Correlation between copy number variations of arm-level result and molecular subtypes
Testicular Germ Cell Tumors (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/C1DR2V0G
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 75 arm-level events and 10 molecular subtypes across 150 patients, 362 significant findings detected with P value < 0.05 and Q value < 0.25.

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

  • 1q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

  • 2q gain cnv correlated to 'METHLYATION_CNMF'.

  • 3p gain cnv correlated to 'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

  • 6q gain cnv correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

  • 11p gain cnv correlated to 'RPPA_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 11q gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

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

  • 16p gain cnv correlated to 'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 16q gain cnv correlated to 'RPPA_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

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

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

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

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

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

  • 1p loss cnv correlated to 'MIRSEQ_CNMF'.

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

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

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

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

  • 5p loss cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.

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

  • 6p loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

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

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

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

  • 9p loss cnv correlated to 'CN_CNMF'.

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

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

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

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

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

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

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

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

  • 16p loss cnv correlated to 'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 16q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

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

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

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

  • 18q loss cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 20p loss cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • xp loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 75 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 362 significant findings detected.

Clinical
Features
CN
CNMF
METHLYATION
CNMF
RPPA
CNMF
RPPA
CHIERARCHICAL
MRNASEQ
CNMF
MRNASEQ
CHIERARCHICAL
MIRSEQ
CNMF
MIRSEQ
CHIERARCHICAL
MIRSEQ
MATURE
CNMF
MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
1p gain 37 (25%) 113 0.014
(0.0401)
0.00307
(0.0127)
0.00022
(0.00162)
0.00249
(0.0109)
0.00189
(0.00909)
0.00051
(0.00311)
5e-05
(0.000463)
1e-05
(0.000134)
1e-05
(0.000134)
0.00047
(0.00291)
8q gain 111 (74%) 39 0.0115
(0.0346)
0.00711
(0.0243)
0.0128
(0.0376)
0.00228
(0.0104)
4e-05
(4e-04)
0.00032
(0.00212)
0.0002
(0.00153)
8e-05
(0.00069)
0.00028
(0.00193)
0.00172
(0.00843)
15q gain 51 (34%) 99 0.0323
(0.0742)
0.0167
(0.0457)
0.00191
(0.00912)
0.00039
(0.00252)
2e-05
(0.000234)
4e-05
(4e-04)
0.00011
(0.000907)
2e-05
(0.000234)
1e-05
(0.000134)
1e-05
(0.000134)
17p gain 40 (27%) 110 0.00111
(0.00595)
1e-05
(0.000134)
4e-05
(4e-04)
1e-05
(0.000134)
1e-05
(0.000134)
1e-05
(0.000134)
2e-05
(0.000234)
1e-05
(0.000134)
1e-05
(0.000134)
1e-05
(0.000134)
17q gain 50 (33%) 100 0.007
(0.0242)
3e-05
(0.000326)
1e-05
(0.000134)
1e-05
(0.000134)
1e-05
(0.000134)
2e-05
(0.000234)
1e-05
(0.000134)
1e-05
(0.000134)
1e-05
(0.000134)
1e-05
(0.000134)
10p loss 77 (51%) 73 0.00247
(0.0109)
0.0229
(0.0575)
0.00819
(0.0266)
0.00734
(0.025)
0.031
(0.0718)
0.00553
(0.0197)
0.0421
(0.0916)
0.00062
(0.00369)
0.00194
(0.00915)
0.00285
(0.0122)
15q loss 29 (19%) 121 0.0176
(0.0474)
0.00026
(0.00182)
1e-05
(0.000134)
1e-05
(0.000134)
1e-05
(0.000134)
1e-05
(0.000134)
1e-05
(0.000134)
1e-05
(0.000134)
1e-05
(0.000134)
1e-05
(0.000134)
19p loss 49 (33%) 101 1e-05
(0.000134)
1e-05
(0.000134)
1e-05
(0.000134)
1e-05
(0.000134)
1e-05
(0.000134)
1e-05
(0.000134)
1e-05
(0.000134)
1e-05
(0.000134)
1e-05
(0.000134)
1e-05
(0.000134)
19q loss 53 (35%) 97 1e-05
(0.000134)
1e-05
(0.000134)
1e-05
(0.000134)
1e-05
(0.000134)
1e-05
(0.000134)
1e-05
(0.000134)
1e-05
(0.000134)
1e-05
(0.000134)
1e-05
(0.000134)
1e-05
(0.000134)
22q loss 43 (29%) 107 3e-05
(0.000326)
5e-05
(0.000463)
0.00166
(0.00824)
3e-05
(0.000326)
4e-05
(4e-04)
4e-05
(4e-04)
0.00014
(0.00113)
1e-05
(0.000134)
1e-05
(0.000134)
1e-05
(0.000134)
8p gain 110 (73%) 40 0.0587
(0.115)
0.00081
(0.0046)
0.00091
(0.00495)
0.00011
(0.000907)
2e-05
(0.000234)
0.00021
(0.00156)
0.00016
(0.00128)
1e-05
(0.000134)
2e-05
(0.000234)
0.0001
(0.000852)
19p gain 37 (25%) 113 0.00418
(0.016)
0.0147
(0.0413)
0.0133
(0.0388)
0.00694
(0.0242)
0.00217
(0.00992)
0.00118
(0.00628)
0.0657
(0.126)
0.00014
(0.00113)
0.00087
(0.00483)
0.00092
(0.00496)
19q gain 29 (19%) 121 5e-05
(0.000463)
0.00153
(0.00786)
0.00198
(0.00928)
0.00248
(0.0109)
0.00051
(0.00311)
0.00056
(0.00336)
0.134
(0.22)
5e-05
(0.000463)
0.00035
(0.0023)
0.0002
(0.00153)
xp gain 22 (15%) 128 0.0509
(0.105)
0.0197
(0.0511)
0.0383
(0.0847)
0.00922
(0.0292)
0.00355
(0.014)
0.00308
(0.0127)
0.00023
(0.00166)
0.00018
(0.00142)
0.00166
(0.00824)
8e-05
(0.00069)
3q gain 35 (23%) 115 0.117
(0.198)
0.0101
(0.0315)
0.00214
(0.00985)
0.00332
(0.0133)
0.00027
(0.00187)
0.0138
(0.0398)
0.0495
(0.103)
0.0104
(0.0321)
0.0194
(0.0509)
0.0561
(0.111)
20q gain 41 (27%) 109 0.0494
(0.103)
0.00289
(0.0122)
0.0422
(0.0916)
0.0281
(0.0672)
0.00512
(0.0189)
0.0508
(0.105)
0.0335
(0.0766)
0.0124
(0.0366)
0.0166
(0.0456)
0.0641
(0.124)
22q gain 39 (26%) 111 1e-05
(0.000134)
0.0569
(0.112)
0.0165
(0.0456)
0.00444
(0.0167)
2e-05
(0.000234)
4e-05
(4e-04)
0.0978
(0.171)
5e-05
(0.000463)
0.00024
(0.00171)
5e-05
(0.000463)
xq gain 23 (15%) 127 0.368
(0.465)
0.0521
(0.106)
0.0392
(0.0864)
0.00755
(0.0254)
0.0082
(0.0266)
0.00257
(0.0111)
0.00161
(0.0081)
0.00032
(0.00212)
0.00083
(0.00465)
0.00045
(0.00286)
3p loss 31 (21%) 119 0.0633
(0.122)
0.00334
(0.0133)
0.017
(0.0463)
0.317
(0.415)
0.002
(0.00932)
0.00231
(0.0104)
0.0008
(0.00458)
0.00046
(0.0029)
0.00186
(0.009)
0.00045
(0.00286)
5q loss 101 (67%) 49 6e-05
(0.000542)
0.0224
(0.0568)
0.0397
(0.087)
0.261
(0.355)
0.00277
(0.0119)
0.00349
(0.0138)
0.387
(0.482)
0.0101
(0.0315)
0.0201
(0.0519)
0.0189
(0.0499)
8p loss 12 (8%) 138 0.372
(0.466)
0.0687
(0.131)
0.0276
(0.0667)
0.00923
(0.0292)
0.0215
(0.055)
0.0477
(0.1)
0.00966
(0.0304)
0.00193
(0.00915)
0.00739
(0.0251)
0.0163
(0.0452)
10q loss 71 (47%) 79 0.00019
(0.00148)
0.0115
(0.0346)
0.0544
(0.109)
0.0238
(0.0591)
0.00438
(0.0166)
0.00142
(0.00734)
0.0677
(0.13)
0.00029
(0.00196)
0.00067
(0.00393)
0.00023
(0.00166)
14q loss 20 (13%) 130 0.1
(0.174)
0.0241
(0.0596)
0.0279
(0.0671)
0.0921
(0.164)
0.00459
(0.0171)
3e-05
(0.000326)
0.0367
(0.0826)
0.00322
(0.0131)
0.00238
(0.0107)
0.00089
(0.00487)
17p loss 37 (25%) 113 1e-05
(0.000134)
0.177
(0.264)
0.0447
(0.095)
0.00313
(0.0128)
0.00065
(0.00384)
0.00021
(0.00156)
0.0933
(0.166)
0.00334
(0.0133)
0.0016
(0.0081)
1e-05
(0.000134)
2p gain 47 (31%) 103 0.373
(0.467)
0.0101
(0.0315)
0.0699
(0.133)
0.0374
(0.0834)
0.0302
(0.071)
0.0991
(0.172)
0.0293
(0.0694)
0.0131
(0.0381)
0.0181
(0.0483)
0.019
(0.0499)
3p gain 26 (17%) 124 0.161
(0.246)
0.0554
(0.11)
0.00171
(0.00843)
0.0134
(0.0388)
6e-05
(0.000542)
0.00307
(0.0127)
0.0527
(0.107)
0.00545
(0.0197)
0.00602
(0.0213)
0.0268
(0.0655)
5p gain 6 (4%) 144 0.87
(0.906)
0.0313
(0.0723)
0.00901
(0.0289)
0.15
(0.235)
0.057
(0.112)
0.00799
(0.0265)
0.00415
(0.016)
0.00697
(0.0242)
0.00378
(0.0148)
0.0229
(0.0575)
7p gain 121 (81%) 29 0.0507
(0.105)
0.15
(0.235)
0.0155
(0.0434)
0.0213
(0.0548)
0.00076
(0.00438)
0.00859
(0.0276)
0.0116
(0.0348)
0.00747
(0.0252)
0.00706
(0.0243)
0.0576
(0.113)
7q gain 104 (69%) 46 0.142
(0.227)
0.0452
(0.0956)
0.184
(0.273)
0.472
(0.567)
3e-05
(0.000326)
0.00813
(0.0266)
0.0243
(0.06)
0.0142
(0.0406)
0.0124
(0.0365)
0.00796
(0.0265)
8q loss 5 (3%) 145 0.341
(0.437)
0.192
(0.281)
0.122
(0.204)
0.0145
(0.0412)
0.0116
(0.0348)
0.0119
(0.0352)
0.00158
(0.00806)
0.00256
(0.0111)
0.00247
(0.0109)
0.00291
(0.0123)
11q loss 116 (77%) 34 0.00288
(0.0122)
0.105
(0.181)
0.147
(0.231)
0.0772
(0.143)
7e-05
(0.000625)
1e-05
(0.000134)
8e-05
(0.00069)
0.00011
(0.000907)
0.00089
(0.00487)
1e-05
(0.000134)
6p gain 28 (19%) 122 0.371
(0.466)
0.76
(0.82)
0.428
(0.521)
0.0417
(0.0913)
0.0308
(0.0717)
0.00082
(0.00462)
0.0053
(0.0193)
0.00648
(0.0227)
0.0544
(0.109)
0.0201
(0.0519)
4q loss 109 (73%) 41 0.0688
(0.131)
0.0568
(0.112)
0.492
(0.585)
0.564
(0.647)
0.0293
(0.0694)
0.00553
(0.0197)
0.00174
(0.00847)
0.00498
(0.0185)
0.0298
(0.0704)
0.00792
(0.0265)
11p loss 99 (66%) 51 0.0813
(0.148)
0.0441
(0.0942)
0.0934
(0.166)
0.204
(0.295)
0.0921
(0.164)
0.00038
(0.00248)
0.00026
(0.00182)
0.00029
(0.00196)
0.00448
(0.0168)
0.00546
(0.0197)
13q loss 113 (75%) 37 0.0157
(0.0439)
0.227
(0.321)
0.0943
(0.167)
0.052
(0.106)
0.00047
(0.00291)
0.0012
(0.00629)
0.027
(0.0657)
0.0232
(0.058)
0.0978
(0.171)
0.0007
(0.00407)
xq loss 28 (19%) 122 2e-05
(0.000234)
0.00139
(0.00724)
0.0744
(0.139)
0.802
(0.852)
0.0227
(0.0574)
0.145
(0.229)
0.0235
(0.0587)
0.0115
(0.0346)
0.0975
(0.171)
0.00518
(0.019)
6q gain 23 (15%) 127 0.18
(0.268)
0.407
(0.5)
0.836
(0.877)
0.217
(0.31)
0.00636
(0.0224)
0.00021
(0.00156)
0.0021
(0.00972)
0.00432
(0.0164)
0.0512
(0.105)
0.0216
(0.0552)
16p gain 17 (11%) 133 0.1
(0.174)
0.125
(0.208)
0.0535
(0.108)
0.00366
(0.0144)
0.188
(0.276)
0.0364
(0.0823)
0.00391
(0.0152)
0.0166
(0.0456)
0.00838
(0.0271)
0.0709
(0.134)
16q gain 15 (10%) 135 0.102
(0.176)
0.484
(0.576)
0.0535
(0.108)
0.00807
(0.0265)
0.326
(0.425)
0.0871
(0.157)
0.0217
(0.0552)
0.0383
(0.0847)
0.0259
(0.0638)
0.0424
(0.0916)
4p loss 94 (63%) 56 0.23
(0.323)
0.026
(0.0638)
0.354
(0.45)
0.666
(0.739)
0.0426
(0.0919)
0.0777
(0.143)
0.0176
(0.0474)
0.0445
(0.0948)
0.0623
(0.121)
0.0137
(0.0395)
5q gain 3 (2%) 147 0.839
(0.879)
0.222
(0.316)
0.122
(0.204)
0.0423
(0.0916)
0.112
(0.191)
0.0146
(0.0412)
0.0119
(0.0352)
0.0431
(0.0923)
3q loss 23 (15%) 127 0.986
(1.00)
0.238
(0.332)
0.0471
(0.0993)
0.152
(0.237)
0.0808
(0.148)
0.0351
(0.0797)
0.0616
(0.12)
0.0491
(0.103)
0.0337
(0.0769)
0.171
(0.258)
18p loss 118 (79%) 32 0.268
(0.36)
0.0487
(0.102)
0.716
(0.78)
1
(1.00)
0.52
(0.607)
0.233
(0.326)
0.00587
(0.0209)
0.0196
(0.0511)
0.16
(0.246)
0.0369
(0.0827)
18q loss 122 (81%) 28 0.0293
(0.0694)
0.153
(0.238)
0.506
(0.597)
0.875
(0.909)
0.213
(0.306)
0.123
(0.205)
0.0175
(0.0473)
0.0309
(0.0717)
0.203
(0.294)
0.00803
(0.0265)
xp loss 29 (19%) 121 0.00316
(0.0129)
0.0052
(0.019)
0.763
(0.821)
0.917
(0.942)
0.0449
(0.0951)
0.178
(0.265)
0.0919
(0.164)
0.0921
(0.164)
0.0539
(0.108)
0.0167
(0.0457)
6q loss 16 (11%) 134 0.174
(0.262)
0.122
(0.204)
0.159
(0.245)
0.0623
(0.121)
0.0605
(0.118)
0.00119
(0.00629)
0.115
(0.195)
0.0277
(0.0667)
0.0355
(0.0805)
0.19
(0.279)
16p loss 44 (29%) 106 0.121
(0.203)
0.0111
(0.034)
0.29
(0.384)
0.249
(0.344)
0.233
(0.326)
0.263
(0.355)
0.00305
(0.0127)
0.0113
(0.0343)
0.0792
(0.146)
0.139
(0.224)
1q gain 60 (40%) 90 0.0368
(0.0826)
0.19
(0.279)
0.193
(0.282)
0.389
(0.483)
0.284
(0.378)
0.0375
(0.0834)
0.0742
(0.139)
0.563
(0.647)
0.225
(0.32)
0.0762
(0.142)
11p gain 9 (6%) 141 0.45
(0.545)
0.578
(0.66)
0.0499
(0.103)
0.168
(0.256)
0.0856
(0.155)
0.0394
(0.0866)
0.28
(0.374)
0.29
(0.384)
0.331
(0.428)
0.208
(0.299)
20p gain 35 (23%) 115 0.0182
(0.0484)
0.0106
(0.0327)
0.227
(0.321)
0.136
(0.221)
0.119
(0.2)
0.327
(0.425)
0.21
(0.301)
0.142
(0.227)
0.0737
(0.139)
0.167
(0.255)
5p loss 103 (69%) 47 0.0197
(0.0511)
0.138
(0.223)
0.0274
(0.0666)
0.477
(0.572)
0.116
(0.197)
0.134
(0.22)
0.518
(0.607)
0.0841
(0.153)
0.11
(0.189)
0.158
(0.244)
9q loss 58 (39%) 92 1e-05
(0.000134)
0.227
(0.321)
0.144
(0.228)
0.175
(0.262)
0.289
(0.384)
0.0178
(0.0477)
0.76
(0.82)
0.396
(0.49)
0.368
(0.465)
0.266
(0.359)
16q loss 51 (34%) 99 0.0186
(0.0494)
0.0947
(0.167)
0.658
(0.731)
0.59
(0.667)
0.714
(0.779)
0.482
(0.575)
0.0109
(0.0335)
0.121
(0.203)
0.33
(0.427)
0.13
(0.214)
17q loss 19 (13%) 131 0.00397
(0.0153)
0.819
(0.864)
0.765
(0.822)
0.352
(0.448)
0.142
(0.227)
0.0281
(0.0672)
0.338
(0.435)
0.159
(0.245)
0.142
(0.227)
0.136
(0.221)
20p loss 29 (19%) 121 0.382
(0.477)
0.436
(0.53)
0.415
(0.507)
0.451
(0.545)
0.208
(0.299)
0.26
(0.354)
0.0307
(0.0717)
0.246
(0.341)
0.182
(0.27)
0.00912
(0.0291)
2q gain 42 (28%) 108 0.807
(0.854)
0.0319
(0.0735)
0.928
(0.951)
0.253
(0.349)
0.128
(0.212)
0.75
(0.811)
0.595
(0.67)
0.399
(0.492)
0.348
(0.445)
0.611
(0.685)
11q gain 3 (2%) 147 0.144
(0.229)
0.581
(0.661)
0.135
(0.22)
0.315
(0.413)
0.231
(0.323)
0.0308
(0.0717)
0.281
(0.374)
0.149
(0.234)
0.156
(0.242)
0.171
(0.259)
1p loss 20 (13%) 130 0.0708
(0.134)
0.473
(0.567)
0.339
(0.435)
0.263
(0.355)
0.263
(0.355)
0.871
(0.906)
0.0428
(0.0919)
0.203
(0.294)
0.0717
(0.135)
0.689
(0.76)
6p loss 13 (9%) 137 0.239
(0.333)
0.0959
(0.169)
0.31
(0.407)
0.0815
(0.148)
0.241
(0.335)
0.0146
(0.0412)
0.268
(0.36)
0.114
(0.195)
0.185
(0.273)
0.482
(0.575)
9p loss 64 (43%) 86 0.00055
(0.00333)
0.718
(0.781)
0.514
(0.604)
0.26
(0.354)
0.4
(0.492)
0.388
(0.482)
0.818
(0.864)
0.773
(0.826)
0.83
(0.873)
0.831
(0.873)
4p gain 3 (2%) 147 0.605
(0.679)
0.579
(0.66)
0.862
(0.899)
1
(1.00)
0.768
(0.823)
0.683
(0.756)
0.502
(0.595)
1
(1.00)
1
(1.00)
0.779
(0.832)
9p gain 16 (11%) 134 0.35
(0.446)
0.52
(0.607)
0.43
(0.524)
0.694
(0.761)
0.593
(0.669)
0.296
(0.391)
0.251
(0.347)
0.141
(0.227)
0.176
(0.263)
0.459
(0.554)
9q gain 17 (11%) 133 0.0863
(0.156)
0.53
(0.617)
0.803
(0.852)
0.535
(0.621)
0.163
(0.249)
0.077
(0.143)
0.445
(0.541)
0.895
(0.926)
0.54
(0.626)
0.0978
(0.171)
10p gain 6 (4%) 144 0.0538
(0.108)
0.269
(0.36)
0.642
(0.716)
0.824
(0.868)
0.153
(0.238)
0.346
(0.443)
0.152
(0.237)
0.321
(0.42)
0.37
(0.466)
0.138
(0.224)
10q gain 10 (7%) 140 0.227
(0.321)
0.531
(0.617)
0.694
(0.761)
0.507
(0.598)
0.137
(0.223)
0.327
(0.425)
0.221
(0.315)
0.494
(0.587)
0.586
(0.664)
0.269
(0.36)
12p gain 146 (97%) 4 0.23
(0.323)
0.421
(0.515)
0.518
(0.607)
0.542
(0.627)
0.132
(0.217)
0.371
(0.466)
0.252
(0.348)
0.583
(0.661)
0.692
(0.761)
0.187
(0.276)
12q gain 100 (67%) 50 0.772
(0.825)
0.331
(0.427)
0.267
(0.359)
0.547
(0.632)
0.146
(0.23)
0.338
(0.435)
0.106
(0.182)
0.176
(0.263)
0.076
(0.142)
0.0779
(0.144)
14q gain 51 (34%) 99 0.0681
(0.13)
0.687
(0.759)
0.588
(0.665)
0.568
(0.651)
0.917
(0.942)
0.397
(0.49)
0.762
(0.821)
0.306
(0.402)
0.203
(0.294)
0.768
(0.823)
18p gain 4 (3%) 146 0.629
(0.703)
0.513
(0.604)
0.691
(0.761)
1
(1.00)
0.469
(0.565)
0.784
(0.835)
0.679
(0.753)
0.48
(0.574)
0.575
(0.657)
0.882
(0.914)
21q gain 126 (84%) 24 0.142
(0.227)
0.173
(0.261)
0.118
(0.199)
0.553
(0.638)
0.104
(0.179)
0.259
(0.354)
0.26
(0.354)
0.0912
(0.164)
0.171
(0.258)
0.195
(0.284)
1q loss 9 (6%) 141 0.166
(0.254)
0.503
(0.595)
0.92
(0.944)
1
(1.00)
0.738
(0.802)
0.653
(0.727)
0.574
(0.657)
0.615
(0.688)
0.299
(0.394)
0.878
(0.91)
2p loss 4 (3%) 146 1
(1.00)
0.904
(0.934)
1
(1.00)
0.911
(0.938)
1
(1.00)
1
(1.00)
1
(1.00)
0.704
(0.77)
2q loss 5 (3%) 145 0.908
(0.937)
0.748
(0.81)
0.862
(0.899)
0.598
(0.673)
0.654
(0.727)
0.583
(0.661)
0.855
(0.894)
0.52
(0.607)
0.376
(0.47)
0.256
(0.351)
7q loss 4 (3%) 146 0.134
(0.22)
1
(1.00)
0.406
(0.5)
0.0522
(0.106)
0.795
(0.846)
0.258
(0.354)
0.384
(0.479)
0.697
(0.763)
0.812
(0.859)
0.0799
(0.147)
20q loss 15 (10%) 135 0.956
(0.978)
0.744
(0.808)
0.553
(0.638)
0.328
(0.425)
0.17
(0.257)
0.357
(0.453)
0.216
(0.31)
0.415
(0.507)
0.364
(0.461)
0.461
(0.556)
'1p gain' versus 'CN_CNMF'

