Correlation between copy number variations of arm-level result and molecular subtypes
Stomach and Esophageal carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
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 (2016): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1FX78ZX
Overview
Introduction

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

Summary

Testing the association between copy number variation 82 arm-level events and 10 molecular subtypes across 625 patients, 493 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

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

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

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

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

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

  • 4q gain cnv correlated to 'MRNASEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 5q gain cnv correlated to 'CN_CNMF'.

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

  • 6q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 7q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

  • 8q gain cnv correlated to 'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 9q gain cnv correlated to 'CN_CNMF'.

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

  • 10q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

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

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

  • 12q gain cnv correlated to 'CN_CNMF'.

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

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

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

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

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

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

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

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

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

  • 19p gain cnv correlated to 'CN_CNMF' and 'RPPA_CHIERARCHICAL'.

  • 19q gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

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

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

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

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

  • 2p loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 2q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 3q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_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_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',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

  • 7q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

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

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

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

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

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

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

  • 12q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 15q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

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

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

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

  • 18p loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

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

  • 20p loss cnv correlated to 'CN_CNMF'.

  • 20q loss cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 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',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 493 significant findings detected.

Clinical
Features
CN
CNMF
METHLYATION
CNMF
RPPA
CNMF
RPPA
CHIERARCHICAL
MRNASEQ
CNMF
MRNASEQ
CHIERARCHICAL
MIRSEQ
CNMF
MIRSEQ
CHIERARCHICAL
MIRSEQ
MATURE
CNMF
MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
6p gain 118 (19%) 507 1e-05
(4.38e-05)
1e-05
(4.38e-05)
0.0239
(0.044)
0.031
(0.0544)
0.0251
(0.0457)
1e-05
(4.38e-05)
0.0104
(0.0216)
1e-05
(4.38e-05)
0.00442
(0.0103)
2e-05
(8.24e-05)
xq loss 98 (16%) 527 1e-05
(4.38e-05)
0.00027
(0.000839)
0.0284
(0.0505)
0.0022
(0.0055)
6e-05
(0.000217)
0.00048
(0.00141)
0.00107
(0.00292)
0.0004
(0.0012)
0.0275
(0.0492)
0.0358
(0.0617)
5p gain 179 (29%) 446 1e-05
(4.38e-05)
1e-05
(4.38e-05)
0.572
(0.64)
0.0198
(0.0378)
6e-05
(0.000217)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
5e-05
(0.000187)
1e-05
(4.38e-05)
6q gain 100 (16%) 525 1e-05
(4.38e-05)
0.00013
(0.000425)
0.0419
(0.0707)
0.0373
(0.0637)
0.0103
(0.0214)
0.00054
(0.00156)
0.0716
(0.113)
1e-05
(4.38e-05)
0.0234
(0.0434)
1e-05
(4.38e-05)
18p gain 135 (22%) 490 1e-05
(4.38e-05)
1e-05
(4.38e-05)
0.584
(0.651)
0.0187
(0.0364)
0.00303
(0.00737)
1e-05
(4.38e-05)
0.00076
(0.00215)
0.00015
(0.000484)
0.0018
(0.0046)
0.00077
(0.00216)
5q loss 195 (31%) 430 1e-05
(4.38e-05)
1e-05
(4.38e-05)
0.0149
(0.0297)
0.412
(0.49)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
2e-05
(8.24e-05)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
8p loss 156 (25%) 469 1e-05
(4.38e-05)
0.0084
(0.0182)
0.131
(0.19)
0.00618
(0.0139)
0.00197
(0.005)
1e-05
(4.38e-05)
4e-05
(0.000151)
1e-05
(4.38e-05)
0.0395
(0.067)
3e-05
(0.000117)
xp loss 123 (20%) 502 1e-05
(4.38e-05)
1e-05
(4.38e-05)
0.275
(0.348)
0.00254
(0.00629)
1e-05
(4.38e-05)
0.00049
(0.00143)
0.0001
(0.000339)
9e-05
(0.000306)
0.00612
(0.0139)
0.00086
(0.0024)
2p gain 137 (22%) 488 1e-05
(4.38e-05)
1e-05
(4.38e-05)
0.521
(0.595)
0.6
(0.668)
9e-05
(0.000306)
2e-05
(8.24e-05)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
5e-05
(0.000187)
1e-05
(4.38e-05)
2q gain 113 (18%) 512 1e-05
(4.38e-05)
3e-05
(0.000117)
0.993
(0.993)
0.848
(0.886)
0.00619
(0.0139)
0.00016
(0.000515)
0.00044
(0.00131)
0.00069
(0.00196)
0.00858
(0.0185)
0.0257
(0.0466)
3q gain 170 (27%) 455 1e-05
(4.38e-05)
1e-05
(4.38e-05)
0.161
(0.221)
0.922
(0.945)
0.00039
(0.00118)
0.00013
(0.000425)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
6e-05
(0.000217)
1e-05
(4.38e-05)
7p gain 308 (49%) 317 1e-05
(4.38e-05)
1e-05
(4.38e-05)
0.541
(0.615)
0.364
(0.441)
0.00025
(0.000779)
0.00377
(0.00893)
0.003
(0.00732)
0.00012
(0.000398)
0.017
(0.0335)
0.00908
(0.0194)
12p gain 149 (24%) 476 1e-05
(4.38e-05)
8e-05
(0.000276)
0.877
(0.907)
0.233
(0.302)
0.022
(0.041)
0.00195
(0.00497)
0.00032
(0.000983)
0.0004
(0.0012)
0.00065
(0.00186)
6e-05
(0.000217)
13q gain 197 (32%) 428 1e-05
(4.38e-05)
0.0323
(0.0563)
0.113
(0.168)
0.778
(0.826)
3e-05
(0.000117)
1e-05
(4.38e-05)
0.0127
(0.0256)
1e-05
(4.38e-05)
0.0126
(0.0255)
1e-05
(4.38e-05)
14q gain 76 (12%) 549 1e-05
(4.38e-05)
8e-05
(0.000276)
0.558
(0.627)
0.156
(0.215)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
6e-05
(0.000217)
1e-05
(4.38e-05)
16q gain 86 (14%) 539 1e-05
(4.38e-05)
0.00111
(0.00301)
0.0863
(0.133)
0.415
(0.493)
0.00624
(0.014)
0.00018
(0.000568)
0.00328
(0.00789)
4e-05
(0.000151)
0.00688
(0.0152)
3e-05
(0.000117)
17p gain 61 (10%) 564 1e-05
(4.38e-05)
0.00344
(0.00825)
0.455
(0.53)
0.377
(0.455)
0.0167
(0.033)
0.021
(0.0395)
4e-05
(0.000151)
0.0195
(0.0375)
0.00596
(0.0136)
0.0013
(0.00344)
22q gain 63 (10%) 562 1e-05
(4.38e-05)
1e-05
(4.38e-05)
0.976
(0.981)
0.744
(0.793)
9e-05
(0.000306)
7e-05
(0.000247)
3e-05
(0.000117)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
xq gain 93 (15%) 532 1e-05
(4.38e-05)
3e-05
(0.000117)
0.427
(0.505)
0.208
(0.275)
0.00882
(0.019)
8e-05
(0.000276)
0.00206
(0.0052)
0.00023
(0.00072)
0.0343
(0.0596)
0.00017
(0.000538)
3p loss 187 (30%) 438 1e-05
(4.38e-05)
1e-05
(4.38e-05)
0.733
(0.784)
0.181
(0.243)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
4p loss 274 (44%) 351 1e-05
(4.38e-05)
1e-05
(4.38e-05)
0.755
(0.804)
0.863
(0.898)
0.0017
(0.00438)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
5p loss 110 (18%) 515 1e-05
(4.38e-05)
1e-05
(4.38e-05)
0.135
(0.194)
0.354
(0.432)
8e-05
(0.000276)
1e-05
(4.38e-05)
0.00023
(0.00072)
1e-05
(4.38e-05)
0.0108
(0.0223)
1e-05
(4.38e-05)
9p loss 249 (40%) 376 1e-05
(4.38e-05)
8e-05
(0.000276)
0.47
(0.544)
0.15
(0.21)
7e-05
(0.000247)
1e-05
(4.38e-05)
0.00051
(0.00148)
1e-05
(4.38e-05)
0.00098
(0.00271)
0.00012
(0.000398)
9q loss 173 (28%) 452 1e-05
(4.38e-05)
4e-05
(0.000151)
0.24
(0.31)
0.499
(0.573)
0.00687
(0.0152)
1e-05
(4.38e-05)
0.00017
(0.000538)
1e-05
(4.38e-05)
3e-05
(0.000117)
2e-05
(8.24e-05)
10p loss 118 (19%) 507 1e-05
(4.38e-05)
1e-05
(4.38e-05)
0.913
(0.937)
0.707
(0.762)
0.00377
(0.00893)
1e-05
(4.38e-05)
0.00272
(0.00668)
1e-05
(4.38e-05)
0.00156
(0.00406)
1e-05
(4.38e-05)
10q loss 118 (19%) 507 1e-05
(4.38e-05)
1e-05
(4.38e-05)
0.364
(0.441)
0.564
(0.634)
0.00077
(0.00216)
1e-05
(4.38e-05)
0.00356
(0.00851)
1e-05
(4.38e-05)
0.00212
(0.00533)
2e-05
(8.24e-05)
11p loss 117 (19%) 508 1e-05
(4.38e-05)
6e-05
(0.000217)
0.419
(0.495)
0.0906
(0.138)
7e-05
(0.000247)
4e-05
(0.000151)
2e-05
(8.24e-05)
0.00015
(0.000484)
0.00359
(0.00856)
0.00556
(0.0127)
11q loss 122 (20%) 503 1e-05
(4.38e-05)
1e-05
(4.38e-05)
0.479
(0.553)
0.393
(0.47)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
13q loss 103 (16%) 522 1e-05
(4.38e-05)
3e-05
(0.000117)
0.96
(0.968)
0.0547
(0.0895)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
17p loss 237 (38%) 388 1e-05
(4.38e-05)
3e-05
(0.000117)
0.14
(0.198)
0.131
(0.19)
0.00056
(0.00161)
1e-05
(4.38e-05)
0.00012
(0.000398)
1e-05
(4.38e-05)
0.0194
(0.0373)
7e-05
(0.000247)
19p loss 182 (29%) 443 1e-05
(4.38e-05)
1e-05
(4.38e-05)
0.13
(0.189)
0.0826
(0.129)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
19q loss 142 (23%) 483 1e-05
(4.38e-05)
1e-05
(4.38e-05)
0.213
(0.28)
0.113
(0.168)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
1e-05
(4.38e-05)
2e-05
(8.24e-05)
1e-05
(4.38e-05)
21q loss 287 (46%) 338 1e-05
(4.38e-05)
0.0264
(0.0474)
0.947
(0.963)
0.836
(0.876)
0.00045
(0.00133)
1e-05
(4.38e-05)
0.0352
(0.0608)
1e-05
(4.38e-05)
0.00017
(0.000538)
0.0199
(0.0379)
22q loss 218 (35%) 407 1e-05
(4.38e-05)
0.0104
(0.0216)
0.615
(0.681)
0.455
(0.53)
0.0133
(0.0268)
1e-05
(4.38e-05)
0.0489
(0.0814)
1e-05
(4.38e-05)
0.00244
(0.00606)
0.00012
(0.000398)
1q gain 170 (27%) 455 1e-05
(4.38e-05)
1e-05
(4.38e-05)
0.856
(0.893)
0.119
(0.176)
0.125
(0.183)
0.00466
(0.0108)
0.00036
(0.0011)
1e-05
(4.38e-05)
0.00172
(0.00442)
0.00084
(0.00235)
15q gain 67 (11%) 558 1e-05
(4.38e-05)
0.0157
(0.0312)
0.197
(0.262)
0.191
(0.255)
0.00255
(0.0063)
0.0013
(0.00344)
0.0372
(0.0637)
0.0707
(0.112)
0.0192
(0.0372)
0.00131
(0.00345)
20p gain 349 (56%) 276 1e-05
(4.38e-05)
0.00149
(0.00389)
0.133
(0.191)
0.074
(0.116)
0.301
(0.374)
0.001
(0.00275)
0.00669
(0.0148)
3e-05
(0.000117)
0.0124
(0.0251)
2e-05
(8.24e-05)
21q gain 39 (6%) 586 3e-05
(0.000117)
4e-05
(0.000151)
0.924
(0.946)
0.636
(0.701)
0.00799
(0.0174)
0.0141
(0.0282)
0.00466
(0.0108)
0.00217
(0.00544)
0.0766
(0.12)
0.0468
(0.0784)
xp gain 75 (12%) 550 0.00614
(0.0139)
2e-05
(8.24e-05)
0.807
(0.853)
0.214
(0.28)
0.0408
(0.069)
0.0338
(0.0589)
0.0436
(0.0734)
0.00324
(0.00781)
0.0829
(0.129)
0.0219
(0.0409)
1p loss 97 (16%) 528 1e-05
(4.38e-05)
0.00039
(0.00118)
0.227
(0.296)
0.452
(0.528)
0.00033
(0.00101)
0.0239
(0.044)
0.0256
(0.0465)
0.00091
(0.00253)
0.13
(0.189)
0.035
(0.0605)
4q loss 256 (41%) 369 1e-05
(4.38e-05)
0.00013
(0.000425)
0.328
(0.404)
0.302
(0.374)
0.113
(0.168)
8e-05
(0.000276)
0.00625
(0.014)
1e-05
(4.38e-05)
0.00755
(0.0166)
1e-05
(4.38e-05)
6p loss 93 (15%) 532 1e-05
(4.38e-05)
0.00807
(0.0175)
0.211
(0.278)
0.281
(0.353)
0.0156
(0.0309)
0.00094
(0.0026)
0.0385
(0.0654)
0.00118
(0.00317)
0.15
(0.21)
0.0205
(0.0389)
12p loss 98 (16%) 527 1e-05
(4.38e-05)
0.0118
(0.0242)
0.107
(0.161)
0.875
(0.906)
0.00032
(0.000983)
1e-05
(4.38e-05)
0.0866
(0.133)
1e-05
(4.38e-05)
0.00883
(0.019)
0.00011
(0.000371)
14q loss 157 (25%) 468 1e-05
(4.38e-05)
0.0073
(0.016)
0.538
(0.612)
0.285
(0.358)
0.0202
(0.0384)
1e-05
(4.38e-05)
0.83
(0.872)
1e-05
(4.38e-05)
0.0474
(0.0793)
0.00013
(0.000425)
16p loss 154 (25%) 471 1e-05
(4.38e-05)
0.0111
(0.023)
0.16
(0.22)
0.371
(0.448)
0.0285
(0.0505)
1e-05
(4.38e-05)
0.0911
(0.138)
1e-05
(4.38e-05)
0.00044
(0.00131)
2e-05
(8.24e-05)
1p gain 84 (13%) 541 1e-05
(4.38e-05)
0.00148
(0.00388)
0.667
(0.728)
0.273
(0.347)
0.653
(0.715)
0.0006
(0.00172)
0.0297
(0.0525)
0.00115
(0.0031)
0.0247
(0.0451)
0.0596
(0.0963)
11q gain 102 (16%) 523 1e-05
(4.38e-05)
0.0373
(0.0637)
0.201
(0.267)
0.154
(0.213)
0.075
(0.118)
0.00109
(0.00297)
0.0883
(0.135)
0.00132
(0.00347)
0.0032
(0.00774)
0.00128
(0.00341)
17q gain 108 (17%) 517 1e-05
(4.38e-05)
0.00781
(0.017)
0.829
(0.872)
0.862
(0.898)
0.0135
(0.027)
0.0179
(0.035)
0.00383
(0.00905)
0.177
(0.238)
0.0522
(0.0862)
0.0123
(0.025)
19q gain 119 (19%) 506 1e-05
(4.38e-05)
0.333
(0.408)
0.00918
(0.0196)
0.0277
(0.0494)
0.0296
(0.0525)
0.334
(0.41)
0.266
(0.339)
0.00161
(0.00416)
0.134
(0.193)
0.031
(0.0544)
3q loss 92 (15%) 533 1e-05
(4.38e-05)
0.00127
(0.00339)
0.0571
(0.0928)
0.118
(0.174)
0.0141
(0.0282)
1e-05
(4.38e-05)
0.0663
(0.106)
1e-05
(4.38e-05)
0.0841
(0.13)
0.0113
(0.0233)
12q loss 87 (14%) 538 1e-05
(4.38e-05)
0.0621
(0.0999)
0.293
(0.365)
0.743
(0.793)
0.00046
(0.00136)
1e-05
(4.38e-05)
0.122
(0.179)
6e-05
(0.000217)
0.00556
(0.0127)
0.024
(0.044)
17q loss 102 (16%) 523 1e-05
(4.38e-05)
0.0209
(0.0394)
0.327
(0.403)
0.0853
(0.132)
0.21
(0.277)
4e-05
(0.000151)
0.0209
(0.0394)
0.00051
(0.00148)
0.442
(0.517)
0.0102
(0.0213)
18q loss 257 (41%) 368 1e-05
(4.38e-05)
0.00598
(0.0136)
0.955
(0.966)
0.168
(0.229)
0.00306
(0.00742)
0.00042
(0.00126)
0.0669
(0.107)
0.00076
(0.00215)
0.055
(0.0896)
0.0277
(0.0494)
4p gain 37 (6%) 588 0.0197
(0.0378)
0.17
(0.232)
0.136
(0.194)
0.817
(0.862)
0.00537
(0.0123)
0.00997
(0.021)
0.218
(0.285)
0.00768
(0.0168)
0.186
(0.25)
0.0193
(0.0373)
11p gain 98 (16%) 527 1e-05
(4.38e-05)
0.0016
(0.00415)
0.661
(0.722)
0.361
(0.439)
0.419
(0.495)
0.0125
(0.0254)
0.501
(0.574)
0.00658
(0.0146)
0.012
(0.0246)
0.0542
(0.0889)
16p gain 100 (16%) 525 1e-05
(4.38e-05)
0.00412
(0.00968)
0.0901
(0.137)
0.661
(0.722)
0.115
(0.17)
0.00955
(0.0203)
0.122
(0.179)
6e-05
(0.000217)
0.292
(0.364)
0.00114
(0.00309)
20q gain 395 (63%) 230 1e-05
(4.38e-05)
0.0871
(0.133)
0.391
(0.468)
0.153
(0.213)
0.00639
(0.0142)
1e-05
(4.38e-05)
0.108
(0.163)
1e-05
(4.38e-05)
0.142
(0.202)
1e-05
(4.38e-05)
2q loss 49 (8%) 576 1e-05
(4.38e-05)
0.0599
(0.0964)
0.824
(0.867)
0.214
(0.28)
0.0321
(0.0561)
0.02
(0.0381)
0.287
(0.36)
0.0101
(0.0213)
0.0678
(0.108)
0.0189
(0.0367)
16q loss 167 (27%) 458 1e-05
(4.38e-05)
0.082
(0.128)
0.867
(0.901)
0.168
(0.229)
0.163
(0.223)
1e-05
(4.38e-05)
0.21
(0.277)
1e-05
(4.38e-05)
0.0044
(0.0103)
1e-05
(4.38e-05)
18q gain 79 (13%) 546 0.00203
(0.00514)
0.431
(0.507)
0.991
(0.992)
0.388
(0.467)
0.0224
(0.0416)
0.00983
(0.0208)
0.0345
(0.0598)
0.0587
(0.0949)
0.16
(0.22)
0.0718
(0.113)
2p loss 36 (6%) 589 0.00017
(0.000538)
0.478
(0.553)
0.0261
(0.0472)
0.0859
(0.132)
0.536
(0.611)
0.0181
(0.0354)
0.604
(0.671)
0.0219
(0.0409)
0.229
(0.297)
0.0549
(0.0896)
7q loss 50 (8%) 575 1e-05
(4.38e-05)
0.083
(0.129)
0.145
(0.204)
0.537
(0.612)
0.258
(0.331)
0.0045
(0.0105)
0.024
(0.044)
0.152
(0.212)
0.0094
(0.02)
0.176
(0.238)
8q loss 59 (9%) 566 1e-05
(4.38e-05)
0.305
(0.377)
0.955
(0.966)
0.0559
(0.091)
0.0262
(0.0472)
0.0175
(0.0343)
0.159
(0.22)
0.43
(0.507)
0.652
(0.715)
0.0314
(0.0551)
4q gain 30 (5%) 595 0.131
(0.19)
0.353
(0.431)
0.125
(0.183)
0.176
(0.238)
0.0242
(0.0443)
0.0874
(0.134)
0.551
(0.623)
0.00257
(0.00633)
0.152
(0.212)
0.0105
(0.0217)
8q gain 337 (54%) 288 0.869
(0.902)
0.00519
(0.012)
0.435
(0.512)
0.511
(0.586)
0.236
(0.305)
0.438
(0.514)
0.012
(0.0246)
0.0101
(0.0213)
0.464
(0.539)
0.804
(0.85)
10p gain 136 (22%) 489 1e-05
(4.38e-05)
0.0373
(0.0637)
0.949
(0.963)
0.845
(0.885)
0.628
(0.694)
0.0527
(0.087)
0.6
(0.668)
0.00121
(0.00324)
0.0847
(0.131)
0.0509
(0.0846)
10q gain 98 (16%) 527 1e-05
(4.38e-05)
0.159
(0.22)
0.902
(0.927)
0.784
(0.83)
0.709
(0.763)
0.00492
(0.0114)
0.989
(0.992)
0.0674
(0.107)
0.0175
(0.0343)
0.111
(0.166)
1q loss 47 (8%) 578 1e-05
(4.38e-05)
0.109
(0.164)
0.715
(0.769)
0.14
(0.198)
0.0531
(0.0875)
0.0662
(0.106)
0.0376
(0.0641)
0.0493
(0.082)
0.125
(0.183)
0.177
(0.238)
6q loss 112 (18%) 513 1e-05
(4.38e-05)
0.0227
(0.0421)
0.672
(0.731)
0.382
(0.46)
0.133
(0.191)
0.00222
(0.00553)
0.344
(0.42)
0.102
(0.154)
0.488
(0.561)
0.145
(0.204)
7p loss 33 (5%) 592 0.00105
(0.00288)
0.00993
(0.021)
0.262
(0.334)
0.399
(0.476)
0.739
(0.79)
0.195
(0.26)
0.144
(0.203)
0.248
(0.32)
0.0366
(0.0629)
0.44
(0.516)
15q loss 149 (24%) 476 1e-05
(4.38e-05)
0.204
(0.271)
0.301
(0.374)
0.391
(0.468)
0.225
(0.293)
0.0005
(0.00146)
0.58
(0.648)
0.0003
(0.000928)
0.208
(0.275)
0.611
(0.677)
3p gain 85 (14%) 540 7e-05
(0.000247)
0.0452
(0.0759)
0.324
(0.4)
0.136
(0.194)
0.389
(0.467)
0.19
(0.255)
0.153
(0.213)
0.329
(0.405)
0.273
(0.347)
0.275
(0.348)
7q gain 257 (41%) 368 1e-05
(4.38e-05)
2e-05
(8.24e-05)
0.556
(0.627)
0.277
(0.349)
0.0658
(0.106)
0.19
(0.255)
0.468
(0.542)
0.235
(0.305)
0.288
(0.36)
0.337
(0.413)
8p gain 248 (40%) 377 0.0209
(0.0394)
0.0266
(0.0477)
0.888
(0.917)
0.12
(0.177)
0.069
(0.109)
0.152
(0.212)
0.0909
(0.138)
0.572
(0.64)
0.275
(0.348)
0.657
(0.72)
19p gain 83 (13%) 542 2e-05
(8.24e-05)
0.64
(0.705)
0.148
(0.207)
0.0483
(0.0807)
0.732
(0.784)
0.682
(0.741)
0.766
(0.814)
0.573
(0.641)
0.967
(0.973)
0.965
(0.973)
18p loss 187 (30%) 438 1e-05
(4.38e-05)
0.253
(0.325)
0.0512
(0.0848)
0.781
(0.829)
0.163
(0.223)
0.441
(0.517)
0.948
(0.963)
0.12
(0.177)
0.024
(0.044)
0.453
(0.528)
20q loss 8 (1%) 617 0.137
(0.196)
0.0672
(0.107)
0.0574
(0.093)
0.55
(0.623)
0.0161
(0.0319)
0.0301
(0.0531)
0.0541
(0.0889)
0.144
(0.204)
0.648
(0.713)
0.134
(0.192)
5q gain 64 (10%) 561 0.00014
(0.000456)
0.622
(0.688)
0.89
(0.917)
0.402
(0.48)
0.703
(0.761)
0.926
(0.946)
0.415
(0.493)
0.548
(0.621)
0.294
(0.366)
0.177
(0.238)
9q gain 109 (17%) 516 0.00174
(0.00446)
0.728
(0.781)
0.374
(0.451)
0.821
(0.865)
0.485
(0.56)
0.941
(0.958)
0.926
(0.946)
0.369
(0.447)
0.557
(0.627)
0.94
(0.958)
12q gain 116 (19%) 509 0.00411
(0.00968)
0.26
(0.333)
0.985
(0.988)
0.262
(0.334)
0.718
(0.772)
0.636
(0.701)
0.112
(0.167)
0.208
(0.275)
0.132
(0.19)
0.293
(0.365)
20p loss 42 (7%) 583 0.00278
(0.0068)
0.557
(0.627)
0.093
(0.141)
0.263
(0.335)
0.243
(0.313)
0.107
(0.161)
0.956
(0.966)
0.194
(0.26)
0.487
(0.561)
0.691
(0.749)
9p gain 78 (12%) 547 0.276
(0.348)
0.672
(0.731)
0.7
(0.759)
0.519
(0.594)
0.89
(0.917)
0.951
(0.964)
0.849
(0.886)
0.872
(0.904)
0.892
(0.917)
0.706
(0.762)
'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
1P GAIN MUTATED 24 19 37 4
1P GAIN WILD-TYPE 127 79 145 190

