.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.044

Table S82.  Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
17Q GAIN MUTATED 2 23 3
17Q GAIN WILD-TYPE 139 196 152

Figure S82.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S83.  Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
18P GAIN MUTATED 3 5 59 1 0
18P GAIN WILD-TYPE 302 43 95 11 5

Figure S83.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S84.  Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
18P GAIN MUTATED 41 13 4
18P GAIN WILD-TYPE 117 73 162

Figure S84.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S85.  Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
18P GAIN MUTATED 61 3 4
18P GAIN WILD-TYPE 163 147 141

Figure S85.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S86.  Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
18P GAIN MUTATED 56 8 4
18P GAIN WILD-TYPE 107 205 139

Figure S86.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S87.  Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
18P GAIN MUTATED 6 58 4
18P GAIN WILD-TYPE 135 161 151

Figure S87.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S88.  Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
18P GAIN MUTATED 2 55 3 8
18P GAIN WILD-TYPE 53 107 113 174

Figure S88.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S89.  Gene #32: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 177 94
18P GAIN MUTATED 3 38 15
18P GAIN WILD-TYPE 118 139 79

Figure S89.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S90.  Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 108 113
18P GAIN MUTATED 34 3 19
18P GAIN WILD-TYPE 137 105 94

Figure S90.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S91.  Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
18Q GAIN MUTATED 3 3 34 1 0
18Q GAIN WILD-TYPE 302 45 120 11 5

Figure S91.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S92.  Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
18Q GAIN MUTATED 25 7 3
18Q GAIN WILD-TYPE 133 79 163

Figure S92.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S93.  Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
18Q GAIN MUTATED 36 2 3
18Q GAIN WILD-TYPE 188 148 142

Figure S93.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S94.  Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
18Q GAIN MUTATED 31 7 3
18Q GAIN WILD-TYPE 132 206 140

Figure S94.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S95.  Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
18Q GAIN MUTATED 6 33 2
18Q GAIN WILD-TYPE 135 186 153

Figure S95.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S96.  Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
18Q GAIN MUTATED 1 30 2 8
18Q GAIN WILD-TYPE 54 132 114 174

Figure S96.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.028

Table S97.  Gene #33: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 177 94
18Q GAIN MUTATED 1 25 7
18Q GAIN WILD-TYPE 120 152 87

Figure S97.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S98.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
19P GAIN MUTATED 0 2 46 2 0
19P GAIN WILD-TYPE 305 46 108 10 5

Figure S98.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.13

Table S99.  Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
19P GAIN MUTATED 28 10 7
19P GAIN WILD-TYPE 130 76 159

Figure S99.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S100.  Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
19P GAIN MUTATED 44 1 4
19P GAIN WILD-TYPE 180 149 141

Figure S100.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S101.  Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
19P GAIN MUTATED 36 10 3
19P GAIN WILD-TYPE 127 203 140

Figure S101.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S102.  Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
19P GAIN MUTATED 3 42 5
19P GAIN WILD-TYPE 138 177 150

Figure S102.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S103.  Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
19P GAIN MUTATED 1 35 5 9
19P GAIN WILD-TYPE 54 127 111 173

Figure S103.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S104.  Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
19Q GAIN MUTATED 0 3 50 2 0
19Q GAIN WILD-TYPE 305 45 104 10 5

Figure S104.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S105.  Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
19Q GAIN MUTATED 32 11 6
19Q GAIN WILD-TYPE 126 75 160

Figure S105.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S106.  Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
19Q GAIN MUTATED 51 1 3
19Q GAIN WILD-TYPE 173 149 142

Figure S106.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S107.  Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
19Q GAIN MUTATED 44 9 2
19Q GAIN WILD-TYPE 119 204 141

Figure S107.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S108.  Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
19Q GAIN MUTATED 4 47 4
19Q GAIN WILD-TYPE 137 172 151

Figure S108.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S109.  Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
19Q GAIN MUTATED 1 43 4 7
19Q GAIN WILD-TYPE 54 119 112 175

Figure S109.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S110.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
20P GAIN MUTATED 6 22 76 1 2
20P GAIN WILD-TYPE 299 26 78 11 3

Figure S110.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S111.  Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
20P GAIN MUTATED 68 13 17
20P GAIN WILD-TYPE 90 73 149

Figure S111.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S112.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
20P GAIN MUTATED 84 9 14
20P GAIN WILD-TYPE 140 141 131

Figure S112.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S113.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
20P GAIN MUTATED 72 20 15
20P GAIN WILD-TYPE 91 193 128

Figure S113.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S114.  Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
20P GAIN MUTATED 13 79 14
20P GAIN WILD-TYPE 128 140 141

Figure S114.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S115.  Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
20P GAIN MUTATED 5 67 14 20
20P GAIN WILD-TYPE 50 95 102 162

Figure S115.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.044

Table S116.  Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 177 94
20P GAIN MUTATED 17 60 16
20P GAIN WILD-TYPE 104 117 78

Figure S116.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S117.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
20Q GAIN MUTATED 7 25 90 1 2
20Q GAIN WILD-TYPE 298 23 64 11 3

Figure S117.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S118.  Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
20Q GAIN MUTATED 76 16 21
20Q GAIN WILD-TYPE 82 70 145

Figure S118.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S119.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
20Q GAIN MUTATED 97 10 18
20Q GAIN WILD-TYPE 127 140 127

Figure S119.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S120.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
20Q GAIN MUTATED 83 23 19
20Q GAIN WILD-TYPE 80 190 124

