Correlation between copy number variations of arm-level result and molecular subtypes
Lung Squamous Cell Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1JS9PVV
Overview
Introduction

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

Summary

Testing the association between copy number variation 82 arm-level events and 12 molecular subtypes across 501 patients, 434 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'CN_CNMF'.

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

  • 2p gain 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'.

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

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

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

  • 4q gain cnv correlated to 'CN_CNMF'.

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

  • 5q gain cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 6q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

  • 8p gain cnv correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 9p gain cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

  • 10p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 11p gain cnv correlated to 'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • 13q gain cnv correlated to 'CN_CNMF'.

  • 14q gain cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

  • 16p gain cnv correlated to 'CN_CNMF'.

  • 16q gain cnv correlated to 'CN_CNMF'.

  • 17p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

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

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

  • 18q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

  • 20p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • 20q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • 22q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

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

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

  • 2p loss cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 2q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

  • 4p 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'.

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

  • 5p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.

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

  • 6p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

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

  • 7q loss cnv correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • 9q 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'.

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

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

  • 11p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 11q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 12p loss cnv correlated to 'MRNA_CNMF' and 'MRNA_CHIERARCHICAL'.

  • 12q loss cnv correlated to 'MIRSEQ_CNMF'.

  • 13q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

  • 15q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 16p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

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

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

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

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

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

  • 19q loss cnv correlated to 'CN_CNMF'.

  • 20p loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 20q loss cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