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

'1p gain' versus 'METHLYATION_CNMF'

P value = 0.00148 (Fisher's exact test), Q value = 0.0039

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
1P GAIN MUTATED 31 34 13
1P GAIN WILD-TYPE 210 127 162

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

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-04 (Fisher's exact test), Q value = 0.0017

Table S3.  Gene #1: '1p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
1P GAIN MUTATED 26 22 9 19 6
1P GAIN WILD-TYPE 105 94 89 102 124

Figure S3.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_CNMF'

P value = 0.0297 (Fisher's exact test), Q value = 0.053

Table S4.  Gene #1: '1p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
1P GAIN MUTATED 31 37 15
1P GAIN WILD-TYPE 136 241 157

Figure S4.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00115 (Fisher's exact test), Q value = 0.0031

Table S5.  Gene #1: '1p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
1P GAIN MUTATED 27 21 11 17 7
1P GAIN WILD-TYPE 100 122 153 77 82

Figure S5.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0247 (Fisher's exact test), Q value = 0.045

Table S6.  Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
1P GAIN MUTATED 24 23 13 6 3
1P GAIN WILD-TYPE 99 132 108 41 70

Figure S6.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
1Q GAIN MUTATED 53 37 66 14
1Q GAIN WILD-TYPE 98 61 116 180

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

'1q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
1Q GAIN MUTATED 62 70 28
1Q GAIN WILD-TYPE 179 91 147

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

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00466 (Fisher's exact test), Q value = 0.011

Table S9.  Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
1Q GAIN MUTATED 46 27 28 41 22
1Q GAIN WILD-TYPE 85 89 70 80 108

Figure S9.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.0011

Table S10.  Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
1Q GAIN MUTATED 63 73 31
1Q GAIN WILD-TYPE 104 205 141

Figure S10.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
1Q GAIN MUTATED 49 44 19 37 18
1Q GAIN WILD-TYPE 78 99 145 57 71

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

'1q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00172 (Fisher's exact test), Q value = 0.0044

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
1Q GAIN MUTATED 49 43 23 14 13
1Q GAIN WILD-TYPE 74 112 98 33 60

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

'1q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00084 (Fisher's exact test), Q value = 0.0024

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
1Q GAIN MUTATED 20 37 25 24 36
1Q GAIN WILD-TYPE 31 87 119 84 56

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

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
2P GAIN MUTATED 39 23 65 10
2P GAIN WILD-TYPE 112 75 117 184

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
2P GAIN MUTATED 54 60 17
2P GAIN WILD-TYPE 187 101 158

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

'2p gain' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00031

Table S16.  Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
2P GAIN MUTATED 53 62 18
2P GAIN WILD-TYPE 117 211 135

Figure S16.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8.2e-05

Table S17.  Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
2P GAIN MUTATED 33 20 20 46 14
2P GAIN WILD-TYPE 98 96 78 75 116