Figure S120.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S121.  Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
20Q GAIN MUTATED 13 92 18
20Q GAIN WILD-TYPE 128 127 137

Figure S121.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S122.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
20Q GAIN MUTATED 6 77 16 24
20Q GAIN WILD-TYPE 49 85 100 158

Figure S122.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.11

Table S123.  Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 177 94
20Q GAIN MUTATED 21 67 20
20Q GAIN WILD-TYPE 100 110 74

Figure S123.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S124.  Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
21Q GAIN MUTATED 1 2 32 1 0
21Q GAIN WILD-TYPE 304 46 122 11 5

Figure S124.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S125.  Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
21Q GAIN MUTATED 30 2 4
21Q GAIN WILD-TYPE 194 148 141

Figure S125.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S126.  Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
21Q GAIN MUTATED 28 4 4
21Q GAIN WILD-TYPE 135 209 139

Figure S126.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S127.  Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
21Q GAIN MUTATED 2 30 4
21Q GAIN WILD-TYPE 139 189 151

Figure S127.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S128.  Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
21Q GAIN MUTATED 1 28 3 4
21Q GAIN WILD-TYPE 54 134 113 178

Figure S128.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S129.  Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
22Q GAIN MUTATED 3 3 24 0 1
22Q GAIN WILD-TYPE 302 45 130 12 4

Figure S129.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S130.  Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
22Q GAIN MUTATED 26 1 1
22Q GAIN WILD-TYPE 132 85 165

Figure S130.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S131.  Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
22Q GAIN MUTATED 31 0 0
22Q GAIN WILD-TYPE 193 150 145

Figure S131.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S132.  Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
22Q GAIN MUTATED 28 3 0
22Q GAIN WILD-TYPE 135 210 143

Figure S132.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S133.  Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
22Q GAIN MUTATED 0 29 1
22Q GAIN WILD-TYPE 141 190 154

Figure S133.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S134.  Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
22Q GAIN MUTATED 0 26 2 2
22Q GAIN WILD-TYPE 55 136 114 180

Figure S134.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S135.  Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 177 94
22Q GAIN MUTATED 1 25 2
22Q GAIN WILD-TYPE 120 152 92

Figure S135.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S136.  Gene #40: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
XQ GAIN MUTATED 10 19 23 9 2
XQ GAIN WILD-TYPE 295 29 131 3 3

Figure S136.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S137.  Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
1P LOSS MUTATED 0 5 15 0 2
1P LOSS WILD-TYPE 305 43 139 12 3

Figure S137.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S138.  Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
1P LOSS MUTATED 17 1 0
1P LOSS WILD-TYPE 141 85 166

Figure S138.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.028

Table S139.  Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
1P LOSS MUTATED 20 1 1
1P LOSS WILD-TYPE 204 149 144

Figure S139.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S140.  Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
1P LOSS MUTATED 17 5 0
1P LOSS WILD-TYPE 146 208 143

Figure S140.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.038

Table S141.  Gene #41: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
1P LOSS MUTATED 2 19 1
1P LOSS WILD-TYPE 139 200 154

Figure S141.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.033

Table S142.  Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
1P LOSS MUTATED 0 17 0 5
1P LOSS WILD-TYPE 55 145 116 177

Figure S142.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.049

Table S143.  Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
1Q LOSS MUTATED 0 2 11 0 0
1Q LOSS WILD-TYPE 305 46 143 12 5

Figure S143.  Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'1q loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S144.  Gene #42: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
1Q LOSS MUTATED 11 0 0
1Q LOSS WILD-TYPE 147 86 166

Figure S144.  Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S145.  Gene #42: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
1Q LOSS MUTATED 13 0 0
1Q LOSS WILD-TYPE 211 150 145

Figure S145.  Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.038

Table S146.  Gene #42: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
1Q LOSS MUTATED 11 2 0
1Q LOSS WILD-TYPE 152 211 143

Figure S146.  Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.028

Table S147.  Gene #42: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
1Q LOSS MUTATED 0 13 0
1Q LOSS WILD-TYPE 141 206 155

Figure S147.  Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.06

Table S148.  Gene #42: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
1Q LOSS MUTATED 0 12 0 1
1Q LOSS WILD-TYPE 55 150 116 181

Figure S148.  Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S149.  Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
2Q LOSS MUTATED 0 2 14 0 0
2Q LOSS WILD-TYPE 305 46 140 12 5

Figure S149.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S150.  Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
3P LOSS MUTATED 0 5 44 0 1
3P LOSS WILD-TYPE 305 43 110 12 4

Figure S150.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S151.  Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
3P LOSS MUTATED 32 6 3
3P LOSS WILD-TYPE 126 80 163

Figure S151.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S152.  Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
3P LOSS MUTATED 46 1 2
3P LOSS WILD-TYPE 178 149 143

Figure S152.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S153.  Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
3P LOSS MUTATED 40 7 2
3P LOSS WILD-TYPE 123 206 141

Figure S153.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S154.  Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
3P LOSS MUTATED 6 39 3
3P LOSS WILD-TYPE 135 180 152

Figure S154.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S155.  Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
3P LOSS MUTATED 1 37 2 8
3P LOSS WILD-TYPE 54 125 114 174

Figure S155.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S156.  Gene #46: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
3Q LOSS MUTATED 0 3 26 0 1
3Q LOSS WILD-TYPE 305 45 128 12 4

Figure S156.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.06

Table S157.  Gene #46: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
3Q LOSS MUTATED 19 3 2
3Q LOSS WILD-TYPE 139 83 164

