Correlation between copy number variation genes (focal events) and molecular subtypes
Breast Invasive Carcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1NS0S80
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1NS0S80
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.

Summary

Testing the association between copy number variation 40 focal events and 12 molecular subtypes across 1007 patients, 414 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

  • 2p cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 2q cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 3p cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

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

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

  • 6q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

  • 16q cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

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

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

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

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

  • 21q cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 22q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

  • xq cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 40 focal events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 414 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Chi-square test Fisher's exact test Chi-square test Chi-square 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 421 (42%) 586 8.22e-06
(0.00131) 		0.000129
(0.0158) 		5.1e-22
(2.26e-19) 		6.19e-07
(0.000121) 		4.01e-05
(0.00542) 		0.00217
(0.163) 		2.57e-09
(6.52e-07) 		6.95e-10
(1.85e-07) 		3.72e-07
(7.48e-05) 		1.07e-06
(0.000198) 		6.99e-06
(0.00115) 		0.000868
(0.0764)
2p 283 (28%) 724 4.34e-05
(0.00581) 		2.04e-06
(0.000372) 		6.37e-18
(2.69e-15) 		5.66e-08
(1.27e-05) 		4.52e-05
(0.00597) 		1.3e-05
(0.00198) 		5.52e-12
(1.71e-09) 		1.76e-13
(6.12e-11) 		5.31e-11
(1.54e-08) 		2.68e-10
(7.32e-08) 		6.52e-11
(1.87e-08) 		6.2e-06
(0.00104)
2q 262 (26%) 745 0.00136
(0.109) 		6.28e-05
(0.00804) 		3.39e-16
(1.34e-13) 		1.65e-07
(3.46e-05) 		3.45e-06
(0.000598) 		2.08e-05
(0.00308) 		9.83e-09
(2.33e-06) 		1.26e-09
(3.31e-07) 		8.86e-08
(1.95e-05) 		1.54e-07
(3.29e-05) 		6.65e-09
(1.63e-06) 		9.5e-05
(0.012)
3p 308 (31%) 699 1.48e-07
(3.17e-05) 		9.19e-07
(0.000172) 		1.03e-26
(4.67e-24) 		1.44e-15
(5.53e-13) 		0.000198
(0.0226) 		0.000283
(0.0297) 		6.5e-16
(2.54e-13) 		2.21e-15
(8.39e-13) 		7.52e-17
(3.05e-14) 		4.68e-14
(1.71e-11) 		7.85e-13
(2.57e-10) 		5.83e-09
(1.44e-06)
4p 403 (40%) 604 3.37e-11
(9.99e-09) 		5.18e-12
(1.61e-09) 		5.5e-39
(2.62e-36) 		6.48e-18
(2.72e-15) 		3.77e-06
(0.000649) 		4.47e-05
(0.00595) 		1.89e-27
(8.61e-25) 		4.08e-26
(1.85e-23) 		1.46e-21
(6.46e-19) 		1.61e-25
(7.26e-23) 		3.02e-19
(1.31e-16) 		7.2e-16
(2.79e-13)
5q 411 (41%) 596 3.29e-10
(8.96e-08) 		7.14e-09
(1.74e-06) 		5.35e-39
(2.55e-36) 		2.53e-20
(1.1e-17) 		0.000934
(0.0785) 		0.000373
(0.0384) 		1.92e-21
(8.5e-19) 		4.74e-23
(2.12e-20) 		3.56e-22
(1.58e-19) 		3.29e-25
(1.48e-22) 		1.95e-16
(7.78e-14) 		2.12e-16
(8.46e-14)
9p 427 (42%) 580 6.44e-07
(0.000124) 		1.27e-07
(2.74e-05) 		1.45e-39
(6.93e-37) 		7.66e-18
(3.21e-15) 		1.65e-07
(3.46e-05) 		3.98e-05
(0.00541) 		1.43e-14
(5.29e-12) 		1.08e-16
(4.35e-14) 		1.8e-16
(7.25e-14) 		7.09e-16
(2.76e-13) 		2.69e-13
(9.27e-11) 		1.18e-08
(2.74e-06)
9q 381 (38%) 626 0.000147
(0.0175) 		2.31e-06
(0.000414) 		1.52e-28
(6.97e-26) 		1.18e-14
(4.37e-12) 		3.14e-05
(0.0044) 		6.5e-06
(0.00108) 		2.83e-16
(1.12e-13) 		1.16e-15
(4.48e-13) 		6.8e-15
(2.55e-12) 		2.03e-15
(7.73e-13) 		2.9e-11
(8.64e-09) 		9.94e-09
(2.35e-06)
10p 359 (36%) 648 3.79e-09
(9.52e-07) 		1.61e-07
(3.4e-05) 		1.29e-33
(6.04e-31) 		1.91e-20
(8.37e-18) 		1.86e-05
(0.00277) 		0.000132
(0.016) 		3.16e-21
(1.39e-18) 		1.25e-18
(5.36e-16) 		7.4e-15
(2.77e-12) 		6.83e-21
(3e-18) 		1.82e-12
(5.88e-10) 		8.94e-11
(2.54e-08)
10q 327 (32%) 680 1.12e-05
(0.00171) 		7.46e-06
(0.00121) 		2.16e-25
(9.74e-23) 		6.12e-16
(2.4e-13) 		4.89e-06
(0.000836) 		0.000228
(0.0252) 		1.65e-14
(6.1e-12) 		6.97e-14
(2.52e-11) 		8.09e-10
(2.15e-07) 		6.92e-13
(2.29e-10) 		1.42e-09
(3.67e-07) 		7.57e-06
(0.00122)
12p 360 (36%) 647 1.36e-07
(2.92e-05) 		3.82e-08
(8.71e-06) 		3.2e-31
(1.49e-28) 		4.65e-18
(1.98e-15) 		0.000954
(0.0792) 		2.72e-05
(0.00386) 		2.31e-17
(9.6e-15) 		7.27e-17
(2.95e-14) 		1.56e-15
(5.98e-13) 		6.13e-17
(2.51e-14) 		2.19e-11
(6.59e-09) 		3.24e-07
(6.64e-05)
14q 379 (38%) 628 6.95e-08
(1.54e-05) 		9.07e-07
(0.00017) 		9.33e-32
(4.34e-29) 		3.24e-17
(1.34e-14) 		2.84e-06
(5e-04) 		0.000749
(0.0674) 		8.2e-19
(3.54e-16) 		2.47e-20
(1.08e-17) 		2.75e-16
(1.09e-13) 		2.55e-17
(1.06e-14) 		1.42e-12
(4.61e-10) 		3.69e-13
(1.26e-10)
15q 387 (38%) 620 8.63e-09
(2.07e-06) 		5.92e-07
(0.000116) 		8.57e-37
(4.07e-34) 		2.24e-17
(9.33e-15) 		0.000514
(0.0499) 		0.000127
(0.0157) 		5.19e-21
(2.28e-18) 		1.5e-19
(6.51e-17) 		1.78e-15
(6.82e-13) 		5.79e-18
(2.45e-15) 		3.78e-11
(1.11e-08) 		7.07e-10
(1.88e-07)
16q 687 (68%) 320 1.96e-07
(4.07e-05) 		8.93e-08
(1.95e-05) 		3.33e-07
(6.77e-05) 		5.06e-11
(1.47e-08) 		0.000897
(0.078) 		6.47e-06
(0.00108) 		7.27e-12
(2.25e-09) 		1.36e-12
(4.44e-10) 		1.98e-07
(4.09e-05) 		4.18e-11
(1.23e-08) 		0.000135
(0.0163) 		5.32e-05
(0.00686)
17q 462 (46%) 545 6.31e-10
(1.69e-07) 		1.68e-05
(0.00252) 		3.62e-29
(1.67e-26) 		2.99e-12
(9.46e-10) 		7.27e-07
(0.00014) 		0.000237
(0.0256) 		1.34e-09
(3.51e-07) 		4.91e-09
(1.22e-06) 		1.15e-08
(2.68e-06) 		1.52e-13
(5.33e-11) 		9.38e-08
(2.04e-05) 		0.000219
(0.0245)
18p 463 (46%) 544 5.82e-07
(0.000115) 		2.67e-06
(0.000473) 		1.85e-33
(8.66e-31) 		1.99e-13
(6.9e-11) 		0.000148
(0.0175) 		0.000204
(0.0231) 		5.27e-17
(2.16e-14) 		1.93e-16
(7.74e-14) 		3.31e-14
(1.21e-11) 		1.48e-13
(5.21e-11) 		2.61e-13
(9.02e-11) 		7.1e-09
(1.73e-06)
19p 350 (35%) 657 8.91e-06
(0.00139) 		2.33e-06
(0.000415) 		1.93e-28
(8.85e-26) 		7.21e-13
(2.38e-10) 		1.53e-05
(0.00231) 		5.02e-05
(0.00653) 		6.71e-13
(2.23e-10) 		6.96e-14
(2.52e-11) 		2.48e-16
(9.87e-14) 		1.16e-13
(4.11e-11) 		9.3e-14
(3.31e-11) 		3.26e-06
(0.000568)
21q 350 (35%) 657 1.47e-09
(3.78e-07) 		2.31e-05
(0.0034) 		5.6e-27
(2.54e-24) 		2.06e-10
(5.74e-08) 		0.000275
(0.0291) 		0.00189
(0.146) 		2.28e-15
(8.63e-13) 		7.25e-17
(2.95e-14) 		7.97e-13
(2.6e-10) 		3.78e-12
(1.19e-09) 		2.46e-10
(6.77e-08) 		7.63e-09
(1.84e-06)
3q 296 (29%) 711 1.15e-08
(2.68e-06) 		3.15e-09
(7.93e-07) 		2.27e-28
(1.04e-25) 		4.12e-17
(1.7e-14) 		0.000618
(0.0579) 		0.00967
(0.532) 		2.8e-17
(1.16e-14) 		3.86e-18
(1.65e-15) 		1.06e-18
(4.56e-16) 		3.26e-16
(1.29e-13) 		1.56e-14
(5.76e-12) 		1.07e-10
(3.02e-08)
5p 423 (42%) 584 4.03e-07
(8.07e-05) 		2.19e-06
(0.000395) 		2.54e-32
(1.19e-29) 		1.55e-13
(5.41e-11) 		0.00296
(0.207) 		0.00511
(0.322) 		5.62e-15
(2.11e-12) 		5.2e-16
(2.04e-13) 		2.22e-13
(7.7e-11) 		5.03e-18
(2.13e-15) 		4.88e-14
(1.78e-11) 		1.72e-11
(5.23e-09)
12q 303 (30%) 704 0.000294
(0.0305) 		3.31e-05
(0.00461) 		9.48e-23
(4.23e-20) 		8.06e-16
(3.11e-13) 		0.0084
(0.47) 		0.00239
(0.174) 		6.45e-11
(1.86e-08) 		4.44e-11
(1.3e-08) 		2.37e-09
(6.04e-07) 		1.11e-08
(2.6e-06) 		6.69e-08
(1.49e-05) 		0.000426
(0.043)
17p 644 (64%) 363 4.91e-13
(1.65e-10) 		0.0501
(1.00) 		4.02e-34
(1.89e-31) 		2.51e-12
(8e-10) 		7.42e-07
(0.000142) 		0.00231
(0.171) 		1.07e-07
(2.32e-05) 		2.59e-05
(0.00375) 		6e-09
(1.48e-06) 		5.61e-08
(1.27e-05) 		1.77e-07
(3.68e-05) 		0.00327
(0.219)
18q 443 (44%) 564 9.47e-05
(0.012) 		0.000137
(0.0165) 		1.44e-34
(6.77e-32) 		4.2e-13
(1.42e-10) 		0.000616
(0.0579) 		0.00783
(0.446) 		8.86e-14
(3.17e-11) 		1.93e-11
(5.84e-09) 		2.48e-11
(7.45e-09) 		2.44e-10
(6.75e-08) 		1.14e-11
(3.5e-09) 		8.22e-06
(0.00131)
19q 354 (35%) 653 2.49e-05
(0.00364) 		1.06e-05
(0.00165) 		2.11e-27
(9.62e-25) 		1.09e-10
(3.08e-08) 		0.000631
(0.0581) 		0.00727
(0.422) 		8.6e-11
(2.45e-08) 		5.52e-14
(2e-11) 		5.27e-13
(1.77e-10) 		3.31e-12
(1.04e-09) 		4e-10
(1.08e-07) 		2.68e-05
(0.00383)
20p 477 (47%) 530 3.96e-09
(9.89e-07) 		8.63e-06
(0.00135) 		6.94e-48
(3.33e-45) 		6.63e-17
(2.7e-14) 		0.000234
(0.0255) 		0.0107
(0.569) 		6.76e-16
(2.64e-13) 		1.65e-14
(6.1e-12) 		1.44e-13
(5.1e-11) 		5.18e-13
(1.74e-10) 		1.45e-08
(3.34e-06) 		8.81e-09
(2.1e-06)
4q 362 (36%) 645 2.79e-05
(0.00394) 		4.73e-07
(9.36e-05) 		2.05e-29
(9.48e-27) 		3.18e-11
(9.43e-09) 		0.00499
(0.319) 		0.038
(1.00) 		1.02e-18
(4.38e-16) 		3.25e-17
(1.34e-14) 		3.83e-13
(1.31e-10) 		2.21e-15
(8.38e-13) 		2.12e-12
(6.84e-10) 		2.7e-09
(6.82e-07)
7p 395 (39%) 612 0.000916
(0.0785) 		0.00239
(0.174) 		4.44e-18
(1.89e-15) 		2.04e-08
(4.68e-06) 		0.077
(1.00) 		0.0278
(1.00) 		7.52e-09
(1.82e-06) 		4.5e-11
(1.32e-08) 		3.46e-07
(6.99e-05) 		1.82e-06
(0.000335) 		0.000165
(0.0193) 		0.00214
(0.163)
8p 641 (64%) 366 3.3e-07
(6.73e-05) 		3.72e-05
(0.0051) 		2.7e-30
(1.25e-27) 		7.53e-16
(2.91e-13) 		0.255
(1.00) 		0.136
(1.00) 		2.38e-12
(7.64e-10) 		3.49e-13
(1.2e-10) 		2.77e-11
(8.29e-09) 		6.4e-13
(2.13e-10) 		4.88e-12
(1.52e-09) 		1.06e-06
(0.000196)
8q 581 (58%) 426 8.1e-06
(0.0013) 		0.000195
(0.0224) 		6.79e-32
(3.17e-29) 		6.4e-18
(2.69e-15) 		0.101
(1.00) 		0.109
(1.00) 		1.16e-10
(3.26e-08) 		4.46e-12
(1.4e-09) 		1.17e-13
(4.14e-11) 		2.71e-12
(8.61e-10) 		3.85e-13
(1.31e-10) 		3.41e-08
(7.82e-06)
13q 497 (49%) 510 8.48e-07
(0.000161) 		5.2e-08
(1.18e-05) 		2.48e-35
(1.17e-32) 		2.67e-14
(9.8e-12) 		0.0936
(1.00) 		0.0271
(1.00) 		3.23e-15
(1.22e-12) 		1.67e-16
(6.74e-14) 		1.68e-13
(5.85e-11) 		7.45e-14
(2.68e-11) 		2e-10
(5.59e-08) 		2.14e-06
(0.000387)
20q 473 (47%) 534 5.28e-06
(0.000892) 		0.00129
(0.104) 		1.03e-45
(4.95e-43) 		1.31e-18
(5.59e-16) 		0.00648
(0.389) 		0.0961
(1.00) 		2.96e-12
(9.38e-10) 		1.89e-11
(5.73e-09) 		4.24e-10
(1.15e-07) 		2.58e-10
(7.08e-08) 		6.93e-08
(1.54e-05) 		4.21e-07
(8.38e-05)
xq 299 (30%) 708 3.38e-05
(0.00466) 		8.93e-07
(0.000169) 		4.84e-23
(2.16e-20) 		2.26e-09
(5.78e-07) 		0.0343
(1.00) 		0.000598
(0.0568) 		1.49e-11
(4.57e-09) 		7.6e-13
(2.5e-10) 		9.05e-14
(3.23e-11) 		8.95e-09
(2.13e-06) 		3.19e-06
(0.000559) 		0.00533
(0.33)
11q 440 (44%) 567 0.000379
(0.0386) 		0.172
(1.00) 		5.97e-36
(2.83e-33) 		2.16e-10
(5.99e-08) 		0.675
(1.00) 		0.824
(1.00) 		0.000257
(0.0275) 		0.000429
(0.043) 		0.00158
(0.125) 		6.2e-07
(0.000121) 		0.000768
(0.0683) 		0.00064
(0.0582)
6p 370 (37%) 637 0.179
(1.00) 		0.0176
(0.864) 		8.58e-28
(3.92e-25) 		9.16e-15
(3.42e-12) 		0.0137
(0.711) 		0.236
(1.00) 		1.38e-09
(3.58e-07) 		6.32e-13
(2.11e-10) 		1.47e-10
(4.12e-08) 		8.73e-10
(2.3e-07) 		1.53e-09
(3.93e-07) 		1.11e-05
(0.00171)
7q 360 (36%) 647 0.0288
(1.00) 		0.0169
(0.843) 		8.67e-14
(3.11e-11) 		7.15e-06
(0.00117) 		0.0379
(1.00) 		0.0597
(1.00) 		6.88e-06
(0.00113) 		5.87e-10
(1.58e-07) 		2.62e-05
(0.00378) 		4.89e-06
(0.000836) 		0.00238
(0.174) 		0.00323
(0.219)
11p 388 (39%) 619 0.00394
(0.26) 		0.0828
(1.00) 		9.86e-36
(4.66e-33) 		4.78e-13
(1.61e-10) 		0.0192
(0.92) 		0.0754
(1.00) 		1.51e-11
(4.62e-09) 		8.42e-12
(2.59e-09) 		8.21e-11
(2.35e-08) 		1.54e-12
(4.99e-10) 		6.19e-11
(1.79e-08) 		5.72e-09
(1.42e-06)
6q 396 (39%) 611 0.55
(1.00) 		0.352
(1.00) 		7.12e-19
(3.09e-16) 		1.6e-07
(3.4e-05) 		0.0364
(1.00) 		0.759
(1.00) 		0.00655
(0.389) 		0.000431
(0.043) 		0.000118
(0.0148) 		0.000488
(0.0478) 		0.000183
(0.0212) 		0.0156
(0.796)
16p 603 (60%) 404 0.00546
(0.333) 		0.0031
(0.214) 		6.64e-08
(1.49e-05) 		4.9e-05
(0.00642) 		0.0105
(0.569) 		0.037
(1.00) 		0.000913
(0.0785) 		0.000542
(0.052) 		0.182
(1.00) 		0.49
(1.00) 		0.313
(1.00) 		0.141
(1.00)
22q 545 (54%) 462 0.0603
(1.00) 		0.163
(1.00) 		1.1e-17
(4.61e-15) 		1.12e-09
(2.94e-07) 		0.494
(1.00) 		0.212
(1.00) 		0.000227
(0.0252) 		0.0041
(0.267) 		0.00127
(0.104) 		0.0369
(1.00) 		0.0384
(1.00) 		0.173
(1.00)
1q 706 (70%) 301 0.00167
(0.131) 		0.101
(1.00) 		2.48e-12
(7.95e-10) 		2.06e-06
(0.000375) 		0.239
(1.00) 		0.0995
(1.00) 		0.548
(1.00) 		0.318
(1.00) 		0.964
(1.00) 		0.0471
(1.00) 		0.785
(1.00) 		0.725
(1.00)
'1p' versus 'MRNA_CNMF'

