Correlation between copy number variations of arm-level result and molecular subtypes
Lung Adenocarcinoma (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/C1WD400S
Overview
Introduction

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

Summary

Testing the association between copy number variation 82 arm-level events and 12 molecular subtypes across 516 patients, 500 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

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

  • 4q gain cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

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

  • 6q gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

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

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

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

  • 9q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 10p 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'.

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

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

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

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

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

  • 13q gain cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_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', and 'MRNASEQ_CHIERARCHICAL'.

  • 16p gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

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

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

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

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

  • 20p 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'.

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

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

  • 22q gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • xp gain cnv correlated to 'METHLYATION_CNMF' and 'MIRSEQ_MATURE_CNMF'.

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

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

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

  • 2p loss cnv correlated to 'MIRSEQ_CNMF'.

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

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

  • 4p 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'.

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

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

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

  • 6p loss cnv correlated to 'METHLYATION_CNMF'.

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

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

  • 7q loss cnv correlated to 'CN_CNMF'.

  • 8p 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'.

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

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

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

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

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

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

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

  • 12p loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

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

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

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

  • 16q 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'.

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

  • 17q loss cnv correlated to 'CN_CNMF'.

  • 18p loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 18q loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 19p 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'.

  • 19q 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'.

  • 20p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 21q 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'.

  • 22q 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'.

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

  • xq loss cnv correlated to 'METHLYATION_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 500 significant findings detected.

Clinical
Features
MRNA
CNMF
MRNA
CHIERARCHICAL
CN
CNMF
METHLYATION
CNMF
RPPA
CNMF
RPPA
CHIERARCHICAL
MRNASEQ
CNMF
MRNASEQ
CHIERARCHICAL
MIRSEQ
CNMF
MIRSEQ
CHIERARCHICAL
MIRSEQ
MATURE
CNMF
MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
20q gain 201 (39%) 315 0.0222
(0.0518)
0.0239
(0.0543)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
0.0203
(0.0482)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
2e-05
(0.000144)
0.00191
(0.00674)
1e-05
(8.2e-05)
4q loss 136 (26%) 380 0.00519
(0.0157)
0.00706
(0.0196)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
0.0267
(0.0596)
0.0184
(0.0441)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
0.00015
(0.000745)
0.0003
(0.00135)
5q loss 143 (28%) 373 0.03
(0.0655)
0.0351
(0.0742)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
4e-05
(0.000243)
6e-05
(0.000339)
2e-05
(0.000144)
2e-05
(0.000144)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
8q gain 245 (47%) 271 0.0376
(0.0789)
0.0438
(0.0892)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
0.0763
(0.14)
0.692
(0.782)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
6e-05
(0.000339)
2e-05
(0.000144)
0.00033
(0.00146)
10p gain 112 (22%) 404 1e-05
(8.2e-05)
1e-05
(8.2e-05)
0.00465
(0.0143)
0.0207
(0.0486)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
0.00027
(0.00125)
1e-05
(8.2e-05)
0.00084
(0.00323)
0.00028
(0.00129)
12p gain 138 (27%) 378 0.0275
(0.061)
0.0463
(0.093)
1e-05
(8.2e-05)
5e-05
(0.000296)
0.0517
(0.101)
0.082
(0.148)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
0.00253
(0.00867)
2e-05
(0.000144)
4p loss 119 (23%) 397 0.403
(0.51)
0.408
(0.514)
1e-05
(8.2e-05)
0.0027
(0.00916)
0.00117
(0.00436)
0.00464
(0.0143)
0.00048
(0.002)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
0.00866
(0.0235)
0.00339
(0.0112)
8p loss 200 (39%) 316 0.182
(0.28)
0.0796
(0.145)
1e-05
(8.2e-05)
0.0299
(0.0653)
0.0371
(0.0779)
0.0333
(0.0712)
2e-05
(0.000144)
8e-05
(0.00044)
0.0311
(0.0675)
0.023
(0.0526)
0.00067
(0.00268)
0.0318
(0.0685)
16p loss 107 (21%) 409 0.466
(0.57)
0.483
(0.584)
1e-05
(8.2e-05)
0.00022
(0.00105)
0.00331
(0.0109)
0.00045
(0.00191)
1e-05
(8.2e-05)
0.00014
(0.000706)
0.00696
(0.0196)
0.00044
(0.00188)
9e-05
(0.000487)
0.00205
(0.0072)
16q loss 137 (27%) 379 0.79
(0.862)
0.622
(0.723)
1e-05
(8.2e-05)
3e-05
(0.000198)
0.00029
(0.00132)
0.00478
(0.0146)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
0.00602
(0.0175)
0.00113
(0.00423)
0.00132
(0.00485)
0.00497
(0.015)
19q loss 159 (31%) 357 0.686
(0.779)
0.467
(0.57)
0.00014
(0.000706)
1e-05
(8.2e-05)
0.0318
(0.0685)
0.00073
(0.00287)
0.00227
(0.00792)
4e-05
(0.000243)
0.00099
(0.00376)
0.00067
(0.00268)
0.00331
(0.0109)
0.0113
(0.0295)
21q loss 166 (32%) 350 0.0879
(0.156)
0.141
(0.23)
1e-05
(8.2e-05)
0.00424
(0.0133)
2e-05
(0.000144)
0.0068
(0.0193)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
3e-05
(0.000198)
0.00031
(0.00139)
0.0001
(0.000532)
1e-05
(8.2e-05)
22q loss 221 (43%) 295 0.314
(0.42)
0.168
(0.263)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
0.0165
(0.0408)
0.0112
(0.0295)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
4e-05
(0.000243)
1e-05
(8.2e-05)
0.00582
(0.017)
0.00048
(0.002)
7p gain 267 (52%) 249 0.248
(0.355)
0.315
(0.421)
1e-05
(8.2e-05)
0.083
(0.149)
0.00434
(0.0136)
0.00577
(0.0169)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
0.00293
(0.00981)
1e-05
(8.2e-05)
12q gain 133 (26%) 383 0.0872
(0.156)
0.142
(0.23)
1e-05
(8.2e-05)
6e-05
(0.000339)
0.0331
(0.0709)
0.232
(0.337)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
0.00012
(0.000625)
2e-05
(0.000144)
20p gain 175 (34%) 341 0.113
(0.193)
0.137
(0.224)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
0.253
(0.361)
0.00181
(0.00643)
2e-05
(0.000144)
1e-05
(8.2e-05)
3e-05
(0.000198)
0.00019
(0.000912)
0.00776
(0.0213)
7e-05
(0.000389)
1p loss 80 (16%) 436 0.0131
(0.0337)
0.038
(0.0795)
1e-05
(8.2e-05)
0.00047
(0.00198)
0.0385
(0.0805)
0.634
(0.734)
4e-05
(0.000243)
4e-05
(0.000243)
0.376
(0.483)
0.00722
(0.02)
0.00577
(0.0169)
0.516
(0.617)
5p loss 45 (9%) 471 0.296
(0.405)
0.308
(0.417)
4e-05
(0.000243)
0.018
(0.0434)
0.009
(0.0243)
0.00023
(0.00108)
0.106
(0.183)
0.00595
(0.0173)
0.0203
(0.0482)
0.0175
(0.0424)
0.0146
(0.0368)
0.00235
(0.00814)
19p loss 245 (47%) 271 1
(1.00)
1
(1.00)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
0.00152
(0.00548)
0.168
(0.263)
2e-05
(0.000144)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
4e-05
(0.000243)
3e-05
(0.000198)
0.00142
(0.00518)
2p gain 154 (30%) 362 0.114
(0.195)
0.182
(0.28)
1e-05
(8.2e-05)
3e-05
(0.000198)
0.238
(0.344)
0.535
(0.638)
4e-05
(0.000243)
0.00019
(0.000912)
1e-05
(8.2e-05)
0.00045
(0.00191)
0.0012
(0.00444)
7e-05
(0.000389)
2q gain 143 (28%) 373 0.205
(0.307)
0.317
(0.423)
2e-05
(0.000144)
0.00029
(0.00132)
0.566
(0.671)
0.9
(0.951)
0.0297
(0.0651)
0.0115
(0.0299)
0.0013
(0.00479)
0.0139
(0.0355)
0.00557
(0.0165)
0.00479
(0.0146)
3q gain 90 (17%) 426 0.201
(0.303)
0.297
(0.406)
3e-05
(0.000198)
0.00057
(0.00234)
0.0166
(0.041)
0.22
(0.324)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
0.0179
(0.0432)
0.192
(0.292)
0.00064
(0.00258)
0.027
(0.06)
10q gain 79 (15%) 437 0.00051
(0.00212)
0.00032
(0.00142)
0.0459
(0.0926)
0.74
(0.822)
0.00076
(0.00297)
1e-05
(8.2e-05)
0.108
(0.185)
0.00543
(0.0162)
0.0241
(0.0546)
0.0174
(0.0424)
11q gain 118 (23%) 398 0.0178
(0.0432)
0.0169
(0.0413)
1e-05
(8.2e-05)
0.209
(0.311)
0.245
(0.353)
0.318
(0.423)
0.0308
(0.0669)
5e-05
(0.000296)
0.00017
(0.000828)
6e-05
(0.000339)
0.065
(0.122)
0.00306
(0.0102)
14q gain 129 (25%) 387 0.841
(0.906)
0.844
(0.907)
1e-05
(8.2e-05)
0.0292
(0.0643)
0.0818
(0.148)
0.136
(0.223)
0.00047
(0.00198)
1e-05
(8.2e-05)
0.00043
(0.00185)
0.00015
(0.000745)
0.00626
(0.018)
0.0248
(0.0559)
17q gain 191 (37%) 325 1
(1.00)
0.635
(0.735)
1e-05
(8.2e-05)
0.00073
(0.00287)
0.34
(0.445)
0.216
(0.318)
4e-05
(0.000243)
1e-05
(8.2e-05)
0.00094
(0.00359)
7e-05
(0.000389)
0.00286
(0.0096)
0.00013
(0.000666)
18p gain 92 (18%) 424 1
(1.00)
1
(1.00)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
0.688
(0.78)
0.95
(0.995)
0.0137
(0.0349)
0.00106
(0.004)
0.00229
(0.00796)
0.0356
(0.0751)
0.00482
(0.0146)
4e-05
(0.000243)
18q gain 69 (13%) 447 0.318
(0.423)
0.405
(0.511)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
0.078
(0.143)
0.451
(0.556)
4e-05
(0.000243)
4e-05
(0.000243)
0.00702
(0.0196)
0.00166
(0.00592)
1e-05
(8.2e-05)
0.00052
(0.00215)
10q loss 132 (26%) 384 0.776
(0.857)
0.788
(0.862)
1e-05
(8.2e-05)
0.042
(0.0862)
0.0557
(0.107)
0.398
(0.506)
0.00267
(0.00912)
1e-05
(8.2e-05)
0.00934
(0.025)
0.00017
(0.000828)
0.0425
(0.0871)
0.007
(0.0196)
11p loss 111 (22%) 405 0.0343
(0.0728)
0.0704
(0.131)
1e-05
(8.2e-05)
0.00011
(0.000576)
0.292
(0.402)
0.023
(0.0526)
0.00064
(0.00258)
0.00016
(0.000787)
0.111
(0.189)
0.0417
(0.086)
3e-05
(0.000198)
0.241
(0.348)
15q loss 244 (47%) 272 0.81
(0.88)
0.655
(0.755)
1e-05
(8.2e-05)
0.00034
(0.00148)
0.135
(0.222)
0.224
(0.327)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
4e-05
(0.000243)
0.00022
(0.00105)
0.00419
(0.0132)
0.00029
(0.00132)
17p loss 219 (42%) 297 0.302
(0.41)
0.144
(0.232)
1e-05
(8.2e-05)
6e-05
(0.000339)
0.0184
(0.0441)
0.364
(0.471)
0.00076
(0.00297)
6e-05
(0.000339)
0.416
(0.522)
0.011
(0.029)
6e-05
(0.000339)
0.0202
(0.0481)
1q gain 319 (62%) 197 0.9
(0.951)
1
(1.00)
2e-05
(0.000144)
0.00103
(0.0039)
5e-05
(0.000296)
0.00282
(0.0095)
0.00187
(0.00662)
0.0264
(0.0591)
0.346
(0.451)
2e-05
(0.000144)
0.57
(0.675)
0.385
(0.494)
3p gain 44 (9%) 472 0.00827
(0.0225)
0.00069
(0.00275)
0.0216
(0.0505)
0.78
(0.858)
3e-05
(0.000198)
0.00093
(0.00356)
0.0802
(0.145)
0.49
(0.59)
0.00239
(0.00825)
0.0131
(0.0337)
7q gain 220 (43%) 296 0.529
(0.632)
0.389
(0.497)
1e-05
(8.2e-05)
0.419
(0.524)
0.0594
(0.113)
0.598
(0.702)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
0.00402
(0.0128)
0.00119
(0.00442)
0.048
(0.0957)
3e-05
(0.000198)
11p gain 94 (18%) 422 0.00859
(0.0233)
0.0107
(0.0283)
0.00241
(0.00829)
0.683
(0.777)
0.128
(0.213)
0.479
(0.582)
0.129
(0.214)
2e-05
(0.000144)
6e-05
(0.000339)
2e-05
(0.000144)
0.0697
(0.13)
0.00274
(0.00927)
3p loss 211 (41%) 305 0.149
(0.238)
0.242
(0.348)
1e-05
(8.2e-05)
0.00019
(0.000912)
0.348
(0.453)
0.189
(0.289)
0.058
(0.111)
2e-05
(0.000144)
0.00813
(0.0222)
0.00029
(0.00132)
0.0112
(0.0295)
0.0343
(0.0728)
13q loss 251 (49%) 265 0.418
(0.523)
0.622
(0.723)
1e-05
(8.2e-05)
0.109
(0.187)
9e-05
(0.000487)
0.282
(0.391)
1e-05
(8.2e-05)
2e-05
(0.000144)
0.00321
(0.0107)
0.00164
(0.00587)
0.078
(0.143)
0.0215
(0.0503)
18q loss 215 (42%) 301 0.0945
(0.166)
0.205
(0.307)
1e-05
(8.2e-05)
0.447
(0.552)
0.0149
(0.0374)
0.0786
(0.143)
1e-05
(8.2e-05)
3e-05
(0.000198)
0.00614
(0.0178)
0.932
(0.98)
0.0104
(0.0277)
0.0247
(0.0558)
20p loss 113 (22%) 403 0.79
(0.862)
0.621
(0.723)
0.0232
(0.0528)
0.0113
(0.0295)
0.00698
(0.0196)
0.0573
(0.11)
0.00464
(0.0143)
0.00078
(0.00303)
1
(1.00)
0.636
(0.735)
0.0139
(0.0355)
0.0234
(0.0533)
5p gain 279 (54%) 237 0.481
(0.583)
0.666
(0.761)
1e-05
(8.2e-05)
0.0599
(0.114)
0.262
(0.371)
0.0472
(0.0945)
0.00032
(0.00142)
0.00635
(0.0182)
0.106
(0.183)
0.116
(0.196)
0.0472
(0.0945)
0.00034
(0.00148)
16p gain 137 (27%) 379 0.553
(0.657)
0.337
(0.443)
0.00023
(0.00108)
0.673
(0.769)
0.00342
(0.0112)
0.135
(0.222)
0.0206
(0.0486)
0.00702
(0.0196)
0.0302
(0.0658)
0.00556
(0.0165)
0.181
(0.28)
0.345
(0.451)
17p gain 84 (16%) 432 0.405
(0.511)
0.314
(0.42)
0.00268
(0.00912)
0.0628
(0.119)
0.119
(0.201)
0.0159
(0.0395)
0.0407
(0.0843)
0.0225
(0.0519)
0.00948
(0.0253)
0.00015
(0.000745)
0.0534
(0.104)
0.158
(0.249)
9q loss 249 (48%) 267 1
(1.00)
0.902
(0.952)
1e-05
(8.2e-05)
0.0035
(0.0114)
0.291
(0.4)
0.106
(0.183)
0.205
(0.307)
0.00026
(0.00121)
0.00448
(0.014)
3e-05
(0.000198)
0.0521
(0.102)
0.0127
(0.0328)
10p loss 110 (21%) 406 0.777
(0.857)
0.786
(0.862)
1e-05
(8.2e-05)
0.169
(0.264)
0.0483
(0.0958)
0.888
(0.944)
0.00112
(0.00421)
1e-05
(8.2e-05)
0.00757
(0.0208)
0.0006
(0.00244)
0.242
(0.348)
0.235
(0.34)
14q loss 114 (22%) 402 0.403
(0.51)
0.409
(0.515)
0.0003
(0.00135)
0.0253
(0.0567)
0.00222
(0.00777)
0.181
(0.28)
0.401
(0.509)
0.00928
(0.0249)
0.0155
(0.0388)
0.0283
(0.0624)
0.676
(0.771)
0.319
(0.423)
18p loss 180 (35%) 336 0.125
(0.209)
0.236
(0.343)
1e-05
(8.2e-05)
0.946
(0.992)
0.0451
(0.0912)
0.00618
(0.0178)
0.0016
(0.00575)
0.00016
(0.000787)
0.00413
(0.0131)
0.489
(0.589)
0.32
(0.423)
0.191
(0.291)
1p gain 142 (28%) 374 1
(1.00)
1
(1.00)
1e-05
(8.2e-05)
0.789
(0.862)
0.00034
(0.00148)
0.0491
(0.0966)
0.00151
(0.00546)
0.0253
(0.0567)
0.197
(0.299)
0.17
(0.266)
0.303
(0.411)
0.153
(0.242)
5q gain 132 (26%) 384 0.37
(0.477)
0.33
(0.435)
0.004
(0.0128)
0.213
(0.315)
0.0953
(0.167)
0.00381
(0.0123)
0.0229
(0.0526)
0.046
(0.0926)
0.185
(0.284)
0.00651
(0.0185)
0.0965
(0.169)
0.375
(0.483)
6p gain 146 (28%) 370 0.0825
(0.149)
0.088
(0.156)
0.00038
(0.00165)
0.00011
(0.000576)
0.32
(0.423)
0.84
(0.905)
0.044
(0.0895)
0.0225
(0.0519)
0.0763
(0.14)
0.0297
(0.0651)
0.0719
(0.133)
0.0509
(0.0998)
6q gain 60 (12%) 456 1
(1.00)
1
(1.00)
0.0157
(0.0391)
0.0782
(0.143)
0.0488
(0.0962)
0.432
(0.536)
0.211
(0.313)
0.0168
(0.0412)
0.0127
(0.0327)
0.0314
(0.068)
0.285
(0.393)
0.151
(0.24)
8p gain 125 (24%) 391 0.253
(0.361)
0.253
(0.361)
1e-05
(8.2e-05)
0.0271
(0.0602)
0.275
(0.383)
0.887
(0.944)
0.0168
(0.0412)
0.00385
(0.0124)
0.416
(0.522)
0.707
(0.795)
0.0343
(0.0728)
0.838
(0.904)
19q gain 78 (15%) 438 0.00082
(0.00316)
0.00737
(0.0203)
0.0418
(0.086)
0.233
(0.339)
0.127
(0.213)
0.039
(0.0812)
0.065
(0.122)
0.135
(0.222)
0.44
(0.544)
0.0279
(0.0617)
9p loss 269 (52%) 247 0.591
(0.696)
0.601
(0.704)
1e-05
(8.2e-05)
0.00344
(0.0112)
0.61
(0.713)
0.399
(0.507)
0.0882
(0.156)
5e-05
(0.000296)
0.051
(0.0998)
0.0121
(0.0312)
0.18
(0.279)
0.0329
(0.0707)
11q loss 87 (17%) 429 0.467
(0.57)
0.482
(0.584)
1e-05
(8.2e-05)
0.0001
(0.000532)
0.588
(0.692)
0.125
(0.21)
0.00138
(0.00505)
0.00356
(0.0116)
0.067
(0.126)
0.0658
(0.124)
0.00644
(0.0184)
0.88
(0.94)
4p gain 83 (16%) 433 1
(1.00)
1
(1.00)
3e-05
(0.000198)
0.00376
(0.0122)
0.498
(0.599)
0.14
(0.228)
0.00554
(0.0165)
0.0477
(0.0953)
0.0677
(0.127)
0.128
(0.213)
0.936
(0.982)
0.134
(0.222)
4q gain 49 (9%) 467 0.427
(0.532)
0.37
(0.478)
0.00073
(0.00287)
0.712
(0.798)
0.958
(1.00)
0.0485
(0.0959)
0.00887
(0.024)
0.0216
(0.0505)
0.0646
(0.122)
0.13
(0.215)
0.174
(0.271)
0.338
(0.443)
9p gain 45 (9%) 471 9e-05
(0.000487)
0.0225
(0.0519)
0.684
(0.777)
0.257
(0.365)
0.0115
(0.0299)
0.00526
(0.0158)
0.0795
(0.145)
0.124
(0.208)
0.8
(0.871)
0.623
(0.723)
15q gain 38 (7%) 478 0.2
(0.303)
0.146
(0.235)
0.00151
(0.00546)
0.0146
(0.0368)
0.659
(0.757)
0.965
(1.00)
1e-05
(8.2e-05)
1e-05
(8.2e-05)
0.837
(0.904)
0.734
(0.818)
0.193
(0.293)
0.816
(0.886)
21q gain 98 (19%) 418 0.31
(0.417)
0.265
(0.374)
1e-05
(8.2e-05)
0.866
(0.928)
0.033
(0.0707)
0.326
(0.43)
0.00456
(0.0142)
0.00026
(0.00121)
0.714
(0.799)
0.878
(0.939)
0.689
(0.78)
0.275
(0.383)
1q loss 28 (5%) 488 0.00569
(0.0168)
0.00409
(0.013)
0.0559
(0.108)
0.0855
(0.153)
0.0178
(0.0432)
0.342
(0.447)
0.594
(0.698)
0.274
(0.383)
0.0357
(0.0752)
0.106
(0.183)
3q loss 144 (28%) 372 0.228
(0.333)
0.286
(0.394)
1e-05
(8.2e-05)
0.0394
(0.0819)
0.318
(0.423)
0.808
(0.878)
0.314
(0.42)
0.00538
(0.0161)
0.46
(0.564)
0.0225
(0.0519)
0.194
(0.294)
0.979
(1.00)
6q loss 217 (42%) 299 0.43
(0.534)
0.541
(0.643)
0.215
(0.318)
1e-05
(8.2e-05)
0.455
(0.559)
0.716
(0.8)
0.267
(0.376)
0.00014
(0.000706)
0.563
(0.668)
0.00081
(0.00314)
0.212
(0.315)
0.0206
(0.0486)
7p loss 34 (7%) 482 1
(1.00)
1
(1.00)
0.00013
(0.000666)
0.0443
(0.0899)
0.772
(0.854)
0.71
(0.797)
0.00999
(0.0266)
0.0001
(0.000532)
0.147
(0.235)
0.364
(0.471)
0.132
(0.219)
0.173
(0.271)
12p loss 109 (21%) 407 1
(1.00)
0.882
(0.941)
1e-05
(8.2e-05)
0.269
(0.379)
0.00708
(0.0196)
0.103
(0.18)
0.00039
(0.00168)
0.00011
(0.000576)
0.0714
(0.133)
0.18
(0.279)
0.136
(0.223)
0.184
(0.284)
12q loss 94 (18%) 422 0.579
(0.685)
0.428
(0.533)
1e-05
(8.2e-05)
0.118
(0.201)
0.105
(0.182)
0.149
(0.237)
8e-05
(0.00044)
0.00013
(0.000666)
0.0941
(0.166)
0.0214
(0.0503)
0.188
(0.288)
0.22
(0.324)
xp loss 106 (21%) 410 0.702
(0.79)
0.893
(0.947)
0.00904
(0.0243)
0.043
(0.0879)
0.00684
(0.0193)
0.142
(0.23)
0.0977
(0.171)
0.00477
(0.0146)
0.757
(0.839)
0.452
(0.557)
0.389
(0.497)
0.661
(0.759)
16q gain 101 (20%) 415 0.298
(0.406)
0.31
(0.417)
0.0165
(0.0408)
0.338
(0.443)
0.297
(0.406)
0.425
(0.531)
0.346
(0.451)
0.203
(0.305)
0.0152
(0.0382)
0.0146
(0.0368)
0.513
(0.615)
0.486
(0.587)
xq gain 86 (17%) 430 0.394
(0.503)
0.246
(0.353)
0.00059
(0.00241)
0.187
(0.286)
0.921
(0.971)
0.336
(0.442)
0.0485
(0.0959)
0.0169
(0.0414)
0.17
(0.266)
0.436
(0.54)
0.389
(0.497)
0.054
(0.104)
9q gain 34 (7%) 482 0.0045
(0.014)
0.106
(0.183)
0.274
(0.383)
0.138
(0.225)
0.178
(0.277)
0.0483
(0.0958)
0.223
(0.326)
0.889
(0.944)
0.698
(0.787)
0.312
(0.419)
13q gain 43 (8%) 473 0.63
(0.732)
0.539
(0.642)
0.0554
(0.107)
0.0143
(0.0362)
0.0718
(0.133)
0.723
(0.807)
0.304
(0.412)
0.0227
(0.0523)
0.935
(0.981)
0.162
(0.255)
0.363
(0.471)
0.483
(0.584)
xp gain 53 (10%) 463 0.293
(0.402)
0.221
(0.324)
0.0739
(0.136)
0.00635
(0.0182)
0.363
(0.471)
0.827
(0.895)
0.149
(0.237)
0.124
(0.208)
0.0837
(0.15)
0.332
(0.437)
0.0446
(0.0904)
0.191
(0.291)
8q loss 56 (11%) 460 1
(1.00)
0.583
(0.687)
1e-05
(8.2e-05)
0.418
(0.523)
0.088
(0.156)
0.103
(0.18)
0.0738
(0.136)
0.0412
(0.0851)
0.662
(0.76)
0.652
(0.752)
0.824
(0.893)
0.263
(0.372)
22q gain 62 (12%) 454 0.11
(0.188)
0.122
(0.206)
0.0522
(0.102)
0.678
(0.772)
0.858
(0.92)
0.144
(0.232)
0.226
(0.329)
0.0426
(0.0871)
0.613
(0.716)
0.835
(0.903)
0.372
(0.479)
0.276
(0.385)
2p loss 24 (5%) 492 0.427
(0.532)
0.581
(0.686)
0.666
(0.761)
0.889
(0.944)
1
(1.00)
0.297
(0.406)
0.998
(1.00)
0.751
(0.833)
0.039
(0.0812)
0.923
(0.971)
0.142
(0.23)
0.462
(0.566)
6p loss 101 (20%) 415 0.0635
(0.12)
0.0935
(0.165)
0.0582
(0.111)
0.00398
(0.0128)
0.788
(0.862)
0.467
(0.57)
0.452
(0.557)
0.278
(0.386)
0.146
(0.235)
0.0975
(0.171)
0.205
(0.307)
0.156
(0.246)
7q loss 41 (8%) 475 0.255
(0.363)
0.256
(0.364)
0.0194
(0.0463)
0.273
(0.383)
0.78
(0.858)
0.6
(0.704)
0.309
(0.417)
0.091
(0.161)
0.473
(0.575)
0.149
(0.237)
0.788
(0.862)
0.732
(0.816)
17q loss 60 (12%) 456 0.52
(0.622)
0.844
(0.907)
0.00053
(0.00218)
0.378
(0.485)
0.115
(0.195)
0.773
(0.855)
0.3
(0.409)
0.277
(0.385)
0.602
(0.705)
0.137
(0.223)
0.396
(0.504)
0.471
(0.574)
xq loss 61 (12%) 455 0.0827
(0.149)
0.054
(0.104)
0.203
(0.305)
0.0056
(0.0165)
0.256
(0.363)
0.697
(0.787)
0.187
(0.286)
0.157
(0.248)
0.0718
(0.133)
0.051
(0.0998)
0.155
(0.246)
0.303
(0.411)
19p gain 33 (6%) 483 0.0642
(0.122)
0.73
(0.815)
0.275
(0.383)
0.663
(0.76)
0.898
(0.951)
0.707
(0.795)
0.505
(0.607)
0.658
(0.757)
0.886
(0.944)
0.513
(0.615)
2q loss 25 (5%) 491 1
(1.00)
1
(1.00)
0.212
(0.315)
0.242
(0.348)
0.777
(0.857)
0.271
(0.381)
0.213
(0.315)
0.44
(0.545)
0.21
(0.312)
0.923
(0.971)
0.31
(0.417)
0.285
(0.394)
20q loss 67 (13%) 449 1
(1.00)
1
(1.00)
0.986
(1.00)
0.69
(0.78)
0.126
(0.21)
0.282
(0.391)
0.871
(0.933)
0.105
(0.183)
0.739
(0.821)
0.807
(0.878)
0.123
(0.207)
0.655
(0.755)
'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
1P GAIN MUTATED 81 28 18 15
1P GAIN WILD-TYPE 91 110 114 59