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

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

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

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 434 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
4p loss 315 (63%) 186 0.00049
(0.00319)
5e-05
(0.000518)
1e-05
(0.000135)
2e-05
(0.000232)
0.00471
(0.0193)
0.0266
(0.0727)
1e-05
(0.000135)
1e-05
(0.000135)
1e-05
(0.000135)
0.0492
(0.112)
6e-05
(0.000602)
8e-05
(0.000779)
9q loss 247 (49%) 254 2e-05
(0.000232)
1e-05
(0.000135)
1e-05
(0.000135)
1e-05
(0.000135)
0.00071
(0.00421)
0.00169
(0.0088)
1e-05
(0.000135)
1e-05
(0.000135)
1e-05
(0.000135)
1e-05
(0.000135)
0.00264
(0.0122)
0.0011
(0.00595)
7q gain 220 (44%) 281 0.00379
(0.0164)
0.00032
(0.00235)
1e-05
(0.000135)
0.00018
(0.00146)
0.0323
(0.0825)
0.624
(0.72)
1e-05
(0.000135)
1e-05
(0.000135)
9e-05
(0.000868)
0.00089
(0.005)
0.0146
(0.0468)
0.0178
(0.0538)
12p gain 226 (45%) 275 0.0146
(0.0468)
0.0254
(0.0702)
1e-05
(0.000135)
0.00442
(0.0187)
0.0386
(0.0933)
0.624
(0.72)
1e-05
(0.000135)
0.00197
(0.00979)
0.0118
(0.0395)
0.0053
(0.0212)
0.00066
(0.00398)
0.0133
(0.0437)
17q gain 158 (32%) 343 0.00021
(0.00161)
0.00102
(0.00555)
1e-05
(0.000135)
1e-05
(0.000135)
1e-05
(0.000135)
0.207
(0.315)
1e-05
(0.000135)
1e-05
(0.000135)
2e-05
(0.000232)
0.00769
(0.0282)
0.00011
(0.00101)
0.00037
(0.00264)
1p loss 155 (31%) 346 1e-05
(0.000135)
1e-05
(0.000135)
1e-05
(0.000135)
1e-05
(0.000135)
0.0219
(0.064)
0.348
(0.465)
1e-05
(0.000135)
1e-05
(0.000135)
0.00014
(0.00121)
1e-05
(0.000135)
0.00017
(0.00139)
0.00558
(0.022)
2p gain 223 (45%) 278 0.142
(0.245)
0.017
(0.0518)
1e-05
(0.000135)
1e-05
(0.000135)
0.0168
(0.0514)
0.125
(0.227)
1e-05
(0.000135)
2e-05
(0.000232)
0.00289
(0.0131)
0.0315
(0.0809)
0.00169
(0.0088)
0.00291
(0.0131)
9q gain 91 (18%) 410 0.0294
(0.0763)
0.00175
(0.00897)
1e-05
(0.000135)
1e-05
(0.000135)
4e-05
(0.000423)
0.00317
(0.0141)
1e-05
(0.000135)
1e-05
(0.000135)
0.00013
(0.00115)
8e-05
(0.000779)
0.304
(0.421)
0.0947
(0.186)
9p loss 315 (63%) 186 0.0237
(0.0672)
0.0026
(0.0122)
1e-05
(0.000135)
0.00172
(0.00891)
0.186
(0.293)
0.0978
(0.19)
1e-05
(0.000135)
3e-05
(0.000324)
0.00807
(0.0292)
0.00046
(0.0031)
2e-05
(0.000232)
0.0155
(0.0485)
10q loss 229 (46%) 272 0.00464
(0.0192)
0.00021
(0.00161)
1e-05
(0.000135)
8e-05
(0.000779)
0.00687
(0.0261)
0.175
(0.282)
1e-05
(0.000135)
1e-05
(0.000135)
0.0005
(0.00324)
1e-05
(0.000135)
0.00046
(0.0031)
0.117
(0.215)
14q loss 167 (33%) 334 1e-05
(0.000135)
0.0002
(0.00159)
1e-05
(0.000135)
0.0399
(0.0954)
0.00291
(0.0131)
0.143
(0.245)
1e-05
(0.000135)
1e-05
(0.000135)
0.00028
(0.0021)
1e-05
(0.000135)
0.0824
(0.167)
0.00067
(0.00402)
18p gain 148 (30%) 353 0.0147
(0.0468)
0.00066
(0.00398)
1e-05
(0.000135)
3e-05
(0.000324)
0.106
(0.202)
0.0195
(0.0584)
0.00093
(0.00514)
1e-05
(0.000135)
0.0133
(0.0437)
0.28
(0.399)
0.181
(0.287)
0.0474
(0.108)
4q loss 297 (59%) 204 0.00176
(0.00897)
0.00256
(0.0121)
1e-05
(0.000135)
0.00066
(0.00398)
0.141
(0.245)
0.157
(0.263)
1e-05
(0.000135)
0.00039
(0.00272)
1e-05
(0.000135)
0.0504
(0.113)
0.00066
(0.00398)
0.00815
(0.0294)
17p loss 292 (58%) 209 0.0202
(0.0596)
0.171
(0.279)
6e-05
(0.000602)
0.0114
(0.0386)
0.656
(0.743)
0.0327
(0.083)
0.00404
(0.0173)
0.00098
(0.00536)
0.00591
(0.023)
0.00243
(0.0116)
0.0574
(0.126)
0.0368
(0.0899)
1q gain 202 (40%) 299 0.787
(0.84)
0.668
(0.752)
0.0001
(0.000955)
0.00662
(0.0253)
0.0807
(0.165)
0.984
(0.988)
0.00752
(0.0278)
0.00053
(0.00334)
0.00026
(0.00197)
0.00304
(0.0136)
0.0221
(0.0642)
0.0204
(0.06)
7p gain 238 (48%) 263 0.0695
(0.148)
0.0104
(0.0356)
1e-05
(0.000135)
0.00289
(0.0131)
0.136
(0.238)
0.693
(0.77)
3e-05
(0.000324)
1e-05
(0.000135)
0.00222
(0.0107)
0.00063
(0.0039)
0.0197
(0.0585)
0.319
(0.436)
9p gain 62 (12%) 439 0.121
(0.221)
0.0272
(0.0737)
2e-05
(0.000232)
0.0009
(0.00503)
0.106
(0.202)
0.0294
(0.0763)
3e-05
(0.000324)
1e-05
(0.000135)
0.0784
(0.162)
0.0328
(0.0831)
0.0405
(0.0962)
0.166
(0.272)
12q gain 151 (30%) 350 0.0776
(0.16)
0.494
(0.604)
5e-05
(0.000518)
0.00136
(0.00727)
0.0441
(0.103)
0.356
(0.47)
0.00751
(0.0278)
0.00285
(0.013)
0.0155
(0.0486)
0.176
(0.283)
0.0294
(0.0763)
0.00073
(0.00425)
17p gain 65 (13%) 436 0.00511
(0.0207)
0.0396
(0.0948)
0.00015
(0.00127)
0.0047
(0.0193)
0.0123
(0.041)
0.224
(0.337)
0.00037
(0.00264)
0.00061
(0.0038)
0.00262
(0.0122)
0.129
(0.232)
0.106
(0.202)
0.157
(0.263)
19p gain 115 (23%) 386 0.0253
(0.0702)
0.15
(0.254)
1e-05
(0.000135)
0.00575
(0.0225)
0.017
(0.0518)
0.321
(0.437)
0.00014
(0.00121)
0.00386
(0.0166)
0.00626
(0.0241)
0.00194
(0.00969)
0.0763
(0.158)
0.0887
(0.177)
5q loss 290 (58%) 211 0.153
(0.259)
0.0375
(0.0912)
2e-05
(0.000232)
0.0045
(0.0188)
0.224
(0.337)
0.289
(0.408)
0.00985
(0.0344)
0.0008
(0.0046)
0.0309
(0.0797)
0.0444
(0.103)
0.00356
(0.0155)
0.182
(0.288)
6p loss 114 (23%) 387 0.028
(0.0748)
0.00732
(0.0275)
0.00073
(0.00425)
0.00051
(0.00326)
0.797
(0.848)
0.495
(0.605)
2e-05
(0.000232)
1e-05
(0.000135)
0.304
(0.421)
0.0391
(0.094)
0.0317
(0.0814)
0.683
(0.764)
10p loss 215 (43%) 286 0.398
(0.511)
0.262
(0.379)
1e-05
(0.000135)
0.00021
(0.00161)
0.00749
(0.0278)
0.138
(0.24)
2e-05
(0.000232)
0.00014
(0.00121)
0.00011
(0.00101)
1e-05
(0.000135)
0.00336
(0.0148)
0.156
(0.263)
17q loss 91 (18%) 410 0.0135
(0.0443)
0.00608
(0.0236)
0.00024
(0.00183)
0.00905
(0.0321)
0.0975
(0.19)
0.131
(0.234)
0.00021
(0.00161)
1e-05
(0.000135)
0.01
(0.0348)
0.0073
(0.0275)
0.181
(0.287)
0.131
(0.234)
xp loss 145 (29%) 356 0.284
(0.402)
0.633
(0.722)
1e-05
(0.000135)
1e-05
(0.000135)
0.162
(0.27)
0.364
(0.477)
0.00174
(0.00896)
0.0267
(0.0727)
0.00526
(0.0212)
0.00157
(0.00831)
0.00069
(0.00411)
0.0209
(0.0613)
15q gain 107 (21%) 394 0.748
(0.805)
0.427
(0.542)
1e-05
(0.000135)
0.00082
(0.00466)
0.969
(0.981)
0.663
(0.748)
0.00139
(0.00739)
0.0119
(0.04)
0.0024
(0.0115)
0.0253
(0.0702)
0.0198
(0.0586)
0.0888
(0.177)
16q loss 184 (37%) 317 0.882
(0.913)
0.0981
(0.19)
0.0267
(0.0727)
0.0684
(0.146)
0.0022
(0.0107)
0.0998
(0.193)
0.0274
(0.074)
0.0222
(0.0642)
0.00259
(0.0122)
0.312
(0.43)
0.0255
(0.0702)
0.00531
(0.0212)
xq loss 114 (23%) 387 0.187
(0.294)
0.353
(0.468)
1e-05
(0.000135)
1e-05
(0.000135)
0.315
(0.432)
0.363
(0.477)
0.00722
(0.0273)
0.981
(0.986)
0.00011
(0.00101)
0.012
(0.0401)
0.00218
(0.0106)
0.00093
(0.00514)
2q gain 143 (29%) 358 0.369
(0.482)
0.147
(0.25)
3e-05
(0.000324)
0.26
(0.377)
0.181
(0.287)
0.121
(0.221)
0.00041
(0.00284)
0.0147
(0.0468)
0.0284
(0.0757)
0.28
(0.399)
0.0178
(0.0538)
0.0446
(0.103)
8q gain 256 (51%) 245 0.0961
(0.188)
0.0264
(0.0725)
0.00045
(0.00307)
0.0615
(0.134)
0.561
(0.663)
0.625
(0.72)
0.00198
(0.00979)
6e-05
(0.000602)
0.00225
(0.0108)
0.00194
(0.00969)
0.49
(0.6)
0.373
(0.487)
11q gain 89 (18%) 412 0.00832
(0.0299)
0.104
(0.2)
0.0157
(0.0489)
0.708
(0.777)
0.626
(0.72)
0.179
(0.285)
0.264
(0.383)
0.0418
(0.0986)
0.0293
(0.0763)
0.0502
(0.113)
0.00051
(0.00326)
0.0329
(0.0831)
18q gain 102 (20%) 399 0.0346
(0.0854)
0.0078
(0.0285)
2e-05
(0.000232)
0.00052
(0.0033)
0.0732
(0.154)
0.354
(0.469)
0.00049
(0.00319)
0.00019
(0.00153)
0.062
(0.134)
0.0517
(0.115)
0.24
(0.356)
0.216
(0.328)
22q gain 222 (44%) 279 0.0149
(0.047)
0.0275
(0.0742)
1e-05
(0.000135)
0.0144
(0.0462)
0.164
(0.271)
0.143
(0.245)
0.00096
(0.00528)
0.00016
(0.00132)
0.272
(0.391)
0.0919
(0.182)
0.614
(0.712)
0.311
(0.428)
6q loss 114 (23%) 387 0.00429
(0.0182)
0.00043
(0.00296)
0.0384
(0.0931)
0.0365
(0.0896)
0.994
(0.995)
0.498
(0.608)
0.00038
(0.00267)
0.00795
(0.029)
0.599
(0.7)
0.517
(0.624)
0.0592
(0.129)
0.246
(0.36)
21q loss 264 (53%) 237 0.932
(0.955)
0.354
(0.469)
1e-05
(0.000135)
0.00682
(0.026)
0.594
(0.695)
0.39
(0.503)
0.0339
(0.0849)
0.0501
(0.113)
0.00032
(0.00235)
0.00057
(0.00357)
0.0173
(0.0526)
0.127
(0.23)
6q gain 92 (18%) 409 0.0245
(0.0685)
0.024
(0.0675)
0.00016
(0.00132)
0.117
(0.215)
0.242
(0.357)
0.695
(0.77)
0.00329
(0.0145)
0.00619
(0.0239)
0.135
(0.237)
0.144
(0.246)
0.683
(0.764)
0.883
(0.913)
10p gain 78 (16%) 423 0.367
(0.48)
0.699
(0.773)
0.0288
(0.0762)
0.32
(0.437)
0.193
(0.299)
0.189
(0.295)
0.034
(0.0849)
0.0389
(0.0939)
0.115
(0.214)
0.00078
(0.00451)
0.482
(0.593)
0.0422
(0.0993)
xq gain 79 (16%) 422 0.159
(0.266)
0.0498
(0.113)
4e-05
(0.000423)
0.00111
(0.00597)
0.121
(0.221)
0.73
(0.794)
0.0188
(0.0565)
0.0106
(0.0362)
0.0658
(0.141)
0.284
(0.402)
0.315
(0.432)
0.661
(0.748)
8p loss 243 (49%) 258 0.979
(0.986)
0.937
(0.958)
0.0131
(0.0434)
0.0137
(0.0446)
0.268
(0.387)
0.472
(0.584)
0.0517
(0.115)
0.0799
(0.165)
0.0333
(0.0838)
0.024
(0.0675)
0.00861
(0.0307)
0.452
(0.564)
16p loss 163 (33%) 338 0.725
(0.791)
0.668
(0.752)
0.00459
(0.0191)
0.0357
(0.0879)
0.0218
(0.064)
0.0557
(0.123)
0.194
(0.3)
0.446
(0.559)
0.015
(0.0472)
0.726
(0.792)
0.00206
(0.0101)
0.0966
(0.189)
19p loss 162 (32%) 339 0.125
(0.227)
0.0822
(0.167)
3e-05
(0.000324)
0.204
(0.312)
0.841
(0.883)
0.699
(0.773)
0.0346
(0.0854)
0.0164
(0.0507)
0.0451
(0.104)
0.00015
(0.00127)
0.118
(0.218)
0.0734
(0.154)
20q loss 49 (10%) 452 0.047
(0.107)
0.0755
(0.157)
0.00049
(0.00319)
0.0951
(0.186)
0.252
(0.367)
0.342
(0.459)
0.00047
(0.00315)
0.00764
(0.0282)
0.00855
(0.0306)
0.129
(0.232)
0.387
(0.5)
0.788
(0.84)
22q loss 98 (20%) 403 0.0234
(0.067)
0.101
(0.194)
0.0018
(0.00908)
0.284
(0.402)
0.0719
(0.152)
0.134
(0.237)
0.00011
(0.00101)
1e-05
(0.000135)
0.359
(0.471)
0.00914
(0.0324)
0.349
(0.465)
0.0548
(0.122)
4p gain 31 (6%) 470 0.357
(0.47)
0.1
(0.194)
0.00036
(0.0026)
0.0415
(0.0981)
0.627
(0.72)
0.154
(0.259)
0.0197
(0.0585)
0.00179
(0.00908)
0.122
(0.223)
0.325
(0.441)
0.307
(0.423)
0.0569
(0.125)
14q gain 126 (25%) 375 0.133
(0.236)
0.0237
(0.0672)
1e-05
(0.000135)
0.377
(0.49)
0.379
(0.492)
0.624
(0.72)
0.116
(0.215)
0.00351
(0.0154)
0.133
(0.236)
0.116
(0.215)
0.0429
(0.1)
0.933
(0.956)
20p gain 263 (52%) 238 0.00799
(0.029)
0.00971
(0.034)
1e-05
(0.000135)
0.0028
(0.0129)
0.307
(0.423)
0.543
(0.647)
0.0756
(0.157)
0.091
(0.18)
0.301
(0.419)
0.744
(0.802)
0.277
(0.397)
0.961
(0.976)
xp gain 64 (13%) 437 0.18
(0.287)
0.136
(0.238)
2e-05
(0.000232)
0.00426
(0.0181)
0.964
(0.977)
0.608
(0.708)
0.01
(0.0348)
0.217
(0.329)
0.00265
(0.0122)
0.244
(0.358)
0.456
(0.568)
0.176
(0.283)
2q loss 44 (9%) 457 0.687
(0.767)
0.744
(0.802)
0.0226
(0.0652)
0.0235
(0.0671)
0.882
(0.913)
0.3
(0.419)
0.224
(0.337)
0.0817
(0.166)
0.00462
(0.0192)
0.145
(0.247)
0.0166
(0.0512)
0.164
(0.271)
3p loss 310 (62%) 191 0.111
(0.21)
0.0811
(0.165)
0.0002
(0.00159)
0.0149
(0.047)
0.451
(0.563)
0.777
(0.832)
0.143
(0.245)
0.243
(0.357)
0.0752
(0.157)
0.00016
(0.00132)
0.00558
(0.022)
0.0902
(0.179)
7p loss 60 (12%) 441 0.391
(0.503)
1
(1.00)
0.00072
(0.00424)
0.0285
(0.0758)
0.713
(0.78)
0.88
(0.913)
0.381
(0.493)
0.14
(0.244)
0.024
(0.0675)
0.00573
(0.0225)
0.674
(0.757)
0.199
(0.306)
7q loss 50 (10%) 451 0.183
(0.289)
0.0888
(0.177)
0.0808
(0.165)
0.359
(0.471)
0.74
(0.802)
0.177
(0.283)
0.00012
(0.00107)
0.00049
(0.00319)
0.0654
(0.14)
0.0404
(0.0962)
0.7
(0.773)
0.0141
(0.0458)
11p loss 169 (34%) 332 0.379
(0.492)
0.442
(0.556)
0.00204
(0.01)
0.0103
(0.0353)
0.17
(0.278)
0.212
(0.322)
0.24
(0.356)
0.588
(0.69)
0.00938
(0.0331)
0.513
(0.621)
0.0393
(0.0944)
0.525
(0.631)
15q loss 141 (28%) 360 0.634
(0.722)
0.743
(0.802)
1e-05
(0.000135)
0.317
(0.435)
0.563
(0.664)
0.13
(0.233)
0.0464
(0.106)
0.239
(0.355)
0.00318
(0.0141)
0.148
(0.251)
0.0234
(0.067)
0.0861
(0.173)
3q gain 315 (63%) 186 0.721
(0.787)
0.735
(0.799)
0.00029
(0.00216)
0.00752
(0.0278)
0.425
(0.541)
0.325
(0.441)
0.284
(0.402)
0.446
(0.559)
0.142
(0.245)
0.0424
(0.0997)
0.0911
(0.18)
0.126
(0.227)
5p gain 309 (62%) 192 0.945
(0.964)
0.626
(0.72)
0.00081
(0.00463)
0.0439
(0.103)
0.695
(0.77)
0.976
(0.986)
0.219
(0.331)
0.349
(0.465)
0.628
(0.72)
0.033
(0.0832)
0.0544
(0.121)
0.172
(0.279)
6p gain 108 (22%) 393 0.113
(0.211)
0.112
(0.21)
1e-05
(0.000135)
0.0626
(0.135)
0.424
(0.54)
0.52
(0.626)
0.00012
(0.00107)
0.00448
(0.0188)
0.137
(0.238)
0.204
(0.312)
0.955
(0.971)
0.578
(0.679)
8p gain 129 (26%) 372 0.631
(0.722)
0.357
(0.47)
0.297
(0.416)
0.19
(0.296)
0.849
(0.889)
0.981
(0.986)
0.0132
(0.0436)
0.0137
(0.0446)
0.169
(0.276)
0.0191
(0.0572)
0.872
(0.907)
0.964
(0.977)
10q gain 44 (9%) 457 0.121
(0.222)
0.144
(0.246)
0.0115
(0.0391)
0.112
(0.211)
0.497
(0.606)
0.554
(0.656)
0.0341
(0.085)
0.00549
(0.0219)
0.89
(0.918)
0.164
(0.271)
0.135
(0.237)
0.473
(0.584)
11p gain 75 (15%) 426 0.503
(0.611)
0.559
(0.662)
0.343
(0.459)
0.238
(0.354)
0.4
(0.512)
0.0803
(0.165)
0.338
(0.456)
0.693
(0.77)
0.0472
(0.108)
0.133
(0.236)
0.00162
(0.00852)
0.00485
(0.0198)
19q gain 163 (33%) 338 0.0598
(0.13)
0.105
(0.201)
0.00012
(0.00107)
0.43
(0.544)
0.658
(0.745)
0.905
(0.931)
0.0254
(0.0702)
0.69
(0.769)
0.218
(0.33)
0.53
(0.636)
0.0559
(0.123)
0.0462
(0.106)
1q loss 60 (12%) 441 0.647
(0.734)
0.867
(0.903)
0.00086
(0.00486)
0.0265
(0.0727)
0.611
(0.71)
0.302
(0.42)
0.0623
(0.135)
0.0277
(0.0742)
0.631
(0.722)
0.0841
(0.17)
0.0683
(0.146)
0.319
(0.436)
2p loss 24 (5%) 477 0.077
(0.16)
0.129
(0.233)
0.0323
(0.0825)
0.472
(0.584)
0.499
(0.608)
0.304
(0.421)
0.811
(0.858)
0.0951
(0.186)
0.00036
(0.0026)
0.38
(0.493)
0.0459
(0.106)
0.0853
(0.172)
5p loss 79 (16%) 422 0.875
(0.91)
0.735
(0.799)
1e-05
(0.000135)
0.00038
(0.00267)
0.163
(0.271)
0.0234
(0.067)
0.163
(0.271)
0.131
(0.234)
0.145
(0.247)
0.293
(0.412)
0.324
(0.441)
0.346
(0.463)
13q loss 311 (62%) 190 0.471
(0.584)
0.712
(0.78)
2e-05
(0.000232)
0.0291
(0.0763)
0.513
(0.621)
0.75
(0.806)
0.396
(0.51)
0.703
(0.774)
0.194
(0.3)
0.106
(0.202)
0.0276
(0.0742)
0.0991
(0.192)
18p loss 141 (28%) 360 0.942
(0.961)
0.743
(0.802)
0.029
(0.0762)
0.0116
(0.0391)
0.817
(0.862)
0.376
(0.489)
0.22
(0.332)
0.0556
(0.123)
0.0896
(0.178)
0.0648
(0.139)
0.0157
(0.0489)
0.199
(0.306)
18q loss 190 (38%) 311 0.489
(0.6)
0.236
(0.351)
0.0038
(0.0164)
0.0463
(0.106)
0.473
(0.584)
0.571
(0.672)
0.515
(0.623)
0.132
(0.235)
0.114
(0.212)
0.164
(0.271)
0.0342
(0.0851)
0.226
(0.339)
20p loss 42 (8%) 459 0.191
(0.297)
0.141
(0.245)
0.13
(0.234)
0.0413
(0.0978)
0.864
(0.901)
0.304
(0.421)
0.164
(0.271)
0.03
(0.0776)
0.28
(0.399)
0.0634
(0.137)
0.0372
(0.0906)
0.439
(0.554)
20q gain 251 (50%) 250 0.503
(0.611)
0.447
(0.559)
1e-05
(0.000135)
0.341
(0.459)
0.632
(0.722)
0.842
(0.883)
0.291
(0.41)
0.175
(0.282)
0.794
(0.845)
0.0345
(0.0854)
0.105
(0.201)
0.202
(0.31)
8q loss 54 (11%) 447 0.07
(0.149)
0.277
(0.397)
0.21
(0.32)
0.189
(0.295)
0.296
(0.415)
0.173
(0.28)
0.111
(0.21)
0.0244
(0.0684)
0.0368
(0.0899)
0.25
(0.365)
0.744
(0.802)
0.534
(0.639)
11q loss 143 (29%) 358 0.988
(0.992)
0.709
(0.778)
0.0161
(0.0498)
0.0143
(0.0462)
0.749
(0.806)
0.692
(0.77)
0.481
(0.593)
0.622
(0.72)
0.611
(0.71)
0.4
(0.512)
0.501
(0.61)
0.69
(0.769)
12p loss 39 (8%) 462 0.034
(0.0849)
0.0056
(0.022)
0.246
(0.36)
0.162
(0.27)
0.399
(0.512)
0.442
(0.556)
0.93
(0.954)
0.112
(0.21)
0.0501
(0.113)
0.0827
(0.167)
0.821
(0.865)
0.258
(0.374)
1p gain 91 (18%) 410 0.113
(0.211)
0.0927
(0.183)
0.0222
(0.0642)
0.822
(0.865)
0.0737
(0.154)
0.978
(0.986)
0.336
(0.454)
0.135
(0.237)
0.0514
(0.115)
0.304
(0.421)
0.173
(0.28)
0.86
(0.898)
4q gain 21 (4%) 480 0.889
(0.918)
0.55
(0.654)
0.0289
(0.0762)
0.84
(0.883)
0.543
(0.647)
0.0716
(0.151)
0.702
(0.774)
0.957
(0.973)
0.279
(0.399)
0.463
(0.575)
0.351
(0.467)
0.179
(0.286)
5q gain 97 (19%) 404 0.776
(0.831)
0.23
(0.344)
0.241
(0.356)
0.269
(0.388)
0.296
(0.415)
0.861
(0.898)
0.27
(0.388)
0.0564
(0.124)
0.34
(0.458)
0.188
(0.294)
0.0827
(0.167)
0.0294
(0.0763)
13q gain 39 (8%) 462 0.677
(0.76)
0.662
(0.748)
0.0107
(0.0363)
0.17
(0.278)
0.56
(0.663)
0.328
(0.444)
0.531
(0.636)
0.707
(0.777)
0.194
(0.3)
0.592
(0.694)
0.164
(0.271)
0.78
(0.834)
16p gain 86 (17%) 415 0.437
(0.553)
0.543
(0.647)
0.00941
(0.0331)
0.82
(0.864)
0.922
(0.948)
0.539
(0.644)
0.633
(0.722)
0.742
(0.802)
0.426
(0.541)
0.0571
(0.125)
0.553
(0.656)
0.431
(0.545)
16q gain 85 (17%) 416 0.992
(0.994)
0.902
(0.929)
0.0102
(0.0353)
0.669
(0.753)
0.416
(0.531)
0.235
(0.351)
0.107
(0.203)
0.605
(0.706)
0.202
(0.31)
0.0707
(0.15)
0.346
(0.463)
0.356
(0.47)
12q loss 47 (9%) 454 0.369
(0.482)
0.141
(0.245)
0.115
(0.214)
0.844
(0.885)
0.62
(0.719)
0.187
(0.294)
0.678
(0.76)
0.803
(0.852)
0.0287
(0.0761)
0.198
(0.305)
0.529
(0.636)
0.134
(0.237)
19q loss 110 (22%) 391 0.604
(0.705)
0.256
(0.373)
0.00503
(0.0205)
0.241
(0.356)
0.177
(0.283)
0.886
(0.916)
0.978
(0.986)
0.486
(0.597)
0.414
(0.529)
0.168
(0.275)
0.19
(0.296)
0.486
(0.597)
3p gain 108 (22%) 393 0.95
(0.968)
0.704
(0.774)
0.111
(0.21)
0.173
(0.28)
0.939
(0.959)
0.639
(0.727)
0.444
(0.558)
0.174
(0.282)
0.326
(0.442)
0.43
(0.544)
0.809
(0.857)
0.227
(0.34)
21q gain 57 (11%) 444 0.851
(0.889)
0.815
(0.861)
0.776
(0.831)
0.541
(0.646)
0.286
(0.403)
0.564
(0.665)
0.282
(0.401)
0.776
(0.831)
0.801
(0.852)
0.466
(0.579)
0.153
(0.259)
0.642
(0.729)
3q loss 73 (15%) 428 0.981
(0.986)
0.927
(0.952)
0.713
(0.78)
0.52
(0.627)
0.177
(0.283)
0.218
(0.329)
0.807
(0.855)
0.271
(0.389)
0.577
(0.678)
0.342
(0.459)
0.445
(0.559)
0.247
(0.361)
'1p gain' versus 'CN_CNMF'