P value = 8.22e-06 (Chi-square test), Q value = 0.0013

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
1P MUTATED 5 9 51 50 35 48 9 12
1P WILD-TYPE 16 27 68 46 74 24 11 28

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

'1p' versus 'MRNA_CHIERARCHICAL'

P value = 0.000129 (Fisher's exact test), Q value = 0.016

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
1P MUTATED 33 65 121
1P WILD-TYPE 89 60 145

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

'1p' versus 'CN_CNMF'

P value = 5.1e-22 (Chi-square test), Q value = 2.3e-19

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
1P MUTATED 79 131 57 134 20
1P WILD-TYPE 292 127 40 102 25

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

'1p' versus 'METHLYATION_CNMF'

P value = 6.19e-07 (Chi-square test), Q value = 0.00012

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
1P MUTATED 60 41 56 68 12 42
1P WILD-TYPE 56 114 52 71 43 70

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

'1p' versus 'RPPA_CNMF'

P value = 4.01e-05 (Fisher's exact test), Q value = 0.0054

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
1P MUTATED 83 51 35
1P WILD-TYPE 64 82 82

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

'1p' versus 'RPPA_CHIERARCHICAL'

P value = 0.00217 (Fisher's exact test), Q value = 0.16

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
1P MUTATED 70 33 66
1P WILD-TYPE 91 77 60

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

'1p' versus 'MRNASEQ_CNMF'

P value = 2.57e-09 (Fisher's exact test), Q value = 6.5e-07

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
1P MUTATED 147 46 226
1P WILD-TYPE 126 140 316

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

'1p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.95e-10 (Fisher's exact test), Q value = 1.9e-07

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
1P MUTATED 118 210 91
1P WILD-TYPE 115 229 238

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

'1p' versus 'MIRSEQ_CNMF'

P value = 3.72e-07 (Fisher's exact test), Q value = 7.5e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
1P MUTATED 156 93 158
1P WILD-TYPE 242 194 134

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

'1p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.07e-06 (Fisher's exact test), Q value = 2e-04

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
1P MUTATED 137 126 144
1P WILD-TYPE 115 173 282

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

'1p' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.99e-06 (Fisher's exact test), Q value = 0.0011

Table S11.  Gene #1: '1p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
1P MUTATED 87 68 105
1P WILD-TYPE 163 151 93

Figure S11.  Get High-res Image Gene #1: '1p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000868 (Fisher's exact test), Q value = 0.076

Table S12.  Gene #1: '1p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
1P MUTATED 75 56 129
1P WILD-TYPE 70 121 216

Figure S12.  Get High-res Image Gene #1: '1p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q' versus 'MRNA_CNMF'

P value = 0.00167 (Chi-square test), Q value = 0.13

Table S13.  Gene #2: '1q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
1Q MUTATED 14 19 72 70 90 57 12 29
1Q WILD-TYPE 7 17 47 26 19 15 8 11

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

'1q' versus 'CN_CNMF'

P value = 2.48e-12 (Chi-square test), Q value = 7.9e-10

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
1Q MUTATED 223 189 97 166 31
1Q WILD-TYPE 148 69 0 70 14

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

'1q' versus 'METHLYATION_CNMF'

P value = 2.06e-06 (Chi-square test), Q value = 0.00038

Table S15.  Gene #2: '1q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
1Q MUTATED 82 128 86 86 32 63
1Q WILD-TYPE 34 27 22 53 23 49

Figure S15.  Get High-res Image Gene #2: '1q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p' versus 'MRNA_CNMF'

P value = 4.34e-05 (Chi-square test), Q value = 0.0058

Table S16.  Gene #3: '2p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
2P MUTATED 4 10 37 39 25 33 3 2
2P WILD-TYPE 17 26 82 57 84 39 17 38

Figure S16.  Get High-res Image Gene #3: '2p' versus Molecular Subtype #1: 'MRNA_CNMF'

'2p' versus 'MRNA_CHIERARCHICAL'

P value = 2.04e-06 (Fisher's exact test), Q value = 0.00037

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
2P MUTATED 16 51 86
2P WILD-TYPE 106 74 180

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

'2p' versus 'CN_CNMF'

P value = 6.37e-18 (Chi-square test), Q value = 2.7e-15

Table S18.  Gene #3: '2p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
2P MUTATED 41 98 37 94 13
2P WILD-TYPE 330 160 60 142 32

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

'2p' versus 'METHLYATION_CNMF'

P value = 5.66e-08 (Chi-square test), Q value = 1.3e-05

Table S19.  Gene #3: '2p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
2P MUTATED 45 25 30 54 6 18
2P WILD-TYPE 71 130 78 85 49 94

Figure S19.  Get High-res Image Gene #3: '2p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p' versus 'RPPA_CNMF'

P value = 4.52e-05 (Fisher's exact test), Q value = 0.006

Table S20.  Gene #3: '2p' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
2P MUTATED 62 38 20
2P WILD-TYPE 85 95 97

Figure S20.  Get High-res Image Gene #3: '2p' versus Molecular Subtype #5: 'RPPA_CNMF'

'2p' versus 'RPPA_CHIERARCHICAL'

P value = 1.3e-05 (Fisher's exact test), Q value = 0.002

Table S21.  Gene #3: '2p' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
2P MUTATED 51 16 53
2P WILD-TYPE 110 94 73

Figure S21.  Get High-res Image Gene #3: '2p' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2p' versus 'MRNASEQ_CNMF'

P value = 5.52e-12 (Fisher's exact test), Q value = 1.7e-09

Table S22.  Gene #3: '2p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
2P MUTATED 108 19 153
2P WILD-TYPE 165 167 389

Figure S22.  Get High-res Image Gene #3: '2p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.76e-13 (Fisher's exact test), Q value = 6.1e-11

Table S23.  Gene #3: '2p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
2P MUTATED 91 145 44
2P WILD-TYPE 142 294 285

Figure S23.  Get High-res Image Gene #3: '2p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p' versus 'MIRSEQ_CNMF'

P value = 5.31e-11 (Fisher's exact test), Q value = 1.5e-08

Table S24.  Gene #3: '2p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
2P MUTATED 113 42 116
2P WILD-TYPE 285 245 176

Figure S24.  Get High-res Image Gene #3: '2p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.68e-10 (Fisher's exact test), Q value = 7.3e-08

Table S25.  Gene #3: '2p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
2P MUTATED 101 95 75
2P WILD-TYPE 151 204 351

Figure S25.  Get High-res Image Gene #3: '2p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.52e-11 (Fisher's exact test), Q value = 1.9e-08

Table S26.  Gene #3: '2p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
2P MUTATED 66 30 86
2P WILD-TYPE 184 189 112

Figure S26.  Get High-res Image Gene #3: '2p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.2e-06 (Fisher's exact test), Q value = 0.001

Table S27.  Gene #3: '2p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
2P MUTATED 58 28 96
2P WILD-TYPE 87 149 249

Figure S27.  Get High-res Image Gene #3: '2p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q' versus 'MRNA_CNMF'

P value = 0.00136 (Chi-square test), Q value = 0.11

Table S28.  Gene #4: '2q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
2Q MUTATED 4 10 35 32 26 31 3 2
2Q WILD-TYPE 17 26 84 64 83 41 17 38

Figure S28.  Get High-res Image Gene #4: '2q' versus Molecular Subtype #1: 'MRNA_CNMF'

'2q' versus 'MRNA_CHIERARCHICAL'

P value = 6.28e-05 (Fisher's exact test), Q value = 0.008

Table S29.  Gene #4: '2q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
2Q MUTATED 16 43 84
2Q WILD-TYPE 106 82 182

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

'2q' versus 'CN_CNMF'

P value = 3.39e-16 (Chi-square test), Q value = 1.3e-13

Table S30.  Gene #4: '2q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
2Q MUTATED 38 93 38 81 12
2Q WILD-TYPE 333 165 59 155 33

Figure S30.  Get High-res Image Gene #4: '2q' versus Molecular Subtype #3: 'CN_CNMF'

'2q' versus 'METHLYATION_CNMF'

P value = 1.65e-07 (Chi-square test), Q value = 3.5e-05

Table S31.  Gene #4: '2q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
2Q MUTATED 39 24 27 51 5 14
2Q WILD-TYPE 77 131 81 88 50 98

Figure S31.  Get High-res Image Gene #4: '2q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2q' versus 'RPPA_CNMF'

P value = 3.45e-06 (Fisher's exact test), Q value = 6e-04

Table S32.  Gene #4: '2q' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
2Q MUTATED 57 38 14
2Q WILD-TYPE 90 95 103

Figure S32.  Get High-res Image Gene #4: '2q' versus Molecular Subtype #5: 'RPPA_CNMF'

'2q' versus 'RPPA_CHIERARCHICAL'

P value = 2.08e-05 (Fisher's exact test), Q value = 0.0031

Table S33.  Gene #4: '2q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
2Q MUTATED 50 13 46
2Q WILD-TYPE 111 97 80

Figure S33.  Get High-res Image Gene #4: '2q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2q' versus 'MRNASEQ_CNMF'

P value = 9.83e-09 (Fisher's exact test), Q value = 2.3e-06

Table S34.  Gene #4: '2q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
2Q MUTATED 95 20 144
2Q WILD-TYPE 178 166 398

Figure S34.  Get High-res Image Gene #4: '2q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.26e-09 (Fisher's exact test), Q value = 3.3e-07

Table S35.  Gene #4: '2q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
2Q MUTATED 76 138 45
2Q WILD-TYPE 157 301 284

Figure S35.  Get High-res Image Gene #4: '2q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q' versus 'MIRSEQ_CNMF'

P value = 8.86e-08 (Fisher's exact test), Q value = 2e-05

Table S36.  Gene #4: '2q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
2Q MUTATED 109 42 101
2Q WILD-TYPE 289 245 191

Figure S36.  Get High-res Image Gene #4: '2q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.54e-07 (Fisher's exact test), Q value = 3.3e-05

Table S37.  Gene #4: '2q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
2Q MUTATED 87 92 73
2Q WILD-TYPE 165 207 353

Figure S37.  Get High-res Image Gene #4: '2q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.65e-09 (Fisher's exact test), Q value = 1.6e-06

Table S38.  Gene #4: '2q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
2Q MUTATED 66 30 79
2Q WILD-TYPE 184 189 119

Figure S38.  Get High-res Image Gene #4: '2q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.5e-05 (Fisher's exact test), Q value = 0.012

Table S39.  Gene #4: '2q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
2Q MUTATED 53 28 94
2Q WILD-TYPE 92 149 251

Figure S39.  Get High-res Image Gene #4: '2q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p' versus 'MRNA_CNMF'

P value = 1.48e-07 (Chi-square test), Q value = 3.2e-05

Table S40.  Gene #5: '3p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
3P MUTATED 4 13 42 48 20 32 12 4
3P WILD-TYPE 17 23 77 48 89 40 8 36

Figure S40.  Get High-res Image Gene #5: '3p' versus Molecular Subtype #1: 'MRNA_CNMF'

'3p' versus 'MRNA_CHIERARCHICAL'

P value = 9.19e-07 (Fisher's exact test), Q value = 0.00017

Table S41.  Gene #5: '3p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
3P MUTATED 23 63 89
3P WILD-TYPE 99 62 177

Figure S41.  Get High-res Image Gene #5: '3p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3p' versus 'CN_CNMF'

P value = 1.03e-26 (Chi-square test), Q value = 4.7e-24

Table S42.  Gene #5: '3p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
3P MUTATED 38 100 36 120 14
3P WILD-TYPE 333 158 61 116 31

Figure S42.  Get High-res Image Gene #5: '3p' versus Molecular Subtype #3: 'CN_CNMF'

'3p' versus 'METHLYATION_CNMF'

P value = 1.44e-15 (Chi-square test), Q value = 5.5e-13

Table S43.  Gene #5: '3p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
3P MUTATED 63 17 39 45 8 19
3P WILD-TYPE 53 138 69 94 47 93

Figure S43.  Get High-res Image Gene #5: '3p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p' versus 'RPPA_CNMF'

P value = 0.000198 (Fisher's exact test), Q value = 0.023

Table S44.  Gene #5: '3p' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
3P MUTATED 71 42 29
3P WILD-TYPE 76 91 88

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

'3p' versus 'RPPA_CHIERARCHICAL'

P value = 0.000283 (Fisher's exact test), Q value = 0.03

Table S45.  Gene #5: '3p' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
3P MUTATED 53 27 62
3P WILD-TYPE 108 83 64

Figure S45.  Get High-res Image Gene #5: '3p' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3p' versus 'MRNASEQ_CNMF'

P value = 6.5e-16 (Fisher's exact test), Q value = 2.5e-13

Table S46.  Gene #5: '3p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
3P MUTATED 131 24 150
3P WILD-TYPE 142 162 392

Figure S46.  Get High-res Image Gene #5: '3p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.21e-15 (Fisher's exact test), Q value = 8.4e-13

Table S47.  Gene #5: '3p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
3P MUTATED 113 138 54
3P WILD-TYPE 120 301 275

Figure S47.  Get High-res Image Gene #5: '3p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p' versus 'MIRSEQ_CNMF'

P value = 7.52e-17 (Fisher's exact test), Q value = 3e-14

Table S48.  Gene #5: '3p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
3P MUTATED 98 52 144
3P WILD-TYPE 300 235 148

Figure S48.  Get High-res Image Gene #5: '3p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.68e-14 (Fisher's exact test), Q value = 1.7e-11

Table S49.  Gene #5: '3p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
3P MUTATED 121 91 82
3P WILD-TYPE 131 208 344

Figure S49.  Get High-res Image Gene #5: '3p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.85e-13 (Fisher's exact test), Q value = 2.6e-10

Table S50.  Gene #5: '3p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
3P MUTATED 59 37 97
3P WILD-TYPE 191 182 101

Figure S50.  Get High-res Image Gene #5: '3p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.83e-09 (Fisher's exact test), Q value = 1.4e-06

Table S51.  Gene #5: '3p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
3P MUTATED 72 35 86
3P WILD-TYPE 73 142 259