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

'1p gain' versus 'RPPA_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0015

Table S2.  Gene #1: '1p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
1P GAIN MUTATED 42 6 17 18 19
1P GAIN WILD-TYPE 49 16 49 57 90

Figure S2.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'1p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0491 (Fisher's exact test), Q value = 0.097

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
1P GAIN MUTATED 50 42 10
1P GAIN WILD-TYPE 117 91 53

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

'1p gain' versus 'MRNASEQ_CNMF'

P value = 0.00151 (Fisher's exact test), Q value = 0.0055

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
1P GAIN MUTATED 53 31 15 29 13
1P GAIN WILD-TYPE 77 88 75 86 45

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

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0253 (Fisher's exact test), Q value = 0.057

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
1P GAIN MUTATED 20 37 37 7 10 12 18
1P GAIN WILD-TYPE 58 73 60 41 43 37 59

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

'1q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
1Q GAIN MUTATED 123 83 60 53
1Q GAIN WILD-TYPE 49 55 72 21

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

'1q gain' versus 'METHLYATION_CNMF'

P value = 0.00103 (Fisher's exact test), Q value = 0.0039

Table S7.  Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
1Q GAIN MUTATED 103 118 63
1Q GAIN WILD-TYPE 53 52 66

Figure S7.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q gain' versus 'RPPA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 3e-04

Table S8.  Gene #2: '1q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
1Q GAIN MUTATED 64 16 53 39 53
1Q GAIN WILD-TYPE 27 6 13 36 56

Figure S8.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'1q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00282 (Fisher's exact test), Q value = 0.0095

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
1Q GAIN MUTATED 119 72 34
1Q GAIN WILD-TYPE 48 61 29

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

'1q gain' versus 'MRNASEQ_CNMF'

P value = 0.00187 (Fisher's exact test), Q value = 0.0066

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
1Q GAIN MUTATED 88 77 40 79 32
1Q GAIN WILD-TYPE 42 42 50 36 26

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

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0264 (Fisher's exact test), Q value = 0.059

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
1Q GAIN MUTATED 49 67 52 37 40 30 41
1Q GAIN WILD-TYPE 29 43 45 11 13 19 36

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

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S12.  Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
1Q GAIN MUTATED 53 35 92 67 56 12
1Q GAIN WILD-TYPE 18 4 53 63 40 17

Figure S12.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
2P GAIN MUTATED 53 59 15 27
2P GAIN WILD-TYPE 119 79 117 47