Figure S17.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S18.  Gene #3: '2p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
2P GAIN MUTATED 60 58 18
2P GAIN WILD-TYPE 107 220 154

Figure S18.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S19.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
2P GAIN MUTATED 36 32 22 37 9
2P GAIN WILD-TYPE 91 111 142 57 80

Figure S19.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00019

Table S20.  Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
2P GAIN MUTATED 46 39 16 7 9
2P GAIN WILD-TYPE 77 116 105 40 64

Figure S20.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S21.  Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
2P GAIN MUTATED 11 38 19 14 35
2P GAIN WILD-TYPE 40 86 125 94 57

Figure S21.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S22.  Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
2Q GAIN MUTATED 35 19 50 9
2Q GAIN WILD-TYPE 116 79 132 185

Figure S22.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00012

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
2Q GAIN MUTATED 49 45 15
2Q GAIN WILD-TYPE 192 116 160

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

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.00619 (Fisher's exact test), Q value = 0.014

Table S24.  Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
2Q GAIN MUTATED 42 52 17
2Q GAIN WILD-TYPE 128 221 136

Figure S24.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00051

Table S25.  Gene #4: '2q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
2Q GAIN MUTATED 35 15 14 34 13
2Q GAIN WILD-TYPE 96 101 84 87 117

Figure S25.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.0013

Table S26.  Gene #4: '2q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
2Q GAIN MUTATED 46 47 19
2Q GAIN WILD-TYPE 121 231 153

Figure S26.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00069 (Fisher's exact test), Q value = 0.002

Table S27.  Gene #4: '2q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
2Q GAIN MUTATED 31 28 19 26 8
2Q GAIN WILD-TYPE 96 115 145 68 81

Figure S27.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00858 (Fisher's exact test), Q value = 0.019

Table S28.  Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
2Q GAIN MUTATED 36 32 19 7 7
2Q GAIN WILD-TYPE 87 123 102 40 66

Figure S28.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0257 (Fisher's exact test), Q value = 0.047

Table S29.  Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
2Q GAIN MUTATED 11 29 21 14 26
2Q GAIN WILD-TYPE 40 95 123 94 66

Figure S29.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00025

Table S30.  Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
3P GAIN MUTATED 17 24 32 12
3P GAIN WILD-TYPE 134 74 150 182

Figure S30.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

'3p gain' versus 'METHLYATION_CNMF'

P value = 0.0452 (Fisher's exact test), Q value = 0.076

Table S31.  Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
3P GAIN MUTATED 35 28 15
3P GAIN WILD-TYPE 206 133 160

Figure S31.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S32.  Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
3Q GAIN MUTATED 26 41 84 19
3Q GAIN WILD-TYPE 125 57 98 175

Figure S32.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S33.  Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
3Q GAIN MUTATED 60 66 32
3Q GAIN WILD-TYPE 181 95 143

Figure S33.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.0012

Table S34.  Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
3Q GAIN MUTATED 65 70 29
3Q GAIN WILD-TYPE 105 203 124

Figure S34.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00042

Table S35.  Gene #6: '3q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
3Q GAIN MUTATED 34 41 17 48 24
3Q GAIN WILD-TYPE 97 75 81 73 106

Figure S35.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S36.  Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
3Q GAIN MUTATED 70 63 34
3Q GAIN WILD-TYPE 97 215 138

Figure S36.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S37.  Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
3Q GAIN MUTATED 38 29 40 46 14
3Q GAIN WILD-TYPE 89 114 124 48 75

Figure S37.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00022

Table S38.  Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
3Q GAIN MUTATED 53 38 22 10 14
3Q GAIN WILD-TYPE 70 117 99 37 59

Figure S38.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S39.  Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
3Q GAIN MUTATED 10 40 28 14 45
3Q GAIN WILD-TYPE 41 84 116 94 47

Figure S39.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 0.0197 (Fisher's exact test), Q value = 0.038

Table S40.  Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
4P GAIN MUTATED 7 7 18 5
4P GAIN WILD-TYPE 144 91 164 189

Figure S40.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 0.00537 (Fisher's exact test), Q value = 0.012

Table S41.  Gene #7: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
4P GAIN MUTATED 15 19 2
4P GAIN WILD-TYPE 155 254 151

Figure S41.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00997 (Fisher's exact test), Q value = 0.021

Table S42.  Gene #7: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
4P GAIN MUTATED 8 10 5 12 1
4P GAIN WILD-TYPE 123 106 93 109 129

Figure S42.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00768 (Fisher's exact test), Q value = 0.017

Table S43.  Gene #7: '4p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
4P GAIN MUTATED 4 13 8 11 1
4P GAIN WILD-TYPE 123 130 156 83 88

Figure S43.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0193 (Fisher's exact test), Q value = 0.037

Table S44.  Gene #7: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
4P GAIN MUTATED 1 11 8 2 11
4P GAIN WILD-TYPE 50 113 136 106 81

Figure S44.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 0.0242 (Fisher's exact test), Q value = 0.044

Table S45.  Gene #8: '4q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
4Q GAIN MUTATED 12 16 2
4Q GAIN WILD-TYPE 158 257 151

Figure S45.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00257 (Fisher's exact test), Q value = 0.0063

Table S46.  Gene #8: '4q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
4Q GAIN MUTATED 2 11 8 9 0
4Q GAIN WILD-TYPE 125 132 156 85 89

Figure S46.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0105 (Fisher's exact test), Q value = 0.022

Table S47.  Gene #8: '4q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
4Q GAIN MUTATED 0 9 7 1 9
4Q GAIN WILD-TYPE 51 115 137 107 83

Figure S47.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S48.  Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
5P GAIN MUTATED 49 23 91 16
5P GAIN WILD-TYPE 102 75 91 178

Figure S48.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S49.  Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
5P GAIN MUTATED 51 83 31
5P GAIN WILD-TYPE 190 78 144

Figure S49.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0198 (Fisher's exact test), Q value = 0.038

Table S50.  Gene #9: '5p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 110 99
5P GAIN MUTATED 89 23 21
5P GAIN WILD-TYPE 184 87 78

Figure S50.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00022

Table S51.  Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
5P GAIN MUTATED 70 73 30
5P GAIN WILD-TYPE 100 200 123

Figure S51.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S52.  Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
5P GAIN MUTATED 53 22 22 55 21
5P GAIN WILD-TYPE 78 94 76 66 109

Figure S52.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S53.  Gene #9: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
5P GAIN MUTATED 75 66 37
5P GAIN WILD-TYPE 92 212 135

Figure S53.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S54.  Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
5P GAIN MUTATED 53 29 34 50 12
5P GAIN WILD-TYPE 74 114 130 44 77

Figure S54.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00019

Table S55.  Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
5P GAIN MUTATED 58 42 23 13 19
5P GAIN WILD-TYPE 65 113 98 34 54

Figure S55.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S56.  Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
5P GAIN MUTATED 18 34 33 20 50
5P GAIN WILD-TYPE 33 90 111 88 42

Figure S56.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00046

Table S57.  Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
5Q GAIN MUTATED 17 7 32 8
5Q GAIN WILD-TYPE 134 91 150 186

Figure S57.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S58.  Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
6P GAIN MUTATED 54 28 29 7
6P GAIN WILD-TYPE 97 70 153 187

Figure S58.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S59.  Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
6P GAIN MUTATED 38 51 17
6P GAIN WILD-TYPE 203 110 158

Figure S59.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p gain' versus 'RPPA_CNMF'

P value = 0.0239 (Fisher's exact test), Q value = 0.044

Table S60.  Gene #11: '6p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 137 136 64
6P GAIN MUTATED 26 33 15 15
6P GAIN WILD-TYPE 119 104 121 49

Figure S60.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'6p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.031 (Fisher's exact test), Q value = 0.054

Table S61.  Gene #11: '6p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 110 99
6P GAIN MUTATED 53 26 10
6P GAIN WILD-TYPE 220 84 89

Figure S61.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 0.0251 (Fisher's exact test), Q value = 0.046

Table S62.  Gene #11: '6p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
6P GAIN MUTATED 33 63 19
6P GAIN WILD-TYPE 137 210 134

Figure S62.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S63.  Gene #11: '6p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
6P GAIN MUTATED 40 24 20 24 7
6P GAIN WILD-TYPE 91 92 78 97 123

Figure S63.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.022

Table S64.  Gene #11: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
6P GAIN MUTATED 43 52 22
6P GAIN WILD-TYPE 124 226 150

Figure S64.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S65.  Gene #11: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
6P GAIN MUTATED 49 29 16 16 7
6P GAIN WILD-TYPE 78 114 148 78 82

Figure S65.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00442 (Fisher's exact test), Q value = 0.01

Table S66.  Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
6P GAIN MUTATED 33 34 11 8 11
6P GAIN WILD-TYPE 90 121 110 39 62

Figure S66.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8.2e-05

Table S67.  Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
6P GAIN MUTATED 20 33 15 13 16
6P GAIN WILD-TYPE 31 91 129 95 76

Figure S67.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S68.  Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
6Q GAIN MUTATED 47 20 25 8
6Q GAIN WILD-TYPE 104 78 157 186

Figure S68.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00042

Table S69.  Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
6Q GAIN MUTATED 37 39 13
6Q GAIN WILD-TYPE 204 122 162

Figure S69.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q gain' versus 'RPPA_CNMF'

P value = 0.0419 (Fisher's exact test), Q value = 0.071

Table S70.  Gene #12: '6q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 137 136 64
6Q GAIN MUTATED 23 28 13 14
6Q GAIN WILD-TYPE 122 109 123 50

Figure S70.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'6q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0373 (Fisher's exact test), Q value = 0.064

Table S71.  Gene #12: '6q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 110 99
6Q GAIN MUTATED 49 21 8
6Q GAIN WILD-TYPE 224 89 91

Figure S71.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'6q gain' versus 'MRNASEQ_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.021

Table S72.  Gene #12: '6q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
6Q GAIN MUTATED 26 57 15
6Q GAIN WILD-TYPE 144 216 138

Figure S72.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00054 (Fisher's exact test), Q value = 0.0016

Table S73.  Gene #12: '6q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
6Q GAIN MUTATED 31 21 18 21 7
6Q GAIN WILD-TYPE 100 95 80 100 123

Figure S73.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S74.  Gene #12: '6q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
6Q GAIN MUTATED 37 29 13 14 6
6Q GAIN WILD-TYPE 90 114 151 80 83

Figure S74.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0234 (Fisher's exact test), Q value = 0.043

Table S75.  Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
6Q GAIN MUTATED 23 33 10 8 8
6Q GAIN WILD-TYPE 100 122 111 39 65

Figure S75.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S76.  Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
6Q GAIN MUTATED 14 33 10 11 14
6Q GAIN WILD-TYPE 37 91 134 97 78

Figure S76.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S77.  Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
7P GAIN MUTATED 91 42 126 49
7P GAIN WILD-TYPE 60 56 56 145

Figure S77.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S78.  Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
7P GAIN MUTATED 134 96 58
7P GAIN WILD-TYPE 107 65 117

Figure S78.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.00078

Table S79.  Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
7P GAIN MUTATED 92 150 54
7P GAIN WILD-TYPE 78 123 99

Figure S79.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00377 (Fisher's exact test), Q value = 0.0089

Table S80.  Gene #13: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
7P GAIN MUTATED 76 51 51 69 49
7P GAIN WILD-TYPE 55 65 47 52 81

Figure S80.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.003 (Fisher's exact test), Q value = 0.0073

Table S81.  Gene #13: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
7P GAIN MUTATED 94 142 66
7P GAIN WILD-TYPE 73 136 106

Figure S81.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 4e-04

Table S82.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
7P GAIN MUTATED 71 82 69 52 28
7P GAIN WILD-TYPE 56 61 95 42 61

Figure S82.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.017 (Fisher's exact test), Q value = 0.034

Table S83.  Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
7P GAIN MUTATED 72 83 46 24 33
7P GAIN WILD-TYPE 51 72 75 23 40

Figure S83.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00908 (Fisher's exact test), Q value = 0.019

Table S84.  Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
7P GAIN MUTATED 30 71 66 40 51
7P GAIN WILD-TYPE 21 53 78 68 41

Figure S84.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S85.  Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
7Q GAIN MUTATED 76 32 104 45
7Q GAIN WILD-TYPE 75 66 78 149

Figure S85.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.2e-05

Table S86.  Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
7Q GAIN MUTATED 110 79 47
7Q GAIN WILD-TYPE 131 82 128

Figure S86.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 0.0209 (Fisher's exact test), Q value = 0.039

Table S87.  Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
8P GAIN MUTATED 57 39 59 93
8P GAIN WILD-TYPE 94 59 123 101

Figure S87.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.0266 (Fisher's exact test), Q value = 0.048

Table S88.  Gene #15: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
8P GAIN MUTATED 108 60 56
8P GAIN WILD-TYPE 133 101 119

Figure S88.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.00519 (Fisher's exact test), Q value = 0.012

Table S89.  Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
8Q GAIN MUTATED 140 94 76
8Q GAIN WILD-TYPE 101 67 99

Figure S89.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 0.025

Table S90.  Gene #16: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
8Q GAIN MUTATED 95 161 76
8Q GAIN WILD-TYPE 72 117 96

Figure S90.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0101 (Fisher's exact test), Q value = 0.021

Table S91.  Gene #16: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
8Q GAIN MUTATED 75 89 73 53 42
8Q GAIN WILD-TYPE 52 54 91 41 47

Figure S91.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 0.00174 (Fisher's exact test), Q value = 0.0045

Table S92.  Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
9Q GAIN MUTATED 33 9 43 24
9Q GAIN WILD-TYPE 118 89 139 170

Figure S92.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S93.  Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
10P GAIN MUTATED 52 42 32 10
10P GAIN WILD-TYPE 99 56 150 184

Figure S93.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 0.0373 (Fisher's exact test), Q value = 0.064

Table S94.  Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
10P GAIN MUTATED 62 35 27
10P GAIN WILD-TYPE 179 126 148

Figure S94.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00121 (Fisher's exact test), Q value = 0.0032

Table S95.  Gene #19: '10p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
10P GAIN MUTATED 43 33 24 14 19
10P GAIN WILD-TYPE 84 110 140 80 70

Figure S95.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S96.  Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
10Q GAIN MUTATED 31 39 17 11
10Q GAIN WILD-TYPE 120 59 165 183

Figure S96.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

'10q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00492 (Fisher's exact test), Q value = 0.011

Table S97.  Gene #20: '10q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
10Q GAIN MUTATED 28 28 9 13 17
10Q GAIN WILD-TYPE 103 88 89 108 113

Figure S97.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0175 (Fisher's exact test), Q value = 0.034