Figure S51.  Get High-res Image Gene #5: '3p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q' versus 'MRNA_CNMF'

P value = 1.15e-08 (Chi-square test), Q value = 2.7e-06

Table S52.  Gene #6: '3q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
3Q MUTATED 2 10 43 45 18 31 11 2
3Q WILD-TYPE 19 26 76 51 91 41 9 38

Figure S52.  Get High-res Image Gene #6: '3q' versus Molecular Subtype #1: 'MRNA_CNMF'

'3q' versus 'MRNA_CHIERARCHICAL'

P value = 3.15e-09 (Fisher's exact test), Q value = 7.9e-07

Table S53.  Gene #6: '3q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
3Q MUTATED 15 60 87
3Q WILD-TYPE 107 65 179

Figure S53.  Get High-res Image Gene #6: '3q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3q' versus 'CN_CNMF'

P value = 2.27e-28 (Chi-square test), Q value = 1e-25

Table S54.  Gene #6: '3q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
3Q MUTATED 33 94 35 120 14
3Q WILD-TYPE 338 164 62 116 31

Figure S54.  Get High-res Image Gene #6: '3q' versus Molecular Subtype #3: 'CN_CNMF'

'3q' versus 'METHLYATION_CNMF'

P value = 4.12e-17 (Chi-square test), Q value = 1.7e-14

Table S55.  Gene #6: '3q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
3Q MUTATED 65 17 34 43 9 15
3Q WILD-TYPE 51 138 74 96 46 97

Figure S55.  Get High-res Image Gene #6: '3q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q' versus 'RPPA_CNMF'

P value = 0.000618 (Fisher's exact test), Q value = 0.058

Table S56.  Gene #6: '3q' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
3Q MUTATED 66 40 27
3Q WILD-TYPE 81 93 90

Figure S56.  Get High-res Image Gene #6: '3q' versus Molecular Subtype #5: 'RPPA_CNMF'

'3q' versus 'MRNASEQ_CNMF'

P value = 2.8e-17 (Fisher's exact test), Q value = 1.2e-14

Table S57.  Gene #6: '3q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
3Q MUTATED 127 19 148
3Q WILD-TYPE 146 167 394

Figure S57.  Get High-res Image Gene #6: '3q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.86e-18 (Fisher's exact test), Q value = 1.6e-15

Table S58.  Gene #6: '3q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
3Q MUTATED 111 138 45
3Q WILD-TYPE 122 301 284

Figure S58.  Get High-res Image Gene #6: '3q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q' versus 'MIRSEQ_CNMF'

P value = 1.06e-18 (Fisher's exact test), Q value = 4.6e-16

Table S59.  Gene #6: '3q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
3Q MUTATED 95 46 143
3Q WILD-TYPE 303 241 149

Figure S59.  Get High-res Image Gene #6: '3q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.26e-16 (Fisher's exact test), Q value = 1.3e-13

Table S60.  Gene #6: '3q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
3Q MUTATED 121 89 74
3Q WILD-TYPE 131 210 352

Figure S60.  Get High-res Image Gene #6: '3q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.56e-14 (Fisher's exact test), Q value = 5.8e-12

Table S61.  Gene #6: '3q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
3Q MUTATED 56 34 98
3Q WILD-TYPE 194 185 100

Figure S61.  Get High-res Image Gene #6: '3q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.07e-10 (Fisher's exact test), Q value = 3e-08

Table S62.  Gene #6: '3q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
3Q MUTATED 74 33 81
3Q WILD-TYPE 71 144 264

Figure S62.  Get High-res Image Gene #6: '3q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p' versus 'MRNA_CNMF'

P value = 3.37e-11 (Chi-square test), Q value = 1e-08

Table S63.  Gene #7: '4p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
4P MUTATED 5 9 45 62 25 45 8 9
4P WILD-TYPE 16 27 74 34 84 27 12 31

Figure S63.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #1: 'MRNA_CNMF'

'4p' versus 'MRNA_CHIERARCHICAL'

P value = 5.18e-12 (Fisher's exact test), Q value = 1.6e-09

Table S64.  Gene #7: '4p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
4P MUTATED 24 80 104
4P WILD-TYPE 98 45 162

Figure S64.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4p' versus 'CN_CNMF'

P value = 5.5e-39 (Chi-square test), Q value = 2.6e-36

Table S65.  Gene #7: '4p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
4P MUTATED 58 114 48 165 18
4P WILD-TYPE 313 144 49 71 27

Figure S65.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #3: 'CN_CNMF'

'4p' versus 'METHLYATION_CNMF'

P value = 6.48e-18 (Chi-square test), Q value = 2.7e-15

Table S66.  Gene #7: '4p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
4P MUTATED 86 37 45 55 11 31
4P WILD-TYPE 30 118 63 84 44 81

Figure S66.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p' versus 'RPPA_CNMF'

P value = 3.77e-06 (Fisher's exact test), Q value = 0.00065

Table S67.  Gene #7: '4p' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
4P MUTATED 84 51 32
4P WILD-TYPE 63 82 85

Figure S67.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #5: 'RPPA_CNMF'

'4p' versus 'RPPA_CHIERARCHICAL'

P value = 4.47e-05 (Fisher's exact test), Q value = 0.006

Table S68.  Gene #7: '4p' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
4P MUTATED 60 34 73
4P WILD-TYPE 101 76 53

Figure S68.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4p' versus 'MRNASEQ_CNMF'

P value = 1.89e-27 (Fisher's exact test), Q value = 8.6e-25

Table S69.  Gene #7: '4p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
4P MUTATED 178 31 190
4P WILD-TYPE 95 155 352

Figure S69.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.08e-26 (Fisher's exact test), Q value = 1.8e-23

Table S70.  Gene #7: '4p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
4P MUTATED 155 173 71
4P WILD-TYPE 78 266 258

Figure S70.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p' versus 'MIRSEQ_CNMF'

P value = 1.46e-21 (Fisher's exact test), Q value = 6.5e-19

Table S71.  Gene #7: '4p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
4P MUTATED 145 63 178
4P WILD-TYPE 253 224 114

Figure S71.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.61e-25 (Fisher's exact test), Q value = 7.3e-23

Table S72.  Gene #7: '4p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
4P MUTATED 167 113 106
4P WILD-TYPE 85 186 320

Figure S72.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.02e-19 (Fisher's exact test), Q value = 1.3e-16

Table S73.  Gene #7: '4p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
4P MUTATED 87 47 128
4P WILD-TYPE 163 172 70

Figure S73.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.2e-16 (Fisher's exact test), Q value = 2.8e-13

Table S74.  Gene #7: '4p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
4P MUTATED 97 39 126
4P WILD-TYPE 48 138 219

Figure S74.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q' versus 'MRNA_CNMF'

P value = 2.79e-05 (Chi-square test), Q value = 0.0039

Table S75.  Gene #8: '4q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
4Q MUTATED 5 9 46 48 24 38 7 9
4Q WILD-TYPE 16 27 73 48 85 34 13 31

Figure S75.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q' versus 'MRNA_CHIERARCHICAL'

P value = 4.73e-07 (Fisher's exact test), Q value = 9.4e-05

Table S76.  Gene #8: '4q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
4Q MUTATED 23 64 99
4Q WILD-TYPE 99 61 167

Figure S76.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4q' versus 'CN_CNMF'

P value = 2.05e-29 (Chi-square test), Q value = 9.5e-27

Table S77.  Gene #8: '4q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
4Q MUTATED 53 104 47 140 18
4Q WILD-TYPE 318 154 50 96 27

Figure S77.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #3: 'CN_CNMF'

'4q' versus 'METHLYATION_CNMF'

P value = 3.18e-11 (Chi-square test), Q value = 9.4e-09

Table S78.  Gene #8: '4q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
4Q MUTATED 73 37 39 49 11 29
4Q WILD-TYPE 43 118 69 90 44 83

Figure S78.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q' versus 'MRNASEQ_CNMF'

P value = 1.02e-18 (Fisher's exact test), Q value = 4.4e-16

Table S79.  Gene #8: '4q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
4Q MUTATED 149 27 182
4Q WILD-TYPE 124 159 360

Figure S79.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.25e-17 (Fisher's exact test), Q value = 1.3e-14

Table S80.  Gene #8: '4q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
4Q MUTATED 129 163 66
4Q WILD-TYPE 104 276 263

Figure S80.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q' versus 'MIRSEQ_CNMF'

P value = 3.83e-13 (Fisher's exact test), Q value = 1.3e-10

Table S81.  Gene #8: '4q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
4Q MUTATED 137 60 148
4Q WILD-TYPE 261 227 144

Figure S81.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.21e-15 (Fisher's exact test), Q value = 8.4e-13

Table S82.  Gene #8: '4q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
4Q MUTATED 140 102 103
4Q WILD-TYPE 112 197 323

Figure S82.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.12e-12 (Fisher's exact test), Q value = 6.8e-10

Table S83.  Gene #8: '4q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
4Q MUTATED 81 43 106
4Q WILD-TYPE 169 176 92

Figure S83.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.7e-09 (Fisher's exact test), Q value = 6.8e-07

Table S84.  Gene #8: '4q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
4Q MUTATED 77 35 118
4Q WILD-TYPE 68 142 227

Figure S84.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p' versus 'MRNA_CNMF'

P value = 4.03e-07 (Chi-square test), Q value = 8.1e-05

Table S85.  Gene #9: '5p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
5P MUTATED 6 15 41 63 36 39 13 10
5P WILD-TYPE 15 21 78 33 73 33 7 30

Figure S85.  Get High-res Image Gene #9: '5p' versus Molecular Subtype #1: 'MRNA_CNMF'

'5p' versus 'MRNA_CHIERARCHICAL'

P value = 2.19e-06 (Fisher's exact test), Q value = 0.00039

Table S86.  Gene #9: '5p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
5P MUTATED 44 79 100
5P WILD-TYPE 78 46 166

Figure S86.  Get High-res Image Gene #9: '5p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5p' versus 'CN_CNMF'

P value = 2.54e-32 (Chi-square test), Q value = 1.2e-29

Table S87.  Gene #9: '5p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
5P MUTATED 68 124 55 156 20
5P WILD-TYPE 303 134 42 80 25

Figure S87.  Get High-res Image Gene #9: '5p' versus Molecular Subtype #3: 'CN_CNMF'

'5p' versus 'METHLYATION_CNMF'

P value = 1.55e-13 (Chi-square test), Q value = 5.4e-11

Table S88.  Gene #9: '5p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
5P MUTATED 84 43 49 53 13 38
5P WILD-TYPE 32 112 59 86 42 74

Figure S88.  Get High-res Image Gene #9: '5p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p' versus 'RPPA_CNMF'

P value = 0.00296 (Fisher's exact test), Q value = 0.21

Table S89.  Gene #9: '5p' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
5P MUTATED 83 51 46
5P WILD-TYPE 64 82 71

Figure S89.  Get High-res Image Gene #9: '5p' versus Molecular Subtype #5: 'RPPA_CNMF'

'5p' versus 'MRNASEQ_CNMF'

P value = 5.62e-15 (Fisher's exact test), Q value = 2.1e-12

Table S90.  Gene #9: '5p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
5P MUTATED 170 55 195
5P WILD-TYPE 103 131 347

Figure S90.  Get High-res Image Gene #9: '5p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.2e-16 (Fisher's exact test), Q value = 2e-13

Table S91.  Gene #9: '5p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
5P MUTATED 148 179 93
5P WILD-TYPE 85 260 236

Figure S91.  Get High-res Image Gene #9: '5p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p' versus 'MIRSEQ_CNMF'

P value = 2.22e-13 (Fisher's exact test), Q value = 7.7e-11

Table S92.  Gene #9: '5p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
5P MUTATED 148 87 175
5P WILD-TYPE 250 200 117

Figure S92.  Get High-res Image Gene #9: '5p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.03e-18 (Fisher's exact test), Q value = 2.1e-15

Table S93.  Gene #9: '5p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
5P MUTATED 165 112 133
5P WILD-TYPE 87 187 293

Figure S93.  Get High-res Image Gene #9: '5p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.88e-14 (Fisher's exact test), Q value = 1.8e-11

Table S94.  Gene #9: '5p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
5P MUTATED 95 57 125
5P WILD-TYPE 155 162 73

Figure S94.  Get High-res Image Gene #9: '5p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.72e-11 (Fisher's exact test), Q value = 5.2e-09

Table S95.  Gene #9: '5p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
5P MUTATED 95 49 133
5P WILD-TYPE 50 128 212

Figure S95.  Get High-res Image Gene #9: '5p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q' versus 'MRNA_CNMF'

P value = 3.29e-10 (Chi-square test), Q value = 9e-08

Table S96.  Gene #10: '5q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
5Q MUTATED 7 13 38 68 33 36 11 7
5Q WILD-TYPE 14 23 81 28 76 36 9 33

Figure S96.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #1: 'MRNA_CNMF'

'5q' versus 'MRNA_CHIERARCHICAL'

P value = 7.14e-09 (Fisher's exact test), Q value = 1.7e-06

Table S97.  Gene #10: '5q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
5Q MUTATED 37 81 95
5Q WILD-TYPE 85 44 171

Figure S97.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5q' versus 'CN_CNMF'

P value = 5.35e-39 (Chi-square test), Q value = 2.6e-36

Table S98.  Gene #10: '5q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
5Q MUTATED 63 107 53 168 20
5Q WILD-TYPE 308 151 44 68 25

Figure S98.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #3: 'CN_CNMF'

'5q' versus 'METHLYATION_CNMF'

P value = 2.53e-20 (Chi-square test), Q value = 1.1e-17

Table S99.  Gene #10: '5q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
5Q MUTATED 93 40 41 55 11 38
5Q WILD-TYPE 23 115 67 84 44 74

Figure S99.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q' versus 'RPPA_CNMF'

P value = 0.000934 (Fisher's exact test), Q value = 0.078

Table S100.  Gene #10: '5q' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
5Q MUTATED 83 48 45
5Q WILD-TYPE 64 85 72

Figure S100.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #5: 'RPPA_CNMF'

'5q' versus 'RPPA_CHIERARCHICAL'

P value = 0.000373 (Fisher's exact test), Q value = 0.038

Table S101.  Gene #10: '5q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
5Q MUTATED 63 39 74
5Q WILD-TYPE 98 71 52

Figure S101.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5q' versus 'MRNASEQ_CNMF'

P value = 1.92e-21 (Fisher's exact test), Q value = 8.5e-19

Table S102.  Gene #10: '5q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
5Q MUTATED 178 48 183
5Q WILD-TYPE 95 138 359

Figure S102.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.74e-23 (Fisher's exact test), Q value = 2.1e-20

Table S103.  Gene #10: '5q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
5Q MUTATED 158 166 85
5Q WILD-TYPE 75 273 244

Figure S103.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q' versus 'MIRSEQ_CNMF'

P value = 3.56e-22 (Fisher's exact test), Q value = 1.6e-19

Table S104.  Gene #10: '5q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
5Q MUTATED 130 79 188
5Q WILD-TYPE 268 208 104

Figure S104.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.29e-25 (Fisher's exact test), Q value = 1.5e-22

Table S105.  Gene #10: '5q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
5Q MUTATED 173 103 121
5Q WILD-TYPE 79 196 305

Figure S105.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.95e-16 (Fisher's exact test), Q value = 7.8e-14

Table S106.  Gene #10: '5q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
5Q MUTATED 88 55 128
5Q WILD-TYPE 162 164 70

Figure S106.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.12e-16 (Fisher's exact test), Q value = 8.5e-14

Table S107.  Gene #10: '5q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
5Q MUTATED 102 46 123
5Q WILD-TYPE 43 131 222

Figure S107.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p' versus 'CN_CNMF'

P value = 8.58e-28 (Chi-square test), Q value = 3.9e-25

Table S108.  Gene #11: '6p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
6P MUTATED 54 120 40 133 23
6P WILD-TYPE 317 138 57 103 22

Figure S108.  Get High-res Image Gene #11: '6p' versus Molecular Subtype #3: 'CN_CNMF'

'6p' versus 'METHLYATION_CNMF'

P value = 9.16e-15 (Chi-square test), Q value = 3.4e-12

Table S109.  Gene #11: '6p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
6P MUTATED 67 28 43 68 6 31
6P WILD-TYPE 49 127 65 71 49 81

Figure S109.  Get High-res Image Gene #11: '6p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p' versus 'MRNASEQ_CNMF'

P value = 1.38e-09 (Fisher's exact test), Q value = 3.6e-07

Table S110.  Gene #11: '6p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
6P MUTATED 131 36 200
6P WILD-TYPE 142 150 342

Figure S110.  Get High-res Image Gene #11: '6p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.32e-13 (Fisher's exact test), Q value = 2.1e-10

Table S111.  Gene #11: '6p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
6P MUTATED 115 182 70
6P WILD-TYPE 118 257 259