P value = 0.014 (Fisher's exact test), Q value = 0.04

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
1P GAIN MUTATED 11 6 20 0
1P GAIN WILD-TYPE 37 28 34 14

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

'1p gain' versus 'METHLYATION_CNMF'

P value = 0.00307 (Fisher's exact test), Q value = 0.013

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
1P GAIN MUTATED 8 4 17 8
1P GAIN WILD-TYPE 37 16 17 43

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

'1p gain' versus 'RPPA_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0016

Table S3.  Gene #1: '1p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
1P GAIN MUTATED 5 2 4 9 12
1P GAIN WILD-TYPE 40 6 6 28 6

Figure S3.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'1p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00249 (Fisher's exact test), Q value = 0.011

Table S4.  Gene #1: '1p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
1P GAIN MUTATED 6 8 18
1P GAIN WILD-TYPE 45 17 24

Figure S4.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'1p gain' versus 'MRNASEQ_CNMF'

P value = 0.00189 (Fisher's exact test), Q value = 0.0091

Table S5.  Gene #1: '1p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
1P GAIN MUTATED 4 3 17 4 2 7 0
1P GAIN WILD-TYPE 30 27 16 18 6 15 1

Figure S5.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.0031

Table S6.  Gene #1: '1p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
1P GAIN MUTATED 5 3 3 8 4 13 1
1P GAIN WILD-TYPE 38 24 9 16 4 10 12

Figure S6.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00046

Table S7.  Gene #1: '1p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
1P GAIN MUTATED 4 24 9
1P GAIN WILD-TYPE 47 33 33

Figure S7.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S8.  Gene #1: '1p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
1P GAIN MUTATED 8 20 9
1P GAIN WILD-TYPE 62 18 33

Figure S8.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S9.  Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
1P GAIN MUTATED 7 21 9
1P GAIN WILD-TYPE 62 15 36

Figure S9.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.0029

Table S10.  Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
1P GAIN MUTATED 4 4 11 6 9 3
1P GAIN WILD-TYPE 30 32 8 21 10 12

Figure S10.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q gain' versus 'CN_CNMF'

P value = 0.0368 (Fisher's exact test), Q value = 0.083

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
1Q GAIN MUTATED 16 19 23 2
1Q GAIN WILD-TYPE 32 15 31 12

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

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0375 (Fisher's exact test), Q value = 0.083

Table S12.  Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
1Q GAIN MUTATED 11 15 2 12 3 13 4
1Q GAIN WILD-TYPE 32 12 10 12 5 10 9

Figure S12.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'METHLYATION_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.031

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
2P GAIN MUTATED 8 3 14 22
2P GAIN WILD-TYPE 37 17 20 29

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

'2p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0374 (Fisher's exact test), Q value = 0.083

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
2P GAIN MUTATED 9 10 16
2P GAIN WILD-TYPE 42 15 26

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

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.0302 (Fisher's exact test), Q value = 0.071

Table S15.  Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
2P GAIN MUTATED 7 7 11 6 2 14 0
2P GAIN WILD-TYPE 27 23 22 16 6 8 1

Figure S15.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p gain' versus 'MIRSEQ_CNMF'

P value = 0.0293 (Fisher's exact test), Q value = 0.069

Table S16.  Gene #3: '2p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
2P GAIN MUTATED 10 18 19
2P GAIN WILD-TYPE 41 39 23

Figure S16.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0131 (Fisher's exact test), Q value = 0.038

Table S17.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
2P GAIN MUTATED 14 14 19
2P GAIN WILD-TYPE 56 24 23

Figure S17.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 0.048

Table S18.  Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
2P GAIN MUTATED 14 13 20
2P GAIN WILD-TYPE 55 23 25

