Correlation between copy number variation genes (focal events) and molecular subtypes

Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)

15 January 2014 | analyses__2014_01_15

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1JD4V92

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 514 patients, 316 significant findings detected with P value < 0.05 and Q value < 0.25.

1p cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
1q cnv correlated to 'CN_CNMF'.
2p cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
2q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
3p cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
3q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
4p cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
4q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
5p cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
5q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', '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', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
6q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
7p cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
7q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
8p cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
8q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
9p 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'.
9q 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'.
10p cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
10q cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
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 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
12p cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
12q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
13q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
14q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', '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', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
16p 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'.
16q 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'.
17p 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'.
17q 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'.
18p cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
18q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
19p cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
19q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
20p cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
20q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
21q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
22q cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
xq cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 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, 316 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Chi-square test	Fisher's exact test	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test
9p	120 (23%)	394	0.000601 (0.103)	3.97e-05 (0.00826)	4.45e-48 (2.1e-45)	1.57e-13 (5.47e-11)	0.000613 (0.104)	0.0395 (1.00)	7.1e-21 (2.96e-18)	1.36e-18 (5.45e-16)	5.15e-20 (2.12e-17)	5.85e-12 (1.91e-09)	0.000391 (0.0696)	5.39e-06 (0.00122)
9q	126 (25%)	388	2.35e-05 (0.00498)	1.13e-06 (0.000265)	3.08e-51 (1.46e-48)	5.93e-12 (1.93e-09)	0.000337 (0.0607)	0.0656 (1.00)	5.35e-22 (2.27e-19)	6.88e-20 (2.82e-17)	5.18e-25 (2.26e-22)	1.54e-12 (5.14e-10)	0.000178 (0.0338)	6.34e-06 (0.00143)
15q	112 (22%)	402	0.000567 (0.0992)	4.17e-05 (0.00864)	1.47e-44 (6.87e-42)	4.5e-13 (1.52e-10)	0.00104 (0.17)	0.157 (1.00)	8.41e-23 (3.61e-20)	7.75e-22 (3.28e-19)	9.68e-20 (3.96e-17)	3.97e-15 (1.45e-12)	3.05e-06 (0.000703)	3.79e-08 (9.81e-06)
4p	110 (21%)	404	0.00888 (1.00)	0.000595 (0.102)	9.98e-44 (4.65e-41)	2.71e-16 (1.01e-13)	0.000505 (0.0889)	0.0297 (1.00)	3.7e-26 (1.62e-23)	4.77e-23 (2.05e-20)	8.65e-21 (3.6e-18)	6.18e-17 (2.38e-14)	4.5e-07 (0.000108)	8.74e-10 (2.6e-07)
16p	116 (23%)	398	0.000567 (0.0992)	4.17e-05 (0.00864)	5.59e-45 (2.63e-42)	2.44e-12 (8.09e-10)	0.115 (1.00)	0.411 (1.00)	1.17e-22 (5.03e-20)	9.66e-18 (3.81e-15)	2.3e-17 (8.94e-15)	5.63e-11 (1.77e-08)	8.35e-05 (0.0167)	2.67e-07 (6.63e-05)
16q	144 (28%)	370	0.000771 (0.128)	9.8e-05 (0.0192)	5.3e-51 (2.52e-48)	3.5e-14 (1.24e-11)	0.202 (1.00)	0.698 (1.00)	2.96e-26 (1.3e-23)	5.12e-20 (2.11e-17)	3.13e-19 (1.27e-16)	8.51e-12 (2.74e-09)	2.8e-06 (0.000646)	3.82e-09 (1.09e-06)
17p	132 (26%)	382	0.000771 (0.128)	9.8e-05 (0.0192)	1.31e-62 (6.24e-60)	1.02e-16 (3.9e-14)	0.00568 (0.812)	0.535 (1.00)	1.01e-29 (4.52e-27)	1.72e-22 (7.35e-20)	4.55e-23 (1.96e-20)	6.15e-12 (1.99e-09)	0.000263 (0.0487)	7.5e-07 (0.000178)
17q	114 (22%)	400	0.000567 (0.0992)	4.17e-05 (0.00864)	1.9e-49 (9e-47)	8.34e-13 (2.8e-10)	0.115 (1.00)	0.378 (1.00)	4.19e-22 (1.78e-19)	4.52e-16 (1.67e-13)	4.15e-16 (1.54e-13)	1.86e-08 (5.03e-06)	0.000631 (0.106)	2.19e-05 (0.00466)
8p	188 (37%)	326	0.00295 (0.457)	0.00421 (0.631)	1.31e-36 (6.02e-34)	2.92e-08 (7.61e-06)	0.000359 (0.0642)	0.607 (1.00)	3.9e-15 (1.43e-12)	4.12e-13 (1.41e-10)	2.73e-12 (9.03e-10)	3.66e-09 (1.05e-06)	9.23e-05 (0.0183)	1.84e-05 (0.00394)
19p	107 (21%)	407	0.00202 (0.317)	0.000218 (0.0406)	6.49e-44 (3.03e-41)	1.78e-16 (6.75e-14)	0.0621 (1.00)	0.102 (1.00)	5.12e-24 (2.23e-21)	1.63e-22 (6.97e-20)	4.01e-20 (1.65e-17)	4.39e-12 (1.44e-09)	1.36e-06 (0.000317)	5.66e-09 (1.59e-06)
22q	136 (26%)	378	0.00381 (0.576)	0.000454 (0.0803)	2.3e-58 (1.1e-55)	1.85e-19 (7.57e-17)	0.0116 (1.00)	0.659 (1.00)	2.56e-30 (1.15e-27)	8.79e-28 (3.91e-25)	1.32e-21 (5.58e-19)	3.19e-14 (1.14e-11)	1.11e-06 (0.000262)	4.27e-13 (1.45e-10)
1p	67 (13%)	447	0.206 (1.00)	0.136 (1.00)	3.98e-18 (1.58e-15)	1.21e-08 (3.32e-06)	0.0807 (1.00)	0.0559 (1.00)	1.36e-10 (4.19e-08)	2.23e-08 (5.9e-06)	3.09e-08 (8.04e-06)	8.39e-10 (2.51e-07)	4.81e-05 (0.00977)	4.15e-06 (0.000947)
2p	98 (19%)	416	0.855 (1.00)	0.683 (1.00)	1.62e-34 (7.38e-32)	7.98e-09 (2.21e-06)	0.0567 (1.00)	0.535 (1.00)	4.78e-10 (1.44e-07)	1.99e-09 (5.8e-07)	3.25e-07 (8.04e-05)	1.76e-07 (4.46e-05)	0.000271 (0.0498)	3.68e-05 (0.00768)
2q	87 (17%)	427	0.284 (1.00)	0.667 (1.00)	4.04e-32 (1.83e-29)	3.34e-07 (8.19e-05)	0.0464 (1.00)	1 (1.00)	2.39e-09 (6.9e-07)	4.29e-09 (1.22e-06)	9.6e-08 (2.46e-05)	2.31e-08 (6.1e-06)	0.000321 (0.0581)	2.39e-05 (0.00505)
3p	91 (18%)	423	0.037 (1.00)	0.158 (1.00)	1.23e-31 (5.56e-29)	1.02e-09 (3.03e-07)	0.0581 (1.00)	0.157 (1.00)	7.04e-17 (2.7e-14)	3.07e-14 (1.1e-11)	9e-09 (2.48e-06)	1.34e-08 (3.63e-06)	0.000115 (0.0224)	2.57e-07 (6.4e-05)
3q	105 (20%)	409	0.0192 (1.00)	0.0426 (1.00)	2.17e-35 (9.9e-33)	1.2e-14 (4.35e-12)	0.022 (1.00)	0.0131 (1.00)	3.28e-21 (1.38e-18)	3.55e-19 (1.43e-16)	1.16e-10 (3.59e-08)	1.36e-11 (4.31e-09)	1.23e-05 (0.0027)	3.08e-10 (9.36e-08)
4q	105 (20%)	409	0.175 (1.00)	0.0623 (1.00)	1.93e-42 (8.94e-40)	1.11e-16 (4.21e-14)	0.0128 (1.00)	0.168 (1.00)	1.7e-26 (7.48e-24)	3.83e-21 (1.61e-18)	2.82e-16 (1.05e-13)	1.59e-16 (6.05e-14)	6.34e-07 (0.000151)	2.13e-09 (6.17e-07)
5p	103 (20%)	411	0.101 (1.00)	0.00447 (0.657)	5.14e-39 (2.37e-36)	1.62e-17 (6.34e-15)	0.00942 (1.00)	0.133 (1.00)	5.61e-21 (2.34e-18)	3.77e-20 (1.56e-17)	2.35e-16 (8.81e-14)	5.16e-14 (1.82e-11)	1.34e-08 (3.63e-06)	3.42e-12 (1.13e-09)
5q	91 (18%)	423	0.0129 (1.00)	0.00193 (0.307)	9.45e-36 (4.32e-33)	7.84e-16 (2.89e-13)	0.00623 (0.879)	0.0653 (1.00)	1.82e-18 (7.25e-16)	6.05e-18 (2.39e-15)	1.91e-13 (6.62e-11)	2.73e-13 (9.37e-11)	3.44e-07 (8.39e-05)	2.4e-10 (7.33e-08)
8q	174 (34%)	340	0.00295 (0.457)	0.00421 (0.631)	6.68e-31 (3e-28)	0.000203 (0.0379)	0.000197 (0.037)	0.864 (1.00)	6.16e-09 (1.72e-06)	1.06e-08 (2.92e-06)	2.18e-08 (5.79e-06)	1.02e-05 (0.00226)	0.000605 (0.103)	0.0019 (0.303)
11p	93 (18%)	421	0.00202 (0.317)	0.00755 (1.00)	5.99e-36 (2.74e-33)	6.09e-12 (1.97e-09)	0.313 (1.00)	0.638 (1.00)	3.44e-17 (1.33e-14)	1.93e-16 (7.27e-14)	1.51e-14 (5.41e-12)	3.44e-09 (9.88e-07)	9.41e-05 (0.0185)	2.84e-08 (7.44e-06)
11q	87 (17%)	427			2.53e-32 (1.15e-29)	8.06e-11 (2.52e-08)	0.499 (1.00)	0.802 (1.00)	1.28e-14 (4.61e-12)	9.11e-14 (3.2e-11)	1.86e-13 (6.47e-11)	2.2e-07 (5.52e-05)	0.000127 (0.0242)	3.48e-10 (1.05e-07)
12p	107 (21%)	407	0.157 (1.00)	0.175 (1.00)	1.26e-27 (5.6e-25)	5.35e-10 (1.61e-07)	0.0927 (1.00)	0.225 (1.00)	2.46e-15 (9.06e-13)	1.29e-11 (4.12e-09)	1.49e-09 (4.42e-07)	5.42e-08 (1.39e-05)	2.47e-07 (6.17e-05)	2.56e-08 (6.73e-06)
12q	85 (17%)	429	0.255 (1.00)	0.434 (1.00)	7.71e-18 (3.05e-15)	4.22e-07 (0.000102)	0.222 (1.00)	0.133 (1.00)	2.48e-10 (7.57e-08)	2.04e-08 (5.48e-06)	6.57e-05 (0.0133)	8.93e-06 (0.002)	2.65e-05 (0.00556)	4.57e-06 (0.00104)
14q	95 (18%)	419	0.0192 (1.00)	0.0426 (1.00)	3.2e-32 (1.45e-29)	2.8e-13 (9.61e-11)	0.0185 (1.00)	0.0131 (1.00)	1.25e-25 (5.46e-23)	2.88e-19 (1.17e-16)	2.54e-13 (8.75e-11)	1.03e-13 (3.62e-11)	1.48e-05 (0.00324)	4.79e-08 (1.24e-05)
18p	117 (23%)	397	0.188 (1.00)	0.0951 (1.00)	1.5e-45 (7.05e-43)	3.97e-19 (1.59e-16)	0.0291 (1.00)	0.133 (1.00)	4.09e-23 (1.77e-20)	3.81e-21 (1.6e-18)	2.16e-20 (8.94e-18)	7.9e-17 (3.03e-14)	2.5e-09 (7.21e-07)	2.94e-12 (9.7e-10)
18q	105 (20%)	409	0.0515 (1.00)	0.0276 (1.00)	3.96e-38 (1.82e-35)	8.91e-15 (3.23e-12)	0.145 (1.00)	0.186 (1.00)	5.35e-18 (2.13e-15)	1.86e-19 (7.57e-17)	3.67e-17 (1.42e-14)	8.32e-15 (3.04e-12)	1.74e-07 (4.42e-05)	1.93e-09 (5.67e-07)
19q	107 (21%)	407	0.037 (1.00)	0.00755 (1.00)	3.69e-43 (1.71e-40)	5.26e-13 (1.77e-10)	0.017 (1.00)	0.346 (1.00)	3.52e-23 (1.53e-20)	5.74e-24 (2.49e-21)	3.22e-19 (1.3e-16)	6.28e-13 (2.11e-10)	9.66e-06 (0.00215)	1.52e-09 (4.49e-07)
20p	124 (24%)	390	0.0515 (1.00)	0.00755 (1.00)	6.36e-45 (2.98e-42)	4.95e-12 (1.62e-09)	0.0563 (1.00)	0.274 (1.00)	2.14e-17 (8.36e-15)	1.68e-16 (6.37e-14)	6.11e-14 (2.15e-11)	1.73e-10 (5.32e-08)	1.59e-05 (0.00345)	1.96e-08 (5.27e-06)
20q	133 (26%)	381	0.0129 (1.00)	0.00193 (0.307)	1.73e-50 (8.2e-48)	4.25e-13 (1.45e-10)	0.0339 (1.00)	0.301 (1.00)	2.36e-19 (9.59e-17)	1.29e-17 (5.05e-15)	1.22e-14 (4.4e-12)	5.26e-11 (1.66e-08)	1.73e-05 (0.00374)	2.02e-09 (5.87e-07)
21q	87 (17%)	427	0.0515 (1.00)	0.00755 (1.00)	4.14e-30 (1.85e-27)	1.72e-09 (5.06e-07)	0.038 (1.00)	0.0698 (1.00)	1.05e-17 (4.11e-15)	8.72e-15 (3.17e-12)	3.18e-16 (1.18e-13)	1.32e-13 (4.62e-11)	3.85e-07 (9.31e-05)	4.99e-10 (1.5e-07)
xq	130 (25%)	384	0.0336 (1.00)	0.00722 (1.00)	1.51e-40 (7.01e-38)	1e-05 (0.00223)	0.00164 (0.265)	0.471 (1.00)	1.07e-11 (3.43e-09)	2.05e-08 (5.48e-06)	4.71e-09 (1.33e-06)	9.11e-05 (0.0181)	0.000186 (0.0351)	4.76e-05 (0.00971)
6p	90 (18%)	424	0.0872 (1.00)	0.0426 (1.00)	1.71e-31 (7.72e-29)	6.35e-09 (1.76e-06)	0.0341 (1.00)	0.0487 (1.00)	4.27e-13 (1.45e-10)	5.62e-11 (1.77e-08)	1.21e-08 (3.32e-06)	5.48e-09 (1.54e-06)	0.00345 (0.525)	0.000679 (0.113)
13q	114 (22%)	400	0.154 (1.00)	0.0276 (1.00)	1.6e-39 (7.39e-37)	1.07e-10 (3.34e-08)	0.00524 (0.76)	0.0901 (1.00)	2.12e-16 (7.96e-14)	6.06e-17 (2.34e-14)	4.8e-14 (1.7e-11)	6.05e-11 (1.89e-08)	0.00426 (0.631)	8.18e-05 (0.0164)
6q	83 (16%)	431	0.0872 (1.00)	0.0426 (1.00)	2.04e-27 (9.05e-25)	4.8e-07 (0.000115)	0.0194 (1.00)	0.0487 (1.00)	2.27e-10 (6.96e-08)	5.01e-09 (1.41e-06)	1.94e-06 (0.000452)	2.08e-07 (5.24e-05)	0.054 (1.00)	0.00509 (0.743)
7p	105 (20%)	409	0.115 (1.00)	0.128 (1.00)	9.08e-27 (4.01e-24)	0.000122 (0.0236)	0.23 (1.00)	0.665 (1.00)	2.47e-11 (7.84e-09)	1.12e-07 (2.85e-05)	3.46e-06 (0.000792)	1.81e-05 (0.00389)	0.0224 (1.00)	0.0392 (1.00)
7q	101 (20%)	413	0.682 (1.00)	0.889 (1.00)	1.85e-26 (8.13e-24)	1.48e-05 (0.00324)	0.778 (1.00)	0.274 (1.00)	9.75e-12 (3.13e-09)	3.29e-07 (8.1e-05)	3.47e-07 (8.44e-05)	2.2e-06 (0.00051)	0.00524 (0.76)	0.00312 (0.477)
10p	152 (30%)	362	0.0337 (1.00)	0.0929 (1.00)	4.15e-14 (1.47e-11)	0.0293 (1.00)	0.119 (1.00)	0.406 (1.00)	0.000314 (0.0571)	0.000289 (0.0528)	0.00174 (0.281)	0.2 (1.00)	0.864 (1.00)	0.243 (1.00)
10q	142 (28%)	372	0.0101 (1.00)	0.0365 (1.00)	1.52e-12 (5.06e-10)	0.0496 (1.00)	0.142 (1.00)	0.247 (1.00)	0.001 (0.164)	0.00591 (0.839)	0.0091 (1.00)	0.497 (1.00)	0.445 (1.00)	0.0958 (1.00)
1q	188 (37%)	326	0.0934 (1.00)	0.133 (1.00)	0.000123 (0.0237)	0.0449 (1.00)	0.158 (1.00)	0.0458 (1.00)	0.0191 (1.00)	0.106 (1.00)	0.0298 (1.00)	0.136 (1.00)	0.656 (1.00)	0.0172 (1.00)