Table S98.  Gene #20: '10q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
10Q GAIN MUTATED 17 37 16 5 6
10Q GAIN WILD-TYPE 106 118 105 42 67

Figure S98.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S99.  Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
11P GAIN MUTATED 38 18 35 7
11P GAIN WILD-TYPE 113 80 147 187

Figure S99.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 0.0016 (Fisher's exact test), Q value = 0.0042

Table S100.  Gene #21: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
11P GAIN MUTATED 32 40 20
11P GAIN WILD-TYPE 209 121 155

Figure S100.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0125 (Fisher's exact test), Q value = 0.025

Table S101.  Gene #21: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
11P GAIN MUTATED 30 17 15 22 10
11P GAIN WILD-TYPE 101 99 83 99 120

Figure S101.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00658 (Fisher's exact test), Q value = 0.015

Table S102.  Gene #21: '11p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
11P GAIN MUTATED 30 22 19 17 6
11P GAIN WILD-TYPE 97 121 145 77 83

Figure S102.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 0.025

Table S103.  Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
11P GAIN MUTATED 24 29 13 10 4
11P GAIN WILD-TYPE 99 126 108 37 69

Figure S103.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S104.  Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
11Q GAIN MUTATED 42 18 32 10
11Q GAIN WILD-TYPE 109 80 150 184

Figure S104.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 0.0373 (Fisher's exact test), Q value = 0.064

Table S105.  Gene #22: '11q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
11Q GAIN MUTATED 38 35 20
11Q GAIN WILD-TYPE 203 126 155

Figure S105.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00109 (Fisher's exact test), Q value = 0.003

Table S106.  Gene #22: '11q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
11Q GAIN MUTATED 35 20 18 16 10
11Q GAIN WILD-TYPE 96 96 80 105 120

Figure S106.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00132 (Fisher's exact test), Q value = 0.0035

Table S107.  Gene #22: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
11Q GAIN MUTATED 32 26 25 11 5
11Q GAIN WILD-TYPE 95 117 139 83 84

Figure S107.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0032 (Fisher's exact test), Q value = 0.0077

Table S108.  Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
11Q GAIN MUTATED 21 36 11 9 5
11Q GAIN WILD-TYPE 102 119 110 38 68

Figure S108.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00128 (Fisher's exact test), Q value = 0.0034

Table S109.  Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
11Q GAIN MUTATED 14 29 20 8 11
11Q GAIN WILD-TYPE 37 95 124 100 81

Figure S109.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S110.  Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
12P GAIN MUTATED 29 31 66 23
12P GAIN WILD-TYPE 122 67 116 171

Figure S110.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00028

Table S111.  Gene #23: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
12P GAIN MUTATED 49 61 34
12P GAIN WILD-TYPE 192 100 141

Figure S111.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 0.022 (Fisher's exact test), Q value = 0.041

Table S112.  Gene #23: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
12P GAIN MUTATED 55 59 32
12P GAIN WILD-TYPE 115 214 121

Figure S112.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00195 (Fisher's exact test), Q value = 0.005

Table S113.  Gene #23: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
12P GAIN MUTATED 37 22 22 44 21
12P GAIN WILD-TYPE 94 94 76 77 109

Figure S113.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.00098

Table S114.  Gene #23: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
12P GAIN MUTATED 59 58 30
12P GAIN WILD-TYPE 108 220 142

Figure S114.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.0012

Table S115.  Gene #23: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
12P GAIN MUTATED 28 32 36 39 12
12P GAIN WILD-TYPE 99 111 128 55 77

Figure S115.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.0019

Table S116.  Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
12P GAIN MUTATED 47 39 21 6 15
12P GAIN WILD-TYPE 76 116 100 41 58

Figure S116.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00022

Table S117.  Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
12P GAIN MUTATED 11 30 35 13 39
12P GAIN WILD-TYPE 40 94 109 95 53

Figure S117.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 0.00411 (Fisher's exact test), Q value = 0.0097

Table S118.  Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
12Q GAIN MUTATED 26 29 37 24
12Q GAIN WILD-TYPE 125 69 145 170

Figure S118.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S119.  Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
13Q GAIN MUTATED 109 10 46 32
13Q GAIN WILD-TYPE 42 88 136 162

Figure S119.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 0.0323 (Fisher's exact test), Q value = 0.056

Table S120.  Gene #25: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
13Q GAIN MUTATED 83 55 41
13Q GAIN WILD-TYPE 158 106 134

Figure S120.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00012

Table S121.  Gene #25: '13q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
13Q GAIN MUTATED 37 113 38
13Q GAIN WILD-TYPE 133 160 115

Figure S121.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S122.  Gene #25: '13q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
13Q GAIN MUTATED 54 33 50 21 30
13Q GAIN WILD-TYPE 77 83 48 100 100

Figure S122.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 0.0127 (Fisher's exact test), Q value = 0.026

Table S123.  Gene #25: '13q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
13Q GAIN MUTATED 47 103 42
13Q GAIN WILD-TYPE 120 175 130

Figure S123.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'13q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S124.  Gene #25: '13q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
13Q GAIN MUTATED 62 68 29 9 24
13Q GAIN WILD-TYPE 65 75 135 85 65

Figure S124.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0126 (Fisher's exact test), Q value = 0.026

Table S125.  Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
13Q GAIN MUTATED 33 58 24 18 24
13Q GAIN WILD-TYPE 90 97 97 29 49

Figure S125.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'13q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S126.  Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
13Q GAIN MUTATED 27 47 39 35 9
13Q GAIN WILD-TYPE 24 77 105 73 83

Figure S126.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S127.  Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
14Q GAIN MUTATED 14 7 50 5
14Q GAIN WILD-TYPE 137 91 132 189

Figure S127.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00028

Table S128.  Gene #26: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
14Q GAIN MUTATED 22 38 13
14Q GAIN WILD-TYPE 219 123 162

Figure S128.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S129.  Gene #26: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
14Q GAIN MUTATED 41 25 9
14Q GAIN WILD-TYPE 129 248 144

Figure S129.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S130.  Gene #26: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
14Q GAIN MUTATED 16 8 7 38 6
14Q GAIN WILD-TYPE 115 108 91 83 124

Figure S130.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S131.  Gene #26: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
14Q GAIN MUTATED 40 20 15
14Q GAIN WILD-TYPE 127 258 157

Figure S131.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S132.  Gene #26: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
14Q GAIN MUTATED 10 17 7 34 7
14Q GAIN WILD-TYPE 117 126 157 60 82

Figure S132.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00022

Table S133.  Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
14Q GAIN MUTATED 30 15 14 8 1
14Q GAIN WILD-TYPE 93 140 107 39 72

Figure S133.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S134.  Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
14Q GAIN MUTATED 7 14 6 7 34
14Q GAIN WILD-TYPE 44 110 138 101 58

Figure S134.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S135.  Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
15Q GAIN MUTATED 21 19 25 2
15Q GAIN WILD-TYPE 130 79 157 192

Figure S135.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

'15q gain' versus 'METHLYATION_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.031

Table S136.  Gene #27: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
15Q GAIN MUTATED 29 24 10
15Q GAIN WILD-TYPE 212 137 165

Figure S136.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q gain' versus 'MRNASEQ_CNMF'

P value = 0.00255 (Fisher's exact test), Q value = 0.0063

Table S137.  Gene #27: '15q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
15Q GAIN MUTATED 25 32 6
15Q GAIN WILD-TYPE 145 241 147

Figure S137.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0013 (Fisher's exact test), Q value = 0.0034

Table S138.  Gene #27: '15q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
15Q GAIN MUTATED 16 15 9 20 3
15Q GAIN WILD-TYPE 115 101 89 101 127

Figure S138.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q gain' versus 'MIRSEQ_CNMF'

P value = 0.0372 (Fisher's exact test), Q value = 0.064

Table S139.  Gene #27: '15q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
15Q GAIN MUTATED 25 29 11
15Q GAIN WILD-TYPE 142 249 161

Figure S139.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.037

Table S140.  Gene #27: '15q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
15Q GAIN MUTATED 22 19 6 3 7
15Q GAIN WILD-TYPE 101 136 115 44 66

Figure S140.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'15q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00131 (Fisher's exact test), Q value = 0.0035

Table S141.  Gene #27: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
15Q GAIN MUTATED 4 25 9 6 13
15Q GAIN WILD-TYPE 47 99 135 102 79

Figure S141.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S142.  Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
16P GAIN MUTATED 20 18 52 10
16P GAIN WILD-TYPE 131 80 130 184

Figure S142.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 0.00412 (Fisher's exact test), Q value = 0.0097

Table S143.  Gene #28: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
16P GAIN MUTATED 27 38 26
16P GAIN WILD-TYPE 214 123 149

Figure S143.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00955 (Fisher's exact test), Q value = 0.02

Table S144.  Gene #28: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
16P GAIN MUTATED 21 19 12 32 13
16P GAIN WILD-TYPE 110 97 86 89 117

Figure S144.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00022

Table S145.  Gene #28: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
16P GAIN MUTATED 23 12 22 30 11
16P GAIN WILD-TYPE 104 131 142 64 78

Figure S145.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00114 (Fisher's exact test), Q value = 0.0031

Table S146.  Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
16P GAIN MUTATED 6 15 21 10 28
16P GAIN WILD-TYPE 45 109 123 98 64

Figure S146.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S147.  Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
16Q GAIN MUTATED 17 11 49 9
16Q GAIN WILD-TYPE 134 87 133 185

Figure S147.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.003

Table S148.  Gene #29: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
16Q GAIN MUTATED 23 36 20
16Q GAIN WILD-TYPE 218 125 155

Figure S148.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 0.00624 (Fisher's exact test), Q value = 0.014

Table S149.  Gene #29: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
16Q GAIN MUTATED 36 32 15
16Q GAIN WILD-TYPE 134 241 138

Figure S149.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.00057

Table S150.  Gene #29: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
16Q GAIN MUTATED 18 12 10 33 10
16Q GAIN WILD-TYPE 113 104 88 88 120

Figure S150.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CNMF'

P value = 0.00328 (Fisher's exact test), Q value = 0.0079

Table S151.  Gene #29: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
16Q GAIN MUTATED 35 26 23
16Q GAIN WILD-TYPE 132 252 149

Figure S151.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00015

Table S152.  Gene #29: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
16Q GAIN MUTATED 15 13 17 30 9
16Q GAIN WILD-TYPE 112 130 147 64 80

Figure S152.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00688 (Fisher's exact test), Q value = 0.015

Table S153.  Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
16Q GAIN MUTATED 29 16 13 4 6
16Q GAIN WILD-TYPE 94 139 108 43 67

Figure S153.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00012

Table S154.  Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
16Q GAIN MUTATED 5 11 17 7 28
16Q GAIN WILD-TYPE 46 113 127 101 64

Figure S154.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S155.  Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
17P GAIN MUTATED 17 10 31 3
17P GAIN WILD-TYPE 134 88 151 191

Figure S155.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 0.00344 (Fisher's exact test), Q value = 0.0082

Table S156.  Gene #30: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
17P GAIN MUTATED 22 26 9
17P GAIN WILD-TYPE 219 135 166

Figure S156.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 0.0167 (Fisher's exact test), Q value = 0.033

Table S157.  Gene #30: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
17P GAIN MUTATED 25 26 8
17P GAIN WILD-TYPE 145 247 145

Figure S157.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.021 (Fisher's exact test), Q value = 0.039

Table S158.  Gene #30: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
17P GAIN MUTATED 18 9 5 19 8
17P GAIN WILD-TYPE 113 107 93 102 122

Figure S158.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00015

Table S159.  Gene #30: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
17P GAIN MUTATED 32 15 13
17P GAIN WILD-TYPE 135 263 159

Figure S159.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0195 (Fisher's exact test), Q value = 0.037

Table S160.  Gene #30: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
17P GAIN MUTATED 14 9 13 18 6
17P GAIN WILD-TYPE 113 134 151 76 83

Figure S160.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00596 (Fisher's exact test), Q value = 0.014

Table S161.  Gene #30: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
17P GAIN MUTATED 23 10 7 5 5
17P GAIN WILD-TYPE 100 145 114 42 68

Figure S161.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0013 (Fisher's exact test), Q value = 0.0034

Table S162.  Gene #30: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
17P GAIN MUTATED 7 10 9 5 19
17P GAIN WILD-TYPE 44 114 135 103 73

Figure S162.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S163.  Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
17Q GAIN MUTATED 33 21 48 6
17Q GAIN WILD-TYPE 118 77 134 188

Figure S163.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 0.00781 (Fisher's exact test), Q value = 0.017

Table S164.  Gene #31: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
17Q GAIN MUTATED 47 37 19
17Q GAIN WILD-TYPE 194 124 156

Figure S164.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.027

Table S165.  Gene #31: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
17Q GAIN MUTATED 40 47 17
17Q GAIN WILD-TYPE 130 226 136

Figure S165.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0179 (Fisher's exact test), Q value = 0.035

Table S166.  Gene #31: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
17Q GAIN MUTATED 32 20 10 26 16
17Q GAIN WILD-TYPE 99 96 88 95 114

Figure S166.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 0.00383 (Fisher's exact test), Q value = 0.0091

Table S167.  Gene #31: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
17Q GAIN MUTATED 43 40 23
17Q GAIN WILD-TYPE 124 238 149

Figure S167.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0123 (Fisher's exact test), Q value = 0.025

Table S168.  Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
17Q GAIN MUTATED 12 22 24 8 22
17Q GAIN WILD-TYPE 39 102 120 100 70

Figure S168.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S169.  Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
18P GAIN MUTATED 38 22 60 15
18P GAIN WILD-TYPE 113 76 122 179

Figure S169.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S170.  Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
18P GAIN MUTATED 42 57 28
18P GAIN WILD-TYPE 199 104 147

Figure S170.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0187 (Fisher's exact test), Q value = 0.036

Table S171.  Gene #32: '18p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 110 99
18P GAIN MUTATED 69 15 16
18P GAIN WILD-TYPE 204 95 83

Figure S171.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 0.00303 (Fisher's exact test), Q value = 0.0074

Table S172.  Gene #32: '18p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
18P GAIN MUTATED 44 67 19
18P GAIN WILD-TYPE 126 206 134

Figure S172.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S173.  Gene #32: '18p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
18P GAIN MUTATED 43 29 19 30 9
18P GAIN WILD-TYPE 88 87 79 91 121

Figure S173.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.0021

Table S174.  Gene #32: '18p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
18P GAIN MUTATED 49 63 22
18P GAIN WILD-TYPE 118 215 150