Figure S157.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S158.  Gene #46: '3q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
3Q LOSS MUTATED 27 0 2
3Q LOSS WILD-TYPE 197 150 143

Figure S158.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S159.  Gene #46: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
3Q LOSS MUTATED 24 3 2
3Q LOSS WILD-TYPE 139 210 141

Figure S159.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S160.  Gene #46: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
3Q LOSS MUTATED 1 24 3
3Q LOSS WILD-TYPE 140 195 152

Figure S160.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S161.  Gene #46: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
3Q LOSS MUTATED 0 22 2 4
3Q LOSS WILD-TYPE 55 140 114 178

Figure S161.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S162.  Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
4P LOSS MUTATED 4 11 82 1 2
4P LOSS WILD-TYPE 301 37 72 11 3

Figure S162.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S163.  Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
4P LOSS MUTATED 67 16 6
4P LOSS WILD-TYPE 91 70 160

Figure S163.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S164.  Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
4P LOSS MUTATED 87 6 7
4P LOSS WILD-TYPE 137 144 138

Figure S164.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S165.  Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
4P LOSS MUTATED 73 21 6
4P LOSS WILD-TYPE 90 192 137

Figure S165.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S166.  Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
4P LOSS MUTATED 8 81 9
4P LOSS WILD-TYPE 133 138 146

Figure S166.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S167.  Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
4P LOSS MUTATED 2 70 3 23
4P LOSS WILD-TYPE 53 92 113 159

Figure S167.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S168.  Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 177 94
4P LOSS MUTATED 10 55 24
4P LOSS WILD-TYPE 111 122 70

Figure S168.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S169.  Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 108 113
4P LOSS MUTATED 53 9 27
4P LOSS WILD-TYPE 118 99 86

Figure S169.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S170.  Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
4Q LOSS MUTATED 3 10 83 1 2
4Q LOSS WILD-TYPE 302 38 71 11 3

Figure S170.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S171.  Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
4Q LOSS MUTATED 67 15 5
4Q LOSS WILD-TYPE 91 71 161

Figure S171.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S172.  Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
4Q LOSS MUTATED 86 7 6
4Q LOSS WILD-TYPE 138 143 139

Figure S172.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S173.  Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
4Q LOSS MUTATED 73 20 6
4Q LOSS WILD-TYPE 90 193 137

Figure S173.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S174.  Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
4Q LOSS MUTATED 8 80 9
4Q LOSS WILD-TYPE 133 139 146

Figure S174.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S175.  Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
4Q LOSS MUTATED 2 71 3 21
4Q LOSS WILD-TYPE 53 91 113 161

Figure S175.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S176.  Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 177 94
4Q LOSS MUTATED 9 52 26
4Q LOSS WILD-TYPE 112 125 68

Figure S176.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S177.  Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 108 113
4Q LOSS MUTATED 49 8 30
4Q LOSS WILD-TYPE 122 100 83

Figure S177.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S178.  Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
5P LOSS MUTATED 0 9 43 1 1
5P LOSS WILD-TYPE 305 39 111 11 4

Figure S178.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S179.  Gene #49: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
5P LOSS MUTATED 36 6 3
5P LOSS WILD-TYPE 122 80 163

Figure S179.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S180.  Gene #49: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
5P LOSS MUTATED 45 4 5
5P LOSS WILD-TYPE 179 146 140

Figure S180.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S181.  Gene #49: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
5P LOSS MUTATED 39 10 5
5P LOSS WILD-TYPE 124 203 138

Figure S181.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S182.  Gene #49: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
5P LOSS MUTATED 5 42 7
5P LOSS WILD-TYPE 136 177 148

Figure S182.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S183.  Gene #49: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
5P LOSS MUTATED 1 38 3 12
5P LOSS WILD-TYPE 54 124 113 170

Figure S183.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S184.  Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
5Q LOSS MUTATED 0 9 61 1 1
5Q LOSS WILD-TYPE 305 39 93 11 4

Figure S184.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S185.  Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
5Q LOSS MUTATED 51 6 3
5Q LOSS WILD-TYPE 107 80 163

Figure S185.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S186.  Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
5Q LOSS MUTATED 62 4 6
5Q LOSS WILD-TYPE 162 146 139

Figure S186.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S187.  Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
5Q LOSS MUTATED 54 11 7
5Q LOSS WILD-TYPE 109 202 136

Figure S187.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S188.  Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
5Q LOSS MUTATED 6 58 7
5Q LOSS WILD-TYPE 135 161 148

Figure S188.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S189.  Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
5Q LOSS MUTATED 1 52 4 14
5Q LOSS WILD-TYPE 54 110 112 168

Figure S189.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S190.  Gene #50: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 177 94
5Q LOSS MUTATED 5 39 14
5Q LOSS WILD-TYPE 116 138 80

Figure S190.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S191.  Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
6P LOSS MUTATED 0 3 14 0 0
6P LOSS WILD-TYPE 305 45 140 12 5

Figure S191.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S192.  Gene #51: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
6P LOSS MUTATED 14 3 0
6P LOSS WILD-TYPE 149 210 143

Figure S192.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S193.  Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
6Q LOSS MUTATED 0 3 21 0 0
6Q LOSS WILD-TYPE 305 45 133 12 5

Figure S193.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.028

Table S194.  Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
6Q LOSS MUTATED 14 4 0
6Q LOSS WILD-TYPE 144 82 166

Figure S194.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S195.  Gene #52: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
6Q LOSS MUTATED 22 1 1
6Q LOSS WILD-TYPE 202 149 144