'1p' versus 'CN_CNMF'

P value = 3.98e-18 (Chi-square test), Q value = 1.6e-15

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
1P MUTATED	6	8	49	3	1	0
1P WILD-TYPE	294	16	103	19	14	1

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

'1p' versus 'METHLYATION_CNMF'

P value = 1.21e-08 (Fisher's exact test), Q value = 3.3e-06

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
1P MUTATED	43	6	9
1P WILD-TYPE	109	82	151

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

'1p' versus 'MRNASEQ_CNMF'

P value = 1.36e-10 (Fisher's exact test), Q value = 4.2e-08

Table S3. Gene #1: '1p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
1P MUTATED	49	7	5	6
1P WILD-TYPE	125	79	110	124

Figure S3. Get High-res Image Gene #1: '1p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.23e-08 (Fisher's exact test), Q value = 5.9e-06

Table S4. Gene #1: '1p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
1P MUTATED	54	4	9
1P WILD-TYPE	185	80	173

Figure S4. Get High-res Image Gene #1: '1p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p' versus 'MIRSEQ_CNMF'

P value = 3.09e-08 (Chi-square test), Q value = 8e-06

Table S5. Gene #1: '1p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
1P MUTATED	40	4	4	8	10
1P WILD-TYPE	109	134	45	45	106

Figure S5. Get High-res Image Gene #1: '1p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.39e-10 (Fisher's exact test), Q value = 2.5e-07

Table S6. Gene #1: '1p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
1P MUTATED	1	6	59
1P WILD-TYPE	12	208	219

Figure S6. Get High-res Image Gene #1: '1p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.81e-05 (Fisher's exact test), Q value = 0.0098

Table S7. Gene #1: '1p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
1P MUTATED	42	9	7
1P WILD-TYPE	134	81	109

Figure S7. Get High-res Image Gene #1: '1p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.15e-06 (Fisher's exact test), Q value = 0.00095

Table S8. Gene #1: '1p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
1P MUTATED	14	31	9	4
1P WILD-TYPE	87	69	137	31

Figure S8. Get High-res Image Gene #1: '1p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q' versus 'CN_CNMF'

P value = 0.000123 (Chi-square test), Q value = 0.024

Table S9. Gene #2: '1q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
1Q MUTATED	90	17	60	11	9	1
1Q WILD-TYPE	210	7	92	11	6	0

Figure S9. Get High-res Image Gene #2: '1q' versus Molecular Subtype #3: 'CN_CNMF'

'2p' versus 'CN_CNMF'

P value = 1.62e-34 (Chi-square test), Q value = 7.4e-32

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
2P MUTATED	8	21	60	4	5	0
2P WILD-TYPE	292	3	92	18	10	1

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

'2p' versus 'METHLYATION_CNMF'

P value = 7.98e-09 (Fisher's exact test), Q value = 2.2e-06

Table S11. Gene #3: '2p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
2P MUTATED	52	13	12
2P WILD-TYPE	100	75	148

Figure S11. Get High-res Image Gene #3: '2p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p' versus 'MRNASEQ_CNMF'

P value = 4.78e-10 (Fisher's exact test), Q value = 1.4e-07

Table S12. Gene #3: '2p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
2P MUTATED	62	11	13	10
2P WILD-TYPE	112	75	102	120

Figure S12. Get High-res Image Gene #3: '2p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.99e-09 (Fisher's exact test), Q value = 5.8e-07

Table S13. Gene #3: '2p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
2P MUTATED	73	8	15
2P WILD-TYPE	166	76	167

Figure S13. Get High-res Image Gene #3: '2p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p' versus 'MIRSEQ_CNMF'

P value = 3.25e-07 (Chi-square test), Q value = 8e-05

Table S14. Gene #3: '2p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
2P MUTATED	49	11	13	11	13
2P WILD-TYPE	100	127	36	42	103

Figure S14. Get High-res Image Gene #3: '2p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.76e-07 (Fisher's exact test), Q value = 4.5e-05

Table S15. Gene #3: '2p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
2P MUTATED	0	20	77
2P WILD-TYPE	13	194	201

Figure S15. Get High-res Image Gene #3: '2p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000271 (Fisher's exact test), Q value = 0.05

Table S16. Gene #3: '2p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
2P MUTATED	45	20	9
2P WILD-TYPE	131	70	107

Figure S16. Get High-res Image Gene #3: '2p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.68e-05 (Fisher's exact test), Q value = 0.0077

Table S17. Gene #3: '2p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
2P MUTATED	26	30	12	6
2P WILD-TYPE	75	70	134	29

Figure S17. Get High-res Image Gene #3: '2p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q' versus 'CN_CNMF'

P value = 4.04e-32 (Chi-square test), Q value = 1.8e-29

Table S18. Gene #4: '2q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
2Q MUTATED	5	19	55	4	4	0
2Q WILD-TYPE	295	5	97	18	11	1

Figure S18. Get High-res Image Gene #4: '2q' versus Molecular Subtype #3: 'CN_CNMF'

'2q' versus 'METHLYATION_CNMF'

P value = 3.34e-07 (Fisher's exact test), Q value = 8.2e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
2Q MUTATED	47	13	12
2Q WILD-TYPE	105	75	148

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

'2q' versus 'MRNASEQ_CNMF'

P value = 2.39e-09 (Fisher's exact test), Q value = 6.9e-07

Table S20. Gene #4: '2q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
2Q MUTATED	56	10	10	9
2Q WILD-TYPE	118	76	105	121

Figure S20. Get High-res Image Gene #4: '2q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.29e-09 (Fisher's exact test), Q value = 1.2e-06

Table S21. Gene #4: '2q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
2Q MUTATED	66	6	13
2Q WILD-TYPE	173	78	169

Figure S21. Get High-res Image Gene #4: '2q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q' versus 'MIRSEQ_CNMF'

P value = 9.6e-08 (Chi-square test), Q value = 2.5e-05

Table S22. Gene #4: '2q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
2Q MUTATED	47	9	11	9	11
2Q WILD-TYPE	102	129	38	44	105

Figure S22. Get High-res Image Gene #4: '2q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.31e-08 (Fisher's exact test), Q value = 6.1e-06

Table S23. Gene #4: '2q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
2Q MUTATED	0	15	72
2Q WILD-TYPE	13	199	206

Figure S23. Get High-res Image Gene #4: '2q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000321 (Fisher's exact test), Q value = 0.058

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
2Q MUTATED	42	19	8
2Q WILD-TYPE	134	71	108

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

'2q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.39e-05 (Fisher's exact test), Q value = 0.0051

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
2Q MUTATED	26	27	10	6
2Q WILD-TYPE	75	73	136	29

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

'3p' versus 'CN_CNMF'

P value = 1.23e-31 (Chi-square test), Q value = 5.6e-29

Table S26. Gene #5: '3p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
3P MUTATED	2	6	67	7	9	0
3P WILD-TYPE	298	18	85	15	6	1

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

'3p' versus 'METHLYATION_CNMF'

P value = 1.02e-09 (Fisher's exact test), Q value = 3e-07

Table S27. Gene #5: '3p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
3P MUTATED	52	14	10
3P WILD-TYPE	100	74	150

Figure S27. Get High-res Image Gene #5: '3p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p' versus 'MRNASEQ_CNMF'

P value = 7.04e-17 (Fisher's exact test), Q value = 2.7e-14

Table S28. Gene #5: '3p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
3P MUTATED	67	8	4	10
3P WILD-TYPE	107	78	111	120

Figure S28. Get High-res Image Gene #5: '3p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.07e-14 (Fisher's exact test), Q value = 1.1e-11

Table S29. Gene #5: '3p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
3P MUTATED	75	4	10
3P WILD-TYPE	164	80	172

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

'3p' versus 'MIRSEQ_CNMF'

P value = 9e-09 (Chi-square test), Q value = 2.5e-06

Table S30. Gene #5: '3p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
3P MUTATED	51	10	9	6	13
3P WILD-TYPE	98	128	40	47	103

Figure S30. Get High-res Image Gene #5: '3p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.34e-08 (Fisher's exact test), Q value = 3.6e-06

Table S31. Gene #5: '3p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
3P MUTATED	5	14	70
3P WILD-TYPE	8	200	208

Figure S31. Get High-res Image Gene #5: '3p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000115 (Fisher's exact test), Q value = 0.022

Table S32. Gene #5: '3p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
3P MUTATED	49	14	10
3P WILD-TYPE	127	76	106

Figure S32. Get High-res Image Gene #5: '3p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.57e-07 (Fisher's exact test), Q value = 6.4e-05

Table S33. Gene #5: '3p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
3P MUTATED	18	38	12	5
3P WILD-TYPE	83	62	134	30

Figure S33. Get High-res Image Gene #5: '3p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q' versus 'CN_CNMF'

P value = 2.17e-35 (Chi-square test), Q value = 9.9e-33

Table S34. Gene #6: '3q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
3Q MUTATED	5	6	77	7	10	0
3Q WILD-TYPE	295	18	75	15	5	1

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

'3q' versus 'METHLYATION_CNMF'

P value = 1.2e-14 (Fisher's exact test), Q value = 4.3e-12

Table S35. Gene #6: '3q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
3Q MUTATED	65	14	10
3Q WILD-TYPE	87	74	150

Figure S35. Get High-res Image Gene #6: '3q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q' versus 'MRNASEQ_CNMF'