Figure S174.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00048

Table S175.  Gene #32: '18p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
18P GAIN MUTATED 42 30 25 27 10
18P GAIN WILD-TYPE 85 113 139 67 79

Figure S175.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0018 (Fisher's exact test), Q value = 0.0046

Table S176.  Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
18P GAIN MUTATED 39 42 18 5 12
18P GAIN WILD-TYPE 84 113 103 42 61

Figure S176.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00077 (Fisher's exact test), Q value = 0.0022

Table S177.  Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
18P GAIN MUTATED 19 34 23 14 26
18P GAIN WILD-TYPE 32 90 121 94 66

Figure S177.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 0.00203 (Fisher's exact test), Q value = 0.0051

Table S178.  Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
18Q GAIN MUTATED 24 18 26 11
18Q GAIN WILD-TYPE 127 80 156 183

Figure S178.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 0.0224 (Fisher's exact test), Q value = 0.042

Table S179.  Gene #33: '18q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
18Q GAIN MUTATED 19 46 12
18Q GAIN WILD-TYPE 151 227 141

Figure S179.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00983 (Fisher's exact test), Q value = 0.021

Table S180.  Gene #33: '18q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
18Q GAIN MUTATED 24 20 13 13 7
18Q GAIN WILD-TYPE 107 96 85 108 123

Figure S180.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CNMF'

P value = 0.0345 (Fisher's exact test), Q value = 0.06

Table S181.  Gene #33: '18q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
18Q GAIN MUTATED 27 39 13
18Q GAIN WILD-TYPE 140 239 159

Figure S181.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.2e-05

Table S182.  Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
19P GAIN MUTATED 28 21 26 8
19P GAIN WILD-TYPE 123 77 156 186

Figure S182.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0483 (Fisher's exact test), Q value = 0.081

Table S183.  Gene #34: '19p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 110 99
19P GAIN MUTATED 46 9 10
19P GAIN WILD-TYPE 227 101 89

Figure S183.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S184.  Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
19Q GAIN MUTATED 42 28 38 11
19Q GAIN WILD-TYPE 109 70 144 183

Figure S184.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'RPPA_CNMF'

P value = 0.00918 (Fisher's exact test), Q value = 0.02

Table S185.  Gene #35: '19q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 137 136 64
19Q GAIN MUTATED 39 18 18 11
19Q GAIN WILD-TYPE 106 119 118 53

Figure S185.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'19q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0277 (Fisher's exact test), Q value = 0.049

Table S186.  Gene #35: '19q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 110 99
19Q GAIN MUTATED 60 14 12
19Q GAIN WILD-TYPE 213 96 87

Figure S186.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 0.0296 (Fisher's exact test), Q value = 0.052

Table S187.  Gene #35: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
19Q GAIN MUTATED 27 66 23
19Q GAIN WILD-TYPE 143 207 130

Figure S187.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00161 (Fisher's exact test), Q value = 0.0042

Table S188.  Gene #35: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
19Q GAIN MUTATED 40 28 24 16 10
19Q GAIN WILD-TYPE 87 115 140 78 79

Figure S188.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.031 (Fisher's exact test), Q value = 0.054

Table S189.  Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
19Q GAIN MUTATED 18 26 25 15 15
19Q GAIN WILD-TYPE 33 98 119 93 77

Figure S189.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S190.  Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
20P GAIN MUTATED 116 61 115 57
20P GAIN WILD-TYPE 35 37 67 137

Figure S190.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.00149 (Fisher's exact test), Q value = 0.0039

Table S191.  Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
20P GAIN MUTATED 135 106 81
20P GAIN WILD-TYPE 106 55 94

Figure S191.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.001 (Fisher's exact test), Q value = 0.0028

Table S192.  Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
20P GAIN MUTATED 94 58 47 68 69
20P GAIN WILD-TYPE 37 58 51 53 61

Figure S192.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 0.00669 (Fisher's exact test), Q value = 0.015

Table S193.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
20P GAIN MUTATED 108 155 82
20P GAIN WILD-TYPE 59 123 90

Figure S193.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00012

Table S194.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
20P GAIN MUTATED 94 86 75 50 40
20P GAIN WILD-TYPE 33 57 89 44 49

Figure S194.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.025

Table S195.  Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
20P GAIN MUTATED 83 84 57 28 35
20P GAIN WILD-TYPE 40 71 64 19 38

Figure S195.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8.2e-05

Table S196.  Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
20P GAIN MUTATED 44 73 65 55 50
20P GAIN WILD-TYPE 7 51 79 53 42

Figure S196.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S197.  Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
20Q GAIN MUTATED 131 75 129 60
20Q GAIN WILD-TYPE 20 23 53 134

Figure S197.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 0.00639 (Fisher's exact test), Q value = 0.014

Table S198.  Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
20Q GAIN MUTATED 98 193 90
20Q GAIN WILD-TYPE 72 80 63

Figure S198.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S199.  Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
20Q GAIN MUTATED 112 74 56 65 74
20Q GAIN WILD-TYPE 19 42 42 56 56

Figure S199.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S200.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
20Q GAIN MUTATED 114 98 86 47 44
20Q GAIN WILD-TYPE 13 45 78 47 45

Figure S200.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S201.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
20Q GAIN MUTATED 46 92 76 67 47
20Q GAIN WILD-TYPE 5 32 68 41 45

Figure S201.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00012

Table S202.  Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
21Q GAIN MUTATED 9 10 19 1
21Q GAIN WILD-TYPE 142 88 163 193

Figure S202.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00015

Table S203.  Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
21Q GAIN MUTATED 11 23 4
21Q GAIN WILD-TYPE 230 138 171

Figure S203.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 0.00799 (Fisher's exact test), Q value = 0.017

Table S204.  Gene #38: '21q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
21Q GAIN MUTATED 17 18 3
21Q GAIN WILD-TYPE 153 255 150

Figure S204.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0141 (Fisher's exact test), Q value = 0.028

Table S205.  Gene #38: '21q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
21Q GAIN MUTATED 14 5 6 11 2
21Q GAIN WILD-TYPE 117 111 92 110 128

Figure S205.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 0.00466 (Fisher's exact test), Q value = 0.011

Table S206.  Gene #38: '21q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
21Q GAIN MUTATED 18 16 4
21Q GAIN WILD-TYPE 149 262 168

Figure S206.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00217 (Fisher's exact test), Q value = 0.0054

Table S207.  Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
21Q GAIN MUTATED 14 6 6 11 1
21Q GAIN WILD-TYPE 113 137 158 83 88

Figure S207.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0468 (Fisher's exact test), Q value = 0.078

Table S208.  Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
21Q GAIN MUTATED 6 8 7 3 11
21Q GAIN WILD-TYPE 45 116 137 105 81

Figure S208.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S209.  Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
22Q GAIN MUTATED 11 8 40 4
22Q GAIN WILD-TYPE 140 90 142 190

Figure S209.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S210.  Gene #39: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
22Q GAIN MUTATED 15 37 9
22Q GAIN WILD-TYPE 226 124 166

Figure S210.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00031

Table S211.  Gene #39: '22q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
22Q GAIN MUTATED 33 21 9
22Q GAIN WILD-TYPE 137 252 144

Figure S211.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00025

Table S212.  Gene #39: '22q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
22Q GAIN MUTATED 13 7 9 28 6
22Q GAIN WILD-TYPE 118 109 89 93 124

Figure S212.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00012

Table S213.  Gene #39: '22q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
22Q GAIN MUTATED 34 18 11
22Q GAIN WILD-TYPE 133 260 161

Figure S213.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S214.  Gene #39: '22q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
22Q GAIN MUTATED 11 10 10 28 4
22Q GAIN WILD-TYPE 116 133 154 66 85

Figure S214.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S215.  Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
22Q GAIN MUTATED 32 11 9 2 4
22Q GAIN WILD-TYPE 91 144 112 45 69

Figure S215.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S216.  Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
22Q GAIN MUTATED 5 8 12 5 28
22Q GAIN WILD-TYPE 46 116 132 103 64

Figure S216.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp gain' versus 'CN_CNMF'

P value = 0.00614 (Fisher's exact test), Q value = 0.014

Table S217.  Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
XP GAIN MUTATED 26 10 27 12
XP GAIN WILD-TYPE 125 88 155 182

Figure S217.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

'xp gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.2e-05

Table S218.  Gene #40: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
XP GAIN MUTATED 30 32 7
XP GAIN WILD-TYPE 211 129 168

Figure S218.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp gain' versus 'MRNASEQ_CNMF'

P value = 0.0408 (Fisher's exact test), Q value = 0.069

Table S219.  Gene #40: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
XP GAIN MUTATED 24 38 10
XP GAIN WILD-TYPE 146 235 143

Figure S219.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0338 (Fisher's exact test), Q value = 0.059

Table S220.  Gene #40: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
XP GAIN MUTATED 18 10 17 19 8
XP GAIN WILD-TYPE 113 106 81 102 122

Figure S220.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_CNMF'

P value = 0.0436 (Fisher's exact test), Q value = 0.073

Table S221.  Gene #40: 'xp gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
XP GAIN MUTATED 28 30 14
XP GAIN WILD-TYPE 139 248 158

Figure S221.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xp gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00324 (Fisher's exact test), Q value = 0.0078

Table S222.  Gene #40: 'xp gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
XP GAIN MUTATED 18 24 8 15 7
XP GAIN WILD-TYPE 109 119 156 79 82

Figure S222.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0219 (Fisher's exact test), Q value = 0.041

Table S223.  Gene #40: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
XP GAIN MUTATED 5 20 7 11 14
XP GAIN WILD-TYPE 46 104 137 97 78

Figure S223.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S224.  Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
XQ GAIN MUTATED 29 7 43 14
XQ GAIN WILD-TYPE 122 91 139 180

Figure S224.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00012

Table S225.  Gene #41: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
XQ GAIN MUTATED 37 40 11
XQ GAIN WILD-TYPE 204 121 164

Figure S225.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 0.00882 (Fisher's exact test), Q value = 0.019

Table S226.  Gene #41: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
XQ GAIN MUTATED 32 46 12
XQ GAIN WILD-TYPE 138 227 141

Figure S226.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00028

Table S227.  Gene #41: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
XQ GAIN MUTATED 15 10 24 30 11
XQ GAIN WILD-TYPE 116 106 74 91 119

Figure S227.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_CNMF'

P value = 0.00206 (Fisher's exact test), Q value = 0.0052

Table S228.  Gene #41: 'xq gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
XQ GAIN MUTATED 36 40 14
XQ GAIN WILD-TYPE 131 238 158

Figure S228.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xq gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.00072

Table S229.  Gene #41: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
XQ GAIN MUTATED 20 25 11 25 9
XQ GAIN WILD-TYPE 107 118 153 69 80

Figure S229.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0343 (Fisher's exact test), Q value = 0.06

Table S230.  Gene #41: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
XQ GAIN MUTATED 26 26 9 7 9
XQ GAIN WILD-TYPE 97 129 112 40 64

Figure S230.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00054

Table S231.  Gene #41: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
XQ GAIN MUTATED 5 25 9 14 24
XQ GAIN WILD-TYPE 46 99 135 94 68

Figure S231.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S232.  Gene #42: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
1P LOSS MUTATED 43 21 33 0
1P LOSS WILD-TYPE 108 77 149 194

Figure S232.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.0012

Table S233.  Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
1P LOSS MUTATED 48 32 13
1P LOSS WILD-TYPE 193 129 162

Figure S233.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.001

Table S234.  Gene #42: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
1P LOSS MUTATED 29 53 9
1P LOSS WILD-TYPE 141 220 144

Figure S234.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0239 (Fisher's exact test), Q value = 0.044

Table S235.  Gene #42: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
1P LOSS MUTATED 26 18 18 20 9
1P LOSS WILD-TYPE 105 98 80 101 121

Figure S235.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 0.0256 (Fisher's exact test), Q value = 0.046

Table S236.  Gene #42: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
1P LOSS MUTATED 34 44 17
1P LOSS WILD-TYPE 133 234 155

Figure S236.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00091 (Fisher's exact test), Q value = 0.0025

Table S237.  Gene #42: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
1P LOSS MUTATED 29 31 15 13 7
1P LOSS WILD-TYPE 98 112 149 81 82

Figure S237.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.035 (Fisher's exact test), Q value = 0.061

Table S238.  Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
1P LOSS MUTATED 13 27 16 13 13
1P LOSS WILD-TYPE 38 97 128 95 79

Figure S238.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S239.  Gene #43: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
1Q LOSS MUTATED 17 14 16 0
1Q LOSS WILD-TYPE 134 84 166 194

Figure S239.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'MIRSEQ_CNMF'

P value = 0.0376 (Fisher's exact test), Q value = 0.064

Table S240.  Gene #43: '1q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
1Q LOSS MUTATED 17 23 6
1Q LOSS WILD-TYPE 150 255 166

Figure S240.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0493 (Fisher's exact test), Q value = 0.082

Table S241.  Gene #43: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
1Q LOSS MUTATED 12 17 9 6 2
1Q LOSS WILD-TYPE 115 126 155 88 87

Figure S241.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00054

Table S242.  Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
2P LOSS MUTATED 14 8 13 1
2P LOSS WILD-TYPE 137 90 169 193

Figure S242.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'RPPA_CNMF'

P value = 0.0261 (Fisher's exact test), Q value = 0.047

Table S243.  Gene #44: '2p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 137 136 64
2P LOSS MUTATED 9 15 3 3
2P LOSS WILD-TYPE 136 122 133 61

Figure S243.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0181 (Fisher's exact test), Q value = 0.035

Table S244.  Gene #44: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
2P LOSS MUTATED 15 6 5 7 2
2P LOSS WILD-TYPE 116 110 93 114 128

Figure S244.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0219 (Fisher's exact test), Q value = 0.041

Table S245.  Gene #44: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
2P LOSS MUTATED 12 8 3 9 4
2P LOSS WILD-TYPE 115 135 161 85 85

Figure S245.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S246.  Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
2Q LOSS MUTATED 17 11 20 1
2Q LOSS WILD-TYPE 134 87 162 193

Figure S246.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 0.0321 (Fisher's exact test), Q value = 0.056

Table S247.  Gene #45: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
2Q LOSS MUTATED 21 19 7
2Q LOSS WILD-TYPE 149 254 146

Figure S247.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.02 (Fisher's exact test), Q value = 0.038

Table S248.  Gene #45: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
2Q LOSS MUTATED 14 8 7 15 3
2Q LOSS WILD-TYPE 117 108 91 106 127

Figure S248.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0101 (Fisher's exact test), Q value = 0.021