Figure S111.  Get High-res Image Gene #11: '6p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p' versus 'MIRSEQ_CNMF'

P value = 1.47e-10 (Fisher's exact test), Q value = 4.1e-08

Table S112.  Gene #11: '6p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
6P MUTATED 138 69 148
6P WILD-TYPE 260 218 144

Figure S112.  Get High-res Image Gene #11: '6p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.73e-10 (Fisher's exact test), Q value = 2.3e-07

Table S113.  Gene #11: '6p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
6P MUTATED 125 120 110
6P WILD-TYPE 127 179 316

Figure S113.  Get High-res Image Gene #11: '6p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.53e-09 (Fisher's exact test), Q value = 3.9e-07

Table S114.  Gene #11: '6p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
6P MUTATED 84 50 104
6P WILD-TYPE 166 169 94

Figure S114.  Get High-res Image Gene #11: '6p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.11e-05 (Fisher's exact test), Q value = 0.0017

Table S115.  Gene #11: '6p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
6P MUTATED 75 47 116
6P WILD-TYPE 70 130 229

Figure S115.  Get High-res Image Gene #11: '6p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q' versus 'CN_CNMF'

P value = 7.12e-19 (Chi-square test), Q value = 3.1e-16

Table S116.  Gene #12: '6q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
6Q MUTATED 76 133 41 120 26
6Q WILD-TYPE 295 125 56 116 19

Figure S116.  Get High-res Image Gene #12: '6q' versus Molecular Subtype #3: 'CN_CNMF'

'6q' versus 'METHLYATION_CNMF'

P value = 1.6e-07 (Chi-square test), Q value = 3.4e-05

Table S117.  Gene #12: '6q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
6Q MUTATED 59 46 43 74 9 34
6Q WILD-TYPE 57 109 65 65 46 78

Figure S117.  Get High-res Image Gene #12: '6q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000431 (Fisher's exact test), Q value = 0.043

Table S118.  Gene #12: '6q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
6Q MUTATED 104 188 101
6Q WILD-TYPE 129 251 228

Figure S118.  Get High-res Image Gene #12: '6q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q' versus 'MIRSEQ_CNMF'

P value = 0.000118 (Fisher's exact test), Q value = 0.015

Table S119.  Gene #12: '6q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
6Q MUTATED 145 95 144
6Q WILD-TYPE 253 192 148

Figure S119.  Get High-res Image Gene #12: '6q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000488 (Fisher's exact test), Q value = 0.048

Table S120.  Gene #12: '6q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
6Q MUTATED 113 133 138
6Q WILD-TYPE 139 166 288

Figure S120.  Get High-res Image Gene #12: '6q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000183 (Fisher's exact test), Q value = 0.021

Table S121.  Gene #12: '6q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
6Q MUTATED 98 66 99
6Q WILD-TYPE 152 153 99

Figure S121.  Get High-res Image Gene #12: '6q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7p' versus 'MRNA_CNMF'

P value = 0.000916 (Chi-square test), Q value = 0.078

Table S122.  Gene #13: '7p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
7P MUTATED 6 12 46 50 38 40 8 7
7P WILD-TYPE 15 24 73 46 71 32 12 33

Figure S122.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #1: 'MRNA_CNMF'

'7p' versus 'MRNA_CHIERARCHICAL'

P value = 0.00239 (Fisher's exact test), Q value = 0.17

Table S123.  Gene #13: '7p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
7P MUTATED 36 64 107
7P WILD-TYPE 86 61 159

Figure S123.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7p' versus 'CN_CNMF'

P value = 4.44e-18 (Chi-square test), Q value = 1.9e-15

Table S124.  Gene #13: '7p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
7P MUTATED 81 111 56 130 17
7P WILD-TYPE 290 147 41 106 28

Figure S124.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #3: 'CN_CNMF'

'7p' versus 'METHLYATION_CNMF'

P value = 2.04e-08 (Chi-square test), Q value = 4.7e-06

Table S125.  Gene #13: '7p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
7P MUTATED 69 43 47 60 14 28
7P WILD-TYPE 47 112 61 79 41 84

Figure S125.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p' versus 'MRNASEQ_CNMF'

P value = 7.52e-09 (Fisher's exact test), Q value = 1.8e-06

Table S126.  Gene #13: '7p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
7P MUTATED 143 46 202
7P WILD-TYPE 130 140 340

Figure S126.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.5e-11 (Fisher's exact test), Q value = 1.3e-08

Table S127.  Gene #13: '7p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
7P MUTATED 123 185 83
7P WILD-TYPE 110 254 246

Figure S127.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p' versus 'MIRSEQ_CNMF'

P value = 3.46e-07 (Fisher's exact test), Q value = 7e-05

Table S128.  Gene #13: '7p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
7P MUTATED 143 85 149
7P WILD-TYPE 255 202 143

Figure S128.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.82e-06 (Fisher's exact test), Q value = 0.00033

Table S129.  Gene #13: '7p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
7P MUTATED 129 115 133
7P WILD-TYPE 123 184 293

Figure S129.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000165 (Fisher's exact test), Q value = 0.019

Table S130.  Gene #13: '7p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
7P MUTATED 87 68 99
7P WILD-TYPE 163 151 99

Figure S130.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00214 (Fisher's exact test), Q value = 0.16

Table S131.  Gene #13: '7p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
7P MUTATED 73 57 124
7P WILD-TYPE 72 120 221

Figure S131.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q' versus 'CN_CNMF'

P value = 8.67e-14 (Chi-square test), Q value = 3.1e-11

Table S132.  Gene #14: '7q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
7Q MUTATED 78 103 54 111 14
7Q WILD-TYPE 293 155 43 125 31

Figure S132.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #3: 'CN_CNMF'

'7q' versus 'METHLYATION_CNMF'

P value = 7.15e-06 (Chi-square test), Q value = 0.0012

Table S133.  Gene #14: '7q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
7Q MUTATED 61 42 39 51 14 24
7Q WILD-TYPE 55 113 69 88 41 88

Figure S133.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q' versus 'MRNASEQ_CNMF'

P value = 6.88e-06 (Fisher's exact test), Q value = 0.0011

Table S134.  Gene #14: '7q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
7Q MUTATED 123 43 190
7Q WILD-TYPE 150 143 352

Figure S134.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.87e-10 (Fisher's exact test), Q value = 1.6e-07

Table S135.  Gene #14: '7q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
7Q MUTATED 108 175 73
7Q WILD-TYPE 125 264 256

Figure S135.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q' versus 'MIRSEQ_CNMF'

P value = 2.62e-05 (Fisher's exact test), Q value = 0.0038

Table S136.  Gene #14: '7q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
7Q MUTATED 127 83 134
7Q WILD-TYPE 271 204 158

Figure S136.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.89e-06 (Fisher's exact test), Q value = 0.00084

Table S137.  Gene #14: '7q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
7Q MUTATED 121 97 126
7Q WILD-TYPE 131 202 300

Figure S137.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00238 (Fisher's exact test), Q value = 0.17

Table S138.  Gene #14: '7q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
7Q MUTATED 80 65 89
7Q WILD-TYPE 170 154 109

Figure S138.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00323 (Fisher's exact test), Q value = 0.22

Table S139.  Gene #14: '7q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
7Q MUTATED 68 53 113
7Q WILD-TYPE 77 124 232

Figure S139.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p' versus 'MRNA_CNMF'

P value = 3.3e-07 (Chi-square test), Q value = 6.7e-05

Table S140.  Gene #15: '8p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
8P MUTATED 12 18 94 73 52 56 15 21
8P WILD-TYPE 9 18 25 23 57 16 5 19

Figure S140.  Get High-res Image Gene #15: '8p' versus Molecular Subtype #1: 'MRNA_CNMF'

'8p' versus 'MRNA_CHIERARCHICAL'

P value = 3.72e-05 (Fisher's exact test), Q value = 0.0051

Table S141.  Gene #15: '8p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
8P MUTATED 61 95 185
8P WILD-TYPE 61 30 81

Figure S141.  Get High-res Image Gene #15: '8p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8p' versus 'CN_CNMF'

P value = 2.7e-30 (Chi-square test), Q value = 1.3e-27

Table S142.  Gene #15: '8p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
8P MUTATED 154 194 58 193 42
8P WILD-TYPE 217 64 39 43 3

Figure S142.  Get High-res Image Gene #15: '8p' versus Molecular Subtype #3: 'CN_CNMF'

'8p' versus 'METHLYATION_CNMF'

P value = 7.53e-16 (Chi-square test), Q value = 2.9e-13

Table S143.  Gene #15: '8p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
8P MUTATED 96 60 72 107 25 60
8P WILD-TYPE 20 95 36 32 30 52

Figure S143.  Get High-res Image Gene #15: '8p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p' versus 'MRNASEQ_CNMF'

P value = 2.38e-12 (Fisher's exact test), Q value = 7.6e-10

Table S144.  Gene #15: '8p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
8P MUTATED 209 80 347
8P WILD-TYPE 64 106 195

Figure S144.  Get High-res Image Gene #15: '8p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.49e-13 (Fisher's exact test), Q value = 1.2e-10

Table S145.  Gene #15: '8p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
8P MUTATED 179 300 157
8P WILD-TYPE 54 139 172

Figure S145.  Get High-res Image Gene #15: '8p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p' versus 'MIRSEQ_CNMF'

P value = 2.77e-11 (Fisher's exact test), Q value = 8.3e-09

Table S146.  Gene #15: '8p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
8P MUTATED 251 144 227
8P WILD-TYPE 147 143 65

Figure S146.  Get High-res Image Gene #15: '8p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.4e-13 (Fisher's exact test), Q value = 2.1e-10

Table S147.  Gene #15: '8p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
8P MUTATED 203 195 224
8P WILD-TYPE 49 104 202

Figure S147.  Get High-res Image Gene #15: '8p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.88e-12 (Fisher's exact test), Q value = 1.5e-09

Table S148.  Gene #15: '8p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
8P MUTATED 155 102 159
8P WILD-TYPE 95 117 39

Figure S148.  Get High-res Image Gene #15: '8p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.06e-06 (Fisher's exact test), Q value = 2e-04

Table S149.  Gene #15: '8p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
8P MUTATED 115 92 209
8P WILD-TYPE 30 85 136

Figure S149.  Get High-res Image Gene #15: '8p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q' versus 'MRNA_CNMF'

P value = 8.1e-06 (Chi-square test), Q value = 0.0013

Table S150.  Gene #16: '8q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
8Q MUTATED 15 17 85 68 50 49 16 16
8Q WILD-TYPE 6 19 34 28 59 23 4 24

Figure S150.  Get High-res Image Gene #16: '8q' versus Molecular Subtype #1: 'MRNA_CNMF'

'8q' versus 'MRNA_CHIERARCHICAL'

P value = 0.000195 (Fisher's exact test), Q value = 0.022

Table S151.  Gene #16: '8q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
8Q MUTATED 56 87 173
8Q WILD-TYPE 66 38 93

Figure S151.  Get High-res Image Gene #16: '8q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8q' versus 'CN_CNMF'

P value = 6.79e-32 (Chi-square test), Q value = 3.2e-29

Table S152.  Gene #16: '8q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
8Q MUTATED 127 183 55 173 43
8Q WILD-TYPE 244 75 42 63 2

Figure S152.  Get High-res Image Gene #16: '8q' versus Molecular Subtype #3: 'CN_CNMF'

'8q' versus 'METHLYATION_CNMF'

P value = 6.4e-18 (Chi-square test), Q value = 2.7e-15

Table S153.  Gene #16: '8q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
8Q MUTATED 91 45 64 99 22 55
8Q WILD-TYPE 25 110 44 40 33 57

Figure S153.  Get High-res Image Gene #16: '8q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q' versus 'MRNASEQ_CNMF'

P value = 1.16e-10 (Fisher's exact test), Q value = 3.3e-08

Table S154.  Gene #16: '8q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
8Q MUTATED 187 69 321
8Q WILD-TYPE 86 117 221

Figure S154.  Get High-res Image Gene #16: '8q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.46e-12 (Fisher's exact test), Q value = 1.4e-09

Table S155.  Gene #16: '8q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
8Q MUTATED 165 273 139
8Q WILD-TYPE 68 166 190

Figure S155.  Get High-res Image Gene #16: '8q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q' versus 'MIRSEQ_CNMF'

P value = 1.17e-13 (Fisher's exact test), Q value = 4.1e-11

Table S156.  Gene #16: '8q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
8Q MUTATED 231 118 212
8Q WILD-TYPE 167 169 80

Figure S156.  Get High-res Image Gene #16: '8q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.71e-12 (Fisher's exact test), Q value = 8.6e-10

Table S157.  Gene #16: '8q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
8Q MUTATED 186 180 195
8Q WILD-TYPE 66 119 231

Figure S157.  Get High-res Image Gene #16: '8q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.85e-13 (Fisher's exact test), Q value = 1.3e-10

Table S158.  Gene #16: '8q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
8Q MUTATED 141 84 148
8Q WILD-TYPE 109 135 50

Figure S158.  Get High-res Image Gene #16: '8q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.41e-08 (Fisher's exact test), Q value = 7.8e-06

Table S159.  Gene #16: '8q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
8Q MUTATED 108 75 190
8Q WILD-TYPE 37 102 155

Figure S159.  Get High-res Image Gene #16: '8q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p' versus 'MRNA_CNMF'

P value = 6.44e-07 (Chi-square test), Q value = 0.00012

Table S160.  Gene #17: '9p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
9P MUTATED 8 12 56 64 32 42 9 11
9P WILD-TYPE 13 24 63 32 77 30 11 29

Figure S160.  Get High-res Image Gene #17: '9p' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p' versus 'MRNA_CHIERARCHICAL'

P value = 1.27e-07 (Fisher's exact test), Q value = 2.7e-05

Table S161.  Gene #17: '9p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
9P MUTATED 33 78 123
9P WILD-TYPE 89 47 143

Figure S161.  Get High-res Image Gene #17: '9p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p' versus 'CN_CNMF'

P value = 1.45e-39 (Chi-square test), Q value = 6.9e-37

Table S162.  Gene #17: '9p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
9P MUTATED 58 156 46 150 17
9P WILD-TYPE 313 102 51 86 28

Figure S162.  Get High-res Image Gene #17: '9p' versus Molecular Subtype #3: 'CN_CNMF'

'9p' versus 'METHLYATION_CNMF'

P value = 7.66e-18 (Chi-square test), Q value = 3.2e-15

Table S163.  Gene #17: '9p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
9P MUTATED 74 33 49 81 12 27
9P WILD-TYPE 42 122 59 58 43 85

Figure S163.  Get High-res Image Gene #17: '9p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p' versus 'RPPA_CNMF'

P value = 1.65e-07 (Fisher's exact test), Q value = 3.5e-05

Table S164.  Gene #17: '9p' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
9P MUTATED 96 49 42
9P WILD-TYPE 51 84 75

Figure S164.  Get High-res Image Gene #17: '9p' versus Molecular Subtype #5: 'RPPA_CNMF'

'9p' versus 'RPPA_CHIERARCHICAL'

P value = 3.98e-05 (Fisher's exact test), Q value = 0.0054

Table S165.  Gene #17: '9p' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
9P MUTATED 66 41 80
9P WILD-TYPE 95 69 46

Figure S165.  Get High-res Image Gene #17: '9p' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9p' versus 'MRNASEQ_CNMF'

P value = 1.43e-14 (Fisher's exact test), Q value = 5.3e-12

Table S166.  Gene #17: '9p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
9P MUTATED 156 38 231
9P WILD-TYPE 117 148 311

Figure S166.  Get High-res Image Gene #17: '9p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.08e-16 (Fisher's exact test), Q value = 4.3e-14

Table S167.  Gene #17: '9p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
9P MUTATED 136 208 81
9P WILD-TYPE 97 231 248

Figure S167.  Get High-res Image Gene #17: '9p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p' versus 'MIRSEQ_CNMF'

P value = 1.8e-16 (Fisher's exact test), Q value = 7.3e-14

Table S168.  Gene #17: '9p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
9P MUTATED 170 70 172
9P WILD-TYPE 228 217 120

Figure S168.  Get High-res Image Gene #17: '9p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.09e-16 (Fisher's exact test), Q value = 2.8e-13

Table S169.  Gene #17: '9p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
9P MUTATED 156 131 125
9P WILD-TYPE 96 168 301

Figure S169.  Get High-res Image Gene #17: '9p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.69e-13 (Fisher's exact test), Q value = 9.3e-11

Table S170.  Gene #17: '9p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
9P MUTATED 103 52 119
9P WILD-TYPE 147 167 79

Figure S170.  Get High-res Image Gene #17: '9p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.18e-08 (Fisher's exact test), Q value = 2.7e-06

Table S171.  Gene #17: '9p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
9P MUTATED 82 43 149
9P WILD-TYPE 63 134 196

Figure S171.  Get High-res Image Gene #17: '9p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q' versus 'MRNA_CNMF'