P value = 3.28e-21 (Fisher's exact test), Q value = 1.4e-18

Table S36. Gene #6: '3q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
3Q MUTATED	76	14	2	11
3Q WILD-TYPE	98	72	113	119

Figure S36. Get High-res Image Gene #6: '3q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.55e-19 (Fisher's exact test), Q value = 1.4e-16

Table S37. Gene #6: '3q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
3Q MUTATED	89	3	11
3Q WILD-TYPE	150	81	171

Figure S37. Get High-res Image Gene #6: '3q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q' versus 'MIRSEQ_CNMF'

P value = 1.16e-10 (Chi-square test), Q value = 3.6e-08

Table S38. Gene #6: '3q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
3Q MUTATED	57	12	14	3	17
3Q WILD-TYPE	92	126	35	50	99

Figure S38. Get High-res Image Gene #6: '3q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.36e-11 (Fisher's exact test), Q value = 4.3e-09

Table S39. Gene #6: '3q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
3Q MUTATED	4	14	85
3Q WILD-TYPE	9	200	193

Figure S39. Get High-res Image Gene #6: '3q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.23e-05 (Fisher's exact test), Q value = 0.0027

Table S40. Gene #6: '3q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
3Q MUTATED	55	22	10
3Q WILD-TYPE	121	68	106

Figure S40. Get High-res Image Gene #6: '3q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.08e-10 (Fisher's exact test), Q value = 9.4e-08

Table S41. Gene #6: '3q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
3Q MUTATED	27	44	12	4
3Q WILD-TYPE	74	56	134	31

Figure S41. Get High-res Image Gene #6: '3q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p' versus 'MRNA_CHIERARCHICAL'

P value = 0.000595 (Fisher's exact test), Q value = 0.1

Table S42. Gene #7: '4p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	19	19	15
4P MUTATED	2	0	7
4P WILD-TYPE	17	19	8

Figure S42. Get High-res Image Gene #7: '4p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4p' versus 'CN_CNMF'

P value = 9.98e-44 (Chi-square test), Q value = 4.6e-41

Table S43. Gene #7: '4p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
4P MUTATED	4	9	91	5	1	0
4P WILD-TYPE	296	15	61	17	14	1

Figure S43. Get High-res Image Gene #7: '4p' versus Molecular Subtype #3: 'CN_CNMF'

'4p' versus 'METHLYATION_CNMF'

P value = 2.71e-16 (Fisher's exact test), Q value = 1e-13

Table S44. Gene #7: '4p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
4P MUTATED	67	20	8
4P WILD-TYPE	85	68	152

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

'4p' versus 'RPPA_CNMF'

P value = 0.000505 (Chi-square test), Q value = 0.089

Table S45. Gene #7: '4p' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
4P MUTATED	7	10	0	1	1	7
4P WILD-TYPE	34	27	39	11	40	17

Figure S45. Get High-res Image Gene #7: '4p' versus Molecular Subtype #5: 'RPPA_CNMF'

'4p' versus 'MRNASEQ_CNMF'

P value = 3.7e-26 (Fisher's exact test), Q value = 1.6e-23

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
4P MUTATED	87	9	7	7
4P WILD-TYPE	87	77	108	123

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

'4p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.77e-23 (Fisher's exact test), Q value = 2.1e-20

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
4P MUTATED	97	2	11
4P WILD-TYPE	142	82	171

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

'4p' versus 'MIRSEQ_CNMF'

P value = 8.65e-21 (Chi-square test), Q value = 3.6e-18

Table S48. Gene #7: '4p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
4P MUTATED	72	8	12	8	8
4P WILD-TYPE	77	130	37	45	108

Figure S48. Get High-res Image Gene #7: '4p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.18e-17 (Fisher's exact test), Q value = 2.4e-14

Table S49. Gene #7: '4p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
4P MUTATED	2	10	96
4P WILD-TYPE	11	204	182

Figure S49. Get High-res Image Gene #7: '4p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.5e-07 (Fisher's exact test), Q value = 0.00011

Table S50. Gene #7: '4p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
4P MUTATED	62	23	10
4P WILD-TYPE	114	67	106

Figure S50. Get High-res Image Gene #7: '4p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.74e-10 (Fisher's exact test), Q value = 2.6e-07

Table S51. Gene #7: '4p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
4P MUTATED	32	43	12	8
4P WILD-TYPE	69	57	134	27

Figure S51. Get High-res Image Gene #7: '4p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q' versus 'CN_CNMF'

P value = 1.93e-42 (Chi-square test), Q value = 8.9e-40

Table S52. Gene #8: '4q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
4Q MUTATED	3	8	88	5	1	0
4Q WILD-TYPE	297	16	64	17	14	1

Figure S52. Get High-res Image Gene #8: '4q' versus Molecular Subtype #3: 'CN_CNMF'

'4q' versus 'METHLYATION_CNMF'

P value = 1.11e-16 (Fisher's exact test), Q value = 4.2e-14

Table S53. Gene #8: '4q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
4Q MUTATED	66	19	7
4Q WILD-TYPE	86	69	153

Figure S53. Get High-res Image Gene #8: '4q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q' versus 'MRNASEQ_CNMF'

P value = 1.7e-26 (Fisher's exact test), Q value = 7.5e-24

Table S54. Gene #8: '4q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
4Q MUTATED	85	7	6	7
4Q WILD-TYPE	89	79	109	123

Figure S54. Get High-res Image Gene #8: '4q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.83e-21 (Fisher's exact test), Q value = 1.6e-18

Table S55. Gene #8: '4q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
4Q MUTATED	92	2	11
4Q WILD-TYPE	147	82	171

Figure S55. Get High-res Image Gene #8: '4q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q' versus 'MIRSEQ_CNMF'

P value = 2.82e-16 (Chi-square test), Q value = 1.1e-13

Table S56. Gene #8: '4q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
4Q MUTATED	64	9	14	8	8
4Q WILD-TYPE	85	129	35	45	108

Figure S56. Get High-res Image Gene #8: '4q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.59e-16 (Fisher's exact test), Q value = 6e-14

Table S57. Gene #8: '4q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
4Q MUTATED	2	9	92
4Q WILD-TYPE	11	205	186

Figure S57. Get High-res Image Gene #8: '4q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.34e-07 (Fisher's exact test), Q value = 0.00015

Table S58. Gene #8: '4q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
4Q MUTATED	58	25	9
4Q WILD-TYPE	118	65	107

Figure S58. Get High-res Image Gene #8: '4q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.13e-09 (Fisher's exact test), Q value = 6.2e-07

Table S59. Gene #8: '4q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
4Q MUTATED	34	39	11	8
4Q WILD-TYPE	67	61	135	27

Figure S59. Get High-res Image Gene #8: '4q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p' versus 'CN_CNMF'

P value = 5.14e-39 (Chi-square test), Q value = 2.4e-36

Table S60. Gene #9: '5p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
5P MUTATED	3	8	83	8	1	0
5P WILD-TYPE	297	16	69	14	14	1

Figure S60. Get High-res Image Gene #9: '5p' versus Molecular Subtype #3: 'CN_CNMF'

'5p' versus 'METHLYATION_CNMF'

P value = 1.62e-17 (Fisher's exact test), Q value = 6.3e-15

Table S61. Gene #9: '5p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
5P MUTATED	67	11	8
5P WILD-TYPE	85	77	152

Figure S61. Get High-res Image Gene #9: '5p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p' versus 'MRNASEQ_CNMF'

P value = 5.61e-21 (Fisher's exact test), Q value = 2.3e-18

Table S62. Gene #9: '5p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
5P MUTATED	78	9	11	5
5P WILD-TYPE	96	77	104	125

Figure S62. Get High-res Image Gene #9: '5p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.77e-20 (Fisher's exact test), Q value = 1.6e-17

Table S63. Gene #9: '5p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
5P MUTATED	90	3	10
5P WILD-TYPE	149	81	172

Figure S63. Get High-res Image Gene #9: '5p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p' versus 'MIRSEQ_CNMF'

P value = 2.35e-16 (Chi-square test), Q value = 8.8e-14

Table S64. Gene #9: '5p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
5P MUTATED	65	6	9	10	12
5P WILD-TYPE	84	132	40	43	104

Figure S64. Get High-res Image Gene #9: '5p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.16e-14 (Fisher's exact test), Q value = 1.8e-11

Table S65. Gene #9: '5p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
5P MUTATED	3	11	88
5P WILD-TYPE	10	203	190

Figure S65. Get High-res Image Gene #9: '5p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.34e-08 (Fisher's exact test), Q value = 3.6e-06

Table S66. Gene #9: '5p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
5P MUTATED	60	16	7
5P WILD-TYPE	116	74	109

Figure S66. Get High-res Image Gene #9: '5p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.42e-12 (Fisher's exact test), Q value = 1.1e-09

Table S67. Gene #9: '5p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
5P MUTATED	26	44	8	5
5P WILD-TYPE	75	56	138	30

Figure S67. Get High-res Image Gene #9: '5p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q' versus 'CN_CNMF'

P value = 9.45e-36 (Chi-square test), Q value = 4.3e-33

Table S68. Gene #10: '5q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
5Q MUTATED	1	6	75	8	1	0
5Q WILD-TYPE	299	18	77	14	14	1

Figure S68. Get High-res Image Gene #10: '5q' versus Molecular Subtype #3: 'CN_CNMF'

'5q' versus 'METHLYATION_CNMF'

P value = 7.84e-16 (Fisher's exact test), Q value = 2.9e-13

Table S69. Gene #10: '5q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
5Q MUTATED	61	10	7
5Q WILD-TYPE	91	78	153

Figure S69. Get High-res Image Gene #10: '5q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q' versus 'MRNASEQ_CNMF'

P value = 1.82e-18 (Fisher's exact test), Q value = 7.2e-16

Table S70. Gene #10: '5q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
5Q MUTATED	70	8	7	6
5Q WILD-TYPE	104	78	108	124

Figure S70. Get High-res Image Gene #10: '5q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.05e-18 (Fisher's exact test), Q value = 2.4e-15

Table S71. Gene #10: '5q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
5Q MUTATED	80	2	9
5Q WILD-TYPE	159	82	173

Figure S71. Get High-res Image Gene #10: '5q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q' versus 'MIRSEQ_CNMF'

P value = 1.91e-13 (Chi-square test), Q value = 6.6e-11

Table S72. Gene #10: '5q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
5Q MUTATED	55	5	12	9	9
5Q WILD-TYPE	94	133	37	44	107

Figure S72. Get High-res Image Gene #10: '5q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.73e-13 (Fisher's exact test), Q value = 9.4e-11

Table S73. Gene #10: '5q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
5Q MUTATED	1	9	80
5Q WILD-TYPE	12	205	198

Figure S73. Get High-res Image Gene #10: '5q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.44e-07 (Fisher's exact test), Q value = 8.4e-05

Table S74. Gene #10: '5q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
5Q MUTATED	52	16	6
5Q WILD-TYPE	124	74	110

Figure S74. Get High-res Image Gene #10: '5q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.4e-10 (Fisher's exact test), Q value = 7.3e-08

Table S75. Gene #10: '5q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
5Q MUTATED	24	37	6	7
5Q WILD-TYPE	77	63	140	28

Figure S75. Get High-res Image Gene #10: '5q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p' versus 'CN_CNMF'

P value = 1.71e-31 (Chi-square test), Q value = 7.7e-29

Table S76. Gene #11: '6p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
6P MUTATED	5	5	69	2	9	0
6P WILD-TYPE	295	19	83	20	6	1

Figure S76. Get High-res Image Gene #11: '6p' versus Molecular Subtype #3: 'CN_CNMF'

'6p' versus 'METHLYATION_CNMF'

P value = 6.35e-09 (Fisher's exact test), Q value = 1.8e-06

Table S77. Gene #11: '6p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
6P MUTATED	50	16	10
6P WILD-TYPE	102	72	150

Figure S77. Get High-res Image Gene #11: '6p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p' versus 'MRNASEQ_CNMF'

P value = 4.27e-13 (Fisher's exact test), Q value = 1.5e-10

Table S78. Gene #11: '6p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
6P MUTATED	63	6	6	15
6P WILD-TYPE	111	80	109	115

Figure S78. Get High-res Image Gene #11: '6p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.62e-11 (Fisher's exact test), Q value = 1.8e-08

Table S79. Gene #11: '6p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
6P MUTATED	71	3	16
6P WILD-TYPE	168	81	166

Figure S79. Get High-res Image Gene #11: '6p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p' versus 'MIRSEQ_CNMF'

P value = 1.21e-08 (Chi-square test), Q value = 3.3e-06

Table S80. Gene #11: '6p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
6P MUTATED	49	12	12	6	9
6P WILD-TYPE	100	126	37	47	107

Figure S80. Get High-res Image Gene #11: '6p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.48e-09 (Fisher's exact test), Q value = 1.5e-06

Table S81. Gene #11: '6p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
6P MUTATED	2	13	73
6P WILD-TYPE	11	201	205

Figure S81. Get High-res Image Gene #11: '6p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000679 (Fisher's exact test), Q value = 0.11

Table S82. Gene #11: '6p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
6P MUTATED	22	31	15	7
6P WILD-TYPE	79	69	131	28

Figure S82. Get High-res Image Gene #11: '6p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q' versus 'CN_CNMF'

P value = 2.04e-27 (Chi-square test), Q value = 9e-25

Table S83. Gene #12: '6q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
6Q MUTATED	5	5	63	2	8	0
6Q WILD-TYPE	295	19	89	20	7	1

Figure S83. Get High-res Image Gene #12: '6q' versus Molecular Subtype #3: 'CN_CNMF'

'6q' versus 'METHLYATION_CNMF'