Table S249.  Gene #45: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
2Q LOSS MUTATED 14 11 6 14 4
2Q LOSS WILD-TYPE 113 132 158 80 85

Figure S249.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0189 (Fisher's exact test), Q value = 0.037

Table S250.  Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
2Q LOSS MUTATED 4 10 8 3 14
2Q LOSS WILD-TYPE 47 114 136 105 78

Figure S250.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S251.  Gene #46: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
3P LOSS MUTATED 62 26 91 8
3P LOSS WILD-TYPE 89 72 91 186

Figure S251.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S252.  Gene #46: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
3P LOSS MUTATED 68 78 34
3P LOSS WILD-TYPE 173 83 141

Figure S252.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S253.  Gene #46: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
3P LOSS MUTATED 81 74 22
3P LOSS WILD-TYPE 89 199 131

Figure S253.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S254.  Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
3P LOSS MUTATED 44 21 25 75 12
3P LOSS WILD-TYPE 87 95 73 46 118

Figure S254.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S255.  Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
3P LOSS MUTATED 78 75 32
3P LOSS WILD-TYPE 89 203 140

Figure S255.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S256.  Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
3P LOSS MUTATED 41 49 17 66 12
3P LOSS WILD-TYPE 86 94 147 28 77

Figure S256.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S257.  Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
3P LOSS MUTATED 60 47 31 15 9
3P LOSS WILD-TYPE 63 108 90 32 64

Figure S257.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S258.  Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
3P LOSS MUTATED 16 37 23 21 65
3P LOSS WILD-TYPE 35 87 121 87 27

Figure S258.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S259.  Gene #47: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
3Q LOSS MUTATED 48 9 32 3
3Q LOSS WILD-TYPE 103 89 150 191

Figure S259.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 0.00127 (Fisher's exact test), Q value = 0.0034

Table S260.  Gene #47: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
3Q LOSS MUTATED 43 32 13
3Q LOSS WILD-TYPE 198 129 162

Figure S260.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.028

Table S261.  Gene #47: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
3Q LOSS MUTATED 30 46 12
3Q LOSS WILD-TYPE 140 227 141

Figure S261.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S262.  Gene #47: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
3Q LOSS MUTATED 29 7 20 26 6
3Q LOSS WILD-TYPE 102 109 78 95 124

Figure S262.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S263.  Gene #47: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
3Q LOSS MUTATED 26 31 6 20 7
3Q LOSS WILD-TYPE 101 112 158 74 82

Figure S263.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.023

Table S264.  Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
3Q LOSS MUTATED 14 15 14 15 20
3Q LOSS WILD-TYPE 37 109 130 93 72

Figure S264.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S265.  Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
4P LOSS MUTATED 100 67 96 11
4P LOSS WILD-TYPE 51 31 86 183

Figure S265.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S266.  Gene #48: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
4P LOSS MUTATED 99 99 56
4P LOSS WILD-TYPE 142 62 119

Figure S266.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.0017 (Fisher's exact test), Q value = 0.0044

Table S267.  Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
4P LOSS MUTATED 90 121 51
4P LOSS WILD-TYPE 80 152 102

Figure S267.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S268.  Gene #48: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
4P LOSS MUTATED 77 46 36 68 35
4P LOSS WILD-TYPE 54 70 62 53 95

Figure S268.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S269.  Gene #48: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
4P LOSS MUTATED 103 112 57
4P LOSS WILD-TYPE 64 166 115

Figure S269.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S270.  Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
4P LOSS MUTATED 82 65 41 56 28
4P LOSS WILD-TYPE 45 78 123 38 61

Figure S270.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S271.  Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
4P LOSS MUTATED 79 69 46 22 17
4P LOSS WILD-TYPE 44 86 75 25 56

Figure S271.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S272.  Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
4P LOSS MUTATED 36 61 39 41 56
4P LOSS WILD-TYPE 15 63 105 67 36

Figure S272.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S273.  Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
4Q LOSS MUTATED 98 68 81 9
4Q LOSS WILD-TYPE 53 30 101 185

Figure S273.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00042

Table S274.  Gene #49: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
4Q LOSS MUTATED 101 85 53
4Q LOSS WILD-TYPE 140 76 122

Figure S274.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00028

Table S275.  Gene #49: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
4Q LOSS MUTATED 74 45 34 54 37
4Q LOSS WILD-TYPE 57 71 64 67 93

Figure S275.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 0.00625 (Fisher's exact test), Q value = 0.014

Table S276.  Gene #49: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
4Q LOSS MUTATED 85 110 59
4Q LOSS WILD-TYPE 82 168 113

Figure S276.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S277.  Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
4Q LOSS MUTATED 81 63 41 42 27
4Q LOSS WILD-TYPE 46 80 123 52 62

Figure S277.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00755 (Fisher's exact test), Q value = 0.017

Table S278.  Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
4Q LOSS MUTATED 66 67 47 20 20
4Q LOSS WILD-TYPE 57 88 74 27 53

Figure S278.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S279.  Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
4Q LOSS MUTATED 35 59 40 44 42
4Q LOSS WILD-TYPE 16 65 104 64 50

Figure S279.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S280.  Gene #50: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
5P LOSS MUTATED 46 26 35 3
5P LOSS WILD-TYPE 105 72 147 191

Figure S280.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S281.  Gene #50: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
5P LOSS MUTATED 57 37 11
5P LOSS WILD-TYPE 184 124 164

Figure S281.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00028

Table S282.  Gene #50: '5p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
5P LOSS MUTATED 36 59 11
5P LOSS WILD-TYPE 134 214 142

Figure S282.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S283.  Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
5P LOSS MUTATED 40 22 16 22 6
5P LOSS WILD-TYPE 91 94 82 99 124

Figure S283.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.00072

Table S284.  Gene #50: '5p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
5P LOSS MUTATED 35 59 14
5P LOSS WILD-TYPE 132 219 158

Figure S284.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S285.  Gene #50: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
5P LOSS MUTATED 42 39 11 11 5
5P LOSS WILD-TYPE 85 104 153 83 84

Figure S285.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.022

Table S286.  Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
5P LOSS MUTATED 31 36 14 7 8
5P LOSS WILD-TYPE 92 119 107 40 65

Figure S286.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S287.  Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
5P LOSS MUTATED 22 32 16 15 11
5P LOSS WILD-TYPE 29 92 128 93 81

Figure S287.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S288.  Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
5Q LOSS MUTATED 70 42 80 3
5Q LOSS WILD-TYPE 81 56 102 191

Figure S288.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S289.  Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
5Q LOSS MUTATED 79 82 26
5Q LOSS WILD-TYPE 162 79 149

Figure S289.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'RPPA_CNMF'

P value = 0.0149 (Fisher's exact test), Q value = 0.03

Table S290.  Gene #51: '5q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 137 136 64
5Q LOSS MUTATED 51 42 28 25
5Q LOSS WILD-TYPE 94 95 108 39

Figure S290.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S291.  Gene #51: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
5Q LOSS MUTATED 72 95 23
5Q LOSS WILD-TYPE 98 178 130

Figure S291.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S292.  Gene #51: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
5Q LOSS MUTATED 69 34 24 51 12
5Q LOSS WILD-TYPE 62 82 74 70 118

Figure S292.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.2e-05

Table S293.  Gene #51: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
5Q LOSS MUTATED 74 87 32
5Q LOSS WILD-TYPE 93 191 140

Figure S293.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S294.  Gene #51: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
5Q LOSS MUTATED 70 51 24 38 10
5Q LOSS WILD-TYPE 57 92 140 56 79

Figure S294.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S295.  Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
5Q LOSS MUTATED 64 56 32 8 15
5Q LOSS WILD-TYPE 59 99 89 39 58

Figure S295.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S296.  Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
5Q LOSS MUTATED 32 48 30 27 38
5Q LOSS WILD-TYPE 19 76 114 81 54

Figure S296.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S297.  Gene #52: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
6P LOSS MUTATED 23 15 48 7
6P LOSS WILD-TYPE 128 83 134 187

Figure S297.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.00807 (Fisher's exact test), Q value = 0.018

Table S298.  Gene #52: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
6P LOSS MUTATED 33 37 19
6P LOSS WILD-TYPE 208 124 156

Figure S298.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 0.0156 (Fisher's exact test), Q value = 0.031

Table S299.  Gene #52: '6p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
6P LOSS MUTATED 35 41 14
6P LOSS WILD-TYPE 135 232 139

Figure S299.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00094 (Fisher's exact test), Q value = 0.0026

Table S300.  Gene #52: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
6P LOSS MUTATED 25 19 10 28 8
6P LOSS WILD-TYPE 106 97 88 93 122

Figure S300.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CNMF'

P value = 0.0385 (Fisher's exact test), Q value = 0.065

Table S301.  Gene #52: '6p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
6P LOSS MUTATED 35 37 20
6P LOSS WILD-TYPE 132 241 152

Figure S301.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00118 (Fisher's exact test), Q value = 0.0032

Table S302.  Gene #52: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
6P LOSS MUTATED 22 24 17 24 5
6P LOSS WILD-TYPE 105 119 147 70 84

Figure S302.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0205 (Fisher's exact test), Q value = 0.039

Table S303.  Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
6P LOSS MUTATED 7 20 18 10 24
6P LOSS WILD-TYPE 44 104 126 98 68

Figure S303.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S304.  Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
6Q LOSS MUTATED 29 18 56 9
6Q LOSS WILD-TYPE 122 80 126 185

Figure S304.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.0227 (Fisher's exact test), Q value = 0.042

Table S305.  Gene #53: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
6Q LOSS MUTATED 38 41 26
6Q LOSS WILD-TYPE 203 120 149

Figure S305.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00222 (Fisher's exact test), Q value = 0.0055

Table S306.  Gene #53: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
6Q LOSS MUTATED 31 25 10 28 13
6Q LOSS WILD-TYPE 100 91 88 93 117

Figure S306.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p loss' versus 'CN_CNMF'

P value = 0.00105 (Fisher's exact test), Q value = 0.0029

Table S307.  Gene #54: '7p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
7P LOSS MUTATED 12 10 9 2
7P LOSS WILD-TYPE 139 88 173 192

Figure S307.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #1: 'CN_CNMF'

'7p loss' versus 'METHLYATION_CNMF'

P value = 0.00993 (Fisher's exact test), Q value = 0.021

Table S308.  Gene #54: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
7P LOSS MUTATED 9 16 5
7P LOSS WILD-TYPE 232 145 170

Figure S308.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0366 (Fisher's exact test), Q value = 0.063

Table S309.  Gene #54: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
7P LOSS MUTATED 9 8 3 6 1
7P LOSS WILD-TYPE 114 147 118 41 72

Figure S309.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S310.  Gene #55: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
7Q LOSS MUTATED 16 17 15 2
7Q LOSS WILD-TYPE 135 81 167 192

Figure S310.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

'7q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0045 (Fisher's exact test), Q value = 0.01

Table S311.  Gene #55: '7q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
7Q LOSS MUTATED 20 10 7 10 3
7Q LOSS WILD-TYPE 111 106 91 111 127

Figure S311.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_CNMF'

P value = 0.024 (Fisher's exact test), Q value = 0.044

Table S312.  Gene #55: '7q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
7Q LOSS MUTATED 21 20 8
7Q LOSS WILD-TYPE 146 258 164

Figure S312.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0094 (Fisher's exact test), Q value = 0.02

Table S313.  Gene #55: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
7Q LOSS MUTATED 12 13 5 10 3
7Q LOSS WILD-TYPE 111 142 116 37 70

Figure S313.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S314.  Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
8P LOSS MUTATED 49 26 72 9
8P LOSS WILD-TYPE 102 72 110 185

Figure S314.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 0.0084 (Fisher's exact test), Q value = 0.018

Table S315.  Gene #56: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
8P LOSS MUTATED 61 53 32
8P LOSS WILD-TYPE 180 108 143

Figure S315.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00618 (Fisher's exact test), Q value = 0.014

Table S316.  Gene #56: '8p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 110 99
8P LOSS MUTATED 83 19 18
8P LOSS WILD-TYPE 190 91 81

Figure S316.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 0.00197 (Fisher's exact test), Q value = 0.005

Table S317.  Gene #56: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
8P LOSS MUTATED 53 72 23
8P LOSS WILD-TYPE 117 201 130

Figure S317.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S318.  Gene #56: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
8P LOSS MUTATED 48 29 22 40 9
8P LOSS WILD-TYPE 83 87 76 81 121

Figure S318.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00015

Table S319.  Gene #56: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
8P LOSS MUTATED 60 70 23
8P LOSS WILD-TYPE 107 208 149

Figure S319.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S320.  Gene #56: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
8P LOSS MUTATED 38 42 27 37 9
8P LOSS WILD-TYPE 89 101 137 57 80

Figure S320.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0395 (Fisher's exact test), Q value = 0.067

Table S321.  Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
8P LOSS MUTATED 44 38 24 12 14
8P LOSS WILD-TYPE 79 117 97 35 59

Figure S321.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00012

Table S322.  Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
8P LOSS MUTATED 21 29 31 14 37
8P LOSS WILD-TYPE 30 95 113 94 55

Figure S322.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S323.  Gene #57: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
8Q LOSS MUTATED 19 12 25 3
8Q LOSS WILD-TYPE 132 86 157 191

Figure S323.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 0.0262 (Fisher's exact test), Q value = 0.047

Table S324.  Gene #57: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
8Q LOSS MUTATED 17 34 7
8Q LOSS WILD-TYPE 153 239 146

Figure S324.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0175 (Fisher's exact test), Q value = 0.034

Table S325.  Gene #57: '8q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
8Q LOSS MUTATED 17 16 10 11 4
8Q LOSS WILD-TYPE 114 100 88 110 126

Figure S325.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0314 (Fisher's exact test), Q value = 0.055

Table S326.  Gene #57: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
8Q LOSS MUTATED 7 15 11 3 11
8Q LOSS WILD-TYPE 44 109 133 105 81

Figure S326.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S327.  Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
9P LOSS MUTATED 75 63 105 6
9P LOSS WILD-TYPE 76 35 77 188

Figure S327.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00028

Table S328.  Gene #58: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
9P LOSS MUTATED 90 89 56
9P LOSS WILD-TYPE 151 72 119

Figure S328.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00025

Table S329.  Gene #58: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
9P LOSS MUTATED 82 120 40
9P LOSS WILD-TYPE 88 153 113

Figure S329.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S330.  Gene #58: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
9P LOSS MUTATED 80 51 27 60 24
9P LOSS WILD-TYPE 51 65 71 61 106

