Correlation between copy number variations of arm-level result and molecular subtypes
Brain Lower Grade Glioma (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/C1833RFN
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 81 arm-level events and 12 molecular subtypes across 513 patients, 459 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p 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'.

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

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

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

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

  • 3q gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

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

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

  • 6p gain cnv correlated to 'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

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

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

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

  • 8q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 9p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 9q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 10p gain cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 10q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 11q gain cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 14q gain cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 15q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 16p gain cnv correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 17p gain cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.

  • 17q gain cnv correlated to 'RPPA_CNMF' and 'RPPA_CHIERARCHICAL'.

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

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

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

  • 19q 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'.

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

  • 20q 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'.

  • 21q gain cnv correlated to 'CN_CNMF'.

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

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

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

  • 1p 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'.

  • 1q loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

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

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

  • 3p loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 4p 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'.

  • 4q 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'.

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

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

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

  • 6q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 7q loss cnv correlated to 'RPPA_CNMF'.

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

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

  • 9p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.

  • 9q loss cnv correlated to 'RPPA_CHIERARCHICAL' and 'MRNASEQ_CHIERARCHICAL'.

  • 10p 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'.

  • 10q 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'.

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

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

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

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

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

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

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

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

  • 16q loss cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 17q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

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

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

  • 19p loss cnv correlated to 'MIRSEQ_MATURE_CNMF'.

  • 19q loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_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' and 'METHLYATION_CNMF'.

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

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

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

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

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 81 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, 459 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
1p loss 184 (36%) 329 0.029
(0.0694)
0.00016
(0.000978)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
0.00312
(0.0114)
0.00106
(0.00468)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
7p gain 120 (23%) 393 1
(1.00)
1
(1.00)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
0.0097
(0.0293)
0.0179
(0.0475)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
0.00141
(0.00591)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
10p gain 57 (11%) 456 1
(1.00)
0.0423
(0.0938)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
0.00748
(0.0235)
0.00185
(0.00746)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
0.0273
(0.0664)
0.296
(0.428)
0.0179
(0.0475)
1e-05
(8.6e-05)
20q gain 44 (9%) 469 1e-05
(8.6e-05)
1e-05
(8.6e-05)
0.0007
(0.00335)
0.00369
(0.0133)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
0.0452
(0.0978)
1e-05
(8.6e-05)
9e-05
(0.000607)
1e-05
(8.6e-05)
8p loss 17 (3%) 496 0.618
(0.774)
0.0435
(0.0956)
2e-05
(0.000156)
0.0002
(0.00116)
0.0161
(0.0439)
0.0102
(0.0305)
1e-05
(8.6e-05)
4e-05
(0.00029)
0.297
(0.429)
0.00146
(0.00609)
0.00782
(0.0243)
1e-05
(8.6e-05)
10p loss 83 (16%) 430 0.271
(0.403)
0.883
(1.00)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
0.00742
(0.0235)
0.00031
(0.00168)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
0.00016
(0.000978)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
10q loss 97 (19%) 416 0.27
(0.403)
0.881
(1.00)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
0.00907
(0.0275)
9e-05
(0.000607)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
6e-05
(0.000423)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
11p loss 63 (12%) 450 1
(1.00)
0.0311
(0.0731)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
0.0114
(0.0335)
0.317
(0.455)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
2e-05
(0.000156)
4e-05
(0.00029)
0.00092
(0.00418)
1e-05
(8.6e-05)
19q loss 209 (41%) 304 0.184
(0.293)
0.0133
(0.0379)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
0.0598
(0.123)
0.00821
(0.0253)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
22q loss 57 (11%) 456 0.816
(0.973)
0.00658
(0.0215)
1e-05
(8.6e-05)
2e-05
(0.000156)
0.00036
(0.00192)
0.0389
(0.0878)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
0.513
(0.663)
0.0003
(0.00164)
0.00165
(0.0068)
2e-05
(0.000156)
1p gain 13 (3%) 500 7e-05
(0.000483)
0.00028
(0.00156)
0.0233
(0.0589)
0.296
(0.428)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
0.00656
(0.0215)
1e-05
(8.6e-05)
0.00291
(0.0108)
0.0011
(0.00479)
5p gain 11 (2%) 502 0.00132
(0.0056)
0.0172
(0.046)
0.128
(0.222)
0.036
(0.0828)
0.00012
(0.000772)
0.00043
(0.00225)
0.0257
(0.0634)
0.0268
(0.0653)
2e-05
(0.000156)
0.00078
(0.00368)
19q gain 25 (5%) 488 1e-05
(8.6e-05)
1e-05
(8.6e-05)
0.133
(0.229)
0.0138
(0.039)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
0.00247
(0.00945)
1e-05
(8.6e-05)
0.00013
(0.000815)
1e-05
(8.6e-05)
20p gain 45 (9%) 468 1e-05
(8.6e-05)
1e-05
(8.6e-05)
0.00484
(0.0166)
0.0154
(0.0425)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
0.105
(0.19)
1e-05
(8.6e-05)
0.00027
(0.00151)
1e-05
(8.6e-05)
xq gain 42 (8%) 471 1e-05
(8.6e-05)
1e-05
(8.6e-05)
0.0262
(0.0642)
0.0249
(0.0621)
0.00013
(0.000815)
1e-05
(8.6e-05)
0.0101
(0.0302)
0.461
(0.609)
0.0366
(0.0839)
0.00196
(0.00781)
4p loss 72 (14%) 441 1
(1.00)
0.781
(0.937)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
0.0118
(0.0344)
0.932
(1.00)
0.00012
(0.000772)
1e-05
(8.6e-05)
7e-05
(0.000483)
0.00105
(0.00468)
0.00056
(0.00278)
1e-05
(8.6e-05)
4q loss 94 (18%) 419 1
(1.00)
0.408
(0.558)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
0.0186
(0.0488)
0.402
(0.554)
0.00119
(0.00512)
1e-05
(8.6e-05)
0.00047
(0.00242)
0.00347
(0.0126)
0.0072
(0.0229)
2e-05
(0.000156)
xq loss 70 (14%) 443 0.838
(0.994)
0.266
(0.398)
0.0076
(0.0237)
0.00018
(0.00107)
7e-05
(0.000483)
0.0167
(0.045)
0.00021
(0.00121)
1e-05
(8.6e-05)
4e-05
(0.00029)
0.26
(0.391)
0.00011
(0.000727)
0.00069
(0.00334)
7q gain 150 (29%) 363 0.863
(1.00)
0.781
(0.937)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
0.0798
(0.154)
0.0779
(0.151)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
0.00285
(0.0107)
1e-05
(8.6e-05)
2e-05
(0.000156)
1e-05
(8.6e-05)
19p gain 99 (19%) 414 0.221
(0.342)
1
(1.00)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
0.279
(0.414)
0.00389
(0.014)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
0.0024
(0.00926)
0.055
(0.114)
0.0002
(0.00116)
1e-05
(8.6e-05)
5q loss 32 (6%) 481 0.449
(0.596)
0.237
(0.363)
0.00081
(0.00379)
4e-05
(0.00029)
0.0022
(0.00866)
0.183
(0.292)
0.0137
(0.0387)
1e-05
(8.6e-05)
0.0001
(0.000666)
0.116
(0.206)
0.0155
(0.0425)
3e-05
(0.000226)
13q loss 115 (22%) 398 0.179
(0.288)
2e-05
(0.000156)
1e-05
(8.6e-05)
0.0433
(0.0955)
0.0128
(0.0368)
0.445
(0.593)
0.0181
(0.0477)
0.00117
(0.00505)
0.0514
(0.108)
0.0206
(0.0531)
0.455
(0.603)
0.0447
(0.0974)
14q loss 81 (16%) 432 0.467
(0.614)
0.266
(0.398)
1e-05
(8.6e-05)
0.00178
(0.00724)
0.0528
(0.11)
0.295
(0.428)
1e-05
(8.6e-05)
0.00019
(0.00112)
0.0191
(0.0497)
0.00126
(0.0054)
0.0123
(0.0359)
0.00149
(0.00616)
1q gain 23 (4%) 490 3e-05
(0.000226)
0.00267
(0.0102)
0.47
(0.618)
0.833
(0.99)
9e-05
(0.000607)
0.00299
(0.0111)
0.0188
(0.049)
0.0304
(0.0719)
0.0115
(0.0338)
0.27
(0.403)
5q gain 9 (2%) 504 0.00302
(0.0112)
0.00832
(0.0256)
0.44
(0.59)
0.0614
(0.126)
0.0011
(0.00479)
0.00041
(0.00217)
0.0819
(0.157)
0.00613
(0.0203)
0.00012
(0.000772)
0.00076
(0.0036)
8q gain 55 (11%) 458 0.0507
(0.107)
0.406
(0.557)
0.00021
(0.00121)
5e-05
(0.000357)
0.00758
(0.0237)
0.0436
(0.0956)
0.0014
(0.00589)
0.00068
(0.0033)
0.132
(0.228)
0.0989
(0.181)
0.0637
(0.128)
0.0006
(0.00296)
11p gain 30 (6%) 483 0.00432
(0.0153)
0.0003
(0.00164)
0.51
(0.66)
0.158
(0.259)
0.00681
(0.022)
0.00857
(0.0263)
0.0377
(0.0852)
0.0265
(0.0647)
0.126
(0.22)
0.00749
(0.0235)
18q gain 13 (3%) 500 0.00183
(0.00741)
2e-05
(0.000156)
0.451
(0.599)
0.483
(0.63)
0.00026
(0.00147)
0.00048
(0.00244)
0.525
(0.675)
0.0174
(0.0462)
0.0292
(0.0699)
0.00679
(0.022)
22q gain 23 (4%) 490 0.00086
(0.004)
1e-05
(8.6e-05)
0.75
(0.909)
0.109
(0.197)
0.00081
(0.00379)
0.00048
(0.00244)
0.0453
(0.0978)
0.528
(0.679)
0.00045
(0.00233)
0.00177
(0.00723)
8q loss 11 (2%) 502 3e-05
(0.000226)
0.00092
(0.00418)
0.0998
(0.182)
0.105
(0.19)
0.00018
(0.00107)
0.00036
(0.00192)
0.288
(0.423)
0.0007
(0.00335)
0.0498
(0.106)
2e-05
(0.000156)
11q loss 21 (4%) 492 2e-05
(0.000156)
0.00018
(0.00107)
0.133
(0.229)
0.162
(0.265)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
0.0958
(0.177)
0.0001
(0.000666)
0.00631
(0.0208)
0.00138
(0.00583)
21q loss 38 (7%) 475 0.505
(0.654)
0.00692
(0.0222)
0.00013
(0.000815)
5e-05
(0.000357)
0.15
(0.25)
0.457
(0.604)
0.00129
(0.0055)
1e-05
(8.6e-05)
0.352
(0.496)
0.0486
(0.103)
0.126
(0.22)
0.0254
(0.063)
xp loss 99 (19%) 414 0.84
(0.995)
0.0662
(0.132)
0.98
(1.00)
0.00286
(0.0107)
0.00246
(0.00945)
0.00588
(0.0196)
0.116
(0.206)
1e-05
(8.6e-05)
0.0238
(0.06)
0.279
(0.414)
0.00107
(0.00471)
0.00033
(0.00178)
2q gain 13 (3%) 500 0.00017
(0.00103)
0.145
(0.243)
0.251
(0.382)
0.422
(0.573)
0.04
(0.0897)
0.00071
(0.00338)
0.522
(0.673)
0.017
(0.0455)
0.0122
(0.0357)
0.0282
(0.0677)
4p gain 12 (2%) 501 0.00236
(0.00914)
0.024
(0.0604)
0.384
(0.535)
0.48
(0.626)
0.00716
(0.0228)
0.0135
(0.0384)
0.315
(0.453)
0.0452
(0.0978)
0.00313
(0.0114)
0.0762
(0.149)
8p gain 45 (9%) 468 0.00063
(0.00308)
0.00328
(0.0119)
0.0184
(0.0483)
0.0616
(0.126)
0.0166
(0.0448)
0.0141
(0.0397)
0.263
(0.395)
0.344
(0.489)
0.111
(0.199)
0.00621
(0.0205)
9q gain 24 (5%) 489 0.00689
(0.0222)
0.00233
(0.0091)
0.00694
(0.0222)
0.866
(1.00)
0.0433
(0.0955)
0.00472
(0.0163)
0.444
(0.593)
0.0105
(0.0314)
0.444
(0.593)
0.0694
(0.137)
12p gain 32 (6%) 481 0.754
(0.911)
0.579
(0.738)
4e-05
(0.00029)
0.0259
(0.0639)
0.177
(0.286)
0.374
(0.523)
0.0518
(0.109)
0.0421
(0.0936)
0.0477
(0.102)
0.0278
(0.0672)
0.117
(0.207)
0.0227
(0.0577)
15q gain 11 (2%) 502 0.011
(0.0326)
0.0319
(0.0745)
0.00893
(0.0271)
0.0126
(0.0364)
0.047
(0.101)
0.063
(0.128)
0.17
(0.276)
0.288
(0.423)
0.0197
(0.051)
0.0576
(0.119)
2q loss 18 (4%) 495 0.0153
(0.0425)
0.00863
(0.0264)
0.0479
(0.102)
0.769
(0.926)
0.455
(0.603)
0.00186
(0.00747)
0.0257
(0.0634)
0.811
(0.969)
0.143
(0.241)
0.00206
(0.00817)
6q loss 63 (12%) 450 1e-05
(8.6e-05)
0.00097
(0.00436)
0.457
(0.604)
0.0339
(0.0789)
0.0649
(0.13)
0.0529
(0.11)
0.00191
(0.00764)
0.172
(0.278)
0.0133
(0.0379)
0.00451
(0.0156)
12q loss 52 (10%) 461 1
(1.00)
0.58
(0.738)
1e-05
(8.6e-05)
1e-05
(8.6e-05)
0.604
(0.759)
0.956
(1.00)
0.00089
(0.00412)
1e-05
(8.6e-05)
0.00306
(0.0113)
0.395
(0.546)
0.24
(0.366)
1e-05
(8.6e-05)
15q loss 51 (10%) 462 1
(1.00)
0.708
(0.868)
0.0159
(0.0433)
1e-05
(8.6e-05)
0.0145
(0.0408)
0.0871
(0.164)
0.00276
(0.0105)
3e-05
(0.000226)
0.123
(0.216)
0.473
(0.62)
0.0937
(0.174)
0.00053
(0.00266)
2p gain 14 (3%) 499 6e-05
(0.000423)
0.159
(0.26)
0.251
(0.382)
0.425
(0.575)
0.0155
(0.0425)
0.00166
(0.00681)
0.645
(0.803)
0.021
(0.0539)
0.0045
(0.0156)
0.0638
(0.128)
4q gain 7 (1%) 506 0.00392
(0.014)
0.0522
(0.109)
0.0736
(0.144)
0.728
(0.887)
0.0053
(0.0179)
0.00225
(0.00882)
0.24
(0.366)
0.0543
(0.113)
0.0362
(0.0831)
0.0355
(0.0821)
10q gain 11 (2%) 502 0.0124
(0.0359)
0.00116
(0.00503)
0.0675
(0.134)
0.0398
(0.0894)
0.202
(0.318)
0.00027
(0.00151)
0.103
(0.187)
0.0656
(0.131)
0.738
(0.899)
0.00148
(0.00615)
12q gain 15 (3%) 498 2e-05
(0.000156)
0.632
(0.79)
0.0048
(0.0165)
0.211
(0.329)
0.00503
(0.0171)
0.0926
(0.173)
0.0565
(0.117)
0.0279
(0.0672)
0.0859
(0.163)
0.0153
(0.0425)
18p gain 18 (4%) 495 0.0065
(0.0213)
0.00025
(0.00143)
0.681
(0.842)
0.939
(1.00)
0.00563
(0.0189)
0.022
(0.0562)
0.936
(1.00)
0.135
(0.231)
0.236
(0.363)
0.0226
(0.0577)
5p loss 35 (7%) 478 0.745
(0.904)
0.0668
(0.133)
0.00049
(0.00247)
0.00026
(0.00147)
0.0902
(0.17)
0.969
(1.00)
0.0405
(0.0905)
0.00106
(0.00468)
0.112
(0.201)
0.254
(0.385)
0.181
(0.29)
0.00013
(0.000815)
9p loss 118 (23%) 395 0.385
(0.535)
0.266
(0.398)
1e-05
(8.6e-05)
0.00409
(0.0146)
0.00056
(0.00278)
1e-05
(8.6e-05)
0.104
(0.188)
0.00015
(0.000935)
0.972
(1.00)
0.223
(0.344)
0.371
(0.519)
0.0851
(0.162)
12p loss 28 (5%) 485 0.0149
(0.0416)
0.0003
(0.00164)
0.946
(1.00)
1
(1.00)
0.0987
(0.181)
0.00507
(0.0172)
0.0428
(0.0949)
0.243
(0.371)
0.486
(0.631)
0.0477
(0.102)
16q loss 22 (4%) 491 0.0056
(0.0188)
0.0855
(0.162)
0.294
(0.428)
0.00567
(0.0189)
0.0211
(0.054)
0.0206
(0.0531)
0.699
(0.861)
0.00376
(0.0135)
0.286
(0.421)
0.128
(0.222)
17p loss 14 (3%) 499 0.00094
(0.00425)
0.0101
(0.0302)
0.908
(1.00)
0.616
(0.772)
0.00049
(0.00247)
0.0633
(0.128)
0.0985
(0.181)
0.00214
(0.00846)
0.439
(0.589)
0.0452
(0.0978)
6p gain 7 (1%) 506 0.102
(0.186)
0.00016
(0.000978)
0.00818
(0.0253)
0.43
(0.579)
0.475
(0.622)
0.00449
(0.0156)
0.0261
(0.0642)
0.066
(0.132)
0.119
(0.209)
0.115
(0.204)
9p gain 17 (3%) 496 0.00499
(0.017)
0.0305
(0.0719)
0.0372
(0.0847)
0.771
(0.927)
0.0808
(0.156)
0.0794
(0.153)
0.882
(1.00)
0.0279
(0.0672)
0.987
(1.00)
0.201
(0.317)
11q gain 58 (11%) 455 0.613
(0.768)
0.581
(0.738)
1
(1.00)
0.00414
(0.0147)
0.203
(0.318)
0.0673
(0.133)
0.0463
(0.0998)
0.0638
(0.128)
0.392
(0.544)
0.0468
(0.101)
0.278
(0.413)
0.0277
(0.0672)
16q gain 19 (4%) 494 0.00679
(0.022)
0.152
(0.252)
0.636
(0.793)
0.944
(1.00)
0.0937
(0.174)
0.00043
(0.00225)
0.0485
(0.103)
0.0996
(0.182)
0.141
(0.238)
0.0307
(0.0723)
xp gain 22 (4%) 491 0.00284
(0.0107)
1e-05
(8.6e-05)
0.404
(0.556)
0.603
(0.759)
0.0295
(0.0702)
0.0187
(0.049)
0.403
(0.554)
0.74
(0.9)
0.861
(1.00)
0.198
(0.313)
3p loss 30 (6%) 483 0.0231
(0.0584)
0.151
(0.251)
0.0113
(0.0335)
0.0839
(0.16)
0.0758
(0.148)
0.0656
(0.131)
0.00105
(0.00468)
0.00039
(0.00207)
0.0711
(0.14)
0.13
(0.225)
18q loss 62 (12%) 451 0.344
(0.489)
0.149
(0.249)
0.00091
(0.00417)
0.00091
(0.00417)
0.362
(0.508)
0.0921
(0.173)
0.0538
(0.112)
0.0154
(0.0425)
0.0181
(0.0477)
0.712
(0.871)
0.238
(0.364)
0.287
(0.423)
3q gain 8 (2%) 505 0.00012
(0.000772)
0.467
(0.614)
0.00439
(0.0154)
0.21
(0.328)
0.0715
(0.141)
0.00434
(0.0153)
0.387
(0.537)
0.135
(0.231)
0.839
(0.994)
0.119
(0.209)
2p loss 21 (4%) 492 0.0252
(0.0628)
0.0351
(0.0813)
0.101
(0.185)
0.953
(1.00)
0.18
(0.288)
0.0439
(0.0961)
0.0777
(0.151)
0.399
(0.55)
0.232
(0.357)
0.137
(0.234)
3q loss 28 (5%) 485 0.175
(0.283)
0.881
(1.00)
0.156
(0.256)
0.14
(0.237)
0.154
(0.255)
0.0811
(0.156)
0.148
(0.248)
0.0317
(0.0742)
0.095
(0.176)
0.0165
(0.0446)
0.112
(0.201)
0.0158
(0.0432)
16p loss 14 (3%) 499 0.0304
(0.0719)
0.414
(0.565)
0.704
(0.864)
0.0632
(0.128)
0.0375
(0.0852)
0.0227
(0.0577)
0.811
(0.969)
0.356
(0.501)
0.701
(0.862)
0.326
(0.465)
3p gain 11 (2%) 502 0.00062
(0.00304)
0.281
(0.416)
0.0764
(0.149)
0.2
(0.316)
0.111
(0.2)
0.0369
(0.0843)
0.133
(0.229)
0.291
(0.425)
0.425
(0.575)
0.253
(0.384)
16p gain 16 (3%) 497 0.119
(0.209)
0.139
(0.237)
0.564
(0.72)
0.94
(1.00)
0.158
(0.259)
0.00235
(0.00914)
0.155
(0.255)
0.0502
(0.106)
0.138
(0.235)
0.0376
(0.0852)
17p gain 20 (4%) 493 0.0128
(0.0368)
0.122
(0.213)
0.0162
(0.044)
0.377
(0.526)
0.206
(0.323)
0.0638
(0.128)
0.199
(0.314)
0.485
(0.631)
0.585
(0.739)
0.371
(0.519)
17q gain 23 (4%) 490 0.144
(0.242)
0.548
(0.704)
0.0126
(0.0363)
0.0244
(0.0611)
0.347
(0.491)
0.257
(0.387)
0.113
(0.202)
0.701
(0.862)
0.417
(0.569)
0.11
(0.198)
6p loss 30 (6%) 483 0.00018
(0.00107)
0.18
(0.289)
0.886
(1.00)
0.349
(0.493)
0.473
(0.62)
0.155
(0.255)
0.446
(0.593)
0.405
(0.556)
0.385
(0.535)
0.0334
(0.0778)
9q loss 51 (10%) 462 0.497
(0.644)
0.743
(0.903)
0.0852
(0.162)
0.00451
(0.0156)
0.584
(0.739)
0.0441
(0.0963)
0.42
(0.572)
0.823
(0.981)
0.894
(1.00)
0.678
(0.839)
17q loss 9 (2%) 504 0.00291
(0.0108)
0.0533
(0.111)
0.596
(0.751)
0.229
(0.352)
0.0109
(0.0324)
0.295
(0.428)
0.0819
(0.157)
0.097
(0.179)
0.424
(0.575)
0.128
(0.222)
18p loss 67 (13%) 446 0.323
(0.462)
0.0302
(0.0717)
0.00749
(0.0235)
0.0756
(0.148)
0.587
(0.741)
0.113
(0.202)
0.179
(0.288)
0.0943
(0.175)
0.287
(0.423)
0.86
(1.00)
0.558
(0.715)
0.554
(0.71)
20p loss 7 (1%) 506 0.0151
(0.0423)
0.0369
(0.0843)
0.655
(0.813)
0.727
(0.887)
0.291
(0.426)
0.217
(0.336)
0.429
(0.578)
0.486
(0.631)
0.751
(0.909)
0.283
(0.418)
20q loss 3 (1%) 510 0.32
(0.458)
0.039
(0.0878)
0.0345
(0.08)
0.0779
(0.151)
0.331
(0.472)
1
(1.00)
0.163
(0.266)
0.196
(0.311)
14q gain 4 (1%) 509 0.205
(0.321)
0.09
(0.17)
0.792
(0.948)
0.42
(0.572)
0.754
(0.911)
0.709
(0.868)
0.196
(0.311)
0.681
(0.842)
1
(1.00)
0.0245
(0.0611)
21q gain 23 (4%) 490 0.00044
(0.00229)
0.192
(0.304)
0.215
(0.333)
0.142
(0.241)
0.634
(0.791)
0.226
(0.348)
0.26
(0.391)
0.0622
(0.127)
0.765
(0.923)
0.177
(0.286)
1q loss 26 (5%) 487 0.343
(0.488)
0.15
(0.25)
0.151
(0.251)
0.132
(0.228)
0.571
(0.729)
0.119
(0.209)
0.315
(0.453)
0.00877
(0.0267)
0.082
(0.157)
0.293
(0.428)
0.683
(0.843)
0.295
(0.428)
7q loss 4 (1%) 509 0.15
(0.25)
0.442
(0.592)
0.0169
(0.0455)
0.254
(0.385)
0.438
(0.589)
0.0933
(0.174)
1
(1.00)
0.833
(0.99)
0.561
(0.717)
0.908
(1.00)
19p loss 26 (5%) 487 0.847
(1.00)
0.429
(0.578)
0.933
(1.00)
0.843
(0.997)
0.352
(0.496)
0.396
(0.547)
0.677
(0.839)
0.186
(0.295)
0.214
(0.332)
0.408
(0.558)
0.0411
(0.0916)
0.0961
(0.178)
13q gain 6 (1%) 507 0.584
(0.739)
0.181
(0.289)
0.165
(0.268)
0.144
(0.242)
0.302
(0.436)
0.48
(0.626)
0.349
(0.493)
0.585
(0.739)
0.594
(0.748)
0.95
(1.00)
7p loss 3 (1%) 510 0.321
(0.459)
0.649
(0.807)
1
(1.00)
0.792
(0.948)
1
(1.00)
1
(1.00)
'1p gain' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00048