P value = 4.8e-07 (Fisher's exact test), Q value = 0.00011

Table S84. Gene #12: '6q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
6Q MUTATED	45	13	11
6Q WILD-TYPE	107	75	149

Figure S84. Get High-res Image Gene #12: '6q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q' versus 'MRNASEQ_CNMF'

P value = 2.27e-10 (Fisher's exact test), Q value = 7e-08

Table S85. Gene #12: '6q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
6Q MUTATED	56	6	6	15
6Q WILD-TYPE	118	80	109	115

Figure S85. Get High-res Image Gene #12: '6q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.01e-09 (Fisher's exact test), Q value = 1.4e-06

Table S86. Gene #12: '6q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
6Q MUTATED	64	3	16
6Q WILD-TYPE	175	81	166

Figure S86. Get High-res Image Gene #12: '6q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q' versus 'MIRSEQ_CNMF'

P value = 1.94e-06 (Chi-square test), Q value = 0.00045

Table S87. Gene #12: '6q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
6Q MUTATED	42	12	12	7	8
6Q WILD-TYPE	107	126	37	46	108

Figure S87. Get High-res Image Gene #12: '6q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.08e-07 (Fisher's exact test), Q value = 5.2e-05

Table S88. Gene #12: '6q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
6Q MUTATED	2	13	66
6Q WILD-TYPE	11	201	212

Figure S88. Get High-res Image Gene #12: '6q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p' versus 'CN_CNMF'

P value = 9.08e-27 (Chi-square test), Q value = 4e-24

Table S89. Gene #13: '7p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
7P MUTATED	11	15	64	8	7	0
7P WILD-TYPE	289	9	88	14	8	1

Figure S89. Get High-res Image Gene #13: '7p' versus Molecular Subtype #3: 'CN_CNMF'

'7p' versus 'METHLYATION_CNMF'

P value = 0.000122 (Fisher's exact test), Q value = 0.024

Table S90. Gene #13: '7p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
7P MUTATED	49	13	22
7P WILD-TYPE	103	75	138

Figure S90. Get High-res Image Gene #13: '7p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p' versus 'MRNASEQ_CNMF'

P value = 2.47e-11 (Fisher's exact test), Q value = 7.8e-09

Table S91. Gene #13: '7p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
7P MUTATED	67	6	15	15
7P WILD-TYPE	107	80	100	115

Figure S91. Get High-res Image Gene #13: '7p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.12e-07 (Fisher's exact test), Q value = 2.9e-05

Table S92. Gene #13: '7p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
7P MUTATED	74	7	22
7P WILD-TYPE	165	77	160

Figure S92. Get High-res Image Gene #13: '7p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p' versus 'MIRSEQ_CNMF'

P value = 3.46e-06 (Chi-square test), Q value = 0.00079

Table S93. Gene #13: '7p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
7P MUTATED	52	16	11	11	14
7P WILD-TYPE	97	122	38	42	102

Figure S93. Get High-res Image Gene #13: '7p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.81e-05 (Fisher's exact test), Q value = 0.0039

Table S94. Gene #13: '7p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
7P MUTATED	3	24	77
7P WILD-TYPE	10	190	201

Figure S94. Get High-res Image Gene #13: '7p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q' versus 'CN_CNMF'

P value = 1.85e-26 (Chi-square test), Q value = 8.1e-24

Table S95. Gene #14: '7q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
7Q MUTATED	11	16	61	6	7	0
7Q WILD-TYPE	289	8	91	16	8	1

Figure S95. Get High-res Image Gene #14: '7q' versus Molecular Subtype #3: 'CN_CNMF'

'7q' versus 'METHLYATION_CNMF'

P value = 1.48e-05 (Fisher's exact test), Q value = 0.0032

Table S96. Gene #14: '7q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
7Q MUTATED	50	11	21
7Q WILD-TYPE	102	77	139

Figure S96. Get High-res Image Gene #14: '7q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q' versus 'MRNASEQ_CNMF'

P value = 9.75e-12 (Fisher's exact test), Q value = 3.1e-09

Table S97. Gene #14: '7q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
7Q MUTATED	66	6	13	14
7Q WILD-TYPE	108	80	102	116

Figure S97. Get High-res Image Gene #14: '7q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.29e-07 (Fisher's exact test), Q value = 8.1e-05

Table S98. Gene #14: '7q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
7Q MUTATED	71	7	21
7Q WILD-TYPE	168	77	161

Figure S98. Get High-res Image Gene #14: '7q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q' versus 'MIRSEQ_CNMF'

P value = 3.47e-07 (Chi-square test), Q value = 8.4e-05

Table S99. Gene #14: '7q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
7Q MUTATED	53	14	9	11	14
7Q WILD-TYPE	96	124	40	42	102

Figure S99. Get High-res Image Gene #14: '7q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.2e-06 (Fisher's exact test), Q value = 0.00051

Table S100. Gene #14: '7q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
7Q MUTATED	1	22	78
7Q WILD-TYPE	12	192	200

Figure S100. Get High-res Image Gene #14: '7q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p' versus 'CN_CNMF'

P value = 1.31e-36 (Chi-square test), Q value = 6e-34

Table S101. Gene #15: '8p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
8P MUTATED	42	8	107	15	15	1
8P WILD-TYPE	258	16	45	7	0	0

Figure S101. Get High-res Image Gene #15: '8p' versus Molecular Subtype #3: 'CN_CNMF'

'8p' versus 'METHLYATION_CNMF'

P value = 2.92e-08 (Fisher's exact test), Q value = 7.6e-06

Table S102. Gene #15: '8p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
8P MUTATED	88	32	41
8P WILD-TYPE	64	56	119

Figure S102. Get High-res Image Gene #15: '8p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p' versus 'RPPA_CNMF'

P value = 0.000359 (Chi-square test), Q value = 0.064

Table S103. Gene #15: '8p' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
8P MUTATED	12	12	7	2	2	13
8P WILD-TYPE	29	25	32	10	39	11

Figure S103. Get High-res Image Gene #15: '8p' versus Molecular Subtype #5: 'RPPA_CNMF'

'8p' versus 'MRNASEQ_CNMF'

P value = 3.9e-15 (Fisher's exact test), Q value = 1.4e-12

Table S104. Gene #15: '8p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
8P MUTATED	107	19	30	29
8P WILD-TYPE	67	67	85	101

Figure S104. Get High-res Image Gene #15: '8p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.12e-13 (Fisher's exact test), Q value = 1.4e-10

Table S105. Gene #15: '8p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
8P MUTATED	128	16	41
8P WILD-TYPE	111	68	141

Figure S105. Get High-res Image Gene #15: '8p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p' versus 'MIRSEQ_CNMF'

P value = 2.73e-12 (Chi-square test), Q value = 9e-10

Table S106. Gene #15: '8p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
8P MUTATED	90	32	17	21	24
8P WILD-TYPE	59	106	32	32	92

Figure S106. Get High-res Image Gene #15: '8p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.66e-09 (Fisher's exact test), Q value = 1e-06

Table S107. Gene #15: '8p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
8P MUTATED	5	46	133
8P WILD-TYPE	8	168	145

Figure S107. Get High-res Image Gene #15: '8p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.23e-05 (Fisher's exact test), Q value = 0.018

Table S108. Gene #15: '8p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
8P MUTATED	88	37	29
8P WILD-TYPE	88	53	87

Figure S108. Get High-res Image Gene #15: '8p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.84e-05 (Fisher's exact test), Q value = 0.0039

Table S109. Gene #15: '8p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
8P MUTATED	42	58	39	15
8P WILD-TYPE	59	42	107	20

Figure S109. Get High-res Image Gene #15: '8p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q' versus 'CN_CNMF'

P value = 6.68e-31 (Chi-square test), Q value = 3e-28

Table S110. Gene #16: '8q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
8Q MUTATED	41	8	93	16	15	1
8Q WILD-TYPE	259	16	59	6	0	0

Figure S110. Get High-res Image Gene #16: '8q' versus Molecular Subtype #3: 'CN_CNMF'

'8q' versus 'METHLYATION_CNMF'

P value = 0.000203 (Fisher's exact test), Q value = 0.038

Table S111. Gene #16: '8q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
8Q MUTATED	75	28	44
8Q WILD-TYPE	77	60	116

Figure S111. Get High-res Image Gene #16: '8q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q' versus 'RPPA_CNMF'

P value = 0.000197 (Chi-square test), Q value = 0.037

Table S112. Gene #16: '8q' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
8Q MUTATED	9	14	8	2	2	13
8Q WILD-TYPE	32	23	31	10	39	11

Figure S112. Get High-res Image Gene #16: '8q' versus Molecular Subtype #5: 'RPPA_CNMF'

'8q' versus 'MRNASEQ_CNMF'

P value = 6.16e-09 (Fisher's exact test), Q value = 1.7e-06

Table S113. Gene #16: '8q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
8Q MUTATED	92	19	30	31
8Q WILD-TYPE	82	67	85	99

Figure S113. Get High-res Image Gene #16: '8q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.06e-08 (Fisher's exact test), Q value = 2.9e-06

Table S114. Gene #16: '8q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
8Q MUTATED	113	15	44
8Q WILD-TYPE	126	69	138

Figure S114. Get High-res Image Gene #16: '8q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q' versus 'MIRSEQ_CNMF'

P value = 2.18e-08 (Chi-square test), Q value = 5.8e-06

Table S115. Gene #16: '8q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
8Q MUTATED	79	35	14	20	22
8Q WILD-TYPE	70	103	35	33	94

Figure S115. Get High-res Image Gene #16: '8q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.02e-05 (Fisher's exact test), Q value = 0.0023

Table S116. Gene #16: '8q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
8Q MUTATED	4	48	118
8Q WILD-TYPE	9	166	160

Figure S116. Get High-res Image Gene #16: '8q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000605 (Fisher's exact test), Q value = 0.1

Table S117. Gene #16: '8q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
8Q MUTATED	83	27	31
8Q WILD-TYPE	93	63	85

Figure S117. Get High-res Image Gene #16: '8q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p' versus 'MRNA_CNMF'

P value = 0.000601 (Fisher's exact test), Q value = 0.1

Table S118. Gene #17: '9p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
9P MUTATED	2	9	0	0
9P WILD-TYPE	12	8	12	10

Figure S118. Get High-res Image Gene #17: '9p' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p' versus 'MRNA_CHIERARCHICAL'

P value = 3.97e-05 (Fisher's exact test), Q value = 0.0083

Table S119. Gene #17: '9p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	19	19	15
9P MUTATED	2	0	9
9P WILD-TYPE	17	19	6

Figure S119. Get High-res Image Gene #17: '9p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p' versus 'CN_CNMF'

P value = 4.45e-48 (Chi-square test), Q value = 2.1e-45

Table S120. Gene #17: '9p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
9P MUTATED	6	8	99	7	0	0
9P WILD-TYPE	294	16	53	15	15	1

Figure S120. Get High-res Image Gene #17: '9p' versus Molecular Subtype #3: 'CN_CNMF'

'9p' versus 'METHLYATION_CNMF'

P value = 1.57e-13 (Fisher's exact test), Q value = 5.5e-11

Table S121. Gene #17: '9p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
9P MUTATED	67	24	12
9P WILD-TYPE	85	64	148

Figure S121. Get High-res Image Gene #17: '9p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p' versus 'RPPA_CNMF'

P value = 0.000613 (Chi-square test), Q value = 0.1

Table S122. Gene #17: '9p' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
9P MUTATED	8	12	1	1	1	6
9P WILD-TYPE	33	25	38	11	40	18

Figure S122. Get High-res Image Gene #17: '9p' versus Molecular Subtype #5: 'RPPA_CNMF'

'9p' versus 'MRNASEQ_CNMF'

P value = 7.1e-21 (Fisher's exact test), Q value = 3e-18

Table S123. Gene #17: '9p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
9P MUTATED	87	9	10	14
9P WILD-TYPE	87	77	105	116

Figure S123. Get High-res Image Gene #17: '9p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.36e-18 (Fisher's exact test), Q value = 5.4e-16

Table S124. Gene #17: '9p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
9P MUTATED	99	5	16
9P WILD-TYPE	140	79	166

Figure S124. Get High-res Image Gene #17: '9p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p' versus 'MIRSEQ_CNMF'

P value = 5.15e-20 (Chi-square test), Q value = 2.1e-17

Table S125. Gene #17: '9p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
9P MUTATED	76	14	10	9	8
9P WILD-TYPE	73	124	39	44	108

Figure S125. Get High-res Image Gene #17: '9p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.85e-12 (Fisher's exact test), Q value = 1.9e-09

Table S126. Gene #17: '9p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
9P MUTATED	3	18	96
9P WILD-TYPE	10	196	182

Figure S126. Get High-res Image Gene #17: '9p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000391 (Fisher's exact test), Q value = 0.07

Table S127. Gene #17: '9p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
9P MUTATED	60	24	16
9P WILD-TYPE	116	66	100

Figure S127. Get High-res Image Gene #17: '9p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.39e-06 (Fisher's exact test), Q value = 0.0012

Table S128. Gene #17: '9p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
9P MUTATED	29	43	20	8
9P WILD-TYPE	72	57	126	27

Figure S128. Get High-res Image Gene #17: '9p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q' versus 'MRNA_CNMF'

P value = 2.35e-05 (Fisher's exact test), Q value = 0.005

Table S129. Gene #18: '9q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
9Q MUTATED	0	9	0	0
9Q WILD-TYPE	14	8	12	10

Figure S129. Get High-res Image Gene #18: '9q' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q' versus 'MRNA_CHIERARCHICAL'