Figure S18.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.019 (Fisher's exact test), Q value = 0.05

Table S19.  Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
2P GAIN MUTATED 4 10 9 13 5 6
2P GAIN WILD-TYPE 30 26 10 14 14 9

Figure S19.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'METHLYATION_CNMF'

P value = 0.0319 (Fisher's exact test), Q value = 0.073

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
2Q GAIN MUTATED 11 1 11 19
2Q GAIN WILD-TYPE 34 19 23 32

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

'3p gain' versus 'RPPA_CNMF'

P value = 0.00171 (Fisher's exact test), Q value = 0.0084

Table S21.  Gene #5: '3p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
3P GAIN MUTATED 3 0 0 14 3
3P GAIN WILD-TYPE 42 8 10 23 15

Figure S21.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'3p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0134 (Fisher's exact test), Q value = 0.039

Table S22.  Gene #5: '3p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
3P GAIN MUTATED 3 7 10
3P GAIN WILD-TYPE 48 18 32

Figure S22.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00054

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
3P GAIN MUTATED 2 2 6 2 1 13 0
3P GAIN WILD-TYPE 32 28 27 20 7 9 1

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

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00307 (Fisher's exact test), Q value = 0.013

Table S24.  Gene #5: '3p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
3P GAIN MUTATED 3 2 3 5 3 3 7
3P GAIN WILD-TYPE 40 25 9 19 5 20 6

Figure S24.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00545 (Fisher's exact test), Q value = 0.02

Table S25.  Gene #5: '3p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
3P GAIN MUTATED 5 9 12
3P GAIN WILD-TYPE 65 29 30

Figure S25.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00602 (Fisher's exact test), Q value = 0.021

Table S26.  Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
3P GAIN MUTATED 5 8 13
3P GAIN WILD-TYPE 64 28 32

Figure S26.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0268 (Fisher's exact test), Q value = 0.066

Table S27.  Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
3P GAIN MUTATED 3 2 5 8 3 5
3P GAIN WILD-TYPE 31 34 14 19 16 10

Figure S27.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q gain' versus 'METHLYATION_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.031

Table S28.  Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
3Q GAIN MUTATED 5 2 13 15
3Q GAIN WILD-TYPE 40 18 21 36

Figure S28.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q gain' versus 'RPPA_CNMF'

P value = 0.00214 (Fisher's exact test), Q value = 0.0098

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
3Q GAIN MUTATED 4 0 2 16 4
3Q GAIN WILD-TYPE 41 8 8 21 14

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

'3q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00332 (Fisher's exact test), Q value = 0.013

Table S30.  Gene #6: '3q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
3Q GAIN MUTATED 4 9 13
3Q GAIN WILD-TYPE 47 16 29

Figure S30.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0019

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
3Q GAIN MUTATED 2 6 10 2 2 13 0
3Q GAIN WILD-TYPE 32 24 23 20 6 9 1

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

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0138 (Fisher's exact test), Q value = 0.04

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
3Q GAIN MUTATED 4 5 5 5 3 6 7
3Q GAIN WILD-TYPE 39 22 7 19 5 17 6

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

'3q gain' versus 'MIRSEQ_CNMF'

P value = 0.0495 (Fisher's exact test), Q value = 0.1

Table S33.  Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
3Q GAIN MUTATED 6 17 12
3Q GAIN WILD-TYPE 45 40 30

Figure S33.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 0.032

Table S34.  Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
3Q GAIN MUTATED 9 14 12
3Q GAIN WILD-TYPE 61 24 30

Figure S34.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0194 (Fisher's exact test), Q value = 0.051

Table S35.  Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
3Q GAIN MUTATED 9 12 14
3Q GAIN WILD-TYPE 60 24 31

Figure S35.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.0313 (Fisher's exact test), Q value = 0.072

Table S36.  Gene #8: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
5P GAIN MUTATED 2 0 4 0
5P GAIN WILD-TYPE 43 20 30 51

Figure S36.  Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'RPPA_CNMF'

P value = 0.00901 (Fisher's exact test), Q value = 0.029

Table S37.  Gene #8: '5p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
5P GAIN MUTATED 1 0 0 0 4
5P GAIN WILD-TYPE 44 8 10 37 14

Figure S37.  Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00799 (Fisher's exact test), Q value = 0.027

Table S38.  Gene #8: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
5P GAIN MUTATED 0 1 0 0 2 3 0
5P GAIN WILD-TYPE 43 26 12 24 6 20 13

Figure S38.  Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 0.00415 (Fisher's exact test), Q value = 0.016

Table S39.  Gene #8: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
5P GAIN MUTATED 0 6 0
5P GAIN WILD-TYPE 51 51 42

Figure S39.  Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00697 (Fisher's exact test), Q value = 0.024

Table S40.  Gene #8: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
5P GAIN MUTATED 1 5 0
5P GAIN WILD-TYPE 69 33 42

Figure S40.  Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00378 (Fisher's exact test), Q value = 0.015

Table S41.  Gene #8: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
5P GAIN MUTATED 1 5 0
5P GAIN WILD-TYPE 68 31 45

Figure S41.  Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0229 (Fisher's exact test), Q value = 0.057

Table S42.  Gene #8: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
5P GAIN MUTATED 0 1 2 0 3 0
5P GAIN WILD-TYPE 34 35 17 27 16 15

Figure S42.  Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0423 (Fisher's exact test), Q value = 0.092

Table S43.  Gene #9: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
5Q GAIN MUTATED 0 0 0 0 1 2 0
5Q GAIN WILD-TYPE 43 27 12 24 7 21 13

Figure S43.  Get High-res Image Gene #9: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0146 (Fisher's exact test), Q value = 0.041

Table S44.  Gene #9: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
5Q GAIN MUTATED 0 3 0
5Q GAIN WILD-TYPE 70 35 42

Figure S44.  Get High-res Image Gene #9: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.035

Table S45.  Gene #9: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
5Q GAIN MUTATED 0 3 0
5Q GAIN WILD-TYPE 69 33 45

Figure S45.  Get High-res Image Gene #9: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0431 (Fisher's exact test), Q value = 0.092

Table S46.  Gene #9: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
5Q GAIN MUTATED 0 0 2 0 1 0
5Q GAIN WILD-TYPE 34 36 17 27 18 15

Figure S46.  Get High-res Image Gene #9: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0417 (Fisher's exact test), Q value = 0.091

Table S47.  Gene #10: '6p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
6P GAIN MUTATED 6 9 6
6P GAIN WILD-TYPE 45 16 36

Figure S47.  Get High-res Image Gene #10: '6p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 0.0308 (Fisher's exact test), Q value = 0.072

Table S48.  Gene #10: '6p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
6P GAIN MUTATED 8 1 5 7 0 7 0
6P GAIN WILD-TYPE 26 29 28 15 8 15 1

Figure S48.  Get High-res Image Gene #10: '6p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00082 (Fisher's exact test), Q value = 0.0046

Table S49.  Gene #10: '6p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
6P GAIN MUTATED 8 1 0 12 0 5 2
6P GAIN WILD-TYPE 35 26 12 12 8 18 11

Figure S49.  Get High-res Image Gene #10: '6p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 0.0053 (Fisher's exact test), Q value = 0.019

Table S50.  Gene #10: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
6P GAIN MUTATED 7 6 15
6P GAIN WILD-TYPE 44 51 27

Figure S50.  Get High-res Image Gene #10: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00648 (Fisher's exact test), Q value = 0.023

Table S51.  Gene #10: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
6P GAIN MUTATED 9 4 15
6P GAIN WILD-TYPE 61 34 27

Figure S51.  Get High-res Image Gene #10: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0201 (Fisher's exact test), Q value = 0.052

Table S52.  Gene #10: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
6P GAIN MUTATED 7 2 4 9 1 5
6P GAIN WILD-TYPE 27 34 15 18 18 10

Figure S52.  Get High-res Image Gene #10: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q gain' versus 'MRNASEQ_CNMF'

P value = 0.00636 (Fisher's exact test), Q value = 0.022

Table S53.  Gene #11: '6q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
6Q GAIN MUTATED 8 0 3 7 0 5 0
6Q GAIN WILD-TYPE 26 30 30 15 8 17 1

Figure S53.  Get High-res Image Gene #11: '6q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S54.  Gene #11: '6q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
6Q GAIN MUTATED 8 0 0 11 0 3 1
6Q GAIN WILD-TYPE 35 27 12 13 8 20 12

Figure S54.  Get High-res Image Gene #11: '6q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_CNMF'

P value = 0.0021 (Fisher's exact test), Q value = 0.0097

Table S55.  Gene #11: '6q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
6Q GAIN MUTATED 7 3 13
6Q GAIN WILD-TYPE 44 54 29

Figure S55.  Get High-res Image Gene #11: '6q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00432 (Fisher's exact test), Q value = 0.016

Table S56.  Gene #11: '6q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
6Q GAIN MUTATED 8 2 13
6Q GAIN WILD-TYPE 62 36 29

Figure S56.  Get High-res Image Gene #11: '6q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0216 (Fisher's exact test), Q value = 0.055

Table S57.  Gene #11: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
6Q GAIN MUTATED 6 2 3 8 0 4
6Q GAIN WILD-TYPE 28 34 16 19 19 11

Figure S57.  Get High-res Image Gene #11: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'RPPA_CNMF'

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

Table S58.  Gene #12: '7p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
7P GAIN MUTATED 39 8 5 25 16
7P GAIN WILD-TYPE 6 0 5 12 2

Figure S58.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'7p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0213 (Fisher's exact test), Q value = 0.055

Table S59.  Gene #12: '7p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
7P GAIN MUTATED 45 15 33
7P GAIN WILD-TYPE 6 10 9

Figure S59.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.0044

Table S60.  Gene #12: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
7P GAIN MUTATED 32 27 28 11 6 17 0
7P GAIN WILD-TYPE 2 3 5 11 2 5 1

Figure S60.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00859 (Fisher's exact test), Q value = 0.028

Table S61.  Gene #12: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
7P GAIN MUTATED 38 24 7 16 6 22 8
7P GAIN WILD-TYPE 5 3 5 8 2 1 5

Figure S61.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.0116 (Fisher's exact test), Q value = 0.035

Table S62.  Gene #12: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
7P GAIN MUTATED 44 50 27
7P GAIN WILD-TYPE 7 7 15

Figure S62.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00747 (Fisher's exact test), Q value = 0.025

Table S63.  Gene #12: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
7P GAIN MUTATED 62 32 27
7P GAIN WILD-TYPE 8 6 15

Figure S63.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00706 (Fisher's exact test), Q value = 0.024

Table S64.  Gene #12: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
7P GAIN MUTATED 61 31 29
7P GAIN WILD-TYPE 8 5 16

Figure S64.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 0.0452 (Fisher's exact test), Q value = 0.096

Table S65.  Gene #13: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
7Q GAIN MUTATED 33 12 29 30
7Q GAIN WILD-TYPE 12 8 5 21

Figure S65.  Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00033

Table S66.  Gene #13: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
7Q GAIN MUTATED 30 18 27 6 6 17 0
7Q GAIN WILD-TYPE 4 12 6 16 2 5 1

Figure S66.  Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00813 (Fisher's exact test), Q value = 0.027

Table S67.  Gene #13: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
7Q GAIN MUTATED 36 15 8 11 6 20 8
7Q GAIN WILD-TYPE 7 12 4 13 2 3 5

Figure S67.  Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 0.0243 (Fisher's exact test), Q value = 0.06

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
7Q GAIN MUTATED 38 44 22
7Q GAIN WILD-TYPE 13 13 20

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

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0142 (Fisher's exact test), Q value = 0.041

Table S69.  Gene #13: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
7Q GAIN MUTATED 51 31 22
7Q GAIN WILD-TYPE 19 7 20

Figure S69.  Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.037

Table S70.  Gene #13: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
7Q GAIN MUTATED 50 30 24
7Q GAIN WILD-TYPE 19 6 21

Figure S70.  Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00796 (Fisher's exact test), Q value = 0.027

Table S71.  Gene #13: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
7Q GAIN MUTATED 29 22 14 13 17 9
7Q GAIN WILD-TYPE 5 14 5 14 2 6

Figure S71.  Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'METHLYATION_CNMF'

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

Table S72.  Gene #14: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
8P GAIN MUTATED 37 20 22 31
8P GAIN WILD-TYPE 8 0 12 20

Figure S72.  Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p gain' versus 'RPPA_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.0049

Table S73.  Gene #14: '8p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
8P GAIN MUTATED 41 6 4 22 12
8P GAIN WILD-TYPE 4 2 6 15 6

Figure S73.  Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'8p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00091

Table S74.  Gene #14: '8p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
8P GAIN MUTATED 46 12 27
8P GAIN WILD-TYPE 5 13 15

Figure S74.  Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8p gain' versus 'MRNASEQ_CNMF'

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

Table S75.  Gene #14: '8p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
8P GAIN MUTATED 30 29 23 13 5 9 1
8P GAIN WILD-TYPE 4 1 10 9 3 13 0

Figure S75.  Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S76.  Gene #14: '8p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
8P GAIN MUTATED 37 26 8 14 5 15 5
8P GAIN WILD-TYPE 6 1 4 10 3 8 8

Figure S76.  Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_CNMF'

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

Table S77.  Gene #14: '8p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
8P GAIN MUTATED 45 44 21
8P GAIN WILD-TYPE 6 13 21

Figure S77.  Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8p gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S78.  Gene #14: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
8P GAIN MUTATED 63 26 21
8P GAIN WILD-TYPE 7 12 21

Figure S78.  Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S79.  Gene #14: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
8P GAIN MUTATED 62 24 24
8P GAIN WILD-TYPE 7 12 21

Figure S79.  Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00085

Table S80.  Gene #14: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
8P GAIN MUTATED 29 34 14 14 12 7
8P GAIN WILD-TYPE 5 2 5 13 7 8