Figure S195.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S196.  Gene #52: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
6Q LOSS MUTATED 21 3 0
6Q LOSS WILD-TYPE 142 210 143

Figure S196.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S197.  Gene #52: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
6Q LOSS MUTATED 0 17 0 5
6Q LOSS WILD-TYPE 55 145 116 177

Figure S197.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S198.  Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
7P LOSS MUTATED 3 1 38 0 1
7P LOSS WILD-TYPE 302 47 116 12 4

Figure S198.  Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

'7p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S199.  Gene #53: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
7P LOSS MUTATED 38 1 4
7P LOSS WILD-TYPE 186 149 141

Figure S199.  Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S200.  Gene #53: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
7P LOSS MUTATED 31 8 4
7P LOSS WILD-TYPE 132 205 139

Figure S200.  Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S201.  Gene #53: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
7P LOSS MUTATED 2 34 7
7P LOSS WILD-TYPE 139 185 148

Figure S201.  Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S202.  Gene #53: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
7P LOSS MUTATED 0 30 4 9
7P LOSS WILD-TYPE 55 132 112 173

Figure S202.  Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S203.  Gene #54: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
7Q LOSS MUTATED 0 0 40 0 1
7Q LOSS WILD-TYPE 305 48 114 12 4

Figure S203.  Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

'7q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S204.  Gene #54: '7q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
7Q LOSS MUTATED 28 9 1
7Q LOSS WILD-TYPE 130 77 165

Figure S204.  Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S205.  Gene #54: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
7Q LOSS MUTATED 40 0 1
7Q LOSS WILD-TYPE 184 150 144

Figure S205.  Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S206.  Gene #54: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
7Q LOSS MUTATED 35 4 2
7Q LOSS WILD-TYPE 128 209 141

Figure S206.  Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S207.  Gene #54: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
7Q LOSS MUTATED 1 37 3
7Q LOSS WILD-TYPE 140 182 152

Figure S207.  Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S208.  Gene #54: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
7Q LOSS MUTATED 0 35 2 4
7Q LOSS WILD-TYPE 55 127 114 178

Figure S208.  Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.06

Table S209.  Gene #55: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
8P LOSS MUTATED 0 5 0 0 0
8P LOSS WILD-TYPE 14 4 7 7 16

Figure S209.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S210.  Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
8P LOSS MUTATED 4 3 67 0 1
8P LOSS WILD-TYPE 301 45 87 12 4

Figure S210.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S211.  Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
8P LOSS MUTATED 53 11 2
8P LOSS WILD-TYPE 105 75 164

Figure S211.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S212.  Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
8P LOSS MUTATED 68 3 3
8P LOSS WILD-TYPE 156 147 142

Figure S212.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S213.  Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
8P LOSS MUTATED 63 7 4
8P LOSS WILD-TYPE 100 206 139

Figure S213.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S214.  Gene #55: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
8P LOSS MUTATED 2 66 4
8P LOSS WILD-TYPE 139 153 151

Figure S214.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S215.  Gene #55: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
8P LOSS MUTATED 1 60 3 8
8P LOSS WILD-TYPE 54 102 113 174

Figure S215.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S216.  Gene #55: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 177 94
8P LOSS MUTATED 3 41 18
8P LOSS WILD-TYPE 118 136 76

Figure S216.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.028

Table S217.  Gene #55: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 108 113
8P LOSS MUTATED 37 4 21
8P LOSS WILD-TYPE 134 104 92

Figure S217.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S218.  Gene #56: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
8Q LOSS MUTATED 1 1 23 0 0
8Q LOSS WILD-TYPE 304 47 131 12 5

Figure S218.  Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S219.  Gene #56: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
8Q LOSS MUTATED 20 3 0
8Q LOSS WILD-TYPE 138 83 166

Figure S219.  Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S220.  Gene #56: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
8Q LOSS MUTATED 23 0 2
8Q LOSS WILD-TYPE 201 150 143

Figure S220.  Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S221.  Gene #56: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
8Q LOSS MUTATED 22 1 2
8Q LOSS WILD-TYPE 141 212 141

Figure S221.  Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S222.  Gene #56: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
8Q LOSS MUTATED 0 22 2
8Q LOSS WILD-TYPE 141 197 153

Figure S222.  Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S223.  Gene #56: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
8Q LOSS MUTATED 0 21 2 1
8Q LOSS WILD-TYPE 55 141 114 181

Figure S223.  Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S224.  Gene #57: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
9P LOSS MUTATED 2 7 0 0 0
9P LOSS WILD-TYPE 12 2 7 7 16

Figure S224.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S225.  Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
9P LOSS MUTATED 2 14 83 0 0
9P LOSS WILD-TYPE 303 34 71 12 5

Figure S225.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S226.  Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
9P LOSS MUTATED 55 20 9
9P LOSS WILD-TYPE 103 66 157

Figure S226.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S227.  Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
9P LOSS MUTATED 80 6 13
9P LOSS WILD-TYPE 144 144 132

Figure S227.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S228.  Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
9P LOSS MUTATED 71 15 13
9P LOSS WILD-TYPE 92 198 130

Figure S228.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S229.  Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
9P LOSS MUTATED 9 72 15
9P LOSS WILD-TYPE 132 147 140

Figure S229.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S230.  Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
9P LOSS MUTATED 2 66 10 18
9P LOSS WILD-TYPE 53 96 106 164

Figure S230.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S231.  Gene #58: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
9Q LOSS MUTATED 0 9 0 0
9Q LOSS WILD-TYPE 14 8 12 10