P value = 1.13e-06 (Fisher's exact test), Q value = 0.00027

Table S130. Gene #18: '9q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	19	19	15
9Q MUTATED	0	0	9
9Q WILD-TYPE	19	19	6

Figure S130. Get High-res Image Gene #18: '9q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9q' versus 'CN_CNMF'

P value = 3.08e-51 (Chi-square test), Q value = 1.5e-48

Table S131. Gene #18: '9q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
9Q MUTATED	6	7	103	10	0	0
9Q WILD-TYPE	294	17	49	12	15	1

Figure S131. Get High-res Image Gene #18: '9q' versus Molecular Subtype #3: 'CN_CNMF'

'9q' versus 'METHLYATION_CNMF'

P value = 5.93e-12 (Fisher's exact test), Q value = 1.9e-09

Table S132. Gene #18: '9q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
9Q MUTATED	69	25	16
9Q WILD-TYPE	83	63	144

Figure S132. Get High-res Image Gene #18: '9q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q' versus 'RPPA_CNMF'

P value = 0.000337 (Chi-square test), Q value = 0.061

Table S133. Gene #18: '9q' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
9Q MUTATED	7	13	1	2	1	6
9Q WILD-TYPE	34	24	38	10	40	18

Figure S133. Get High-res Image Gene #18: '9q' versus Molecular Subtype #5: 'RPPA_CNMF'

'9q' versus 'MRNASEQ_CNMF'

P value = 5.35e-22 (Fisher's exact test), Q value = 2.3e-19

Table S134. Gene #18: '9q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
9Q MUTATED	91	9	11	15
9Q WILD-TYPE	83	77	104	115

Figure S134. Get High-res Image Gene #18: '9q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.88e-20 (Fisher's exact test), Q value = 2.8e-17

Table S135. Gene #18: '9q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
9Q MUTATED	104	5	17
9Q WILD-TYPE	135	79	165

Figure S135. Get High-res Image Gene #18: '9q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q' versus 'MIRSEQ_CNMF'

P value = 5.18e-25 (Chi-square test), Q value = 2.3e-22

Table S136. Gene #18: '9q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
9Q MUTATED	83	15	11	9	5
9Q WILD-TYPE	66	123	38	44	111

Figure S136. Get High-res Image Gene #18: '9q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.54e-12 (Fisher's exact test), Q value = 5.1e-10

Table S137. Gene #18: '9q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
9Q MUTATED	4	19	100
9Q WILD-TYPE	9	195	178

Figure S137. Get High-res Image Gene #18: '9q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000178 (Fisher's exact test), Q value = 0.034

Table S138. Gene #18: '9q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
9Q MUTATED	64	26	17
9Q WILD-TYPE	112	64	99

Figure S138. Get High-res Image Gene #18: '9q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.34e-06 (Fisher's exact test), Q value = 0.0014

Table S139. Gene #18: '9q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
9Q MUTATED	28	46	23	10
9Q WILD-TYPE	73	54	123	25

Figure S139. Get High-res Image Gene #18: '9q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p' versus 'CN_CNMF'

P value = 4.15e-14 (Chi-square test), Q value = 1.5e-11

Table S140. Gene #19: '10p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
10P MUTATED	47	15	75	8	7	0
10P WILD-TYPE	253	9	77	14	8	1

Figure S140. Get High-res Image Gene #19: '10p' versus Molecular Subtype #3: 'CN_CNMF'

'10p' versus 'MRNASEQ_CNMF'

P value = 0.000314 (Fisher's exact test), Q value = 0.057

Table S141. Gene #19: '10p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
10P MUTATED	71	16	25	37
10P WILD-TYPE	103	70	90	93

Figure S141. Get High-res Image Gene #19: '10p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000289 (Fisher's exact test), Q value = 0.053

Table S142. Gene #19: '10p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
10P MUTATED	85	11	53
10P WILD-TYPE	154	73	129

Figure S142. Get High-res Image Gene #19: '10p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q' versus 'CN_CNMF'

P value = 1.52e-12 (Chi-square test), Q value = 5.1e-10

Table S143. Gene #20: '10q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
10Q MUTATED	47	17	66	6	6	0
10Q WILD-TYPE	253	7	86	16	9	1

Figure S143. Get High-res Image Gene #20: '10q' versus Molecular Subtype #3: 'CN_CNMF'

'10q' versus 'MRNASEQ_CNMF'

P value = 0.001 (Fisher's exact test), Q value = 0.16

Table S144. Gene #20: '10q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
10Q MUTATED	64	13	25	37
10Q WILD-TYPE	110	73	90	93

Figure S144. Get High-res Image Gene #20: '10q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p' versus 'CN_CNMF'

P value = 5.99e-36 (Chi-square test), Q value = 2.7e-33

Table S145. Gene #21: '11p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
11P MUTATED	1	11	74	6	1	0
11P WILD-TYPE	299	13	78	16	14	1

Figure S145. Get High-res Image Gene #21: '11p' versus Molecular Subtype #3: 'CN_CNMF'

'11p' versus 'METHLYATION_CNMF'

P value = 6.09e-12 (Fisher's exact test), Q value = 2e-09

Table S146. Gene #21: '11p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
11P MUTATED	55	21	8
11P WILD-TYPE	97	67	152

Figure S146. Get High-res Image Gene #21: '11p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p' versus 'MRNASEQ_CNMF'

P value = 3.44e-17 (Fisher's exact test), Q value = 1.3e-14

Table S147. Gene #21: '11p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
11P MUTATED	70	7	7	9
11P WILD-TYPE	104	79	108	121

Figure S147. Get High-res Image Gene #21: '11p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.93e-16 (Fisher's exact test), Q value = 7.3e-14

Table S148. Gene #21: '11p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
11P MUTATED	79	1	13
11P WILD-TYPE	160	83	169

Figure S148. Get High-res Image Gene #21: '11p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p' versus 'MIRSEQ_CNMF'

P value = 1.51e-14 (Chi-square test), Q value = 5.4e-12

Table S149. Gene #21: '11p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
11P MUTATED	59	11	9	8	5
11P WILD-TYPE	90	127	40	45	111

Figure S149. Get High-res Image Gene #21: '11p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.44e-09 (Fisher's exact test), Q value = 9.9e-07

Table S150. Gene #21: '11p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
11P MUTATED	2	14	76
11P WILD-TYPE	11	200	202

Figure S150. Get High-res Image Gene #21: '11p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.41e-05 (Fisher's exact test), Q value = 0.019

Table S151. Gene #21: '11p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
11P MUTATED	54	16	12
11P WILD-TYPE	122	74	104

Figure S151. Get High-res Image Gene #21: '11p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.84e-08 (Fisher's exact test), Q value = 7.4e-06

Table S152. Gene #21: '11p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
11P MUTATED	22	42	14	4
11P WILD-TYPE	79	58	132	31

Figure S152. Get High-res Image Gene #21: '11p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q' versus 'CN_CNMF'

P value = 2.53e-32 (Chi-square test), Q value = 1.1e-29

Table S153. Gene #22: '11q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
11Q MUTATED	1	12	66	7	1	0
11Q WILD-TYPE	299	12	86	15	14	1

Figure S153. Get High-res Image Gene #22: '11q' versus Molecular Subtype #3: 'CN_CNMF'

'11q' versus 'METHLYATION_CNMF'

P value = 8.06e-11 (Fisher's exact test), Q value = 2.5e-08

Table S154. Gene #22: '11q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
11Q MUTATED	54	18	9
11Q WILD-TYPE	98	70	151

Figure S154. Get High-res Image Gene #22: '11q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q' versus 'MRNASEQ_CNMF'

P value = 1.28e-14 (Fisher's exact test), Q value = 4.6e-12

Table S155. Gene #22: '11q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
11Q MUTATED	64	6	6	11
11Q WILD-TYPE	110	80	109	119

Figure S155. Get High-res Image Gene #22: '11q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.11e-14 (Fisher's exact test), Q value = 3.2e-11

Table S156. Gene #22: '11q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
11Q MUTATED	72	1	14
11Q WILD-TYPE	167	83	168

Figure S156. Get High-res Image Gene #22: '11q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q' versus 'MIRSEQ_CNMF'

P value = 1.86e-13 (Chi-square test), Q value = 6.5e-11

Table S157. Gene #22: '11q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
11Q MUTATED	56	13	6	8	4
11Q WILD-TYPE	93	125	43	45	112

Figure S157. Get High-res Image Gene #22: '11q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.2e-07 (Fisher's exact test), Q value = 5.5e-05

Table S158. Gene #22: '11q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
11Q MUTATED	2	15	70
11Q WILD-TYPE	11	199	208

Figure S158. Get High-res Image Gene #22: '11q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000127 (Fisher's exact test), Q value = 0.024

Table S159. Gene #22: '11q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
11Q MUTATED	53	13	13
11Q WILD-TYPE	123	77	103

Figure S159. Get High-res Image Gene #22: '11q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.48e-10 (Fisher's exact test), Q value = 1.1e-07

Table S160. Gene #22: '11q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
11Q MUTATED	17	45	14	3
11Q WILD-TYPE	84	55	132	32

Figure S160. Get High-res Image Gene #22: '11q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p' versus 'CN_CNMF'

P value = 1.26e-27 (Chi-square test), Q value = 5.6e-25

Table S161. Gene #23: '12p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
12P MUTATED	12	9	74	10	2	0
12P WILD-TYPE	288	15	78	12	13	1

Figure S161. Get High-res Image Gene #23: '12p' versus Molecular Subtype #3: 'CN_CNMF'

'12p' versus 'METHLYATION_CNMF'

P value = 5.35e-10 (Fisher's exact test), Q value = 1.6e-07

Table S162. Gene #23: '12p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
12P MUTATED	55	20	11
12P WILD-TYPE	97	68	149

Figure S162. Get High-res Image Gene #23: '12p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p' versus 'MRNASEQ_CNMF'

P value = 2.46e-15 (Fisher's exact test), Q value = 9.1e-13

Table S163. Gene #23: '12p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
12P MUTATED	74	10	9	13
12P WILD-TYPE	100	76	106	117

Figure S163. Get High-res Image Gene #23: '12p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.29e-11 (Fisher's exact test), Q value = 4.1e-09

Table S164. Gene #23: '12p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
12P MUTATED	82	6	18
12P WILD-TYPE	157	78	164

Figure S164. Get High-res Image Gene #23: '12p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p' versus 'MIRSEQ_CNMF'

P value = 1.49e-09 (Chi-square test), Q value = 4.4e-07

Table S165. Gene #23: '12p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
12P MUTATED	56	12	15	8	14
12P WILD-TYPE	93	126	34	45	102

Figure S165. Get High-res Image Gene #23: '12p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.42e-08 (Fisher's exact test), Q value = 1.4e-05

Table S166. Gene #23: '12p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
12P MUTATED	0	22	83
12P WILD-TYPE	13	192	195

Figure S166. Get High-res Image Gene #23: '12p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.47e-07 (Fisher's exact test), Q value = 6.2e-05

Table S167. Gene #23: '12p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
12P MUTATED	59	15	9
12P WILD-TYPE	117	75	107

Figure S167. Get High-res Image Gene #23: '12p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.56e-08 (Fisher's exact test), Q value = 6.7e-06

Table S168. Gene #23: '12p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
12P MUTATED	23	41	12	7
12P WILD-TYPE	78	59	134	28

Figure S168. Get High-res Image Gene #23: '12p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q' versus 'CN_CNMF'

P value = 7.71e-18 (Chi-square test), Q value = 3e-15

Table S169. Gene #24: '12q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
12Q MUTATED	12	8	53	10	2	0
12Q WILD-TYPE	288	16	99	12	13	1

Figure S169. Get High-res Image Gene #24: '12q' versus Molecular Subtype #3: 'CN_CNMF'

'12q' versus 'METHLYATION_CNMF'

P value = 4.22e-07 (Fisher's exact test), Q value = 1e-04

Table S170. Gene #24: '12q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
12Q MUTATED	42	16	9
12Q WILD-TYPE	110	72	151

Figure S170. Get High-res Image Gene #24: '12q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q' versus 'MRNASEQ_CNMF'

P value = 2.48e-10 (Fisher's exact test), Q value = 7.6e-08

Table S171. Gene #24: '12q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
12Q MUTATED	57	9	7	11
12Q WILD-TYPE	117	77	108	119

Figure S171. Get High-res Image Gene #24: '12q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.04e-08 (Fisher's exact test), Q value = 5.5e-06

Table S172. Gene #24: '12q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
12Q MUTATED	64	4	16
12Q WILD-TYPE	175	80	166

Figure S172. Get High-res Image Gene #24: '12q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q' versus 'MIRSEQ_CNMF'

P value = 6.57e-05 (Chi-square test), Q value = 0.013

Table S173. Gene #24: '12q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
12Q MUTATED	39	10	13	7	14
12Q WILD-TYPE	110	128	36	46	102

Figure S173. Get High-res Image Gene #24: '12q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.93e-06 (Fisher's exact test), Q value = 0.002

Table S174. Gene #24: '12q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
12Q MUTATED	0	18	65
12Q WILD-TYPE	13	196	213

Figure S174. Get High-res Image Gene #24: '12q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.65e-05 (Fisher's exact test), Q value = 0.0056

Table S175. Gene #24: '12q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
12Q MUTATED	45	12	7
12Q WILD-TYPE	131	78	109

Figure S175. Get High-res Image Gene #24: '12q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.57e-06 (Fisher's exact test), Q value = 0.001

Table S176. Gene #24: '12q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
12Q MUTATED	19	31	9	5
12Q WILD-TYPE	82	69	137	30

Figure S176. Get High-res Image Gene #24: '12q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q' versus 'CN_CNMF'