Figure S80.  Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.035

Table S81.  Gene #15: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
8Q GAIN MUTATED 32 29 36 14
8Q GAIN WILD-TYPE 16 5 18 0

Figure S81.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.00711 (Fisher's exact test), Q value = 0.024

Table S82.  Gene #15: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
8Q GAIN MUTATED 40 17 23 31
8Q GAIN WILD-TYPE 5 3 11 20

Figure S82.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'RPPA_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 0.038

Table S83.  Gene #15: '8q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
8Q GAIN MUTATED 40 6 6 21 13
8Q GAIN WILD-TYPE 5 2 4 16 5

Figure S83.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'8q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00228 (Fisher's exact test), Q value = 0.01

Table S84.  Gene #15: '8q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
8Q GAIN MUTATED 45 14 27
8Q GAIN WILD-TYPE 6 11 15

Figure S84.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 4e-04

Table S85.  Gene #15: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
8Q GAIN MUTATED 33 25 24 14 5 9 1
8Q GAIN WILD-TYPE 1 5 9 8 3 13 0

Figure S85.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.0021

Table S86.  Gene #15: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
8Q GAIN MUTATED 40 22 8 15 5 17 4
8Q GAIN WILD-TYPE 3 5 4 9 3 6 9

Figure S86.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0015

Table S87.  Gene #15: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
8Q GAIN MUTATED 46 43 22
8Q GAIN WILD-TYPE 5 14 20

Figure S87.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00069

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
8Q GAIN MUTATED 62 27 22
8Q GAIN WILD-TYPE 8 11 20

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

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0019

Table S89.  Gene #15: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
8Q GAIN MUTATED 61 25 25
8Q GAIN WILD-TYPE 8 11 20

Figure S89.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00172 (Fisher's exact test), Q value = 0.0084

Table S90.  Gene #15: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
8Q GAIN MUTATED 31 31 14 15 13 7
8Q GAIN WILD-TYPE 3 5 5 12 6 8

Figure S90.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p gain' versus 'RPPA_CNMF'

P value = 0.0499 (Fisher's exact test), Q value = 0.1

Table S91.  Gene #20: '11p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
11P GAIN MUTATED 1 0 2 1 3
11P GAIN WILD-TYPE 44 8 8 36 15

Figure S91.  Get High-res Image Gene #20: '11p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0394 (Fisher's exact test), Q value = 0.087

Table S92.  Gene #20: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
11P GAIN MUTATED 1 1 0 1 2 1 3
11P GAIN WILD-TYPE 42 26 12 23 6 22 10

Figure S92.  Get High-res Image Gene #20: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0308 (Fisher's exact test), Q value = 0.072

Table S93.  Gene #21: '11q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
11Q GAIN MUTATED 0 0 0 0 0 1 2
11Q GAIN WILD-TYPE 43 27 12 24 8 22 11

Figure S93.  Get High-res Image Gene #21: '11q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q gain' versus 'CN_CNMF'

P value = 0.0323 (Fisher's exact test), Q value = 0.074

Table S94.  Gene #25: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
15Q GAIN MUTATED 19 17 12 3
15Q GAIN WILD-TYPE 29 17 42 11

Figure S94.  Get High-res Image Gene #25: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

'15q gain' versus 'METHLYATION_CNMF'

P value = 0.0167 (Fisher's exact test), Q value = 0.046

Table S95.  Gene #25: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
15Q GAIN MUTATED 24 5 8 14
15Q GAIN WILD-TYPE 21 15 26 37

Figure S95.  Get High-res Image Gene #25: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q gain' versus 'RPPA_CNMF'

P value = 0.00191 (Fisher's exact test), Q value = 0.0091

Table S96.  Gene #25: '15q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
15Q GAIN MUTATED 24 2 2 5 4
15Q GAIN WILD-TYPE 21 6 8 32 14

Figure S96.  Get High-res Image Gene #25: '15q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'15q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.0025

Table S97.  Gene #25: '15q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
15Q GAIN MUTATED 26 3 8
15Q GAIN WILD-TYPE 25 22 34

Figure S97.  Get High-res Image Gene #25: '15q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'15q gain' versus 'MRNASEQ_CNMF'

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

Table S98.  Gene #25: '15q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
15Q GAIN MUTATED 23 13 8 3 2 2 0
15Q GAIN WILD-TYPE 11 17 25 19 6 20 1

Figure S98.  Get High-res Image Gene #25: '15q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 4e-04

Table S99.  Gene #25: '15q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
15Q GAIN MUTATED 26 12 1 4 0 7 1
15Q GAIN WILD-TYPE 17 15 11 20 8 16 12

Figure S99.  Get High-res Image Gene #25: '15q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q gain' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00091

Table S100.  Gene #25: '15q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
15Q GAIN MUTATED 27 19 5
15Q GAIN WILD-TYPE 24 38 37

Figure S100.  Get High-res Image Gene #25: '15q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S101.  Gene #25: '15q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
15Q GAIN MUTATED 38 8 5
15Q GAIN WILD-TYPE 32 30 37

Figure S101.  Get High-res Image Gene #25: '15q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S102.  Gene #25: '15q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
15Q GAIN MUTATED 37 8 6
15Q GAIN WILD-TYPE 32 28 39

Figure S102.  Get High-res Image Gene #25: '15q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'15q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S103.  Gene #25: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
15Q GAIN MUTATED 22 16 6 3 2 2
15Q GAIN WILD-TYPE 12 20 13 24 17 13

Figure S103.  Get High-res Image Gene #25: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00366 (Fisher's exact test), Q value = 0.014

Table S104.  Gene #26: '16p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
16P GAIN MUTATED 2 8 5
16P GAIN WILD-TYPE 49 17 37

Figure S104.  Get High-res Image Gene #26: '16p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0364 (Fisher's exact test), Q value = 0.082

Table S105.  Gene #26: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
16P GAIN MUTATED 2 2 1 8 0 2 2
16P GAIN WILD-TYPE 41 25 11 16 8 21 11

Figure S105.  Get High-res Image Gene #26: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 0.00391 (Fisher's exact test), Q value = 0.015

Table S106.  Gene #26: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
16P GAIN MUTATED 1 6 10
16P GAIN WILD-TYPE 50 51 32

Figure S106.  Get High-res Image Gene #26: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0166 (Fisher's exact test), Q value = 0.046

Table S107.  Gene #26: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
16P GAIN MUTATED 4 3 10
16P GAIN WILD-TYPE 66 35 32

Figure S107.  Get High-res Image Gene #26: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00838 (Fisher's exact test), Q value = 0.027

Table S108.  Gene #26: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
16P GAIN MUTATED 4 2 11
16P GAIN WILD-TYPE 65 34 34

Figure S108.  Get High-res Image Gene #26: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00807 (Fisher's exact test), Q value = 0.027

Table S109.  Gene #27: '16q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
16Q GAIN MUTATED 1 6 5
16Q GAIN WILD-TYPE 50 19 37

Figure S109.  Get High-res Image Gene #27: '16q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CNMF'

P value = 0.0217 (Fisher's exact test), Q value = 0.055

Table S110.  Gene #27: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
16Q GAIN MUTATED 1 6 8
16Q GAIN WILD-TYPE 50 51 34

Figure S110.  Get High-res Image Gene #27: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0383 (Fisher's exact test), Q value = 0.085

Table S111.  Gene #27: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
16Q GAIN MUTATED 3 4 8
16Q GAIN WILD-TYPE 67 34 34

Figure S111.  Get High-res Image Gene #27: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S112.  Gene #27: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
16Q GAIN MUTATED 3 3 9
16Q GAIN WILD-TYPE 66 33 36

Figure S112.  Get High-res Image Gene #27: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0424 (Fisher's exact test), Q value = 0.092

Table S113.  Gene #27: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
16Q GAIN MUTATED 0 3 3 6 1 2
16Q GAIN WILD-TYPE 34 33 16 21 18 13

Figure S113.  Get High-res Image Gene #27: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.0059

Table S114.  Gene #28: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
17P GAIN MUTATED 9 3 24 4
17P GAIN WILD-TYPE 39 31 30 10

Figure S114.  Get High-res Image Gene #28: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

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

Table S115.  Gene #28: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
17P GAIN MUTATED 2 3 18 17
17P GAIN WILD-TYPE 43 17 16 34

Figure S115.  Get High-res Image Gene #28: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'RPPA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 4e-04

Table S116.  Gene #28: '17p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
17P GAIN MUTATED 2 0 5 15 8
17P GAIN WILD-TYPE 43 8 5 22 10

Figure S116.  Get High-res Image Gene #28: '17p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'17p gain' versus 'RPPA_CHIERARCHICAL'

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

Table S117.  Gene #28: '17p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
17P GAIN MUTATED 2 11 17
17P GAIN WILD-TYPE 49 14 25

Figure S117.  Get High-res Image Gene #28: '17p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'17p gain' versus 'MRNASEQ_CNMF'

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

Table S118.  Gene #28: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
17P GAIN MUTATED 0 2 17 7 2 11 1
17P GAIN WILD-TYPE 34 28 16 15 6 11 0

Figure S118.  Get High-res Image Gene #28: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S119.  Gene #28: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
17P GAIN MUTATED 2 1 5 11 4 12 5
17P GAIN WILD-TYPE 41 26 7 13 4 11 8

Figure S119.  Get High-res Image Gene #28: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CNMF'

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

Table S120.  Gene #28: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
17P GAIN MUTATED 2 20 18
17P GAIN WILD-TYPE 49 37 24

Figure S120.  Get High-res Image Gene #28: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S121.  Gene #28: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
17P GAIN MUTATED 3 19 18
17P GAIN WILD-TYPE 67 19 24

Figure S121.  Get High-res Image Gene #28: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S122.  Gene #28: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
17P GAIN MUTATED 3 17 20
17P GAIN WILD-TYPE 66 19 25

Figure S122.  Get High-res Image Gene #28: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S123.  Gene #28: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
17P GAIN MUTATED 1 2 11 11 9 6
17P GAIN WILD-TYPE 33 34 8 16 10 9

Figure S123.  Get High-res Image Gene #28: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 0.007 (Fisher's exact test), Q value = 0.024

Table S124.  Gene #29: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
17Q GAIN MUTATED 12 6 27 5
17Q GAIN WILD-TYPE 36 28 27 9

Figure S124.  Get High-res Image Gene #29: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00033

Table S125.  Gene #29: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
17Q GAIN MUTATED 4 6 20 20
17Q GAIN WILD-TYPE 41 14 14 31

Figure S125.  Get High-res Image Gene #29: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'RPPA_CNMF'

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

Table S126.  Gene #29: '17q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
17Q GAIN MUTATED 5 0 5 19 10
17Q GAIN WILD-TYPE 40 8 5 18 8

Figure S126.  Get High-res Image Gene #29: '17q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'17q gain' versus 'RPPA_CHIERARCHICAL'

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

Table S127.  Gene #29: '17q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
17Q GAIN MUTATED 5 12 22
17Q GAIN WILD-TYPE 46 13 20

Figure S127.  Get High-res Image Gene #29: '17q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'17q gain' versus 'MRNASEQ_CNMF'

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

Table S128.  Gene #29: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
17Q GAIN MUTATED 2 4 20 8 2 13 1
17Q GAIN WILD-TYPE 32 26 13 14 6 9 0

Figure S128.  Get High-res Image Gene #29: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S129.  Gene #29: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
17Q GAIN MUTATED 4 3 6 13 4 14 6
17Q GAIN WILD-TYPE 39 24 6 11 4 9 7

Figure S129.  Get High-res Image Gene #29: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

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

Table S130.  Gene #29: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
17Q GAIN MUTATED 4 24 22
17Q GAIN WILD-TYPE 47 33 20

Figure S130.  Get High-res Image Gene #29: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S131.  Gene #29: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
17Q GAIN MUTATED 7 21 22
17Q GAIN WILD-TYPE 63 17 20

Figure S131.  Get High-res Image Gene #29: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S132.  Gene #29: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
17Q GAIN MUTATED 6 20 24
17Q GAIN WILD-TYPE 63 16 21

Figure S132.  Get High-res Image Gene #29: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S133.  Gene #29: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
17Q GAIN MUTATED 2 5 10 13 11 9
17Q GAIN WILD-TYPE 32 31 9 14 8 6

Figure S133.  Get High-res Image Gene #29: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 0.00418 (Fisher's exact test), Q value = 0.016

Table S134.  Gene #31: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
19P GAIN MUTATED 10 16 7 4
19P GAIN WILD-TYPE 38 18 47 10

Figure S134.  Get High-res Image Gene #31: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 0.0147 (Fisher's exact test), Q value = 0.041

Table S135.  Gene #31: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
19P GAIN MUTATED 13 10 4 10
19P GAIN WILD-TYPE 32 10 30 41

Figure S135.  Get High-res Image Gene #31: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p gain' versus 'RPPA_CNMF'

P value = 0.0133 (Fisher's exact test), Q value = 0.039

Table S136.  Gene #31: '19p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
19P GAIN MUTATED 20 1 1 5 4
19P GAIN WILD-TYPE 25 7 9 32 14

Figure S136.  Get High-res Image Gene #31: '19p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'19p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00694 (Fisher's exact test), Q value = 0.024

Table S137.  Gene #31: '19p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
19P GAIN MUTATED 21 3 7
19P GAIN WILD-TYPE 30 22 35

Figure S137.  Get High-res Image Gene #31: '19p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 0.00217 (Fisher's exact test), Q value = 0.0099

Table S138.  Gene #31: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
19P GAIN MUTATED 12 15 4 3 1 2 0
19P GAIN WILD-TYPE 22 15 29 19 7 20 1

Figure S138.  Get High-res Image Gene #31: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00118 (Fisher's exact test), Q value = 0.0063