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 2e-04

Table S14.  Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
2P GAIN MUTATED 64 47 20
2P GAIN WILD-TYPE 92 123 109

Figure S14.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00024

Table S15.  Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
2P GAIN MUTATED 43 17 28 50 16
2P GAIN WILD-TYPE 87 102 62 65 42

Figure S15.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00091

Table S16.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
2P GAIN MUTATED 15 32 35 8 25 23 16
2P GAIN WILD-TYPE 63 78 62 40 28 26 61

Figure S16.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S17.  Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
2P GAIN MUTATED 37 92 24
2P GAIN WILD-TYPE 149 129 79

Figure S17.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0019

Table S18.  Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
2P GAIN MUTATED 13 17 51 29 39 4
2P GAIN WILD-TYPE 58 22 94 101 57 25

Figure S18.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0012 (Fisher's exact test), Q value = 0.0044

Table S19.  Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
2P GAIN MUTATED 8 41 27 9 18 23
2P GAIN WILD-TYPE 51 49 68 34 52 54

Figure S19.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00039

Table S20.  Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
2P GAIN MUTATED 15 88 23
2P GAIN WILD-TYPE 89 150 69

Figure S20.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S21.  Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
2Q GAIN MUTATED 50 49 15 29
2Q GAIN WILD-TYPE 122 89 117 45

Figure S21.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.0013

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
2Q GAIN MUTATED 57 46 20
2Q GAIN WILD-TYPE 99 124 109

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

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.0297 (Fisher's exact test), Q value = 0.065

Table S23.  Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
2Q GAIN MUTATED 37 22 26 43 15
2Q GAIN WILD-TYPE 93 97 64 72 43

Figure S23.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0115 (Fisher's exact test), Q value = 0.03

Table S24.  Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
2Q GAIN MUTATED 14 30 34 12 18 21 14
2Q GAIN WILD-TYPE 64 80 63 36 35 28 63

Figure S24.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CNMF'

P value = 0.0013 (Fisher's exact test), Q value = 0.0048

Table S25.  Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
2Q GAIN MUTATED 39 80 23
2Q GAIN WILD-TYPE 147 141 80

Figure S25.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0139 (Fisher's exact test), Q value = 0.035

Table S26.  Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
2Q GAIN MUTATED 13 13 48 31 34 3
2Q GAIN WILD-TYPE 58 26 97 99 62 26

Figure S26.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00557 (Fisher's exact test), Q value = 0.017

Table S27.  Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
2Q GAIN MUTATED 8 36 28 7 16 20
2Q GAIN WILD-TYPE 51 54 67 36 54 57

Figure S27.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00479 (Fisher's exact test), Q value = 0.015

Table S28.  Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
2Q GAIN MUTATED 16 76 23
2Q GAIN WILD-TYPE 88 162 69

Figure S28.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 0.00827 (Fisher's exact test), Q value = 0.023

Table S29.  Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
3P GAIN MUTATED 16 17 3 8
3P GAIN WILD-TYPE 156 121 129 66

Figure S29.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

'3p gain' versus 'METHLYATION_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0027

Table S30.  Gene #5: '3p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
3P GAIN MUTATED 18 20 2
3P GAIN WILD-TYPE 138 150 127

Figure S30.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p gain' versus 'RPPA_CNMF'

P value = 0.0216 (Fisher's exact test), Q value = 0.05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
3P GAIN MUTATED 7 3 5 13 4
3P GAIN WILD-TYPE 84 19 61 62 105

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

'3p gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 2e-04

Table S32.  Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
3P GAIN MUTATED 19 0 8 14 3
3P GAIN WILD-TYPE 111 119 82 101 55

Figure S32.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00093 (Fisher's exact test), Q value = 0.0036

Table S33.  Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
3P GAIN MUTATED 3 13 19 3 2 2 2
3P GAIN WILD-TYPE 75 97 78 45 51 47 75

Figure S33.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00239 (Fisher's exact test), Q value = 0.0083

Table S34.  Gene #5: '3p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
3P GAIN MUTATED 0 6 16 1 8 8
3P GAIN WILD-TYPE 59 84 79 42 62 69

Figure S34.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0131 (Fisher's exact test), Q value = 0.034

Table S35.  Gene #5: '3p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
3P GAIN MUTATED 3 23 13
3P GAIN WILD-TYPE 101 215 79

Figure S35.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 2e-04

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
3Q GAIN MUTATED 30 40 9 11
3Q GAIN WILD-TYPE 142 98 123 63

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

'3q gain' versus 'METHLYATION_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.0023

Table S37.  Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
3Q GAIN MUTATED 40 31 11
3Q GAIN WILD-TYPE 116 139 118

Figure S37.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q gain' versus 'RPPA_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.041

Table S38.  Gene #6: '3q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
3Q GAIN MUTATED 15 5 10 23 12
3Q GAIN WILD-TYPE 76 17 56 52 97

Figure S38.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S39.  Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
3Q GAIN MUTATED 31 3 23 26 7
3Q GAIN WILD-TYPE 99 116 67 89 51

Figure S39.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S40.  Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
3Q GAIN MUTATED 4 24 39 3 6 8 6
3Q GAIN WILD-TYPE 74 86 58 45 47 41 71

Figure S40.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 0.0179 (Fisher's exact test), Q value = 0.043

Table S41.  Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
3Q GAIN MUTATED 27 51 12
3Q GAIN WILD-TYPE 159 170 91

Figure S41.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00064 (Fisher's exact test), Q value = 0.0026

Table S42.  Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
3Q GAIN MUTATED 2 18 27 3 15 14
3Q GAIN WILD-TYPE 57 72 68 40 55 63

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

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.027 (Fisher's exact test), Q value = 0.06

Table S43.  Gene #6: '3q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
3Q GAIN MUTATED 10 50 19
3Q GAIN WILD-TYPE 94 188 73

Figure S43.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 2e-04

Table S44.  Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
4P GAIN MUTATED 40 29 8 6
4P GAIN WILD-TYPE 132 109 124 68

Figure S44.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'4p gain' versus 'METHLYATION_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
4P GAIN MUTATED 36 28 11
4P GAIN WILD-TYPE 120 142 118

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

'4p gain' versus 'MRNASEQ_CNMF'

P value = 0.00554 (Fisher's exact test), Q value = 0.017

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
4P GAIN MUTATED 32 9 15 20 7
4P GAIN WILD-TYPE 98 110 75 95 51

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

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0477 (Fisher's exact test), Q value = 0.095

Table S47.  Gene #7: '4p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
4P GAIN MUTATED 6 24 19 6 8 12 8
4P GAIN WILD-TYPE 72 86 78 42 45 37 69

Figure S47.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q gain' versus 'CN_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.0029

Table S48.  Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
4Q GAIN MUTATED 27 14 7 1
4Q GAIN WILD-TYPE 145 124 125 73

Figure S48.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

'4q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0485 (Fisher's exact test), Q value = 0.096

Table S49.  Gene #8: '4q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
4Q GAIN MUTATED 9 18 5
4Q GAIN WILD-TYPE 158 115 58

Figure S49.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 0.00887 (Fisher's exact test), Q value = 0.024

Table S50.  Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
4Q GAIN MUTATED 23 6 7 7 6
4Q GAIN WILD-TYPE 107 113 83 108 52

Figure S50.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0216 (Fisher's exact test), Q value = 0.05

Table S51.  Gene #8: '4q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
4Q GAIN MUTATED 5 17 15 1 2 4 5
4Q GAIN WILD-TYPE 73 93 82 47 51 45 72

Figure S51.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S52.  Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
5P GAIN MUTATED 135 60 39 45
5P GAIN WILD-TYPE 37 78 93 29

Figure S52.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0472 (Fisher's exact test), Q value = 0.094

Table S53.  Gene #9: '5p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
5P GAIN MUTATED 93 64 42
5P GAIN WILD-TYPE 74 69 21

Figure S53.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0014

Table S54.  Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
5P GAIN MUTATED 87 55 35 66 34
5P GAIN WILD-TYPE 43 64 55 49 24

Figure S54.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00635 (Fisher's exact test), Q value = 0.018

Table S55.  Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
5P GAIN MUTATED 42 69 59 16 32 26 33
5P GAIN WILD-TYPE 36 41 38 32 21 23 44

Figure S55.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0472 (Fisher's exact test), Q value = 0.094

Table S56.  Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
5P GAIN MUTATED 24 60 52 22 35 45
5P GAIN WILD-TYPE 35 30 43 21 35 32

Figure S56.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.0015

Table S57.  Gene #9: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
5P GAIN MUTATED 40 148 50
5P GAIN WILD-TYPE 64 90 42

Figure S57.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 0.004 (Fisher's exact test), Q value = 0.013

Table S58.  Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
5Q GAIN MUTATED 60 24 32 16
5Q GAIN WILD-TYPE 112 114 100 58

Figure S58.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00381 (Fisher's exact test), Q value = 0.012

Table S59.  Gene #10: '5q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
5Q GAIN MUTATED 49 22 23
5Q GAIN WILD-TYPE 118 111 40

Figure S59.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.0229 (Fisher's exact test), Q value = 0.053

Table S60.  Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
5Q GAIN MUTATED 31 41 16 23 19
5Q GAIN WILD-TYPE 99 78 74 92 39

Figure S60.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S61.  Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
5Q GAIN MUTATED 32 24 27 10 12 10 15
5Q GAIN WILD-TYPE 46 86 70 38 41 39 62

Figure S61.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00651 (Fisher's exact test), Q value = 0.019

Table S62.  Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
5Q GAIN MUTATED 27 10 26 37 19 12
5Q GAIN WILD-TYPE 44 29 119 93 77 17

Figure S62.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0016

Table S63.  Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
6P GAIN MUTATED 54 36 23 33
6P GAIN WILD-TYPE 118 102 109 41

Figure S63.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

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

Table S64.  Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
6P GAIN MUTATED 60 46 21
6P GAIN WILD-TYPE 96 124 108

Figure S64.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 0.044 (Fisher's exact test), Q value = 0.089

Table S65.  Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
6P GAIN MUTATED 38 31 17 44 16
6P GAIN WILD-TYPE 92 88 73 71 42

Figure S65.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0225 (Fisher's exact test), Q value = 0.052

Table S66.  Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
6P GAIN MUTATED 17 26 39 18 17 14 15
6P GAIN WILD-TYPE 61 84 58 30 36 35 62

Figure S66.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0297 (Fisher's exact test), Q value = 0.065

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
6P GAIN MUTATED 16 12 49 24 34 8
6P GAIN WILD-TYPE 55 27 96 106 62 21

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

'6q gain' versus 'CN_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.039

Table S68.  Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
6Q GAIN MUTATED 23 21 6 10
6Q GAIN WILD-TYPE 149 117 126 64

Figure S68.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'RPPA_CNMF'

P value = 0.0488 (Fisher's exact test), Q value = 0.096

Table S69.  Gene #12: '6q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
6Q GAIN MUTATED 5 2 11 14 10
6Q GAIN WILD-TYPE 86 20 55 61 99

Figure S69.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0168 (Fisher's exact test), Q value = 0.041

Table S70.  Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
6Q GAIN MUTATED 11 7 21 5 6 6 4
6Q GAIN WILD-TYPE 67 103 76 43 47 43 73

Figure S70.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_CNMF'

P value = 0.0127 (Fisher's exact test), Q value = 0.033

Table S71.  Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
6Q GAIN MUTATED 13 36 10
6Q GAIN WILD-TYPE 173 185 93

Figure S71.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0314 (Fisher's exact test), Q value = 0.068

Table S72.  Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
6Q GAIN MUTATED 3 6 22 9 16 3
6Q GAIN WILD-TYPE 68 33 123 121 80 26

Figure S72.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S73.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
7P GAIN MUTATED 138 82 19 28
7P GAIN WILD-TYPE 34 56 113 46

Figure S73.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 0.00434 (Fisher's exact test), Q value = 0.014

Table S74.  Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
7P GAIN MUTATED 59 11 26 47 50
7P GAIN WILD-TYPE 32 11 40 28 59

Figure S74.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00577 (Fisher's exact test), Q value = 0.017

Table S75.  Gene #13: '7p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
7P GAIN MUTATED 81 85 27
7P GAIN WILD-TYPE 86 48 36

Figure S75.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S76.  Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
7P GAIN MUTATED 101 34 47 51 30
7P GAIN WILD-TYPE 29 85 43 64 28

Figure S76.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S77.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
7P GAIN MUTATED 31 80 60 9 22 28 33
7P GAIN WILD-TYPE 47 30 37 39 31 21 44

Figure S77.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S78.  Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
7P GAIN MUTATED 71 125 67
7P GAIN WILD-TYPE 115 96 36

Figure S78.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S79.  Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
7P GAIN MUTATED 20 18 95 56 56 18
7P GAIN WILD-TYPE 51 21 50 74 40 11

Figure S79.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00293 (Fisher's exact test), Q value = 0.0098

Table S80.  Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
7P GAIN MUTATED 17 48 52 25 36 49
7P GAIN WILD-TYPE 42 42 43 18 34 28

Figure S80.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S81.  Gene #13: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
7P GAIN MUTATED 31 138 58
7P GAIN WILD-TYPE 73 100 34

Figure S81.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S82.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
7Q GAIN MUTATED 113 66 17 24
7Q GAIN WILD-TYPE 59 72 115 50

Figure S82.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S83.  Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
7Q GAIN MUTATED 87 28 40 35 26
7Q GAIN WILD-TYPE 43 91 50 80 32

Figure S83.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S84.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
7Q GAIN MUTATED 25 72 45 7 17 23 27
7Q GAIN WILD-TYPE 53 38 52 41 36 26 50

Figure S84.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 0.00402 (Fisher's exact test), Q value = 0.013

Table S85.  Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
7Q GAIN MUTATED 61 106 49
7Q GAIN WILD-TYPE 125 115 54

Figure S85.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00119 (Fisher's exact test), Q value = 0.0044

Table S86.  Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
7Q GAIN MUTATED 17 18 75 46 45 15
7Q GAIN WILD-TYPE 54 21 70 84 51 14

Figure S86.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S87.  Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
7Q GAIN MUTATED 16 35 44 21 26 40
7Q GAIN WILD-TYPE 43 55 51 22 44 37

Figure S87.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 2e-04

Table S88.  Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
7Q GAIN MUTATED 23 112 47
7Q GAIN WILD-TYPE 81 126 45

Figure S88.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S89.  Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
8P GAIN MUTATED 34 36 17 38
8P GAIN WILD-TYPE 138 102 115 36

Figure S89.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.0271 (Fisher's exact test), Q value = 0.06

Table S90.  Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
8P GAIN MUTATED 48 41 22
8P GAIN WILD-TYPE 108 129 107

Figure S90.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.0168 (Fisher's exact test), Q value = 0.041

Table S91.  Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
8P GAIN MUTATED 29 20 19 41 14
8P GAIN WILD-TYPE 101 99 71 74 44

Figure S91.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00385 (Fisher's exact test), Q value = 0.012

Table S92.  Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
8P GAIN MUTATED 13 24 20 14 24 15 13
8P GAIN WILD-TYPE 65 86 77 34 29 34 64

Figure S92.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0343 (Fisher's exact test), Q value = 0.073

Table S93.  Gene #15: '8p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
8P GAIN MUTATED 8 31 27 7 18 15
8P GAIN WILD-TYPE 51 59 68 36 52 62

Figure S93.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MRNA_CNMF'

P value = 0.0376 (Fisher's exact test), Q value = 0.079

Table S94.  Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 10 7
8Q GAIN MUTATED 4 5 6
8Q GAIN WILD-TYPE 11 5 1

Figure S94.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'8q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0438 (Fisher's exact test), Q value = 0.089

Table S95.  Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
8Q GAIN MUTATED 4 5 6
8Q GAIN WILD-TYPE 10 6 1