P value = 0.000147 (Chi-square test), Q value = 0.018

Table S172.  Gene #18: '9q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
9Q MUTATED 8 8 48 57 34 31 9 9
9Q WILD-TYPE 13 28 71 39 75 41 11 31

Figure S172.  Get High-res Image Gene #18: '9q' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q' versus 'MRNA_CHIERARCHICAL'

P value = 2.31e-06 (Fisher's exact test), Q value = 0.00041

Table S173.  Gene #18: '9q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
9Q MUTATED 27 66 111
9Q WILD-TYPE 95 59 155

Figure S173.  Get High-res Image Gene #18: '9q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9q' versus 'CN_CNMF'

P value = 1.52e-28 (Chi-square test), Q value = 7e-26

Table S174.  Gene #18: '9q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
9Q MUTATED 56 128 46 134 17
9Q WILD-TYPE 315 130 51 102 28

Figure S174.  Get High-res Image Gene #18: '9q' versus Molecular Subtype #3: 'CN_CNMF'

'9q' versus 'METHLYATION_CNMF'

P value = 1.18e-14 (Chi-square test), Q value = 4.4e-12

Table S175.  Gene #18: '9q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
9Q MUTATED 70 34 43 70 8 26
9Q WILD-TYPE 46 121 65 69 47 86

Figure S175.  Get High-res Image Gene #18: '9q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q' versus 'RPPA_CNMF'

P value = 3.14e-05 (Fisher's exact test), Q value = 0.0044

Table S176.  Gene #18: '9q' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
9Q MUTATED 80 43 35
9Q WILD-TYPE 67 90 82

Figure S176.  Get High-res Image Gene #18: '9q' versus Molecular Subtype #5: 'RPPA_CNMF'

'9q' versus 'RPPA_CHIERARCHICAL'

P value = 6.5e-06 (Fisher's exact test), Q value = 0.0011

Table S177.  Gene #18: '9q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
9Q MUTATED 55 31 72
9Q WILD-TYPE 106 79 54

Figure S177.  Get High-res Image Gene #18: '9q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9q' versus 'MRNASEQ_CNMF'

P value = 2.83e-16 (Fisher's exact test), Q value = 1.1e-13

Table S178.  Gene #18: '9q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
9Q MUTATED 146 29 204
9Q WILD-TYPE 127 157 338

Figure S178.  Get High-res Image Gene #18: '9q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.16e-15 (Fisher's exact test), Q value = 4.5e-13

Table S179.  Gene #18: '9q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
9Q MUTATED 123 187 69
9Q WILD-TYPE 110 252 260

Figure S179.  Get High-res Image Gene #18: '9q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q' versus 'MIRSEQ_CNMF'

P value = 6.8e-15 (Fisher's exact test), Q value = 2.6e-12

Table S180.  Gene #18: '9q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
9Q MUTATED 146 62 157
9Q WILD-TYPE 252 225 135

Figure S180.  Get High-res Image Gene #18: '9q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.03e-15 (Fisher's exact test), Q value = 7.7e-13

Table S181.  Gene #18: '9q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
9Q MUTATED 142 117 106
9Q WILD-TYPE 110 182 320

Figure S181.  Get High-res Image Gene #18: '9q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.9e-11 (Fisher's exact test), Q value = 8.6e-09

Table S182.  Gene #18: '9q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
9Q MUTATED 87 49 109
9Q WILD-TYPE 163 170 89

Figure S182.  Get High-res Image Gene #18: '9q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.94e-09 (Fisher's exact test), Q value = 2.3e-06

Table S183.  Gene #18: '9q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
9Q MUTATED 77 37 131
9Q WILD-TYPE 68 140 214

Figure S183.  Get High-res Image Gene #18: '9q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p' versus 'MRNA_CNMF'

P value = 3.79e-09 (Chi-square test), Q value = 9.5e-07

Table S184.  Gene #19: '10p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
10P MUTATED 6 9 42 56 24 41 9 6
10P WILD-TYPE 15 27 77 40 85 31 11 34

Figure S184.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #1: 'MRNA_CNMF'

'10p' versus 'MRNA_CHIERARCHICAL'

P value = 1.61e-07 (Fisher's exact test), Q value = 3.4e-05

Table S185.  Gene #19: '10p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
10P MUTATED 28 71 94
10P WILD-TYPE 94 54 172

Figure S185.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10p' versus 'CN_CNMF'

P value = 1.29e-33 (Chi-square test), Q value = 6e-31

Table S186.  Gene #19: '10p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
10P MUTATED 52 100 38 151 18
10P WILD-TYPE 319 158 59 85 27

Figure S186.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #3: 'CN_CNMF'

'10p' versus 'METHLYATION_CNMF'

P value = 1.91e-20 (Chi-square test), Q value = 8.4e-18

Table S187.  Gene #19: '10p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
10P MUTATED 83 28 39 55 11 25
10P WILD-TYPE 33 127 69 84 44 87

Figure S187.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p' versus 'RPPA_CNMF'

P value = 1.86e-05 (Fisher's exact test), Q value = 0.0028

Table S188.  Gene #19: '10p' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
10P MUTATED 79 41 34
10P WILD-TYPE 68 92 83

Figure S188.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #5: 'RPPA_CNMF'

'10p' versus 'RPPA_CHIERARCHICAL'

P value = 0.000132 (Fisher's exact test), Q value = 0.016

Table S189.  Gene #19: '10p' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
10P MUTATED 53 33 68
10P WILD-TYPE 108 77 58

Figure S189.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10p' versus 'MRNASEQ_CNMF'

P value = 3.16e-21 (Fisher's exact test), Q value = 1.4e-18

Table S190.  Gene #19: '10p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
10P MUTATED 156 28 173
10P WILD-TYPE 117 158 369

Figure S190.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.25e-18 (Fisher's exact test), Q value = 5.4e-16

Table S191.  Gene #19: '10p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
10P MUTATED 134 156 67
10P WILD-TYPE 99 283 262

Figure S191.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p' versus 'MIRSEQ_CNMF'

P value = 7.4e-15 (Fisher's exact test), Q value = 2.8e-12

Table S192.  Gene #19: '10p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
10P MUTATED 126 65 157
10P WILD-TYPE 272 222 135

Figure S192.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.83e-21 (Fisher's exact test), Q value = 3e-18

Table S193.  Gene #19: '10p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
10P MUTATED 149 104 95
10P WILD-TYPE 103 195 331

Figure S193.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.82e-12 (Fisher's exact test), Q value = 5.9e-10

Table S194.  Gene #19: '10p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
10P MUTATED 76 46 108
10P WILD-TYPE 174 173 90

Figure S194.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.94e-11 (Fisher's exact test), Q value = 2.5e-08

Table S195.  Gene #19: '10p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
10P MUTATED 84 41 105
10P WILD-TYPE 61 136 240

Figure S195.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q' versus 'MRNA_CNMF'

P value = 1.12e-05 (Chi-square test), Q value = 0.0017

Table S196.  Gene #20: '10q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
10Q MUTATED 8 8 41 49 23 32 8 5
10Q WILD-TYPE 13 28 78 47 86 40 12 35

Figure S196.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #1: 'MRNA_CNMF'

'10q' versus 'MRNA_CHIERARCHICAL'

P value = 7.46e-06 (Fisher's exact test), Q value = 0.0012

Table S197.  Gene #20: '10q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
10Q MUTATED 24 61 89
10Q WILD-TYPE 98 64 177

Figure S197.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10q' versus 'CN_CNMF'

P value = 2.16e-25 (Chi-square test), Q value = 9.7e-23

Table S198.  Gene #20: '10q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
10Q MUTATED 47 97 37 127 19
10Q WILD-TYPE 324 161 60 109 26

Figure S198.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #3: 'CN_CNMF'

'10q' versus 'METHLYATION_CNMF'

P value = 6.12e-16 (Chi-square test), Q value = 2.4e-13

Table S199.  Gene #20: '10q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
10Q MUTATED 68 24 41 57 10 19
10Q WILD-TYPE 48 131 67 82 45 93

Figure S199.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q' versus 'RPPA_CNMF'

P value = 4.89e-06 (Fisher's exact test), Q value = 0.00084

Table S200.  Gene #20: '10q' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
10Q MUTATED 76 36 31
10Q WILD-TYPE 71 97 86

Figure S200.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #5: 'RPPA_CNMF'

'10q' versus 'RPPA_CHIERARCHICAL'

P value = 0.000228 (Fisher's exact test), Q value = 0.025

Table S201.  Gene #20: '10q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
10Q MUTATED 52 28 63
10Q WILD-TYPE 109 82 63

Figure S201.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10q' versus 'MRNASEQ_CNMF'

P value = 1.65e-14 (Fisher's exact test), Q value = 6.1e-12

Table S202.  Gene #20: '10q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
10Q MUTATED 129 24 172
10Q WILD-TYPE 144 162 370

Figure S202.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.97e-14 (Fisher's exact test), Q value = 2.5e-11

Table S203.  Gene #20: '10q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
10Q MUTATED 110 157 58
10Q WILD-TYPE 123 282 271

Figure S203.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q' versus 'MIRSEQ_CNMF'

P value = 8.09e-10 (Fisher's exact test), Q value = 2.1e-07

Table S204.  Gene #20: '10q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
10Q MUTATED 118 63 136
10Q WILD-TYPE 280 224 156

Figure S204.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.92e-13 (Fisher's exact test), Q value = 2.3e-10

Table S205.  Gene #20: '10q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
10Q MUTATED 127 95 95
10Q WILD-TYPE 125 204 331

Figure S205.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.42e-09 (Fisher's exact test), Q value = 3.7e-07

Table S206.  Gene #20: '10q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
10Q MUTATED 74 45 98
10Q WILD-TYPE 176 174 100

Figure S206.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.57e-06 (Fisher's exact test), Q value = 0.0012

Table S207.  Gene #20: '10q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
10Q MUTATED 71 43 103
10Q WILD-TYPE 74 134 242

Figure S207.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p' versus 'CN_CNMF'

P value = 9.86e-36 (Chi-square test), Q value = 4.7e-33

Table S208.  Gene #21: '11p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
11P MUTATED 50 145 42 136 15
11P WILD-TYPE 321 113 55 100 30

Figure S208.  Get High-res Image Gene #21: '11p' versus Molecular Subtype #3: 'CN_CNMF'

'11p' versus 'METHLYATION_CNMF'

P value = 4.78e-13 (Chi-square test), Q value = 1.6e-10

Table S209.  Gene #21: '11p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
11P MUTATED 65 35 45 75 12 24
11P WILD-TYPE 51 120 63 64 43 88

Figure S209.  Get High-res Image Gene #21: '11p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p' versus 'MRNASEQ_CNMF'

P value = 1.51e-11 (Fisher's exact test), Q value = 4.6e-09

Table S210.  Gene #21: '11p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
11P MUTATED 140 36 212
11P WILD-TYPE 133 150 330

Figure S210.  Get High-res Image Gene #21: '11p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.42e-12 (Fisher's exact test), Q value = 2.6e-09

Table S211.  Gene #21: '11p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
11P MUTATED 117 193 78
11P WILD-TYPE 116 246 251

Figure S211.  Get High-res Image Gene #21: '11p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p' versus 'MIRSEQ_CNMF'

P value = 8.21e-11 (Fisher's exact test), Q value = 2.3e-08

Table S212.  Gene #21: '11p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
11P MUTATED 151 70 151
11P WILD-TYPE 247 217 141

Figure S212.  Get High-res Image Gene #21: '11p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.54e-12 (Fisher's exact test), Q value = 5e-10

Table S213.  Gene #21: '11p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
11P MUTATED 131 132 109
11P WILD-TYPE 121 167 317

Figure S213.  Get High-res Image Gene #21: '11p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.19e-11 (Fisher's exact test), Q value = 1.8e-08

Table S214.  Gene #21: '11p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
11P MUTATED 100 45 103
11P WILD-TYPE 150 174 95

Figure S214.  Get High-res Image Gene #21: '11p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.72e-09 (Fisher's exact test), Q value = 1.4e-06

Table S215.  Gene #21: '11p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
11P MUTATED 76 36 136
11P WILD-TYPE 69 141 209

Figure S215.  Get High-res Image Gene #21: '11p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q' versus 'MRNA_CNMF'

P value = 0.000379 (Chi-square test), Q value = 0.039

Table S216.  Gene #22: '11q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
11Q MUTATED 8 21 73 36 36 38 9 15
11Q WILD-TYPE 13 15 46 60 73 34 11 25

Figure S216.  Get High-res Image Gene #22: '11q' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q' versus 'CN_CNMF'

P value = 5.97e-36 (Chi-square test), Q value = 2.8e-33

Table S217.  Gene #22: '11q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
11Q MUTATED 71 179 46 127 17
11Q WILD-TYPE 300 79 51 109 28

Figure S217.  Get High-res Image Gene #22: '11q' versus Molecular Subtype #3: 'CN_CNMF'

'11q' versus 'METHLYATION_CNMF'

P value = 2.16e-10 (Chi-square test), Q value = 6e-08

Table S218.  Gene #22: '11q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
11Q MUTATED 60 49 55 86 16 28
11Q WILD-TYPE 56 106 53 53 39 84

Figure S218.  Get High-res Image Gene #22: '11q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q' versus 'MRNASEQ_CNMF'

P value = 0.000257 (Fisher's exact test), Q value = 0.028

Table S219.  Gene #22: '11q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
11Q MUTATED 128 57 254
11Q WILD-TYPE 145 129 288

Figure S219.  Get High-res Image Gene #22: '11q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000429 (Fisher's exact test), Q value = 0.043

Table S220.  Gene #22: '11q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
11Q MUTATED 107 216 116
11Q WILD-TYPE 126 223 213

Figure S220.  Get High-res Image Gene #22: '11q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q' versus 'MIRSEQ_CNMF'

P value = 0.00158 (Fisher's exact test), Q value = 0.12

Table S221.  Gene #22: '11q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
11Q MUTATED 172 103 148
11Q WILD-TYPE 226 184 144

Figure S221.  Get High-res Image Gene #22: '11q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.2e-07 (Fisher's exact test), Q value = 0.00012

Table S222.  Gene #22: '11q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
11Q MUTATED 123 156 144
11Q WILD-TYPE 129 143 282

Figure S222.  Get High-res Image Gene #22: '11q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000768 (Fisher's exact test), Q value = 0.068

Table S223.  Gene #22: '11q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
11Q MUTATED 114 69 95
11Q WILD-TYPE 136 150 103

Figure S223.  Get High-res Image Gene #22: '11q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00064 (Fisher's exact test), Q value = 0.058

Table S224.  Gene #22: '11q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
11Q MUTATED 71 53 154
11Q WILD-TYPE 74 124 191

Figure S224.  Get High-res Image Gene #22: '11q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p' versus 'MRNA_CNMF'

P value = 1.36e-07 (Chi-square test), Q value = 2.9e-05

Table S225.  Gene #23: '12p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
12P MUTATED 5 12 45 58 24 32 7 6
12P WILD-TYPE 16 24 74 38 85 40 13 34

Figure S225.  Get High-res Image Gene #23: '12p' versus Molecular Subtype #1: 'MRNA_CNMF'

'12p' versus 'MRNA_CHIERARCHICAL'

P value = 3.82e-08 (Fisher's exact test), Q value = 8.7e-06

Table S226.  Gene #23: '12p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
12P MUTATED 24 69 96
12P WILD-TYPE 98 56 170

Figure S226.  Get High-res Image Gene #23: '12p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12p' versus 'CN_CNMF'

P value = 3.2e-31 (Chi-square test), Q value = 1.5e-28

Table S227.  Gene #23: '12p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
12P MUTATED 50 120 40 138 12
12P WILD-TYPE 321 138 57 98 33

Figure S227.  Get High-res Image Gene #23: '12p' versus Molecular Subtype #3: 'CN_CNMF'

'12p' versus 'METHLYATION_CNMF'

P value = 4.65e-18 (Chi-square test), Q value = 2e-15

Table S228.  Gene #23: '12p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
12P MUTATED 75 27 35 66 13 22
12P WILD-TYPE 41 128 73 73 42 90

Figure S228.  Get High-res Image Gene #23: '12p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p' versus 'RPPA_CNMF'

P value = 0.000954 (Fisher's exact test), Q value = 0.079

Table S229.  Gene #23: '12p' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
12P MUTATED 75 46 35
12P WILD-TYPE 72 87 82

Figure S229.  Get High-res Image Gene #23: '12p' versus Molecular Subtype #5: 'RPPA_CNMF'

'12p' versus 'RPPA_CHIERARCHICAL'

P value = 2.72e-05 (Fisher's exact test), Q value = 0.0039

Table S230.  Gene #23: '12p' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
12P MUTATED 58 29 69
12P WILD-TYPE 103 81 57