Table S139.  Gene #31: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
19P GAIN MUTATED 14 14 0 4 0 4 1
19P GAIN WILD-TYPE 29 13 12 20 8 19 12

Figure S139.  Get High-res Image Gene #31: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.0011

Table S140.  Gene #31: '19p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
19P GAIN MUTATED 28 3 6
19P GAIN WILD-TYPE 42 35 36

Figure S140.  Get High-res Image Gene #31: '19p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.0048

Table S141.  Gene #31: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
19P GAIN MUTATED 27 5 5
19P GAIN WILD-TYPE 42 31 40

Figure S141.  Get High-res Image Gene #31: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00092 (Fisher's exact test), Q value = 0.005

Table S142.  Gene #31: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
19P GAIN MUTATED 10 18 3 3 1 2
19P GAIN WILD-TYPE 24 18 16 24 18 13

Figure S142.  Get High-res Image Gene #31: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00046

Table S143.  Gene #32: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
19Q GAIN MUTATED 8 16 3 2
19Q GAIN WILD-TYPE 40 18 51 12

Figure S143.  Get High-res Image Gene #32: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 0.00153 (Fisher's exact test), Q value = 0.0079

Table S144.  Gene #32: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
19Q GAIN MUTATED 10 9 1 9
19Q GAIN WILD-TYPE 35 11 33 42

Figure S144.  Get High-res Image Gene #32: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q gain' versus 'RPPA_CNMF'

P value = 0.00198 (Fisher's exact test), Q value = 0.0093

Table S145.  Gene #32: '19q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
19Q GAIN MUTATED 18 0 1 4 1
19Q GAIN WILD-TYPE 27 8 9 33 17

Figure S145.  Get High-res Image Gene #32: '19q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'19q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00248 (Fisher's exact test), Q value = 0.011

Table S146.  Gene #32: '19q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
19Q GAIN MUTATED 18 2 4
19Q GAIN WILD-TYPE 33 23 38

Figure S146.  Get High-res Image Gene #32: '19q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.0031

Table S147.  Gene #32: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
19Q GAIN MUTATED 10 13 1 3 1 1 0
19Q GAIN WILD-TYPE 24 17 32 19 7 21 1

Figure S147.  Get High-res Image Gene #32: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.0034

Table S148.  Gene #32: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
19Q GAIN MUTATED 11 13 0 3 0 1 1
19Q GAIN WILD-TYPE 32 14 12 21 8 22 12

Figure S148.  Get High-res Image Gene #32: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00046

Table S149.  Gene #32: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
19Q GAIN MUTATED 24 1 4
19Q GAIN WILD-TYPE 46 37 38

Figure S149.  Get High-res Image Gene #32: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0023

Table S150.  Gene #32: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
19Q GAIN MUTATED 23 2 4
19Q GAIN WILD-TYPE 46 34 41

Figure S150.  Get High-res Image Gene #32: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.0015

Table S151.  Gene #32: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
19Q GAIN MUTATED 8 16 1 3 0 1
19Q GAIN WILD-TYPE 26 20 18 24 19 14

Figure S151.  Get High-res Image Gene #32: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 0.0182 (Fisher's exact test), Q value = 0.048

Table S152.  Gene #33: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
20P GAIN MUTATED 5 7 17 6
20P GAIN WILD-TYPE 43 27 37 8

Figure S152.  Get High-res Image Gene #33: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.033

Table S153.  Gene #33: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
20P GAIN MUTATED 4 4 8 19
20P GAIN WILD-TYPE 41 16 26 32

Figure S153.  Get High-res Image Gene #33: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 0.0494 (Fisher's exact test), Q value = 0.1

Table S154.  Gene #34: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
20Q GAIN MUTATED 8 7 20 6
20Q GAIN WILD-TYPE 40 27 34 8

Figure S154.  Get High-res Image Gene #34: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 0.00289 (Fisher's exact test), Q value = 0.012

Table S155.  Gene #34: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
20Q GAIN MUTATED 5 3 12 21
20Q GAIN WILD-TYPE 40 17 22 30

Figure S155.  Get High-res Image Gene #34: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 0.0422 (Fisher's exact test), Q value = 0.092

Table S156.  Gene #34: '20q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
20Q GAIN MUTATED 7 1 3 13 9
20Q GAIN WILD-TYPE 38 7 7 24 9

Figure S156.  Get High-res Image Gene #34: '20q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0281 (Fisher's exact test), Q value = 0.067

Table S157.  Gene #34: '20q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
20Q GAIN MUTATED 8 10 15
20Q GAIN WILD-TYPE 43 15 27

Figure S157.  Get High-res Image Gene #34: '20q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 0.00512 (Fisher's exact test), Q value = 0.019

Table S158.  Gene #34: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
20Q GAIN MUTATED 6 5 10 4 2 14 0
20Q GAIN WILD-TYPE 28 25 23 18 6 8 1

Figure S158.  Get High-res Image Gene #34: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 0.0335 (Fisher's exact test), Q value = 0.077

Table S159.  Gene #34: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
20Q GAIN MUTATED 10 13 18
20Q GAIN WILD-TYPE 41 44 24

Figure S159.  Get High-res Image Gene #34: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0124 (Fisher's exact test), Q value = 0.037

Table S160.  Gene #34: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
20Q GAIN MUTATED 12 11 18
20Q GAIN WILD-TYPE 58 27 24

Figure S160.  Get High-res Image Gene #34: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.046

Table S161.  Gene #34: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
20Q GAIN MUTATED 12 10 19
20Q GAIN WILD-TYPE 57 26 26

Figure S161.  Get High-res Image Gene #34: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'CN_CNMF'

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

Table S162.  Gene #36: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
22Q GAIN MUTATED 11 21 5 2
22Q GAIN WILD-TYPE 37 13 49 12

Figure S162.  Get High-res Image Gene #36: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

'22q gain' versus 'RPPA_CNMF'

P value = 0.0165 (Fisher's exact test), Q value = 0.046

Table S163.  Gene #36: '22q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
22Q GAIN MUTATED 18 2 3 4 2
22Q GAIN WILD-TYPE 27 6 7 33 16

Figure S163.  Get High-res Image Gene #36: '22q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'22q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00444 (Fisher's exact test), Q value = 0.017

Table S164.  Gene #36: '22q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
22Q GAIN MUTATED 20 2 7
22Q GAIN WILD-TYPE 31 23 35

Figure S164.  Get High-res Image Gene #36: '22q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'22q gain' versus 'MRNASEQ_CNMF'

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

Table S165.  Gene #36: '22q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
22Q GAIN MUTATED 9 20 2 4 1 3 0
22Q GAIN WILD-TYPE 25 10 31 18 7 19 1

Figure S165.  Get High-res Image Gene #36: '22q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 4e-04

Table S166.  Gene #36: '22q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
22Q GAIN MUTATED 12 18 1 4 1 1 2
22Q GAIN WILD-TYPE 31 9 11 20 7 22 11

Figure S166.  Get High-res Image Gene #36: '22q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00046

Table S167.  Gene #36: '22q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
22Q GAIN MUTATED 30 3 6
22Q GAIN WILD-TYPE 40 35 36

Figure S167.  Get High-res Image Gene #36: '22q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0017

Table S168.  Gene #36: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
22Q GAIN MUTATED 29 4 6
22Q GAIN WILD-TYPE 40 32 39

Figure S168.  Get High-res Image Gene #36: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00046

Table S169.  Gene #36: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
22Q GAIN MUTATED 9 21 1 4 2 2
22Q GAIN WILD-TYPE 25 15 18 23 17 13

Figure S169.  Get High-res Image Gene #36: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp gain' versus 'METHLYATION_CNMF'

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

Table S170.  Gene #37: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
XP GAIN MUTATED 2 1 7 12
XP GAIN WILD-TYPE 43 19 27 39

Figure S170.  Get High-res Image Gene #37: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp gain' versus 'RPPA_CNMF'

P value = 0.0383 (Fisher's exact test), Q value = 0.085

Table S171.  Gene #37: 'xp gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
XP GAIN MUTATED 3 0 2 10 5
XP GAIN WILD-TYPE 42 8 8 27 13

Figure S171.  Get High-res Image Gene #37: 'xp gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'xp gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00922 (Fisher's exact test), Q value = 0.029

Table S172.  Gene #37: 'xp gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
XP GAIN MUTATED 3 5 12
XP GAIN WILD-TYPE 48 20 30

Figure S172.  Get High-res Image Gene #37: 'xp gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'xp gain' versus 'MRNASEQ_CNMF'

P value = 0.00355 (Fisher's exact test), Q value = 0.014

Table S173.  Gene #37: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
XP GAIN MUTATED 2 1 5 5 0 9 0
XP GAIN WILD-TYPE 32 29 28 17 8 13 1

Figure S173.  Get High-res Image Gene #37: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00308 (Fisher's exact test), Q value = 0.013

Table S174.  Gene #37: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
XP GAIN MUTATED 2 1 3 7 0 4 5
XP GAIN WILD-TYPE 41 26 9 17 8 19 8

Figure S174.  Get High-res Image Gene #37: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0017

Table S175.  Gene #37: 'xp gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
XP GAIN MUTATED 2 6 14
XP GAIN WILD-TYPE 49 51 28

Figure S175.  Get High-res Image Gene #37: 'xp gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xp gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.0014

Table S176.  Gene #37: 'xp gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
XP GAIN MUTATED 3 5 14
XP GAIN WILD-TYPE 67 33 28

Figure S176.  Get High-res Image Gene #37: 'xp gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00166 (Fisher's exact test), Q value = 0.0082

Table S177.  Gene #37: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
XP GAIN MUTATED 3 7 12
XP GAIN WILD-TYPE 66 29 33

Figure S177.  Get High-res Image Gene #37: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xp gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00069

Table S178.  Gene #37: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
XP GAIN MUTATED 2 1 6 11 1 1
XP GAIN WILD-TYPE 32 35 13 16 18 14

Figure S178.  Get High-res Image Gene #37: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq gain' versus 'RPPA_CNMF'

P value = 0.0392 (Fisher's exact test), Q value = 0.086

Table S179.  Gene #38: 'xq gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
XQ GAIN MUTATED 3 1 4 8 5
XQ GAIN WILD-TYPE 42 7 6 29 13

Figure S179.  Get High-res Image Gene #38: 'xq gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'xq gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00755 (Fisher's exact test), Q value = 0.025

Table S180.  Gene #38: 'xq gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
XQ GAIN MUTATED 3 6 12
XQ GAIN WILD-TYPE 48 19 30

Figure S180.  Get High-res Image Gene #38: 'xq gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 0.0082 (Fisher's exact test), Q value = 0.027

Table S181.  Gene #38: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
XQ GAIN MUTATED 2 1 7 5 0 8 0
XQ GAIN WILD-TYPE 32 29 26 17 8 14 1

Figure S181.  Get High-res Image Gene #38: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00257 (Fisher's exact test), Q value = 0.011

Table S182.  Gene #38: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
XQ GAIN MUTATED 2 1 3 7 0 5 5
XQ GAIN WILD-TYPE 41 26 9 17 8 18 8

Figure S182.  Get High-res Image Gene #38: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_CNMF'

P value = 0.00161 (Fisher's exact test), Q value = 0.0081

Table S183.  Gene #38: 'xq gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
XQ GAIN MUTATED 2 8 13
XQ GAIN WILD-TYPE 49 49 29

Figure S183.  Get High-res Image Gene #38: 'xq gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xq gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.0021

Table S184.  Gene #38: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
XQ GAIN MUTATED 3 7 13
XQ GAIN WILD-TYPE 67 31 29

Figure S184.  Get High-res Image Gene #38: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00083 (Fisher's exact test), Q value = 0.0046

Table S185.  Gene #38: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
XQ GAIN MUTATED 3 7 13
XQ GAIN WILD-TYPE 66 29 32

Figure S185.  Get High-res Image Gene #38: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0029

Table S186.  Gene #38: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
XQ GAIN MUTATED 2 1 5 11 2 2
XQ GAIN WILD-TYPE 32 35 14 16 17 13

Figure S186.  Get High-res Image Gene #38: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 0.0428 (Fisher's exact test), Q value = 0.092

Table S187.  Gene #39: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
1P LOSS MUTATED 11 3 6
1P LOSS WILD-TYPE 40 54 36

Figure S187.  Get High-res Image Gene #39: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 0.00334 (Fisher's exact test), Q value = 0.013

Table S188.  Gene #43: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
3P LOSS MUTATED 12 4 12 3
3P LOSS WILD-TYPE 33 16 22 48

Figure S188.  Get High-res Image Gene #43: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'RPPA_CNMF'

P value = 0.017 (Fisher's exact test), Q value = 0.046

Table S189.  Gene #43: '3p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
3P LOSS MUTATED 8 3 2 1 5
3P LOSS WILD-TYPE 37 5 8 36 13

Figure S189.  Get High-res Image Gene #43: '3p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 0.002 (Fisher's exact test), Q value = 0.0093

Table S190.  Gene #43: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
3P LOSS MUTATED 11 5 11 1 3 0 0
3P LOSS WILD-TYPE 23 25 22 21 5 22 1

Figure S190.  Get High-res Image Gene #43: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00231 (Fisher's exact test), Q value = 0.01

Table S191.  Gene #43: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
3P LOSS MUTATED 14 4 1 1 1 10 0
3P LOSS WILD-TYPE 29 23 11 23 7 13 13

Figure S191.  Get High-res Image Gene #43: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.0046

Table S192.  Gene #43: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
3P LOSS MUTATED 13 17 1
3P LOSS WILD-TYPE 38 40 41

Figure S192.  Get High-res Image Gene #43: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.0029

Table S193.  Gene #43: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
3P LOSS MUTATED 18 12 1
3P LOSS WILD-TYPE 52 26 41

Figure S193.  Get High-res Image Gene #43: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00186 (Fisher's exact test), Q value = 0.009