P value = 1.6e-39 (Chi-square test), Q value = 7.4e-37

Table S177. Gene #25: '13q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
13Q MUTATED	6	9	88	9	2	0
13Q WILD-TYPE	294	15	64	13	13	1

Figure S177. Get High-res Image Gene #25: '13q' versus Molecular Subtype #3: 'CN_CNMF'

'13q' versus 'METHLYATION_CNMF'

P value = 1.07e-10 (Fisher's exact test), Q value = 3.3e-08

Table S178. Gene #25: '13q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
13Q MUTATED	60	25	13
13Q WILD-TYPE	92	63	147

Figure S178. Get High-res Image Gene #25: '13q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q' versus 'MRNASEQ_CNMF'

P value = 2.12e-16 (Fisher's exact test), Q value = 8e-14

Table S179. Gene #25: '13q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
13Q MUTATED	79	7	12	16
13Q WILD-TYPE	95	79	103	114

Figure S179. Get High-res Image Gene #25: '13q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.06e-17 (Fisher's exact test), Q value = 2.3e-14

Table S180. Gene #25: '13q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
13Q MUTATED	91	1	22
13Q WILD-TYPE	148	83	160

Figure S180. Get High-res Image Gene #25: '13q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q' versus 'MIRSEQ_CNMF'

P value = 4.8e-14 (Chi-square test), Q value = 1.7e-11

Table S181. Gene #25: '13q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
13Q MUTATED	67	16	8	13	9
13Q WILD-TYPE	82	122	41	40	107

Figure S181. Get High-res Image Gene #25: '13q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.05e-11 (Fisher's exact test), Q value = 1.9e-08

Table S182. Gene #25: '13q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
13Q MUTATED	5	18	90
13Q WILD-TYPE	8	196	188

Figure S182. Get High-res Image Gene #25: '13q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.18e-05 (Fisher's exact test), Q value = 0.016

Table S183. Gene #25: '13q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
13Q MUTATED	28	41	22	7
13Q WILD-TYPE	73	59	124	28

Figure S183. Get High-res Image Gene #25: '13q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q' versus 'CN_CNMF'

P value = 3.2e-32 (Chi-square test), Q value = 1.4e-29

Table S184. Gene #26: '14q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
14Q MUTATED	4	7	75	5	4	0
14Q WILD-TYPE	296	17	77	17	11	1

Figure S184. Get High-res Image Gene #26: '14q' versus Molecular Subtype #3: 'CN_CNMF'

'14q' versus 'METHLYATION_CNMF'

P value = 2.8e-13 (Fisher's exact test), Q value = 9.6e-11

Table S185. Gene #26: '14q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
14Q MUTATED	58	13	8
14Q WILD-TYPE	94	75	152

Figure S185. Get High-res Image Gene #26: '14q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q' versus 'MRNASEQ_CNMF'

P value = 1.25e-25 (Fisher's exact test), Q value = 5.5e-23

Table S186. Gene #26: '14q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
14Q MUTATED	78	2	4	10
14Q WILD-TYPE	96	84	111	120

Figure S186. Get High-res Image Gene #26: '14q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.88e-19 (Fisher's exact test), Q value = 1.2e-16

Table S187. Gene #26: '14q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
14Q MUTATED	82	0	12
14Q WILD-TYPE	157	84	170

Figure S187. Get High-res Image Gene #26: '14q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q' versus 'MIRSEQ_CNMF'

P value = 2.54e-13 (Chi-square test), Q value = 8.7e-11

Table S188. Gene #26: '14q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
14Q MUTATED	58	9	9	9	8
14Q WILD-TYPE	91	129	40	44	108

Figure S188. Get High-res Image Gene #26: '14q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.03e-13 (Fisher's exact test), Q value = 3.6e-11

Table S189. Gene #26: '14q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
14Q MUTATED	2	9	82
14Q WILD-TYPE	11	205	196

Figure S189. Get High-res Image Gene #26: '14q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.48e-05 (Fisher's exact test), Q value = 0.0032

Table S190. Gene #26: '14q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
14Q MUTATED	54	16	10
14Q WILD-TYPE	122	74	106

Figure S190. Get High-res Image Gene #26: '14q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.79e-08 (Fisher's exact test), Q value = 1.2e-05

Table S191. Gene #26: '14q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
14Q MUTATED	23	39	11	7
14Q WILD-TYPE	78	61	135	28

Figure S191. Get High-res Image Gene #26: '14q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q' versus 'MRNA_CNMF'

P value = 0.000567 (Fisher's exact test), Q value = 0.099

Table S192. Gene #27: '15q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
15Q MUTATED	0	7	0	0
15Q WILD-TYPE	14	10	12	10

Figure S192. Get High-res Image Gene #27: '15q' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q' versus 'MRNA_CHIERARCHICAL'

P value = 4.17e-05 (Fisher's exact test), Q value = 0.0086

Table S193. Gene #27: '15q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	19	19	15
15Q MUTATED	0	0	7
15Q WILD-TYPE	19	19	8

Figure S193. Get High-res Image Gene #27: '15q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'15q' versus 'CN_CNMF'

P value = 1.47e-44 (Chi-square test), Q value = 6.9e-42

Table S194. Gene #27: '15q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
15Q MUTATED	5	5	91	11	0	0
15Q WILD-TYPE	295	19	61	11	15	1

Figure S194. Get High-res Image Gene #27: '15q' versus Molecular Subtype #3: 'CN_CNMF'

'15q' versus 'METHLYATION_CNMF'

P value = 4.5e-13 (Fisher's exact test), Q value = 1.5e-10

Table S195. Gene #27: '15q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
15Q MUTATED	64	23	11
15Q WILD-TYPE	88	65	149

Figure S195. Get High-res Image Gene #27: '15q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q' versus 'RPPA_CNMF'

P value = 0.00104 (Chi-square test), Q value = 0.17

Table S196. Gene #27: '15q' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
15Q MUTATED	2	11	2	1	1	4
15Q WILD-TYPE	39	26	37	11	40	20

Figure S196. Get High-res Image Gene #27: '15q' versus Molecular Subtype #5: 'RPPA_CNMF'

'15q' versus 'MRNASEQ_CNMF'

P value = 8.41e-23 (Fisher's exact test), Q value = 3.6e-20

Table S197. Gene #27: '15q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
15Q MUTATED	85	6	12	9
15Q WILD-TYPE	89	80	103	121

Figure S197. Get High-res Image Gene #27: '15q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.75e-22 (Fisher's exact test), Q value = 3.3e-19

Table S198. Gene #27: '15q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
15Q MUTATED	97	2	13
15Q WILD-TYPE	142	82	169

Figure S198. Get High-res Image Gene #27: '15q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q' versus 'MIRSEQ_CNMF'

P value = 9.68e-20 (Chi-square test), Q value = 4e-17

Table S199. Gene #27: '15q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
15Q MUTATED	71	10	13	10	6
15Q WILD-TYPE	78	128	36	43	110

Figure S199. Get High-res Image Gene #27: '15q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.97e-15 (Fisher's exact test), Q value = 1.5e-12

Table S200. Gene #27: '15q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
15Q MUTATED	4	12	94
15Q WILD-TYPE	9	202	184

Figure S200. Get High-res Image Gene #27: '15q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.05e-06 (Fisher's exact test), Q value = 7e-04

Table S201. Gene #27: '15q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
15Q MUTATED	64	19	13
15Q WILD-TYPE	112	71	103

Figure S201. Get High-res Image Gene #27: '15q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.79e-08 (Fisher's exact test), Q value = 9.8e-06

Table S202. Gene #27: '15q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
15Q MUTATED	26	46	17	7
15Q WILD-TYPE	75	54	129	28

Figure S202. Get High-res Image Gene #27: '15q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p' versus 'MRNA_CNMF'

P value = 0.000567 (Fisher's exact test), Q value = 0.099

Table S203. Gene #28: '16p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
16P MUTATED	0	7	0	0
16P WILD-TYPE	14	10	12	10

Figure S203. Get High-res Image Gene #28: '16p' versus Molecular Subtype #1: 'MRNA_CNMF'

'16p' versus 'MRNA_CHIERARCHICAL'

P value = 4.17e-05 (Fisher's exact test), Q value = 0.0086

Table S204. Gene #28: '16p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	19	19	15
16P MUTATED	0	0	7
16P WILD-TYPE	19	19	8

Figure S204. Get High-res Image Gene #28: '16p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16p' versus 'CN_CNMF'

P value = 5.59e-45 (Chi-square test), Q value = 2.6e-42

Table S205. Gene #28: '16p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
16P MUTATED	6	6	96	6	2	0
16P WILD-TYPE	294	18	56	16	13	1

Figure S205. Get High-res Image Gene #28: '16p' versus Molecular Subtype #3: 'CN_CNMF'

'16p' versus 'METHLYATION_CNMF'

P value = 2.44e-12 (Fisher's exact test), Q value = 8.1e-10

Table S206. Gene #28: '16p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
16P MUTATED	67	23	14
16P WILD-TYPE	85	65	146

Figure S206. Get High-res Image Gene #28: '16p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p' versus 'MRNASEQ_CNMF'

P value = 1.17e-22 (Fisher's exact test), Q value = 5e-20

Table S207. Gene #28: '16p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
16P MUTATED	87	7	11	11
16P WILD-TYPE	87	79	104	119

Figure S207. Get High-res Image Gene #28: '16p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.66e-18 (Fisher's exact test), Q value = 3.8e-15

Table S208. Gene #28: '16p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
16P MUTATED	95	3	18
16P WILD-TYPE	144	81	164

Figure S208. Get High-res Image Gene #28: '16p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p' versus 'MIRSEQ_CNMF'

P value = 2.3e-17 (Chi-square test), Q value = 8.9e-15

Table S209. Gene #28: '16p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
16P MUTATED	71	13	12	8	9
16P WILD-TYPE	78	125	37	45	107

Figure S209. Get High-res Image Gene #28: '16p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.63e-11 (Fisher's exact test), Q value = 1.8e-08

Table S210. Gene #28: '16p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
16P MUTATED	3	18	92
16P WILD-TYPE	10	196	186

Figure S210. Get High-res Image Gene #28: '16p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.35e-05 (Fisher's exact test), Q value = 0.017

Table S211. Gene #28: '16p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
16P MUTATED	58	28	14
16P WILD-TYPE	118	62	102

Figure S211. Get High-res Image Gene #28: '16p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.67e-07 (Fisher's exact test), Q value = 6.6e-05

Table S212. Gene #28: '16p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
16P MUTATED	35	41	17	7
16P WILD-TYPE	66	59	129	28

Figure S212. Get High-res Image Gene #28: '16p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q' versus 'MRNA_CNMF'

P value = 0.000771 (Fisher's exact test), Q value = 0.13

Table S213. Gene #29: '16q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
16Q MUTATED	0	8	1	0
16Q WILD-TYPE	14	9	11	10

Figure S213. Get High-res Image Gene #29: '16q' versus Molecular Subtype #1: 'MRNA_CNMF'

'16q' versus 'MRNA_CHIERARCHICAL'

P value = 9.8e-05 (Fisher's exact test), Q value = 0.019

Table S214. Gene #29: '16q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	19	19	15
16Q MUTATED	0	1	8
16Q WILD-TYPE	19	18	7

Figure S214. Get High-res Image Gene #29: '16q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16q' versus 'CN_CNMF'

P value = 5.3e-51 (Chi-square test), Q value = 2.5e-48

Table S215. Gene #29: '16q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
16Q MUTATED	15	9	113	6	1	0
16Q WILD-TYPE	285	15	39	16	14	1

Figure S215. Get High-res Image Gene #29: '16q' versus Molecular Subtype #3: 'CN_CNMF'

'16q' versus 'METHLYATION_CNMF'

P value = 3.5e-14 (Fisher's exact test), Q value = 1.2e-11

Table S216. Gene #29: '16q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
16Q MUTATED	78	30	18
16Q WILD-TYPE	74	58	142

Figure S216. Get High-res Image Gene #29: '16q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q' versus 'MRNASEQ_CNMF'

P value = 2.96e-26 (Fisher's exact test), Q value = 1.3e-23

Table S217. Gene #29: '16q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
16Q MUTATED	103	9	16	15
16Q WILD-TYPE	71	77	99	115

Figure S217. Get High-res Image Gene #29: '16q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.12e-20 (Fisher's exact test), Q value = 2.1e-17

Table S218. Gene #29: '16q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
16Q MUTATED	114	6	23
16Q WILD-TYPE	125	78	159

Figure S218. Get High-res Image Gene #29: '16q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q' versus 'MIRSEQ_CNMF'

P value = 3.13e-19 (Chi-square test), Q value = 1.3e-16

Table S219. Gene #29: '16q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
16Q MUTATED	84	16	14	11	15
16Q WILD-TYPE	65	122	35	42	101

Figure S219. Get High-res Image Gene #29: '16q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.51e-12 (Fisher's exact test), Q value = 2.7e-09

Table S220. Gene #29: '16q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
16Q MUTATED	3	26	111
16Q WILD-TYPE	10	188	167

Figure S220. Get High-res Image Gene #29: '16q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.8e-06 (Fisher's exact test), Q value = 0.00065

Table S221. Gene #29: '16q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
16Q MUTATED	73	32	17
16Q WILD-TYPE	103	58	99

Figure S221. Get High-res Image Gene #29: '16q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.82e-09 (Fisher's exact test), Q value = 1.1e-06

Table S222. Gene #29: '16q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
16Q MUTATED	40	52	23	7
16Q WILD-TYPE	61	48	123	28

Figure S222. Get High-res Image Gene #29: '16q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p' versus 'MRNA_CNMF'