Figure S231.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S232.  Gene #58: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
9Q LOSS MUTATED 2 7 0 0 0
9Q LOSS WILD-TYPE 12 2 7 7 16

Figure S232.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S233.  Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
9Q LOSS MUTATED 3 19 95 0 0
9Q LOSS WILD-TYPE 302 29 59 12 5

Figure S233.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S234.  Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
9Q LOSS MUTATED 66 22 13
9Q LOSS WILD-TYPE 92 64 153

Figure S234.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'RPPA_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.16

Table S235.  Gene #58: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
9Q LOSS MUTATED 6 12 1 2 1 6
9Q LOSS WILD-TYPE 35 25 38 10 40 18

Figure S235.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S236.  Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
9Q LOSS MUTATED 94 8 15
9Q LOSS WILD-TYPE 130 142 130

Figure S236.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S237.  Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
9Q LOSS MUTATED 82 20 15
9Q LOSS WILD-TYPE 81 193 128

Figure S237.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S238.  Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
9Q LOSS MUTATED 12 85 17
9Q LOSS WILD-TYPE 129 134 138

Figure S238.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S239.  Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
9Q LOSS MUTATED 2 75 11 26
9Q LOSS WILD-TYPE 53 87 105 156

Figure S239.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S240.  Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
10P LOSS MUTATED 0 2 38 0 0
10P LOSS WILD-TYPE 305 46 116 12 5

Figure S240.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S241.  Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
10P LOSS MUTATED 28 5 1
10P LOSS WILD-TYPE 130 81 165

Figure S241.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S242.  Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
10P LOSS MUTATED 36 1 3
10P LOSS WILD-TYPE 188 149 142

Figure S242.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S243.  Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
10P LOSS MUTATED 32 5 3
10P LOSS WILD-TYPE 131 208 140

Figure S243.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S244.  Gene #59: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
10P LOSS MUTATED 3 33 2
10P LOSS WILD-TYPE 138 186 153

Figure S244.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S245.  Gene #59: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
10P LOSS MUTATED 1 29 1 7
10P LOSS WILD-TYPE 54 133 115 175

Figure S245.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S246.  Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
10Q LOSS MUTATED 1 2 36 0 0
10Q LOSS WILD-TYPE 304 46 118 12 5

Figure S246.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S247.  Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
10Q LOSS MUTATED 27 6 1
10Q LOSS WILD-TYPE 131 80 165

Figure S247.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S248.  Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
10Q LOSS MUTATED 34 1 4
10Q LOSS WILD-TYPE 190 149 141

Figure S248.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S249.  Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
10Q LOSS MUTATED 28 7 4
10Q LOSS WILD-TYPE 135 206 139

Figure S249.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S250.  Gene #60: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
10Q LOSS MUTATED 4 31 3
10Q LOSS WILD-TYPE 137 188 152

Figure S250.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S251.  Gene #60: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
10Q LOSS MUTATED 1 27 2 8
10Q LOSS WILD-TYPE 54 135 114 174

Figure S251.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S252.  Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
11P LOSS MUTATED 1 9 60 0 2
11P LOSS WILD-TYPE 304 39 94 12 3

Figure S252.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S253.  Gene #61: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
11P LOSS MUTATED 50 12 5
11P LOSS WILD-TYPE 108 74 161

Figure S253.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S254.  Gene #61: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
11P LOSS MUTATED 62 4 6
11P LOSS WILD-TYPE 162 146 139

Figure S254.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S255.  Gene #61: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
11P LOSS MUTATED 52 13 7
11P LOSS WILD-TYPE 111 200 136

Figure S255.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S256.  Gene #61: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
11P LOSS MUTATED 7 56 8
11P LOSS WILD-TYPE 134 163 147

Figure S256.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S257.  Gene #61: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
11P LOSS MUTATED 0 48 6 17
11P LOSS WILD-TYPE 55 114 110 165

Figure S257.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S258.  Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
11Q LOSS MUTATED 1 11 54 0 2
11Q LOSS WILD-TYPE 304 37 100 12 3

Figure S258.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S259.  Gene #62: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
11Q LOSS MUTATED 48 11 6
11Q LOSS WILD-TYPE 110 75 160

Figure S259.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S260.  Gene #62: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
11Q LOSS MUTATED 56 4 8
11Q LOSS WILD-TYPE 168 146 137

Figure S260.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S261.  Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
11Q LOSS MUTATED 50 10 8
11Q LOSS WILD-TYPE 113 203 135

Figure S261.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S262.  Gene #62: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
11Q LOSS MUTATED 7 52 9
11Q LOSS WILD-TYPE 134 167 146

Figure S262.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S263.  Gene #62: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
11Q LOSS MUTATED 0 46 7 15
11Q LOSS WILD-TYPE 55 116 109 167

Figure S263.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.16

Table S264.  Gene #62: '11q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 177 94
11Q LOSS MUTATED 10 44 11
11Q LOSS WILD-TYPE 111 133 83

Figure S264.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.23

Table S265.  Gene #62: '11q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 108 113
11Q LOSS MUTATED 43 10 12
11Q LOSS WILD-TYPE 128 98 101

Figure S265.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S266.  Gene #63: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
12P LOSS MUTATED 0 3 38 1 0
12P LOSS WILD-TYPE 305 45 116 11 5

Figure S266.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S267.  Gene #63: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
12P LOSS MUTATED 28 3 4
12P LOSS WILD-TYPE 130 83 162

Figure S267.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S268.  Gene #63: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
12P LOSS MUTATED 37 0 5
12P LOSS WILD-TYPE 187 150 140