Figure S95.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S96.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
8Q GAIN MUTATED 75 82 28 60
8Q GAIN WILD-TYPE 97 56 104 14

Figure S96.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S97.  Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
8Q GAIN MUTATED 88 91 39
8Q GAIN WILD-TYPE 68 79 90

Figure S97.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S98.  Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
8Q GAIN MUTATED 65 35 39 78 24
8Q GAIN WILD-TYPE 65 84 51 37 34

Figure S98.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
8Q GAIN MUTATED 28 54 49 20 42 26 22
8Q GAIN WILD-TYPE 50 56 48 28 11 23 55

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

'8q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S100.  Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
8Q GAIN MUTATED 60 126 56
8Q GAIN WILD-TYPE 126 95 47

Figure S100.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00034

Table S101.  Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
8Q GAIN MUTATED 25 29 77 47 53 11
8Q GAIN WILD-TYPE 46 10 68 83 43 18

Figure S101.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S102.  Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
8Q GAIN MUTATED 13 58 45 17 38 38
8Q GAIN WILD-TYPE 46 32 50 26 32 39

Figure S102.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.0015

Table S103.  Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
8Q GAIN MUTATED 34 133 42
8Q GAIN WILD-TYPE 70 105 50

Figure S103.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

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

Table S104.  Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
9P GAIN MUTATED 19 8 3 15
9P GAIN WILD-TYPE 153 130 129 59

Figure S104.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 0.0225 (Fisher's exact test), Q value = 0.052

Table S105.  Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
9P GAIN MUTATED 20 18 5
9P GAIN WILD-TYPE 136 152 124

Figure S105.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p gain' versus 'MRNASEQ_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.03

Table S106.  Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
9P GAIN MUTATED 12 5 3 17 7
9P GAIN WILD-TYPE 118 114 87 98 51

Figure S106.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00526 (Fisher's exact test), Q value = 0.016

Table S107.  Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
9P GAIN MUTATED 1 11 13 2 9 1 7
9P GAIN WILD-TYPE 77 99 84 46 44 48 70

Figure S107.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 0.0045 (Fisher's exact test), Q value = 0.014

Table S108.  Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
9Q GAIN MUTATED 14 8 2 10
9Q GAIN WILD-TYPE 158 130 130 64

Figure S108.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0483 (Fisher's exact test), Q value = 0.096

Table S109.  Gene #18: '9q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
9Q GAIN MUTATED 1 7 12 2 6 2 3
9Q GAIN WILD-TYPE 77 103 85 46 47 47 74

Figure S109.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S110.  Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
10P GAIN MUTATED 31 44 9 28
10P GAIN WILD-TYPE 141 94 123 46

Figure S110.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S111.  Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
10P GAIN MUTATED 45 47 9
10P GAIN WILD-TYPE 111 123 120

Figure S111.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p gain' versus 'RPPA_CNMF'

P value = 0.00465 (Fisher's exact test), Q value = 0.014

Table S112.  Gene #19: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
10P GAIN MUTATED 11 2 19 22 33
10P GAIN WILD-TYPE 80 20 47 53 76

Figure S112.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'10p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0207 (Fisher's exact test), Q value = 0.049

Table S113.  Gene #19: '10p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
10P GAIN MUTATED 30 35 22
10P GAIN WILD-TYPE 137 98 41

Figure S113.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S114.  Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
10P GAIN MUTATED 27 10 22 43 9
10P GAIN WILD-TYPE 103 109 68 72 49

Figure S114.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S115.  Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
10P GAIN MUTATED 5 19 20 14 26 17 10
10P GAIN WILD-TYPE 73 91 77 34 27 32 67

Figure S115.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0013

Table S116.  Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
10P GAIN MUTATED 24 65 21
10P GAIN WILD-TYPE 162 156 82

Figure S116.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S117.  Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
10P GAIN MUTATED 12 15 44 12 25 2
10P GAIN WILD-TYPE 59 24 101 118 71 27

Figure S117.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00084 (Fisher's exact test), Q value = 0.0032

Table S118.  Gene #19: '10p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
10P GAIN MUTATED 4 32 26 10 12 15
10P GAIN WILD-TYPE 55 58 69 33 58 62

Figure S118.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.0013

Table S119.  Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
10P GAIN MUTATED 10 69 20
10P GAIN WILD-TYPE 94 169 72

Figure S119.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.0021

Table S120.  Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
10Q GAIN MUTATED 24 29 8 18
10Q GAIN WILD-TYPE 148 109 124 56

Figure S120.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10q gain' versus 'METHLYATION_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0014

Table S121.  Gene #20: '10q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
10Q GAIN MUTATED 30 34 7
10Q GAIN WILD-TYPE 126 136 122

Figure S121.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q gain' versus 'RPPA_CNMF'

P value = 0.0459 (Fisher's exact test), Q value = 0.093

Table S122.  Gene #20: '10q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
10Q GAIN MUTATED 8 1 16 13 20
10Q GAIN WILD-TYPE 83 21 50 62 89

Figure S122.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'10q gain' versus 'MRNASEQ_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.003

Table S123.  Gene #20: '10q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
10Q GAIN MUTATED 17 8 17 30 6
10Q GAIN WILD-TYPE 113 111 73 85 52

Figure S123.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S124.  Gene #20: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
10Q GAIN MUTATED 3 15 8 13 19 13 7
10Q GAIN WILD-TYPE 75 95 89 35 34 36 70

Figure S124.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00543 (Fisher's exact test), Q value = 0.016

Table S125.  Gene #20: '10q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
10Q GAIN MUTATED 10 12 29 12 13 1
10Q GAIN WILD-TYPE 61 27 116 118 83 28

Figure S125.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0241 (Fisher's exact test), Q value = 0.055

Table S126.  Gene #20: '10q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
10Q GAIN MUTATED 3 21 18 9 7 12
10Q GAIN WILD-TYPE 56 69 77 34 63 65

Figure S126.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0174 (Fisher's exact test), Q value = 0.042

Table S127.  Gene #20: '10q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
10Q GAIN MUTATED 8 46 16
10Q GAIN WILD-TYPE 96 192 76

Figure S127.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p gain' versus 'MRNA_CNMF'

P value = 0.00859 (Fisher's exact test), Q value = 0.023

Table S128.  Gene #21: '11p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 10 7
11P GAIN MUTATED 2 0 4
11P GAIN WILD-TYPE 13 10 3

Figure S128.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'11p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0107 (Fisher's exact test), Q value = 0.028

Table S129.  Gene #21: '11p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
11P GAIN MUTATED 2 0 4
11P GAIN WILD-TYPE 12 11 3

Figure S129.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11p gain' versus 'CN_CNMF'

P value = 0.00241 (Fisher's exact test), Q value = 0.0083

Table S130.  Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
11P GAIN MUTATED 40 26 11 17
11P GAIN WILD-TYPE 132 112 121 57

Figure S130.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S131.  Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
11P GAIN MUTATED 18 18 29 0 15 7 7
11P GAIN WILD-TYPE 60 92 68 48 38 42 70

Figure S131.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00034

Table S132.  Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
11P GAIN MUTATED 16 48 29
11P GAIN WILD-TYPE 170 173 74

Figure S132.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S133.  Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
11P GAIN MUTATED 4 11 25 13 31 9
11P GAIN WILD-TYPE 67 28 120 117 65 20

Figure S133.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00274 (Fisher's exact test), Q value = 0.0093

Table S134.  Gene #21: '11p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
11P GAIN MUTATED 8 49 22
11P GAIN WILD-TYPE 96 189 70

Figure S134.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q gain' versus 'MRNA_CNMF'

P value = 0.0178 (Fisher's exact test), Q value = 0.043

Table S135.  Gene #22: '11q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 10 7
11Q GAIN MUTATED 3 1 5
11Q GAIN WILD-TYPE 12 9 2

Figure S135.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0169 (Fisher's exact test), Q value = 0.041

Table S136.  Gene #22: '11q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
11Q GAIN MUTATED 3 1 5
11Q GAIN WILD-TYPE 11 10 2

Figure S136.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S137.  Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
11Q GAIN MUTATED 59 31 11 17
11Q GAIN WILD-TYPE 113 107 121 57

Figure S137.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 0.0308 (Fisher's exact test), Q value = 0.067

Table S138.  Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
11Q GAIN MUTATED 38 20 15 34 11
11Q GAIN WILD-TYPE 92 99 75 81 47

Figure S138.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 3e-04

Table S139.  Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
11Q GAIN MUTATED 19 31 28 0 18 10 12
11Q GAIN WILD-TYPE 59 79 69 48 35 39 65

Figure S139.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CNMF'

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

Table S140.  Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
11Q GAIN MUTATED 24 59 32
11Q GAIN WILD-TYPE 162 162 71

Figure S140.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00034

Table S141.  Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
11Q GAIN MUTATED 5 11 36 20 33 10
11Q GAIN WILD-TYPE 66 28 109 110 63 19

Figure S141.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S142.  Gene #22: '11q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
11Q GAIN MUTATED 12 61 27
11Q GAIN WILD-TYPE 92 177 65

Figure S142.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p gain' versus 'MRNA_CNMF'

P value = 0.0275 (Fisher's exact test), Q value = 0.061

Table S143.  Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 10 7
12P GAIN MUTATED 1 3 4
12P GAIN WILD-TYPE 14 7 3

Figure S143.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'12p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0463 (Fisher's exact test), Q value = 0.093

Table S144.  Gene #23: '12p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
12P GAIN MUTATED 1 3 4
12P GAIN WILD-TYPE 13 8 3

Figure S144.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S145.  Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
12P GAIN MUTATED 26 80 13 19
12P GAIN WILD-TYPE 146 58 119 55

Figure S145.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 3e-04

Table S146.  Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
12P GAIN MUTATED 59 44 19
12P GAIN WILD-TYPE 97 126 110

Figure S146.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S147.  Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
12P GAIN MUTATED 36 7 39 44 12
12P GAIN WILD-TYPE 94 112 51 71 46

Figure S147.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S148.  Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
12P GAIN MUTATED 8 30 31 4 27 25 13
12P GAIN WILD-TYPE 70 80 66 44 26 24 64

Figure S148.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S149.  Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
12P GAIN MUTATED 27 82 27
12P GAIN WILD-TYPE 159 139 76

Figure S149.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S150.  Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
12P GAIN MUTATED 10 16 40 18 45 7
12P GAIN WILD-TYPE 61 23 105 112 51 22

Figure S150.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00253 (Fisher's exact test), Q value = 0.0087

Table S151.  Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
12P GAIN MUTATED 6 35 28 11 14 23
12P GAIN WILD-TYPE 53 55 67 32 56 54

Figure S151.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S152.  Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
12P GAIN MUTATED 13 84 20
12P GAIN WILD-TYPE 91 154 72

Figure S152.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S153.  Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
12Q GAIN MUTATED 21 78 13 21
12Q GAIN WILD-TYPE 151 60 119 53

Figure S153.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00034

Table S154.  Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
12Q GAIN MUTATED 56 44 17
12Q GAIN WILD-TYPE 100 126 112

Figure S154.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q gain' versus 'RPPA_CNMF'

P value = 0.0331 (Fisher's exact test), Q value = 0.071

Table S155.  Gene #24: '12q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
12Q GAIN MUTATED 20 3 20 30 25
12Q GAIN WILD-TYPE 71 19 46 45 84

Figure S155.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S156.  Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
12Q GAIN MUTATED 30 6 37 51 9
12Q GAIN WILD-TYPE 100 113 53 64 49

Figure S156.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S157.  Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
12Q GAIN MUTATED 8 30 25 4 32 26 8
12Q GAIN WILD-TYPE 70 80 72 44 21 23 69

Figure S157.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S158.  Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
12Q GAIN MUTATED 26 82 23
12Q GAIN WILD-TYPE 160 139 80

Figure S158.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S159.  Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
12Q GAIN MUTATED 13 19 35 13 42 9
12Q GAIN WILD-TYPE 58 20 110 117 54 20

Figure S159.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00062

Table S160.  Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
12Q GAIN MUTATED 3 35 28 12 15 19
12Q GAIN WILD-TYPE 56 55 67 31 55 58

Figure S160.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S161.  Gene #24: '12q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
12Q GAIN MUTATED 12 81 19
12Q GAIN WILD-TYPE 92 157 73

Figure S161.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q gain' versus 'METHLYATION_CNMF'

P value = 0.0143 (Fisher's exact test), Q value = 0.036

Table S162.  Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
13Q GAIN MUTATED 17 14 3
13Q GAIN WILD-TYPE 139 156 126

Figure S162.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0227 (Fisher's exact test), Q value = 0.052

Table S163.  Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
13Q GAIN MUTATED 8 4 9 8 3 8 3
13Q GAIN WILD-TYPE 70 106 88 40 50 41 74

Figure S163.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S164.  Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
14Q GAIN MUTATED 51 35 13 30
14Q GAIN WILD-TYPE 121 103 119 44

Figure S164.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 0.0292 (Fisher's exact test), Q value = 0.064

Table S165.  Gene #26: '14q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
14Q GAIN MUTATED 51 40 25
14Q GAIN WILD-TYPE 105 130 104

Figure S165.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.002

Table S166.  Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
14Q GAIN MUTATED 40 21 13 42 12
14Q GAIN WILD-TYPE 90 98 77 73 46

Figure S166.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S167.  Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
14Q GAIN MUTATED 15 27 42 7 21 7 9
14Q GAIN WILD-TYPE 63 83 55 41 32 42 68

Figure S167.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

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

Table S168.  Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
14Q GAIN MUTATED 29 60 36
14Q GAIN WILD-TYPE 157 161 67

Figure S168.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00075

Table S169.  Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
14Q GAIN MUTATED 12 13 38 17 32 13
14Q GAIN WILD-TYPE 59 26 107 113 64 16

Figure S169.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00626 (Fisher's exact test), Q value = 0.018

Table S170.  Gene #26: '14q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
14Q GAIN MUTATED 6 33 23 14 14 19
14Q GAIN WILD-TYPE 53 57 72 29 56 58

Figure S170.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0248 (Fisher's exact test), Q value = 0.056

Table S171.  Gene #26: '14q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
14Q GAIN MUTATED 16 69 24
14Q GAIN WILD-TYPE 88 169 68

Figure S171.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q gain' versus 'CN_CNMF'

P value = 0.00151 (Fisher's exact test), Q value = 0.0055

Table S172.  Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
15Q GAIN MUTATED 8 21 7 2
15Q GAIN WILD-TYPE 164 117 125 72

Figure S172.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

'15q gain' versus 'METHLYATION_CNMF'

P value = 0.0146 (Fisher's exact test), Q value = 0.037

Table S173.  Gene #27: '15q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
15Q GAIN MUTATED 18 6 7
15Q GAIN WILD-TYPE 138 164 122

Figure S173.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S174.  Gene #27: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
15Q GAIN MUTATED 3 6 20 7 2
15Q GAIN WILD-TYPE 127 113 70 108 56

Figure S174.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S175.  Gene #27: '15q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
15Q GAIN MUTATED 2 1 4 3 4 16 8
15Q GAIN WILD-TYPE 76 109 93 45 49 33 69

Figure S175.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0011

Table S176.  Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
16P GAIN MUTATED 66 33 25 13
16P GAIN WILD-TYPE 106 105 107 61

Figure S176.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'16p gain' versus 'RPPA_CNMF'

P value = 0.00342 (Fisher's exact test), Q value = 0.011

Table S177.  Gene #28: '16p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
16P GAIN MUTATED 36 7 20 16 18
16P GAIN WILD-TYPE 55 15 46 59 91

Figure S177.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.0206 (Fisher's exact test), Q value = 0.049

Table S178.  Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
16P GAIN MUTATED 39 39 15 24 20
16P GAIN WILD-TYPE 91 80 75 91 38

Figure S178.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00702 (Fisher's exact test), Q value = 0.02

Table S179.  Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
16P GAIN MUTATED 33 26 33 9 9 10 17
16P GAIN WILD-TYPE 45 84 64 39 44 39 60