P value = 0.000771 (Fisher's exact test), Q value = 0.13

Table S223. Gene #30: '17p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
17P MUTATED	0	8	1	0
17P WILD-TYPE	14	9	11	10

Figure S223. Get High-res Image Gene #30: '17p' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p' versus 'MRNA_CHIERARCHICAL'

P value = 9.8e-05 (Fisher's exact test), Q value = 0.019

Table S224. Gene #30: '17p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	19	19	15
17P MUTATED	1	0	8
17P WILD-TYPE	18	19	7

Figure S224. Get High-res Image Gene #30: '17p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p' versus 'CN_CNMF'

P value = 1.31e-62 (Chi-square test), Q value = 6.2e-60

Table S225. Gene #30: '17p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
17P MUTATED	3	5	115	8	1	0
17P WILD-TYPE	297	19	37	14	14	1

Figure S225. Get High-res Image Gene #30: '17p' versus Molecular Subtype #3: 'CN_CNMF'

'17p' versus 'METHLYATION_CNMF'

P value = 1.02e-16 (Fisher's exact test), Q value = 3.9e-14

Table S226. Gene #30: '17p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
17P MUTATED	77	25	13
17P WILD-TYPE	75	63	147

Figure S226. Get High-res Image Gene #30: '17p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p' versus 'MRNASEQ_CNMF'

P value = 1.01e-29 (Fisher's exact test), Q value = 4.5e-27

Table S227. Gene #30: '17p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
17P MUTATED	100	10	7	13
17P WILD-TYPE	74	76	108	117

Figure S227. Get High-res Image Gene #30: '17p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.72e-22 (Fisher's exact test), Q value = 7.3e-20

Table S228. Gene #30: '17p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
17P MUTATED	109	4	17
17P WILD-TYPE	130	80	165

Figure S228. Get High-res Image Gene #30: '17p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p' versus 'MIRSEQ_CNMF'

P value = 4.55e-23 (Chi-square test), Q value = 2e-20

Table S229. Gene #30: '17p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
17P MUTATED	84	16	12	8	9
17P WILD-TYPE	65	122	37	45	107

Figure S229. Get High-res Image Gene #30: '17p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.15e-12 (Fisher's exact test), Q value = 2e-09

Table S230. Gene #30: '17p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
17P MUTATED	3	22	104
17P WILD-TYPE	10	192	174

Figure S230. Get High-res Image Gene #30: '17p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000263 (Fisher's exact test), Q value = 0.049

Table S231. Gene #30: '17p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
17P MUTATED	67	26	19
17P WILD-TYPE	109	64	97

Figure S231. Get High-res Image Gene #30: '17p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.5e-07 (Fisher's exact test), Q value = 0.00018

Table S232. Gene #30: '17p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
17P MUTATED	35	47	23	7
17P WILD-TYPE	66	53	123	28

Figure S232. Get High-res Image Gene #30: '17p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q' versus 'MRNA_CNMF'

P value = 0.000567 (Fisher's exact test), Q value = 0.099

Table S233. Gene #31: '17q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
17Q MUTATED	0	7	0	0
17Q WILD-TYPE	14	10	12	10

Figure S233. Get High-res Image Gene #31: '17q' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q' versus 'MRNA_CHIERARCHICAL'

P value = 4.17e-05 (Fisher's exact test), Q value = 0.0086

Table S234. Gene #31: '17q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	19	19	15
17Q MUTATED	0	0	7
17Q WILD-TYPE	19	19	8

Figure S234. Get High-res Image Gene #31: '17q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q' versus 'CN_CNMF'

P value = 1.9e-49 (Chi-square test), Q value = 9e-47

Table S235. Gene #31: '17q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
17Q MUTATED	2	6	97	8	1	0
17Q WILD-TYPE	298	18	55	14	14	1

Figure S235. Get High-res Image Gene #31: '17q' versus Molecular Subtype #3: 'CN_CNMF'

'17q' versus 'METHLYATION_CNMF'

P value = 8.34e-13 (Fisher's exact test), Q value = 2.8e-10

Table S236. Gene #31: '17q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
17Q MUTATED	65	23	12
17Q WILD-TYPE	87	65	148

Figure S236. Get High-res Image Gene #31: '17q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q' versus 'MRNASEQ_CNMF'

P value = 4.19e-22 (Fisher's exact test), Q value = 1.8e-19

Table S237. Gene #31: '17q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
17Q MUTATED	84	9	6	13
17Q WILD-TYPE	90	77	109	117

Figure S237. Get High-res Image Gene #31: '17q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.52e-16 (Fisher's exact test), Q value = 1.7e-13

Table S238. Gene #31: '17q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
17Q MUTATED	91	4	17
17Q WILD-TYPE	148	80	165

Figure S238. Get High-res Image Gene #31: '17q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q' versus 'MIRSEQ_CNMF'

P value = 4.15e-16 (Chi-square test), Q value = 1.5e-13

Table S239. Gene #31: '17q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
17Q MUTATED	69	15	11	8	8
17Q WILD-TYPE	80	123	38	45	108

Figure S239. Get High-res Image Gene #31: '17q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.86e-08 (Fisher's exact test), Q value = 5e-06

Table S240. Gene #31: '17q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
17Q MUTATED	3	21	87
17Q WILD-TYPE	10	193	191

Figure S240. Get High-res Image Gene #31: '17q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000631 (Fisher's exact test), Q value = 0.11

Table S241. Gene #31: '17q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
17Q MUTATED	61	19	18
17Q WILD-TYPE	115	71	98

Figure S241. Get High-res Image Gene #31: '17q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.19e-05 (Fisher's exact test), Q value = 0.0047

Table S242. Gene #31: '17q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
17Q MUTATED	26	43	22	7
17Q WILD-TYPE	75	57	124	28

Figure S242. Get High-res Image Gene #31: '17q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p' versus 'CN_CNMF'

P value = 1.5e-45 (Chi-square test), Q value = 7.1e-43

Table S243. Gene #32: '18p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
18P MUTATED	4	9	94	9	1	0
18P WILD-TYPE	296	15	58	13	14	1

Figure S243. Get High-res Image Gene #32: '18p' versus Molecular Subtype #3: 'CN_CNMF'

'18p' versus 'METHLYATION_CNMF'

P value = 3.97e-19 (Fisher's exact test), Q value = 1.6e-16

Table S244. Gene #32: '18p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
18P MUTATED	72	22	7
18P WILD-TYPE	80	66	153

Figure S244. Get High-res Image Gene #32: '18p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p' versus 'MRNASEQ_CNMF'

P value = 4.09e-23 (Fisher's exact test), Q value = 1.8e-20

Table S245. Gene #32: '18p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
18P MUTATED	87	11	8	10
18P WILD-TYPE	87	75	107	120

Figure S245. Get High-res Image Gene #32: '18p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.81e-21 (Fisher's exact test), Q value = 1.6e-18

Table S246. Gene #32: '18p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
18P MUTATED	99	3	14
18P WILD-TYPE	140	81	168

Figure S246. Get High-res Image Gene #32: '18p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p' versus 'MIRSEQ_CNMF'

P value = 2.16e-20 (Chi-square test), Q value = 8.9e-18

Table S247. Gene #32: '18p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
18P MUTATED	74	9	13	12	8
18P WILD-TYPE	75	129	36	41	108

Figure S247. Get High-res Image Gene #32: '18p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.9e-17 (Fisher's exact test), Q value = 3e-14

Table S248. Gene #32: '18p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
18P MUTATED	1	13	102
18P WILD-TYPE	12	201	176

Figure S248. Get High-res Image Gene #32: '18p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.5e-09 (Fisher's exact test), Q value = 7.2e-07

Table S249. Gene #32: '18p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
18P MUTATED	69	21	9
18P WILD-TYPE	107	69	107

Figure S249. Get High-res Image Gene #32: '18p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.94e-12 (Fisher's exact test), Q value = 9.7e-10

Table S250. Gene #32: '18p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
18P MUTATED	29	50	12	8
18P WILD-TYPE	72	50	134	27

Figure S250. Get High-res Image Gene #32: '18p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q' versus 'CN_CNMF'

P value = 3.96e-38 (Chi-square test), Q value = 1.8e-35

Table S251. Gene #33: '18q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
18Q MUTATED	4	8	82	10	1	0
18Q WILD-TYPE	296	16	70	12	14	1

Figure S251. Get High-res Image Gene #33: '18q' versus Molecular Subtype #3: 'CN_CNMF'

'18q' versus 'METHLYATION_CNMF'

P value = 8.91e-15 (Fisher's exact test), Q value = 3.2e-12

Table S252. Gene #33: '18q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
18Q MUTATED	63	22	8
18Q WILD-TYPE	89	66	152

Figure S252. Get High-res Image Gene #33: '18q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q' versus 'MRNASEQ_CNMF'

P value = 5.35e-18 (Fisher's exact test), Q value = 2.1e-15

Table S253. Gene #33: '18q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
18Q MUTATED	76	10	8	10
18Q WILD-TYPE	98	76	107	120

Figure S253. Get High-res Image Gene #33: '18q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.86e-19 (Fisher's exact test), Q value = 7.6e-17

Table S254. Gene #33: '18q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
18Q MUTATED	89	1	14
18Q WILD-TYPE	150	83	168

Figure S254. Get High-res Image Gene #33: '18q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q' versus 'MIRSEQ_CNMF'

P value = 3.67e-17 (Chi-square test), Q value = 1.4e-14

Table S255. Gene #33: '18q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
18Q MUTATED	66	10	11	11	6
18Q WILD-TYPE	83	128	38	42	110

Figure S255. Get High-res Image Gene #33: '18q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.32e-15 (Fisher's exact test), Q value = 3e-12

Table S256. Gene #33: '18q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
18Q MUTATED	2	11	91
18Q WILD-TYPE	11	203	187

Figure S256. Get High-res Image Gene #33: '18q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.74e-07 (Fisher's exact test), Q value = 4.4e-05

Table S257. Gene #33: '18q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
18Q MUTATED	63	18	10
18Q WILD-TYPE	113	72	106

Figure S257. Get High-res Image Gene #33: '18q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.93e-09 (Fisher's exact test), Q value = 5.7e-07

Table S258. Gene #33: '18q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
18Q MUTATED	25	45	13	8
18Q WILD-TYPE	76	55	133	27

Figure S258. Get High-res Image Gene #33: '18q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p' versus 'MRNA_CHIERARCHICAL'

P value = 0.000218 (Fisher's exact test), Q value = 0.041

Table S259. Gene #34: '19p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	19	19	15
19P MUTATED	0	0	6
19P WILD-TYPE	19	19	9

Figure S259. Get High-res Image Gene #34: '19p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19p' versus 'CN_CNMF'

P value = 6.49e-44 (Chi-square test), Q value = 3e-41

Table S260. Gene #34: '19p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
19P MUTATED	1	8	89	7	2	0
19P WILD-TYPE	299	16	63	15	13	1

Figure S260. Get High-res Image Gene #34: '19p' versus Molecular Subtype #3: 'CN_CNMF'

'19p' versus 'METHLYATION_CNMF'

P value = 1.78e-16 (Fisher's exact test), Q value = 6.7e-14

Table S261. Gene #34: '19p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
19P MUTATED	69	18	9
19P WILD-TYPE	83	70	151

Figure S261. Get High-res Image Gene #34: '19p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p' versus 'MRNASEQ_CNMF'

P value = 5.12e-24 (Fisher's exact test), Q value = 2.2e-21

Table S262. Gene #34: '19p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
19P MUTATED	83	9	6	8
19P WILD-TYPE	91	77	109	122

Figure S262. Get High-res Image Gene #34: '19p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.63e-22 (Fisher's exact test), Q value = 7e-20

Table S263. Gene #34: '19p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
19P MUTATED	94	2	10
19P WILD-TYPE	145	82	172

Figure S263. Get High-res Image Gene #34: '19p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p' versus 'MIRSEQ_CNMF'

P value = 4.01e-20 (Chi-square test), Q value = 1.7e-17

Table S264. Gene #34: '19p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
19P MUTATED	71	10	10	6	8
19P WILD-TYPE	78	128	39	47	108

Figure S264. Get High-res Image Gene #34: '19p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.39e-12 (Fisher's exact test), Q value = 1.4e-09

Table S265. Gene #34: '19p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
19P MUTATED	4	14	87
19P WILD-TYPE	9	200	191

Figure S265. Get High-res Image Gene #34: '19p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.36e-06 (Fisher's exact test), Q value = 0.00032

Table S266. Gene #34: '19p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
19P MUTATED	62	20	11
19P WILD-TYPE	114	70	105

Figure S266. Get High-res Image Gene #34: '19p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.66e-09 (Fisher's exact test), Q value = 1.6e-06

Table S267. Gene #34: '19p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
19P MUTATED	25	46	15	7
19P WILD-TYPE	76	54	131	28

Figure S267. Get High-res Image Gene #34: '19p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q' versus 'CN_CNMF'

P value = 3.69e-43 (Chi-square test), Q value = 1.7e-40

Table S268. Gene #35: '19q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
19Q MUTATED	2	8	89	6	2	0
19Q WILD-TYPE	298	16	63	16	13	1

Figure S268. Get High-res Image Gene #35: '19q' versus Molecular Subtype #3: 'CN_CNMF'

'19q' versus 'METHLYATION_CNMF'

P value = 5.26e-13 (Fisher's exact test), Q value = 1.8e-10

Table S269. Gene #35: '19q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
19Q MUTATED	62	22	10
19Q WILD-TYPE	90	66	150

Figure S269. Get High-res Image Gene #35: '19q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q' versus 'MRNASEQ_CNMF'