Figure S230.  Get High-res Image Gene #23: '12p' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'12p' versus 'MRNASEQ_CNMF'

P value = 2.31e-17 (Fisher's exact test), Q value = 9.6e-15

Table S231.  Gene #23: '12p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
12P MUTATED 150 31 178
12P WILD-TYPE 123 155 364

Figure S231.  Get High-res Image Gene #23: '12p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.27e-17 (Fisher's exact test), Q value = 3e-14

Table S232.  Gene #23: '12p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
12P MUTATED 129 163 67
12P WILD-TYPE 104 276 262

Figure S232.  Get High-res Image Gene #23: '12p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p' versus 'MIRSEQ_CNMF'

P value = 1.56e-15 (Fisher's exact test), Q value = 6e-13

Table S233.  Gene #23: '12p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
12P MUTATED 122 65 158
12P WILD-TYPE 276 222 134

Figure S233.  Get High-res Image Gene #23: '12p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.13e-17 (Fisher's exact test), Q value = 2.5e-14

Table S234.  Gene #23: '12p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
12P MUTATED 141 106 98
12P WILD-TYPE 111 193 328

Figure S234.  Get High-res Image Gene #23: '12p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.19e-11 (Fisher's exact test), Q value = 6.6e-09

Table S235.  Gene #23: '12p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
12P MUTATED 78 48 107
12P WILD-TYPE 172 171 91

Figure S235.  Get High-res Image Gene #23: '12p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.24e-07 (Fisher's exact test), Q value = 6.6e-05

Table S236.  Gene #23: '12p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
12P MUTATED 77 43 113
12P WILD-TYPE 68 134 232

Figure S236.  Get High-res Image Gene #23: '12p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q' versus 'MRNA_CNMF'

P value = 0.000294 (Chi-square test), Q value = 0.031

Table S237.  Gene #24: '12q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
12Q MUTATED 3 10 40 44 22 28 4 6
12Q WILD-TYPE 18 26 79 52 87 44 16 34

Figure S237.  Get High-res Image Gene #24: '12q' versus Molecular Subtype #1: 'MRNA_CNMF'

'12q' versus 'MRNA_CHIERARCHICAL'

P value = 3.31e-05 (Fisher's exact test), Q value = 0.0046

Table S238.  Gene #24: '12q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
12Q MUTATED 20 53 84
12Q WILD-TYPE 102 72 182

Figure S238.  Get High-res Image Gene #24: '12q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12q' versus 'CN_CNMF'

P value = 9.48e-23 (Chi-square test), Q value = 4.2e-20

Table S239.  Gene #24: '12q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
12Q MUTATED 40 109 39 103 12
12Q WILD-TYPE 331 149 58 133 33

Figure S239.  Get High-res Image Gene #24: '12q' versus Molecular Subtype #3: 'CN_CNMF'

'12q' versus 'METHLYATION_CNMF'

P value = 8.06e-16 (Chi-square test), Q value = 3.1e-13

Table S240.  Gene #24: '12q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
12Q MUTATED 62 24 34 61 8 15
12Q WILD-TYPE 54 131 74 78 47 97

Figure S240.  Get High-res Image Gene #24: '12q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q' versus 'RPPA_CHIERARCHICAL'

P value = 0.00239 (Fisher's exact test), Q value = 0.17

Table S241.  Gene #24: '12q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
12Q MUTATED 50 24 54
12Q WILD-TYPE 111 86 72

Figure S241.  Get High-res Image Gene #24: '12q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'12q' versus 'MRNASEQ_CNMF'

P value = 6.45e-11 (Fisher's exact test), Q value = 1.9e-08

Table S242.  Gene #24: '12q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
12Q MUTATED 116 25 160
12Q WILD-TYPE 157 161 382

Figure S242.  Get High-res Image Gene #24: '12q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.44e-11 (Fisher's exact test), Q value = 1.3e-08

Table S243.  Gene #24: '12q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
12Q MUTATED 99 146 56
12Q WILD-TYPE 134 293 273

Figure S243.  Get High-res Image Gene #24: '12q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q' versus 'MIRSEQ_CNMF'

P value = 2.37e-09 (Fisher's exact test), Q value = 6e-07

Table S244.  Gene #24: '12q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
12Q MUTATED 106 57 126
12Q WILD-TYPE 292 230 166

Figure S244.  Get High-res Image Gene #24: '12q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.11e-08 (Fisher's exact test), Q value = 2.6e-06

Table S245.  Gene #24: '12q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
12Q MUTATED 108 92 89
12Q WILD-TYPE 144 207 337

Figure S245.  Get High-res Image Gene #24: '12q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.69e-08 (Fisher's exact test), Q value = 1.5e-05

Table S246.  Gene #24: '12q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
12Q MUTATED 71 42 89
12Q WILD-TYPE 179 177 109

Figure S246.  Get High-res Image Gene #24: '12q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000426 (Fisher's exact test), Q value = 0.043

Table S247.  Gene #24: '12q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
12Q MUTATED 62 40 100
12Q WILD-TYPE 83 137 245

Figure S247.  Get High-res Image Gene #24: '12q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q' versus 'MRNA_CNMF'

P value = 8.48e-07 (Chi-square test), Q value = 0.00016

Table S248.  Gene #25: '13q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
13Q MUTATED 10 17 73 65 42 44 10 8
13Q WILD-TYPE 11 19 46 31 67 28 10 32

Figure S248.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q' versus 'MRNA_CHIERARCHICAL'

P value = 5.2e-08 (Fisher's exact test), Q value = 1.2e-05

Table S249.  Gene #25: '13q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
13Q MUTATED 39 85 145
13Q WILD-TYPE 83 40 121

Figure S249.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q' versus 'CN_CNMF'

P value = 2.48e-35 (Chi-square test), Q value = 1.2e-32

Table S250.  Gene #25: '13q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
13Q MUTATED 84 167 60 156 30
13Q WILD-TYPE 287 91 37 80 15

Figure S250.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #3: 'CN_CNMF'

'13q' versus 'METHLYATION_CNMF'

P value = 2.67e-14 (Chi-square test), Q value = 9.8e-12

Table S251.  Gene #25: '13q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
13Q MUTATED 83 50 64 77 11 41
13Q WILD-TYPE 33 105 44 62 44 71

Figure S251.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q' versus 'MRNASEQ_CNMF'

P value = 3.23e-15 (Fisher's exact test), Q value = 1.2e-12

Table S252.  Gene #25: '13q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
13Q MUTATED 178 50 266
13Q WILD-TYPE 95 136 276

Figure S252.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.67e-16 (Fisher's exact test), Q value = 6.7e-14

Table S253.  Gene #25: '13q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
13Q MUTATED 156 233 105
13Q WILD-TYPE 77 206 224

Figure S253.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q' versus 'MIRSEQ_CNMF'

P value = 1.68e-13 (Fisher's exact test), Q value = 5.9e-11

Table S254.  Gene #25: '13q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
13Q MUTATED 194 98 192
13Q WILD-TYPE 204 189 100

Figure S254.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.45e-14 (Fisher's exact test), Q value = 2.7e-11

Table S255.  Gene #25: '13q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
13Q MUTATED 170 156 158
13Q WILD-TYPE 82 143 268

Figure S255.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-10 (Fisher's exact test), Q value = 5.6e-08

Table S256.  Gene #25: '13q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
13Q MUTATED 107 76 131
13Q WILD-TYPE 143 143 67

Figure S256.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'13q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.14e-06 (Fisher's exact test), Q value = 0.00039

Table S257.  Gene #25: '13q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
13Q MUTATED 94 66 154
13Q WILD-TYPE 51 111 191

Figure S257.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q' versus 'MRNA_CNMF'

P value = 6.95e-08 (Chi-square test), Q value = 1.5e-05

Table S258.  Gene #26: '14q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
14Q MUTATED 6 9 46 56 25 34 12 6
14Q WILD-TYPE 15 27 73 40 84 38 8 34

Figure S258.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q' versus 'MRNA_CHIERARCHICAL'

P value = 9.07e-07 (Fisher's exact test), Q value = 0.00017

Table S259.  Gene #26: '14q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
14Q MUTATED 28 69 97
14Q WILD-TYPE 94 56 169

Figure S259.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q' versus 'CN_CNMF'

P value = 9.33e-32 (Chi-square test), Q value = 4.3e-29

Table S260.  Gene #26: '14q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
14Q MUTATED 57 114 41 150 17
14Q WILD-TYPE 314 144 56 86 28

Figure S260.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #3: 'CN_CNMF'

'14q' versus 'METHLYATION_CNMF'

P value = 3.24e-17 (Chi-square test), Q value = 1.3e-14

Table S261.  Gene #26: '14q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
14Q MUTATED 79 30 46 58 11 27
14Q WILD-TYPE 37 125 62 81 44 85

Figure S261.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q' versus 'RPPA_CNMF'

P value = 2.84e-06 (Fisher's exact test), Q value = 5e-04

Table S262.  Gene #26: '14q' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
14Q MUTATED 79 34 38
14Q WILD-TYPE 68 99 79

Figure S262.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #5: 'RPPA_CNMF'

'14q' versus 'RPPA_CHIERARCHICAL'

P value = 0.000749 (Fisher's exact test), Q value = 0.067

Table S263.  Gene #26: '14q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
14Q MUTATED 53 33 65
14Q WILD-TYPE 108 77 61

Figure S263.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'14q' versus 'MRNASEQ_CNMF'

P value = 8.2e-19 (Fisher's exact test), Q value = 3.5e-16

Table S264.  Gene #26: '14q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
14Q MUTATED 155 30 192
14Q WILD-TYPE 118 156 350

Figure S264.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.47e-20 (Fisher's exact test), Q value = 1.1e-17

Table S265.  Gene #26: '14q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
14Q MUTATED 140 168 69
14Q WILD-TYPE 93 271 260

Figure S265.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q' versus 'MIRSEQ_CNMF'

P value = 2.75e-16 (Fisher's exact test), Q value = 1.1e-13

Table S266.  Gene #26: '14q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
14Q MUTATED 139 64 163
14Q WILD-TYPE 259 223 129

Figure S266.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.55e-17 (Fisher's exact test), Q value = 1.1e-14

Table S267.  Gene #26: '14q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
14Q MUTATED 152 98 116
14Q WILD-TYPE 100 201 310

Figure S267.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.42e-12 (Fisher's exact test), Q value = 4.6e-10

Table S268.  Gene #26: '14q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
14Q MUTATED 91 53 117
14Q WILD-TYPE 159 166 81

Figure S268.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.69e-13 (Fisher's exact test), Q value = 1.3e-10

Table S269.  Gene #26: '14q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
14Q MUTATED 95 46 120
14Q WILD-TYPE 50 131 225

Figure S269.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q' versus 'MRNA_CNMF'

P value = 8.63e-09 (Chi-square test), Q value = 2.1e-06

Table S270.  Gene #27: '15q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
15Q MUTATED 6 13 42 56 25 42 12 7
15Q WILD-TYPE 15 23 77 40 84 30 8 33

Figure S270.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q' versus 'MRNA_CHIERARCHICAL'

P value = 5.92e-07 (Fisher's exact test), Q value = 0.00012

Table S271.  Gene #27: '15q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
15Q MUTATED 28 70 105
15Q WILD-TYPE 94 55 161

Figure S271.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'15q' versus 'CN_CNMF'

P value = 8.57e-37 (Chi-square test), Q value = 4.1e-34

Table S272.  Gene #27: '15q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
15Q MUTATED 56 107 52 157 15
15Q WILD-TYPE 315 151 45 79 30

Figure S272.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #3: 'CN_CNMF'

'15q' versus 'METHLYATION_CNMF'

P value = 2.24e-17 (Chi-square test), Q value = 9.3e-15

Table S273.  Gene #27: '15q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
15Q MUTATED 82 29 45 58 16 29
15Q WILD-TYPE 34 126 63 81 39 83

Figure S273.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q' versus 'RPPA_CNMF'

P value = 0.000514 (Fisher's exact test), Q value = 0.05

Table S274.  Gene #27: '15q' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
15Q MUTATED 80 46 40
15Q WILD-TYPE 67 87 77

Figure S274.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #5: 'RPPA_CNMF'

'15q' versus 'RPPA_CHIERARCHICAL'

P value = 0.000127 (Fisher's exact test), Q value = 0.016

Table S275.  Gene #27: '15q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
15Q MUTATED 58 36 72
15Q WILD-TYPE 103 74 54

Figure S275.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'15q' versus 'MRNASEQ_CNMF'

P value = 5.19e-21 (Fisher's exact test), Q value = 2.3e-18

Table S276.  Gene #27: '15q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
15Q MUTATED 159 28 197
15Q WILD-TYPE 114 158 345

Figure S276.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.5e-19 (Fisher's exact test), Q value = 6.5e-17

Table S277.  Gene #27: '15q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
15Q MUTATED 136 180 68
15Q WILD-TYPE 97 259 261

Figure S277.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q' versus 'MIRSEQ_CNMF'

P value = 1.78e-15 (Fisher's exact test), Q value = 6.8e-13

Table S278.  Gene #27: '15q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
15Q MUTATED 143 66 163
15Q WILD-TYPE 255 221 129

Figure S278.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.79e-18 (Fisher's exact test), Q value = 2.4e-15

Table S279.  Gene #27: '15q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
15Q MUTATED 154 103 115
15Q WILD-TYPE 98 196 311

Figure S279.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.78e-11 (Fisher's exact test), Q value = 1.1e-08

Table S280.  Gene #27: '15q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
15Q MUTATED 94 48 108
15Q WILD-TYPE 156 171 90

Figure S280.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.07e-10 (Fisher's exact test), Q value = 1.9e-07

Table S281.  Gene #27: '15q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
15Q MUTATED 85 42 123
15Q WILD-TYPE 60 135 222

Figure S281.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p' versus 'MRNA_CHIERARCHICAL'

P value = 0.0031 (Fisher's exact test), Q value = 0.21

Table S282.  Gene #28: '16p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
16P MUTATED 68 68 185
16P WILD-TYPE 54 57 81

Figure S282.  Get High-res Image Gene #28: '16p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16p' versus 'CN_CNMF'

P value = 6.64e-08 (Chi-square test), Q value = 1.5e-05

Table S283.  Gene #28: '16p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
16P MUTATED 188 164 82 142 27
16P WILD-TYPE 183 94 15 94 18

Figure S283.  Get High-res Image Gene #28: '16p' versus Molecular Subtype #3: 'CN_CNMF'

'16p' versus 'METHLYATION_CNMF'

P value = 4.9e-05 (Chi-square test), Q value = 0.0064

Table S284.  Gene #28: '16p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
16P MUTATED 66 102 74 73 19 53
16P WILD-TYPE 50 53 34 66 36 59

Figure S284.  Get High-res Image Gene #28: '16p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p' versus 'MRNASEQ_CNMF'

P value = 0.000913 (Fisher's exact test), Q value = 0.078

Table S285.  Gene #28: '16p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
16P MUTATED 144 102 353
16P WILD-TYPE 129 84 189

Figure S285.  Get High-res Image Gene #28: '16p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000542 (Fisher's exact test), Q value = 0.052

Table S286.  Gene #28: '16p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
16P MUTATED 118 289 192
16P WILD-TYPE 115 150 137

Figure S286.  Get High-res Image Gene #28: '16p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q' versus 'MRNA_CNMF'

P value = 1.96e-07 (Chi-square test), Q value = 4.1e-05

Table S287.  Gene #29: '16q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
16Q MUTATED 14 25 80 44 94 48 16 33
16Q WILD-TYPE 7 11 39 52 15 24 4 7

Figure S287.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #1: 'MRNA_CNMF'

'16q' versus 'MRNA_CHIERARCHICAL'

P value = 8.93e-08 (Fisher's exact test), Q value = 2e-05

Table S288.  Gene #29: '16q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
16Q MUTATED 91 60 203
16Q WILD-TYPE 31 65 63

Figure S288.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16q' versus 'CN_CNMF'

P value = 3.33e-07 (Chi-square test), Q value = 6.8e-05

Table S289.  Gene #29: '16q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
16Q MUTATED 253 180 87 134 33
16Q WILD-TYPE 118 78 10 102 12

Figure S289.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #3: 'CN_CNMF'

'16q' versus 'METHLYATION_CNMF'

P value = 5.06e-11 (Chi-square test), Q value = 1.5e-08

Table S290.  Gene #29: '16q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
16Q MUTATED 63 132 88 87 27 63
16Q WILD-TYPE 53 23 20 52 28 49

Figure S290.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q' versus 'RPPA_CNMF'

P value = 0.000897 (Fisher's exact test), Q value = 0.078

Table S291.  Gene #29: '16q' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
16Q MUTATED 83 103 80
16Q WILD-TYPE 64 30 37

Figure S291.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #5: 'RPPA_CNMF'

'16q' versus 'RPPA_CHIERARCHICAL'