Figure S179.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 0.0302 (Fisher's exact test), Q value = 0.066

Table S180.  Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
16P GAIN MUTATED 42 56 38
16P GAIN WILD-TYPE 144 165 65

Figure S180.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00556 (Fisher's exact test), Q value = 0.017

Table S181.  Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
16P GAIN MUTATED 17 13 34 29 26 17
16P GAIN WILD-TYPE 54 26 111 101 70 12

Figure S181.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 0.0165 (Fisher's exact test), Q value = 0.041

Table S182.  Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
16Q GAIN MUTATED 46 27 17 11
16Q GAIN WILD-TYPE 126 111 115 63

Figure S182.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'16q gain' versus 'MIRSEQ_CNMF'

P value = 0.0152 (Fisher's exact test), Q value = 0.038

Table S183.  Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
16Q GAIN MUTATED 26 45 29
16Q GAIN WILD-TYPE 160 176 74

Figure S183.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0146 (Fisher's exact test), Q value = 0.037

Table S184.  Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
16Q GAIN MUTATED 8 8 28 22 21 13
16Q GAIN WILD-TYPE 63 31 117 108 75 16

Figure S184.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 0.00268 (Fisher's exact test), Q value = 0.0091

Table S185.  Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
17P GAIN MUTATED 30 30 9 15
17P GAIN WILD-TYPE 142 108 123 59

Figure S185.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0159 (Fisher's exact test), Q value = 0.04

Table S186.  Gene #30: '17p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
17P GAIN MUTATED 30 25 3
17P GAIN WILD-TYPE 137 108 60

Figure S186.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 0.0407 (Fisher's exact test), Q value = 0.084

Table S187.  Gene #30: '17p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
17P GAIN MUTATED 24 11 12 27 10
17P GAIN WILD-TYPE 106 108 78 88 48

Figure S187.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0225 (Fisher's exact test), Q value = 0.052

Table S188.  Gene #30: '17p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
17P GAIN MUTATED 12 14 22 4 16 8 8
17P GAIN WILD-TYPE 66 96 75 44 37 41 69

Figure S188.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CNMF'

P value = 0.00948 (Fisher's exact test), Q value = 0.025

Table S189.  Gene #30: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
17P GAIN MUTATED 19 47 16
17P GAIN WILD-TYPE 167 174 87

Figure S189.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00075

Table S190.  Gene #30: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
17P GAIN MUTATED 4 16 23 15 20 4
17P GAIN WILD-TYPE 67 23 122 115 76 25

Figure S190.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S191.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
17Q GAIN MUTATED 88 61 16 26
17Q GAIN WILD-TYPE 84 77 116 48

Figure S191.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.0029

Table S192.  Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
17Q GAIN MUTATED 57 77 31
17Q GAIN WILD-TYPE 99 93 98

Figure S192.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00024

Table S193.  Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
17Q GAIN MUTATED 68 27 29 46 20
17Q GAIN WILD-TYPE 62 92 61 69 38

Figure S193.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S194.  Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
17Q GAIN MUTATED 29 53 45 5 27 12 19
17Q GAIN WILD-TYPE 49 57 52 43 26 37 58

Figure S194.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 0.00094 (Fisher's exact test), Q value = 0.0036

Table S195.  Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
17Q GAIN MUTATED 50 98 41
17Q GAIN WILD-TYPE 136 123 62

Figure S195.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00039

Table S196.  Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
17Q GAIN MUTATED 18 23 59 32 47 10
17Q GAIN WILD-TYPE 53 16 86 98 49 19

Figure S196.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00286 (Fisher's exact test), Q value = 0.0096

Table S197.  Gene #31: '17q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
17Q GAIN MUTATED 9 39 42 16 24 33
17Q GAIN WILD-TYPE 50 51 53 27 46 44

Figure S197.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S198.  Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
17Q GAIN MUTATED 21 103 39
17Q GAIN WILD-TYPE 83 135 53

Figure S198.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S199.  Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
18P GAIN MUTATED 36 25 7 24
18P GAIN WILD-TYPE 136 113 125 50

Figure S199.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S200.  Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
18P GAIN MUTATED 41 34 7
18P GAIN WILD-TYPE 115 136 122

Figure S200.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.035

Table S201.  Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
18P GAIN MUTATED 25 14 11 32 9
18P GAIN WILD-TYPE 105 105 79 83 49

Figure S201.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00106 (Fisher's exact test), Q value = 0.004

Table S202.  Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
18P GAIN MUTATED 10 15 26 4 19 6 11
18P GAIN WILD-TYPE 68 95 71 44 34 43 66

Figure S202.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_CNMF'

P value = 0.00229 (Fisher's exact test), Q value = 0.008

Table S203.  Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
18P GAIN MUTATED 20 53 18
18P GAIN WILD-TYPE 166 168 85

Figure S203.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0356 (Fisher's exact test), Q value = 0.075

Table S204.  Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
18P GAIN MUTATED 6 9 29 18 25 4
18P GAIN WILD-TYPE 65 30 116 112 71 25

Figure S204.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00482 (Fisher's exact test), Q value = 0.015

Table S205.  Gene #32: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
18P GAIN MUTATED 5 28 14 8 8 17
18P GAIN WILD-TYPE 54 62 81 35 62 60

Figure S205.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00024

Table S206.  Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
18P GAIN MUTATED 6 59 15
18P GAIN WILD-TYPE 98 179 77

Figure S206.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S207.  Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
18Q GAIN MUTATED 21 22 5 21
18Q GAIN WILD-TYPE 151 116 127 53

Figure S207.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S208.  Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
18Q GAIN MUTATED 37 21 3
18Q GAIN WILD-TYPE 119 149 126

Figure S208.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00024

Table S209.  Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
18Q GAIN MUTATED 12 11 8 33 4
18Q GAIN WILD-TYPE 118 108 82 82 54

Figure S209.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00024

Table S210.  Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
18Q GAIN MUTATED 5 8 19 6 19 5 6
18Q GAIN WILD-TYPE 73 102 78 42 34 44 71

Figure S210.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CNMF'

P value = 0.00702 (Fisher's exact test), Q value = 0.02

Table S211.  Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
18Q GAIN MUTATED 15 41 12
18Q GAIN WILD-TYPE 171 180 91

Figure S211.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00166 (Fisher's exact test), Q value = 0.0059

Table S212.  Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
18Q GAIN MUTATED 5 10 17 11 23 2
18Q GAIN WILD-TYPE 66 29 128 119 73 27

Figure S212.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S213.  Gene #33: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
18Q GAIN MUTATED 4 30 8 5 4 8
18Q GAIN WILD-TYPE 55 60 87 38 66 69

Figure S213.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.0021

Table S214.  Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
18Q GAIN MUTATED 5 45 9
18Q GAIN WILD-TYPE 99 193 83

Figure S214.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 0.00082 (Fisher's exact test), Q value = 0.0032

Table S215.  Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
19Q GAIN MUTATED 22 29 9 18
19Q GAIN WILD-TYPE 150 109 123 56

Figure S215.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 0.00737 (Fisher's exact test), Q value = 0.02

Table S216.  Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
19Q GAIN MUTATED 37 20 16
19Q GAIN WILD-TYPE 119 150 113

Figure S216.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q gain' versus 'RPPA_CNMF'

P value = 0.0418 (Fisher's exact test), Q value = 0.086

Table S217.  Gene #35: '19q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
19Q GAIN MUTATED 10 2 10 21 15
19Q GAIN WILD-TYPE 81 20 56 54 94

Figure S217.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.039 (Fisher's exact test), Q value = 0.081

Table S218.  Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
19Q GAIN MUTATED 5 13 16 11 10 12 9
19Q GAIN WILD-TYPE 73 97 81 37 43 37 68

Figure S218.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0279 (Fisher's exact test), Q value = 0.062

Table S219.  Gene #35: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
19Q GAIN MUTATED 17 46 7
19Q GAIN WILD-TYPE 87 192 85

Figure S219.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S220.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
20P GAIN MUTATED 63 59 15 38
20P GAIN WILD-TYPE 109 79 117 36

Figure S220.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S221.  Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
20P GAIN MUTATED 75 48 30
20P GAIN WILD-TYPE 81 122 99

Figure S221.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00181 (Fisher's exact test), Q value = 0.0064

Table S222.  Gene #36: '20p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
20P GAIN MUTATED 43 60 19
20P GAIN WILD-TYPE 124 73 44

Figure S222.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S223.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
20P GAIN MUTATED 42 27 31 59 12
20P GAIN WILD-TYPE 88 92 59 56 46

Figure S223.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S224.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
20P GAIN MUTATED 12 33 54 14 27 16 15
20P GAIN WILD-TYPE 66 77 43 34 26 33 62

Figure S224.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 2e-04

Table S225.  Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
20P GAIN MUTATED 39 92 41
20P GAIN WILD-TYPE 147 129 62

Figure S225.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00091

Table S226.  Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
20P GAIN MUTATED 15 14 56 29 47 11
20P GAIN WILD-TYPE 56 25 89 101 49 18

Figure S226.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00776 (Fisher's exact test), Q value = 0.021

Table S227.  Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
20P GAIN MUTATED 14 42 24 20 21 25
20P GAIN WILD-TYPE 45 48 71 23 49 52

Figure S227.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00039

Table S228.  Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
20P GAIN MUTATED 22 101 23
20P GAIN WILD-TYPE 82 137 69

Figure S228.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'MRNA_CNMF'

P value = 0.0222 (Fisher's exact test), Q value = 0.052

Table S229.  Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 10 7
20Q GAIN MUTATED 2 2 5
20Q GAIN WILD-TYPE 13 8 2

Figure S229.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0239 (Fisher's exact test), Q value = 0.054

Table S230.  Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
20Q GAIN MUTATED 2 2 5
20Q GAIN WILD-TYPE 12 9 2

Figure S230.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S231.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
20Q GAIN MUTATED 76 71 14 40
20Q GAIN WILD-TYPE 96 67 118 34

Figure S231.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S232.  Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
20Q GAIN MUTATED 84 60 32
20Q GAIN WILD-TYPE 72 110 97

Figure S232.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 0.0203 (Fisher's exact test), Q value = 0.048

Table S233.  Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
20Q GAIN MUTATED 33 8 18 41 44
20Q GAIN WILD-TYPE 58 14 48 34 65

Figure S233.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S234.  Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
20Q GAIN MUTATED 47 73 24
20Q GAIN WILD-TYPE 120 60 39

Figure S234.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S235.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
20Q GAIN MUTATED 53 26 36 65 17
20Q GAIN WILD-TYPE 77 93 54 50 41

Figure S235.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S236.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
20Q GAIN MUTATED 12 46 61 14 29 18 17
20Q GAIN WILD-TYPE 66 64 36 34 24 31 60

Figure S236.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S237.  Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
20Q GAIN MUTATED 47 106 43
20Q GAIN WILD-TYPE 139 115 60

Figure S237.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S238.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
20Q GAIN MUTATED 15 15 71 35 50 10
20Q GAIN WILD-TYPE 56 24 74 95 46 19

Figure S238.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00191 (Fisher's exact test), Q value = 0.0067

Table S239.  Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
20Q GAIN MUTATED 13 48 32 21 23 31
20Q GAIN WILD-TYPE 46 42 63 22 47 46

Figure S239.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S240.  Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
20Q GAIN MUTATED 20 118 30
20Q GAIN WILD-TYPE 84 120 62

Figure S240.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S241.  Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
21Q GAIN MUTATED 62 13 15 8
21Q GAIN WILD-TYPE 110 125 117 66

Figure S241.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'21q gain' versus 'RPPA_CNMF'

P value = 0.033 (Fisher's exact test), Q value = 0.071

Table S242.  Gene #38: '21q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
21Q GAIN MUTATED 29 3 12 11 17
21Q GAIN WILD-TYPE 62 19 54 64 92

Figure S242.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 0.00456 (Fisher's exact test), Q value = 0.014

Table S243.  Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
21Q GAIN MUTATED 35 30 11 15 7
21Q GAIN WILD-TYPE 95 89 79 100 51

Figure S243.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.0012

Table S244.  Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
21Q GAIN MUTATED 24 25 26 3 4 7 9
21Q GAIN WILD-TYPE 54 85 71 45 49 42 68

Figure S244.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0426 (Fisher's exact test), Q value = 0.087

Table S245.  Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
22Q GAIN MUTATED 7 12 19 2 4 10 7
22Q GAIN WILD-TYPE 71 98 78 46 49 39 70

Figure S245.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xp gain' versus 'METHLYATION_CNMF'

P value = 0.00635 (Fisher's exact test), Q value = 0.018

Table S246.  Gene #40: 'xp gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
XP GAIN MUTATED 25 16 6
XP GAIN WILD-TYPE 131 154 123

Figure S246.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xp gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0446 (Fisher's exact test), Q value = 0.09

Table S247.  Gene #40: 'xp gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
XP GAIN MUTATED 3 16 9 7 3 7
XP GAIN WILD-TYPE 56 74 86 36 67 70

Figure S247.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 0.0024

Table S248.  Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
XQ GAIN MUTATED 43 16 12 15
XQ GAIN WILD-TYPE 129 122 120 59

Figure S248.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 0.0485 (Fisher's exact test), Q value = 0.096

Table S249.  Gene #41: 'xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
XQ GAIN MUTATED 31 19 10 21 5
XQ GAIN WILD-TYPE 99 100 80 94 53

Figure S249.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0169 (Fisher's exact test), Q value = 0.041

Table S250.  Gene #41: 'xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
XQ GAIN MUTATED 12 23 27 5 6 4 9
XQ GAIN WILD-TYPE 66 87 70 43 47 45 68

Figure S250.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MRNA_CNMF'

P value = 0.0131 (Fisher's exact test), Q value = 0.034

Table S251.  Gene #42: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 10 7
1P LOSS MUTATED 0 4 1
1P LOSS WILD-TYPE 15 6 6

Figure S251.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.038 (Fisher's exact test), Q value = 0.08

Table S252.  Gene #42: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
1P LOSS MUTATED 0 4 1
1P LOSS WILD-TYPE 14 7 6

Figure S252.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S253.  Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
1P LOSS MUTATED 9 35 10 26
1P LOSS WILD-TYPE 163 103 122 48

Figure S253.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.002

Table S254.  Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
1P LOSS MUTATED 33 27 7
1P LOSS WILD-TYPE 123 143 122

Figure S254.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'RPPA_CNMF'

P value = 0.0385 (Fisher's exact test), Q value = 0.081

Table S255.  Gene #42: '1p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
1P LOSS MUTATED 7 2 16 15 18
1P LOSS WILD-TYPE 84 20 50 60 91

Figure S255.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00024

Table S256.  Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
1P LOSS MUTATED 14 10 20 31 3
1P LOSS WILD-TYPE 116 109 70 84 55

Figure S256.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00024

Table S257.  Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
1P LOSS MUTATED 7 17 10 10 19 12 3
1P LOSS WILD-TYPE 71 93 87 38 34 37 74

Figure S257.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00722 (Fisher's exact test), Q value = 0.02

Table S258.  Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
1P LOSS MUTATED 9 15 23 14 13 4
1P LOSS WILD-TYPE 62 24 122 116 83 25

Figure S258.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00577 (Fisher's exact test), Q value = 0.017

Table S259.  Gene #42: '1p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
1P LOSS MUTATED 3 23 14 8 9 6
1P LOSS WILD-TYPE 56 67 81 35 61 71

Figure S259.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1q loss' versus 'CN_CNMF'

P value = 0.00569 (Fisher's exact test), Q value = 0.017

Table S260.  Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
1Q LOSS MUTATED 3 10 6 9
1Q LOSS WILD-TYPE 169 128 126 65

Figure S260.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'1q loss' versus 'METHLYATION_CNMF'

P value = 0.00409 (Fisher's exact test), Q value = 0.013

Table S261.  Gene #43: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
1Q LOSS MUTATED 14 10 1
1Q LOSS WILD-TYPE 142 160 128