Table S194.  Gene #43: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
3P LOSS MUTATED 18 11 2
3P LOSS WILD-TYPE 51 25 43

Figure S194.  Get High-res Image Gene #43: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0029

Table S195.  Gene #43: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
3P LOSS MUTATED 11 7 3 0 9 1
3P LOSS WILD-TYPE 23 29 16 27 10 14

Figure S195.  Get High-res Image Gene #43: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'RPPA_CNMF'

P value = 0.0471 (Fisher's exact test), Q value = 0.099

Table S196.  Gene #44: '3q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
3Q LOSS MUTATED 7 3 1 1 3
3Q LOSS WILD-TYPE 38 5 9 36 15

Figure S196.  Get High-res Image Gene #44: '3q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0351 (Fisher's exact test), Q value = 0.08

Table S197.  Gene #44: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
3Q LOSS MUTATED 12 3 0 2 0 6 0
3Q LOSS WILD-TYPE 31 24 12 22 8 17 13

Figure S197.  Get High-res Image Gene #44: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0491 (Fisher's exact test), Q value = 0.1

Table S198.  Gene #44: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
3Q LOSS MUTATED 15 6 2
3Q LOSS WILD-TYPE 55 32 40

Figure S198.  Get High-res Image Gene #44: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0337 (Fisher's exact test), Q value = 0.077

Table S199.  Gene #44: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
3Q LOSS MUTATED 15 6 2
3Q LOSS WILD-TYPE 54 30 43

Figure S199.  Get High-res Image Gene #44: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 0.026 (Fisher's exact test), Q value = 0.064

Table S200.  Gene #45: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
4P LOSS MUTATED 28 17 24 25
4P LOSS WILD-TYPE 17 3 10 26

Figure S200.  Get High-res Image Gene #45: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.0426 (Fisher's exact test), Q value = 0.092

Table S201.  Gene #45: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
4P LOSS MUTATED 20 23 25 9 3 13 1
4P LOSS WILD-TYPE 14 7 8 13 5 9 0

Figure S201.  Get High-res Image Gene #45: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 0.0176 (Fisher's exact test), Q value = 0.047

Table S202.  Gene #45: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
4P LOSS MUTATED 31 43 20
4P LOSS WILD-TYPE 20 14 22

Figure S202.  Get High-res Image Gene #45: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0445 (Fisher's exact test), Q value = 0.095

Table S203.  Gene #45: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
4P LOSS MUTATED 46 28 20
4P LOSS WILD-TYPE 24 10 22

Figure S203.  Get High-res Image Gene #45: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0137 (Fisher's exact test), Q value = 0.04

Table S204.  Gene #45: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
4P LOSS MUTATED 21 25 12 9 15 12
4P LOSS WILD-TYPE 13 11 7 18 4 3

Figure S204.  Get High-res Image Gene #45: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 0.0293 (Fisher's exact test), Q value = 0.069

Table S205.  Gene #46: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
4Q LOSS MUTATED 21 26 29 14 5 13 1
4Q LOSS WILD-TYPE 13 4 4 8 3 9 0

Figure S205.  Get High-res Image Gene #46: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00553 (Fisher's exact test), Q value = 0.02

Table S206.  Gene #46: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
4Q LOSS MUTATED 27 24 10 13 7 21 7
4Q LOSS WILD-TYPE 16 3 2 11 1 2 6

Figure S206.  Get High-res Image Gene #46: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 0.00174 (Fisher's exact test), Q value = 0.0085

Table S207.  Gene #46: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
4Q LOSS MUTATED 35 50 24
4Q LOSS WILD-TYPE 16 7 18

Figure S207.  Get High-res Image Gene #46: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00498 (Fisher's exact test), Q value = 0.018

Table S208.  Gene #46: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
4Q LOSS MUTATED 51 34 24
4Q LOSS WILD-TYPE 19 4 18

Figure S208.  Get High-res Image Gene #46: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0298 (Fisher's exact test), Q value = 0.07

Table S209.  Gene #46: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
4Q LOSS MUTATED 51 31 27
4Q LOSS WILD-TYPE 18 5 18

Figure S209.  Get High-res Image Gene #46: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00792 (Fisher's exact test), Q value = 0.027

Table S210.  Gene #46: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
4Q LOSS MUTATED 22 29 15 13 18 12
4Q LOSS WILD-TYPE 12 7 4 14 1 3

Figure S210.  Get High-res Image Gene #46: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

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

Table S211.  Gene #47: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
5P LOSS MUTATED 31 30 35 7
5P LOSS WILD-TYPE 17 4 19 7

Figure S211.  Get High-res Image Gene #47: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

'5p loss' versus 'RPPA_CNMF'

P value = 0.0274 (Fisher's exact test), Q value = 0.067

Table S212.  Gene #47: '5p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
5P LOSS MUTATED 31 7 4 27 7
5P LOSS WILD-TYPE 14 1 6 10 11

Figure S212.  Get High-res Image Gene #47: '5p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00054

Table S213.  Gene #48: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
5Q LOSS MUTATED 31 32 33 5
5Q LOSS WILD-TYPE 17 2 21 9

Figure S213.  Get High-res Image Gene #48: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 0.0224 (Fisher's exact test), Q value = 0.057

Table S214.  Gene #48: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
5Q LOSS MUTATED 33 17 16 35
5Q LOSS WILD-TYPE 12 3 18 16

Figure S214.  Get High-res Image Gene #48: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'RPPA_CNMF'

P value = 0.0397 (Fisher's exact test), Q value = 0.087

Table S215.  Gene #48: '5q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
5Q LOSS MUTATED 33 6 4 26 7
5Q LOSS WILD-TYPE 12 2 6 11 11

Figure S215.  Get High-res Image Gene #48: '5q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 0.00277 (Fisher's exact test), Q value = 0.012

Table S216.  Gene #48: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
5Q LOSS MUTATED 23 28 16 16 4 13 1
5Q LOSS WILD-TYPE 11 2 17 6 4 9 0

Figure S216.  Get High-res Image Gene #48: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00349 (Fisher's exact test), Q value = 0.014

Table S217.  Gene #48: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
5Q LOSS MUTATED 29 26 8 15 3 12 8
5Q LOSS WILD-TYPE 14 1 4 9 5 11 5

Figure S217.  Get High-res Image Gene #48: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0101 (Fisher's exact test), Q value = 0.031

Table S218.  Gene #48: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
5Q LOSS MUTATED 55 19 27
5Q LOSS WILD-TYPE 15 19 15

Figure S218.  Get High-res Image Gene #48: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0201 (Fisher's exact test), Q value = 0.052

Table S219.  Gene #48: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
5Q LOSS MUTATED 54 19 28
5Q LOSS WILD-TYPE 15 17 17

Figure S219.  Get High-res Image Gene #48: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0189 (Fisher's exact test), Q value = 0.05

Table S220.  Gene #48: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
5Q LOSS MUTATED 25 30 9 16 9 12
5Q LOSS WILD-TYPE 9 6 10 11 10 3

Figure S220.  Get High-res Image Gene #48: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0146 (Fisher's exact test), Q value = 0.041

Table S221.  Gene #49: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
6P LOSS MUTATED 1 2 2 0 1 3 4
6P LOSS WILD-TYPE 42 25 10 24 7 20 9

Figure S221.  Get High-res Image Gene #49: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00119 (Fisher's exact test), Q value = 0.0063

Table S222.  Gene #50: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
6Q LOSS MUTATED 1 2 2 0 2 4 5
6Q LOSS WILD-TYPE 42 25 10 24 6 19 8

Figure S222.  Get High-res Image Gene #50: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S223.  Gene #50: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
6Q LOSS MUTATED 3 8 5
6Q LOSS WILD-TYPE 67 30 37

Figure S223.  Get High-res Image Gene #50: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0355 (Fisher's exact test), Q value = 0.08

Table S224.  Gene #50: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
6Q LOSS MUTATED 3 7 6
6Q LOSS WILD-TYPE 66 29 39

Figure S224.  Get High-res Image Gene #50: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'RPPA_CNMF'

P value = 0.0276 (Fisher's exact test), Q value = 0.067

Table S225.  Gene #52: '8p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
8P LOSS MUTATED 0 0 0 5 3
8P LOSS WILD-TYPE 45 8 10 32 15

Figure S225.  Get High-res Image Gene #52: '8p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'8p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00923 (Fisher's exact test), Q value = 0.029

Table S226.  Gene #52: '8p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
8P LOSS MUTATED 0 4 4
8P LOSS WILD-TYPE 51 21 38

Figure S226.  Get High-res Image Gene #52: '8p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 0.0215 (Fisher's exact test), Q value = 0.055

Table S227.  Gene #52: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
8P LOSS MUTATED 1 0 3 2 0 6 0
8P LOSS WILD-TYPE 33 30 30 20 8 16 1

Figure S227.  Get High-res Image Gene #52: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S228.  Gene #52: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
8P LOSS MUTATED 1 0 1 3 1 3 3
8P LOSS WILD-TYPE 42 27 11 21 7 20 10

Figure S228.  Get High-res Image Gene #52: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 0.00966 (Fisher's exact test), Q value = 0.03

Table S229.  Gene #52: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
8P LOSS MUTATED 1 3 8
8P LOSS WILD-TYPE 50 54 34

Figure S229.  Get High-res Image Gene #52: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00193 (Fisher's exact test), Q value = 0.0092

Table S230.  Gene #52: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
8P LOSS MUTATED 1 3 8
8P LOSS WILD-TYPE 69 35 34

Figure S230.  Get High-res Image Gene #52: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00739 (Fisher's exact test), Q value = 0.025

Table S231.  Gene #52: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
8P LOSS MUTATED 1 4 7
8P LOSS WILD-TYPE 68 32 38

Figure S231.  Get High-res Image Gene #52: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0163 (Fisher's exact test), Q value = 0.045

Table S232.  Gene #52: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
8P LOSS MUTATED 1 0 2 3 2 4
8P LOSS WILD-TYPE 33 36 17 24 17 11

Figure S232.  Get High-res Image Gene #52: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0145 (Fisher's exact test), Q value = 0.041

Table S233.  Gene #53: '8q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
8Q LOSS MUTATED 0 3 1
8Q LOSS WILD-TYPE 51 22 41

Figure S233.  Get High-res Image Gene #53: '8q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 0.0116 (Fisher's exact test), Q value = 0.035

Table S234.  Gene #53: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
8Q LOSS MUTATED 0 0 0 1 0 4 0
8Q LOSS WILD-TYPE 34 30 33 21 8 18 1

Figure S234.  Get High-res Image Gene #53: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0119 (Fisher's exact test), Q value = 0.035

Table S235.  Gene #53: '8q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
8Q LOSS MUTATED 0 0 0 3 0 0 2
8Q LOSS WILD-TYPE 43 27 12 21 8 23 11

Figure S235.  Get High-res Image Gene #53: '8q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_CNMF'

P value = 0.00158 (Fisher's exact test), Q value = 0.0081

Table S236.  Gene #53: '8q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
8Q LOSS MUTATED 0 0 5
8Q LOSS WILD-TYPE 51 57 37

Figure S236.  Get High-res Image Gene #53: '8q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00256 (Fisher's exact test), Q value = 0.011

Table S237.  Gene #53: '8q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
8Q LOSS MUTATED 0 0 5
8Q LOSS WILD-TYPE 70 38 37

Figure S237.  Get High-res Image Gene #53: '8q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00247 (Fisher's exact test), Q value = 0.011

Table S238.  Gene #53: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
8Q LOSS MUTATED 0 0 5
8Q LOSS WILD-TYPE 69 36 40

Figure S238.  Get High-res Image Gene #53: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00291 (Fisher's exact test), Q value = 0.012

Table S239.  Gene #53: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
8Q LOSS MUTATED 0 0 0 2 0 3
8Q LOSS WILD-TYPE 34 36 19 25 19 12

Figure S239.  Get High-res Image Gene #53: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.0033

Table S240.  Gene #54: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
9P LOSS MUTATED 14 18 31 1
9P LOSS WILD-TYPE 34 16 23 13

Figure S240.  Get High-res Image Gene #54: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'CN_CNMF'

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

Table S241.  Gene #55: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
9Q LOSS MUTATED 10 15 33 0
9Q LOSS WILD-TYPE 38 19 21 14

Figure S241.  Get High-res Image Gene #55: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0178 (Fisher's exact test), Q value = 0.048

Table S242.  Gene #55: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
9Q LOSS MUTATED 13 10 8 13 0 11 3
9Q LOSS WILD-TYPE 30 17 4 11 8 12 10

Figure S242.  Get High-res Image Gene #55: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 0.00247 (Fisher's exact test), Q value = 0.011

Table S243.  Gene #56: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
10P LOSS MUTATED 19 12 38 8
10P LOSS WILD-TYPE 29 22 16 6

Figure S243.  Get High-res Image Gene #56: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.0229 (Fisher's exact test), Q value = 0.057

Table S244.  Gene #56: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
10P LOSS MUTATED 18 10 25 24
10P LOSS WILD-TYPE 27 10 9 27

Figure S244.  Get High-res Image Gene #56: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'RPPA_CNMF'

P value = 0.00819 (Fisher's exact test), Q value = 0.027

Table S245.  Gene #56: '10p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
10P LOSS MUTATED 16 3 4 24 14
10P LOSS WILD-TYPE 29 5 6 13 4

Figure S245.  Get High-res Image Gene #56: '10p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'10p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00734 (Fisher's exact test), Q value = 0.025

Table S246.  Gene #56: '10p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
10P LOSS MUTATED 18 15 28
10P LOSS WILD-TYPE 33 10 14

Figure S246.  Get High-res Image Gene #56: '10p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.031 (Fisher's exact test), Q value = 0.072

Table S247.  Gene #56: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
10P LOSS MUTATED 13 12 25 11 4 12 0
10P LOSS WILD-TYPE 21 18 8 11 4 10 1