P value = 0.0222 (Fisher's exact test), Q value = 0.064

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
1P GAIN MUTATED 11 13 7 15 27 18
1P GAIN WILD-TYPE 32 102 22 72 142 40

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

'1q gain' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00096

Table S2.  Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
1Q GAIN MUTATED 17 34 12 22 88 29
1Q GAIN WILD-TYPE 26 81 17 65 81 29

Figure S2.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1q gain' versus 'METHLYATION_CNMF'

P value = 0.00662 (Fisher's exact test), Q value = 0.025

Table S3.  Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
1Q GAIN MUTATED 32 42 30 35
1Q GAIN WILD-TYPE 58 53 27 90

Figure S3.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 0.00752 (Fisher's exact test), Q value = 0.028

Table S4.  Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
1Q GAIN MUTATED 34 77 63 28
1Q GAIN WILD-TYPE 72 73 96 55

Figure S4.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00053 (Fisher's exact test), Q value = 0.0033

Table S5.  Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
1Q GAIN MUTATED 53 93 56
1Q GAIN WILD-TYPE 125 96 75

Figure S5.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.002

Table S6.  Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
1Q GAIN MUTATED 81 29 34 44
1Q GAIN WILD-TYPE 103 58 90 36

Figure S6.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00304 (Fisher's exact test), Q value = 0.014

Table S7.  Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
1Q GAIN MUTATED 49 50 65 24
1Q GAIN WILD-TYPE 40 68 134 45

Figure S7.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0221 (Fisher's exact test), Q value = 0.064

Table S8.  Gene #2: '1q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
1Q GAIN MUTATED 17 51 17 39
1Q GAIN WILD-TYPE 44 64 49 53

Figure S8.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0204 (Fisher's exact test), Q value = 0.06

Table S9.  Gene #2: '1q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
1Q GAIN MUTATED 11 82 31
1Q GAIN WILD-TYPE 26 106 78

Figure S9.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.017 (Fisher's exact test), Q value = 0.052

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
2P GAIN MUTATED 17 31 15
2P GAIN WILD-TYPE 30 25 36

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

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
2P GAIN MUTATED 14 30 12 25 106 36
2P GAIN WILD-TYPE 29 85 17 62 63 22

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S12.  Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
2P GAIN MUTATED 31 61 35 44
2P GAIN WILD-TYPE 59 34 22 81

Figure S12.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p gain' versus 'RPPA_CNMF'

P value = 0.0168 (Fisher's exact test), Q value = 0.051

Table S13.  Gene #3: '2p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 109 86 26
2P GAIN MUTATED 45 44 53 11
2P GAIN WILD-TYPE 60 65 33 15

Figure S13.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S14.  Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
2P GAIN MUTATED 33 93 71 24
2P GAIN WILD-TYPE 73 57 88 59

Figure S14.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00023

Table S15.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
2P GAIN MUTATED 61 112 48
2P GAIN WILD-TYPE 117 77 83

Figure S15.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CNMF'

P value = 0.00289 (Fisher's exact test), Q value = 0.013

Table S16.  Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
2P GAIN MUTATED 84 49 40 41
2P GAIN WILD-TYPE 100 38 84 39

Figure S16.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0315 (Fisher's exact test), Q value = 0.081

Table S17.  Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
2P GAIN MUTATED 44 50 99 21
2P GAIN WILD-TYPE 45 68 100 48

Figure S17.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00169 (Fisher's exact test), Q value = 0.0088

Table S18.  Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
2P GAIN MUTATED 26 61 18 51
2P GAIN WILD-TYPE 35 54 48 41

Figure S18.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00291 (Fisher's exact test), Q value = 0.013

Table S19.  Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
2P GAIN MUTATED 15 103 38
2P GAIN WILD-TYPE 22 85 71

Figure S19.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00032

Table S20.  Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
2Q GAIN MUTATED 8 20 8 15 68 24
2Q GAIN WILD-TYPE 35 95 21 72 101 34

Figure S20.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.0028

Table S21.  Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
2Q GAIN MUTATED 22 58 48 13
2Q GAIN WILD-TYPE 84 92 111 70

Figure S21.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0147 (Fisher's exact test), Q value = 0.047

Table S22.  Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
2Q GAIN MUTATED 39 67 35
2Q GAIN WILD-TYPE 139 122 96

Figure S22.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CNMF'

P value = 0.0284 (Fisher's exact test), Q value = 0.076

Table S23.  Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
2Q GAIN MUTATED 60 29 23 24
2Q GAIN WILD-TYPE 124 58 101 56

Figure S23.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0178 (Fisher's exact test), Q value = 0.054

Table S24.  Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
2Q GAIN MUTATED 13 42 12 32
2Q GAIN WILD-TYPE 48 73 54 60

Figure S24.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0446 (Fisher's exact test), Q value = 0.1

Table S25.  Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
2Q GAIN MUTATED 6 65 28
2Q GAIN WILD-TYPE 31 123 81

Figure S25.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.0022

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
3Q GAIN MUTATED 27 54 23 58 107 46
3Q GAIN WILD-TYPE 16 61 6 29 62 12

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

'3q gain' versus 'METHLYATION_CNMF'

P value = 0.00752 (Fisher's exact test), Q value = 0.028

Table S27.  Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
3Q GAIN MUTATED 64 58 43 66
3Q GAIN WILD-TYPE 26 37 14 59

Figure S27.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0424 (Fisher's exact test), Q value = 0.1

Table S28.  Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
3Q GAIN MUTATED 56 74 134 33
3Q GAIN WILD-TYPE 33 44 65 36

Figure S28.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.0026

Table S29.  Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
4P GAIN MUTATED 4 5 5 5 3 9
4P GAIN WILD-TYPE 39 110 24 82 166 49

Figure S29.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'4p gain' versus 'METHLYATION_CNMF'

P value = 0.0415 (Fisher's exact test), Q value = 0.098

Table S30.  Gene #7: '4p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
4P GAIN MUTATED 9 1 2 6
4P GAIN WILD-TYPE 81 94 55 119

Figure S30.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 0.0197 (Fisher's exact test), Q value = 0.059

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
4P GAIN MUTATED 5 3 16 6
4P GAIN WILD-TYPE 101 147 143 77

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

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00179 (Fisher's exact test), Q value = 0.0091

Table S32.  Gene #7: '4p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
4P GAIN MUTATED 15 3 12
4P GAIN WILD-TYPE 163 186 119

Figure S32.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q gain' versus 'CN_CNMF'

P value = 0.0289 (Fisher's exact test), Q value = 0.076

Table S33.  Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
4Q GAIN MUTATED 2 2 5 4 5 3
4Q GAIN WILD-TYPE 41 113 24 83 164 55

Figure S33.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 0.00081 (Fisher's exact test), Q value = 0.0046

Table S34.  Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
5P GAIN MUTATED 27 66 19 46 101 50
5P GAIN WILD-TYPE 16 49 10 41 68 8

Figure S34.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.0439 (Fisher's exact test), Q value = 0.1

Table S35.  Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
5P GAIN MUTATED 67 52 35 78
5P GAIN WILD-TYPE 23 43 22 47

Figure S35.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.033 (Fisher's exact test), Q value = 0.083

Table S36.  Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
5P GAIN MUTATED 56 66 137 36
5P GAIN WILD-TYPE 33 52 62 33

Figure S36.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0294 (Fisher's exact test), Q value = 0.076

Table S37.  Gene #10: '5q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
5Q GAIN MUTATED 13 36 16
5Q GAIN WILD-TYPE 24 152 93

Figure S37.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S38.  Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
6P GAIN MUTATED 9 11 5 20 37 26
6P GAIN WILD-TYPE 34 104 24 67 132 32

Figure S38.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0011

Table S39.  Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
6P GAIN MUTATED 11 26 51 19
6P GAIN WILD-TYPE 95 124 108 64

Figure S39.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00448 (Fisher's exact test), Q value = 0.019

Table S40.  Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
6P GAIN MUTATED 36 30 41
6P GAIN WILD-TYPE 142 159 90

Figure S40.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q gain' versus 'MRNA_CNMF'

P value = 0.0245 (Fisher's exact test), Q value = 0.069

Table S41.  Gene #12: '6q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
6Q GAIN MUTATED 9 3 6 9
6Q GAIN WILD-TYPE 32 47 28 20

Figure S41.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'6q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.024 (Fisher's exact test), Q value = 0.068

Table S42.  Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
6Q GAIN MUTATED 10 4 13
6Q GAIN WILD-TYPE 37 52 38

Figure S42.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.0013

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
6Q GAIN MUTATED 8 9 3 16 34 22
6Q GAIN WILD-TYPE 35 106 26 71 135 36

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

'6q gain' versus 'MRNASEQ_CNMF'

P value = 0.00329 (Fisher's exact test), Q value = 0.015

Table S44.  Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
6Q GAIN MUTATED 13 20 44 15
6Q GAIN WILD-TYPE 93 130 115 68

Figure S44.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00619 (Fisher's exact test), Q value = 0.024

Table S45.  Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
6Q GAIN MUTATED 35 23 34
6Q GAIN WILD-TYPE 143 166 97

Figure S45.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 0.036

Table S46.  Gene #13: '7p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
7P GAIN MUTATED 23 38 20
7P GAIN WILD-TYPE 24 18 31

Figure S46.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S47.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
7P GAIN MUTATED 28 46 14 18 102 30
7P GAIN WILD-TYPE 15 69 15 69 67 28

Figure S47.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 0.00289 (Fisher's exact test), Q value = 0.013

Table S48.  Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
7P GAIN MUTATED 39 59 24 47
7P GAIN WILD-TYPE 51 36 33 78

Figure S48.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00032

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
7P GAIN MUTATED 44 94 69 29
7P GAIN WILD-TYPE 62 56 90 54

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

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S50.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
7P GAIN MUTATED 65 119 52
7P GAIN WILD-TYPE 113 70 79

Figure S50.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.00222 (Fisher's exact test), Q value = 0.011

Table S51.  Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
7P GAIN MUTATED 98 42 43 47
7P GAIN WILD-TYPE 86 45 81 33

Figure S51.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00063 (Fisher's exact test), Q value = 0.0039

Table S52.  Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
7P GAIN MUTATED 60 57 84 29
7P GAIN WILD-TYPE 29 61 115 40

Figure S52.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0197 (Fisher's exact test), Q value = 0.059

Table S53.  Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
7P GAIN MUTATED 25 51 23 54
7P GAIN WILD-TYPE 36 64 43 38

Figure S53.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MRNA_CNMF'

P value = 0.00379 (Fisher's exact test), Q value = 0.016

Table S54.  Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
7Q GAIN MUTATED 20 34 11 10
7Q GAIN WILD-TYPE 21 16 23 19

Figure S54.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'7q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.0023

Table S55.  Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
7Q GAIN MUTATED 22 38 15
7Q GAIN WILD-TYPE 25 18 36

Figure S55.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S56.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
7Q GAIN MUTATED 26 33 15 13 106 27
7Q GAIN WILD-TYPE 17 82 14 74 63 31

Figure S56.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0015

Table S57.  Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
7Q GAIN MUTATED 34 57 24 39
7Q GAIN WILD-TYPE 56 38 33 86

Figure S57.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'RPPA_CNMF'

P value = 0.0323 (Fisher's exact test), Q value = 0.082

Table S58.  Gene #14: '7q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 109 86 26
7Q GAIN MUTATED 41 41 48 14
7Q GAIN WILD-TYPE 64 68 38 12

Figure S58.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
7Q GAIN MUTATED 38 97 52 31
7Q GAIN WILD-TYPE 68 53 107 52

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

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S60.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
7Q GAIN MUTATED 55 120 43
7Q GAIN WILD-TYPE 123 69 88

Figure S60.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00087

Table S61.  Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
7Q GAIN MUTATED 88 38 37 49
7Q GAIN WILD-TYPE 96 49 87 31

Figure S61.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00089 (Fisher's exact test), Q value = 0.005

Table S62.  Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
7Q GAIN MUTATED 57 47 81 27
7Q GAIN WILD-TYPE 32 71 118 42

Figure S62.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0146 (Fisher's exact test), Q value = 0.047

Table S63.  Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
7Q GAIN MUTATED 20 49 21 50
7Q GAIN WILD-TYPE 41 66 45 42

Figure S63.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0178 (Fisher's exact test), Q value = 0.054

Table S64.  Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
7Q GAIN MUTATED 8 87 45
7Q GAIN WILD-TYPE 29 101 64

Figure S64.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.0132 (Fisher's exact test), Q value = 0.044

Table S65.  Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
8P GAIN MUTATED 25 26 50 27
8P GAIN WILD-TYPE 81 124 109 56

Figure S65.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0137 (Fisher's exact test), Q value = 0.045

Table S66.  Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
8P GAIN MUTATED 54 35 39
8P GAIN WILD-TYPE 124 154 92

Figure S66.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0191 (Fisher's exact test), Q value = 0.057

Table S67.  Gene #15: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
8P GAIN MUTATED 16 22 62 21
8P GAIN WILD-TYPE 73 96 137 48

Figure S67.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0264 (Fisher's exact test), Q value = 0.072

Table S68.  Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
8Q GAIN MUTATED 27 20 30
8Q GAIN WILD-TYPE 20 36 21

Figure S68.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.0031

Table S69.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
8Q GAIN MUTATED 30 53 19 42 72 40
8Q GAIN WILD-TYPE 13 62 10 45 97 18

Figure S69.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 0.00198 (Fisher's exact test), Q value = 0.0098