Figure S261.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 0.0178 (Fisher's exact test), Q value = 0.043

Table S262.  Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
1Q LOSS MUTATED 6 3 9 10 0
1Q LOSS WILD-TYPE 124 116 81 105 58

Figure S262.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0357 (Fisher's exact test), Q value = 0.075

Table S263.  Gene #43: '1q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
1Q LOSS MUTATED 1 9 7 2 0 6
1Q LOSS WILD-TYPE 58 81 88 41 70 71

Figure S263.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 0.039 (Fisher's exact test), Q value = 0.081

Table S264.  Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
2P LOSS MUTATED 7 7 10
2P LOSS WILD-TYPE 179 214 93

Figure S264.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S265.  Gene #46: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
3P LOSS MUTATED 84 68 21 38
3P LOSS WILD-TYPE 88 70 111 36

Figure S265.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00091

Table S266.  Gene #46: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
3P LOSS MUTATED 82 65 37
3P LOSS WILD-TYPE 74 105 92

Figure S266.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S267.  Gene #46: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
3P LOSS MUTATED 29 38 49 17 34 24 17
3P LOSS WILD-TYPE 49 72 48 31 19 25 60

Figure S267.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 0.00813 (Fisher's exact test), Q value = 0.022

Table S268.  Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
3P LOSS MUTATED 59 100 48
3P LOSS WILD-TYPE 127 121 55

Figure S268.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.0013

Table S269.  Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
3P LOSS MUTATED 29 25 51 41 52 9
3P LOSS WILD-TYPE 42 14 94 89 44 20

Figure S269.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0112 (Fisher's exact test), Q value = 0.03

Table S270.  Gene #46: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
3P LOSS MUTATED 21 52 38 18 25 24
3P LOSS WILD-TYPE 38 38 57 25 45 53

Figure S270.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0343 (Fisher's exact test), Q value = 0.073

Table S271.  Gene #46: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
3P LOSS MUTATED 32 109 37
3P LOSS WILD-TYPE 72 129 55

Figure S271.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S272.  Gene #47: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
3Q LOSS MUTATED 58 37 18 31
3Q LOSS WILD-TYPE 114 101 114 43

Figure S272.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 0.0394 (Fisher's exact test), Q value = 0.082

Table S273.  Gene #47: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
3Q LOSS MUTATED 50 51 25
3Q LOSS WILD-TYPE 106 119 104

Figure S273.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00538 (Fisher's exact test), Q value = 0.016

Table S274.  Gene #47: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
3Q LOSS MUTATED 24 29 20 17 24 15 12
3Q LOSS WILD-TYPE 54 81 77 31 29 34 65

Figure S274.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0225 (Fisher's exact test), Q value = 0.052

Table S275.  Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
3Q LOSS MUTATED 25 19 37 30 25 5
3Q LOSS WILD-TYPE 46 20 108 100 71 24

Figure S275.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S276.  Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
4P LOSS MUTATED 39 46 8 26
4P LOSS WILD-TYPE 133 92 124 48

Figure S276.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 0.0027 (Fisher's exact test), Q value = 0.0092

Table S277.  Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
4P LOSS MUTATED 49 30 21
4P LOSS WILD-TYPE 107 140 108

Figure S277.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'RPPA_CNMF'

P value = 0.00117 (Fisher's exact test), Q value = 0.0044

Table S278.  Gene #48: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
4P LOSS MUTATED 20 7 10 32 21
4P LOSS WILD-TYPE 71 15 56 43 88

Figure S278.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00464 (Fisher's exact test), Q value = 0.014

Table S279.  Gene #48: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
4P LOSS MUTATED 40 43 7
4P LOSS WILD-TYPE 127 90 56

Figure S279.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.002

Table S280.  Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
4P LOSS MUTATED 29 13 22 40 14
4P LOSS WILD-TYPE 101 106 68 75 44

Figure S280.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S281.  Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
4P LOSS MUTATED 13 17 39 2 21 14 12
4P LOSS WILD-TYPE 65 93 58 46 32 35 65

Figure S281.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S282.  Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
4P LOSS MUTATED 22 75 21
4P LOSS WILD-TYPE 164 146 82

Figure S282.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S283.  Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
4P LOSS MUTATED 6 16 39 19 36 2
4P LOSS WILD-TYPE 65 23 106 111 60 27

Figure S283.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00866 (Fisher's exact test), Q value = 0.023

Table S284.  Gene #48: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
4P LOSS MUTATED 5 31 22 8 18 15
4P LOSS WILD-TYPE 54 59 73 35 52 62

Figure S284.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00339 (Fisher's exact test), Q value = 0.011

Table S285.  Gene #48: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
4P LOSS MUTATED 16 69 14
4P LOSS WILD-TYPE 88 169 78

Figure S285.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'MRNA_CNMF'

P value = 0.00519 (Fisher's exact test), Q value = 0.016

Table S286.  Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 10 7
4Q LOSS MUTATED 1 2 5
4Q LOSS WILD-TYPE 14 8 2

Figure S286.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00706 (Fisher's exact test), Q value = 0.02

Table S287.  Gene #49: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
4Q LOSS MUTATED 1 2 5
4Q LOSS WILD-TYPE 13 9 2

Figure S287.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S288.  Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
4Q LOSS MUTATED 41 57 7 31
4Q LOSS WILD-TYPE 131 81 125 43

Figure S288.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S289.  Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
4Q LOSS MUTATED 62 31 22
4Q LOSS WILD-TYPE 94 139 107

Figure S289.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'RPPA_CNMF'

P value = 0.0267 (Fisher's exact test), Q value = 0.06

Table S290.  Gene #49: '4q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
4Q LOSS MUTATED 25 6 12 32 28
4Q LOSS WILD-TYPE 66 16 54 43 81

Figure S290.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4q loss' versus 'RPPA_CHIERARCHICAL'

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

Table S291.  Gene #49: '4q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
4Q LOSS MUTATED 44 48 11
4Q LOSS WILD-TYPE 123 85 52

Figure S291.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S292.  Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
4Q LOSS MUTATED 34 11 27 50 13
4Q LOSS WILD-TYPE 96 108 63 65 45

Figure S292.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S293.  Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
4Q LOSS MUTATED 11 17 43 5 28 20 11
4Q LOSS WILD-TYPE 67 93 54 43 25 29 66

Figure S293.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S294.  Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
4Q LOSS MUTATED 24 82 29
4Q LOSS WILD-TYPE 162 139 74

Figure S294.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S295.  Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
4Q LOSS MUTATED 8 16 45 19 44 3
4Q LOSS WILD-TYPE 63 23 100 111 52 26

Figure S295.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00075

Table S296.  Gene #49: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
4Q LOSS MUTATED 5 38 23 11 20 16
4Q LOSS WILD-TYPE 54 52 72 32 50 61

Figure S296.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.0013

Table S297.  Gene #49: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
4Q LOSS MUTATED 16 80 17
4Q LOSS WILD-TYPE 88 158 75

Figure S297.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00024

Table S298.  Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
5P LOSS MUTATED 9 23 3 10
5P LOSS WILD-TYPE 163 115 129 64

Figure S298.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 0.018 (Fisher's exact test), Q value = 0.043

Table S299.  Gene #50: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
5P LOSS MUTATED 20 11 5
5P LOSS WILD-TYPE 136 159 124

Figure S299.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p loss' versus 'RPPA_CNMF'

P value = 0.009 (Fisher's exact test), Q value = 0.024

Table S300.  Gene #50: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
5P LOSS MUTATED 6 1 3 15 6
5P LOSS WILD-TYPE 85 21 63 60 103

Figure S300.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.0011

Table S301.  Gene #50: '5p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
5P LOSS MUTATED 7 22 2
5P LOSS WILD-TYPE 160 111 61

Figure S301.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00595 (Fisher's exact test), Q value = 0.017

Table S302.  Gene #50: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
5P LOSS MUTATED 4 8 12 2 7 9 1
5P LOSS WILD-TYPE 74 102 85 46 46 40 76

Figure S302.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CNMF'

P value = 0.0203 (Fisher's exact test), Q value = 0.048

Table S303.  Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
5P LOSS MUTATED 8 26 9
5P LOSS WILD-TYPE 178 195 94

Figure S303.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0175 (Fisher's exact test), Q value = 0.042

Table S304.  Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
5P LOSS MUTATED 2 4 13 6 16 2
5P LOSS WILD-TYPE 69 35 132 124 80 27

Figure S304.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0146 (Fisher's exact test), Q value = 0.037

Table S305.  Gene #50: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
5P LOSS MUTATED 0 13 8 5 4 4
5P LOSS WILD-TYPE 59 77 87 38 66 73

Figure S305.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00235 (Fisher's exact test), Q value = 0.0081

Table S306.  Gene #50: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
5P LOSS MUTATED 1 26 7
5P LOSS WILD-TYPE 103 212 85

Figure S306.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'MRNA_CNMF'

P value = 0.03 (Fisher's exact test), Q value = 0.066

Table S307.  Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 10 7
5Q LOSS MUTATED 1 4 4
5Q LOSS WILD-TYPE 14 6 3

Figure S307.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0351 (Fisher's exact test), Q value = 0.074

Table S308.  Gene #51: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
5Q LOSS MUTATED 1 4 4
5Q LOSS WILD-TYPE 13 7 3

Figure S308.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S309.  Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
5Q LOSS MUTATED 51 53 6 33
5Q LOSS WILD-TYPE 121 85 126 41

Figure S309.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S310.  Gene #51: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
5Q LOSS MUTATED 59 53 13
5Q LOSS WILD-TYPE 97 117 116

Figure S310.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'RPPA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00024

Table S311.  Gene #51: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
5Q LOSS MUTATED 30 6 12 36 18
5Q LOSS WILD-TYPE 61 16 54 39 91

Figure S311.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5q loss' versus 'RPPA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00034

Table S312.  Gene #51: '5q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
5Q LOSS MUTATED 36 57 9
5Q LOSS WILD-TYPE 131 76 54

Figure S312.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S313.  Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
5Q LOSS MUTATED 46 14 22 47 12
5Q LOSS WILD-TYPE 84 105 68 68 46

Figure S313.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S314.  Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
5Q LOSS MUTATED 6 37 34 9 21 18 16
5Q LOSS WILD-TYPE 72 73 63 39 32 31 61

Figure S314.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S315.  Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
5Q LOSS MUTATED 29 83 28
5Q LOSS WILD-TYPE 157 138 75

Figure S315.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S316.  Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
5Q LOSS MUTATED 8 13 50 20 45 4
5Q LOSS WILD-TYPE 63 26 95 110 51 25

Figure S316.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S317.  Gene #51: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
5Q LOSS MUTATED 4 41 30 9 13 24
5Q LOSS WILD-TYPE 55 49 65 34 57 53

Figure S317.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S318.  Gene #51: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
5Q LOSS MUTATED 11 88 22
5Q LOSS WILD-TYPE 93 150 70

Figure S318.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.00398 (Fisher's exact test), Q value = 0.013

Table S319.  Gene #52: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
6P LOSS MUTATED 23 48 20
6P LOSS WILD-TYPE 133 122 109

Figure S319.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S320.  Gene #53: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
6Q LOSS MUTATED 59 98 37
6Q LOSS WILD-TYPE 97 72 92

Figure S320.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S321.  Gene #53: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
6Q LOSS MUTATED 29 58 27 28 30 18 24
6Q LOSS WILD-TYPE 49 52 70 20 23 31 53

Figure S321.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00081 (Fisher's exact test), Q value = 0.0031

Table S322.  Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
6Q LOSS MUTATED 31 18 77 43 29 17
6Q LOSS WILD-TYPE 40 21 68 87 67 12

Figure S322.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0206 (Fisher's exact test), Q value = 0.049

Table S323.  Gene #53: '6q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
6Q LOSS MUTATED 37 96 50
6Q LOSS WILD-TYPE 67 142 42

Figure S323.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p loss' versus 'CN_CNMF'

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

Table S324.  Gene #54: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
7P LOSS MUTATED 2 16 7 9
7P LOSS WILD-TYPE 170 122 125 65

Figure S324.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

'7p loss' versus 'METHLYATION_CNMF'

P value = 0.0443 (Fisher's exact test), Q value = 0.09

Table S325.  Gene #54: '7p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
7P LOSS MUTATED 16 9 4
7P LOSS WILD-TYPE 140 161 125

Figure S325.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p loss' versus 'MRNASEQ_CNMF'

P value = 0.00999 (Fisher's exact test), Q value = 0.027

Table S326.  Gene #54: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
7P LOSS MUTATED 3 6 8 15 2
7P LOSS WILD-TYPE 127 113 82 100 56

Figure S326.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00053

Table S327.  Gene #54: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
7P LOSS MUTATED 2 3 7 7 8 7 0
7P LOSS WILD-TYPE 76 107 90 41 45 42 77

Figure S327.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q loss' versus 'CN_CNMF'

P value = 0.0194 (Fisher's exact test), Q value = 0.046

Table S328.  Gene #55: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
7Q LOSS MUTATED 9 19 6 7
7Q LOSS WILD-TYPE 163 119 126 67

Figure S328.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S329.  Gene #56: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
8P LOSS MUTATED 96 61 23 20
8P LOSS WILD-TYPE 76 77 109 54

Figure S329.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 0.0299 (Fisher's exact test), Q value = 0.065

Table S330.  Gene #56: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
8P LOSS MUTATED 59 77 39
8P LOSS WILD-TYPE 97 93 90

Figure S330.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'RPPA_CNMF'

P value = 0.0371 (Fisher's exact test), Q value = 0.078

Table S331.  Gene #56: '8p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
8P LOSS MUTATED 41 11 21 35 32
8P LOSS WILD-TYPE 50 11 45 40 77

Figure S331.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'8p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0333 (Fisher's exact test), Q value = 0.071

Table S332.  Gene #56: '8p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
8P LOSS MUTATED 56 63 21
8P LOSS WILD-TYPE 111 70 42

Figure S332.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S333.  Gene #56: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
8P LOSS MUTATED 75 36 29 43 16
8P LOSS WILD-TYPE 55 83 61 72 42

Figure S333.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00044

Table S334.  Gene #56: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
8P LOSS MUTATED 33 54 51 8 15 15 23
8P LOSS WILD-TYPE 45 56 46 40 38 34 54

Figure S334.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 0.0311 (Fisher's exact test), Q value = 0.067

Table S335.  Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
8P LOSS MUTATED 59 98 41
8P LOSS WILD-TYPE 127 123 62

Figure S335.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.023 (Fisher's exact test), Q value = 0.053

Table S336.  Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
8P LOSS MUTATED 22 14 72 40 40 10
8P LOSS WILD-TYPE 49 25 73 90 56 19

Figure S336.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0027

Table S337.  Gene #56: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
8P LOSS MUTATED 12 33 40 10 35 38
8P LOSS WILD-TYPE 47 57 55 33 35 39

Figure S337.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0318 (Fisher's exact test), Q value = 0.068

Table S338.  Gene #56: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
8P LOSS MUTATED 29 100 39
8P LOSS WILD-TYPE 75 138 53

Figure S338.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S339.  Gene #57: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
8Q LOSS MUTATED 36 11 6 3
8Q LOSS WILD-TYPE 136 127 126 71

Figure S339.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0412 (Fisher's exact test), Q value = 0.085

Table S340.  Gene #57: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
8Q LOSS MUTATED 15 13 12 2 1 5 8
8Q LOSS WILD-TYPE 63 97 85 46 52 44 69

Figure S340.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S341.  Gene #58: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
9P LOSS MUTATED 101 94 46 28
9P LOSS WILD-TYPE 71 44 86 46

Figure S341.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 0.00344 (Fisher's exact test), Q value = 0.011

Table S342.  Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
9P LOSS MUTATED 96 85 54
9P LOSS WILD-TYPE 60 85 75