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
1P GAIN MUTATED 2 10 1
1P GAIN WILD-TYPE 225 101 174

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

'1p gain' versus 'METHLYATION_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0016

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
1P GAIN MUTATED 3 8 0 2
1P GAIN WILD-TYPE 206 126 157 11

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

'1p gain' versus 'RPPA_CNMF'

P value = 0.0233 (Fisher's exact test), Q value = 0.059

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
1P GAIN MUTATED 2 5 1 0
1P GAIN WILD-TYPE 89 90 124 115

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

'1p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
1P GAIN MUTATED 0 13 0 0 0
1P GAIN WILD-TYPE 130 102 105 133 30

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

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

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 135 71 36 68 90 41 72
1P GAIN MUTATED 0 8 0 0 0 5 0
1P GAIN WILD-TYPE 135 63 36 68 90 36 72

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

'1p gain' versus 'MIRSEQ_CNMF'

P value = 0.00656 (Fisher's exact test), Q value = 0.021

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
1P GAIN MUTATED 8 4 0 1
1P GAIN WILD-TYPE 132 103 82 179

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

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S7.  Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
1P GAIN MUTATED 3 0 10
1P GAIN WILD-TYPE 219 184 93

Figure S7.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00291 (Fisher's exact test), Q value = 0.011

Table S8.  Gene #1: '1p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
1P GAIN MUTATED 4 8 0 1
1P GAIN WILD-TYPE 123 111 105 153

Figure S8.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0011 (Fisher's exact test), Q value = 0.0048

Table S9.  Gene #1: '1p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
1P GAIN MUTATED 1 4 0 0 6 2
1P GAIN WILD-TYPE 98 73 118 56 57 90

Figure S9.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00023

Table S10.  Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
1Q GAIN MUTATED 4 15 4
1Q GAIN WILD-TYPE 223 96 171

Figure S10.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1q gain' versus 'METHLYATION_CNMF'

P value = 0.00267 (Fisher's exact test), Q value = 0.01

Table S11.  Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
1Q GAIN MUTATED 7 12 2 2
1Q GAIN WILD-TYPE 202 122 155 11

Figure S11.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00061

Table S12.  Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
1Q GAIN MUTATED 2 14 0 5 2
1Q GAIN WILD-TYPE 128 101 105 128 28

Figure S12.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00299 (Fisher's exact test), Q value = 0.011

Table S13.  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 135 71 36 68 90 41 72
1Q GAIN MUTATED 3 9 1 2 1 5 2
1Q GAIN WILD-TYPE 132 62 35 66 89 36 70

Figure S13.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CNMF'

P value = 0.0188 (Fisher's exact test), Q value = 0.049

Table S14.  Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
1Q GAIN MUTATED 12 4 0 7
1Q GAIN WILD-TYPE 128 103 82 173

Figure S14.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0304 (Fisher's exact test), Q value = 0.072

Table S15.  Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
1Q GAIN MUTATED 7 6 10
1Q GAIN WILD-TYPE 215 178 93

Figure S15.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.034

Table S16.  Gene #2: '1q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
1Q GAIN MUTATED 5 10 0 8
1Q GAIN WILD-TYPE 122 109 105 146

Figure S16.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00042

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
2P GAIN MUTATED 1 10 3
2P GAIN WILD-TYPE 226 101 172

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

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.0155 (Fisher's exact test), Q value = 0.043

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
2P GAIN MUTATED 1 9 2 2 0
2P GAIN WILD-TYPE 129 106 103 131 30

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

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00166 (Fisher's exact test), Q value = 0.0068

Table S19.  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 135 71 36 68 90 41 72
2P GAIN MUTATED 0 5 1 2 2 4 0
2P GAIN WILD-TYPE 135 66 35 66 88 37 72

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

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.021 (Fisher's exact test), Q value = 0.054

Table S20.  Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
2P GAIN MUTATED 5 2 7
2P GAIN WILD-TYPE 217 182 96

Figure S20.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0045 (Fisher's exact test), Q value = 0.016

Table S21.  Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
2P GAIN MUTATED 2 9 0 3
2P GAIN WILD-TYPE 125 110 105 151

Figure S21.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2q gain' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.001

Table S22.  Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
2Q GAIN MUTATED 1 9 3
2Q GAIN WILD-TYPE 226 102 172