Figure S268.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S269.  Gene #63: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
12P LOSS MUTATED 33 3 6
12P LOSS WILD-TYPE 130 210 137

Figure S269.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S270.  Gene #63: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
12P LOSS MUTATED 2 33 5
12P LOSS WILD-TYPE 139 186 150

Figure S270.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S271.  Gene #63: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
12P LOSS MUTATED 0 32 3 5
12P LOSS WILD-TYPE 55 130 113 177

Figure S271.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S272.  Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
12Q LOSS MUTATED 0 2 31 1 0
12Q LOSS WILD-TYPE 305 46 123 11 5

Figure S272.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S273.  Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
12Q LOSS MUTATED 25 1 2
12Q LOSS WILD-TYPE 133 85 164

Figure S273.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S274.  Gene #64: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
12Q LOSS MUTATED 31 0 3
12Q LOSS WILD-TYPE 193 150 142

Figure S274.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S275.  Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
12Q LOSS MUTATED 29 1 4
12Q LOSS WILD-TYPE 134 212 139

Figure S275.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.033

Table S276.  Gene #64: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
12Q LOSS MUTATED 3 26 3
12Q LOSS WILD-TYPE 138 193 152

Figure S276.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S277.  Gene #64: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
12Q LOSS MUTATED 0 28 1 3
12Q LOSS WILD-TYPE 55 134 115 179

Figure S277.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S278.  Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
13Q LOSS MUTATED 4 20 63 1 1
13Q LOSS WILD-TYPE 301 28 91 11 4

Figure S278.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S279.  Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
13Q LOSS MUTATED 48 17 12
13Q LOSS WILD-TYPE 110 69 154

Figure S279.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S280.  Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
13Q LOSS MUTATED 65 8 16
13Q LOSS WILD-TYPE 159 142 129

Figure S280.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S281.  Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
13Q LOSS MUTATED 49 25 15
13Q LOSS WILD-TYPE 114 188 128

Figure S281.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S282.  Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
13Q LOSS MUTATED 16 58 14
13Q LOSS WILD-TYPE 125 161 141

Figure S282.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S283.  Gene #65: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
13Q LOSS MUTATED 2 49 9 28
13Q LOSS WILD-TYPE 53 113 107 154

Figure S283.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S284.  Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
14Q LOSS MUTATED 0 4 49 1 2
14Q LOSS WILD-TYPE 305 44 105 11 3

Figure S284.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S285.  Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
14Q LOSS MUTATED 36 7 1
14Q LOSS WILD-TYPE 122 79 165

Figure S285.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S286.  Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
14Q LOSS MUTATED 49 3 4
14Q LOSS WILD-TYPE 175 147 141

Figure S286.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S287.  Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
14Q LOSS MUTATED 44 8 4
14Q LOSS WILD-TYPE 119 205 139

Figure S287.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S288.  Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
14Q LOSS MUTATED 7 44 3
14Q LOSS WILD-TYPE 134 175 152

Figure S288.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S289.  Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
14Q LOSS MUTATED 0 40 1 13
14Q LOSS WILD-TYPE 55 122 115 169

Figure S289.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S290.  Gene #66: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 177 94
14Q LOSS MUTATED 3 34 8
14Q LOSS WILD-TYPE 118 143 86

Figure S290.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S291.  Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
15Q LOSS MUTATED 1 6 0 0 0
15Q LOSS WILD-TYPE 13 3 7 7 16

Figure S291.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S292.  Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
15Q LOSS MUTATED 4 14 86 0 2
15Q LOSS WILD-TYPE 301 34 68 12 3

Figure S292.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S293.  Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
15Q LOSS MUTATED 67 18 8
15Q LOSS WILD-TYPE 91 68 158

Figure S293.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S294.  Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
15Q LOSS MUTATED 91 7 8
15Q LOSS WILD-TYPE 133 143 137

Figure S294.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S295.  Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
15Q LOSS MUTATED 77 21 8
15Q LOSS WILD-TYPE 86 192 135

Figure S295.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S296.  Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
15Q LOSS MUTATED 11 84 9
15Q LOSS WILD-TYPE 130 135 146

Figure S296.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S297.  Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
15Q LOSS MUTATED 0 71 5 28
15Q LOSS WILD-TYPE 55 91 111 154

Figure S297.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S298.  Gene #67: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 177 94
15Q LOSS MUTATED 10 62 20
15Q LOSS WILD-TYPE 111 115 74

Figure S298.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S299.  Gene #67: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 108 113
15Q LOSS MUTATED 59 10 23
15Q LOSS WILD-TYPE 112 98 90

Figure S299.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S300.  Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
16P LOSS MUTATED 5 9 80 0 0
16P LOSS WILD-TYPE 300 39 74 12 5

Figure S300.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S301.  Gene #68: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
16P LOSS MUTATED 58 20 6
16P LOSS WILD-TYPE 100 66 160

Figure S301.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S302.  Gene #68: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
16P LOSS MUTATED 82 5 7
16P LOSS WILD-TYPE 142 145 138

Figure S302.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S303.  Gene #68: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
16P LOSS MUTATED 67 19 8
16P LOSS WILD-TYPE 96 194 135

Figure S303.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S304.  Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
16P LOSS MUTATED 10 72 9
16P LOSS WILD-TYPE 131 147 146

Figure S304.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S305.  Gene #68: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
16P LOSS MUTATED 1 65 7 18
16P LOSS WILD-TYPE 54 97 109 164

Figure S305.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.054

Table S306.  Gene #68: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 177 94
16P LOSS MUTATED 10 48 25
16P LOSS WILD-TYPE 111 129 69