Table S70.  Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
8Q GAIN MUTATED 59 57 93 45
8Q GAIN WILD-TYPE 47 93 66 38

Figure S70.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 6e-04

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
8Q GAIN MUTATED 107 72 75
8Q GAIN WILD-TYPE 71 117 56

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

'8q gain' versus 'MIRSEQ_CNMF'

P value = 0.00225 (Fisher's exact test), Q value = 0.011

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
8Q GAIN MUTATED 89 50 73 27
8Q GAIN WILD-TYPE 95 37 51 53

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

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00194 (Fisher's exact test), Q value = 0.0097

Table S73.  Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
8Q GAIN MUTATED 33 51 116 39
8Q GAIN WILD-TYPE 56 67 83 30

Figure S73.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0272 (Fisher's exact test), Q value = 0.074

Table S74.  Gene #17: '9p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
9P GAIN MUTATED 1 8 9
9P GAIN WILD-TYPE 46 48 42

Figure S74.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00023

Table S75.  Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
9P GAIN MUTATED 6 14 0 1 37 4
9P GAIN WILD-TYPE 37 101 29 86 132 54

Figure S75.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 9e-04 (Fisher's exact test), Q value = 0.005

Table S76.  Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
9P GAIN MUTATED 7 23 10 9
9P GAIN WILD-TYPE 83 72 47 116

Figure S76.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0294 (Fisher's exact test), Q value = 0.076

Table S77.  Gene #17: '9p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 79 67 62 60 30 28
9P GAIN MUTATED 14 5 4 9 0 5
9P GAIN WILD-TYPE 65 62 58 51 30 23

Figure S77.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9p gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00032

Table S78.  Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
9P GAIN MUTATED 3 35 15 9
9P GAIN WILD-TYPE 103 115 144 74

Figure S78.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S79.  Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
9P GAIN MUTATED 6 39 17
9P GAIN WILD-TYPE 172 150 114

Figure S79.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0328 (Fisher's exact test), Q value = 0.083

Table S80.  Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
9P GAIN MUTATED 17 19 16 9
9P GAIN WILD-TYPE 72 99 183 60

Figure S80.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0405 (Fisher's exact test), Q value = 0.096

Table S81.  Gene #17: '9p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
9P GAIN MUTATED 2 13 10 16
9P GAIN WILD-TYPE 59 102 56 76

Figure S81.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q gain' versus 'MRNA_CNMF'

P value = 0.0294 (Fisher's exact test), Q value = 0.076

Table S82.  Gene #18: '9q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
9Q GAIN MUTATED 3 16 6 6
9Q GAIN WILD-TYPE 38 34 28 23

Figure S82.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00175 (Fisher's exact test), Q value = 0.009

Table S83.  Gene #18: '9q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
9Q GAIN MUTATED 3 19 9
9Q GAIN WILD-TYPE 44 37 42

Figure S83.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S84.  Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
9Q GAIN MUTATED 4 17 0 3 64 3
9Q GAIN WILD-TYPE 39 98 29 84 105 55

Figure S84.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

'9q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S85.  Gene #18: '9q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
9Q GAIN MUTATED 7 36 13 10
9Q GAIN WILD-TYPE 83 59 44 115

Figure S85.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q gain' versus 'RPPA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00042

Table S86.  Gene #18: '9q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 109 86 26
9Q GAIN MUTATED 21 7 28 3
9Q GAIN WILD-TYPE 84 102 58 23

Figure S86.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'9q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00317 (Fisher's exact test), Q value = 0.014

Table S87.  Gene #18: '9q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 79 67 62 60 30 28
9Q GAIN MUTATED 22 14 3 12 2 6
9Q GAIN WILD-TYPE 57 53 59 48 28 22

Figure S87.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S88.  Gene #18: '9q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
9Q GAIN MUTATED 5 58 21 7
9Q GAIN WILD-TYPE 101 92 138 76

Figure S88.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S89.  Gene #18: '9q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
9Q GAIN MUTATED 7 64 20
9Q GAIN WILD-TYPE 171 125 111

Figure S89.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.0012

Table S90.  Gene #18: '9q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
9Q GAIN MUTATED 39 12 11 26
9Q GAIN WILD-TYPE 145 75 113 54

Figure S90.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00078

Table S91.  Gene #18: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
9Q GAIN MUTATED 30 26 24 8
9Q GAIN WILD-TYPE 59 92 175 61

Figure S91.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 0.0288 (Fisher's exact test), Q value = 0.076

Table S92.  Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
10P GAIN MUTATED 13 12 2 14 24 13
10P GAIN WILD-TYPE 30 103 27 73 145 45

Figure S92.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 0.034 (Fisher's exact test), Q value = 0.085

Table S93.  Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
10P GAIN MUTATED 23 18 29 7
10P GAIN WILD-TYPE 83 132 130 76

Figure S93.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0389 (Fisher's exact test), Q value = 0.094

Table S94.  Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
10P GAIN MUTATED 26 22 29
10P GAIN WILD-TYPE 152 167 102

Figure S94.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.0045

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
10P GAIN MUTATED 3 18 41 11
10P GAIN WILD-TYPE 86 100 158 58

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

'10p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0422 (Fisher's exact test), Q value = 0.099

Table S96.  Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
10P GAIN MUTATED 5 40 11
10P GAIN WILD-TYPE 32 148 98

Figure S96.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.039

Table S97.  Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
10Q GAIN MUTATED 7 7 0 8 11 11
10Q GAIN WILD-TYPE 36 108 29 79 158 47

Figure S97.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10q gain' versus 'MRNASEQ_CNMF'

P value = 0.0341 (Fisher's exact test), Q value = 0.085

Table S98.  Gene #20: '10q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
10Q GAIN MUTATED 12 7 20 4
10Q GAIN WILD-TYPE 94 143 139 79

Figure S98.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00549 (Fisher's exact test), Q value = 0.022

Table S99.  Gene #20: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
10Q GAIN MUTATED 16 8 19
10Q GAIN WILD-TYPE 162 181 112

Figure S99.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_CNMF'

P value = 0.0472 (Fisher's exact test), Q value = 0.11

Table S100.  Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
11P GAIN MUTATED 37 16 12 9
11P GAIN WILD-TYPE 147 71 112 71

Figure S100.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00162 (Fisher's exact test), Q value = 0.0085

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
11P GAIN MUTATED 6 28 3 12
11P GAIN WILD-TYPE 55 87 63 80

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

'11p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00485 (Fisher's exact test), Q value = 0.02

Table S102.  Gene #21: '11p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
11P GAIN MUTATED 5 37 7
11P GAIN WILD-TYPE 32 151 102

Figure S102.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q gain' versus 'MRNA_CNMF'

P value = 0.00832 (Fisher's exact test), Q value = 0.03

Table S103.  Gene #22: '11q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
11Q GAIN MUTATED 12 5 3 10
11Q GAIN WILD-TYPE 29 45 31 19

Figure S103.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.049

Table S104.  Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
11Q GAIN MUTATED 15 13 8 14 27 12
11Q GAIN WILD-TYPE 28 102 21 73 142 46

Figure S104.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0418 (Fisher's exact test), Q value = 0.099

Table S105.  Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
11Q GAIN MUTATED 40 24 25
11Q GAIN WILD-TYPE 138 165 106

Figure S105.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CNMF'

P value = 0.0293 (Fisher's exact test), Q value = 0.076

Table S106.  Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
11Q GAIN MUTATED 43 19 16 9
11Q GAIN WILD-TYPE 141 68 108 71

Figure S106.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.0033

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
11Q GAIN MUTATED 13 29 2 14
11Q GAIN WILD-TYPE 48 86 64 78

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

'11q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0329 (Fisher's exact test), Q value = 0.083

Table S108.  Gene #22: '11q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
11Q GAIN MUTATED 6 41 11
11Q GAIN WILD-TYPE 31 147 98

Figure S108.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p gain' versus 'MRNA_CNMF'

P value = 0.0146 (Fisher's exact test), Q value = 0.047

Table S109.  Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
12P GAIN MUTATED 11 30 13 12
12P GAIN WILD-TYPE 30 20 21 17

Figure S109.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'12p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0254 (Fisher's exact test), Q value = 0.07

Table S110.  Gene #23: '12p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
12P GAIN MUTATED 15 32 19
12P GAIN WILD-TYPE 32 24 32

Figure S110.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S111.  Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
12P GAIN MUTATED 20 33 11 25 99 38
12P GAIN WILD-TYPE 23 82 18 62 70 20

Figure S111.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 0.00442 (Fisher's exact test), Q value = 0.019

Table S112.  Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
12P GAIN MUTATED 46 51 33 43
12P GAIN WILD-TYPE 44 44 24 82

Figure S112.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'RPPA_CNMF'

P value = 0.0386 (Fisher's exact test), Q value = 0.093

Table S113.  Gene #23: '12p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 109 86 26
12P GAIN MUTATED 43 48 52 11
12P GAIN WILD-TYPE 62 61 34 15

Figure S113.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
12P GAIN MUTATED 32 86 80 26
12P GAIN WILD-TYPE 74 64 79 57

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

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00197 (Fisher's exact test), Q value = 0.0098

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
12P GAIN MUTATED 62 100 62
12P GAIN WILD-TYPE 116 89 69

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

'12p gain' versus 'MIRSEQ_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.039

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
12P GAIN MUTATED 94 41 41 40
12P GAIN WILD-TYPE 90 46 83 40

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

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0053 (Fisher's exact test), Q value = 0.021

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
12P GAIN MUTATED 51 53 92 20
12P GAIN WILD-TYPE 38 65 107 49

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

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.004

Table S118.  Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
12P GAIN MUTATED 25 61 17 50
12P GAIN WILD-TYPE 36 54 49 42

Figure S118.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0133 (Fisher's exact test), Q value = 0.044

Table S119.  Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
12P GAIN MUTATED 12 99 42
12P GAIN WILD-TYPE 25 89 67

Figure S119.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00052

Table S120.  Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
12Q GAIN MUTATED 13 20 6 18 72 22
12Q GAIN WILD-TYPE 30 95 23 69 97 36

Figure S120.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 0.00136 (Fisher's exact test), Q value = 0.0073

Table S121.  Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
12Q GAIN MUTATED 29 35 22 21
12Q GAIN WILD-TYPE 61 60 35 104

Figure S121.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q gain' versus 'RPPA_CNMF'

P value = 0.0441 (Fisher's exact test), Q value = 0.1

Table S122.  Gene #24: '12q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 109 86 26
12Q GAIN MUTATED 31 28 35 4
12Q GAIN WILD-TYPE 74 81 51 22

Figure S122.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 0.00751 (Fisher's exact test), Q value = 0.028

Table S123.  Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
12Q GAIN MUTATED 21 59 47 22
12Q GAIN WILD-TYPE 85 91 112 61

Figure S123.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00285 (Fisher's exact test), Q value = 0.013

Table S124.  Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
12Q GAIN MUTATED 37 64 48
12Q GAIN WILD-TYPE 141 125 83

Figure S124.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 0.0155 (Fisher's exact test), Q value = 0.049

Table S125.  Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
12Q GAIN MUTATED 67 23 25 26
12Q GAIN WILD-TYPE 117 64 99 54

Figure S125.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0294 (Fisher's exact test), Q value = 0.076

Table S126.  Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
12Q GAIN MUTATED 14 35 11 34
12Q GAIN WILD-TYPE 47 80 55 58

Figure S126.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00073 (Fisher's exact test), Q value = 0.0043

Table S127.  Gene #24: '12q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
12Q GAIN MUTATED 2 63 29
12Q GAIN WILD-TYPE 35 125 80

Figure S127.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.036

Table S128.  Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
13Q GAIN MUTATED 2 5 7 3 16 6
13Q GAIN WILD-TYPE 41 110 22 84 153 52

Figure S128.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'14q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0237 (Fisher's exact test), Q value = 0.067

Table S129.  Gene #26: '14q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
14Q GAIN MUTATED 19 11 9
14Q GAIN WILD-TYPE 28 45 42

Figure S129.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S130.  Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
14Q GAIN MUTATED 30 25 13 9 38 11
14Q GAIN WILD-TYPE 13 90 16 78 131 47

Figure S130.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00351 (Fisher's exact test), Q value = 0.015

Table S131.  Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
14Q GAIN MUTATED 60 43 23
14Q GAIN WILD-TYPE 118 146 108

Figure S131.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0429 (Fisher's exact test), Q value = 0.1

Table S132.  Gene #26: '14q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
14Q GAIN MUTATED 19 25 10 30
14Q GAIN WILD-TYPE 42 90 56 62

Figure S132.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S133.  Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
15Q GAIN MUTATED 3 10 9 19 53 13
15Q GAIN WILD-TYPE 40 105 20 68 116 45

Figure S133.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

'15q gain' versus 'METHLYATION_CNMF'

P value = 0.00082 (Fisher's exact test), Q value = 0.0047

Table S134.  Gene #27: '15q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
15Q GAIN MUTATED 19 32 12 14
15Q GAIN WILD-TYPE 71 63 45 111

Figure S134.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q gain' versus 'MRNASEQ_CNMF'

P value = 0.00139 (Fisher's exact test), Q value = 0.0074

Table S135.  Gene #27: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
15Q GAIN MUTATED 14 48 27 16
15Q GAIN WILD-TYPE 92 102 132 67

Figure S135.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0119 (Fisher's exact test), Q value = 0.04

Table S136.  Gene #27: '15q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
15Q GAIN MUTATED 32 53 20
15Q GAIN WILD-TYPE 146 136 111

Figure S136.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q gain' versus 'MIRSEQ_CNMF'

P value = 0.0024 (Fisher's exact test), Q value = 0.011

Table S137.  Gene #27: '15q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
15Q GAIN MUTATED 33 19 20 30
15Q GAIN WILD-TYPE 151 68 104 50

Figure S137.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0253 (Fisher's exact test), Q value = 0.07

Table S138.  Gene #27: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
15Q GAIN MUTATED 29 23 41 9
15Q GAIN WILD-TYPE 60 95 158 60

Figure S138.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0198 (Fisher's exact test), Q value = 0.059

Table S139.  Gene #27: '15q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
15Q GAIN MUTATED 10 31 6 22
15Q GAIN WILD-TYPE 51 84 60 70

Figure S139.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 0.00941 (Fisher's exact test), Q value = 0.033

Table S140.  Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
16P GAIN MUTATED 16 15 5 9 32 9
16P GAIN WILD-TYPE 27 100 24 78 137 49

Figure S140.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'16q gain' versus 'CN_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.035

Table S141.  Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
16Q GAIN MUTATED 13 13 8 8 31 12
16Q GAIN WILD-TYPE 30 102 21 79 138 46

Figure S141.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17p gain' versus 'MRNA_CNMF'