Figure S22.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.04 (Fisher's exact test), Q value = 0.09

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
2Q GAIN MUTATED 1 8 2 2 0
2Q GAIN WILD-TYPE 129 107 103 131 30

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

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00071 (Fisher's exact test), Q value = 0.0034

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 135 71 36 68 90 41 72
2Q GAIN MUTATED 0 5 1 2 1 4 0
2Q GAIN WILD-TYPE 135 66 35 66 89 37 72

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

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.017 (Fisher's exact test), Q value = 0.045

Table S25.  Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
2Q GAIN MUTATED 4 2 7
2Q GAIN WILD-TYPE 218 182 96

Figure S25.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.036

Table S26.  Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
2Q GAIN MUTATED 2 8 0 3
2Q GAIN WILD-TYPE 125 111 105 151

Figure S26.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0282 (Fisher's exact test), Q value = 0.068

Table S27.  Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
2Q GAIN MUTATED 2 4 1 0 5 1
2Q GAIN WILD-TYPE 97 73 117 56 58 91

Figure S27.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.003

Table S28.  Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
3P GAIN MUTATED 2 8 1
3P GAIN WILD-TYPE 225 103 174

Figure S28.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0369 (Fisher's exact test), Q value = 0.084

Table S29.  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 135 71 36 68 90 41 72
3P GAIN MUTATED 2 4 2 0 0 2 1
3P GAIN WILD-TYPE 133 67 34 68 90 39 71

Figure S29.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00077

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
3Q GAIN MUTATED 1 7 0
3Q GAIN WILD-TYPE 226 104 175

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

'3q gain' versus 'RPPA_CNMF'

P value = 0.00439 (Fisher's exact test), Q value = 0.015

Table S31.  Gene #6: '3q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
3Q GAIN MUTATED 0 5 0 1
3Q GAIN WILD-TYPE 91 90 125 114

Figure S31.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00434 (Fisher's exact test), Q value = 0.015

Table S32.  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 135 71 36 68 90 41 72
3Q GAIN MUTATED 0 4 1 0 0 2 1
3Q GAIN WILD-TYPE 135 67 35 68 90 39 71

Figure S32.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 0.00236 (Fisher's exact test), Q value = 0.0091

Table S33.  Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
4P GAIN MUTATED 5 7 0
4P GAIN WILD-TYPE 222 104 175

Figure S33.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'4p gain' versus 'METHLYATION_CNMF'

P value = 0.024 (Fisher's exact test), Q value = 0.06

Table S34.  Gene #7: '4p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
4P GAIN MUTATED 6 5 0 1
4P GAIN WILD-TYPE 203 129 157 12

Figure S34.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 0.00716 (Fisher's exact test), Q value = 0.023

Table S35.  Gene #7: '4p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
4P GAIN MUTATED 3 8 0 1 0
4P GAIN WILD-TYPE 127 107 105 132 30

Figure S35.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0135 (Fisher's exact test), Q value = 0.038

Table S36.  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 135 71 36 68 90 41 72
4P GAIN MUTATED 3 5 0 0 0 3 1
4P GAIN WILD-TYPE 132 66 36 68 90 38 71

Figure S36.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0452 (Fisher's exact test), Q value = 0.098

Table S37.  Gene #7: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
4P GAIN MUTATED 3 3 6
4P GAIN WILD-TYPE 219 181 97

Figure S37.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00313 (Fisher's exact test), Q value = 0.011

Table S38.  Gene #7: '4p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
4P GAIN MUTATED 3 8 0 1
4P GAIN WILD-TYPE 124 111 105 153

Figure S38.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q gain' versus 'CN_CNMF'

P value = 0.00392 (Fisher's exact test), Q value = 0.014

Table S39.  Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
4Q GAIN MUTATED 2 5 0
4Q GAIN WILD-TYPE 225 106 175

Figure S39.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 0.0053 (Fisher's exact test), Q value = 0.018

Table S40.  Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
4Q GAIN MUTATED 0 6 0 1 0
4Q GAIN WILD-TYPE 130 109 105 132 30

Figure S40.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00225 (Fisher's exact test), Q value = 0.0088

Table S41.  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 135 71 36 68 90 41 72
4Q GAIN MUTATED 0 5 0 0 0 1 1
4Q GAIN WILD-TYPE 135 66 36 68 90 40 71

Figure S41.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0362 (Fisher's exact test), Q value = 0.083

Table S42.  Gene #8: '4q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
4Q GAIN MUTATED 1 5 0 1
4Q GAIN WILD-TYPE 126 114 105 153

Figure S42.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0355 (Fisher's exact test), Q value = 0.082

Table S43.  Gene #8: '4q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
4Q GAIN MUTATED 1 1 1 0 4 0
4Q GAIN WILD-TYPE 98 76 117 56 59 92

Figure S43.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 0.00132 (Fisher's exact test), Q value = 0.0056

Table S44.  Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
5P GAIN MUTATED 4 7 0
5P GAIN WILD-TYPE 223 104 175

Figure S44.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.0172 (Fisher's exact test), Q value = 0.046

Table S45.  Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
5P GAIN MUTATED 4 7 0 0
5P GAIN WILD-TYPE 205 127 157 13

Figure S45.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.036 (Fisher's exact test), Q value = 0.083

Table S46.  Gene #9: '5p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
5P GAIN MUTATED 3 0 5
5P GAIN WILD-TYPE 80 158 180

Figure S46.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00077

Table S47.  Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
5P GAIN MUTATED 0 9 0 1 1
5P GAIN WILD-TYPE 130 106 105 132 29

Figure S47.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.0022

Table S48.  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 135 71 36 68 90 41 72
5P GAIN MUTATED 1 7 0 1 0 2 0
5P GAIN WILD-TYPE 134 64 36 67 90 39 72

Figure S48.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 0.0257 (Fisher's exact test), Q value = 0.063

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
5P GAIN MUTATED 5 5 0 1
5P GAIN WILD-TYPE 135 102 82 179

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

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0268 (Fisher's exact test), Q value = 0.065

Table S50.  Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
5P GAIN MUTATED 3 2 6
5P GAIN WILD-TYPE 219 182 97

Figure S50.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00016

Table S51.  Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
5P GAIN MUTATED 0 10 0 1
5P GAIN WILD-TYPE 127 109 105 153

Figure S51.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.0037

Table S52.  Gene #9: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
5P GAIN MUTATED 1 3 0 0 6 1
5P GAIN WILD-TYPE 98 74 118 56 57 91

Figure S52.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 0.00302 (Fisher's exact test), Q value = 0.011

Table S53.  Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
5Q GAIN MUTATED 3 6 0
5Q GAIN WILD-TYPE 224 105 175

Figure S53.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 0.00832 (Fisher's exact test), Q value = 0.026

Table S54.  Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
5Q GAIN MUTATED 2 7 0 0
5Q GAIN WILD-TYPE 207 127 157 13

Figure S54.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.0011 (Fisher's exact test), Q value = 0.0048

Table S55.  Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
5Q GAIN MUTATED 0 7 0 1 1
5Q GAIN WILD-TYPE 130 108 105 132 29

Figure S55.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.0022

Table S56.  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 135 71 36 68 90 41 72
5Q GAIN MUTATED 1 7 0 1 0 0 0
5Q GAIN WILD-TYPE 134 64 36 67 90 41 72

Figure S56.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00613 (Fisher's exact test), Q value = 0.02

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
5Q GAIN MUTATED 2 1 6
5Q GAIN WILD-TYPE 220 183 97

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

'5q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00077

Table S58.  Gene #10: '5q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
5Q GAIN MUTATED 0 8 0 1
5Q GAIN WILD-TYPE 127 111 105 153

Figure S58.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00076 (Fisher's exact test), Q value = 0.0036

Table S59.  Gene #10: '5q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
5Q GAIN MUTATED 1 1 0 0 6 1
5Q GAIN WILD-TYPE 98 76 118 56 57 91

Figure S59.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p gain' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00098

Table S60.  Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
6P GAIN MUTATED 3 1 0 3
6P GAIN WILD-TYPE 206 133 157 10

Figure S60.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p gain' versus 'RPPA_CNMF'

P value = 0.00818 (Fisher's exact test), Q value = 0.025

Table S61.  Gene #11: '6p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
6P GAIN MUTATED 2 4 0 0
6P GAIN WILD-TYPE 89 91 125 115

Figure S61.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00449 (Fisher's exact test), Q value = 0.016

Table S62.  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 135 71 36 68 90 41 72
6P GAIN MUTATED 2 0 0 1 0 4 0
6P GAIN WILD-TYPE 133 71 36 67 90 37 72

Figure S62.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 0.0261 (Fisher's exact test), Q value = 0.064

Table S63.  Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
6P GAIN MUTATED 4 3 0 0
6P GAIN WILD-TYPE 136 104 82 180

Figure S63.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S64.  Gene #12: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
7P GAIN MUTATED 42 66 12
7P GAIN WILD-TYPE 185 45 163

Figure S64.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S65.  Gene #12: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
7P GAIN MUTATED 40 64 15 1
7P GAIN WILD-TYPE 169 70 142 12

Figure S65.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 0.0097 (Fisher's exact test), Q value = 0.029

Table S66.  Gene #12: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
7P GAIN MUTATED 22 32 20 20
7P GAIN WILD-TYPE 69 63 105 95

Figure S66.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0179 (Fisher's exact test), Q value = 0.048

Table S67.  Gene #12: '7p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
7P GAIN MUTATED 13 28 53
7P GAIN WILD-TYPE 70 130 132

Figure S67.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S68.  Gene #12: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
7P GAIN MUTATED 22 59 9 24 6
7P GAIN WILD-TYPE 108 56 96 109 24

Figure S68.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S69.  Gene #12: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
7P GAIN MUTATED 19 51 3 26 8 8 5
7P GAIN WILD-TYPE 116 20 33 42 82 33 67

Figure S69.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.00141 (Fisher's exact test), Q value = 0.0059

Table S70.  Gene #12: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
7P GAIN MUTATED 43 33 12 30
7P GAIN WILD-TYPE 97 74 70 150

Figure S70.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S71.  Gene #12: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
7P GAIN MUTATED 37 26 55
7P GAIN WILD-TYPE 185 158 48

Figure S71.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S72.  Gene #12: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
7P GAIN MUTATED 31 45 11 30
7P GAIN WILD-TYPE 96 74 94 124

Figure S72.  Get High-res Image Gene #12: '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 = 8.6e-05

Table S73.  Gene #12: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
7P GAIN MUTATED 15 11 17 7 47 20
7P GAIN WILD-TYPE 84 66 101 49 16 72

Figure S73.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S74.  Gene #13: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
7Q GAIN MUTATED 57 73 20
7Q GAIN WILD-TYPE 170 38 155

Figure S74.  Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S75.  Gene #13: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
7Q GAIN MUTATED 57 68 23 2
7Q GAIN WILD-TYPE 152 66 134 11

Figure S75.  Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
7Q GAIN MUTATED 35 63 12 32 8
7Q GAIN WILD-TYPE 95 52 93 101 22

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

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
7Q GAIN MUTATED 32 54 4 29 12 7 12
7Q GAIN WILD-TYPE 103 17 32 39 78 34 60

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

'7q gain' versus 'MIRSEQ_CNMF'

P value = 0.00285 (Fisher's exact test), Q value = 0.011

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
7Q GAIN MUTATED 49 41 15 43
7Q GAIN WILD-TYPE 91 66 67 137

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

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
7Q GAIN MUTATED 50 39 59
7Q GAIN WILD-TYPE 172 145 44

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

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
7Q GAIN MUTATED 38 53 14 42
7Q GAIN WILD-TYPE 89 66 91 112

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

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
7Q GAIN MUTATED 21 15 25 7 50 29
7Q GAIN WILD-TYPE 78 62 93 49 13 63

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

'8p gain' versus 'CN_CNMF'

P value = 0.00063 (Fisher's exact test), Q value = 0.0031

Table S82.  Gene #14: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
8P GAIN MUTATED 24 16 5
8P GAIN WILD-TYPE 203 95 170

Figure S82.  Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.00328 (Fisher's exact test), Q value = 0.012

Table S83.  Gene #14: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
8P GAIN MUTATED 29 6 8 2
8P GAIN WILD-TYPE 180 128 149 11

Figure S83.  Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p gain' versus 'RPPA_CNMF'

P value = 0.0184 (Fisher's exact test), Q value = 0.048

Table S84.  Gene #14: '8p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
8P GAIN MUTATED 12 11 10 3
8P GAIN WILD-TYPE 79 84 115 112

Figure S84.  Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.045

Table S85.  Gene #14: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
8P GAIN MUTATED 20 8 4 9 4
8P GAIN WILD-TYPE 110 107 101 124 26

Figure S85.  Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0141 (Fisher's exact test), Q value = 0.04

Table S86.  Gene #14: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
8P GAIN MUTATED 22 3 2 6 3 5 4
8P GAIN WILD-TYPE 113 68 34 62 87 36 68

Figure S86.  Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00621 (Fisher's exact test), Q value = 0.021

Table S87.  Gene #14: '8p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
8P GAIN MUTATED 18 6 5 2 3 10
8P GAIN WILD-TYPE 81 71 113 54 60 82

Figure S87.  Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0012

Table S88.  Gene #15: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
8Q GAIN MUTATED 32 17 6
8Q GAIN WILD-TYPE 195 94 169

Figure S88.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00036

Table S89.  Gene #15: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
8Q GAIN MUTATED 38 7 8 2
8Q GAIN WILD-TYPE 171 127 149 11

Figure S89.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q gain' versus 'RPPA_CNMF'

P value = 0.00758 (Fisher's exact test), Q value = 0.024

Table S90.  Gene #15: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
8Q GAIN MUTATED 14 14 11 4
8Q GAIN WILD-TYPE 77 81 114 111

Figure S90.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'8q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0436 (Fisher's exact test), Q value = 0.096

Table S91.  Gene #15: '8q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
8Q GAIN MUTATED 12 9 22
8Q GAIN WILD-TYPE 71 149 163

Figure S91.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 0.0014 (Fisher's exact test), Q value = 0.0059

Table S92.  Gene #15: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
8Q GAIN MUTATED 26 9 4 12 4
8Q GAIN WILD-TYPE 104 106 101 121 26

Figure S92.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00068 (Fisher's exact test), Q value = 0.0033

Table S93.  Gene #15: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
8Q GAIN MUTATED 27 3 2 9 3 6 5
8Q GAIN WILD-TYPE 108 68 34 59 87 35 67

Figure S93.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-04 (Fisher's exact test), Q value = 0.003

Table S94.  Gene #15: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
8Q GAIN MUTATED 21 8 6 2 3 14
8Q GAIN WILD-TYPE 78 69 112 54 60 78

Figure S94.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 0.00499 (Fisher's exact test), Q value = 0.017

Table S95.  Gene #16: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
9P GAIN MUTATED 8 8 1
9P GAIN WILD-TYPE 219 103 174

Figure S95.  Get High-res Image Gene #16: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 0.0305 (Fisher's exact test), Q value = 0.072

Table S96.  Gene #16: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
9P GAIN MUTATED 6 7 2 2
9P GAIN WILD-TYPE 203 127 155 11