P value = 6.47e-06 (Fisher's exact test), Q value = 0.0011

Table S292.  Gene #29: '16q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
16Q MUTATED 123 80 63
16Q WILD-TYPE 38 30 63

Figure S292.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16q' versus 'MRNASEQ_CNMF'

P value = 7.27e-12 (Fisher's exact test), Q value = 2.2e-09

Table S293.  Gene #29: '16q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
16Q MUTATED 139 145 399
16Q WILD-TYPE 134 41 143

Figure S293.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.36e-12 (Fisher's exact test), Q value = 4.4e-10

Table S294.  Gene #29: '16q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
16Q MUTATED 113 316 254
16Q WILD-TYPE 120 123 75

Figure S294.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q' versus 'MIRSEQ_CNMF'

P value = 1.98e-07 (Fisher's exact test), Q value = 4.1e-05

Table S295.  Gene #29: '16q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
16Q MUTATED 290 215 162
16Q WILD-TYPE 108 72 130

Figure S295.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.18e-11 (Fisher's exact test), Q value = 1.2e-08

Table S296.  Gene #29: '16q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
16Q MUTATED 142 186 339
16Q WILD-TYPE 110 113 87

Figure S296.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000135 (Fisher's exact test), Q value = 0.016

Table S297.  Gene #29: '16q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
16Q MUTATED 174 167 113
16Q WILD-TYPE 76 52 85

Figure S297.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.32e-05 (Fisher's exact test), Q value = 0.0069

Table S298.  Gene #29: '16q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
16Q MUTATED 78 136 240
16Q WILD-TYPE 67 41 105

Figure S298.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p' versus 'MRNA_CNMF'

P value = 4.91e-13 (Chi-square test), Q value = 1.7e-10

Table S299.  Gene #30: '17p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
17P MUTATED 14 28 89 69 37 62 15 23
17P WILD-TYPE 7 8 30 27 72 10 5 17

Figure S299.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p' versus 'CN_CNMF'

P value = 4.02e-34 (Chi-square test), Q value = 1.9e-31

Table S300.  Gene #30: '17p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
17P MUTATED 150 212 58 195 29
17P WILD-TYPE 221 46 39 41 16

Figure S300.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #3: 'CN_CNMF'

'17p' versus 'METHLYATION_CNMF'

P value = 2.51e-12 (Chi-square test), Q value = 8e-10

Table S301.  Gene #30: '17p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
17P MUTATED 88 71 75 113 27 55
17P WILD-TYPE 28 84 33 26 28 57

Figure S301.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p' versus 'RPPA_CNMF'

P value = 7.42e-07 (Fisher's exact test), Q value = 0.00014

Table S302.  Gene #30: '17p' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
17P MUTATED 121 73 70
17P WILD-TYPE 26 60 47

Figure S302.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #5: 'RPPA_CNMF'

'17p' versus 'RPPA_CHIERARCHICAL'

P value = 0.00231 (Fisher's exact test), Q value = 0.17

Table S303.  Gene #30: '17p' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
17P MUTATED 103 63 98
17P WILD-TYPE 58 47 28

Figure S303.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17p' versus 'MRNASEQ_CNMF'

P value = 1.07e-07 (Fisher's exact test), Q value = 2.3e-05

Table S304.  Gene #30: '17p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
17P MUTATED 207 94 339
17P WILD-TYPE 66 92 203

Figure S304.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.59e-05 (Fisher's exact test), Q value = 0.0037

Table S305.  Gene #30: '17p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
17P MUTATED 170 290 180
17P WILD-TYPE 63 149 149

Figure S305.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p' versus 'MIRSEQ_CNMF'

P value = 6e-09 (Fisher's exact test), Q value = 1.5e-06

Table S306.  Gene #30: '17p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
17P MUTATED 248 151 224
17P WILD-TYPE 150 136 68

Figure S306.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.61e-08 (Fisher's exact test), Q value = 1.3e-05

Table S307.  Gene #30: '17p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
17P MUTATED 191 200 232
17P WILD-TYPE 61 99 194

Figure S307.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.77e-07 (Fisher's exact test), Q value = 3.7e-05

Table S308.  Gene #30: '17p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
17P MUTATED 153 114 154
17P WILD-TYPE 97 105 44

Figure S308.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00327 (Fisher's exact test), Q value = 0.22

Table S309.  Gene #30: '17p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
17P MUTATED 105 96 220
17P WILD-TYPE 40 81 125

Figure S309.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q' versus 'MRNA_CNMF'

P value = 6.31e-10 (Chi-square test), Q value = 1.7e-07

Table S310.  Gene #31: '17q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
17Q MUTATED 7 12 69 59 22 45 9 17
17Q WILD-TYPE 14 24 50 37 87 27 11 23

Figure S310.  Get High-res Image Gene #31: '17q' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q' versus 'MRNA_CHIERARCHICAL'

P value = 1.68e-05 (Fisher's exact test), Q value = 0.0025

Table S311.  Gene #31: '17q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
17Q MUTATED 39 77 124
17Q WILD-TYPE 83 48 142

Figure S311.  Get High-res Image Gene #31: '17q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q' versus 'CN_CNMF'

P value = 3.62e-29 (Chi-square test), Q value = 1.7e-26

Table S312.  Gene #31: '17q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
17Q MUTATED 86 164 42 150 20
17Q WILD-TYPE 285 94 55 86 25

Figure S312.  Get High-res Image Gene #31: '17q' versus Molecular Subtype #3: 'CN_CNMF'

'17q' versus 'METHLYATION_CNMF'

P value = 2.99e-12 (Chi-square test), Q value = 9.5e-10

Table S313.  Gene #31: '17q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
17Q MUTATED 71 39 46 85 13 45
17Q WILD-TYPE 45 116 62 54 42 67

Figure S313.  Get High-res Image Gene #31: '17q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q' versus 'RPPA_CNMF'

P value = 7.27e-07 (Fisher's exact test), Q value = 0.00014

Table S314.  Gene #31: '17q' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
17Q MUTATED 96 46 51
17Q WILD-TYPE 51 87 66

Figure S314.  Get High-res Image Gene #31: '17q' versus Molecular Subtype #5: 'RPPA_CNMF'

'17q' versus 'RPPA_CHIERARCHICAL'

P value = 0.000237 (Fisher's exact test), Q value = 0.026

Table S315.  Gene #31: '17q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
17Q MUTATED 65 48 80
17Q WILD-TYPE 96 62 46

Figure S315.  Get High-res Image Gene #31: '17q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17q' versus 'MRNASEQ_CNMF'

P value = 1.34e-09 (Fisher's exact test), Q value = 3.5e-07

Table S316.  Gene #31: '17q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
17Q MUTATED 162 55 241
17Q WILD-TYPE 111 131 301

Figure S316.  Get High-res Image Gene #31: '17q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.91e-09 (Fisher's exact test), Q value = 1.2e-06

Table S317.  Gene #31: '17q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
17Q MUTATED 138 210 110
17Q WILD-TYPE 95 229 219

Figure S317.  Get High-res Image Gene #31: '17q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q' versus 'MIRSEQ_CNMF'

P value = 1.15e-08 (Fisher's exact test), Q value = 2.7e-06

Table S318.  Gene #31: '17q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
17Q MUTATED 172 101 174
17Q WILD-TYPE 226 186 118

Figure S318.  Get High-res Image Gene #31: '17q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.52e-13 (Fisher's exact test), Q value = 5.3e-11

Table S319.  Gene #31: '17q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
17Q MUTATED 153 156 138
17Q WILD-TYPE 99 143 288

Figure S319.  Get High-res Image Gene #31: '17q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.38e-08 (Fisher's exact test), Q value = 2e-05

Table S320.  Gene #31: '17q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
17Q MUTATED 108 78 124
17Q WILD-TYPE 142 141 74

Figure S320.  Get High-res Image Gene #31: '17q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000219 (Fisher's exact test), Q value = 0.025

Table S321.  Gene #31: '17q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
17Q MUTATED 82 61 167
17Q WILD-TYPE 63 116 178

Figure S321.  Get High-res Image Gene #31: '17q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p' versus 'MRNA_CNMF'

P value = 5.82e-07 (Chi-square test), Q value = 0.00011

Table S322.  Gene #32: '18p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
18P MUTATED 7 12 55 62 35 48 13 14
18P WILD-TYPE 14 24 64 34 74 24 7 26

Figure S322.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p' versus 'MRNA_CHIERARCHICAL'

P value = 2.67e-06 (Fisher's exact test), Q value = 0.00047

Table S323.  Gene #32: '18p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
18P MUTATED 39 80 127
18P WILD-TYPE 83 45 139

Figure S323.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p' versus 'CN_CNMF'

P value = 1.85e-33 (Chi-square test), Q value = 8.7e-31

Table S324.  Gene #32: '18p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
18P MUTATED 78 145 59 161 20
18P WILD-TYPE 293 113 38 75 25

Figure S324.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #3: 'CN_CNMF'

'18p' versus 'METHLYATION_CNMF'

P value = 1.99e-13 (Chi-square test), Q value = 6.9e-11

Table S325.  Gene #32: '18p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
18P MUTATED 76 38 59 74 13 39
18P WILD-TYPE 40 117 49 65 42 73

Figure S325.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p' versus 'RPPA_CNMF'

P value = 0.000148 (Fisher's exact test), Q value = 0.018

Table S326.  Gene #32: '18p' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
18P MUTATED 92 54 48
18P WILD-TYPE 55 79 69

Figure S326.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #5: 'RPPA_CNMF'

'18p' versus 'RPPA_CHIERARCHICAL'

P value = 0.000204 (Fisher's exact test), Q value = 0.023

Table S327.  Gene #32: '18p' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
18P MUTATED 72 42 80
18P WILD-TYPE 89 68 46

Figure S327.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18p' versus 'MRNASEQ_CNMF'

P value = 5.27e-17 (Fisher's exact test), Q value = 2.2e-14

Table S328.  Gene #32: '18p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
18P MUTATED 173 43 244
18P WILD-TYPE 100 143 298

Figure S328.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.93e-16 (Fisher's exact test), Q value = 7.7e-14

Table S329.  Gene #32: '18p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
18P MUTATED 149 216 95
18P WILD-TYPE 84 223 234

Figure S329.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p' versus 'MIRSEQ_CNMF'

P value = 3.31e-14 (Fisher's exact test), Q value = 1.2e-11

Table S330.  Gene #32: '18p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
18P MUTATED 172 90 185
18P WILD-TYPE 226 197 107

Figure S330.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.48e-13 (Fisher's exact test), Q value = 5.2e-11

Table S331.  Gene #32: '18p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
18P MUTATED 162 140 145
18P WILD-TYPE 90 159 281

Figure S331.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.61e-13 (Fisher's exact test), Q value = 9e-11

Table S332.  Gene #32: '18p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
18P MUTATED 110 61 128
18P WILD-TYPE 140 158 70

Figure S332.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.1e-09 (Fisher's exact test), Q value = 1.7e-06

Table S333.  Gene #32: '18p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
18P MUTATED 94 55 150
18P WILD-TYPE 51 122 195

Figure S333.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q' versus 'MRNA_CNMF'

P value = 9.47e-05 (Chi-square test), Q value = 0.012

Table S334.  Gene #33: '18q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
18Q MUTATED 7 12 55 56 36 43 11 10
18Q WILD-TYPE 14 24 64 40 73 29 9 30

Figure S334.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q' versus 'MRNA_CHIERARCHICAL'

P value = 0.000137 (Fisher's exact test), Q value = 0.016

Table S335.  Gene #33: '18q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
18Q MUTATED 36 69 125
18Q WILD-TYPE 86 56 141

Figure S335.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q' versus 'CN_CNMF'

P value = 1.44e-34 (Chi-square test), Q value = 6.8e-32

Table S336.  Gene #33: '18q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
18Q MUTATED 69 141 61 153 19
18Q WILD-TYPE 302 117 36 83 26

Figure S336.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #3: 'CN_CNMF'

'18q' versus 'METHLYATION_CNMF'

P value = 4.2e-13 (Chi-square test), Q value = 1.4e-10

Table S337.  Gene #33: '18q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
18Q MUTATED 69 38 60 77 13 33
18Q WILD-TYPE 47 117 48 62 42 79

Figure S337.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q' versus 'RPPA_CNMF'

P value = 0.000616 (Fisher's exact test), Q value = 0.058

Table S338.  Gene #33: '18q' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
18Q MUTATED 85 52 43
18Q WILD-TYPE 62 81 74

Figure S338.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #5: 'RPPA_CNMF'

'18q' versus 'MRNASEQ_CNMF'

P value = 8.86e-14 (Fisher's exact test), Q value = 3.2e-11

Table S339.  Gene #33: '18q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
18Q MUTATED 156 40 243
18Q WILD-TYPE 117 146 299

Figure S339.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.93e-11 (Fisher's exact test), Q value = 5.8e-09

Table S340.  Gene #33: '18q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
18Q MUTATED 131 213 95
18Q WILD-TYPE 102 226 234

Figure S340.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q' versus 'MIRSEQ_CNMF'

P value = 2.48e-11 (Fisher's exact test), Q value = 7.5e-09

Table S341.  Gene #33: '18q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
18Q MUTATED 170 85 170
18Q WILD-TYPE 228 202 122

Figure S341.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.44e-10 (Fisher's exact test), Q value = 6.7e-08

Table S342.  Gene #33: '18q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
18Q MUTATED 149 135 141
18Q WILD-TYPE 103 164 285

Figure S342.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.14e-11 (Fisher's exact test), Q value = 3.5e-09

Table S343.  Gene #33: '18q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
18Q MUTATED 104 59 121
18Q WILD-TYPE 146 160 77

Figure S343.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.22e-06 (Fisher's exact test), Q value = 0.0013

Table S344.  Gene #33: '18q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
18Q MUTATED 83 54 147
18Q WILD-TYPE 62 123 198

Figure S344.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p' versus 'MRNA_CNMF'

P value = 8.91e-06 (Chi-square test), Q value = 0.0014

Table S345.  Gene #34: '19p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
19P MUTATED 8 9 46 49 23 35 9 6
19P WILD-TYPE 13 27 73 47 86 37 11 34

Figure S345.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #1: 'MRNA_CNMF'

'19p' versus 'MRNA_CHIERARCHICAL'

P value = 2.33e-06 (Fisher's exact test), Q value = 0.00041

Table S346.  Gene #34: '19p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
19P MUTATED 23 61 101
19P WILD-TYPE 99 64 165

Figure S346.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19p' versus 'CN_CNMF'

P value = 1.93e-28 (Chi-square test), Q value = 8.9e-26

Table S347.  Gene #34: '19p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
19P MUTATED 48 124 36 127 15
19P WILD-TYPE 323 134 61 109 30

Figure S347.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #3: 'CN_CNMF'

'19p' versus 'METHLYATION_CNMF'

P value = 7.21e-13 (Chi-square test), Q value = 2.4e-10

Table S348.  Gene #34: '19p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
19P MUTATED 60 21 36 66 10 30
19P WILD-TYPE 56 134 72 73 45 82

Figure S348.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p' versus 'RPPA_CNMF'

P value = 1.53e-05 (Fisher's exact test), Q value = 0.0023

Table S349.  Gene #34: '19p' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
19P MUTATED 77 43 30
19P WILD-TYPE 70 90 87

Figure S349.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #5: 'RPPA_CNMF'

'19p' versus 'RPPA_CHIERARCHICAL'

P value = 5.02e-05 (Fisher's exact test), Q value = 0.0065

Table S350.  Gene #34: '19p' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
19P MUTATED 54 29 67
19P WILD-TYPE 107 81 59

Figure S350.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'19p' versus 'MRNASEQ_CNMF'

P value = 6.71e-13 (Fisher's exact test), Q value = 2.2e-10

Table S351.  Gene #34: '19p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
19P MUTATED 138 33 176
19P WILD-TYPE 135 153 366

Figure S351.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.96e-14 (Fisher's exact test), Q value = 2.5e-11

Table S352.  Gene #34: '19p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
19P MUTATED 117 165 65
19P WILD-TYPE 116 274 264

Figure S352.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p' versus 'MIRSEQ_CNMF'

P value = 2.48e-16 (Fisher's exact test), Q value = 9.9e-14

Table S353.  Gene #34: '19p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
19P MUTATED 121 59 155
19P WILD-TYPE 277 228 137

Figure S353.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.16e-13 (Fisher's exact test), Q value = 4.1e-11

Table S354.  Gene #34: '19p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
19P MUTATED 125 117 93
19P WILD-TYPE 127 182 333

Figure S354.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.3e-14 (Fisher's exact test), Q value = 3.3e-11

Table S355.  Gene #34: '19p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
19P MUTATED 76 43 109
19P WILD-TYPE 174 176 89

Figure S355.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.26e-06 (Fisher's exact test), Q value = 0.00057

Table S356.  Gene #34: '19p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
19P MUTATED 74 44 110
19P WILD-TYPE 71 133 235