P value = 0.00511 (Fisher's exact test), Q value = 0.021

Table S142.  Gene #30: '17p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
17P GAIN MUTATED 1 11 1 5
17P GAIN WILD-TYPE 40 39 33 24

Figure S142.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0396 (Fisher's exact test), Q value = 0.095

Table S143.  Gene #30: '17p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
17P GAIN MUTATED 5 11 2
17P GAIN WILD-TYPE 42 45 49

Figure S143.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0013

Table S144.  Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
17P GAIN MUTATED 5 4 4 7 37 8
17P GAIN WILD-TYPE 38 111 25 80 132 50

Figure S144.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 0.0047 (Fisher's exact test), Q value = 0.019

Table S145.  Gene #30: '17p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
17P GAIN MUTATED 13 20 12 8
17P GAIN WILD-TYPE 77 75 45 117

Figure S145.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p gain' versus 'RPPA_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.041

Table S146.  Gene #30: '17p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 109 86 26
17P GAIN MUTATED 12 7 18 1
17P GAIN WILD-TYPE 93 102 68 25

Figure S146.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0026

Table S147.  Gene #30: '17p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
17P GAIN MUTATED 8 35 15 7
17P GAIN WILD-TYPE 98 115 144 76

Figure S147.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00061 (Fisher's exact test), Q value = 0.0038

Table S148.  Gene #30: '17p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
17P GAIN MUTATED 11 37 17
17P GAIN WILD-TYPE 167 152 114

Figure S148.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CNMF'

P value = 0.00262 (Fisher's exact test), Q value = 0.012

Table S149.  Gene #30: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
17P GAIN MUTATED 23 12 7 19
17P GAIN WILD-TYPE 161 75 117 61

Figure S149.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q gain' versus 'MRNA_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0016

Table S150.  Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
17Q GAIN MUTATED 6 27 7 11
17Q GAIN WILD-TYPE 35 23 27 18

Figure S150.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00102 (Fisher's exact test), Q value = 0.0055

Table S151.  Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
17Q GAIN MUTATED 12 29 10
17Q GAIN WILD-TYPE 35 27 41

Figure S151.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S152.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
17Q GAIN MUTATED 12 18 4 10 93 21
17Q GAIN WILD-TYPE 31 97 25 77 76 37

Figure S152.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S153.  Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
17Q GAIN MUTATED 24 46 23 23
17Q GAIN WILD-TYPE 66 49 34 102

Figure S153.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S154.  Gene #31: '17q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 109 86 26
17Q GAIN MUTATED 23 27 46 3
17Q GAIN WILD-TYPE 82 82 40 23

Figure S154.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S155.  Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
17Q GAIN MUTATED 17 77 45 18
17Q GAIN WILD-TYPE 89 73 114 65

Figure S155.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S156.  Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
17Q GAIN MUTATED 30 89 38
17Q GAIN WILD-TYPE 148 100 93

Figure S156.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00023

Table S157.  Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
17Q GAIN MUTATED 65 29 18 35
17Q GAIN WILD-TYPE 119 58 106 45

Figure S157.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00769 (Fisher's exact test), Q value = 0.028

Table S158.  Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
17Q GAIN MUTATED 40 35 58 14
17Q GAIN WILD-TYPE 49 83 141 55

Figure S158.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.001

Table S159.  Gene #31: '17q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
17Q GAIN MUTATED 11 47 10 35
17Q GAIN WILD-TYPE 50 68 56 57

Figure S159.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.0026

Table S160.  Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
17Q GAIN MUTATED 6 74 23
17Q GAIN WILD-TYPE 31 114 86

Figure S160.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'MRNA_CNMF'

P value = 0.0147 (Fisher's exact test), Q value = 0.047

Table S161.  Gene #32: '18p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
18P GAIN MUTATED 7 23 9 6
18P GAIN WILD-TYPE 34 27 25 23

Figure S161.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00066 (Fisher's exact test), Q value = 0.004

Table S162.  Gene #32: '18p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
18P GAIN MUTATED 8 27 10
18P GAIN WILD-TYPE 39 29 41

Figure S162.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S163.  Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
18P GAIN MUTATED 16 21 8 10 79 14
18P GAIN WILD-TYPE 27 94 21 77 90 44

Figure S163.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00032

Table S164.  Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
18P GAIN MUTATED 25 46 18 21
18P GAIN WILD-TYPE 65 49 39 104

Figure S164.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0195 (Fisher's exact test), Q value = 0.058

Table S165.  Gene #32: '18p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 79 67 62 60 30 28
18P GAIN MUTATED 22 18 16 31 8 11
18P GAIN WILD-TYPE 57 49 46 29 22 17

Figure S165.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 0.00093 (Fisher's exact test), Q value = 0.0051

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
18P GAIN MUTATED 26 63 42 16
18P GAIN WILD-TYPE 80 87 117 67

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

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
18P GAIN MUTATED 34 81 32
18P GAIN WILD-TYPE 144 108 99

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

'18p gain' versus 'MIRSEQ_CNMF'

P value = 0.0133 (Fisher's exact test), Q value = 0.044

Table S168.  Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
18P GAIN MUTATED 59 29 23 29
18P GAIN WILD-TYPE 125 58 101 51

Figure S168.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0474 (Fisher's exact test), Q value = 0.11

Table S169.  Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
18P GAIN MUTATED 5 62 31
18P GAIN WILD-TYPE 32 126 78

Figure S169.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'MRNA_CNMF'

P value = 0.0346 (Fisher's exact test), Q value = 0.085

Table S170.  Gene #33: '18q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
18Q GAIN MUTATED 6 19 5 6
18Q GAIN WILD-TYPE 35 31 29 23

Figure S170.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0078 (Fisher's exact test), Q value = 0.029

Table S171.  Gene #33: '18q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
18Q GAIN MUTATED 6 21 9
18Q GAIN WILD-TYPE 41 35 42

Figure S171.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00023

Table S172.  Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
18Q GAIN MUTATED 7 15 5 7 58 10
18Q GAIN WILD-TYPE 36 100 24 80 111 48

Figure S172.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0033

Table S173.  Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
18Q GAIN MUTATED 12 32 13 15
18Q GAIN WILD-TYPE 78 63 44 110

Figure S173.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0032

Table S174.  Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
18Q GAIN MUTATED 14 45 33 8
18Q GAIN WILD-TYPE 92 105 126 75

Figure S174.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.0015

Table S175.  Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
18Q GAIN MUTATED 21 55 24
18Q GAIN WILD-TYPE 157 134 107

Figure S175.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MRNA_CNMF'

P value = 0.0253 (Fisher's exact test), Q value = 0.07

Table S176.  Gene #34: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
19P GAIN MUTATED 7 16 2 6
19P GAIN WILD-TYPE 34 34 32 23

Figure S176.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S177.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
19P GAIN MUTATED 6 18 7 7 64 13
19P GAIN WILD-TYPE 37 97 22 80 105 45

Figure S177.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 0.00575 (Fisher's exact test), Q value = 0.022

Table S178.  Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
19P GAIN MUTATED 21 35 14 20
19P GAIN WILD-TYPE 69 60 43 105

Figure S178.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p gain' versus 'RPPA_CNMF'

P value = 0.017 (Fisher's exact test), Q value = 0.052

Table S179.  Gene #34: '19p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 109 86 26
19P GAIN MUTATED 24 18 31 5
19P GAIN WILD-TYPE 81 91 55 21

Figure S179.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.0012

Table S180.  Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
19P GAIN MUTATED 16 53 34 11
19P GAIN WILD-TYPE 90 97 125 72

Figure S180.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00386 (Fisher's exact test), Q value = 0.017

Table S181.  Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
19P GAIN MUTATED 29 58 27
19P GAIN WILD-TYPE 149 131 104

Figure S181.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 0.00626 (Fisher's exact test), Q value = 0.024

Table S182.  Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
19P GAIN MUTATED 51 16 19 27
19P GAIN WILD-TYPE 133 71 105 53

Figure S182.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00194 (Fisher's exact test), Q value = 0.0097

Table S183.  Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
19P GAIN MUTATED 35 28 36 14
19P GAIN WILD-TYPE 54 90 163 55

Figure S183.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0011

Table S184.  Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
19Q GAIN MUTATED 14 29 10 14 69 27
19Q GAIN WILD-TYPE 29 86 19 73 100 31

Figure S184.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 0.0254 (Fisher's exact test), Q value = 0.07

Table S185.  Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
19Q GAIN MUTATED 26 59 55 20
19Q GAIN WILD-TYPE 80 91 104 63

Figure S185.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0462 (Fisher's exact test), Q value = 0.11

Table S186.  Gene #35: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
19Q GAIN MUTATED 12 71 26
19Q GAIN WILD-TYPE 25 117 83

Figure S186.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p gain' versus 'MRNA_CNMF'

P value = 0.00799 (Fisher's exact test), Q value = 0.029

Table S187.  Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
20P GAIN MUTATED 24 32 10 12
20P GAIN WILD-TYPE 17 18 24 17

Figure S187.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00971 (Fisher's exact test), Q value = 0.034

Table S188.  Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
20P GAIN MUTATED 27 34 17
20P GAIN WILD-TYPE 20 22 34

Figure S188.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S189.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
20P GAIN MUTATED 32 44 18 23 107 39
20P GAIN WILD-TYPE 11 71 11 64 62 19

Figure S189.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.0028 (Fisher's exact test), Q value = 0.013

Table S190.  Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
20P GAIN MUTATED 41 59 39 56
20P GAIN WILD-TYPE 49 36 18 69

Figure S190.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S191.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
20Q GAIN MUTATED 35 49 21 25 84 37
20Q GAIN WILD-TYPE 8 66 8 62 85 21

Figure S191.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0345 (Fisher's exact test), Q value = 0.085

Table S192.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
20Q GAIN MUTATED 36 52 113 36
20Q GAIN WILD-TYPE 53 66 86 33

Figure S192.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'MRNA_CNMF'

P value = 0.0149 (Fisher's exact test), Q value = 0.047

Table S193.  Gene #39: '22q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
22Q GAIN MUTATED 20 30 11 8
22Q GAIN WILD-TYPE 21 20 23 21

Figure S193.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0275 (Fisher's exact test), Q value = 0.074

Table S194.  Gene #39: '22q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
22Q GAIN MUTATED 21 32 16
22Q GAIN WILD-TYPE 26 24 35

Figure S194.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S195.  Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
22Q GAIN MUTATED 20 34 27 20 91 30
22Q GAIN WILD-TYPE 23 81 2 67 78 28

Figure S195.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 0.0144 (Fisher's exact test), Q value = 0.046

Table S196.  Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
22Q GAIN MUTATED 42 52 27 42
22Q GAIN WILD-TYPE 48 43 30 83

Figure S196.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 0.00096 (Fisher's exact test), Q value = 0.0053

Table S197.  Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
22Q GAIN MUTATED 45 86 57 32
22Q GAIN WILD-TYPE 61 64 102 51

Figure S197.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.0013

Table S198.  Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
22Q GAIN MUTATED 84 98 38
22Q GAIN WILD-TYPE 94 91 93

Figure S198.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xp gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00023

Table S199.  Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
XP GAIN MUTATED 9 3 2 11 22 17
XP GAIN WILD-TYPE 34 112 27 76 147 41

Figure S199.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

'xp gain' versus 'METHLYATION_CNMF'

P value = 0.00426 (Fisher's exact test), Q value = 0.018

Table S200.  Gene #40: 'xp gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
XP GAIN MUTATED 13 17 11 6
XP GAIN WILD-TYPE 77 78 46 119

Figure S200.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xp gain' versus 'MRNASEQ_CNMF'

P value = 0.01 (Fisher's exact test), Q value = 0.035

Table S201.  Gene #40: 'xp gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
XP GAIN MUTATED 9 23 28 4
XP GAIN WILD-TYPE 97 127 131 79

Figure S201.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xp gain' versus 'MIRSEQ_CNMF'

P value = 0.00265 (Fisher's exact test), Q value = 0.012

Table S202.  Gene #40: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
XP GAIN MUTATED 30 15 5 9
XP GAIN WILD-TYPE 154 72 119 71

Figure S202.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0498 (Fisher's exact test), Q value = 0.11

Table S203.  Gene #41: 'xq gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
XQ GAIN MUTATED 10 14 4
XQ GAIN WILD-TYPE 37 42 47

Figure S203.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00042

Table S204.  Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
XQ GAIN MUTATED 8 6 3 8 37 17
XQ GAIN WILD-TYPE 35 109 26 79 132 41

Figure S204.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.006

Table S205.  Gene #41: 'xq gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
XQ GAIN MUTATED 11 25 9 9
XQ GAIN WILD-TYPE 79 70 48 116

Figure S205.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 0.0188 (Fisher's exact test), Q value = 0.056

Table S206.  Gene #41: 'xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
XQ GAIN MUTATED 12 35 24 8
XQ GAIN WILD-TYPE 94 115 135 75

Figure S206.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0106 (Fisher's exact test), Q value = 0.036

Table S207.  Gene #41: 'xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
XQ GAIN MUTATED 20 42 17
XQ GAIN WILD-TYPE 158 147 114

Figure S207.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S208.  Gene #42: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
1P LOSS MUTATED 8 29 8 3
1P LOSS WILD-TYPE 33 21 26 26

Figure S208.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S209.  Gene #42: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
1P LOSS MUTATED 8 31 9
1P LOSS WILD-TYPE 39 25 42

Figure S209.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S210.  Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
1P LOSS MUTATED 16 19 7 4 100 9
1P LOSS WILD-TYPE 27 96 22 83 69 49

Figure S210.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S211.  Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
1P LOSS MUTATED 15 50 27 20
1P LOSS WILD-TYPE 75 45 30 105

Figure S211.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'RPPA_CNMF'

P value = 0.0219 (Fisher's exact test), Q value = 0.064

Table S212.  Gene #42: '1p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 109 86 26
1P LOSS MUTATED 33 28 40 8
1P LOSS WILD-TYPE 72 81 46 18

Figure S212.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S213.  Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
1P LOSS MUTATED 20 85 31 18
1P LOSS WILD-TYPE 86 65 128 65

Figure S213.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S214.  Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
1P LOSS MUTATED 28 102 24
1P LOSS WILD-TYPE 150 87 107

Figure S214.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.0012

Table S215.  Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
1P LOSS MUTATED 59 22 25 40
1P LOSS WILD-TYPE 125 65 99 40

Figure S215.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S216.  Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
1P LOSS MUTATED 52 33 51 10
1P LOSS WILD-TYPE 37 85 148 59

Figure S216.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0014

Table S217.  Gene #42: '1p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
1P LOSS MUTATED 15 34 9 42
1P LOSS WILD-TYPE 46 81 57 50

Figure S217.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00558 (Fisher's exact test), Q value = 0.022