Figure S342.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 3e-04

Table S343.  Gene #58: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
9P LOSS MUTATED 41 50 60 20 25 40 31
9P LOSS WILD-TYPE 37 60 37 28 28 9 46

Figure S343.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0121 (Fisher's exact test), Q value = 0.031

Table S344.  Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
9P LOSS MUTATED 31 21 73 58 64 18
9P LOSS WILD-TYPE 40 18 72 72 32 11

Figure S344.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S345.  Gene #58: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
9P LOSS MUTATED 43 134 51
9P LOSS WILD-TYPE 61 104 41

Figure S345.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S346.  Gene #59: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
9Q LOSS MUTATED 94 90 32 33
9Q LOSS WILD-TYPE 78 48 100 41

Figure S346.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 0.0035 (Fisher's exact test), Q value = 0.011

Table S347.  Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
9Q LOSS MUTATED 89 74 49
9Q LOSS WILD-TYPE 67 96 80

Figure S347.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.0012

Table S348.  Gene #59: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
9Q LOSS MUTATED 39 46 58 14 30 32 28
9Q LOSS WILD-TYPE 39 64 39 34 23 17 49

Figure S348.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 0.00448 (Fisher's exact test), Q value = 0.014

Table S349.  Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
9Q LOSS MUTATED 72 115 58
9Q LOSS WILD-TYPE 114 106 45

Figure S349.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 2e-04

Table S350.  Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
9Q LOSS MUTATED 27 24 63 50 65 16
9Q LOSS WILD-TYPE 44 15 82 80 31 13

Figure S350.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0127 (Fisher's exact test), Q value = 0.033

Table S351.  Gene #59: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
9Q LOSS MUTATED 37 126 43
9Q LOSS WILD-TYPE 67 112 49

Figure S351.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S352.  Gene #60: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
10P LOSS MUTATED 66 24 12 8
10P LOSS WILD-TYPE 106 114 120 66

Figure S352.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'RPPA_CNMF'

P value = 0.0483 (Fisher's exact test), Q value = 0.096

Table S353.  Gene #60: '10p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
10P LOSS MUTATED 28 6 12 17 15
10P LOSS WILD-TYPE 63 16 54 58 94

Figure S353.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.00112 (Fisher's exact test), Q value = 0.0042

Table S354.  Gene #60: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
10P LOSS MUTATED 39 18 9 26 17
10P LOSS WILD-TYPE 91 101 81 89 41

Figure S354.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S355.  Gene #60: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
10P LOSS MUTATED 17 27 38 0 10 4 13
10P LOSS WILD-TYPE 61 83 59 48 43 45 64

Figure S355.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 0.00757 (Fisher's exact test), Q value = 0.021

Table S356.  Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
10P LOSS MUTATED 30 45 33
10P LOSS WILD-TYPE 156 176 70

Figure S356.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-04 (Fisher's exact test), Q value = 0.0024

Table S357.  Gene #60: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
10P LOSS MUTATED 9 11 24 24 25 15
10P LOSS WILD-TYPE 62 28 121 106 71 14

Figure S357.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S358.  Gene #61: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
10Q LOSS MUTATED 71 36 12 13
10Q LOSS WILD-TYPE 101 102 120 61

Figure S358.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.042 (Fisher's exact test), Q value = 0.086

Table S359.  Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
10Q LOSS MUTATED 48 42 23
10Q LOSS WILD-TYPE 108 128 106

Figure S359.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 0.00267 (Fisher's exact test), Q value = 0.0091

Table S360.  Gene #61: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
10Q LOSS MUTATED 46 19 16 33 17
10Q LOSS WILD-TYPE 84 100 74 82 41

Figure S360.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S361.  Gene #61: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
10Q LOSS MUTATED 20 31 49 0 10 9 12
10Q LOSS WILD-TYPE 58 79 48 48 43 40 65

Figure S361.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 0.00934 (Fisher's exact test), Q value = 0.025

Table S362.  Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
10Q LOSS MUTATED 35 59 36
10Q LOSS WILD-TYPE 151 162 67

Figure S362.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S363.  Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
10Q LOSS MUTATED 9 9 34 27 36 15
10Q LOSS WILD-TYPE 62 30 111 103 60 14

Figure S363.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0425 (Fisher's exact test), Q value = 0.087

Table S364.  Gene #61: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
10Q LOSS MUTATED 7 29 20 14 19 23
10Q LOSS WILD-TYPE 52 61 75 29 51 54

Figure S364.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.007 (Fisher's exact test), Q value = 0.02

Table S365.  Gene #61: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
10Q LOSS MUTATED 16 74 22
10Q LOSS WILD-TYPE 88 164 70

Figure S365.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'MRNA_CNMF'

P value = 0.0343 (Fisher's exact test), Q value = 0.073

Table S366.  Gene #62: '11p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 10 7
11P LOSS MUTATED 0 3 2
11P LOSS WILD-TYPE 15 7 5

Figure S366.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S367.  Gene #62: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
11P LOSS MUTATED 41 46 8 16
11P LOSS WILD-TYPE 131 92 124 58

Figure S367.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

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

Table S368.  Gene #62: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
11P LOSS MUTATED 48 36 13
11P LOSS WILD-TYPE 108 134 116

Figure S368.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.023 (Fisher's exact test), Q value = 0.053

Table S369.  Gene #62: '11p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
11P LOSS MUTATED 27 39 13
11P LOSS WILD-TYPE 140 94 50

Figure S369.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 0.00064 (Fisher's exact test), Q value = 0.0026

Table S370.  Gene #62: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
11P LOSS MUTATED 36 11 24 29 8
11P LOSS WILD-TYPE 94 108 66 86 50

Figure S370.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S371.  Gene #62: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
11P LOSS MUTATED 6 29 25 9 13 18 8
11P LOSS WILD-TYPE 72 81 72 39 40 31 69

Figure S371.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0417 (Fisher's exact test), Q value = 0.086

Table S372.  Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
11P LOSS MUTATED 14 8 41 20 24 2
11P LOSS WILD-TYPE 57 31 104 110 72 27

Figure S372.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 2e-04

Table S373.  Gene #62: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
11P LOSS MUTATED 7 30 31 3 11 10
11P LOSS WILD-TYPE 52 60 64 40 59 67

Figure S373.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S374.  Gene #63: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
11Q LOSS MUTATED 27 36 6 18
11Q LOSS WILD-TYPE 145 102 126 56

Figure S374.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00053

Table S375.  Gene #63: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
11Q LOSS MUTATED 41 26 10
11Q LOSS WILD-TYPE 115 144 119

Figure S375.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 0.00138 (Fisher's exact test), Q value = 0.005

Table S376.  Gene #63: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
11Q LOSS MUTATED 25 7 18 27 7
11Q LOSS WILD-TYPE 105 112 72 88 51

Figure S376.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00356 (Fisher's exact test), Q value = 0.012

Table S377.  Gene #63: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
11Q LOSS MUTATED 5 20 18 8 15 12 6
11Q LOSS WILD-TYPE 73 90 79 40 38 37 71

Figure S377.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00644 (Fisher's exact test), Q value = 0.018

Table S378.  Gene #63: '11q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
11Q LOSS MUTATED 6 23 21 2 10 8
11Q LOSS WILD-TYPE 53 67 74 41 60 69

Figure S378.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S379.  Gene #64: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
12P LOSS MUTATED 67 8 22 12
12P LOSS WILD-TYPE 105 130 110 62

Figure S379.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12p loss' versus 'RPPA_CNMF'

P value = 0.00708 (Fisher's exact test), Q value = 0.02

Table S380.  Gene #64: '12p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
12P LOSS MUTATED 26 10 16 12 16
12P LOSS WILD-TYPE 65 12 50 63 93

Figure S380.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.0017

Table S381.  Gene #64: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
12P LOSS MUTATED 37 33 8 16 14
12P LOSS WILD-TYPE 93 86 82 99 44

Figure S381.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S382.  Gene #64: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
12P LOSS MUTATED 19 24 32 11 2 3 17
12P LOSS WILD-TYPE 59 86 65 37 51 46 60

Figure S382.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S383.  Gene #65: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
12Q LOSS MUTATED 63 4 18 9
12Q LOSS WILD-TYPE 109 134 114 65

Figure S383.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00044

Table S384.  Gene #65: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
12Q LOSS MUTATED 34 28 7 11 13
12Q LOSS WILD-TYPE 96 91 83 104 45

Figure S384.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S385.  Gene #65: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
12Q LOSS MUTATED 16 21 27 10 1 2 16
12Q LOSS WILD-TYPE 62 89 70 38 52 47 61

Figure S385.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0214 (Fisher's exact test), Q value = 0.05

Table S386.  Gene #65: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
12Q LOSS MUTATED 14 1 32 29 12 5
12Q LOSS WILD-TYPE 57 38 113 101 84 24

Figure S386.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S387.  Gene #66: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
13Q LOSS MUTATED 105 85 24 37
13Q LOSS WILD-TYPE 67 53 108 37

Figure S387.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'RPPA_CNMF'

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

Table S388.  Gene #66: '13q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
13Q LOSS MUTATED 54 7 28 50 39
13Q LOSS WILD-TYPE 37 15 38 25 70

Figure S388.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S389.  Gene #66: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
13Q LOSS MUTATED 82 38 34 69 25
13Q LOSS WILD-TYPE 48 81 56 46 33

Figure S389.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S390.  Gene #66: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
13Q LOSS MUTATED 33 68 53 11 37 18 28
13Q LOSS WILD-TYPE 45 42 44 37 16 31 49

Figure S390.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 0.00321 (Fisher's exact test), Q value = 0.011

Table S391.  Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
13Q LOSS MUTATED 72 120 56
13Q LOSS WILD-TYPE 114 101 47

Figure S391.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00164 (Fisher's exact test), Q value = 0.0059

Table S392.  Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
13Q LOSS MUTATED 31 27 80 47 51 12
13Q LOSS WILD-TYPE 40 12 65 83 45 17

Figure S392.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0215 (Fisher's exact test), Q value = 0.05

Table S393.  Gene #66: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
13Q LOSS MUTATED 40 130 45
13Q LOSS WILD-TYPE 64 108 47

Figure S393.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0013

Table S394.  Gene #67: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
14Q LOSS MUTATED 38 45 15 16
14Q LOSS WILD-TYPE 134 93 117 58

Figure S394.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 0.0253 (Fisher's exact test), Q value = 0.057

Table S395.  Gene #67: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
14Q LOSS MUTATED 42 38 18
14Q LOSS WILD-TYPE 114 132 111

Figure S395.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CNMF'

P value = 0.00222 (Fisher's exact test), Q value = 0.0078

Table S396.  Gene #67: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
14Q LOSS MUTATED 23 2 16 26 13
14Q LOSS WILD-TYPE 68 20 50 49 96

Figure S396.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00928 (Fisher's exact test), Q value = 0.025

Table S397.  Gene #67: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
14Q LOSS MUTATED 12 25 20 10 12 22 12
14Q LOSS WILD-TYPE 66 85 77 38 41 27 65

Figure S397.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 0.0155 (Fisher's exact test), Q value = 0.039

Table S398.  Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
14Q LOSS MUTATED 33 63 18
14Q LOSS WILD-TYPE 153 158 85

Figure S398.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0283 (Fisher's exact test), Q value = 0.062

Table S399.  Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
14Q LOSS MUTATED 18 9 37 22 27 1
14Q LOSS WILD-TYPE 53 30 108 108 69 28

Figure S399.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S400.  Gene #68: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
15Q LOSS MUTATED 111 64 21 48
15Q LOSS WILD-TYPE 61 74 111 26

Figure S400.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0015

Table S401.  Gene #68: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
15Q LOSS MUTATED 75 95 42
15Q LOSS WILD-TYPE 81 75 87

Figure S401.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S402.  Gene #68: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
15Q LOSS MUTATED 90 35 20 66 29
15Q LOSS WILD-TYPE 40 84 70 49 29

Figure S402.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S403.  Gene #68: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
15Q LOSS MUTATED 34 68 56 8 36 9 29
15Q LOSS WILD-TYPE 44 42 41 40 17 40 48

Figure S403.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00024

Table S404.  Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
15Q LOSS MUTATED 63 121 57
15Q LOSS WILD-TYPE 123 100 46

Figure S404.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.001

Table S405.  Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
15Q LOSS MUTATED 25 27 76 46 55 12
15Q LOSS WILD-TYPE 46 12 69 84 41 17

Figure S405.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00419 (Fisher's exact test), Q value = 0.013

Table S406.  Gene #68: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
15Q LOSS MUTATED 14 48 50 21 37 36
15Q LOSS WILD-TYPE 45 42 45 22 33 41

Figure S406.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.0013

Table S407.  Gene #68: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
15Q LOSS MUTATED 32 125 49
15Q LOSS WILD-TYPE 72 113 43

Figure S407.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S408.  Gene #69: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
16P LOSS MUTATED 36 32 9 30
16P LOSS WILD-TYPE 136 106 123 44

Figure S408.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.001

Table S409.  Gene #69: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
16P LOSS MUTATED 42 41 12
16P LOSS WILD-TYPE 114 129 117

Figure S409.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p loss' versus 'RPPA_CNMF'

P value = 0.00331 (Fisher's exact test), Q value = 0.011

Table S410.  Gene #69: '16p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
16P LOSS MUTATED 19 5 8 28 18
16P LOSS WILD-TYPE 72 17 58 47 91

Figure S410.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'16p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0019

Table S411.  Gene #69: '16p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
16P LOSS MUTATED 28 43 7
16P LOSS WILD-TYPE 139 90 56

Figure S411.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S412.  Gene #69: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
16P LOSS MUTATED 39 8 21 32 7
16P LOSS WILD-TYPE 91 111 69 83 51

Figure S412.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S413.  Gene #69: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
16P LOSS MUTATED 8 37 25 8 13 10 6
16P LOSS WILD-TYPE 70 73 72 40 40 39 71

Figure S413.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

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

Table S414.  Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
16P LOSS MUTATED 27 60 20
16P LOSS WILD-TYPE 159 161 83

Figure S414.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.0019

Table S415.  Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
16P LOSS MUTATED 10 5 43 18 29 2
16P LOSS WILD-TYPE 61 34 102 112 67 27

Figure S415.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S416.  Gene #69: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
16P LOSS MUTATED 3 33 23 6 10 18
16P LOSS WILD-TYPE 56 57 72 37 60 59

Figure S416.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00205 (Fisher's exact test), Q value = 0.0072

Table S417.  Gene #69: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
16P LOSS MUTATED 11 64 18
16P LOSS WILD-TYPE 93 174 74

Figure S417.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S418.  Gene #70: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
16Q LOSS MUTATED 51 41 13 32
16Q LOSS WILD-TYPE 121 97 119 42

Figure S418.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 2e-04

Table S419.  Gene #70: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
16Q LOSS MUTATED 49 54 15
16Q LOSS WILD-TYPE 107 116 114

Figure S419.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q loss' versus 'RPPA_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.0013

Table S420.  Gene #70: '16q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
16Q LOSS MUTATED 28 7 10 34 21
16Q LOSS WILD-TYPE 63 15 56 41 88

Figure S420.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'16q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00478 (Fisher's exact test), Q value = 0.015

Table S421.  Gene #70: '16q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
16Q LOSS MUTATED 38 50 12
16Q LOSS WILD-TYPE 129 83 51

Figure S421.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S422.  Gene #70: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
16Q LOSS MUTATED 58 13 24 35 7
16Q LOSS WILD-TYPE 72 106 66 80 51

Figure S422.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S423.  Gene #70: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
16Q LOSS MUTATED 13 50 32 9 14 10 9
16Q LOSS WILD-TYPE 65 60 65 39 39 39 68

Figure S423.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 0.00602 (Fisher's exact test), Q value = 0.017