Figure S96.  Get High-res Image Gene #16: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p gain' versus 'RPPA_CNMF'

P value = 0.0372 (Fisher's exact test), Q value = 0.085

Table S97.  Gene #16: '9p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
9P GAIN MUTATED 4 7 1 2
9P GAIN WILD-TYPE 87 88 124 113

Figure S97.  Get High-res Image Gene #16: '9p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'9p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0279 (Fisher's exact test), Q value = 0.067

Table S98.  Gene #16: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
9P GAIN MUTATED 4 5 8
9P GAIN WILD-TYPE 218 179 95

Figure S98.  Get High-res Image Gene #16: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 0.00689 (Fisher's exact test), Q value = 0.022

Table S99.  Gene #17: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
9Q GAIN MUTATED 10 11 3
9Q GAIN WILD-TYPE 217 100 172

Figure S99.  Get High-res Image Gene #17: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

'9q gain' versus 'METHLYATION_CNMF'

P value = 0.00233 (Fisher's exact test), Q value = 0.0091

Table S100.  Gene #17: '9q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
9Q GAIN MUTATED 10 7 3 4
9Q GAIN WILD-TYPE 199 127 154 9

Figure S100.  Get High-res Image Gene #17: '9q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q gain' versus 'RPPA_CNMF'

P value = 0.00694 (Fisher's exact test), Q value = 0.022

Table S101.  Gene #17: '9q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
9Q GAIN MUTATED 5 10 2 2
9Q GAIN WILD-TYPE 86 85 123 113

Figure S101.  Get High-res Image Gene #17: '9q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'9q gain' versus 'MRNASEQ_CNMF'

P value = 0.0433 (Fisher's exact test), Q value = 0.095

Table S102.  Gene #17: '9q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
9Q GAIN MUTATED 3 12 3 5 1
9Q GAIN WILD-TYPE 127 103 102 128 29

Figure S102.  Get High-res Image Gene #17: '9q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00472 (Fisher's exact test), Q value = 0.016

Table S103.  Gene #17: '9q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
9Q GAIN MUTATED 3 5 1 5 2 7 1
9Q GAIN WILD-TYPE 132 66 35 63 88 34 71

Figure S103.  Get High-res Image Gene #17: '9q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0105 (Fisher's exact test), Q value = 0.031

Table S104.  Gene #17: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
9Q GAIN MUTATED 6 7 11
9Q GAIN WILD-TYPE 216 177 92

Figure S104.  Get High-res Image Gene #17: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0423 (Fisher's exact test), Q value = 0.094

Table S105.  Gene #18: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 7 7 6
10P GAIN MUTATED 0 3 0 0
10P GAIN WILD-TYPE 7 4 7 6

Figure S105.  Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S106.  Gene #18: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
10P GAIN MUTATED 48 9 0
10P GAIN WILD-TYPE 179 102 175

Figure S106.  Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S107.  Gene #18: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
10P GAIN MUTATED 47 3 0 7
10P GAIN WILD-TYPE 162 131 157 6

Figure S107.  Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p gain' versus 'RPPA_CNMF'

P value = 0.00748 (Fisher's exact test), Q value = 0.023

Table S108.  Gene #18: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
10P GAIN MUTATED 16 10 14 4
10P GAIN WILD-TYPE 75 85 111 111

Figure S108.  Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'10p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00185 (Fisher's exact test), Q value = 0.0075

Table S109.  Gene #18: '10p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
10P GAIN MUTATED 15 7 22
10P GAIN WILD-TYPE 68 151 163

Figure S109.  Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S110.  Gene #18: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
10P GAIN MUTATED 25 16 0 13 3
10P GAIN WILD-TYPE 105 99 105 120 27

Figure S110.  Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S111.  Gene #18: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
10P GAIN MUTATED 29 0 0 11 0 14 3
10P GAIN WILD-TYPE 106 71 36 57 90 27 69

Figure S111.  Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_CNMF'

P value = 0.0273 (Fisher's exact test), Q value = 0.066

Table S112.  Gene #18: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
10P GAIN MUTATED 16 20 5 15
10P GAIN WILD-TYPE 124 87 77 165

Figure S112.  Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0179 (Fisher's exact test), Q value = 0.048

Table S113.  Gene #18: '10p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
10P GAIN MUTATED 18 20 6 12
10P GAIN WILD-TYPE 109 99 99 142

Figure S113.  Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S114.  Gene #18: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
10P GAIN MUTATED 21 17 7 0 0 11
10P GAIN WILD-TYPE 78 60 111 56 63 81

Figure S114.  Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.036

Table S115.  Gene #19: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
10Q GAIN MUTATED 9 2 0
10Q GAIN WILD-TYPE 218 109 175

Figure S115.  Get High-res Image Gene #19: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10q gain' versus 'METHLYATION_CNMF'

P value = 0.00116 (Fisher's exact test), Q value = 0.005

Table S116.  Gene #19: '10q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
10Q GAIN MUTATED 8 1 0 2
10Q GAIN WILD-TYPE 201 133 157 11

Figure S116.  Get High-res Image Gene #19: '10q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0398 (Fisher's exact test), Q value = 0.089

Table S117.  Gene #19: '10q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
10Q GAIN MUTATED 1 1 9
10Q GAIN WILD-TYPE 82 157 176

Figure S117.  Get High-res Image Gene #19: '10q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.0015

Table S118.  Gene #19: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
10Q GAIN MUTATED 2 0 0 4 0 5 0
10Q GAIN WILD-TYPE 133 71 36 64 90 36 72

Figure S118.  Get High-res Image Gene #19: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00148 (Fisher's exact test), Q value = 0.0061

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
10Q GAIN MUTATED 0 7 2 0 0 2
10Q GAIN WILD-TYPE 99 70 116 56 63 90

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

'11p gain' versus 'CN_CNMF'

P value = 0.00432 (Fisher's exact test), Q value = 0.015

Table S120.  Gene #20: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
11P GAIN MUTATED 5 10 15
11P GAIN WILD-TYPE 222 101 160

Figure S120.  Get High-res Image Gene #20: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0016

Table S121.  Gene #20: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
11P GAIN MUTATED 8 2 20 0
11P GAIN WILD-TYPE 201 132 137 13

Figure S121.  Get High-res Image Gene #20: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p gain' versus 'MRNASEQ_CNMF'

P value = 0.00681 (Fisher's exact test), Q value = 0.022

Table S122.  Gene #20: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
11P GAIN MUTATED 7 1 13 7 2
11P GAIN WILD-TYPE 123 114 92 126 28

Figure S122.  Get High-res Image Gene #20: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00857 (Fisher's exact test), Q value = 0.026

Table S123.  Gene #20: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
11P GAIN MUTATED 6 0 6 3 9 1 5
11P GAIN WILD-TYPE 129 71 30 65 81 40 67

Figure S123.  Get High-res Image Gene #20: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_CNMF'

P value = 0.0377 (Fisher's exact test), Q value = 0.085

Table S124.  Gene #20: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
11P GAIN MUTATED 6 4 11 9
11P GAIN WILD-TYPE 134 103 71 171

Figure S124.  Get High-res Image Gene #20: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0265 (Fisher's exact test), Q value = 0.065

Table S125.  Gene #20: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
11P GAIN MUTATED 14 15 1
11P GAIN WILD-TYPE 208 169 102

Figure S125.  Get High-res Image Gene #20: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00749 (Fisher's exact test), Q value = 0.023

Table S126.  Gene #20: '11p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
11P GAIN MUTATED 4 2 7 8 0 9
11P GAIN WILD-TYPE 95 75 111 48 63 83

Figure S126.  Get High-res Image Gene #20: '11p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q gain' versus 'METHLYATION_CNMF'

P value = 0.00414 (Fisher's exact test), Q value = 0.015

Table S127.  Gene #21: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
11Q GAIN MUTATED 28 5 24 1
11Q GAIN WILD-TYPE 181 129 133 12

Figure S127.  Get High-res Image Gene #21: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 0.0463 (Fisher's exact test), Q value = 0.1

Table S128.  Gene #21: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
11Q GAIN MUTATED 16 5 17 16 4
11Q GAIN WILD-TYPE 114 110 88 117 26

Figure S128.  Get High-res Image Gene #21: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0468 (Fisher's exact test), Q value = 0.1

Table S129.  Gene #21: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
11Q GAIN MUTATED 30 23 5
11Q GAIN WILD-TYPE 192 161 98

Figure S129.  Get High-res Image Gene #21: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0277 (Fisher's exact test), Q value = 0.067

Table S130.  Gene #21: '11q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
11Q GAIN MUTATED 12 8 12 10 1 15
11Q GAIN WILD-TYPE 87 69 106 46 62 77

Figure S130.  Get High-res Image Gene #21: '11q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00029

Table S131.  Gene #22: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
12P GAIN MUTATED 15 15 2
12P GAIN WILD-TYPE 212 96 173

Figure S131.  Get High-res Image Gene #22: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 0.0259 (Fisher's exact test), Q value = 0.064

Table S132.  Gene #22: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
12P GAIN MUTATED 21 7 4 0
12P GAIN WILD-TYPE 188 127 153 13

Figure S132.  Get High-res Image Gene #22: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0421 (Fisher's exact test), Q value = 0.094

Table S133.  Gene #22: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
12P GAIN MUTATED 12 6 1 6 3 4 0
12P GAIN WILD-TYPE 123 65 35 62 87 37 72

Figure S133.  Get High-res Image Gene #22: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 0.0477 (Fisher's exact test), Q value = 0.1

Table S134.  Gene #22: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
12P GAIN MUTATED 11 11 5 5
12P GAIN WILD-TYPE 129 96 77 175

Figure S134.  Get High-res Image Gene #22: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0278 (Fisher's exact test), Q value = 0.067

Table S135.  Gene #22: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
12P GAIN MUTATED 17 5 10
12P GAIN WILD-TYPE 205 179 93

Figure S135.  Get High-res Image Gene #22: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0227 (Fisher's exact test), Q value = 0.058

Table S136.  Gene #22: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
12P GAIN MUTATED 6 7 1 3 5 10
12P GAIN WILD-TYPE 93 70 117 53 58 82

Figure S136.  Get High-res Image Gene #22: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00016

Table S137.  Gene #23: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
12Q GAIN MUTATED 4 11 0
12Q GAIN WILD-TYPE 223 100 175

Figure S137.  Get High-res Image Gene #23: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'RPPA_CNMF'

P value = 0.0048 (Fisher's exact test), Q value = 0.016

Table S138.  Gene #23: '12q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
12Q GAIN MUTATED 3 8 1 1
12Q GAIN WILD-TYPE 88 87 124 114

Figure S138.  Get High-res Image Gene #23: '12q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 0.00503 (Fisher's exact test), Q value = 0.017

Table S139.  Gene #23: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
12Q GAIN MUTATED 4 9 2 0 0
12Q GAIN WILD-TYPE 126 106 103 133 30

Figure S139.  Get High-res Image Gene #23: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0279 (Fisher's exact test), Q value = 0.067

Table S140.  Gene #23: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
12Q GAIN MUTATED 6 2 7
12Q GAIN WILD-TYPE 216 182 96

Figure S140.  Get High-res Image Gene #23: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0153 (Fisher's exact test), Q value = 0.043

Table S141.  Gene #23: '12q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
12Q GAIN MUTATED 2 2 0 2 6 3
12Q GAIN WILD-TYPE 97 75 118 54 57 89

Figure S141.  Get High-res Image Gene #23: '12q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0245 (Fisher's exact test), Q value = 0.061

Table S142.  Gene #25: '14q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
14Q GAIN MUTATED 0 0 0 2 0 2
14Q GAIN WILD-TYPE 99 77 118 54 63 90

Figure S142.  Get High-res Image Gene #25: '14q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q gain' versus 'CN_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.033

Table S143.  Gene #26: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
15Q GAIN MUTATED 6 5 0
15Q GAIN WILD-TYPE 221 106 175

Figure S143.  Get High-res Image Gene #26: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

'15q gain' versus 'METHLYATION_CNMF'

P value = 0.0319 (Fisher's exact test), Q value = 0.074

Table S144.  Gene #26: '15q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
15Q GAIN MUTATED 7 3 0 1
15Q GAIN WILD-TYPE 202 131 157 12

Figure S144.  Get High-res Image Gene #26: '15q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q gain' versus 'RPPA_CNMF'

P value = 0.00893 (Fisher's exact test), Q value = 0.027

Table S145.  Gene #26: '15q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
15Q GAIN MUTATED 0 4 6 0
15Q GAIN WILD-TYPE 91 91 119 115

Figure S145.  Get High-res Image Gene #26: '15q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'15q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0126 (Fisher's exact test), Q value = 0.036

Table S146.  Gene #26: '15q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
15Q GAIN MUTATED 0 1 9
15Q GAIN WILD-TYPE 83 157 176

Figure S146.  Get High-res Image Gene #26: '15q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'15q gain' versus 'MRNASEQ_CNMF'

P value = 0.047 (Fisher's exact test), Q value = 0.1

Table S147.  Gene #26: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
15Q GAIN MUTATED 4 6 0 1 0
15Q GAIN WILD-TYPE 126 109 105 132 30

Figure S147.  Get High-res Image Gene #26: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0197 (Fisher's exact test), Q value = 0.051

Table S148.  Gene #26: '15q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
15Q GAIN MUTATED 4 6 0 1
15Q GAIN WILD-TYPE 123 113 105 153

Figure S148.  Get High-res Image Gene #26: '15q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00235 (Fisher's exact test), Q value = 0.0091

Table S149.  Gene #27: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
16P GAIN MUTATED 1 1 2 3 1 6 2
16P GAIN WILD-TYPE 134 70 34 65 89 35 70

Figure S149.  Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0376 (Fisher's exact test), Q value = 0.085

Table S150.  Gene #27: '16p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
16P GAIN MUTATED 1 5 4 0 0 6
16P GAIN WILD-TYPE 98 72 114 56 63 86

Figure S150.  Get High-res Image Gene #27: '16p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 0.00679 (Fisher's exact test), Q value = 0.022

Table S151.  Gene #28: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
16Q GAIN MUTATED 6 10 3
16Q GAIN WILD-TYPE 221 101 172

Figure S151.  Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.0022

Table S152.  Gene #28: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
16Q GAIN MUTATED 2 1 1 3 1 8 3
16Q GAIN WILD-TYPE 133 70 35 65 89 33 69

Figure S152.  Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CNMF'

P value = 0.0485 (Fisher's exact test), Q value = 0.1

Table S153.  Gene #28: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
16Q GAIN MUTATED 1 7 2 9
16Q GAIN WILD-TYPE 139 100 80 171

Figure S153.  Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0307 (Fisher's exact test), Q value = 0.072

Table S154.  Gene #28: '16q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
16Q GAIN MUTATED 2 7 5 0 0 5
16Q GAIN WILD-TYPE 97 70 113 56 63 87

Figure S154.  Get High-res Image Gene #28: '16q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 0.037

Table S155.  Gene #29: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
17P GAIN MUTATED 5 10 5
17P GAIN WILD-TYPE 222 101 170