Table S218.  Gene #42: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
1P LOSS MUTATED 4 67 29
1P LOSS WILD-TYPE 33 121 80

Figure S218.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 0.00086 (Fisher's exact test), Q value = 0.0049

Table S219.  Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
1Q LOSS MUTATED 8 7 4 3 32 6
1Q LOSS WILD-TYPE 35 108 25 84 137 52

Figure S219.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'1q loss' versus 'METHLYATION_CNMF'

P value = 0.0265 (Fisher's exact test), Q value = 0.073

Table S220.  Gene #43: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
1Q LOSS MUTATED 9 21 9 11
1Q LOSS WILD-TYPE 81 74 48 114

Figure S220.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0277 (Fisher's exact test), Q value = 0.074

Table S221.  Gene #43: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
1Q LOSS MUTATED 16 32 11
1Q LOSS WILD-TYPE 162 157 120

Figure S221.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 0.0323 (Fisher's exact test), Q value = 0.082

Table S222.  Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
2P LOSS MUTATED 6 3 0 2 8 5
2P LOSS WILD-TYPE 37 112 29 85 161 53

Figure S222.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.0026

Table S223.  Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
2P LOSS MUTATED 18 1 1 2
2P LOSS WILD-TYPE 166 86 123 78

Figure S223.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0459 (Fisher's exact test), Q value = 0.11

Table S224.  Gene #44: '2p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
2P LOSS MUTATED 0 7 0 4
2P LOSS WILD-TYPE 61 108 66 88

Figure S224.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2q loss' versus 'CN_CNMF'

P value = 0.0226 (Fisher's exact test), Q value = 0.065

Table S225.  Gene #45: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
2Q LOSS MUTATED 6 5 0 5 19 9
2Q LOSS WILD-TYPE 37 110 29 82 150 49

Figure S225.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 0.0235 (Fisher's exact test), Q value = 0.067

Table S226.  Gene #45: '2q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
2Q LOSS MUTATED 9 8 9 4
2Q LOSS WILD-TYPE 81 87 48 121

Figure S226.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 0.00462 (Fisher's exact test), Q value = 0.019

Table S227.  Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
2Q LOSS MUTATED 25 9 3 6
2Q LOSS WILD-TYPE 159 78 121 74

Figure S227.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.051

Table S228.  Gene #45: '2q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
2Q LOSS MUTATED 6 11 0 10
2Q LOSS WILD-TYPE 55 104 66 82

Figure S228.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0016

Table S229.  Gene #46: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
3P LOSS MUTATED 33 49 20 59 110 39
3P LOSS WILD-TYPE 10 66 9 28 59 19

Figure S229.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 0.0149 (Fisher's exact test), Q value = 0.047

Table S230.  Gene #46: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
3P LOSS MUTATED 64 61 37 63
3P LOSS WILD-TYPE 26 34 20 62

Figure S230.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.0013

Table S231.  Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
3P LOSS MUTATED 61 81 123 26
3P LOSS WILD-TYPE 28 37 76 43

Figure S231.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00558 (Fisher's exact test), Q value = 0.022

Table S232.  Gene #46: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
3P LOSS MUTATED 38 77 28 62
3P LOSS WILD-TYPE 23 38 38 30

Figure S232.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MRNA_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0032

Table S233.  Gene #48: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
4P LOSS MUTATED 30 39 12 17
4P LOSS WILD-TYPE 11 11 22 12

Figure S233.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4p loss' versus 'MRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00052

Table S234.  Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
4P LOSS MUTATED 33 45 20
4P LOSS WILD-TYPE 14 11 31

Figure S234.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S235.  Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
4P LOSS MUTATED 30 44 15 49 144 33
4P LOSS WILD-TYPE 13 71 14 38 25 25

Figure S235.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00023

Table S236.  Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
4P LOSS MUTATED 54 74 41 60
4P LOSS WILD-TYPE 36 21 16 65

Figure S236.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'RPPA_CNMF'

P value = 0.00471 (Fisher's exact test), Q value = 0.019

Table S237.  Gene #48: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 109 86 26
4P LOSS MUTATED 65 67 71 17
4P LOSS WILD-TYPE 40 42 15 9

Figure S237.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0266 (Fisher's exact test), Q value = 0.073

Table S238.  Gene #48: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 79 67 62 60 30 28
4P LOSS MUTATED 55 50 43 44 16 12
4P LOSS WILD-TYPE 24 17 19 16 14 16

Figure S238.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S239.  Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
4P LOSS MUTATED 69 119 84 42
4P LOSS WILD-TYPE 37 31 75 41

Figure S239.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S240.  Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
4P LOSS MUTATED 98 151 65
4P LOSS WILD-TYPE 80 38 66

Figure S240.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S241.  Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
4P LOSS MUTATED 135 57 52 57
4P LOSS WILD-TYPE 49 30 72 23

Figure S241.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0492 (Fisher's exact test), Q value = 0.11

Table S242.  Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
4P LOSS MUTATED 62 79 126 34
4P LOSS WILD-TYPE 27 39 73 35

Figure S242.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 6e-04

Table S243.  Gene #48: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
4P LOSS MUTATED 34 81 26 68
4P LOSS WILD-TYPE 27 34 40 24

Figure S243.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00078

Table S244.  Gene #48: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
4P LOSS MUTATED 15 136 58
4P LOSS WILD-TYPE 22 52 51

Figure S244.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'MRNA_CNMF'

P value = 0.00176 (Fisher's exact test), Q value = 0.009

Table S245.  Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
4Q LOSS MUTATED 26 37 11 19
4Q LOSS WILD-TYPE 15 13 23 10

Figure S245.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00256 (Fisher's exact test), Q value = 0.012

Table S246.  Gene #49: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
4Q LOSS MUTATED 31 41 21
4Q LOSS WILD-TYPE 16 15 30

Figure S246.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S247.  Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
4Q LOSS MUTATED 29 47 10 41 136 34
4Q LOSS WILD-TYPE 14 68 19 46 33 24

Figure S247.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.004

Table S248.  Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
4Q LOSS MUTATED 51 69 39 59
4Q LOSS WILD-TYPE 39 26 18 66

Figure S248.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S249.  Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
4Q LOSS MUTATED 62 112 86 36
4Q LOSS WILD-TYPE 44 38 73 47

Figure S249.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.0027

Table S250.  Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
4Q LOSS MUTATED 97 133 66
4Q LOSS WILD-TYPE 81 56 65

Figure S250.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S251.  Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
4Q LOSS MUTATED 124 52 49 58
4Q LOSS WILD-TYPE 60 35 75 22

Figure S251.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.004

Table S252.  Gene #49: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
4Q LOSS MUTATED 33 71 26 66
4Q LOSS WILD-TYPE 28 44 40 26

Figure S252.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00815 (Fisher's exact test), Q value = 0.029

Table S253.  Gene #49: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
4Q LOSS MUTATED 19 124 53
4Q LOSS WILD-TYPE 18 64 56

Figure S253.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S254.  Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
5P LOSS MUTATED 11 2 8 21 33 4
5P LOSS WILD-TYPE 32 113 21 66 136 54

Figure S254.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0027

Table S255.  Gene #50: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
5P LOSS MUTATED 19 20 6 6
5P LOSS WILD-TYPE 71 75 51 119

Figure S255.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0234 (Fisher's exact test), Q value = 0.067

Table S256.  Gene #50: '5p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 79 67 62 60 30 28
5P LOSS MUTATED 6 13 10 17 4 2
5P LOSS WILD-TYPE 73 54 52 43 26 26

Figure S256.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0375 (Fisher's exact test), Q value = 0.091

Table S257.  Gene #51: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
5Q LOSS MUTATED 22 40 29
5Q LOSS WILD-TYPE 25 16 22

Figure S257.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00023

Table S258.  Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
5Q LOSS MUTATED 25 43 19 58 113 32
5Q LOSS WILD-TYPE 18 72 10 29 56 26

Figure S258.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 0.0045 (Fisher's exact test), Q value = 0.019

Table S259.  Gene #51: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
5Q LOSS MUTATED 58 63 31 56
5Q LOSS WILD-TYPE 32 32 26 69

Figure S259.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 0.00985 (Fisher's exact test), Q value = 0.034

Table S260.  Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
5Q LOSS MUTATED 57 103 86 41
5Q LOSS WILD-TYPE 49 47 73 42

Figure S260.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-04 (Fisher's exact test), Q value = 0.0046

Table S261.  Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
5Q LOSS MUTATED 90 129 68
5Q LOSS WILD-TYPE 88 60 63

Figure S261.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 0.0309 (Fisher's exact test), Q value = 0.08

Table S262.  Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
5Q LOSS MUTATED 110 57 58 49
5Q LOSS WILD-TYPE 74 30 66 31

Figure S262.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0444 (Fisher's exact test), Q value = 0.1

Table S263.  Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
5Q LOSS MUTATED 55 70 120 29
5Q LOSS WILD-TYPE 34 48 79 40

Figure S263.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00356 (Fisher's exact test), Q value = 0.016

Table S264.  Gene #51: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
5Q LOSS MUTATED 31 81 30 50
5Q LOSS WILD-TYPE 30 34 36 42

Figure S264.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6p loss' versus 'MRNA_CNMF'

P value = 0.028 (Fisher's exact test), Q value = 0.075

Table S265.  Gene #52: '6p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
6P LOSS MUTATED 5 18 6 4
6P LOSS WILD-TYPE 36 32 28 25

Figure S265.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'6p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00732 (Fisher's exact test), Q value = 0.027

Table S266.  Gene #52: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
6P LOSS MUTATED 6 20 7
6P LOSS WILD-TYPE 41 36 44

Figure S266.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.0043

Table S267.  Gene #52: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
6P LOSS MUTATED 13 22 9 11 53 6
6P LOSS WILD-TYPE 30 93 20 76 116 52

Figure S267.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.0033

Table S268.  Gene #52: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
6P LOSS MUTATED 15 37 14 20
6P LOSS WILD-TYPE 75 58 43 105

Figure S268.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00023

Table S269.  Gene #52: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
6P LOSS MUTATED 19 58 20 16
6P LOSS WILD-TYPE 87 92 139 67

Figure S269.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S270.  Gene #52: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
6P LOSS MUTATED 29 68 16
6P LOSS WILD-TYPE 149 121 115

Figure S270.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0391 (Fisher's exact test), Q value = 0.094

Table S271.  Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
6P LOSS MUTATED 30 28 38 12
6P LOSS WILD-TYPE 59 90 161 57

Figure S271.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0317 (Fisher's exact test), Q value = 0.081

Table S272.  Gene #52: '6p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
6P LOSS MUTATED 11 25 9 30
6P LOSS WILD-TYPE 50 90 57 62

Figure S272.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6q loss' versus 'MRNA_CNMF'

P value = 0.00429 (Fisher's exact test), Q value = 0.018

Table S273.  Gene #53: '6q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
6Q LOSS MUTATED 6 21 5 4
6Q LOSS WILD-TYPE 35 29 29 25

Figure S273.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'6q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.003

Table S274.  Gene #53: '6q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
6Q LOSS MUTATED 8 23 5
6Q LOSS WILD-TYPE 39 33 46

Figure S274.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 0.0384 (Fisher's exact test), Q value = 0.093

Table S275.  Gene #53: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
6Q LOSS MUTATED 15 21 7 14 48 9
6Q LOSS WILD-TYPE 28 94 22 73 121 49

Figure S275.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.0365 (Fisher's exact test), Q value = 0.09

Table S276.  Gene #53: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
6Q LOSS MUTATED 18 30 17 21
6Q LOSS WILD-TYPE 72 65 40 104

Figure S276.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0027

Table S277.  Gene #53: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
6Q LOSS MUTATED 19 52 24 18
6Q LOSS WILD-TYPE 87 98 135 65

Figure S277.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00795 (Fisher's exact test), Q value = 0.029

Table S278.  Gene #53: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
6Q LOSS MUTATED 34 57 22
6Q LOSS WILD-TYPE 144 132 109

Figure S278.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p loss' versus 'CN_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.0042

Table S279.  Gene #54: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
7P LOSS MUTATED 9 3 4 13 19 12
7P LOSS WILD-TYPE 34 112 25 74 150 46

Figure S279.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

'7p loss' versus 'METHLYATION_CNMF'

P value = 0.0285 (Fisher's exact test), Q value = 0.076

Table S280.  Gene #54: '7p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
7P LOSS MUTATED 10 8 14 12
7P LOSS WILD-TYPE 80 87 43 113

Figure S280.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p loss' versus 'MIRSEQ_CNMF'

P value = 0.024 (Fisher's exact test), Q value = 0.068

Table S281.  Gene #54: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
7P LOSS MUTATED 32 9 8 7
7P LOSS WILD-TYPE 152 78 116 73

Figure S281.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00573 (Fisher's exact test), Q value = 0.022

Table S282.  Gene #54: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
7P LOSS MUTATED 4 12 35 5
7P LOSS WILD-TYPE 85 106 164 64

Figure S282.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q loss' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0011

Table S283.  Gene #55: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
7Q LOSS MUTATED 10 6 30 4
7Q LOSS WILD-TYPE 96 144 129 79

Figure S283.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.0032

Table S284.  Gene #55: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
7Q LOSS MUTATED 17 9 24
7Q LOSS WILD-TYPE 161 180 107

Figure S284.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0404 (Fisher's exact test), Q value = 0.096

Table S285.  Gene #55: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
7Q LOSS MUTATED 4 14 26 3
7Q LOSS WILD-TYPE 85 104 173 66

Figure S285.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0141 (Fisher's exact test), Q value = 0.046

Table S286.  Gene #55: '7q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
7Q LOSS MUTATED 5 25 4
7Q LOSS WILD-TYPE 32 163 105

Figure S286.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 0.0131 (Fisher's exact test), Q value = 0.043

Table S287.  Gene #56: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
8P LOSS MUTATED 25 39 17 44 90 28
8P LOSS WILD-TYPE 18 76 12 43 79 30

Figure S287.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.045

Table S288.  Gene #56: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
8P LOSS MUTATED 47 55 33 48
8P LOSS WILD-TYPE 43 40 24 77

Figure S288.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 0.0333 (Fisher's exact test), Q value = 0.084

Table S289.  Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
8P LOSS MUTATED 100 44 47 42
8P LOSS WILD-TYPE 84 43 77 38

Figure S289.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.024 (Fisher's exact test), Q value = 0.068

Table S290.  Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
8P LOSS MUTATED 48 68 92 25
8P LOSS WILD-TYPE 41 50 107 44

Figure S290.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00861 (Fisher's exact test), Q value = 0.031

Table S291.  Gene #56: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
8P LOSS MUTATED 37 53 22 51
8P LOSS WILD-TYPE 24 62 44 41