Figure S356.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q' versus 'MRNA_CNMF'

P value = 2.49e-05 (Chi-square test), Q value = 0.0036

Table S357.  Gene #35: '19q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
19Q MUTATED 8 9 48 46 23 37 9 7
19Q WILD-TYPE 13 27 71 50 86 35 11 33

Figure S357.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #1: 'MRNA_CNMF'

'19q' versus 'MRNA_CHIERARCHICAL'

P value = 1.06e-05 (Fisher's exact test), Q value = 0.0017

Table S358.  Gene #35: '19q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
19Q MUTATED 24 59 104
19Q WILD-TYPE 98 66 162

Figure S358.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19q' versus 'CN_CNMF'

P value = 2.11e-27 (Chi-square test), Q value = 9.6e-25

Table S359.  Gene #35: '19q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
19Q MUTATED 49 126 36 123 20
19Q WILD-TYPE 322 132 61 113 25

Figure S359.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #3: 'CN_CNMF'

'19q' versus 'METHLYATION_CNMF'

P value = 1.09e-10 (Chi-square test), Q value = 3.1e-08

Table S360.  Gene #35: '19q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
19Q MUTATED 56 24 37 67 10 31
19Q WILD-TYPE 60 131 71 72 45 81

Figure S360.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q' versus 'RPPA_CNMF'

P value = 0.000631 (Fisher's exact test), Q value = 0.058

Table S361.  Gene #35: '19q' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
19Q MUTATED 70 43 30
19Q WILD-TYPE 77 90 87

Figure S361.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #5: 'RPPA_CNMF'

'19q' versus 'MRNASEQ_CNMF'

P value = 8.6e-11 (Fisher's exact test), Q value = 2.5e-08

Table S362.  Gene #35: '19q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
19Q MUTATED 135 36 181
19Q WILD-TYPE 138 150 361

Figure S362.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.52e-14 (Fisher's exact test), Q value = 2e-11

Table S363.  Gene #35: '19q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
19Q MUTATED 116 171 65
19Q WILD-TYPE 117 268 264

Figure S363.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q' versus 'MIRSEQ_CNMF'

P value = 5.27e-13 (Fisher's exact test), Q value = 1.8e-10

Table S364.  Gene #35: '19q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
19Q MUTATED 126 65 151
19Q WILD-TYPE 272 222 141

Figure S364.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.31e-12 (Fisher's exact test), Q value = 1e-09

Table S365.  Gene #35: '19q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
19Q MUTATED 123 121 98
19Q WILD-TYPE 129 178 328

Figure S365.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-10 (Fisher's exact test), Q value = 1.1e-07

Table S366.  Gene #35: '19q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
19Q MUTATED 78 49 104
19Q WILD-TYPE 172 170 94

Figure S366.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.68e-05 (Fisher's exact test), Q value = 0.0038

Table S367.  Gene #35: '19q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
19Q MUTATED 72 45 114
19Q WILD-TYPE 73 132 231

Figure S367.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p' versus 'MRNA_CNMF'

P value = 3.96e-09 (Chi-square test), Q value = 9.9e-07

Table S368.  Gene #36: '20p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
20P MUTATED 9 15 59 58 36 50 16 7
20P WILD-TYPE 12 21 60 38 73 22 4 33

Figure S368.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p' versus 'MRNA_CHIERARCHICAL'

P value = 8.63e-06 (Fisher's exact test), Q value = 0.0014

Table S369.  Gene #36: '20p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
20P MUTATED 38 76 136
20P WILD-TYPE 84 49 130

Figure S369.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p' versus 'CN_CNMF'

P value = 6.94e-48 (Chi-square test), Q value = 3.3e-45

Table S370.  Gene #36: '20p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
20P MUTATED 62 168 61 163 23
20P WILD-TYPE 309 90 36 73 22

Figure S370.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #3: 'CN_CNMF'

'20p' versus 'METHLYATION_CNMF'

P value = 6.63e-17 (Chi-square test), Q value = 2.7e-14

Table S371.  Gene #36: '20p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
20P MUTATED 79 40 58 90 16 36
20P WILD-TYPE 37 115 50 49 39 76

Figure S371.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p' versus 'RPPA_CNMF'

P value = 0.000234 (Fisher's exact test), Q value = 0.025

Table S372.  Gene #36: '20p' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
20P MUTATED 92 53 51
20P WILD-TYPE 55 80 66

Figure S372.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #5: 'RPPA_CNMF'

'20p' versus 'MRNASEQ_CNMF'

P value = 6.76e-16 (Fisher's exact test), Q value = 2.6e-13

Table S373.  Gene #36: '20p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
20P MUTATED 169 43 263
20P WILD-TYPE 104 143 279

Figure S373.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.65e-14 (Fisher's exact test), Q value = 6.1e-12

Table S374.  Gene #36: '20p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
20P MUTATED 141 235 99
20P WILD-TYPE 92 204 230

Figure S374.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p' versus 'MIRSEQ_CNMF'

P value = 1.44e-13 (Fisher's exact test), Q value = 5.1e-11

Table S375.  Gene #36: '20p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
20P MUTATED 185 90 184
20P WILD-TYPE 213 197 108

Figure S375.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.18e-13 (Fisher's exact test), Q value = 1.7e-10

Table S376.  Gene #36: '20p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
20P MUTATED 160 152 147
20P WILD-TYPE 92 147 279

Figure S376.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.45e-08 (Fisher's exact test), Q value = 3.3e-06

Table S377.  Gene #36: '20p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
20P MUTATED 115 72 123
20P WILD-TYPE 135 147 75

Figure S377.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.81e-09 (Fisher's exact test), Q value = 2.1e-06

Table S378.  Gene #36: '20p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
20P MUTATED 92 53 165
20P WILD-TYPE 53 124 180

Figure S378.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q' versus 'MRNA_CNMF'

P value = 5.28e-06 (Chi-square test), Q value = 0.00089

Table S379.  Gene #37: '20q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
20Q MUTATED 8 15 64 51 36 47 15 10
20Q WILD-TYPE 13 21 55 45 73 25 5 30

Figure S379.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q' versus 'MRNA_CHIERARCHICAL'

P value = 0.00129 (Fisher's exact test), Q value = 0.1

Table S380.  Gene #37: '20q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
20Q MUTATED 41 66 139
20Q WILD-TYPE 81 59 127

Figure S380.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q' versus 'CN_CNMF'

P value = 1.03e-45 (Chi-square test), Q value = 5e-43

Table S381.  Gene #37: '20q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
20Q MUTATED 63 177 60 149 24
20Q WILD-TYPE 308 81 37 87 21

Figure S381.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #3: 'CN_CNMF'

'20q' versus 'METHLYATION_CNMF'

P value = 1.31e-18 (Chi-square test), Q value = 5.6e-16

Table S382.  Gene #37: '20q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
20Q MUTATED 74 39 57 96 13 36
20Q WILD-TYPE 42 116 51 43 42 76

Figure S382.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q' versus 'MRNASEQ_CNMF'

P value = 2.96e-12 (Fisher's exact test), Q value = 9.4e-10

Table S383.  Gene #37: '20q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
20Q MUTATED 155 45 270
20Q WILD-TYPE 118 141 272

Figure S383.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.89e-11 (Fisher's exact test), Q value = 5.7e-09

Table S384.  Gene #37: '20q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
20Q MUTATED 131 236 103
20Q WILD-TYPE 102 203 226

Figure S384.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q' versus 'MIRSEQ_CNMF'

P value = 4.24e-10 (Fisher's exact test), Q value = 1.1e-07

Table S385.  Gene #37: '20q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
20Q MUTATED 194 93 173
20Q WILD-TYPE 204 194 119

Figure S385.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.58e-10 (Fisher's exact test), Q value = 7.1e-08

Table S386.  Gene #37: '20q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
20Q MUTATED 151 158 151
20Q WILD-TYPE 101 141 275

Figure S386.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.93e-08 (Fisher's exact test), Q value = 1.5e-05

Table S387.  Gene #37: '20q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
20Q MUTATED 123 73 121
20Q WILD-TYPE 127 146 77

Figure S387.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.21e-07 (Fisher's exact test), Q value = 8.4e-05

Table S388.  Gene #37: '20q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
20Q MUTATED 88 56 173
20Q WILD-TYPE 57 121 172

Figure S388.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q' versus 'MRNA_CNMF'

P value = 1.47e-09 (Chi-square test), Q value = 3.8e-07

Table S389.  Gene #38: '21q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
21Q MUTATED 4 11 44 44 21 48 10 8
21Q WILD-TYPE 17 25 75 52 88 24 10 32

Figure S389.  Get High-res Image Gene #38: '21q' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q' versus 'MRNA_CHIERARCHICAL'

P value = 2.31e-05 (Fisher's exact test), Q value = 0.0034

Table S390.  Gene #38: '21q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
21Q MUTATED 26 61 103
21Q WILD-TYPE 96 64 163

Figure S390.  Get High-res Image Gene #38: '21q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'21q' versus 'CN_CNMF'

P value = 5.6e-27 (Chi-square test), Q value = 2.5e-24

Table S391.  Gene #38: '21q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
21Q MUTATED 50 107 41 131 21
21Q WILD-TYPE 321 151 56 105 24

Figure S391.  Get High-res Image Gene #38: '21q' versus Molecular Subtype #3: 'CN_CNMF'

'21q' versus 'METHLYATION_CNMF'

P value = 2.06e-10 (Chi-square test), Q value = 5.7e-08

Table S392.  Gene #38: '21q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
21Q MUTATED 64 31 40 55 9 25
21Q WILD-TYPE 52 124 68 84 46 87

Figure S392.  Get High-res Image Gene #38: '21q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q' versus 'RPPA_CNMF'

P value = 0.000275 (Fisher's exact test), Q value = 0.029

Table S393.  Gene #38: '21q' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
21Q MUTATED 75 37 42
21Q WILD-TYPE 72 96 75

Figure S393.  Get High-res Image Gene #38: '21q' versus Molecular Subtype #5: 'RPPA_CNMF'

'21q' versus 'RPPA_CHIERARCHICAL'

P value = 0.00189 (Fisher's exact test), Q value = 0.15

Table S394.  Gene #38: '21q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
21Q MUTATED 53 36 65
21Q WILD-TYPE 108 74 61

Figure S394.  Get High-res Image Gene #38: '21q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'21q' versus 'MRNASEQ_CNMF'

P value = 2.28e-15 (Fisher's exact test), Q value = 8.6e-13

Table S395.  Gene #38: '21q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
21Q MUTATED 142 30 175
21Q WILD-TYPE 131 156 367

Figure S395.  Get High-res Image Gene #38: '21q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.25e-17 (Fisher's exact test), Q value = 2.9e-14

Table S396.  Gene #38: '21q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
21Q MUTATED 121 166 60
21Q WILD-TYPE 112 273 269

Figure S396.  Get High-res Image Gene #38: '21q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q' versus 'MIRSEQ_CNMF'

P value = 7.97e-13 (Fisher's exact test), Q value = 2.6e-10

Table S397.  Gene #38: '21q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
21Q MUTATED 128 61 147
21Q WILD-TYPE 270 226 145

Figure S397.  Get High-res Image Gene #38: '21q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.78e-12 (Fisher's exact test), Q value = 1.2e-09

Table S398.  Gene #38: '21q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
21Q MUTATED 131 101 104
21Q WILD-TYPE 121 198 322

Figure S398.  Get High-res Image Gene #38: '21q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.46e-10 (Fisher's exact test), Q value = 6.8e-08

Table S399.  Gene #38: '21q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
21Q MUTATED 77 45 101
21Q WILD-TYPE 173 174 97

Figure S399.  Get High-res Image Gene #38: '21q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.63e-09 (Fisher's exact test), Q value = 1.8e-06

Table S400.  Gene #38: '21q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 177 345
21Q MUTATED 78 39 106
21Q WILD-TYPE 67 138 239

Figure S400.  Get High-res Image Gene #38: '21q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q' versus 'CN_CNMF'

P value = 1.1e-17 (Chi-square test), Q value = 4.6e-15

Table S401.  Gene #39: '22q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
22Q MUTATED 131 168 69 149 28
22Q WILD-TYPE 240 90 28 87 17

Figure S401.  Get High-res Image Gene #39: '22q' versus Molecular Subtype #3: 'CN_CNMF'

'22q' versus 'METHLYATION_CNMF'

P value = 1.12e-09 (Chi-square test), Q value = 2.9e-07

Table S402.  Gene #39: '22q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
22Q MUTATED 71 63 66 99 18 45
22Q WILD-TYPE 45 92 42 40 37 67

Figure S402.  Get High-res Image Gene #39: '22q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q' versus 'MRNASEQ_CNMF'

P value = 0.000227 (Fisher's exact test), Q value = 0.025

Table S403.  Gene #39: '22q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
22Q MUTATED 151 76 315
22Q WILD-TYPE 122 110 227

Figure S403.  Get High-res Image Gene #39: '22q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q' versus 'MIRSEQ_CNMF'

P value = 0.00127 (Fisher's exact test), Q value = 0.1

Table S404.  Gene #39: '22q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
22Q MUTATED 227 128 169
22Q WILD-TYPE 171 159 123

Figure S404.  Get High-res Image Gene #39: '22q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq' versus 'MRNA_CNMF'

P value = 3.38e-05 (Chi-square test), Q value = 0.0047

Table S405.  Gene #40: 'xq' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
XQ MUTATED 4 7 45 44 25 34 6 5
XQ WILD-TYPE 17 29 74 52 84 38 14 35

Figure S405.  Get High-res Image Gene #40: 'xq' versus Molecular Subtype #1: 'MRNA_CNMF'

'xq' versus 'MRNA_CHIERARCHICAL'

P value = 8.93e-07 (Fisher's exact test), Q value = 0.00017

Table S406.  Gene #40: 'xq' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
XQ MUTATED 20 59 91
XQ WILD-TYPE 102 66 175

Figure S406.  Get High-res Image Gene #40: 'xq' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'xq' versus 'CN_CNMF'

P value = 4.84e-23 (Chi-square test), Q value = 2.2e-20

Table S407.  Gene #40: 'xq' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 371 258 97 236 45
XQ MUTATED 40 101 32 112 14
XQ WILD-TYPE 331 157 65 124 31

Figure S407.  Get High-res Image Gene #40: 'xq' versus Molecular Subtype #3: 'CN_CNMF'

'xq' versus 'METHLYATION_CNMF'

P value = 2.26e-09 (Chi-square test), Q value = 5.8e-07

Table S408.  Gene #40: 'xq' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 116 155 108 139 55 112
XQ MUTATED 49 29 36 50 9 10
XQ WILD-TYPE 67 126 72 89 46 102

Figure S408.  Get High-res Image Gene #40: 'xq' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq' versus 'RPPA_CHIERARCHICAL'

P value = 0.000598 (Fisher's exact test), Q value = 0.057

Table S409.  Gene #40: 'xq' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
XQ MUTATED 55 23 56
XQ WILD-TYPE 106 87 70

Figure S409.  Get High-res Image Gene #40: 'xq' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'xq' versus 'MRNASEQ_CNMF'

P value = 1.49e-11 (Fisher's exact test), Q value = 4.6e-09

Table S410.  Gene #40: 'xq' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 273 186 542
XQ MUTATED 110 21 167
XQ WILD-TYPE 163 165 375

Figure S410.  Get High-res Image Gene #40: 'xq' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.6e-13 (Fisher's exact test), Q value = 2.5e-10

Table S411.  Gene #40: 'xq' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 233 439 329
XQ MUTATED 95 153 50
XQ WILD-TYPE 138 286 279

Figure S411.  Get High-res Image Gene #40: 'xq' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq' versus 'MIRSEQ_CNMF'

P value = 9.05e-14 (Fisher's exact test), Q value = 3.2e-11

Table S412.  Gene #40: 'xq' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 398 287 292
XQ MUTATED 127 39 121
XQ WILD-TYPE 271 248 171

Figure S412.  Get High-res Image Gene #40: 'xq' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.95e-09 (Fisher's exact test), Q value = 2.1e-06

Table S413.  Gene #40: 'xq' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 252 299 426
XQ MUTATED 97 107 83
XQ WILD-TYPE 155 192 343

Figure S413.  Get High-res Image Gene #40: 'xq' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xq' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.19e-06 (Fisher's exact test), Q value = 0.00056

Table S414.  Gene #40: 'xq' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 219 198
XQ MUTATED 69 34 73
XQ WILD-TYPE 181 185 125

Figure S414.  Get High-res Image Gene #40: 'xq' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

  • Molecular subtype file = BRCA-TP.transferedmergedcluster.txt

  • Number of patients = 1007

  • Number of significantly focal cnvs = 40

  • Number of molecular subtypes = 12

  • Exclude genes that fewer than K tumors have alterations, K = 3

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[2] 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)
[3] 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)
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