Figure S306.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.15

Table S307.  Gene #68: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 108 113
16P LOSS MUTATED 45 9 29
16P LOSS WILD-TYPE 126 99 84

Figure S307.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S308.  Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
16Q LOSS MUTATED 15 13 107 0 0
16Q LOSS WILD-TYPE 290 35 47 12 5

Figure S308.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S309.  Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
16Q LOSS MUTATED 77 26 15
16Q LOSS WILD-TYPE 81 60 151

Figure S309.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S310.  Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
16Q LOSS MUTATED 107 15 13
16Q LOSS WILD-TYPE 117 135 132

Figure S310.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S311.  Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
16Q LOSS MUTATED 89 33 13
16Q LOSS WILD-TYPE 74 180 130

Figure S311.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S312.  Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
16Q LOSS MUTATED 20 96 15
16Q LOSS WILD-TYPE 121 123 140

Figure S312.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S313.  Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
16Q LOSS MUTATED 7 84 11 29
16Q LOSS WILD-TYPE 48 78 105 153

Figure S313.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S314.  Gene #69: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 177 94
16Q LOSS MUTATED 16 68 32
16Q LOSS WILD-TYPE 105 109 62

Figure S314.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.033

Table S315.  Gene #69: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 108 113
16Q LOSS MUTATED 65 15 36
16Q LOSS WILD-TYPE 106 93 77

Figure S315.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.086

Table S316.  Gene #70: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
17P LOSS MUTATED 1 6 1 0 0
17P LOSS WILD-TYPE 13 3 6 7 16

Figure S316.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S317.  Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
17P LOSS MUTATED 3 12 107 0 0
17P LOSS WILD-TYPE 302 36 47 12 5

Figure S317.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S318.  Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
17P LOSS MUTATED 76 20 11
17P LOSS WILD-TYPE 82 66 155

Figure S318.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S319.  Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
17P LOSS MUTATED 102 5 14
17P LOSS WILD-TYPE 122 145 131

Figure S319.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S320.  Gene #70: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
17P LOSS MUTATED 86 19 16
17P LOSS WILD-TYPE 77 194 127

Figure S320.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S321.  Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
17P LOSS MUTATED 8 94 17
17P LOSS WILD-TYPE 133 125 138

Figure S321.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S322.  Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
17P LOSS MUTATED 1 80 12 26
17P LOSS WILD-TYPE 54 82 104 156

Figure S322.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S323.  Gene #71: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 14 9 7 7 16
17Q LOSS MUTATED 0 6 0 0 0
17Q LOSS WILD-TYPE 14 3 7 7 16

Figure S323.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S324.  Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
17Q LOSS MUTATED 2 11 75 0 0
17Q LOSS WILD-TYPE 303 37 79 12 5

Figure S324.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S325.  Gene #71: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
17Q LOSS MUTATED 50 17 10
17Q LOSS WILD-TYPE 108 69 156

Figure S325.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S326.  Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
17Q LOSS MUTATED 70 5 12
17Q LOSS WILD-TYPE 154 145 133

Figure S326.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S327.  Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
17Q LOSS MUTATED 56 17 14
17Q LOSS WILD-TYPE 107 196 129

Figure S327.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S328.  Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
17Q LOSS MUTATED 8 62 15
17Q LOSS WILD-TYPE 133 157 140

Figure S328.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S329.  Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
17Q LOSS MUTATED 1 52 9 23
17Q LOSS WILD-TYPE 54 110 107 159

Figure S329.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S330.  Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
18P LOSS MUTATED 1 11 38 0 2
18P LOSS WILD-TYPE 304 37 116 12 3

Figure S330.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S331.  Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
18P LOSS MUTATED 34 8 4
18P LOSS WILD-TYPE 124 78 162

Figure S331.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S332.  Gene #72: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
18P LOSS MUTATED 40 6 6
18P LOSS WILD-TYPE 184 144 139

Figure S332.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.07

Table S333.  Gene #72: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
18P LOSS MUTATED 8 36 7
18P LOSS WILD-TYPE 133 183 148

Figure S333.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.15

Table S334.  Gene #72: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
18P LOSS MUTATED 1 27 4 19
18P LOSS WILD-TYPE 54 135 112 163

Figure S334.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S335.  Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
18Q LOSS MUTATED 1 13 49 0 2
18Q LOSS WILD-TYPE 304 35 105 12 3

Figure S335.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S336.  Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
18Q LOSS MUTATED 42 11 6
18Q LOSS WILD-TYPE 116 75 160

Figure S336.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S337.  Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
18Q LOSS MUTATED 52 6 7
18Q LOSS WILD-TYPE 172 144 138

Figure S337.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S338.  Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
18Q LOSS MUTATED 38 19 8
18Q LOSS WILD-TYPE 125 194 135

Figure S338.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S339.  Gene #73: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
18Q LOSS MUTATED 7 48 9
18Q LOSS WILD-TYPE 134 171 146

Figure S339.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S340.  Gene #73: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
18Q LOSS MUTATED 0 39 5 20
18Q LOSS WILD-TYPE 55 123 111 162

Figure S340.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S341.  Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
19P LOSS MUTATED 1 13 43 0 0
19P LOSS WILD-TYPE 304 35 111 12 5

Figure S341.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S342.  Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
19P LOSS MUTATED 42 7 2
19P LOSS WILD-TYPE 116 79 164

Figure S342.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S343.  Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
19P LOSS MUTATED 48 5 4
19P LOSS WILD-TYPE 176 145 141