P value = 3.52e-23 (Fisher's exact test), Q value = 1.5e-20

Table S270. Gene #35: '19q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
19Q MUTATED	82	10	6	8
19Q WILD-TYPE	92	76	109	122

Figure S270. Get High-res Image Gene #35: '19q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.74e-24 (Fisher's exact test), Q value = 2.5e-21

Table S271. Gene #35: '19q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
19Q MUTATED	95	1	10
19Q WILD-TYPE	144	83	172

Figure S271. Get High-res Image Gene #35: '19q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q' versus 'MIRSEQ_CNMF'

P value = 3.22e-19 (Chi-square test), Q value = 1.3e-16

Table S272. Gene #35: '19q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
19Q MUTATED	70	10	10	7	8
19Q WILD-TYPE	79	128	39	46	108

Figure S272. Get High-res Image Gene #35: '19q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.28e-13 (Fisher's exact test), Q value = 2.1e-10

Table S273. Gene #35: '19q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
19Q MUTATED	4	13	88
19Q WILD-TYPE	9	201	190

Figure S273. Get High-res Image Gene #35: '19q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.66e-06 (Fisher's exact test), Q value = 0.0022

Table S274. Gene #35: '19q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
19Q MUTATED	58	22	11
19Q WILD-TYPE	118	68	105

Figure S274. Get High-res Image Gene #35: '19q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.52e-09 (Fisher's exact test), Q value = 4.5e-07

Table S275. Gene #35: '19q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
19Q MUTATED	25	46	14	6
19Q WILD-TYPE	76	54	132	29

Figure S275. Get High-res Image Gene #35: '19q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p' versus 'CN_CNMF'

P value = 6.36e-45 (Chi-square test), Q value = 3e-42

Table S276. Gene #36: '20p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
20P MUTATED	7	10	89	17	1	0
20P WILD-TYPE	293	14	63	5	14	1

Figure S276. Get High-res Image Gene #36: '20p' versus Molecular Subtype #3: 'CN_CNMF'

'20p' versus 'METHLYATION_CNMF'

P value = 4.95e-12 (Fisher's exact test), Q value = 1.6e-09

Table S277. Gene #36: '20p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
20P MUTATED	72	18	19
20P WILD-TYPE	80	70	141

Figure S277. Get High-res Image Gene #36: '20p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p' versus 'MRNASEQ_CNMF'

P value = 2.14e-17 (Fisher's exact test), Q value = 8.4e-15

Table S278. Gene #36: '20p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
20P MUTATED	84	13	10	16
20P WILD-TYPE	90	73	105	114

Figure S278. Get High-res Image Gene #36: '20p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.68e-16 (Fisher's exact test), Q value = 6.4e-14

Table S279. Gene #36: '20p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
20P MUTATED	97	3	23
20P WILD-TYPE	142	81	159

Figure S279. Get High-res Image Gene #36: '20p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p' versus 'MIRSEQ_CNMF'

P value = 6.11e-14 (Chi-square test), Q value = 2.1e-11

Table S280. Gene #36: '20p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
20P MUTATED	71	16	13	10	13
20P WILD-TYPE	78	122	36	43	103

Figure S280. Get High-res Image Gene #36: '20p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.73e-10 (Fisher's exact test), Q value = 5.3e-08

Table S281. Gene #36: '20p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
20P MUTATED	3	22	98
20P WILD-TYPE	10	192	180

Figure S281. Get High-res Image Gene #36: '20p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.59e-05 (Fisher's exact test), Q value = 0.0034

Table S282. Gene #36: '20p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
20P MUTATED	68	20	17
20P WILD-TYPE	108	70	99

Figure S282. Get High-res Image Gene #36: '20p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.96e-08 (Fisher's exact test), Q value = 5.3e-06

Table S283. Gene #36: '20p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
20P MUTATED	25	51	22	7
20P WILD-TYPE	76	49	124	28

Figure S283. Get High-res Image Gene #36: '20p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q' versus 'CN_CNMF'

P value = 1.73e-50 (Chi-square test), Q value = 8.2e-48

Table S284. Gene #37: '20q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
20Q MUTATED	7	10	97	18	1	0
20Q WILD-TYPE	293	14	55	4	14	1

Figure S284. Get High-res Image Gene #37: '20q' versus Molecular Subtype #3: 'CN_CNMF'

'20q' versus 'METHLYATION_CNMF'

P value = 4.25e-13 (Fisher's exact test), Q value = 1.5e-10

Table S285. Gene #37: '20q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
20Q MUTATED	77	21	20
20Q WILD-TYPE	75	67	140

Figure S285. Get High-res Image Gene #37: '20q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q' versus 'MRNASEQ_CNMF'

P value = 2.36e-19 (Fisher's exact test), Q value = 9.6e-17

Table S286. Gene #37: '20q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
20Q MUTATED	90	15	10	17
20Q WILD-TYPE	84	71	105	113

Figure S286. Get High-res Image Gene #37: '20q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.29e-17 (Fisher's exact test), Q value = 5.1e-15

Table S287. Gene #37: '20q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
20Q MUTATED	104	4	24
20Q WILD-TYPE	135	80	158

Figure S287. Get High-res Image Gene #37: '20q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q' versus 'MIRSEQ_CNMF'

P value = 1.22e-14 (Chi-square test), Q value = 4.4e-12

Table S288. Gene #37: '20q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
20Q MUTATED	75	18	14	10	14
20Q WILD-TYPE	74	120	35	43	102

Figure S288. Get High-res Image Gene #37: '20q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.26e-11 (Fisher's exact test), Q value = 1.7e-08

Table S289. Gene #37: '20q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
20Q MUTATED	3	24	104
20Q WILD-TYPE	10	190	174

Figure S289. Get High-res Image Gene #37: '20q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.73e-05 (Fisher's exact test), Q value = 0.0037

Table S290. Gene #37: '20q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
20Q MUTATED	72	22	19
20Q WILD-TYPE	104	68	97

Figure S290. Get High-res Image Gene #37: '20q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.02e-09 (Fisher's exact test), Q value = 5.9e-07

Table S291. Gene #37: '20q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
20Q MUTATED	27	55	24	7
20Q WILD-TYPE	74	45	122	28

Figure S291. Get High-res Image Gene #37: '20q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q' versus 'CN_CNMF'

P value = 4.14e-30 (Chi-square test), Q value = 1.9e-27

Table S292. Gene #38: '21q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
21Q MUTATED	5	5	71	5	1	0
21Q WILD-TYPE	295	19	81	17	14	1

Figure S292. Get High-res Image Gene #38: '21q' versus Molecular Subtype #3: 'CN_CNMF'

'21q' versus 'METHLYATION_CNMF'

P value = 1.72e-09 (Fisher's exact test), Q value = 5.1e-07

Table S293. Gene #38: '21q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
21Q MUTATED	50	17	9
21Q WILD-TYPE	102	71	151

Figure S293. Get High-res Image Gene #38: '21q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q' versus 'MRNASEQ_CNMF'

P value = 1.05e-17 (Fisher's exact test), Q value = 4.1e-15

Table S294. Gene #38: '21q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
21Q MUTATED	66	11	5	5
21Q WILD-TYPE	108	75	110	125

Figure S294. Get High-res Image Gene #38: '21q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.72e-15 (Fisher's exact test), Q value = 3.2e-12

Table S295. Gene #38: '21q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
21Q MUTATED	74	6	7
21Q WILD-TYPE	165	78	175

Figure S295. Get High-res Image Gene #38: '21q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q' versus 'MIRSEQ_CNMF'

P value = 3.18e-16 (Chi-square test), Q value = 1.2e-13

Table S296. Gene #38: '21q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
21Q MUTATED	58	4	8	5	10
21Q WILD-TYPE	91	134	41	48	106

Figure S296. Get High-res Image Gene #38: '21q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.32e-13 (Fisher's exact test), Q value = 4.6e-11

Table S297. Gene #38: '21q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
21Q MUTATED	0	8	77
21Q WILD-TYPE	13	206	201

Figure S297. Get High-res Image Gene #38: '21q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.85e-07 (Fisher's exact test), Q value = 9.3e-05

Table S298. Gene #38: '21q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
21Q MUTATED	52	17	6
21Q WILD-TYPE	124	73	110

Figure S298. Get High-res Image Gene #38: '21q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.99e-10 (Fisher's exact test), Q value = 1.5e-07

Table S299. Gene #38: '21q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
21Q MUTATED	27	37	8	3
21Q WILD-TYPE	74	63	138	32

Figure S299. Get High-res Image Gene #38: '21q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q' versus 'MRNA_CHIERARCHICAL'

P value = 0.000454 (Fisher's exact test), Q value = 0.08

Table S300. Gene #39: '22q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	19	19	15
22Q MUTATED	1	0	7
22Q WILD-TYPE	18	19	8

Figure S300. Get High-res Image Gene #39: '22q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q' versus 'CN_CNMF'

P value = 2.3e-58 (Chi-square test), Q value = 1.1e-55

Table S301. Gene #39: '22q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
22Q MUTATED	6	9	113	8	0	0
22Q WILD-TYPE	294	15	39	14	15	1

Figure S301. Get High-res Image Gene #39: '22q' versus Molecular Subtype #3: 'CN_CNMF'

'22q' versus 'METHLYATION_CNMF'

P value = 1.85e-19 (Fisher's exact test), Q value = 7.6e-17

Table S302. Gene #39: '22q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
22Q MUTATED	85	25	14
22Q WILD-TYPE	67	63	146

Figure S302. Get High-res Image Gene #39: '22q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q' versus 'MRNASEQ_CNMF'

P value = 2.56e-30 (Fisher's exact test), Q value = 1.1e-27

Table S303. Gene #39: '22q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
22Q MUTATED	103	9	8	15
22Q WILD-TYPE	71	77	107	115

Figure S303. Get High-res Image Gene #39: '22q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.79e-28 (Fisher's exact test), Q value = 3.9e-25

Table S304. Gene #39: '22q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
22Q MUTATED	116	1	18
22Q WILD-TYPE	123	83	164

Figure S304. Get High-res Image Gene #39: '22q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q' versus 'MIRSEQ_CNMF'

P value = 1.32e-21 (Chi-square test), Q value = 5.6e-19

Table S305. Gene #39: '22q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
22Q MUTATED	84	18	13	8	10
22Q WILD-TYPE	65	120	36	45	106

Figure S305. Get High-res Image Gene #39: '22q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.19e-14 (Fisher's exact test), Q value = 1.1e-11

Table S306. Gene #39: '22q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
22Q MUTATED	5	20	108
22Q WILD-TYPE	8	194	170

Figure S306. Get High-res Image Gene #39: '22q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.11e-06 (Fisher's exact test), Q value = 0.00026

Table S307. Gene #39: '22q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
22Q MUTATED	77	25	18
22Q WILD-TYPE	99	65	98

Figure S307. Get High-res Image Gene #39: '22q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.27e-13 (Fisher's exact test), Q value = 1.5e-10

Table S308. Gene #39: '22q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
22Q MUTATED	33	60	21	6
22Q WILD-TYPE	68	40	125	29

Figure S308. Get High-res Image Gene #39: '22q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq' versus 'CN_CNMF'

P value = 1.51e-40 (Chi-square test), Q value = 7e-38

Table S309. Gene #40: 'xq' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	300	24	152	22	15	1
XQ MUTATED	9	15	82	12	12	0
XQ WILD-TYPE	291	9	70	10	3	1

Figure S309. Get High-res Image Gene #40: 'xq' versus Molecular Subtype #3: 'CN_CNMF'

'xq' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0022

Table S310. Gene #40: 'xq' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	152	88	160
XQ MUTATED	56	25	22
XQ WILD-TYPE	96	63	138

Figure S310. Get High-res Image Gene #40: 'xq' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq' versus 'MRNASEQ_CNMF'

P value = 1.07e-11 (Fisher's exact test), Q value = 3.4e-09

Table S311. Gene #40: 'xq' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	174	86	115	130
XQ MUTATED	78	10	17	21
XQ WILD-TYPE	96	76	98	109

Figure S311. Get High-res Image Gene #40: 'xq' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.05e-08 (Fisher's exact test), Q value = 5.5e-06

Table S312. Gene #40: 'xq' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	239	84	182
XQ MUTATED	88	9	29
XQ WILD-TYPE	151	75	153

Figure S312. Get High-res Image Gene #40: 'xq' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq' versus 'MIRSEQ_CNMF'

P value = 4.71e-09 (Chi-square test), Q value = 1.3e-06

Table S313. Gene #40: 'xq' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	149	138	49	53	116
XQ MUTATED	67	23	8	11	18
XQ WILD-TYPE	82	115	41	42	98

Figure S313. Get High-res Image Gene #40: 'xq' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.11e-05 (Fisher's exact test), Q value = 0.018

Table S314. Gene #40: 'xq' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	214	278
XQ MUTATED	5	34	88
XQ WILD-TYPE	8	180	190

Figure S314. Get High-res Image Gene #40: 'xq' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xq' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000186 (Fisher's exact test), Q value = 0.035

Table S315. Gene #40: 'xq' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	90	116
XQ MUTATED	66	16	22
XQ WILD-TYPE	110	74	94

Figure S315. Get High-res Image Gene #40: 'xq' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xq' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.76e-05 (Fisher's exact test), Q value = 0.0097

Table S316. Gene #40: 'xq' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	101	100	146	35
XQ MUTATED	23	45	26	10
XQ WILD-TYPE	78	55	120	25

Figure S316. Get High-res Image Gene #40: 'xq' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = UCEC-TP.transferedmergedcluster.txt
Number of patients = 514
Number of significantly focal cnvs = 40
Number of molecular subtypes = 12
Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

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

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[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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