Figure S291.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0244 (Fisher's exact test), Q value = 0.068

Table S292.  Gene #57: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
8Q LOSS MUTATED 11 28 15
8Q LOSS WILD-TYPE 167 161 116

Figure S292.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_CNMF'

P value = 0.0368 (Fisher's exact test), Q value = 0.09

Table S293.  Gene #57: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
8Q LOSS MUTATED 28 7 7 11
8Q LOSS WILD-TYPE 156 80 117 69

Figure S293.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p loss' versus 'MRNA_CNMF'

P value = 0.0237 (Fisher's exact test), Q value = 0.067

Table S294.  Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
9P LOSS MUTATED 34 27 20 18
9P LOSS WILD-TYPE 7 23 14 11

Figure S294.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0026 (Fisher's exact test), Q value = 0.012

Table S295.  Gene #58: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
9P LOSS MUTATED 39 29 31
9P LOSS WILD-TYPE 8 27 20

Figure S295.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S296.  Gene #58: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
9P LOSS MUTATED 29 51 26 76 91 42
9P LOSS WILD-TYPE 14 64 3 11 78 16

Figure S296.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 0.00172 (Fisher's exact test), Q value = 0.0089

Table S297.  Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
9P LOSS MUTATED 71 52 34 72
9P LOSS WILD-TYPE 19 43 23 53

Figure S297.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S298.  Gene #58: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
9P LOSS MUTATED 83 75 112 42
9P LOSS WILD-TYPE 23 75 47 41

Figure S298.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00032

Table S299.  Gene #58: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
9P LOSS MUTATED 134 97 81
9P LOSS WILD-TYPE 44 92 50

Figure S299.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 0.00807 (Fisher's exact test), Q value = 0.029

Table S300.  Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
9P LOSS MUTATED 122 63 73 39
9P LOSS WILD-TYPE 62 24 51 41

Figure S300.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.0031

Table S301.  Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
9P LOSS MUTATED 45 75 143 34
9P LOSS WILD-TYPE 44 43 56 35

Figure S301.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00023

Table S302.  Gene #58: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
9P LOSS MUTATED 44 85 26 53
9P LOSS WILD-TYPE 17 30 40 39

Figure S302.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0155 (Fisher's exact test), Q value = 0.048

Table S303.  Gene #58: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
9P LOSS MUTATED 29 121 58
9P LOSS WILD-TYPE 8 67 51

Figure S303.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00023

Table S304.  Gene #59: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
9Q LOSS MUTATED 27 10 22 16
9Q LOSS WILD-TYPE 14 40 12 13

Figure S304.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S305.  Gene #59: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
9Q LOSS MUTATED 31 12 32
9Q LOSS WILD-TYPE 16 44 19

Figure S305.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S306.  Gene #59: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
9Q LOSS MUTATED 28 50 23 61 44 41
9Q LOSS WILD-TYPE 15 65 6 26 125 17

Figure S306.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S307.  Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
9Q LOSS MUTATED 67 25 24 66
9Q LOSS WILD-TYPE 23 70 33 59

Figure S307.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'RPPA_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.0042

Table S308.  Gene #59: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 109 86 26
9Q LOSS MUTATED 51 67 28 15
9Q LOSS WILD-TYPE 54 42 58 11

Figure S308.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00169 (Fisher's exact test), Q value = 0.0088

Table S309.  Gene #59: '9q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 79 67 62 60 30 28
9Q LOSS MUTATED 31 23 42 33 16 16
9Q LOSS WILD-TYPE 48 44 20 27 14 12

Figure S309.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S310.  Gene #59: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
9Q LOSS MUTATED 73 29 100 43
9Q LOSS WILD-TYPE 33 121 59 40

Figure S310.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S311.  Gene #59: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
9Q LOSS MUTATED 126 43 76
9Q LOSS WILD-TYPE 52 146 55

Figure S311.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S312.  Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
9Q LOSS MUTATED 86 58 70 18
9Q LOSS WILD-TYPE 98 29 54 62

Figure S312.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S313.  Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
9Q LOSS MUTATED 18 54 129 31
9Q LOSS WILD-TYPE 71 64 70 38

Figure S313.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00264 (Fisher's exact test), Q value = 0.012

Table S314.  Gene #59: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
9Q LOSS MUTATED 42 58 24 43
9Q LOSS WILD-TYPE 19 57 42 49

Figure S314.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0011 (Fisher's exact test), Q value = 0.0059

Table S315.  Gene #59: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
9Q LOSS MUTATED 29 86 52
9Q LOSS WILD-TYPE 8 102 57

Figure S315.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S316.  Gene #60: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
10P LOSS MUTATED 19 32 16 28 98 22
10P LOSS WILD-TYPE 24 83 13 59 71 36

Figure S316.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0016

Table S317.  Gene #60: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
10P LOSS MUTATED 35 53 31 36
10P LOSS WILD-TYPE 55 42 26 89

Figure S317.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'RPPA_CNMF'

P value = 0.00749 (Fisher's exact test), Q value = 0.028

Table S318.  Gene #60: '10p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 109 86 26
10P LOSS MUTATED 33 39 42 16
10P LOSS WILD-TYPE 72 70 44 10

Figure S318.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00023

Table S319.  Gene #60: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
10P LOSS MUTATED 36 91 60 27
10P LOSS WILD-TYPE 70 59 99 56

Figure S319.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.0012

Table S320.  Gene #60: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
10P LOSS MUTATED 67 104 43
10P LOSS WILD-TYPE 111 85 88

Figure S320.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.001

Table S321.  Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
10P LOSS MUTATED 88 37 34 46
10P LOSS WILD-TYPE 96 50 90 34

Figure S321.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S322.  Gene #60: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
10P LOSS MUTATED 58 41 91 15
10P LOSS WILD-TYPE 31 77 108 54

Figure S322.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00336 (Fisher's exact test), Q value = 0.015

Table S323.  Gene #60: '10p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
10P LOSS MUTATED 24 55 15 44
10P LOSS WILD-TYPE 37 60 51 48

Figure S323.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MRNA_CNMF'

P value = 0.00464 (Fisher's exact test), Q value = 0.019

Table S324.  Gene #61: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
10Q LOSS MUTATED 13 32 13 9
10Q LOSS WILD-TYPE 28 18 21 20

Figure S324.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.0016

Table S325.  Gene #61: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
10Q LOSS MUTATED 12 36 19
10Q LOSS WILD-TYPE 35 20 32

Figure S325.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S326.  Gene #61: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
10Q LOSS MUTATED 22 36 13 31 108 19
10Q LOSS WILD-TYPE 21 79 16 56 61 39

Figure S326.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00078

Table S327.  Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
10Q LOSS MUTATED 37 59 33 41
10Q LOSS WILD-TYPE 53 36 24 84

Figure S327.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'RPPA_CNMF'

P value = 0.00687 (Fisher's exact test), Q value = 0.026

Table S328.  Gene #61: '10q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 109 86 26
10Q LOSS MUTATED 40 41 50 15
10Q LOSS WILD-TYPE 65 68 36 11

Figure S328.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S329.  Gene #61: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
10Q LOSS MUTATED 41 101 60 26
10Q LOSS WILD-TYPE 65 49 99 57

Figure S329.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S330.  Gene #61: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
10Q LOSS MUTATED 69 118 41
10Q LOSS WILD-TYPE 109 71 90

Figure S330.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0032

Table S331.  Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
10Q LOSS MUTATED 87 42 40 49
10Q LOSS WILD-TYPE 97 45 84 31

Figure S331.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S332.  Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
10Q LOSS MUTATED 61 43 96 18
10Q LOSS WILD-TYPE 28 75 103 51

Figure S332.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0031

Table S333.  Gene #61: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
10Q LOSS MUTATED 24 63 17 49
10Q LOSS WILD-TYPE 37 52 49 43

Figure S333.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 0.00204 (Fisher's exact test), Q value = 0.01

Table S334.  Gene #62: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
11P LOSS MUTATED 21 22 11 31 59 25
11P LOSS WILD-TYPE 22 93 18 56 110 33

Figure S334.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.035

Table S335.  Gene #62: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
11P LOSS MUTATED 39 32 21 28
11P LOSS WILD-TYPE 51 63 36 97

Figure S335.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 0.00938 (Fisher's exact test), Q value = 0.033

Table S336.  Gene #62: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
11P LOSS MUTATED 78 27 35 19
11P LOSS WILD-TYPE 106 60 89 61

Figure S336.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0393 (Fisher's exact test), Q value = 0.094

Table S337.  Gene #62: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
11P LOSS MUTATED 23 37 13 37
11P LOSS WILD-TYPE 38 78 53 55

Figure S337.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 0.05

Table S338.  Gene #63: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
11Q LOSS MUTATED 11 22 11 19 58 22
11Q LOSS WILD-TYPE 32 93 18 68 111 36

Figure S338.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 0.0143 (Fisher's exact test), Q value = 0.046

Table S339.  Gene #63: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
11Q LOSS MUTATED 32 28 22 24
11Q LOSS WILD-TYPE 58 67 35 101

Figure S339.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p loss' versus 'MRNA_CNMF'

P value = 0.034 (Fisher's exact test), Q value = 0.085

Table S340.  Gene #64: '12p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
12P LOSS MUTATED 0 3 3 5
12P LOSS WILD-TYPE 41 47 31 24

Figure S340.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'12p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0056 (Fisher's exact test), Q value = 0.022

Table S341.  Gene #64: '12p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
12P LOSS MUTATED 0 3 8
12P LOSS WILD-TYPE 47 53 43

Figure S341.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_CNMF'

P value = 0.0287 (Fisher's exact test), Q value = 0.076

Table S342.  Gene #65: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
12Q LOSS MUTATED 12 15 8 9
12Q LOSS WILD-TYPE 172 72 116 71

Figure S342.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00023

Table S343.  Gene #66: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
13Q LOSS MUTATED 33 57 10 68 106 37
13Q LOSS WILD-TYPE 10 58 19 19 63 21

Figure S343.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.0291 (Fisher's exact test), Q value = 0.076

Table S344.  Gene #66: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
13Q LOSS MUTATED 57 68 34 65
13Q LOSS WILD-TYPE 33 27 23 60

Figure S344.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0276 (Fisher's exact test), Q value = 0.074

Table S345.  Gene #66: '13q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
13Q LOSS MUTATED 36 75 31 64
13Q LOSS WILD-TYPE 25 40 35 28

Figure S345.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S346.  Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
14Q LOSS MUTATED 1 21 11 14
14Q LOSS WILD-TYPE 40 29 23 15

Figure S346.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.0016

Table S347.  Gene #67: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
14Q LOSS MUTATED 4 23 20
14Q LOSS WILD-TYPE 43 33 31

Figure S347.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S348.  Gene #67: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
14Q LOSS MUTATED 2 28 3 34 74 26
14Q LOSS WILD-TYPE 41 87 26 53 95 32

Figure S348.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 0.0399 (Fisher's exact test), Q value = 0.095

Table S349.  Gene #67: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
14Q LOSS MUTATED 26 34 29 39
14Q LOSS WILD-TYPE 64 61 28 86

Figure S349.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CNMF'

P value = 0.00291 (Fisher's exact test), Q value = 0.013

Table S350.  Gene #67: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 109 86 26
14Q LOSS MUTATED 42 26 41 7
14Q LOSS WILD-TYPE 63 83 45 19

Figure S350.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S351.  Gene #67: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
14Q LOSS MUTATED 15 63 70 17
14Q LOSS WILD-TYPE 91 87 89 66

Figure S351.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S352.  Gene #67: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
14Q LOSS MUTATED 28 76 61
14Q LOSS WILD-TYPE 150 113 70

Figure S352.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0021

Table S353.  Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
14Q LOSS MUTATED 57 29 29 42
14Q LOSS WILD-TYPE 127 58 95 38

Figure S353.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S354.  Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
14Q LOSS MUTATED 51 35 58 13
14Q LOSS WILD-TYPE 38 83 141 56

Figure S354.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00067 (Fisher's exact test), Q value = 0.004

Table S355.  Gene #67: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
14Q LOSS MUTATED 6 81 29
14Q LOSS WILD-TYPE 31 107 80

Figure S355.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S356.  Gene #68: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
15Q LOSS MUTATED 26 33 6 8 44 24
15Q LOSS WILD-TYPE 17 82 23 79 125 34

Figure S356.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 0.0464 (Fisher's exact test), Q value = 0.11

Table S357.  Gene #68: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
15Q LOSS MUTATED 31 35 57 18
15Q LOSS WILD-TYPE 75 115 102 65

Figure S357.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 0.00318 (Fisher's exact test), Q value = 0.014

Table S358.  Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
15Q LOSS MUTATED 64 29 25 14
15Q LOSS WILD-TYPE 120 58 99 66

Figure S358.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0234 (Fisher's exact test), Q value = 0.067

Table S359.  Gene #68: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
15Q LOSS MUTATED 16 33 9 32
15Q LOSS WILD-TYPE 45 82 57 60

Figure S359.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'CN_CNMF'

P value = 0.00459 (Fisher's exact test), Q value = 0.019

Table S360.  Gene #69: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
16P LOSS MUTATED 11 24 9 29 61 29
16P LOSS WILD-TYPE 32 91 20 58 108 29

Figure S360.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 0.0357 (Fisher's exact test), Q value = 0.088

Table S361.  Gene #69: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
16P LOSS MUTATED 37 28 25 33
16P LOSS WILD-TYPE 53 67 32 92

Figure S361.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p loss' versus 'RPPA_CNMF'

P value = 0.0218 (Fisher's exact test), Q value = 0.064

Table S362.  Gene #69: '16p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 109 86 26
16P LOSS MUTATED 33 37 37 3
16P LOSS WILD-TYPE 72 72 49 23

Figure S362.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 0.015 (Fisher's exact test), Q value = 0.047

Table S363.  Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
16P LOSS MUTATED 65 37 28 25
16P LOSS WILD-TYPE 119 50 96 55

Figure S363.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00206 (Fisher's exact test), Q value = 0.01

Table S364.  Gene #69: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
16P LOSS MUTATED 21 45 10 37
16P LOSS WILD-TYPE 40 70 56 55

Figure S364.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 0.0267 (Fisher's exact test), Q value = 0.073

Table S365.  Gene #70: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
16Q LOSS MUTATED 14 28 12 32 74 24
16Q LOSS WILD-TYPE 29 87 17 55 95 34

Figure S365.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'RPPA_CNMF'

P value = 0.0022 (Fisher's exact test), Q value = 0.011

Table S366.  Gene #70: '16q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 109 86 26
16Q LOSS MUTATED 40 34 46 5
16Q LOSS WILD-TYPE 65 75 40 21