Figure S343.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S344.  Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
19P LOSS MUTATED 41 12 4
19P LOSS WILD-TYPE 122 201 139

Figure S344.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S345.  Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
19P LOSS MUTATED 5 44 6
19P LOSS WILD-TYPE 136 175 149

Figure S345.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S346.  Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
19P LOSS MUTATED 1 37 4 13
19P LOSS WILD-TYPE 54 125 112 169

Figure S346.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S347.  Gene #74: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 177 94
19P LOSS MUTATED 5 38 7
19P LOSS WILD-TYPE 116 139 87

Figure S347.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.08

Table S348.  Gene #74: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 108 113
19P LOSS MUTATED 35 5 10
19P LOSS WILD-TYPE 136 103 103

Figure S348.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S349.  Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
19Q LOSS MUTATED 2 12 39 0 0
19Q LOSS WILD-TYPE 303 36 115 12 5

Figure S349.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S350.  Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
19Q LOSS MUTATED 34 8 4
19Q LOSS WILD-TYPE 124 78 162

Figure S350.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S351.  Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
19Q LOSS MUTATED 42 5 5
19Q LOSS WILD-TYPE 182 145 140

Figure S351.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S352.  Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
19Q LOSS MUTATED 37 10 5
19Q LOSS WILD-TYPE 126 203 138

Figure S352.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S353.  Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
19Q LOSS MUTATED 5 39 7
19Q LOSS WILD-TYPE 136 180 148

Figure S353.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S354.  Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
19Q LOSS MUTATED 1 32 5 13
19Q LOSS WILD-TYPE 54 130 111 169

Figure S354.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.028

Table S355.  Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
20P LOSS MUTATED 1 4 13 0 0
20P LOSS WILD-TYPE 304 44 141 12 5

Figure S355.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S356.  Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
21Q LOSS MUTATED 4 6 41 0 2
21Q LOSS WILD-TYPE 301 42 113 12 3

Figure S356.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S357.  Gene #78: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
21Q LOSS MUTATED 32 7 5
21Q LOSS WILD-TYPE 126 79 161

Figure S357.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S358.  Gene #78: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
21Q LOSS MUTATED 45 7 1
21Q LOSS WILD-TYPE 179 143 144

Figure S358.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S359.  Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
21Q LOSS MUTATED 36 15 2
21Q LOSS WILD-TYPE 127 198 141

Figure S359.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S360.  Gene #78: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
21Q LOSS MUTATED 6 43 2
21Q LOSS WILD-TYPE 135 176 153

Figure S360.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S361.  Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
21Q LOSS MUTATED 2 35 2 12
21Q LOSS WILD-TYPE 53 127 114 170

Figure S361.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S362.  Gene #78: '21q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 177 94
21Q LOSS MUTATED 1 34 9
21Q LOSS WILD-TYPE 120 143 85

Figure S362.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.15

Table S363.  Gene #78: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 108 113
21Q LOSS MUTATED 28 2 14
21Q LOSS WILD-TYPE 143 106 99

Figure S363.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S364.  Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
22Q LOSS MUTATED 3 14 87 0 1
22Q LOSS WILD-TYPE 302 34 67 12 4

Figure S364.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S365.  Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
22Q LOSS MUTATED 63 20 13
22Q LOSS WILD-TYPE 95 66 153

Figure S365.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S366.  Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
22Q LOSS MUTATED 81 7 16
22Q LOSS WILD-TYPE 143 143 129

Figure S366.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S367.  Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
22Q LOSS MUTATED 65 23 16
22Q LOSS WILD-TYPE 98 190 127

Figure S367.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S368.  Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
22Q LOSS MUTATED 10 76 17
22Q LOSS WILD-TYPE 131 143 138

Figure S368.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S369.  Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
22Q LOSS MUTATED 1 64 11 27
22Q LOSS WILD-TYPE 54 98 105 155

Figure S369.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S370.  Gene #80: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 305 48 154 12 5
XQ LOSS MUTATED 1 7 61 0 0
XQ LOSS WILD-TYPE 304 41 93 12 5

Figure S370.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S371.  Gene #80: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 158 86 166
XQ LOSS MUTATED 41 11 6
XQ LOSS WILD-TYPE 117 75 160

Figure S371.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq loss' versus 'RPPA_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.09

Table S372.  Gene #80: 'xq loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
XQ LOSS MUTATED 3 13 2 1 1 1
XQ LOSS WILD-TYPE 38 24 37 11 40 23

Figure S372.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S373.  Gene #80: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 224 150 145
XQ LOSS MUTATED 59 5 4
XQ LOSS WILD-TYPE 165 145 141

Figure S373.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S374.  Gene #80: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 213 143
XQ LOSS MUTATED 46 17 5
XQ LOSS WILD-TYPE 117 196 138

Figure S374.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S375.  Gene #80: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 219 155
XQ LOSS MUTATED 7 50 9
XQ LOSS WILD-TYPE 134 169 146

Figure S375.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S376.  Gene #80: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 162 116 182
XQ LOSS MUTATED 1 45 4 16
XQ LOSS WILD-TYPE 54 117 112 166

Figure S376.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S377.  Gene #80: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 108 113
XQ LOSS MUTATED 42 5 11
XQ LOSS WILD-TYPE 129 103 102

Figure S377.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

  • Molecular subtypes file = UCEC-TP.transferedmergedcluster.txt

  • Number of patients = 524

  • Number of significantly arm-level cnvs = 80

  • Number of molecular subtypes = 12

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)