Figure S155.  Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17p gain' versus 'RPPA_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.044

Table S156.  Gene #29: '17p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
17P GAIN MUTATED 3 8 2 1
17P GAIN WILD-TYPE 88 87 123 114

Figure S156.  Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'17q gain' versus 'RPPA_CNMF'

P value = 0.0126 (Fisher's exact test), Q value = 0.036

Table S157.  Gene #30: '17q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
17Q GAIN MUTATED 5 8 2 1
17Q GAIN WILD-TYPE 86 87 123 114

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

'17q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0244 (Fisher's exact test), Q value = 0.061

Table S158.  Gene #30: '17q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
17Q GAIN MUTATED 7 2 7
17Q GAIN WILD-TYPE 76 156 178

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

'18p gain' versus 'CN_CNMF'

P value = 0.0065 (Fisher's exact test), Q value = 0.021

Table S159.  Gene #31: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
18P GAIN MUTATED 9 8 1
18P GAIN WILD-TYPE 218 103 174

Figure S159.  Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0014

Table S160.  Gene #31: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
18P GAIN MUTATED 8 5 1 4
18P GAIN WILD-TYPE 201 129 156 9

Figure S160.  Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 0.00563 (Fisher's exact test), Q value = 0.019

Table S161.  Gene #31: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
18P GAIN MUTATED 2 8 0 5 3
18P GAIN WILD-TYPE 128 107 105 128 27

Figure S161.  Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.022 (Fisher's exact test), Q value = 0.056

Table S162.  Gene #31: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
18P GAIN MUTATED 4 4 0 3 0 5 2
18P GAIN WILD-TYPE 131 67 36 65 90 36 70

Figure S162.  Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0226 (Fisher's exact test), Q value = 0.058

Table S163.  Gene #31: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
18P GAIN MUTATED 2 8 2 0 3 3
18P GAIN WILD-TYPE 97 69 116 56 60 89

Figure S163.  Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 0.00183 (Fisher's exact test), Q value = 0.0074

Table S164.  Gene #32: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
18Q GAIN MUTATED 6 7 0
18Q GAIN WILD-TYPE 221 104 175

Figure S164.  Get High-res Image Gene #32: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00016

Table S165.  Gene #32: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
18Q GAIN MUTATED 3 6 0 4
18Q GAIN WILD-TYPE 206 128 157 9

Figure S165.  Get High-res Image Gene #32: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0015

Table S166.  Gene #32: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
18Q GAIN MUTATED 1 9 0 1 2
18Q GAIN WILD-TYPE 129 106 105 132 28

Figure S166.  Get High-res Image Gene #32: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00048 (Fisher's exact test), Q value = 0.0024

Table S167.  Gene #32: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
18Q GAIN MUTATED 2 5 0 0 0 5 1
18Q GAIN WILD-TYPE 133 66 36 68 90 36 71

Figure S167.  Get High-res Image Gene #32: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0174 (Fisher's exact test), Q value = 0.046

Table S168.  Gene #32: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
18Q GAIN MUTATED 4 2 7
18Q GAIN WILD-TYPE 218 182 96

Figure S168.  Get High-res Image Gene #32: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0292 (Fisher's exact test), Q value = 0.07

Table S169.  Gene #32: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
18Q GAIN MUTATED 2 8 1 2
18Q GAIN WILD-TYPE 125 111 104 152

Figure S169.  Get High-res Image Gene #32: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00679 (Fisher's exact test), Q value = 0.022

Table S170.  Gene #32: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
18Q GAIN MUTATED 1 6 1 0 4 1
18Q GAIN WILD-TYPE 98 71 117 56 59 91

Figure S170.  Get High-res Image Gene #32: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S171.  Gene #33: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
19P GAIN MUTATED 20 25 54
19P GAIN WILD-TYPE 207 86 121

Figure S171.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S172.  Gene #33: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
19P GAIN MUTATED 10 30 59 0
19P GAIN WILD-TYPE 199 104 98 13

Figure S172.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00389 (Fisher's exact test), Q value = 0.014

Table S173.  Gene #33: '19p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
19P GAIN MUTATED 10 24 50
19P GAIN WILD-TYPE 73 134 135

Figure S173.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S174.  Gene #33: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
19P GAIN MUTATED 5 30 42 21 1
19P GAIN WILD-TYPE 125 85 63 112 29

Figure S174.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S175.  Gene #33: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
19P GAIN MUTATED 6 25 14 7 30 3 14
19P GAIN WILD-TYPE 129 46 22 61 60 38 58

Figure S175.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 0.0024 (Fisher's exact test), Q value = 0.0093

Table S176.  Gene #33: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
19P GAIN MUTATED 21 18 29 31
19P GAIN WILD-TYPE 119 89 53 149

Figure S176.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0012

Table S177.  Gene #33: '19p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
19P GAIN MUTATED 14 24 36 25
19P GAIN WILD-TYPE 113 95 69 129

Figure S177.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S178.  Gene #33: '19p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
19P GAIN MUTATED 8 9 21 24 23 14
19P GAIN WILD-TYPE 91 68 97 32 40 78

Figure S178.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S179.  Gene #34: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
19Q GAIN MUTATED 11 14 0
19Q GAIN WILD-TYPE 216 97 175

Figure S179.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S180.  Gene #34: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
19Q GAIN MUTATED 2 23 0 0
19Q GAIN WILD-TYPE 207 111 157 13

Figure S180.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0138 (Fisher's exact test), Q value = 0.039

Table S181.  Gene #34: '19q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
19Q GAIN MUTATED 1 3 14
19Q GAIN WILD-TYPE 82 155 171

Figure S181.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S182.  Gene #34: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
19Q GAIN MUTATED 1 19 0 4 1
19Q GAIN WILD-TYPE 129 96 105 129 29

Figure S182.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S183.  Gene #34: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
19Q GAIN MUTATED 2 19 0 4 0 0 0
19Q GAIN WILD-TYPE 133 52 36 64 90 41 72

Figure S183.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 0.00247 (Fisher's exact test), Q value = 0.0095

Table S184.  Gene #34: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
19Q GAIN MUTATED 7 12 0 6
19Q GAIN WILD-TYPE 133 95 82 174

Figure S184.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S185.  Gene #34: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
19Q GAIN MUTATED 3 2 20
19Q GAIN WILD-TYPE 219 182 83

Figure S185.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00082

Table S186.  Gene #34: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
19Q GAIN MUTATED 7 14 0 4
19Q GAIN WILD-TYPE 120 105 105 150

Figure S186.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S187.  Gene #34: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
19Q GAIN MUTATED 2 0 3 0 19 1
19Q GAIN WILD-TYPE 97 77 115 56 44 91

Figure S187.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S188.  Gene #35: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
20P GAIN MUTATED 15 28 2
20P GAIN WILD-TYPE 212 83 173

Figure S188.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S189.  Gene #35: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
20P GAIN MUTATED 6 31 6 2
20P GAIN WILD-TYPE 203 103 151 11

Figure S189.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'RPPA_CNMF'

P value = 0.00484 (Fisher's exact test), Q value = 0.017

Table S190.  Gene #35: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
20P GAIN MUTATED 9 17 7 5
20P GAIN WILD-TYPE 82 78 118 110

Figure S190.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0154 (Fisher's exact test), Q value = 0.043

Table S191.  Gene #35: '20p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
20P GAIN MUTATED 5 8 25
20P GAIN WILD-TYPE 78 150 160

Figure S191.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S192.  Gene #35: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
20P GAIN MUTATED 3 30 3 8 1
20P GAIN WILD-TYPE 127 85 102 125 29

Figure S192.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S193.  Gene #35: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
20P GAIN MUTATED 3 23 2 8 2 5 2
20P GAIN WILD-TYPE 132 48 34 60 88 36 70

Figure S193.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S194.  Gene #35: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
20P GAIN MUTATED 9 10 26
20P GAIN WILD-TYPE 213 174 77

Figure S194.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0015

Table S195.  Gene #35: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
20P GAIN MUTATED 14 19 1 11
20P GAIN WILD-TYPE 113 100 104 143

Figure S195.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S196.  Gene #35: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
20P GAIN MUTATED 4 4 9 2 21 5
20P GAIN WILD-TYPE 95 73 109 54 42 87

Figure S196.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S197.  Gene #36: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
20Q GAIN MUTATED 16 26 2
20Q GAIN WILD-TYPE 211 85 173

Figure S197.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S198.  Gene #36: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
20Q GAIN MUTATED 6 30 6 2
20Q GAIN WILD-TYPE 203 104 151 11

Figure S198.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 7e-04 (Fisher's exact test), Q value = 0.0034

Table S199.  Gene #36: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
20Q GAIN MUTATED 9 17 7 3
20Q GAIN WILD-TYPE 82 78 118 112

Figure S199.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00369 (Fisher's exact test), Q value = 0.013

Table S200.  Gene #36: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
20Q GAIN MUTATED 5 6 25
20Q GAIN WILD-TYPE 78 152 160

Figure S200.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S201.  Gene #36: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
20Q GAIN MUTATED 4 30 3 6 1
20Q GAIN WILD-TYPE 126 85 102 127 29

Figure S201.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S202.  Gene #36: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
20Q GAIN MUTATED 4 23 2 7 2 5 1
20Q GAIN WILD-TYPE 131 48 34 61 88 36 71

Figure S202.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 0.0452 (Fisher's exact test), Q value = 0.098

Table S203.  Gene #36: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
20Q GAIN MUTATED 17 13 3 11
20Q GAIN WILD-TYPE 123 94 79 169

Figure S203.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S204.  Gene #36: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
20Q GAIN MUTATED 10 8 26
20Q GAIN WILD-TYPE 212 176 77

Figure S204.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00061

Table S205.  Gene #36: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
20Q GAIN MUTATED 16 18 1 9
20Q GAIN WILD-TYPE 111 101 104 145

Figure S205.  Get High-res Image Gene #36: '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 = 8.6e-05

Table S206.  Gene #36: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
20Q GAIN MUTATED 6 3 7 2 21 5
20Q GAIN WILD-TYPE 93 74 111 54 42 87

Figure S206.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.0023

Table S207.  Gene #37: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
21Q GAIN MUTATED 4 13 6
21Q GAIN WILD-TYPE 223 98 169

Figure S207.  Get High-res Image Gene #37: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 0.00086 (Fisher's exact test), Q value = 0.004

Table S208.  Gene #38: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
22Q GAIN MUTATED 3 4 16
22Q GAIN WILD-TYPE 224 107 159

Figure S208.  Get High-res Image Gene #38: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S209.  Gene #38: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
22Q GAIN MUTATED 1 3 18 1
22Q GAIN WILD-TYPE 208 131 139 12

Figure S209.  Get High-res Image Gene #38: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 0.00081 (Fisher's exact test), Q value = 0.0038

Table S210.  Gene #38: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
22Q GAIN MUTATED 1 4 13 5 0
22Q GAIN WILD-TYPE 129 111 92 128 30

Figure S210.  Get High-res Image Gene #38: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00048 (Fisher's exact test), Q value = 0.0024

Table S211.  Gene #38: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
22Q GAIN MUTATED 0 2 6 2 7 2 4
22Q GAIN WILD-TYPE 135 69 30 66 83 39 68

Figure S211.  Get High-res Image Gene #38: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CNMF'

P value = 0.0453 (Fisher's exact test), Q value = 0.098

Table S212.  Gene #38: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
22Q GAIN MUTATED 4 3 9 7
22Q GAIN WILD-TYPE 136 104 73 173

Figure S212.  Get High-res Image Gene #38: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.0023

Table S213.  Gene #38: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
22Q GAIN MUTATED 1 2 12 8
22Q GAIN WILD-TYPE 126 117 93 146

Figure S213.  Get High-res Image Gene #38: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00177 (Fisher's exact test), Q value = 0.0072

Table S214.  Gene #38: '22q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
22Q GAIN MUTATED 1 1 3 7 2 9
22Q GAIN WILD-TYPE 98 76 115 49 61 83

Figure S214.  Get High-res Image Gene #38: '22q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp gain' versus 'CN_CNMF'

P value = 0.00284 (Fisher's exact test), Q value = 0.011

Table S215.  Gene #39: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
XP GAIN MUTATED 13 8 1
XP GAIN WILD-TYPE 214 103 174

Figure S215.  Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

'xp gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S216.  Gene #39: 'xp gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
XP GAIN MUTATED 18 2 0 2
XP GAIN WILD-TYPE 191 132 157 11

Figure S216.  Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xp gain' versus 'MRNASEQ_CNMF'

P value = 0.0295 (Fisher's exact test), Q value = 0.07

Table S217.  Gene #39: 'xp gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
XP GAIN MUTATED 10 4 0 7 1
XP GAIN WILD-TYPE 120 111 105 126 29

Figure S217.  Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xp gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0187 (Fisher's exact test), Q value = 0.049

Table S218.  Gene #39: 'xp gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
XP GAIN MUTATED 9 2 0 7 0 2 2
XP GAIN WILD-TYPE 126 69 36 61 90 39 70

Figure S218.  Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S219.  Gene #40: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
XQ GAIN MUTATED 29 12 1
XQ GAIN WILD-TYPE 198 99 174

Figure S219.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S220.  Gene #40: 'xq gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
XQ GAIN MUTATED 34 6 0 2
XQ GAIN WILD-TYPE 175 128 157 11

Figure S220.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq gain' versus 'RPPA_CNMF'

P value = 0.0262 (Fisher's exact test), Q value = 0.064

Table S221.  Gene #40: 'xq gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
XQ GAIN MUTATED 10 7 15 3
XQ GAIN WILD-TYPE 81 88 110 112

Figure S221.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'xq gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0249 (Fisher's exact test), Q value = 0.062

Table S222.  Gene #40: 'xq gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
XQ GAIN MUTATED 10 6 19
XQ GAIN WILD-TYPE 73 152 166

Figure S222.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00082

Table S223.  Gene #40: 'xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
XQ GAIN MUTATED 18 9 0 10 5
XQ GAIN WILD-TYPE 112 106 105 123 25

Figure S223.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S224.  Gene #40: 'xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
XQ GAIN MUTATED 24 3 0 8 0 4 3
XQ GAIN WILD-TYPE 111 68 36 60 90 37 69

Figure S224.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.03

Table S225.  Gene #40: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
XQ GAIN MUTATED 18 10 1 12
XQ GAIN WILD-TYPE 122 97 81 168

Figure S225.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0366 (Fisher's exact test), Q value = 0.084

Table S226.  Gene #40: 'xq gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
XQ GAIN MUTATED 15 13 3 10
XQ GAIN WILD-TYPE 112 106 102 144

Figure S226.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00196 (Fisher's exact test), Q value = 0.0078

Table S227.  Gene #40: 'xq gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
XQ GAIN MUTATED 16 7 5 0 3 10
XQ GAIN WILD-TYPE 83 70 113 56 60 82

Figure S227.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'MRNA_CNMF'

P value = 0.029 (Fisher's exact test), Q value = 0.069

Table S228.  Gene #41: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 9 10 8
1P LOSS MUTATED 1 7 2
1P LOSS WILD-TYPE 8 3 6