Figure S330.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.0015

Table S331.  Gene #58: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
9P LOSS MUTATED 86 106 54
9P LOSS WILD-TYPE 81 172 118

Figure S331.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S332.  Gene #58: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
9P LOSS MUTATED 74 62 38 51 21
9P LOSS WILD-TYPE 53 81 126 43 68

Figure S332.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00098 (Fisher's exact test), Q value = 0.0027

Table S333.  Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
9P LOSS MUTATED 69 64 48 19 19
9P LOSS WILD-TYPE 54 91 73 28 54

Figure S333.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 4e-04

Table S334.  Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
9P LOSS MUTATED 29 58 43 38 51
9P LOSS WILD-TYPE 22 66 101 70 41

Figure S334.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S335.  Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
9Q LOSS MUTATED 47 50 71 5
9Q LOSS WILD-TYPE 104 48 111 189

Figure S335.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00015

Table S336.  Gene #59: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
9Q LOSS MUTATED 54 68 41
9Q LOSS WILD-TYPE 187 93 134

Figure S336.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 0.00687 (Fisher's exact test), Q value = 0.015

Table S337.  Gene #59: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
9Q LOSS MUTATED 61 79 31
9Q LOSS WILD-TYPE 109 194 122

Figure S337.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S338.  Gene #59: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
9Q LOSS MUTATED 59 36 13 43 20
9Q LOSS WILD-TYPE 72 80 85 78 110

Figure S338.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00054

Table S339.  Gene #59: '9q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
9Q LOSS MUTATED 68 64 39
9Q LOSS WILD-TYPE 99 214 133

Figure S339.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S340.  Gene #59: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
9Q LOSS MUTATED 58 31 32 37 13
9Q LOSS WILD-TYPE 69 112 132 57 76

Figure S340.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00012

Table S341.  Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
9Q LOSS MUTATED 56 38 33 13 9
9Q LOSS WILD-TYPE 67 117 88 34 64

Figure S341.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8.2e-05

Table S342.  Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
9Q LOSS MUTATED 26 34 26 26 37
9Q LOSS WILD-TYPE 25 90 118 82 55

Figure S342.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S343.  Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
10P LOSS MUTATED 28 11 73 6
10P LOSS WILD-TYPE 123 87 109 188

Figure S343.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S344.  Gene #60: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
10P LOSS MUTATED 35 54 21
10P LOSS WILD-TYPE 206 107 154

Figure S344.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.00377 (Fisher's exact test), Q value = 0.0089

Table S345.  Gene #60: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
10P LOSS MUTATED 46 50 19
10P LOSS WILD-TYPE 124 223 134

Figure S345.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S346.  Gene #60: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
10P LOSS MUTATED 33 22 13 40 7
10P LOSS WILD-TYPE 98 94 85 81 123

Figure S346.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 0.00272 (Fisher's exact test), Q value = 0.0067

Table S347.  Gene #60: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
10P LOSS MUTATED 45 51 21
10P LOSS WILD-TYPE 122 227 151

Figure S347.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S348.  Gene #60: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
10P LOSS MUTATED 31 24 22 36 4
10P LOSS WILD-TYPE 96 119 142 58 85

Figure S348.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00156 (Fisher's exact test), Q value = 0.0041

Table S349.  Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
10P LOSS MUTATED 38 27 19 9 6
10P LOSS WILD-TYPE 85 128 102 38 67

Figure S349.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S350.  Gene #60: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
10P LOSS MUTATED 12 20 19 12 36
10P LOSS WILD-TYPE 39 104 125 96 56

Figure S350.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S351.  Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
10Q LOSS MUTATED 35 7 75 1
10Q LOSS WILD-TYPE 116 91 107 193

Figure S351.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S352.  Gene #61: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
10Q LOSS MUTATED 34 56 19
10Q LOSS WILD-TYPE 207 105 156

Figure S352.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.0022

Table S353.  Gene #61: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
10Q LOSS MUTATED 44 55 15
10Q LOSS WILD-TYPE 126 218 138

Figure S353.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S354.  Gene #61: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
10Q LOSS MUTATED 32 16 18 40 8
10Q LOSS WILD-TYPE 99 100 80 81 122

Figure S354.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 0.00356 (Fisher's exact test), Q value = 0.0085

Table S355.  Gene #61: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
10Q LOSS MUTATED 43 54 20
10Q LOSS WILD-TYPE 124 224 152

Figure S355.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S356.  Gene #61: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
10Q LOSS MUTATED 33 26 18 36 4
10Q LOSS WILD-TYPE 94 117 146 58 85

Figure S356.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00212 (Fisher's exact test), Q value = 0.0053

Table S357.  Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
10Q LOSS MUTATED 38 25 20 7 7
10Q LOSS WILD-TYPE 85 130 101 40 66

Figure S357.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8.2e-05

Table S358.  Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
10Q LOSS MUTATED 11 21 17 12 36
10Q LOSS WILD-TYPE 40 103 127 96 56

Figure S358.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S359.  Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
11P LOSS MUTATED 36 22 53 6
11P LOSS WILD-TYPE 115 76 129 188

Figure S359.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00022

Table S360.  Gene #62: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
11P LOSS MUTATED 46 46 17
11P LOSS WILD-TYPE 195 115 158

Figure S360.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00025

Table S361.  Gene #62: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
11P LOSS MUTATED 47 48 13
11P LOSS WILD-TYPE 123 225 140

Figure S361.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00015

Table S362.  Gene #62: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
11P LOSS MUTATED 32 21 12 34 9
11P LOSS WILD-TYPE 99 95 86 87 121

Figure S362.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.2e-05

Table S363.  Gene #62: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
11P LOSS MUTATED 52 44 20
11P LOSS WILD-TYPE 115 234 152

Figure S363.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00048

Table S364.  Gene #62: '11p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
11P LOSS MUTATED 31 32 21 26 6
11P LOSS WILD-TYPE 96 111 143 68 83

Figure S364.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00359 (Fisher's exact test), Q value = 0.0086

Table S365.  Gene #62: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
11P LOSS MUTATED 38 27 14 7 12
11P LOSS WILD-TYPE 85 128 107 40 61

Figure S365.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00556 (Fisher's exact test), Q value = 0.013

Table S366.  Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
11P LOSS MUTATED 11 31 18 13 25
11P LOSS WILD-TYPE 40 93 126 95 67

Figure S366.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S367.  Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
11Q LOSS MUTATED 32 21 64 5
11Q LOSS WILD-TYPE 119 77 118 189

Figure S367.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S368.  Gene #63: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
11Q LOSS MUTATED 41 57 18
11Q LOSS WILD-TYPE 200 104 157

Figure S368.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S369.  Gene #63: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
11Q LOSS MUTATED 53 43 16
11Q LOSS WILD-TYPE 117 230 137

Figure S369.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S370.  Gene #63: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
11Q LOSS MUTATED 32 16 10 43 11
11Q LOSS WILD-TYPE 99 100 88 78 119

Figure S370.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S371.  Gene #63: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
11Q LOSS MUTATED 61 40 19
11Q LOSS WILD-TYPE 106 238 153

Figure S371.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S372.  Gene #63: '11q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
11Q LOSS MUTATED 29 27 18 38 8
11Q LOSS WILD-TYPE 98 116 146 56 81

Figure S372.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S373.  Gene #63: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
11Q LOSS MUTATED 47 22 16 7 11
11Q LOSS WILD-TYPE 76 133 105 40 62

Figure S373.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S374.  Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
11Q LOSS MUTATED 12 23 18 13 37
11Q LOSS WILD-TYPE 39 101 126 95 55

Figure S374.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S375.  Gene #64: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
12P LOSS MUTATED 49 17 28 4
12P LOSS WILD-TYPE 102 81 154 190

Figure S375.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.024

Table S376.  Gene #64: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
12P LOSS MUTATED 39 33 16
12P LOSS WILD-TYPE 202 128 159

Figure S376.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.00098

Table S377.  Gene #64: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
12P LOSS MUTATED 31 51 9
12P LOSS WILD-TYPE 139 222 144

Figure S377.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S378.  Gene #64: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
12P LOSS MUTATED 39 21 10 16 5
12P LOSS WILD-TYPE 92 95 88 105 125

Figure S378.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S379.  Gene #64: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
12P LOSS MUTATED 44 21 16 9 6
12P LOSS WILD-TYPE 83 122 148 85 83

Figure S379.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00883 (Fisher's exact test), Q value = 0.019

Table S380.  Gene #64: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
12P LOSS MUTATED 26 34 14 3 7
12P LOSS WILD-TYPE 97 121 107 44 66

Figure S380.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00037

Table S381.  Gene #64: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
12P LOSS MUTATED 20 25 17 13 9
12P LOSS WILD-TYPE 31 99 127 95 83

Figure S381.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S382.  Gene #65: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
12Q LOSS MUTATED 37 15 32 3
12Q LOSS WILD-TYPE 114 83 150 191

Figure S382.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

'12q loss' versus 'MRNASEQ_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0014

Table S383.  Gene #65: '12q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
12Q LOSS MUTATED 25 48 8
12Q LOSS WILD-TYPE 145 225 145

Figure S383.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S384.  Gene #65: '12q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
12Q LOSS MUTATED 30 21 10 17 3
12Q LOSS WILD-TYPE 101 95 88 104 127

Figure S384.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00022

Table S385.  Gene #65: '12q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
12Q LOSS MUTATED 33 23 15 9 5
12Q LOSS WILD-TYPE 94 120 149 85 84

Figure S385.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00556 (Fisher's exact test), Q value = 0.013

Table S386.  Gene #65: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
12Q LOSS MUTATED 20 36 13 3 6
12Q LOSS WILD-TYPE 103 119 108 44 67

Figure S386.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.024 (Fisher's exact test), Q value = 0.044

Table S387.  Gene #65: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
12Q LOSS MUTATED 13 26 18 11 10
12Q LOSS WILD-TYPE 38 98 126 97 82

Figure S387.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S388.  Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
13Q LOSS MUTATED 6 39 51 7
13Q LOSS WILD-TYPE 145 59 131 187

Figure S388.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00012

Table S389.  Gene #66: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
13Q LOSS MUTATED 32 46 18
13Q LOSS WILD-TYPE 209 115 157

Figure S389.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S390.  Gene #66: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
13Q LOSS MUTATED 54 32 15
13Q LOSS WILD-TYPE 116 241 138

Figure S390.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S391.  Gene #66: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
13Q LOSS MUTATED 24 19 5 44 9
13Q LOSS WILD-TYPE 107 97 93 77 121

Figure S391.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S392.  Gene #66: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
13Q LOSS MUTATED 50 29 24
13Q LOSS WILD-TYPE 117 249 148

Figure S392.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S393.  Gene #66: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
13Q LOSS MUTATED 21 15 17 43 7
13Q LOSS WILD-TYPE 106 128 147 51 82

Figure S393.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S394.  Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
13Q LOSS MUTATED 40 19 21 8 2
13Q LOSS WILD-TYPE 83 136 100 39 71

Figure S394.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S395.  Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
13Q LOSS MUTATED 8 18 12 10 42
13Q LOSS WILD-TYPE 43 106 132 98 50

Figure S395.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S396.  Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
14Q LOSS MUTATED 61 51 37 8
14Q LOSS WILD-TYPE 90 47 145 186

Figure S396.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 0.0073 (Fisher's exact test), Q value = 0.016

Table S397.  Gene #67: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
14Q LOSS MUTATED 63 52 31
14Q LOSS WILD-TYPE 178 109 144

Figure S397.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 0.0202 (Fisher's exact test), Q value = 0.038

Table S398.  Gene #67: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
14Q LOSS MUTATED 34 84 33
14Q LOSS WILD-TYPE 136 189 120

Figure S398.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S399.  Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
14Q LOSS MUTATED 55 39 17 19 21
14Q LOSS WILD-TYPE 76 77 81 102 109

Figure S399.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S400.  Gene #67: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
14Q LOSS MUTATED 59 37 27 15 16
14Q LOSS WILD-TYPE 68 106 137 79 73

Figure S400.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0474 (Fisher's exact test), Q value = 0.079

Table S401.  Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
14Q LOSS MUTATED 33 50 26 8 12
14Q LOSS WILD-TYPE 90 105 95 39 61

Figure S401.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00042

Table S402.  Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
14Q LOSS MUTATED 24 40 30 20 15
14Q LOSS WILD-TYPE 27 84 114 88 77

Figure S402.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S403.  Gene #68: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
15Q LOSS MUTATED 58 32 54 5
15Q LOSS WILD-TYPE 93 66 128 189

Figure S403.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-04 (Fisher's exact test), Q value = 0.0015

Table S404.  Gene #68: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
15Q LOSS MUTATED 48 28 22 29 17
15Q LOSS WILD-TYPE 83 88 76 92 113

Figure S404.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.00093

Table S405.  Gene #68: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
15Q LOSS MUTATED 45 40 26 23 13
15Q LOSS WILD-TYPE 82 103 138 71 76

Figure S405.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S406.  Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
16P LOSS MUTATED 64 33 49 8
16P LOSS WILD-TYPE 87 65 133 186

Figure S406.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.023

Table S407.  Gene #69: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
16P LOSS MUTATED 58 53 33
16P LOSS WILD-TYPE 183 108 142

Figure S407.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 0.0285 (Fisher's exact test), Q value = 0.051

Table S408.  Gene #69: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
16P LOSS MUTATED 48 74 26
16P LOSS WILD-TYPE 122 199 127

Figure S408.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S409.  Gene #69: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
16P LOSS MUTATED 58 30 19 24 17
16P LOSS WILD-TYPE 73 86 79 97 113

Figure S409.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S410.  Gene #69: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
16P LOSS MUTATED 54 52 18 15 13
16P LOSS WILD-TYPE 73 91 146 79 76

Figure S410.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.0013

Table S411.  Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
16P LOSS MUTATED 39 50 22 12 7
16P LOSS WILD-TYPE 84 105 99 35 66

Figure S411.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8.2e-05

Table S412.  Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
16P LOSS MUTATED 26 41 25 23 15
16P LOSS WILD-TYPE 25 83 119 85 77

Figure S412.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S413.  Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
16Q LOSS MUTATED 70 41 45 11
16Q LOSS WILD-TYPE 81 57 137 183

Figure S413.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S414.  Gene #70: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
16Q LOSS MUTATED 60 37 19 22 23
16Q LOSS WILD-TYPE 71 79 79 99 107

Figure S414.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S415.  Gene #70: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
16Q LOSS MUTATED 63 48 25 12 16
16Q LOSS WILD-TYPE 64 95 139 82 73

Figure S415.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0044 (Fisher's exact test), Q value = 0.01