Figure S247.  Get High-res Image Gene #56: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00553 (Fisher's exact test), Q value = 0.02

Table S248.  Gene #56: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
10P LOSS MUTATED 16 11 9 13 6 18 4
10P LOSS WILD-TYPE 27 16 3 11 2 5 9

Figure S248.  Get High-res Image Gene #56: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 0.0421 (Fisher's exact test), Q value = 0.092

Table S249.  Gene #56: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
10P LOSS MUTATED 20 36 21
10P LOSS WILD-TYPE 31 21 21

Figure S249.  Get High-res Image Gene #56: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.0037

Table S250.  Gene #56: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
10P LOSS MUTATED 27 29 21
10P LOSS WILD-TYPE 43 9 21

Figure S250.  Get High-res Image Gene #56: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00194 (Fisher's exact test), Q value = 0.0092

Table S251.  Gene #56: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
10P LOSS MUTATED 27 27 23
10P LOSS WILD-TYPE 42 9 22

Figure S251.  Get High-res Image Gene #56: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00285 (Fisher's exact test), Q value = 0.012

Table S252.  Gene #56: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
10P LOSS MUTATED 11 16 15 11 14 10
10P LOSS WILD-TYPE 23 20 4 16 5 5

Figure S252.  Get High-res Image Gene #56: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

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

Table S253.  Gene #57: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
10Q LOSS MUTATED 17 9 37 8
10Q LOSS WILD-TYPE 31 25 17 6

Figure S253.  Get High-res Image Gene #57: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.035

Table S254.  Gene #57: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
10Q LOSS MUTATED 16 7 24 24
10Q LOSS WILD-TYPE 29 13 10 27

Figure S254.  Get High-res Image Gene #57: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0238 (Fisher's exact test), Q value = 0.059

Table S255.  Gene #57: '10q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
10Q LOSS MUTATED 16 14 24
10Q LOSS WILD-TYPE 35 11 18

Figure S255.  Get High-res Image Gene #57: '10q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 0.00438 (Fisher's exact test), Q value = 0.017

Table S256.  Gene #57: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
10Q LOSS MUTATED 14 7 24 10 4 12 0
10Q LOSS WILD-TYPE 20 23 9 12 4 10 1

Figure S256.  Get High-res Image Gene #57: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00142 (Fisher's exact test), Q value = 0.0073

Table S257.  Gene #57: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
10Q LOSS MUTATED 16 7 9 12 5 18 4
10Q LOSS WILD-TYPE 27 20 3 12 3 5 9

Figure S257.  Get High-res Image Gene #57: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.002

Table S258.  Gene #57: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
10Q LOSS MUTATED 23 28 20
10Q LOSS WILD-TYPE 47 10 22

Figure S258.  Get High-res Image Gene #57: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0039

Table S259.  Gene #57: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
10Q LOSS MUTATED 23 26 22
10Q LOSS WILD-TYPE 46 10 23

Figure S259.  Get High-res Image Gene #57: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.0017

Table S260.  Gene #57: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
10Q LOSS MUTATED 10 13 15 9 13 11
10Q LOSS WILD-TYPE 24 23 4 18 6 4

Figure S260.  Get High-res Image Gene #57: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'METHLYATION_CNMF'

P value = 0.0441 (Fisher's exact test), Q value = 0.094

Table S261.  Gene #58: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
11P LOSS MUTATED 33 17 22 27
11P LOSS WILD-TYPE 12 3 12 24

Figure S261.  Get High-res Image Gene #58: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.0025

Table S262.  Gene #58: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
11P LOSS MUTATED 32 22 9 12 4 18 2
11P LOSS WILD-TYPE 11 5 3 12 4 5 11

Figure S262.  Get High-res Image Gene #58: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0018

Table S263.  Gene #58: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
11P LOSS MUTATED 37 45 17
11P LOSS WILD-TYPE 14 12 25

Figure S263.  Get High-res Image Gene #58: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.002

Table S264.  Gene #58: '11p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
11P LOSS MUTATED 54 28 17
11P LOSS WILD-TYPE 16 10 25

Figure S264.  Get High-res Image Gene #58: '11p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00448 (Fisher's exact test), Q value = 0.017

Table S265.  Gene #58: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
11P LOSS MUTATED 53 25 21
11P LOSS WILD-TYPE 16 11 24

Figure S265.  Get High-res Image Gene #58: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00546 (Fisher's exact test), Q value = 0.02

Table S266.  Gene #58: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
11P LOSS MUTATED 25 29 15 10 12 8
11P LOSS WILD-TYPE 9 7 4 17 7 7

Figure S266.  Get High-res Image Gene #58: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 0.00288 (Fisher's exact test), Q value = 0.012

Table S267.  Gene #59: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
11Q LOSS MUTATED 30 32 41 13
11Q LOSS WILD-TYPE 18 2 13 1

Figure S267.  Get High-res Image Gene #59: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00062

Table S268.  Gene #59: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
11Q LOSS MUTATED 27 30 27 14 7 11 0
11Q LOSS WILD-TYPE 7 0 6 8 1 11 1

Figure S268.  Get High-res Image Gene #59: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S269.  Gene #59: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
11Q LOSS MUTATED 35 27 11 15 7 18 3
11Q LOSS WILD-TYPE 8 0 1 9 1 5 10

Figure S269.  Get High-res Image Gene #59: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00069

Table S270.  Gene #59: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
11Q LOSS MUTATED 43 51 22
11Q LOSS WILD-TYPE 8 6 20

Figure S270.  Get High-res Image Gene #59: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00091

Table S271.  Gene #59: '11q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
11Q LOSS MUTATED 62 32 22
11Q LOSS WILD-TYPE 8 6 20

Figure S271.  Get High-res Image Gene #59: '11q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.0049

Table S272.  Gene #59: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
11Q LOSS MUTATED 61 29 26
11Q LOSS WILD-TYPE 8 7 19

Figure S272.  Get High-res Image Gene #59: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S273.  Gene #59: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
11Q LOSS MUTATED 26 36 16 12 15 11
11Q LOSS WILD-TYPE 8 0 3 15 4 4

Figure S273.  Get High-res Image Gene #59: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.044

Table S274.  Gene #60: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
13Q LOSS MUTATED 33 32 39 9
13Q LOSS WILD-TYPE 15 2 15 5

Figure S274.  Get High-res Image Gene #60: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0029

Table S275.  Gene #60: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
13Q LOSS MUTATED 24 30 26 16 4 12 1
13Q LOSS WILD-TYPE 10 0 7 6 4 10 0

Figure S275.  Get High-res Image Gene #60: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0012 (Fisher's exact test), Q value = 0.0063

Table S276.  Gene #60: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
13Q LOSS MUTATED 31 27 11 14 6 17 7
13Q LOSS WILD-TYPE 12 0 1 10 2 6 6

Figure S276.  Get High-res Image Gene #60: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 0.027 (Fisher's exact test), Q value = 0.066

Table S277.  Gene #60: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
13Q LOSS MUTATED 42 46 25
13Q LOSS WILD-TYPE 9 11 17

Figure S277.  Get High-res Image Gene #60: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0232 (Fisher's exact test), Q value = 0.058

Table S278.  Gene #60: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
13Q LOSS MUTATED 58 30 25
13Q LOSS WILD-TYPE 12 8 17

Figure S278.  Get High-res Image Gene #60: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-04 (Fisher's exact test), Q value = 0.0041

Table S279.  Gene #60: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
13Q LOSS MUTATED 23 35 14 14 15 12
13Q LOSS WILD-TYPE 11 1 5 13 4 3

Figure S279.  Get High-res Image Gene #60: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'METHLYATION_CNMF'

P value = 0.0241 (Fisher's exact test), Q value = 0.06

Table S280.  Gene #61: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
14Q LOSS MUTATED 3 1 10 6
14Q LOSS WILD-TYPE 42 19 24 45

Figure S280.  Get High-res Image Gene #61: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CNMF'

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

Table S281.  Gene #61: '14q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
14Q LOSS MUTATED 3 1 1 4 7
14Q LOSS WILD-TYPE 42 7 9 33 11

Figure S281.  Get High-res Image Gene #61: '14q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 0.00459 (Fisher's exact test), Q value = 0.017

Table S282.  Gene #61: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
14Q LOSS MUTATED 0 3 10 2 0 5 0
14Q LOSS WILD-TYPE 34 27 23 20 8 17 1

Figure S282.  Get High-res Image Gene #61: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00033

Table S283.  Gene #61: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
14Q LOSS MUTATED 0 3 0 5 0 10 2
14Q LOSS WILD-TYPE 43 24 12 19 8 13 11

Figure S283.  Get High-res Image Gene #61: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 0.0367 (Fisher's exact test), Q value = 0.083

Table S284.  Gene #61: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
14Q LOSS MUTATED 2 11 7
14Q LOSS WILD-TYPE 49 46 35

Figure S284.  Get High-res Image Gene #61: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00322 (Fisher's exact test), Q value = 0.013

Table S285.  Gene #61: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
14Q LOSS MUTATED 3 10 7
14Q LOSS WILD-TYPE 67 28 35

Figure S285.  Get High-res Image Gene #61: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00238 (Fisher's exact test), Q value = 0.011

Table S286.  Gene #61: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
14Q LOSS MUTATED 3 10 7
14Q LOSS WILD-TYPE 66 26 38

Figure S286.  Get High-res Image Gene #61: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00089 (Fisher's exact test), Q value = 0.0049

Table S287.  Gene #61: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
14Q LOSS MUTATED 0 3 6 2 4 5
14Q LOSS WILD-TYPE 34 33 13 25 15 10

Figure S287.  Get High-res Image Gene #61: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 0.0176 (Fisher's exact test), Q value = 0.047

Table S288.  Gene #62: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
15Q LOSS MUTATED 10 1 14 4
15Q LOSS WILD-TYPE 38 33 40 10

Figure S288.  Get High-res Image Gene #62: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0018

Table S289.  Gene #62: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
15Q LOSS MUTATED 3 0 12 14
15Q LOSS WILD-TYPE 42 20 22 37

Figure S289.  Get High-res Image Gene #62: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'RPPA_CNMF'

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

Table S290.  Gene #62: '15q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
15Q LOSS MUTATED 0 0 4 14 7
15Q LOSS WILD-TYPE 45 8 6 23 11

Figure S290.  Get High-res Image Gene #62: '15q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'15q loss' versus 'RPPA_CHIERARCHICAL'

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

Table S291.  Gene #62: '15q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
15Q LOSS MUTATED 0 10 15
15Q LOSS WILD-TYPE 51 15 27

Figure S291.  Get High-res Image Gene #62: '15q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'15q loss' versus 'MRNASEQ_CNMF'

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

Table S292.  Gene #62: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
15Q LOSS MUTATED 0 1 9 9 2 8 0
15Q LOSS WILD-TYPE 34 29 24 13 6 14 1

Figure S292.  Get High-res Image Gene #62: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S293.  Gene #62: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
15Q LOSS MUTATED 0 1 3 7 4 8 6
15Q LOSS WILD-TYPE 43 26 9 17 4 15 7

Figure S293.  Get High-res Image Gene #62: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

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

Table S294.  Gene #62: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
15Q LOSS MUTATED 0 14 15
15Q LOSS WILD-TYPE 51 43 27

Figure S294.  Get High-res Image Gene #62: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S295.  Gene #62: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
15Q LOSS MUTATED 1 13 15
15Q LOSS WILD-TYPE 69 25 27

Figure S295.  Get High-res Image Gene #62: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S296.  Gene #62: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
15Q LOSS MUTATED 1 12 16
15Q LOSS WILD-TYPE 68 24 29

Figure S296.  Get High-res Image Gene #62: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S297.  Gene #62: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
15Q LOSS MUTATED 0 1 4 8 9 7
15Q LOSS WILD-TYPE 34 35 15 19 10 8

Figure S297.  Get High-res Image Gene #62: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'METHLYATION_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.034

Table S298.  Gene #63: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
16P LOSS MUTATED 12 8 16 8
16P LOSS WILD-TYPE 33 12 18 43

Figure S298.  Get High-res Image Gene #63: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 0.00305 (Fisher's exact test), Q value = 0.013

Table S299.  Gene #63: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
16P LOSS MUTATED 11 26 7
16P LOSS WILD-TYPE 40 31 35

Figure S299.  Get High-res Image Gene #63: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.034

Table S300.  Gene #63: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
16P LOSS MUTATED 19 18 7
16P LOSS WILD-TYPE 51 20 35

Figure S300.  Get High-res Image Gene #63: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.049

Table S301.  Gene #64: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
16Q LOSS MUTATED 11 15 16 9
16Q LOSS WILD-TYPE 37 19 38 5

Figure S301.  Get High-res Image Gene #64: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 0.0109 (Fisher's exact test), Q value = 0.034

Table S302.  Gene #64: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
16Q LOSS MUTATED 12 28 11
16Q LOSS WILD-TYPE 39 29 31

Figure S302.  Get High-res Image Gene #64: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p loss' versus 'CN_CNMF'

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

Table S303.  Gene #65: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
17P LOSS MUTATED 4 20 9 4
17P LOSS WILD-TYPE 44 14 45 10

Figure S303.  Get High-res Image Gene #65: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'RPPA_CNMF'

P value = 0.0447 (Fisher's exact test), Q value = 0.095

Table S304.  Gene #65: '17p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
17P LOSS MUTATED 17 2 1 7 1
17P LOSS WILD-TYPE 28 6 9 30 17

Figure S304.  Get High-res Image Gene #65: '17p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'17p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00313 (Fisher's exact test), Q value = 0.013

Table S305.  Gene #65: '17p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
17P LOSS MUTATED 19 1 8
17P LOSS WILD-TYPE 32 24 34

Figure S305.  Get High-res Image Gene #65: '17p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.0038