Figure S228.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00098

Table S229.  Gene #41: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 7 7 6
1P LOSS MUTATED 0 1 7 2
1P LOSS WILD-TYPE 7 6 0 4

Figure S229.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S230.  Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
1P LOSS MUTATED 7 12 165
1P LOSS WILD-TYPE 220 99 10

Figure S230.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S231.  Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
1P LOSS MUTATED 5 23 156 0
1P LOSS WILD-TYPE 204 111 1 13

Figure S231.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'RPPA_CNMF'

P value = 0.00312 (Fisher's exact test), Q value = 0.011

Table S232.  Gene #41: '1p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
1P LOSS MUTATED 24 31 47 58
1P LOSS WILD-TYPE 67 64 78 57

Figure S232.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'1p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00106 (Fisher's exact test), Q value = 0.0047

Table S233.  Gene #41: '1p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
1P LOSS MUTATED 23 77 60
1P LOSS WILD-TYPE 60 81 125

Figure S233.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S234.  Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
1P LOSS MUTATED 3 10 104 58 9
1P LOSS WILD-TYPE 127 105 1 75 21

Figure S234.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S235.  Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
1P LOSS MUTATED 3 6 36 1 87 1 50
1P LOSS WILD-TYPE 132 65 0 67 3 40 22

Figure S235.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S236.  Gene #41: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
1P LOSS MUTATED 27 8 68 81
1P LOSS WILD-TYPE 113 99 14 99

Figure S236.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S237.  Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
1P LOSS MUTATED 80 97 7
1P LOSS WILD-TYPE 142 87 96

Figure S237.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S238.  Gene #41: '1p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
1P LOSS MUTATED 16 17 83 68
1P LOSS WILD-TYPE 111 102 22 86

Figure S238.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S239.  Gene #41: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
1P LOSS MUTATED 6 25 59 55 4 35
1P LOSS WILD-TYPE 93 52 59 1 59 57

Figure S239.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00877 (Fisher's exact test), Q value = 0.027

Table S240.  Gene #42: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
1Q LOSS MUTATED 4 3 5 0 5 1 8
1Q LOSS WILD-TYPE 131 68 31 68 85 40 64

Figure S240.  Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 0.0252 (Fisher's exact test), Q value = 0.063

Table S241.  Gene #43: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
2P LOSS MUTATED 14 5 2
2P LOSS WILD-TYPE 213 106 173

Figure S241.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 0.0351 (Fisher's exact test), Q value = 0.081

Table S242.  Gene #43: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
2P LOSS MUTATED 11 6 2 2
2P LOSS WILD-TYPE 198 128 155 11

Figure S242.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0439 (Fisher's exact test), Q value = 0.096

Table S243.  Gene #43: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
2P LOSS MUTATED 6 4 0 2 2 6 1
2P LOSS WILD-TYPE 129 67 36 66 88 35 71

Figure S243.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.043

Table S244.  Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
2Q LOSS MUTATED 14 2 2
2Q LOSS WILD-TYPE 213 109 173

Figure S244.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 0.00863 (Fisher's exact test), Q value = 0.026

Table S245.  Gene #44: '2q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
2Q LOSS MUTATED 12 2 2 2
2Q LOSS WILD-TYPE 197 132 155 11

Figure S245.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2q loss' versus 'RPPA_CNMF'

P value = 0.0479 (Fisher's exact test), Q value = 0.1

Table S246.  Gene #44: '2q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
2Q LOSS MUTATED 2 9 3 3
2Q LOSS WILD-TYPE 89 86 122 112

Figure S246.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00186 (Fisher's exact test), Q value = 0.0075

Table S247.  Gene #44: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
2Q LOSS MUTATED 5 1 0 3 2 7 0
2Q LOSS WILD-TYPE 130 70 36 65 88 34 72

Figure S247.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 0.0257 (Fisher's exact test), Q value = 0.063

Table S248.  Gene #44: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
2Q LOSS MUTATED 3 9 2 3
2Q LOSS WILD-TYPE 137 98 80 177

Figure S248.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00206 (Fisher's exact test), Q value = 0.0082

Table S249.  Gene #44: '2q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
2Q LOSS MUTATED 1 9 2 1 0 3
2Q LOSS WILD-TYPE 98 68 116 55 63 89

Figure S249.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 0.0231 (Fisher's exact test), Q value = 0.058

Table S250.  Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
3P LOSS MUTATED 13 12 5
3P LOSS WILD-TYPE 214 99 170

Figure S250.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'RPPA_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.033

Table S251.  Gene #45: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
3P LOSS MUTATED 4 13 6 3
3P LOSS WILD-TYPE 87 82 119 112

Figure S251.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 0.00105 (Fisher's exact test), Q value = 0.0047

Table S252.  Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
3P LOSS MUTATED 9 14 4 3
3P LOSS WILD-TYPE 131 93 78 177

Figure S252.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.0021

Table S253.  Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
3P LOSS MUTATED 18 2 10
3P LOSS WILD-TYPE 204 182 93

Figure S253.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0317 (Fisher's exact test), Q value = 0.074

Table S254.  Gene #46: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
3Q LOSS MUTATED 9 4 1 4 2 7 1
3Q LOSS WILD-TYPE 126 67 35 64 88 34 71

Figure S254.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0165 (Fisher's exact test), Q value = 0.045

Table S255.  Gene #46: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
3Q LOSS MUTATED 14 4 10
3Q LOSS WILD-TYPE 208 180 93

Figure S255.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0158 (Fisher's exact test), Q value = 0.043

Table S256.  Gene #46: '3q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
3Q LOSS MUTATED 8 10 2 2 2 3
3Q LOSS WILD-TYPE 91 67 116 54 61 89

Figure S256.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S257.  Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
4P LOSS MUTATED 12 16 44
4P LOSS WILD-TYPE 215 95 131

Figure S257.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S258.  Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
4P LOSS MUTATED 24 3 44 1
4P LOSS WILD-TYPE 185 131 113 12

Figure S258.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'RPPA_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.034

Table S259.  Gene #47: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
4P LOSS MUTATED 6 21 20 12
4P LOSS WILD-TYPE 85 74 105 103

Figure S259.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00077

Table S260.  Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
4P LOSS MUTATED 16 6 29 18 3
4P LOSS WILD-TYPE 114 109 76 115 27

Figure S260.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S261.  Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
4P LOSS MUTATED 14 2 14 7 23 3 9
4P LOSS WILD-TYPE 121 69 22 61 67 38 63

Figure S261.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00048

Table S262.  Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
4P LOSS MUTATED 13 12 26 21
4P LOSS WILD-TYPE 127 95 56 159

Figure S262.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00105 (Fisher's exact test), Q value = 0.0047

Table S263.  Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
4P LOSS MUTATED 39 29 4
4P LOSS WILD-TYPE 183 155 99

Figure S263.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.0028

Table S264.  Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
4P LOSS MUTATED 11 11 28 22
4P LOSS WILD-TYPE 116 108 77 132

Figure S264.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S265.  Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
4P LOSS MUTATED 7 13 13 18 1 20
4P LOSS WILD-TYPE 92 64 105 38 62 72

Figure S265.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S266.  Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
4Q LOSS MUTATED 24 21 49
4Q LOSS WILD-TYPE 203 90 126

Figure S266.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S267.  Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
4Q LOSS MUTATED 37 8 47 2
4Q LOSS WILD-TYPE 172 126 110 11

Figure S267.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'RPPA_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.049

Table S268.  Gene #48: '4q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
4Q LOSS MUTATED 8 25 23 21
4Q LOSS WILD-TYPE 83 70 102 94

Figure S268.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 0.00119 (Fisher's exact test), Q value = 0.0051

Table S269.  Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
4Q LOSS MUTATED 22 11 31 28 2
4Q LOSS WILD-TYPE 108 104 74 105 28

Figure S269.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S270.  Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
4Q LOSS MUTATED 19 2 15 11 24 8 15
4Q LOSS WILD-TYPE 116 69 21 57 66 33 57

Figure S270.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0024

Table S271.  Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
4Q LOSS MUTATED 14 18 27 35
4Q LOSS WILD-TYPE 126 89 55 145

Figure S271.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00347 (Fisher's exact test), Q value = 0.013

Table S272.  Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
4Q LOSS MUTATED 45 41 8
4Q LOSS WILD-TYPE 177 143 95

Figure S272.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0072 (Fisher's exact test), Q value = 0.023

Table S273.  Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
4Q LOSS MUTATED 16 16 30 32
4Q LOSS WILD-TYPE 111 103 75 122

Figure S273.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00016

Table S274.  Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
4Q LOSS MUTATED 9 18 20 18 2 27
4Q LOSS WILD-TYPE 90 59 98 38 61 65

Figure S274.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0025

Table S275.  Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
5P LOSS MUTATED 18 14 3
5P LOSS WILD-TYPE 209 97 172

Figure S275.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0015

Table S276.  Gene #49: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
5P LOSS MUTATED 24 7 2 2
5P LOSS WILD-TYPE 185 127 155 11

Figure S276.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 0.0405 (Fisher's exact test), Q value = 0.091

Table S277.  Gene #49: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
5P LOSS MUTATED 10 11 1 11 2
5P LOSS WILD-TYPE 120 104 104 122 28

Figure S277.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00106 (Fisher's exact test), Q value = 0.0047

Table S278.  Gene #49: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
5P LOSS MUTATED 10 2 0 8 2 9 4
5P LOSS WILD-TYPE 125 69 36 60 88 32 68

Figure S278.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00082

Table S279.  Gene #49: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
5P LOSS MUTATED 3 15 6 0 2 9
5P LOSS WILD-TYPE 96 62 112 56 61 83

Figure S279.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 0.00081 (Fisher's exact test), Q value = 0.0038

Table S280.  Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
5Q LOSS MUTATED 20 10 2
5Q LOSS WILD-TYPE 207 101 173

Figure S280.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00029

Table S281.  Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
5Q LOSS MUTATED 21 5 2 4
5Q LOSS WILD-TYPE 188 129 155 9

Figure S281.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'RPPA_CNMF'

P value = 0.0022 (Fisher's exact test), Q value = 0.0087

Table S282.  Gene #50: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
5Q LOSS MUTATED 6 14 6 2
5Q LOSS WILD-TYPE 85 81 119 113

Figure S282.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.039

Table S283.  Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
5Q LOSS MUTATED 10 13 1 6 2
5Q LOSS WILD-TYPE 120 102 104 127 28

Figure S283.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S284.  Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
5Q LOSS MUTATED 9 2 0 6 2 12 1
5Q LOSS WILD-TYPE 126 69 36 62 88 29 71

Figure S284.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00067

Table S285.  Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
5Q LOSS MUTATED 5 18 2 7
5Q LOSS WILD-TYPE 135 89 80 173

Figure S285.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0155 (Fisher's exact test), Q value = 0.043

Table S286.  Gene #50: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
5Q LOSS MUTATED 12 12 2 6
5Q LOSS WILD-TYPE 115 107 103 148

Figure S286.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00023

Table S287.  Gene #50: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
5Q LOSS MUTATED 4 14 2 0 2 10
5Q LOSS WILD-TYPE 95 63 116 56 61 82

Figure S287.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0011

Table S288.  Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
6P LOSS MUTATED 10 16 4
6P LOSS WILD-TYPE 217 95 171

Figure S288.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0334 (Fisher's exact test), Q value = 0.078

Table S289.  Gene #51: '6p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
6P LOSS MUTATED 6 2 4 3 10 4
6P LOSS WILD-TYPE 93 75 114 53 53 88

Figure S289.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S290.  Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
6Q LOSS MUTATED 23 35 5
6Q LOSS WILD-TYPE 204 76 170

Figure S290.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.00097 (Fisher's exact test), Q value = 0.0044

Table S291.  Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
6Q LOSS MUTATED 32 21 7 3
6Q LOSS WILD-TYPE 177 113 150 10

Figure S291.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0339 (Fisher's exact test), Q value = 0.079

Table S292.  Gene #52: '6q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
6Q LOSS MUTATED 8 14 33
6Q LOSS WILD-TYPE 75 144 152

Figure S292.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CNMF'

P value = 0.00191 (Fisher's exact test), Q value = 0.0076

Table S293.  Gene #52: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
6Q LOSS MUTATED 29 14 4 16
6Q LOSS WILD-TYPE 111 93 78 164

Figure S293.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0133 (Fisher's exact test), Q value = 0.038

Table S294.  Gene #52: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
6Q LOSS MUTATED 22 18 5 16
6Q LOSS WILD-TYPE 105 101 100 138

Figure S294.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00451 (Fisher's exact test), Q value = 0.016

Table S295.  Gene #52: '6q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
6Q LOSS MUTATED 20 5 11 4 14 7
6Q LOSS WILD-TYPE 79 72 107 52 49 85

Figure S295.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q loss' versus 'RPPA_CNMF'

P value = 0.0169 (Fisher's exact test), Q value = 0.045

Table S296.  Gene #54: '7q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
7Q LOSS MUTATED 0 0 4 0
7Q LOSS WILD-TYPE 91 95 121 115

Figure S296.  Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'8p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0435 (Fisher's exact test), Q value = 0.096

Table S297.  Gene #55: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 7 7 6
8P LOSS MUTATED 0 3 0 0
8P LOSS WILD-TYPE 7 4 7 6

Figure S297.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00016

Table S298.  Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
8P LOSS MUTATED 5 12 0
8P LOSS WILD-TYPE 222 99 175

Figure S298.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0012

Table S299.  Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
8P LOSS MUTATED 5 10 0 2
8P LOSS WILD-TYPE 204 124 157 11

Figure S299.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'RPPA_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 0.044

Table S300.  Gene #55: '8p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
8P LOSS MUTATED 0 8 4 3
8P LOSS WILD-TYPE 91 87 121 112

Figure S300.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'8p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.031

Table S301.  Gene #55: '8p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
8P LOSS MUTATED 0 3 12
8P LOSS WILD-TYPE 83 155 173

Figure S301.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S302.  Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
8P LOSS MUTATED 0 13 0 3 1
8P LOSS WILD-TYPE 130 102 105 130 29

Figure S302.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00029

Table S303.  Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
8P LOSS MUTATED 1 8 0 2 0 5 1
8P LOSS WILD-TYPE 134 63 36 66 90 36 71

Figure S303.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00146 (Fisher's exact test), Q value = 0.0061

Table S304.  Gene #55: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
8P LOSS MUTATED 7 1 9
8P LOSS WILD-TYPE 215 183 94

Figure S304.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00782 (Fisher's exact test), Q value = 0.024

Table S305.  Gene #55: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
8P LOSS MUTATED 2 10 1 3
8P LOSS WILD-TYPE 125 109 104 151

Figure S305.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S306.  Gene #55: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
8P LOSS MUTATED 1 6 1 0 8 0
8P LOSS WILD-TYPE 98 71 117 56 55 92

Figure S306.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00023

Table S307.  Gene #56: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
8Q LOSS MUTATED 2 9 0
8Q LOSS WILD-TYPE 225 102 175

Figure S307.  Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8q loss' versus 'METHLYATION_CNMF'

P value = 0.00092 (Fisher's exact test), Q value = 0.0042

Table S308.  Gene #56: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
8Q LOSS MUTATED 2 9 0 0
8Q LOSS WILD-TYPE 207 125 157 13