Table S424.  Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
16Q LOSS MUTATED 36 74 27
16Q LOSS WILD-TYPE 150 147 76

Figure S424.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00113 (Fisher's exact test), Q value = 0.0042

Table S425.  Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
16Q LOSS MUTATED 17 8 52 22 34 4
16Q LOSS WILD-TYPE 54 31 93 108 62 25

Figure S425.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00132 (Fisher's exact test), Q value = 0.0048

Table S426.  Gene #70: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
16Q LOSS MUTATED 5 35 27 9 17 22
16Q LOSS WILD-TYPE 54 55 68 34 53 55

Figure S426.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00497 (Fisher's exact test), Q value = 0.015

Table S427.  Gene #70: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
16Q LOSS MUTATED 16 76 23
16Q LOSS WILD-TYPE 88 162 69

Figure S427.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S428.  Gene #71: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
17P LOSS MUTATED 97 63 26 33
17P LOSS WILD-TYPE 75 75 106 41

Figure S428.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00034

Table S429.  Gene #71: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
17P LOSS MUTATED 63 92 37
17P LOSS WILD-TYPE 93 78 92

Figure S429.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'RPPA_CNMF'

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

Table S430.  Gene #71: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
17P LOSS MUTATED 48 11 20 38 40
17P LOSS WILD-TYPE 43 11 46 37 69

Figure S430.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.003

Table S431.  Gene #71: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
17P LOSS MUTATED 71 33 40 50 23
17P LOSS WILD-TYPE 59 86 50 65 35

Figure S431.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00034

Table S432.  Gene #71: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
17P LOSS MUTATED 29 65 46 8 21 20 28
17P LOSS WILD-TYPE 49 45 51 40 32 29 49

Figure S432.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.011 (Fisher's exact test), Q value = 0.029

Table S433.  Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
17P LOSS MUTATED 26 10 78 49 43 11
17P LOSS WILD-TYPE 45 29 67 81 53 18

Figure S433.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00034

Table S434.  Gene #71: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
17P LOSS MUTATED 13 39 54 14 23 40
17P LOSS WILD-TYPE 46 51 41 29 47 37

Figure S434.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0202 (Fisher's exact test), Q value = 0.048

Table S435.  Gene #71: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
17P LOSS MUTATED 32 106 45
17P LOSS WILD-TYPE 72 132 47

Figure S435.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.0022

Table S436.  Gene #72: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
17Q LOSS MUTATED 30 17 4 9
17Q LOSS WILD-TYPE 142 121 128 65

Figure S436.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S437.  Gene #73: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
18P LOSS MUTATED 77 57 28 18
18P LOSS WILD-TYPE 95 81 104 56

Figure S437.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'RPPA_CNMF'

P value = 0.0451 (Fisher's exact test), Q value = 0.091

Table S438.  Gene #73: '18p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
18P LOSS MUTATED 34 8 22 38 31
18P LOSS WILD-TYPE 57 14 44 37 78

Figure S438.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'18p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00618 (Fisher's exact test), Q value = 0.018

Table S439.  Gene #73: '18p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
18P LOSS MUTATED 50 63 20
18P LOSS WILD-TYPE 117 70 43

Figure S439.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 0.0016 (Fisher's exact test), Q value = 0.0057

Table S440.  Gene #73: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
18P LOSS MUTATED 61 33 37 30 17
18P LOSS WILD-TYPE 69 86 53 85 41

Figure S440.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S441.  Gene #73: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
18P LOSS MUTATED 30 51 37 9 11 23 17
18P LOSS WILD-TYPE 48 59 60 39 42 26 60

Figure S441.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 0.00413 (Fisher's exact test), Q value = 0.013

Table S442.  Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
18P LOSS MUTATED 52 76 49
18P LOSS WILD-TYPE 134 145 54

Figure S442.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S443.  Gene #74: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
18Q LOSS MUTATED 97 64 38 16
18Q LOSS WILD-TYPE 75 74 94 58

Figure S443.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'RPPA_CNMF'

P value = 0.0149 (Fisher's exact test), Q value = 0.037

Table S444.  Gene #74: '18q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
18Q LOSS MUTATED 47 10 25 39 34
18Q LOSS WILD-TYPE 44 12 41 36 75

Figure S444.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S445.  Gene #74: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
18Q LOSS MUTATED 78 40 41 31 23
18Q LOSS WILD-TYPE 52 79 49 84 35

Figure S445.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 2e-04

Table S446.  Gene #74: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
18Q LOSS MUTATED 38 59 45 8 12 23 28
18Q LOSS WILD-TYPE 40 51 52 40 41 26 49

Figure S446.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 0.00614 (Fisher's exact test), Q value = 0.018

Table S447.  Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
18Q LOSS MUTATED 65 91 56
18Q LOSS WILD-TYPE 121 130 47

Figure S447.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.028

Table S448.  Gene #74: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
18Q LOSS MUTATED 21 28 54 17 32 29
18Q LOSS WILD-TYPE 38 62 41 26 38 48

Figure S448.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0247 (Fisher's exact test), Q value = 0.056

Table S449.  Gene #74: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
18Q LOSS MUTATED 36 96 49
18Q LOSS WILD-TYPE 68 142 43

Figure S449.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S450.  Gene #75: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
19P LOSS MUTATED 76 88 37 44
19P LOSS WILD-TYPE 96 50 95 30

Figure S450.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S451.  Gene #75: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
19P LOSS MUTATED 105 77 30
19P LOSS WILD-TYPE 51 93 99

Figure S451.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p loss' versus 'RPPA_CNMF'

P value = 0.00152 (Fisher's exact test), Q value = 0.0055

Table S452.  Gene #75: '19p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
19P LOSS MUTATED 38 13 40 47 41
19P LOSS WILD-TYPE 53 9 26 28 68

Figure S452.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S453.  Gene #75: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
19P LOSS MUTATED 61 39 47 77 19
19P LOSS WILD-TYPE 69 80 43 38 39

Figure S453.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S454.  Gene #75: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
19P LOSS MUTATED 21 46 57 32 35 34 18
19P LOSS WILD-TYPE 57 64 40 16 18 15 59

Figure S454.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S455.  Gene #75: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
19P LOSS MUTATED 66 130 43
19P LOSS WILD-TYPE 120 91 60

Figure S455.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00024

Table S456.  Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
19P LOSS MUTATED 28 21 73 43 63 11
19P LOSS WILD-TYPE 43 18 72 87 33 18

Figure S456.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 2e-04

Table S457.  Gene #75: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
19P LOSS MUTATED 18 62 42 17 34 30
19P LOSS WILD-TYPE 41 28 53 26 36 47

Figure S457.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00142 (Fisher's exact test), Q value = 0.0052

Table S458.  Gene #75: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
19P LOSS MUTATED 39 130 34
19P LOSS WILD-TYPE 65 108 58

Figure S458.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

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

Table S459.  Gene #76: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
19Q LOSS MUTATED 61 53 21 24
19Q LOSS WILD-TYPE 111 85 111 50

Figure S459.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S460.  Gene #76: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
19Q LOSS MUTATED 64 56 17
19Q LOSS WILD-TYPE 92 114 112

Figure S460.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'RPPA_CNMF'

P value = 0.0318 (Fisher's exact test), Q value = 0.068

Table S461.  Gene #76: '19q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
19Q LOSS MUTATED 25 8 28 31 26
19Q LOSS WILD-TYPE 66 14 38 44 83

Figure S461.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'19q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00073 (Fisher's exact test), Q value = 0.0029

Table S462.  Gene #76: '19q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
19Q LOSS MUTATED 55 54 9
19Q LOSS WILD-TYPE 112 79 54

Figure S462.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 0.00227 (Fisher's exact test), Q value = 0.0079

Table S463.  Gene #76: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
19Q LOSS MUTATED 45 24 29 48 12
19Q LOSS WILD-TYPE 85 95 61 67 46

Figure S463.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00024

Table S464.  Gene #76: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
19Q LOSS MUTATED 15 33 41 17 21 22 9
19Q LOSS WILD-TYPE 63 77 56 31 32 27 68

Figure S464.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 0.00099 (Fisher's exact test), Q value = 0.0038

Table S465.  Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
19Q LOSS MUTATED 39 84 31
19Q LOSS WILD-TYPE 147 137 72

Figure S465.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00067 (Fisher's exact test), Q value = 0.0027

Table S466.  Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
19Q LOSS MUTATED 16 12 47 25 44 10
19Q LOSS WILD-TYPE 55 27 98 105 52 19

Figure S466.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00331 (Fisher's exact test), Q value = 0.011

Table S467.  Gene #76: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
19Q LOSS MUTATED 7 38 32 12 21 21
19Q LOSS WILD-TYPE 52 52 63 31 49 56

Figure S467.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.03

Table S468.  Gene #76: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
19Q LOSS MUTATED 21 85 25
19Q LOSS WILD-TYPE 83 153 67

Figure S468.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 0.0232 (Fisher's exact test), Q value = 0.053

Table S469.  Gene #77: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
20P LOSS MUTATED 49 32 22 10
20P LOSS WILD-TYPE 123 106 110 64

Figure S469.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'20p loss' versus 'METHLYATION_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.03

Table S470.  Gene #77: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
20P LOSS MUTATED 24 49 25
20P LOSS WILD-TYPE 132 121 104

Figure S470.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p loss' versus 'RPPA_CNMF'

P value = 0.00698 (Fisher's exact test), Q value = 0.02

Table S471.  Gene #77: '20p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
20P LOSS MUTATED 30 1 16 16 16
20P LOSS WILD-TYPE 61 21 50 59 93

Figure S471.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'20p loss' versus 'MRNASEQ_CNMF'

P value = 0.00464 (Fisher's exact test), Q value = 0.014

Table S472.  Gene #77: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
20P LOSS MUTATED 39 23 24 13 14
20P LOSS WILD-TYPE 91 96 66 102 44

Figure S472.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.003

Table S473.  Gene #77: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
20P LOSS MUTATED 23 37 13 5 7 14 14
20P LOSS WILD-TYPE 55 73 84 43 46 35 63

Figure S473.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0139 (Fisher's exact test), Q value = 0.035

Table S474.  Gene #77: '20p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
20P LOSS MUTATED 7 17 32 5 13 17
20P LOSS WILD-TYPE 52 73 63 38 57 60

Figure S474.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0234 (Fisher's exact test), Q value = 0.053

Table S475.  Gene #77: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
20P LOSS MUTATED 15 48 28
20P LOSS WILD-TYPE 89 190 64

Figure S475.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S476.  Gene #79: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
21Q LOSS MUTATED 33 74 19 40
21Q LOSS WILD-TYPE 139 64 113 34

Figure S476.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 0.00424 (Fisher's exact test), Q value = 0.013

Table S477.  Gene #79: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
21Q LOSS MUTATED 59 54 26
21Q LOSS WILD-TYPE 97 116 103

Figure S477.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q loss' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S478.  Gene #79: '21q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
21Q LOSS MUTATED 16 3 17 41 35
21Q LOSS WILD-TYPE 75 19 49 34 74

Figure S478.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'21q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0068 (Fisher's exact test), Q value = 0.019

Table S479.  Gene #79: '21q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
21Q LOSS MUTATED 38 52 22
21Q LOSS WILD-TYPE 129 81 41

Figure S479.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S480.  Gene #79: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
21Q LOSS MUTATED 32 15 40 62 14
21Q LOSS WILD-TYPE 98 104 50 53 44

Figure S480.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S481.  Gene #79: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
21Q LOSS MUTATED 11 30 36 13 34 23 16
21Q LOSS WILD-TYPE 67 80 61 35 19 26 61

Figure S481.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 2e-04

Table S482.  Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
21Q LOSS MUTATED 39 91 32
21Q LOSS WILD-TYPE 147 130 71

Figure S482.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S483.  Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
21Q LOSS MUTATED 15 15 49 30 47 6
21Q LOSS WILD-TYPE 56 24 96 100 49 23

Figure S483.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00053

Table S484.  Gene #79: '21q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
21Q LOSS MUTATED 7 42 35 9 17 26
21Q LOSS WILD-TYPE 52 48 60 34 53 51

Figure S484.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S485.  Gene #79: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
21Q LOSS MUTATED 18 99 19
21Q LOSS WILD-TYPE 86 139 73

Figure S485.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S486.  Gene #80: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
22Q LOSS MUTATED 78 71 24 48
22Q LOSS WILD-TYPE 94 67 108 26

Figure S486.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S487.  Gene #80: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
22Q LOSS MUTATED 85 84 27
22Q LOSS WILD-TYPE 71 86 102

Figure S487.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CNMF'

P value = 0.0165 (Fisher's exact test), Q value = 0.041

Table S488.  Gene #80: '22q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
22Q LOSS MUTATED 41 5 23 43 44
22Q LOSS WILD-TYPE 50 17 43 32 65

Figure S488.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'22q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0112 (Fisher's exact test), Q value = 0.03

Table S489.  Gene #80: '22q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 167 133 63
22Q LOSS MUTATED 59 70 27
22Q LOSS WILD-TYPE 108 63 36

Figure S489.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S490.  Gene #80: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 119 90 115 58
22Q LOSS MUTATED 68 30 40 66 14
22Q LOSS WILD-TYPE 62 89 50 49 44

Figure S490.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S491.  Gene #80: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
22Q LOSS MUTATED 24 59 46 15 34 23 17
22Q LOSS WILD-TYPE 54 51 51 33 19 26 60

Figure S491.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00024

Table S492.  Gene #80: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 221 103
22Q LOSS MUTATED 58 117 41
22Q LOSS WILD-TYPE 128 104 62

Figure S492.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S493.  Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 39 145 130 96 29
22Q LOSS MUTATED 21 23 77 36 51 8
22Q LOSS WILD-TYPE 50 16 68 94 45 21

Figure S493.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00582 (Fisher's exact test), Q value = 0.017

Table S494.  Gene #80: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 90 95 43 70 77
22Q LOSS MUTATED 15 52 43 18 27 32
22Q LOSS WILD-TYPE 44 38 52 25 43 45

Figure S494.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00048 (Fisher's exact test), Q value = 0.002

Table S495.  Gene #80: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 238 92
22Q LOSS MUTATED 30 121 36
22Q LOSS WILD-TYPE 74 117 56

Figure S495.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'CN_CNMF'

P value = 0.00904 (Fisher's exact test), Q value = 0.024

Table S496.  Gene #81: 'xp loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 172 138 132 74
XP LOSS MUTATED 46 30 15 15
XP LOSS WILD-TYPE 126 108 117 59

Figure S496.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #3: 'CN_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 0.043 (Fisher's exact test), Q value = 0.088

Table S497.  Gene #81: 'xp loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
XP LOSS MUTATED 33 42 17
XP LOSS WILD-TYPE 123 128 112

Figure S497.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xp loss' versus 'RPPA_CNMF'

P value = 0.00684 (Fisher's exact test), Q value = 0.019

Table S498.  Gene #81: 'xp loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 91 22 66 75 109
XP LOSS MUTATED 26 2 5 18 19
XP LOSS WILD-TYPE 65 20 61 57 90

Figure S498.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00477 (Fisher's exact test), Q value = 0.015

Table S499.  Gene #81: 'xp loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 110 97 48 53 49 77
XP LOSS MUTATED 19 36 22 6 6 6 11
XP LOSS WILD-TYPE 59 74 75 42 47 43 66

Figure S499.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.0056 (Fisher's exact test), Q value = 0.017

Table S500.  Gene #82: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 170 129
XQ LOSS MUTATED 23 26 6
XQ LOSS WILD-TYPE 133 144 123

Figure S500.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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/LUAD-TP/22531211/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LUAD-TP/22552673/LUAD-TP.transferedmergedcluster.txt

  • Number of patients = 516

  • Number of significantly arm-level cnvs = 82

  • Number of molecular subtypes = 12

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)