Figure S366.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 0.0274 (Fisher's exact test), Q value = 0.074

Table S367.  Gene #70: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
16Q LOSS MUTATED 33 63 65 21
16Q LOSS WILD-TYPE 73 87 94 62

Figure S367.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0222 (Fisher's exact test), Q value = 0.064

Table S368.  Gene #70: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
16Q LOSS MUTATED 51 78 53
16Q LOSS WILD-TYPE 127 111 78

Figure S368.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 0.00259 (Fisher's exact test), Q value = 0.012

Table S369.  Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
16Q LOSS MUTATED 68 43 31 33
16Q LOSS WILD-TYPE 116 44 93 47

Figure S369.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0255 (Fisher's exact test), Q value = 0.07

Table S370.  Gene #70: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
16Q LOSS MUTATED 19 52 16 37
16Q LOSS WILD-TYPE 42 63 50 55

Figure S370.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00531 (Fisher's exact test), Q value = 0.021

Table S371.  Gene #70: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
16Q LOSS MUTATED 9 84 31
16Q LOSS WILD-TYPE 28 104 78

Figure S371.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'MRNA_CNMF'

P value = 0.0202 (Fisher's exact test), Q value = 0.06

Table S372.  Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
17P LOSS MUTATED 32 25 22 14
17P LOSS WILD-TYPE 9 25 12 15

Figure S372.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 6e-04

Table S373.  Gene #71: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
17P LOSS MUTATED 31 48 16 65 95 37
17P LOSS WILD-TYPE 12 67 13 22 74 21

Figure S373.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.039

Table S374.  Gene #71: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
17P LOSS MUTATED 60 46 38 62
17P LOSS WILD-TYPE 30 49 19 63

Figure S374.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0327 (Fisher's exact test), Q value = 0.083

Table S375.  Gene #71: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 79 67 62 60 30 28
17P LOSS MUTATED 48 46 41 29 15 11
17P LOSS WILD-TYPE 31 21 21 31 15 17

Figure S375.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 0.00404 (Fisher's exact test), Q value = 0.017

Table S376.  Gene #71: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
17P LOSS MUTATED 72 71 101 47
17P LOSS WILD-TYPE 34 79 58 36

Figure S376.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00098 (Fisher's exact test), Q value = 0.0054

Table S377.  Gene #71: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
17P LOSS MUTATED 122 94 75
17P LOSS WILD-TYPE 56 95 56

Figure S377.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 0.00591 (Fisher's exact test), Q value = 0.023

Table S378.  Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
17P LOSS MUTATED 121 57 65 37
17P LOSS WILD-TYPE 63 30 59 43

Figure S378.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00243 (Fisher's exact test), Q value = 0.012

Table S379.  Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
17P LOSS MUTATED 42 75 131 32
17P LOSS WILD-TYPE 47 43 68 37

Figure S379.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0368 (Fisher's exact test), Q value = 0.09

Table S380.  Gene #71: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
17P LOSS MUTATED 25 117 53
17P LOSS WILD-TYPE 12 71 56

Figure S380.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'MRNA_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.044

Table S381.  Gene #72: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
17Q LOSS MUTATED 13 3 6 4
17Q LOSS WILD-TYPE 28 47 28 25

Figure S381.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00608 (Fisher's exact test), Q value = 0.024

Table S382.  Gene #72: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
17Q LOSS MUTATED 13 3 10
17Q LOSS WILD-TYPE 34 53 41

Figure S382.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0018

Table S383.  Gene #72: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
17Q LOSS MUTATED 14 23 9 20 14 11
17Q LOSS WILD-TYPE 29 92 20 67 155 47

Figure S383.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 0.00905 (Fisher's exact test), Q value = 0.032

Table S384.  Gene #72: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
17Q LOSS MUTATED 20 10 6 32
17Q LOSS WILD-TYPE 70 85 51 93

Figure S384.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0016

Table S385.  Gene #72: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
17Q LOSS MUTATED 30 12 31 18
17Q LOSS WILD-TYPE 76 138 128 65

Figure S385.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S386.  Gene #72: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
17Q LOSS MUTATED 56 16 19
17Q LOSS WILD-TYPE 122 173 112

Figure S386.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 0.01 (Fisher's exact test), Q value = 0.035

Table S387.  Gene #72: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
17Q LOSS MUTATED 25 17 35 11
17Q LOSS WILD-TYPE 159 70 89 69

Figure S387.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0073 (Fisher's exact test), Q value = 0.027

Table S388.  Gene #72: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
17Q LOSS MUTATED 8 17 45 18
17Q LOSS WILD-TYPE 81 101 154 51

Figure S388.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 0.029 (Fisher's exact test), Q value = 0.076

Table S389.  Gene #73: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
18P LOSS MUTATED 13 29 14 29 36 20
18P LOSS WILD-TYPE 30 86 15 58 133 38

Figure S389.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 0.0116 (Fisher's exact test), Q value = 0.039

Table S390.  Gene #73: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
18P LOSS MUTATED 23 16 22 41
18P LOSS WILD-TYPE 67 79 35 84

Figure S390.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.049

Table S391.  Gene #73: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
18P LOSS MUTATED 13 27 14 37
18P LOSS WILD-TYPE 48 88 52 55

Figure S391.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 0.0038 (Fisher's exact test), Q value = 0.016

Table S392.  Gene #74: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
18Q LOSS MUTATED 26 34 13 38 54 25
18Q LOSS WILD-TYPE 17 81 16 49 115 33

Figure S392.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 0.0463 (Fisher's exact test), Q value = 0.11

Table S393.  Gene #74: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
18Q LOSS MUTATED 36 27 29 50
18Q LOSS WILD-TYPE 54 68 28 75

Figure S393.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0342 (Fisher's exact test), Q value = 0.085

Table S394.  Gene #74: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
18Q LOSS MUTATED 21 41 20 47
18Q LOSS WILD-TYPE 40 74 46 45

Figure S394.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00032

Table S395.  Gene #75: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
19P LOSS MUTATED 26 24 11 32 44 25
19P LOSS WILD-TYPE 17 91 18 55 125 33

Figure S395.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 0.0346 (Fisher's exact test), Q value = 0.085

Table S396.  Gene #75: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
19P LOSS MUTATED 36 35 58 32
19P LOSS WILD-TYPE 70 115 101 51

Figure S396.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0164 (Fisher's exact test), Q value = 0.051

Table S397.  Gene #75: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
19P LOSS MUTATED 60 48 53
19P LOSS WILD-TYPE 118 141 78

Figure S397.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 0.0451 (Fisher's exact test), Q value = 0.1

Table S398.  Gene #75: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
19P LOSS MUTATED 64 35 32 19
19P LOSS WILD-TYPE 120 52 92 61

Figure S398.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.0013

Table S399.  Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
19P LOSS MUTATED 16 38 82 14
19P LOSS WILD-TYPE 73 80 117 55

Figure S399.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 0.00503 (Fisher's exact test), Q value = 0.02

Table S400.  Gene #76: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
19Q LOSS MUTATED 15 12 9 22 40 12
19Q LOSS WILD-TYPE 28 103 20 65 129 46

Figure S400.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'20p loss' versus 'METHLYATION_CNMF'

P value = 0.0413 (Fisher's exact test), Q value = 0.098

Table S401.  Gene #77: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
20P LOSS MUTATED 14 5 3 7
20P LOSS WILD-TYPE 76 90 54 118

Figure S401.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.03 (Fisher's exact test), Q value = 0.078

Table S402.  Gene #77: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
20P LOSS MUTATED 16 9 17
20P LOSS WILD-TYPE 162 180 114

Figure S402.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0372 (Fisher's exact test), Q value = 0.091

Table S403.  Gene #77: '20p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
20P LOSS MUTATED 6 10 0 7
20P LOSS WILD-TYPE 55 105 66 85

Figure S403.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q loss' versus 'MRNA_CNMF'

P value = 0.047 (Fisher's exact test), Q value = 0.11

Table S404.  Gene #78: '20q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
20Q LOSS MUTATED 1 10 3 2
20Q LOSS WILD-TYPE 40 40 31 27

Figure S404.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q loss' versus 'CN_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0032

Table S405.  Gene #78: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
20Q LOSS MUTATED 1 5 3 5 31 4
20Q LOSS WILD-TYPE 42 110 26 82 138 54

Figure S405.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'

'20q loss' versus 'MRNASEQ_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0031

Table S406.  Gene #78: '20q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
20Q LOSS MUTATED 6 28 12 3
20Q LOSS WILD-TYPE 100 122 147 80

Figure S406.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00764 (Fisher's exact test), Q value = 0.028

Table S407.  Gene #78: '20q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
20Q LOSS MUTATED 11 29 9
20Q LOSS WILD-TYPE 167 160 122

Figure S407.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q loss' versus 'MIRSEQ_CNMF'

P value = 0.00855 (Fisher's exact test), Q value = 0.031

Table S408.  Gene #78: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
20Q LOSS MUTATED 26 11 4 8
20Q LOSS WILD-TYPE 158 76 120 72

Figure S408.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S409.  Gene #79: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
21Q LOSS MUTATED 24 40 21 37 108 34
21Q LOSS WILD-TYPE 19 75 8 50 61 24

Figure S409.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 0.00682 (Fisher's exact test), Q value = 0.026

Table S410.  Gene #79: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
21Q LOSS MUTATED 46 60 32 50
21Q LOSS WILD-TYPE 44 35 25 75

Figure S410.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 0.0339 (Fisher's exact test), Q value = 0.085

Table S411.  Gene #79: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
21Q LOSS MUTATED 50 92 85 36
21Q LOSS WILD-TYPE 56 58 74 47

Figure S411.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0023

Table S412.  Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
21Q LOSS MUTATED 112 52 46 42
21Q LOSS WILD-TYPE 72 35 78 38

Figure S412.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00057 (Fisher's exact test), Q value = 0.0036

Table S413.  Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
21Q LOSS MUTATED 51 64 116 21
21Q LOSS WILD-TYPE 38 54 83 48

Figure S413.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0173 (Fisher's exact test), Q value = 0.053

Table S414.  Gene #79: '21q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
21Q LOSS MUTATED 28 66 23 51
21Q LOSS WILD-TYPE 33 49 43 41

Figure S414.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MRNA_CNMF'

P value = 0.0234 (Fisher's exact test), Q value = 0.067

Table S415.  Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 50 34 29
22Q LOSS MUTATED 7 6 8 12
22Q LOSS WILD-TYPE 34 44 26 17

Figure S415.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 0.0018 (Fisher's exact test), Q value = 0.0091

Table S416.  Gene #80: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
22Q LOSS MUTATED 10 27 0 23 23 15
22Q LOSS WILD-TYPE 33 88 29 64 146 43

Figure S416.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.001

Table S417.  Gene #80: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
22Q LOSS MUTATED 22 14 47 15
22Q LOSS WILD-TYPE 84 136 112 68

Figure S417.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S418.  Gene #80: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
22Q LOSS MUTATED 26 24 48
22Q LOSS WILD-TYPE 152 165 83

Figure S418.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00914 (Fisher's exact test), Q value = 0.032

Table S419.  Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
22Q LOSS MUTATED 10 31 41 7
22Q LOSS WILD-TYPE 79 87 158 62

Figure S419.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xp loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S420.  Gene #81: 'xp loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
XP LOSS MUTATED 9 13 10 33 67 13
XP LOSS WILD-TYPE 34 102 19 54 102 45

Figure S420.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #3: 'CN_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S421.  Gene #81: 'xp loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
XP LOSS MUTATED 34 36 20 14
XP LOSS WILD-TYPE 56 59 37 111

Figure S421.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xp loss' versus 'MRNASEQ_CNMF'

P value = 0.00174 (Fisher's exact test), Q value = 0.009

Table S422.  Gene #81: 'xp loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
XP LOSS MUTATED 30 57 44 12
XP LOSS WILD-TYPE 76 93 115 71

Figure S422.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0267 (Fisher's exact test), Q value = 0.073

Table S423.  Gene #81: 'xp loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
XP LOSS MUTATED 47 67 29
XP LOSS WILD-TYPE 131 122 102

Figure S423.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_CNMF'

P value = 0.00526 (Fisher's exact test), Q value = 0.021

Table S424.  Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
XP LOSS MUTATED 63 26 22 29
XP LOSS WILD-TYPE 121 61 102 51

Figure S424.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xp loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00157 (Fisher's exact test), Q value = 0.0083

Table S425.  Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
XP LOSS MUTATED 35 40 56 9
XP LOSS WILD-TYPE 54 78 143 60

Figure S425.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0041

Table S426.  Gene #81: 'xp loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
XP LOSS MUTATED 13 44 8 29
XP LOSS WILD-TYPE 48 71 58 63

Figure S426.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xp loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0209 (Fisher's exact test), Q value = 0.061

Table S427.  Gene #81: 'xp loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
XP LOSS MUTATED 9 64 21
XP LOSS WILD-TYPE 28 124 88

Figure S427.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S428.  Gene #82: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 43 115 29 87 169 58
XQ LOSS MUTATED 9 9 5 33 46 12
XQ LOSS WILD-TYPE 34 106 24 54 123 46

Figure S428.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00013

Table S429.  Gene #82: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 95 57 125
XQ LOSS MUTATED 34 23 16 9
XQ LOSS WILD-TYPE 56 72 41 116

Figure S429.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 0.00722 (Fisher's exact test), Q value = 0.027

Table S430.  Gene #82: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 106 150 159 83
XQ LOSS MUTATED 24 36 45 8
XQ LOSS WILD-TYPE 82 114 114 75

Figure S430.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.001

Table S431.  Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 184 87 124 80
XQ LOSS MUTATED 54 26 12 18
XQ LOSS WILD-TYPE 130 61 112 62

Figure S431.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.012 (Fisher's exact test), Q value = 0.04

Table S432.  Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
XQ LOSS MUTATED 22 29 53 6
XQ LOSS WILD-TYPE 67 89 146 63

Figure S432.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00218 (Fisher's exact test), Q value = 0.011

Table S433.  Gene #82: 'xq loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 115 66 92
XQ LOSS MUTATED 12 35 5 23
XQ LOSS WILD-TYPE 49 80 61 69

Figure S433.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00093 (Fisher's exact test), Q value = 0.0051

Table S434.  Gene #82: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 188 109
XQ LOSS MUTATED 9 54 12
XQ LOSS WILD-TYPE 28 134 97

Figure S434.  Get High-res Image Gene #82: '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/LUSC-TP/22533933/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LUSC-TP/22552638/LUSC-TP.transferedmergedcluster.txt

  • Number of patients = 501

  • Number of significantly arm-level cnvs = 82

  • Number of molecular subtypes = 12

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)