Figure S308.  Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0011

Table S309.  Gene #56: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
8Q LOSS MUTATED 0 9 0 1 1
8Q LOSS WILD-TYPE 130 106 105 132 29

Figure S309.  Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.0019

Table S310.  Gene #56: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
8Q LOSS MUTATED 1 7 0 1 0 2 0
8Q LOSS WILD-TYPE 134 64 36 67 90 39 72

Figure S310.  Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-04 (Fisher's exact test), Q value = 0.0034

Table S311.  Gene #56: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
8Q LOSS MUTATED 4 0 7
8Q LOSS WILD-TYPE 218 184 96

Figure S311.  Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0498 (Fisher's exact test), Q value = 0.11

Table S312.  Gene #56: '8q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
8Q LOSS MUTATED 2 6 0 2
8Q LOSS WILD-TYPE 125 113 105 152

Figure S312.  Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00016

Table S313.  Gene #56: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
8Q LOSS MUTATED 0 3 0 0 7 0
8Q LOSS WILD-TYPE 99 74 118 56 56 92

Figure S313.  Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S314.  Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
9P LOSS MUTATED 49 47 22
9P LOSS WILD-TYPE 178 64 153

Figure S314.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 0.00409 (Fisher's exact test), Q value = 0.015

Table S315.  Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
9P LOSS MUTATED 58 35 21 4
9P LOSS WILD-TYPE 151 99 136 9

Figure S315.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'RPPA_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.0028

Table S316.  Gene #57: '9p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
9P LOSS MUTATED 13 37 29 22
9P LOSS WILD-TYPE 78 58 96 93

Figure S316.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S317.  Gene #57: '9p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
9P LOSS MUTATED 9 27 65
9P LOSS WILD-TYPE 74 131 120

Figure S317.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00093

Table S318.  Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
9P LOSS MUTATED 33 21 9 25 10 13 7
9P LOSS WILD-TYPE 102 50 27 43 80 28 65

Figure S318.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00451 (Fisher's exact test), Q value = 0.016

Table S319.  Gene #58: '9q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
9Q LOSS MUTATED 3 12 29
9Q LOSS WILD-TYPE 80 146 156

Figure S319.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0441 (Fisher's exact test), Q value = 0.096

Table S320.  Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
9Q LOSS MUTATED 11 11 7 7 7 6 2
9Q LOSS WILD-TYPE 124 60 29 61 83 35 70

Figure S320.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S321.  Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
10P LOSS MUTATED 23 54 6
10P LOSS WILD-TYPE 204 57 169

Figure S321.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S322.  Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
10P LOSS MUTATED 4 73 6 0
10P LOSS WILD-TYPE 205 61 151 13

Figure S322.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'RPPA_CNMF'

P value = 0.00742 (Fisher's exact test), Q value = 0.023

Table S323.  Gene #59: '10p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
10P LOSS MUTATED 10 24 11 16
10P LOSS WILD-TYPE 81 71 114 99

Figure S323.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'10p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.0017

Table S324.  Gene #59: '10p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
10P LOSS MUTATED 4 17 40
10P LOSS WILD-TYPE 79 141 145

Figure S324.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S325.  Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
10P LOSS MUTATED 1 64 1 13 4
10P LOSS WILD-TYPE 129 51 104 120 26

Figure S325.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S326.  Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
10P LOSS MUTATED 1 60 3 12 3 4 0
10P LOSS WILD-TYPE 134 11 33 56 87 37 72

Figure S326.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00098

Table S327.  Gene #59: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
10P LOSS MUTATED 32 26 5 20
10P LOSS WILD-TYPE 108 81 77 160

Figure S327.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S328.  Gene #59: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
10P LOSS MUTATED 11 12 60
10P LOSS WILD-TYPE 211 172 43

Figure S328.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S329.  Gene #59: '10p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
10P LOSS MUTATED 26 37 3 17
10P LOSS WILD-TYPE 101 82 102 137

Figure S329.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S330.  Gene #59: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
10P LOSS MUTATED 4 6 12 1 55 5
10P LOSS WILD-TYPE 95 71 106 55 8 87

Figure S330.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S331.  Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
10Q LOSS MUTATED 32 59 6
10Q LOSS WILD-TYPE 195 52 169

Figure S331.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S332.  Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
10Q LOSS MUTATED 11 74 6 6
10Q LOSS WILD-TYPE 198 60 151 7

Figure S332.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'RPPA_CNMF'

P value = 0.00907 (Fisher's exact test), Q value = 0.027

Table S333.  Gene #60: '10q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
10Q LOSS MUTATED 12 28 17 17
10Q LOSS WILD-TYPE 79 67 108 98

Figure S333.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'10q loss' versus 'RPPA_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00061

Table S334.  Gene #60: '10q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
10Q LOSS MUTATED 6 20 48
10Q LOSS WILD-TYPE 77 138 137

Figure S334.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S335.  Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
10Q LOSS MUTATED 5 71 1 16 4
10Q LOSS WILD-TYPE 125 44 104 117 26

Figure S335.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S336.  Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
10Q LOSS MUTATED 6 60 3 14 3 10 1
10Q LOSS WILD-TYPE 129 11 33 54 87 31 71

Figure S336.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00042

Table S337.  Gene #60: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
10Q LOSS MUTATED 35 32 6 24
10Q LOSS WILD-TYPE 105 75 76 156

Figure S337.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S338.  Gene #60: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
10Q LOSS MUTATED 15 15 67
10Q LOSS WILD-TYPE 207 169 36

Figure S338.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S339.  Gene #60: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
10Q LOSS MUTATED 31 42 5 19
10Q LOSS WILD-TYPE 96 77 100 135

Figure S339.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S340.  Gene #60: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
10Q LOSS MUTATED 8 9 12 1 56 11
10Q LOSS WILD-TYPE 91 68 106 55 7 81

Figure S340.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0311 (Fisher's exact test), Q value = 0.073

Table S341.  Gene #61: '11p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 7 7 6
11P LOSS MUTATED 1 4 0 0
11P LOSS WILD-TYPE 6 3 7 6

Figure S341.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S342.  Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
11P LOSS MUTATED 46 17 0
11P LOSS WILD-TYPE 181 94 175

Figure S342.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S343.  Gene #61: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
11P LOSS MUTATED 38 17 0 8
11P LOSS WILD-TYPE 171 117 157 5

Figure S343.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'RPPA_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.033

Table S344.  Gene #61: '11p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
11P LOSS MUTATED 14 18 8 9
11P LOSS WILD-TYPE 77 77 117 106

Figure S344.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S345.  Gene #61: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
11P LOSS MUTATED 13 31 0 12 7
11P LOSS WILD-TYPE 117 84 105 121 23

Figure S345.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S346.  Gene #61: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
11P LOSS MUTATED 17 9 0 6 0 25 6
11P LOSS WILD-TYPE 118 62 36 62 90 16 66

Figure S346.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00016

Table S347.  Gene #61: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
11P LOSS MUTATED 13 29 4 17
11P LOSS WILD-TYPE 127 78 78 163

Figure S347.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00029

Table S348.  Gene #61: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
11P LOSS MUTATED 22 14 27
11P LOSS WILD-TYPE 200 170 76

Figure S348.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00092 (Fisher's exact test), Q value = 0.0042

Table S349.  Gene #61: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
11P LOSS MUTATED 19 24 4 15
11P LOSS WILD-TYPE 108 95 101 139

Figure S349.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S350.  Gene #61: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
11P LOSS MUTATED 10 27 10 0 8 7
11P LOSS WILD-TYPE 89 50 108 56 55 85

Figure S350.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00016

Table S351.  Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
11Q LOSS MUTATED 9 12 0
11Q LOSS WILD-TYPE 218 99 175

Figure S351.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0011

Table S352.  Gene #62: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
11Q LOSS MUTATED 7 13 0 1
11Q LOSS WILD-TYPE 202 121 157 12

Figure S352.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S353.  Gene #62: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
11Q LOSS MUTATED 0 16 0 3 2
11Q LOSS WILD-TYPE 130 99 105 130 28

Figure S353.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S354.  Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
11Q LOSS MUTATED 2 9 0 2 0 7 1
11Q LOSS WILD-TYPE 133 62 36 66 90 34 71

Figure S354.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00067

Table S355.  Gene #62: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
11Q LOSS MUTATED 5 3 13
11Q LOSS WILD-TYPE 217 181 90

Figure S355.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00631 (Fisher's exact test), Q value = 0.021

Table S356.  Gene #62: '11q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
11Q LOSS MUTATED 6 10 0 4
11Q LOSS WILD-TYPE 121 109 105 150

Figure S356.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00138 (Fisher's exact test), Q value = 0.0058

Table S357.  Gene #62: '11q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
11Q LOSS MUTATED 1 6 3 0 8 2
11Q LOSS WILD-TYPE 98 71 115 56 55 90

Figure S357.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 0.0149 (Fisher's exact test), Q value = 0.042

Table S358.  Gene #63: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
12P LOSS MUTATED 20 3 5
12P LOSS WILD-TYPE 207 108 170

Figure S358.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0016

Table S359.  Gene #63: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
12P LOSS MUTATED 14 4 5 5
12P LOSS WILD-TYPE 195 130 152 8

Figure S359.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00507 (Fisher's exact test), Q value = 0.017

Table S360.  Gene #63: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
12P LOSS MUTATED 10 1 1 1 3 8 4
12P LOSS WILD-TYPE 125 70 35 67 87 33 68

Figure S360.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_CNMF'

P value = 0.0428 (Fisher's exact test), Q value = 0.095

Table S361.  Gene #63: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
12P LOSS MUTATED 4 12 3 9
12P LOSS WILD-TYPE 136 95 79 171

Figure S361.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0477 (Fisher's exact test), Q value = 0.1

Table S362.  Gene #63: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
12P LOSS MUTATED 6 9 7 1 0 5
12P LOSS WILD-TYPE 93 68 111 55 63 87

Figure S362.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S363.  Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
12Q LOSS MUTATED 40 6 6
12Q LOSS WILD-TYPE 187 105 169

Figure S363.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S364.  Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
12Q LOSS MUTATED 33 8 5 6
12Q LOSS WILD-TYPE 176 126 152 7

Figure S364.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q loss' versus 'MRNASEQ_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.0041

Table S365.  Gene #64: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
12Q LOSS MUTATED 17 15 1 14 5
12Q LOSS WILD-TYPE 113 100 104 119 25

Figure S365.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S366.  Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
12Q LOSS MUTATED 21 1 1 6 3 14 6
12Q LOSS WILD-TYPE 114 70 35 62 87 27 66

Figure S366.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_CNMF'

P value = 0.00306 (Fisher's exact test), Q value = 0.011

Table S367.  Gene #64: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
12Q LOSS MUTATED 10 22 5 15
12Q LOSS WILD-TYPE 130 85 77 165

Figure S367.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S368.  Gene #64: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
12Q LOSS MUTATED 13 18 11 1 0 9
12Q LOSS WILD-TYPE 86 59 107 55 63 83

Figure S368.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00016

Table S369.  Gene #65: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 7 7 6
13Q LOSS MUTATED 2 7 0 0
13Q LOSS WILD-TYPE 5 0 7 6

Figure S369.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S370.  Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
13Q LOSS MUTATED 42 46 27
13Q LOSS WILD-TYPE 185 65 148

Figure S370.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.0433 (Fisher's exact test), Q value = 0.095

Table S371.  Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
13Q LOSS MUTATED 52 31 26 6
13Q LOSS WILD-TYPE 157 103 131 7

Figure S371.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'RPPA_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 0.037

Table S372.  Gene #65: '13q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
13Q LOSS MUTATED 13 32 24 25
13Q LOSS WILD-TYPE 78 63 101 90

Figure S372.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 0.048

Table S373.  Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
13Q LOSS MUTATED 31 38 16 25 5
13Q LOSS WILD-TYPE 99 77 89 108 25

Figure S373.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00117 (Fisher's exact test), Q value = 0.0051

Table S374.  Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
13Q LOSS MUTATED 33 19 2 11 17 19 14
13Q LOSS WILD-TYPE 102 52 34 57 73 22 58

Figure S374.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0206 (Fisher's exact test), Q value = 0.053

Table S375.  Gene #65: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
13Q LOSS MUTATED 53 30 31
13Q LOSS WILD-TYPE 169 154 72

Figure S375.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0447 (Fisher's exact test), Q value = 0.097

Table S376.  Gene #65: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
13Q LOSS MUTATED 17 24 20 9 18 26
13Q LOSS WILD-TYPE 82 53 98 47 45 66

Figure S376.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S377.  Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
14Q LOSS MUTATED 22 38 21
14Q LOSS WILD-TYPE 205 73 154

Figure S377.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 0.00178 (Fisher's exact test), Q value = 0.0072

Table S378.  Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
14Q LOSS MUTATED 24 32 20 5
14Q LOSS WILD-TYPE 185 102 137 8

Figure S378.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S379.  Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
14Q LOSS MUTATED 10 36 11 17 7
14Q LOSS WILD-TYPE 120 79 94 116 23

Figure S379.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.0011

Table S380.  Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
14Q LOSS MUTATED 16 25 6 9 8 10 7
14Q LOSS WILD-TYPE 119 46 30 59 82 31 65

Figure S380.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 0.0191 (Fisher's exact test), Q value = 0.05

Table S381.  Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
14Q LOSS MUTATED 34 13 11 22
14Q LOSS WILD-TYPE 106 94 71 158

Figure S381.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00126 (Fisher's exact test), Q value = 0.0054

Table S382.  Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
14Q LOSS MUTATED 28 23 29
14Q LOSS WILD-TYPE 194 161 74

Figure S382.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.036

Table S383.  Gene #66: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
14Q LOSS MUTATED 22 29 10 19
14Q LOSS WILD-TYPE 105 90 95 135

Figure S383.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00149 (Fisher's exact test), Q value = 0.0062

Table S384.  Gene #66: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
14Q LOSS MUTATED 14 16 15 6 21 8
14Q LOSS WILD-TYPE 85 61 103 50 42 84

Figure S384.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 0.0159 (Fisher's exact test), Q value = 0.043

Table S385.  Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
15Q LOSS MUTATED 14 11 26
15Q LOSS WILD-TYPE 213 100 149

Figure S385.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S386.  Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
15Q LOSS MUTATED 13 5 28 5
15Q LOSS WILD-TYPE 196 129 129 8

Figure S386.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'RPPA_CNMF'

P value = 0.0145 (Fisher's exact test), Q value = 0.041

Table S387.  Gene #67: '15q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
15Q LOSS MUTATED 6 16 14 5
15Q LOSS WILD-TYPE 85 79 111 110

Figure S387.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 0.00276 (Fisher's exact test), Q value = 0.01

Table S388.  Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
15Q LOSS MUTATED 5 13 20 10 3
15Q LOSS WILD-TYPE 125 102 85 123 27

Figure S388.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00023

Table S389.  Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
15Q LOSS MUTATED 7 2 6 2 18 10 6
15Q LOSS WILD-TYPE 128 69 30 66 72 31 66

Figure S389.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00053 (Fisher's exact test), Q value = 0.0027