Table S306.  Gene #65: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
17P LOSS MUTATED 9 17 4 4 0 3 0
17P LOSS WILD-TYPE 25 13 29 18 8 19 1

Figure S306.  Get High-res Image Gene #65: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S307.  Gene #65: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
17P LOSS MUTATED 10 16 2 1 0 4 4
17P LOSS WILD-TYPE 33 11 10 23 8 19 9

Figure S307.  Get High-res Image Gene #65: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00334 (Fisher's exact test), Q value = 0.013

Table S308.  Gene #65: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
17P LOSS MUTATED 26 4 7
17P LOSS WILD-TYPE 44 34 35

Figure S308.  Get High-res Image Gene #65: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0016 (Fisher's exact test), Q value = 0.0081

Table S309.  Gene #65: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
17P LOSS MUTATED 26 3 8
17P LOSS WILD-TYPE 43 33 37

Figure S309.  Get High-res Image Gene #65: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S310.  Gene #65: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
17P LOSS MUTATED 6 20 1 3 2 5
17P LOSS WILD-TYPE 28 16 18 24 17 10

Figure S310.  Get High-res Image Gene #65: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 0.00397 (Fisher's exact test), Q value = 0.015

Table S311.  Gene #66: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
17Q LOSS MUTATED 1 8 6 4
17Q LOSS WILD-TYPE 47 26 48 10

Figure S311.  Get High-res Image Gene #66: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0281 (Fisher's exact test), Q value = 0.067

Table S312.  Gene #66: '17q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
17Q LOSS MUTATED 5 8 0 0 0 4 2
17Q LOSS WILD-TYPE 38 19 12 24 8 19 11

Figure S312.  Get High-res Image Gene #66: '17q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'METHLYATION_CNMF'

P value = 0.0487 (Fisher's exact test), Q value = 0.1

Table S313.  Gene #67: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
18P LOSS MUTATED 32 19 30 37
18P LOSS WILD-TYPE 13 1 4 14

Figure S313.  Get High-res Image Gene #67: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 0.00587 (Fisher's exact test), Q value = 0.021

Table S314.  Gene #67: '18p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
18P LOSS MUTATED 38 52 28
18P LOSS WILD-TYPE 13 5 14

Figure S314.  Get High-res Image Gene #67: '18p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0196 (Fisher's exact test), Q value = 0.051

Table S315.  Gene #67: '18p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
18P LOSS MUTATED 55 35 28
18P LOSS WILD-TYPE 15 3 14

Figure S315.  Get High-res Image Gene #67: '18p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0369 (Fisher's exact test), Q value = 0.083

Table S316.  Gene #67: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
18P LOSS MUTATED 24 31 16 16 18 13
18P LOSS WILD-TYPE 10 5 3 11 1 2

Figure S316.  Get High-res Image Gene #67: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 0.0293 (Fisher's exact test), Q value = 0.069

Table S317.  Gene #68: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
18Q LOSS MUTATED 33 32 45 12
18Q LOSS WILD-TYPE 15 2 9 2

Figure S317.  Get High-res Image Gene #68: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 0.0175 (Fisher's exact test), Q value = 0.047

Table S318.  Gene #68: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
18Q LOSS MUTATED 41 52 29
18Q LOSS WILD-TYPE 10 5 13

Figure S318.  Get High-res Image Gene #68: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0309 (Fisher's exact test), Q value = 0.072

Table S319.  Gene #68: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
18Q LOSS MUTATED 58 35 29
18Q LOSS WILD-TYPE 12 3 13

Figure S319.  Get High-res Image Gene #68: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00803 (Fisher's exact test), Q value = 0.027

Table S320.  Gene #68: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
18Q LOSS MUTATED 24 34 16 17 18 13
18Q LOSS WILD-TYPE 10 2 3 10 1 2

Figure S320.  Get High-res Image Gene #68: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

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

Table S321.  Gene #69: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
19P LOSS MUTATED 11 2 31 5
19P LOSS WILD-TYPE 37 32 23 9

Figure S321.  Get High-res Image Gene #69: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

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

Table S322.  Gene #69: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
19P LOSS MUTATED 4 1 23 21
19P LOSS WILD-TYPE 41 19 11 30

Figure S322.  Get High-res Image Gene #69: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p loss' versus 'RPPA_CNMF'

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

Table S323.  Gene #69: '19p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
19P LOSS MUTATED 2 2 4 21 11
19P LOSS WILD-TYPE 43 6 6 16 7

Figure S323.  Get High-res Image Gene #69: '19p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'19p loss' versus 'RPPA_CHIERARCHICAL'

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

Table S324.  Gene #69: '19p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
19P LOSS MUTATED 2 14 24
19P LOSS WILD-TYPE 49 11 18

Figure S324.  Get High-res Image Gene #69: '19p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'19p loss' versus 'MRNASEQ_CNMF'

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

Table S325.  Gene #69: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
19P LOSS MUTATED 0 2 21 12 1 13 0
19P LOSS WILD-TYPE 34 28 12 10 7 9 1

Figure S325.  Get High-res Image Gene #69: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S326.  Gene #69: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
19P LOSS MUTATED 0 2 9 12 5 15 6
19P LOSS WILD-TYPE 43 25 3 12 3 8 7

Figure S326.  Get High-res Image Gene #69: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

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

Table S327.  Gene #69: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
19P LOSS MUTATED 1 27 21
19P LOSS WILD-TYPE 50 30 21

Figure S327.  Get High-res Image Gene #69: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S328.  Gene #69: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
19P LOSS MUTATED 2 26 21
19P LOSS WILD-TYPE 68 12 21

Figure S328.  Get High-res Image Gene #69: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S329.  Gene #69: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
19P LOSS MUTATED 2 23 24
19P LOSS WILD-TYPE 67 13 21

Figure S329.  Get High-res Image Gene #69: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S330.  Gene #69: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
19P LOSS MUTATED 0 2 12 12 13 10
19P LOSS WILD-TYPE 34 34 7 15 6 5

Figure S330.  Get High-res Image Gene #69: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

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

Table S331.  Gene #70: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
19Q LOSS MUTATED 11 1 35 6
19Q LOSS WILD-TYPE 37 33 19 8

Figure S331.  Get High-res Image Gene #70: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

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

Table S332.  Gene #70: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
19Q LOSS MUTATED 4 0 27 22
19Q LOSS WILD-TYPE 41 20 7 29

Figure S332.  Get High-res Image Gene #70: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q loss' versus 'RPPA_CNMF'

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

Table S333.  Gene #70: '19q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
19Q LOSS MUTATED 1 2 4 22 14
19Q LOSS WILD-TYPE 44 6 6 15 4

Figure S333.  Get High-res Image Gene #70: '19q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'19q loss' versus 'RPPA_CHIERARCHICAL'

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

Table S334.  Gene #70: '19q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
19Q LOSS MUTATED 1 14 28
19Q LOSS WILD-TYPE 50 11 14

Figure S334.  Get High-res Image Gene #70: '19q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'19q loss' versus 'MRNASEQ_CNMF'

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

Table S335.  Gene #70: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
19Q LOSS MUTATED 0 1 25 13 1 13 0
19Q LOSS WILD-TYPE 34 29 8 9 7 9 1

Figure S335.  Get High-res Image Gene #70: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S336.  Gene #70: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
19Q LOSS MUTATED 0 1 9 13 5 19 6
19Q LOSS WILD-TYPE 43 26 3 11 3 4 7

Figure S336.  Get High-res Image Gene #70: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

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

Table S337.  Gene #70: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
19Q LOSS MUTATED 1 30 22
19Q LOSS WILD-TYPE 50 27 20

Figure S337.  Get High-res Image Gene #70: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S338.  Gene #70: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
19Q LOSS MUTATED 1 30 22
19Q LOSS WILD-TYPE 69 8 20

Figure S338.  Get High-res Image Gene #70: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S339.  Gene #70: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
19Q LOSS MUTATED 1 27 25
19Q LOSS WILD-TYPE 68 9 20

Figure S339.  Get High-res Image Gene #70: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S340.  Gene #70: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
19Q LOSS MUTATED 0 1 14 13 15 10
19Q LOSS WILD-TYPE 34 35 5 14 4 5

Figure S340.  Get High-res Image Gene #70: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_CNMF'

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

Table S341.  Gene #71: '20p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
20P LOSS MUTATED 5 17 7
20P LOSS WILD-TYPE 46 40 35

Figure S341.  Get High-res Image Gene #71: '20p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00912 (Fisher's exact test), Q value = 0.029

Table S342.  Gene #71: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
20P LOSS MUTATED 2 9 9 5 3 1
20P LOSS WILD-TYPE 32 27 10 22 16 14

Figure S342.  Get High-res Image Gene #71: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00033

Table S343.  Gene #73: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
22Q LOSS MUTATED 7 3 26 7
22Q LOSS WILD-TYPE 41 31 28 7

Figure S343.  Get High-res Image Gene #73: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00046

Table S344.  Gene #73: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
22Q LOSS MUTATED 5 3 19 16
22Q LOSS WILD-TYPE 40 17 15 35

Figure S344.  Get High-res Image Gene #73: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CNMF'

P value = 0.00166 (Fisher's exact test), Q value = 0.0082

Table S345.  Gene #73: '22q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 8 10 37 18
22Q LOSS MUTATED 5 1 4 16 9
22Q LOSS WILD-TYPE 40 7 6 21 9

Figure S345.  Get High-res Image Gene #73: '22q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'22q loss' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00033

Table S346.  Gene #73: '22q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 25 42
22Q LOSS MUTATED 5 14 16
22Q LOSS WILD-TYPE 46 11 26

Figure S346.  Get High-res Image Gene #73: '22q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 4e-04

Table S347.  Gene #73: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
22Q LOSS MUTATED 3 2 19 8 2 9 0
22Q LOSS WILD-TYPE 31 28 14 14 6 13 1

Figure S347.  Get High-res Image Gene #73: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 4e-04

Table S348.  Gene #73: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
22Q LOSS MUTATED 4 2 7 10 4 12 4
22Q LOSS WILD-TYPE 39 25 5 14 4 11 9

Figure S348.  Get High-res Image Gene #73: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.0011

Table S349.  Gene #73: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
22Q LOSS MUTATED 4 22 17
22Q LOSS WILD-TYPE 47 35 25

Figure S349.  Get High-res Image Gene #73: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S350.  Gene #73: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
22Q LOSS MUTATED 6 20 17
22Q LOSS WILD-TYPE 64 18 25

Figure S350.  Get High-res Image Gene #73: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S351.  Gene #73: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 36 45
22Q LOSS MUTATED 6 18 19
22Q LOSS WILD-TYPE 63 18 26

Figure S351.  Get High-res Image Gene #73: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S352.  Gene #73: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
22Q LOSS MUTATED 3 3 13 10 7 7
22Q LOSS WILD-TYPE 31 33 6 17 12 8

Figure S352.  Get High-res Image Gene #73: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'CN_CNMF'

P value = 0.00316 (Fisher's exact test), Q value = 0.013

Table S353.  Gene #74: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
XP LOSS MUTATED 2 7 16 4
XP LOSS WILD-TYPE 46 27 38 10

Figure S353.  Get High-res Image Gene #74: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 0.0052 (Fisher's exact test), Q value = 0.019

Table S354.  Gene #74: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
XP LOSS MUTATED 3 6 4 16
XP LOSS WILD-TYPE 42 14 30 35

Figure S354.  Get High-res Image Gene #74: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp loss' versus 'MRNASEQ_CNMF'

P value = 0.0449 (Fisher's exact test), Q value = 0.095

Table S355.  Gene #74: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
XP LOSS MUTATED 4 7 5 10 0 3 0
XP LOSS WILD-TYPE 30 23 28 12 8 19 1

Figure S355.  Get High-res Image Gene #74: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0167 (Fisher's exact test), Q value = 0.046

Table S356.  Gene #74: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
XP LOSS MUTATED 2 9 3 10 1 4
XP LOSS WILD-TYPE 32 27 16 17 18 11

Figure S356.  Get High-res Image Gene #74: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

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

Table S357.  Gene #75: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 48 34 54 14
XQ LOSS MUTATED 0 7 18 3
XQ LOSS WILD-TYPE 48 27 36 11

Figure S357.  Get High-res Image Gene #75: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.00139 (Fisher's exact test), Q value = 0.0072

Table S358.  Gene #75: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 20 34 51
XQ LOSS MUTATED 2 6 4 16
XQ LOSS WILD-TYPE 43 14 30 35

Figure S358.  Get High-res Image Gene #75: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 0.0227 (Fisher's exact test), Q value = 0.057

Table S359.  Gene #75: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 30 33 22 8 22 1
XQ LOSS MUTATED 4 7 3 10 0 4 0
XQ LOSS WILD-TYPE 30 23 30 12 8 18 1

Figure S359.  Get High-res Image Gene #75: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 0.0235 (Fisher's exact test), Q value = 0.059

Table S360.  Gene #75: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 57 42
XQ LOSS MUTATED 7 7 14
XQ LOSS WILD-TYPE 44 50 28

Figure S360.  Get High-res Image Gene #75: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0115 (Fisher's exact test), Q value = 0.035

Table S361.  Gene #75: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 38 42
XQ LOSS MUTATED 11 3 14
XQ LOSS WILD-TYPE 59 35 28

Figure S361.  Get High-res Image Gene #75: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00518 (Fisher's exact test), Q value = 0.019

Table S362.  Gene #75: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 34 36 19 27 19 15
XQ LOSS MUTATED 2 9 4 10 0 3
XQ LOSS WILD-TYPE 32 27 15 17 19 12

Figure S362.  Get High-res Image Gene #75: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input
  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/TGCT-TP/22533661/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/TGCT-TP/22541961/TGCT-TP.transferedmergedcluster.txt

  • Number of patients = 150

  • Number of significantly arm-level cnvs = 75

  • Number of molecular subtypes = 10

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)