Table S416.  Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
16Q LOSS MUTATED 39 53 25 13 10
16Q LOSS WILD-TYPE 84 102 96 34 63

Figure S416.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S417.  Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
16Q LOSS MUTATED 29 45 26 28 12
16Q LOSS WILD-TYPE 22 79 118 80 80

Figure S417.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S418.  Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
17P LOSS MUTATED 92 57 78 10
17P LOSS WILD-TYPE 59 41 104 184

Figure S418.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00012

Table S419.  Gene #71: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
17P LOSS MUTATED 107 72 42
17P LOSS WILD-TYPE 134 89 133

Figure S419.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.0016

Table S420.  Gene #71: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
17P LOSS MUTATED 63 122 40
17P LOSS WILD-TYPE 107 151 113

Figure S420.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S421.  Gene #71: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
17P LOSS MUTATED 76 54 36 37 22
17P LOSS WILD-TYPE 55 62 62 84 108

Figure S421.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 4e-04

Table S422.  Gene #71: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
17P LOSS MUTATED 66 123 43
17P LOSS WILD-TYPE 101 155 129

Figure S422.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S423.  Gene #71: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
17P LOSS MUTATED 76 66 49 25 16
17P LOSS WILD-TYPE 51 77 115 69 73

Figure S423.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0194 (Fisher's exact test), Q value = 0.037

Table S424.  Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
17P LOSS MUTATED 49 74 37 13 25
17P LOSS WILD-TYPE 74 81 84 34 48

Figure S424.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00025

Table S425.  Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
17P LOSS MUTATED 30 61 50 33 24
17P LOSS WILD-TYPE 21 63 94 75 68

Figure S425.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S426.  Gene #72: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
17Q LOSS MUTATED 47 25 29 1
17Q LOSS WILD-TYPE 104 73 153 193

Figure S426.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 0.0209 (Fisher's exact test), Q value = 0.039

Table S427.  Gene #72: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
17Q LOSS MUTATED 35 36 20
17Q LOSS WILD-TYPE 206 125 155

Figure S427.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00015

Table S428.  Gene #72: '17q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
17Q LOSS MUTATED 37 18 19 12 10
17Q LOSS WILD-TYPE 94 98 79 109 120

Figure S428.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 0.0209 (Fisher's exact test), Q value = 0.039

Table S429.  Gene #72: '17q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
17Q LOSS MUTATED 29 54 17
17Q LOSS WILD-TYPE 138 224 155

Figure S429.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.0015

Table S430.  Gene #72: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
17Q LOSS MUTATED 36 26 18 12 8
17Q LOSS WILD-TYPE 91 117 146 82 81

Figure S430.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.021

Table S431.  Gene #72: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
17Q LOSS MUTATED 18 16 21 17 12
17Q LOSS WILD-TYPE 33 108 123 91 80

Figure S431.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S432.  Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
18P LOSS MUTATED 63 47 58 19
18P LOSS WILD-TYPE 88 51 124 175

Figure S432.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.024 (Fisher's exact test), Q value = 0.044

Table S433.  Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
18P LOSS MUTATED 33 53 34 19 12
18P LOSS WILD-TYPE 90 102 87 28 61

Figure S433.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S434.  Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
18Q LOSS MUTATED 81 52 100 24
18Q LOSS WILD-TYPE 70 46 82 170

Figure S434.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 0.00598 (Fisher's exact test), Q value = 0.014

Table S435.  Gene #74: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
18Q LOSS MUTATED 102 80 57
18Q LOSS WILD-TYPE 139 81 118

Figure S435.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 0.00306 (Fisher's exact test), Q value = 0.0074

Table S436.  Gene #74: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
18Q LOSS MUTATED 83 117 47
18Q LOSS WILD-TYPE 87 156 106

Figure S436.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00042 (Fisher's exact test), Q value = 0.0013

Table S437.  Gene #74: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
18Q LOSS MUTATED 72 43 32 58 42
18Q LOSS WILD-TYPE 59 73 66 63 88

Figure S437.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00076 (Fisher's exact test), Q value = 0.0021

Table S438.  Gene #74: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
18Q LOSS MUTATED 67 60 56 46 25
18Q LOSS WILD-TYPE 60 83 108 48 64

Figure S438.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0277 (Fisher's exact test), Q value = 0.049

Table S439.  Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
18Q LOSS MUTATED 27 53 55 33 45
18Q LOSS WILD-TYPE 24 71 89 75 47

Figure S439.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S440.  Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
19P LOSS MUTATED 71 30 74 7
19P LOSS WILD-TYPE 80 68 108 187

Figure S440.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S441.  Gene #75: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
19P LOSS MUTATED 60 85 27
19P LOSS WILD-TYPE 181 76 148

Figure S441.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S442.  Gene #75: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
19P LOSS MUTATED 67 88 20
19P LOSS WILD-TYPE 103 185 133

Figure S442.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S443.  Gene #75: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
19P LOSS MUTATED 74 32 21 38 10
19P LOSS WILD-TYPE 57 84 77 83 120

Figure S443.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S444.  Gene #75: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
19P LOSS MUTATED 78 75 27
19P LOSS WILD-TYPE 89 203 145

Figure S444.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S445.  Gene #75: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
19P LOSS MUTATED 73 41 23 34 9
19P LOSS WILD-TYPE 54 102 141 60 80

Figure S445.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S446.  Gene #75: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
19P LOSS MUTATED 62 47 20 12 16
19P LOSS WILD-TYPE 61 108 101 35 57

Figure S446.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S447.  Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
19P LOSS MUTATED 32 43 26 22 34
19P LOSS WILD-TYPE 19 81 118 86 58

Figure S447.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S448.  Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
19Q LOSS MUTATED 57 18 60 7
19Q LOSS WILD-TYPE 94 80 122 187

Figure S448.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S449.  Gene #76: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
19Q LOSS MUTATED 41 71 20
19Q LOSS WILD-TYPE 200 90 155

Figure S449.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S450.  Gene #76: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
19Q LOSS MUTATED 60 63 14
19Q LOSS WILD-TYPE 110 210 139

Figure S450.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S451.  Gene #76: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
19Q LOSS MUTATED 58 25 16 32 6
19Q LOSS WILD-TYPE 73 91 82 89 124

Figure S451.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S452.  Gene #76: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
19Q LOSS MUTATED 66 56 19
19Q LOSS WILD-TYPE 101 222 153

Figure S452.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S453.  Gene #76: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
19Q LOSS MUTATED 55 32 14 32 8
19Q LOSS WILD-TYPE 72 111 150 62 81

Figure S453.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8.2e-05

Table S454.  Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
19Q LOSS MUTATED 51 30 15 9 15
19Q LOSS WILD-TYPE 72 125 106 38 58

Figure S454.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S455.  Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
19Q LOSS MUTATED 23 31 17 17 32
19Q LOSS WILD-TYPE 28 93 127 91 60

Figure S455.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 0.00278 (Fisher's exact test), Q value = 0.0068

Table S456.  Gene #77: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
20P LOSS MUTATED 10 12 16 4
20P LOSS WILD-TYPE 141 86 166 190

Figure S456.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

'20q loss' versus 'MRNASEQ_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 0.032

Table S457.  Gene #78: '20q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
20Q LOSS MUTATED 6 2 0
20Q LOSS WILD-TYPE 164 271 153

Figure S457.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0301 (Fisher's exact test), Q value = 0.053

Table S458.  Gene #78: '20q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
20Q LOSS MUTATED 1 2 0 5 0
20Q LOSS WILD-TYPE 130 114 98 116 130

Figure S458.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S459.  Gene #79: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
21Q LOSS MUTATED 96 59 109 23
21Q LOSS WILD-TYPE 55 39 73 171

Figure S459.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 0.0264 (Fisher's exact test), Q value = 0.047

Table S460.  Gene #79: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
21Q LOSS MUTATED 122 81 67
21Q LOSS WILD-TYPE 119 80 108

Figure S460.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.0013

Table S461.  Gene #79: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
21Q LOSS MUTATED 92 132 51
21Q LOSS WILD-TYPE 78 141 102

Figure S461.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S462.  Gene #79: '21q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
21Q LOSS MUTATED 75 58 36 69 37
21Q LOSS WILD-TYPE 56 58 62 52 93

Figure S462.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 0.0352 (Fisher's exact test), Q value = 0.061

Table S463.  Gene #79: '21q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
21Q LOSS MUTATED 84 135 65
21Q LOSS WILD-TYPE 83 143 107

Figure S463.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S464.  Gene #79: '21q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
21Q LOSS MUTATED 74 78 56 49 27
21Q LOSS WILD-TYPE 53 65 108 45 62

Figure S464.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00054

Table S465.  Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
21Q LOSS MUTATED 70 83 43 26 23
21Q LOSS WILD-TYPE 53 72 78 21 50

Figure S465.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'21q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0199 (Fisher's exact test), Q value = 0.038

Table S466.  Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
21Q LOSS MUTATED 30 67 57 43 48
21Q LOSS WILD-TYPE 21 57 87 65 44

Figure S466.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S467.  Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
22Q LOSS MUTATED 83 64 64 7
22Q LOSS WILD-TYPE 68 34 118 187

Figure S467.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.022

Table S468.  Gene #80: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
22Q LOSS MUTATED 91 67 47
22Q LOSS WILD-TYPE 150 94 128

Figure S468.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 0.0133 (Fisher's exact test), Q value = 0.027

Table S469.  Gene #80: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
22Q LOSS MUTATED 55 112 42
22Q LOSS WILD-TYPE 115 161 111

Figure S469.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S470.  Gene #80: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
22Q LOSS MUTATED 68 50 27 35 29
22Q LOSS WILD-TYPE 63 66 71 86 101

Figure S470.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 0.0489 (Fisher's exact test), Q value = 0.081

Table S471.  Gene #80: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
22Q LOSS MUTATED 63 105 47
22Q LOSS WILD-TYPE 104 173 125

Figure S471.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S472.  Gene #80: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
22Q LOSS MUTATED 73 65 33 24 20
22Q LOSS WILD-TYPE 54 78 131 70 69

Figure S472.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00244 (Fisher's exact test), Q value = 0.0061

Table S473.  Gene #80: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
22Q LOSS MUTATED 45 72 32 19 18
22Q LOSS WILD-TYPE 78 83 89 28 55

Figure S473.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 4e-04

Table S474.  Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
22Q LOSS MUTATED 29 57 42 35 23
22Q LOSS WILD-TYPE 22 67 102 73 69

Figure S474.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S475.  Gene #81: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
XP LOSS MUTATED 37 25 54 7
XP LOSS WILD-TYPE 114 73 128 187

Figure S475.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S476.  Gene #81: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
XP LOSS MUTATED 55 45 15
XP LOSS WILD-TYPE 186 116 160

Figure S476.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00254 (Fisher's exact test), Q value = 0.0063

Table S477.  Gene #81: 'xp loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 110 99
XP LOSS MUTATED 67 20 9
XP LOSS WILD-TYPE 206 90 90

Figure S477.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'xp loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S478.  Gene #81: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
XP LOSS MUTATED 53 53 12
XP LOSS WILD-TYPE 117 220 141

Figure S478.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.0014

Table S479.  Gene #81: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
XP LOSS MUTATED 29 25 20 34 10
XP LOSS WILD-TYPE 102 91 78 87 120

Figure S479.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00034

Table S480.  Gene #81: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
XP LOSS MUTATED 47 59 16
XP LOSS WILD-TYPE 120 219 156

Figure S480.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xp loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00031

Table S481.  Gene #81: 'xp loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
XP LOSS MUTATED 29 36 19 30 8
XP LOSS WILD-TYPE 98 107 145 64 81

Figure S481.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00612 (Fisher's exact test), Q value = 0.014

Table S482.  Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
XP LOSS MUTATED 38 36 17 9 9
XP LOSS WILD-TYPE 85 119 104 38 64

Figure S482.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xp loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00086 (Fisher's exact test), Q value = 0.0024

Table S483.  Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
XP LOSS MUTATED 14 31 20 14 30
XP LOSS WILD-TYPE 37 93 124 94 62

Figure S483.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.4e-05

Table S484.  Gene #82: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 98 182 194
XQ LOSS MUTATED 33 26 34 5
XQ LOSS WILD-TYPE 118 72 148 189

Figure S484.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.00084

Table S485.  Gene #82: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 241 161 175
XQ LOSS MUTATED 45 32 12
XQ LOSS WILD-TYPE 196 129 163

Figure S485.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'RPPA_CNMF'

P value = 0.0284 (Fisher's exact test), Q value = 0.051

Table S486.  Gene #82: 'xq loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 137 136 64
XQ LOSS MUTATED 34 18 15 9
XQ LOSS WILD-TYPE 111 119 121 55

Figure S486.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'xq loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0022 (Fisher's exact test), Q value = 0.0055

Table S487.  Gene #82: 'xq loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 110 99
XQ LOSS MUTATED 55 15 6
XQ LOSS WILD-TYPE 218 95 93

Figure S487.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00022

Table S488.  Gene #82: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 170 273 153
XQ LOSS MUTATED 40 44 9
XQ LOSS WILD-TYPE 130 229 144

Figure S488.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00048 (Fisher's exact test), Q value = 0.0014

Table S489.  Gene #82: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 131 116 98 121 130
XQ LOSS MUTATED 30 24 14 18 7
XQ LOSS WILD-TYPE 101 92 84 103 123

Figure S489.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 0.00107 (Fisher's exact test), Q value = 0.0029

Table S490.  Gene #82: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 278 172
XQ LOSS MUTATED 35 49 13
XQ LOSS WILD-TYPE 132 229 159

Figure S490.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.0012

Table S491.  Gene #82: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 127 143 164 94 89
XQ LOSS MUTATED 25 34 17 16 5
XQ LOSS WILD-TYPE 102 109 147 78 84

Figure S491.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0275 (Fisher's exact test), Q value = 0.049

Table S492.  Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 123 155 121 47 73
XQ LOSS MUTATED 28 29 12 6 7
XQ LOSS WILD-TYPE 95 126 109 41 66

Figure S492.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0358 (Fisher's exact test), Q value = 0.062

Table S493.  Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 124 144 108 92
XQ LOSS MUTATED 13 25 18 10 16
XQ LOSS WILD-TYPE 38 99 126 98 76

Figure S493.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input
  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/STES-TP/22532763/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/STES-TP/22555833/STES-TP.transferedmergedcluster.txt

  • Number of patients = 625

  • Number of significantly arm-level cnvs = 82

  • Number of molecular subtypes = 10

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)