Table S390.  Gene #67: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
15Q LOSS MUTATED 7 13 7 14 2 8
15Q LOSS WILD-TYPE 92 64 111 42 61 84

Figure S390.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 0.0304 (Fisher's exact test), Q value = 0.072

Table S391.  Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
16P LOSS MUTATED 7 6 1
16P LOSS WILD-TYPE 220 105 174

Figure S391.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 0.0375 (Fisher's exact test), Q value = 0.085

Table S392.  Gene #68: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
16P LOSS MUTATED 1 8 1 4 0
16P LOSS WILD-TYPE 129 107 104 129 30

Figure S392.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0227 (Fisher's exact test), Q value = 0.058

Table S393.  Gene #68: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
16P LOSS MUTATED 1 4 0 5 2 2 0
16P LOSS WILD-TYPE 134 67 36 63 88 39 72

Figure S393.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 0.0056 (Fisher's exact test), Q value = 0.019

Table S394.  Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
16Q LOSS MUTATED 10 10 2
16Q LOSS WILD-TYPE 217 101 173

Figure S394.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00567 (Fisher's exact test), Q value = 0.019

Table S395.  Gene #69: '16q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
16Q LOSS MUTATED 0 3 13
16Q LOSS WILD-TYPE 83 155 172

Figure S395.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 0.0211 (Fisher's exact test), Q value = 0.054

Table S396.  Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
16Q LOSS MUTATED 4 12 2 4 0
16Q LOSS WILD-TYPE 126 103 103 129 30

Figure S396.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0206 (Fisher's exact test), Q value = 0.053

Table S397.  Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
16Q LOSS MUTATED 4 8 1 5 2 2 0
16Q LOSS WILD-TYPE 131 63 35 63 88 39 72

Figure S397.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00376 (Fisher's exact test), Q value = 0.014

Table S398.  Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
16Q LOSS MUTATED 7 4 11
16Q LOSS WILD-TYPE 215 180 92

Figure S398.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 0.00094 (Fisher's exact test), Q value = 0.0042

Table S399.  Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
17P LOSS MUTATED 4 9 1
17P LOSS WILD-TYPE 223 102 174

Figure S399.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.03

Table S400.  Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
17P LOSS MUTATED 3 7 2 2
17P LOSS WILD-TYPE 206 127 155 11

Figure S400.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0025

Table S401.  Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
17P LOSS MUTATED 0 9 2 1 2
17P LOSS WILD-TYPE 130 106 103 132 28

Figure S401.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00214 (Fisher's exact test), Q value = 0.0085

Table S402.  Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
17P LOSS MUTATED 5 1 8
17P LOSS WILD-TYPE 217 183 95

Figure S402.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0452 (Fisher's exact test), Q value = 0.098

Table S403.  Gene #70: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
17P LOSS MUTATED 3 2 0 1 5 2
17P LOSS WILD-TYPE 96 75 118 55 58 90

Figure S403.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 0.00291 (Fisher's exact test), Q value = 0.011

Table S404.  Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
17Q LOSS MUTATED 3 6 0
17Q LOSS WILD-TYPE 224 105 175

Figure S404.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 0.0109 (Fisher's exact test), Q value = 0.032

Table S405.  Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
17Q LOSS MUTATED 0 5 1 1 2
17Q LOSS WILD-TYPE 130 110 104 132 28

Figure S405.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0302 (Fisher's exact test), Q value = 0.072

Table S406.  Gene #72: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 7 7 6
18P LOSS MUTATED 0 4 1 0
18P LOSS WILD-TYPE 7 3 6 6

Figure S406.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 0.00749 (Fisher's exact test), Q value = 0.023

Table S407.  Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
18P LOSS MUTATED 18 19 30
18P LOSS WILD-TYPE 209 92 145

Figure S407.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.0042

Table S408.  Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
18Q LOSS MUTATED 15 14 33
18Q LOSS WILD-TYPE 212 97 142

Figure S408.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.0042

Table S409.  Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
18Q LOSS MUTATED 19 10 33 0
18Q LOSS WILD-TYPE 190 124 124 13

Figure S409.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0154 (Fisher's exact test), Q value = 0.043

Table S410.  Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
18Q LOSS MUTATED 9 8 7 6 20 6 6
18Q LOSS WILD-TYPE 126 63 29 62 70 35 66

Figure S410.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 0.048

Table S411.  Gene #73: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
18Q LOSS MUTATED 17 7 18 20
18Q LOSS WILD-TYPE 123 100 64 160

Figure S411.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0411 (Fisher's exact test), Q value = 0.092

Table S412.  Gene #74: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
19P LOSS MUTATED 3 9 9 4
19P LOSS WILD-TYPE 124 110 96 150

Figure S412.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0133 (Fisher's exact test), Q value = 0.038

Table S413.  Gene #75: '19q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 7 7 6
19Q LOSS MUTATED 1 6 6 2
19Q LOSS WILD-TYPE 6 1 1 4

Figure S413.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S414.  Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
19Q LOSS MUTATED 22 22 165
19Q LOSS WILD-TYPE 205 89 10

Figure S414.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S415.  Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
19Q LOSS MUTATED 28 24 156 1
19Q LOSS WILD-TYPE 181 110 1 12

Figure S415.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00821 (Fisher's exact test), Q value = 0.025

Table S416.  Gene #75: '19q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
19Q LOSS MUTATED 28 82 71
19Q LOSS WILD-TYPE 55 76 114

Figure S416.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S417.  Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
19Q LOSS MUTATED 16 16 103 63 11
19Q LOSS WILD-TYPE 114 99 2 70 19

Figure S417.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S418.  Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
19Q LOSS MUTATED 16 5 36 8 87 8 49
19Q LOSS WILD-TYPE 119 66 0 60 3 33 23

Figure S418.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S419.  Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
19Q LOSS MUTATED 33 20 70 86
19Q LOSS WILD-TYPE 107 87 12 94

Figure S419.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S420.  Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
19Q LOSS MUTATED 97 103 9
19Q LOSS WILD-TYPE 125 81 94

Figure S420.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S421.  Gene #75: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
19Q LOSS MUTATED 22 26 87 73
19Q LOSS WILD-TYPE 105 93 18 81

Figure S421.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S422.  Gene #75: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
19Q LOSS MUTATED 11 38 62 55 2 40
19Q LOSS WILD-TYPE 88 39 56 1 61 52

Figure S422.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 0.0151 (Fisher's exact test), Q value = 0.042

Table S423.  Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
20P LOSS MUTATED 7 0 0
20P LOSS WILD-TYPE 220 111 175

Figure S423.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'20p loss' versus 'METHLYATION_CNMF'

P value = 0.0369 (Fisher's exact test), Q value = 0.084

Table S424.  Gene #76: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
20P LOSS MUTATED 5 1 0 1
20P LOSS WILD-TYPE 204 133 157 12

Figure S424.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q loss' versus 'METHLYATION_CNMF'

P value = 0.039 (Fisher's exact test), Q value = 0.088

Table S425.  Gene #77: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
20Q LOSS MUTATED 2 0 0 1
20Q LOSS WILD-TYPE 207 134 157 12

Figure S425.  Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q loss' versus 'MRNASEQ_CNMF'

P value = 0.0345 (Fisher's exact test), Q value = 0.08

Table S426.  Gene #77: '20q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
20Q LOSS MUTATED 0 2 0 0 1
20Q LOSS WILD-TYPE 130 113 105 133 29

Figure S426.  Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00692 (Fisher's exact test), Q value = 0.022

Table S427.  Gene #78: '21q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 7 7 6
21Q LOSS MUTATED 0 4 0 0
21Q LOSS WILD-TYPE 7 3 7 6

Figure S427.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00082

Table S428.  Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
21Q LOSS MUTATED 19 16 3
21Q LOSS WILD-TYPE 208 95 172

Figure S428.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00036

Table S429.  Gene #78: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
21Q LOSS MUTATED 23 9 2 4
21Q LOSS WILD-TYPE 186 125 155 9

Figure S429.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 0.00129 (Fisher's exact test), Q value = 0.0055

Table S430.  Gene #78: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
21Q LOSS MUTATED 13 13 1 6 5
21Q LOSS WILD-TYPE 117 102 104 127 25

Figure S430.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S431.  Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
21Q LOSS MUTATED 16 3 2 4 0 11 2
21Q LOSS WILD-TYPE 119 68 34 64 90 30 70

Figure S431.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0486 (Fisher's exact test), Q value = 0.1

Table S432.  Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
21Q LOSS MUTATED 21 7 10
21Q LOSS WILD-TYPE 201 177 93

Figure S432.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0254 (Fisher's exact test), Q value = 0.063

Table S433.  Gene #78: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
21Q LOSS MUTATED 10 12 5 1 3 6
21Q LOSS WILD-TYPE 89 65 113 55 60 86

Figure S433.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00658 (Fisher's exact test), Q value = 0.021

Table S434.  Gene #79: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 7 7 6
22Q LOSS MUTATED 0 4 0 0
22Q LOSS WILD-TYPE 7 3 7 6

Figure S434.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S435.  Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
22Q LOSS MUTATED 21 32 4
22Q LOSS WILD-TYPE 206 79 171

Figure S435.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00016

Table S436.  Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
22Q LOSS MUTATED 22 28 4 3
22Q LOSS WILD-TYPE 187 106 153 10

Figure S436.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.0019

Table S437.  Gene #79: '22q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
22Q LOSS MUTATED 5 23 10 10
22Q LOSS WILD-TYPE 86 72 115 105

Figure S437.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'22q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0389 (Fisher's exact test), Q value = 0.088

Table S438.  Gene #79: '22q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
22Q LOSS MUTATED 5 14 29
22Q LOSS WILD-TYPE 78 144 156

Figure S438.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S439.  Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
22Q LOSS MUTATED 8 31 2 11 5
22Q LOSS WILD-TYPE 122 84 103 122 25

Figure S439.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S440.  Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
22Q LOSS MUTATED 11 21 2 11 2 9 1
22Q LOSS WILD-TYPE 124 50 34 57 88 32 71

Figure S440.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.0016

Table S441.  Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 222 184 103
22Q LOSS MUTATED 18 15 24
22Q LOSS WILD-TYPE 204 169 79

Figure S441.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00165 (Fisher's exact test), Q value = 0.0068

Table S442.  Gene #79: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
22Q LOSS MUTATED 17 23 5 11
22Q LOSS WILD-TYPE 110 96 100 143

Figure S442.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00016

Table S443.  Gene #79: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
22Q LOSS MUTATED 3 15 10 3 17 8
22Q LOSS WILD-TYPE 96 62 108 53 46 84

Figure S443.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'METHLYATION_CNMF'

P value = 0.00286 (Fisher's exact test), Q value = 0.011

Table S444.  Gene #80: 'xp loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
XP LOSS MUTATED 44 16 32 7
XP LOSS WILD-TYPE 165 118 125 6

Figure S444.  Get High-res Image Gene #80: 'xp loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xp loss' versus 'RPPA_CNMF'

P value = 0.00246 (Fisher's exact test), Q value = 0.0095

Table S445.  Gene #80: 'xp loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
XP LOSS MUTATED 10 30 29 18
XP LOSS WILD-TYPE 81 65 96 97

Figure S445.  Get High-res Image Gene #80: 'xp loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'xp loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00588 (Fisher's exact test), Q value = 0.02

Table S446.  Gene #80: 'xp loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
XP LOSS MUTATED 11 25 51
XP LOSS WILD-TYPE 72 133 134

Figure S446.  Get High-res Image Gene #80: 'xp loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S447.  Gene #80: 'xp loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
XP LOSS MUTATED 29 10 10 9 20 18 3
XP LOSS WILD-TYPE 106 61 26 59 70 23 69

Figure S447.  Get High-res Image Gene #80: 'xp loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_CNMF'

P value = 0.0238 (Fisher's exact test), Q value = 0.06

Table S448.  Gene #80: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
XP LOSS MUTATED 22 24 25 28
XP LOSS WILD-TYPE 118 83 57 152

Figure S448.  Get High-res Image Gene #80: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xp loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00107 (Fisher's exact test), Q value = 0.0047

Table S449.  Gene #80: 'xp loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
XP LOSS MUTATED 33 19 29 17
XP LOSS WILD-TYPE 94 100 76 137

Figure S449.  Get High-res Image Gene #80: 'xp loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xp loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.0018

Table S450.  Gene #80: 'xp loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
XP LOSS MUTATED 20 23 9 13 8 25
XP LOSS WILD-TYPE 79 54 109 43 55 67

Figure S450.  Get High-res Image Gene #80: 'xp loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 0.0076 (Fisher's exact test), Q value = 0.024

Table S451.  Gene #81: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 111 175
XQ LOSS MUTATED 20 16 34
XQ LOSS WILD-TYPE 207 95 141

Figure S451.  Get High-res Image Gene #81: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0011

Table S452.  Gene #81: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 209 134 157 13
XQ LOSS MUTATED 20 12 32 6
XQ LOSS WILD-TYPE 189 122 125 7

Figure S452.  Get High-res Image Gene #81: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq loss' versus 'RPPA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00048

Table S453.  Gene #81: 'xq loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 95 125 115
XQ LOSS MUTATED 4 27 15 15
XQ LOSS WILD-TYPE 87 68 110 100

Figure S453.  Get High-res Image Gene #81: 'xq loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'xq loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0167 (Fisher's exact test), Q value = 0.045

Table S454.  Gene #81: 'xq loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 158 185
XQ LOSS MUTATED 5 21 35
XQ LOSS WILD-TYPE 78 137 150

Figure S454.  Get High-res Image Gene #81: 'xq loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0012

Table S455.  Gene #81: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 130 115 105 133 30
XQ LOSS MUTATED 10 23 24 13 0
XQ LOSS WILD-TYPE 120 92 81 120 30

Figure S455.  Get High-res Image Gene #81: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.6e-05

Table S456.  Gene #81: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 135 71 36 68 90 41 72
XQ LOSS MUTATED 9 9 10 7 20 13 2
XQ LOSS WILD-TYPE 126 62 26 61 70 28 70

Figure S456.  Get High-res Image Gene #81: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00029

Table S457.  Gene #81: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 140 107 82 180
XQ LOSS MUTATED 11 16 26 17
XQ LOSS WILD-TYPE 129 91 56 163

Figure S457.  Get High-res Image Gene #81: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00073

Table S458.  Gene #81: 'xq loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 127 119 105 154
XQ LOSS MUTATED 19 11 28 11
XQ LOSS WILD-TYPE 108 108 77 143

Figure S458.  Get High-res Image Gene #81: 'xq loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00069 (Fisher's exact test), Q value = 0.0033

Table S459.  Gene #81: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 99 77 118 56 63 92
XQ LOSS MUTATED 9 17 6 13 7 17
XQ LOSS WILD-TYPE 90 60 112 43 56 75

Figure S459.  Get High-res Image Gene #81: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input
  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LGG-TP/22533657/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LGG-TP/22553887/LGG-TP.transferedmergedcluster.txt

  • Number of patients = 513

  • Number of significantly arm-level cnvs = 81

  • 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)