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

Overview

Introduction

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

Summary

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

1p cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
1q cnv correlated to 'MRNA_CNMF', 'CN_CNMF', and 'METHLYATION_CNMF'.
2p cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
2q cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
3p cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
3q cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
4p cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
4q cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
5p cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
5q cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
6p cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
6q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
7p cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
7q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
8p cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
8q cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
9p cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
9q cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
10p cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
10q cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
11p cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
11q cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
12p cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
12q cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
13q cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
14q cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
15q cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
16p cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
16q cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
17p cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
17q cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
18p cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
18q cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
19p cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
19q cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
20p cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
20q cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
21q cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
22q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
xq cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

Results

Overview of the results

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


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

'1p' versus 'MRNA_CNMF'

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

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

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

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

'1p' versus 'MRNA_CHIERARCHICAL'

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

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

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

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

'1p' versus 'CN_CNMF'

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

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

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

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

'1p' versus 'METHLYATION_CNMF'

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

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

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

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

'1p' versus 'RPPA_CNMF'

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

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

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

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

'1p' versus 'RPPA_CHIERARCHICAL'

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

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

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

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

'1p' versus 'MRNASEQ_CNMF'

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

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

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

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

'1p' versus 'MRNASEQ_CHIERARCHICAL'

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

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

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

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

'1p' versus 'MIRSEQ_CNMF'

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

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

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

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

'1p' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

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

'1p' versus 'MIRSEQ_MATURE_CNMF'

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

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

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

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

'1p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

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

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

'1q' versus 'MRNA_CNMF'

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

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

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

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

'1q' versus 'CN_CNMF'

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

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

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

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

'1q' versus 'METHLYATION_CNMF'

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

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

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

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

'2p' versus 'MRNA_CNMF'

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

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

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

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

'2p' versus 'MRNA_CHIERARCHICAL'

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

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

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

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

'2p' versus 'CN_CNMF'

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

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

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

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

'2p' versus 'METHLYATION_CNMF'

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

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

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

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

'2p' versus 'RPPA_CNMF'

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

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

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

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

'2p' versus 'RPPA_CHIERARCHICAL'

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

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

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

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

'2p' versus 'MRNASEQ_CNMF'

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

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

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

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

'2p' versus 'MRNASEQ_CHIERARCHICAL'

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

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

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

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

'2p' versus 'MIRSEQ_CNMF'

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

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

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

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

'2p' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

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

'2p' versus 'MIRSEQ_MATURE_CNMF'

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

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

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

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

'2p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

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

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

'2q' versus 'MRNA_CNMF'

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

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

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

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

'2q' versus 'MRNA_CHIERARCHICAL'

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

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

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

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

'2q' versus 'CN_CNMF'

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

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

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

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

'2q' versus 'METHLYATION_CNMF'

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

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

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

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

'2q' versus 'RPPA_CNMF'

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

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

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

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

'2q' versus 'RPPA_CHIERARCHICAL'

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

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

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

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

'2q' versus 'MRNASEQ_CNMF'

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

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

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

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

'2q' versus 'MRNASEQ_CHIERARCHICAL'

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

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

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

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

'2q' versus 'MIRSEQ_CNMF'

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

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

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

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

'2q' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

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

'2q' versus 'MIRSEQ_MATURE_CNMF'

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

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

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

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

'2q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

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

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

'3p' versus 'MRNA_CNMF'

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

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

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

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

'3p' versus 'MRNA_CHIERARCHICAL'

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

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

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

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

'3p' versus 'CN_CNMF'

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

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

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

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

'3p' versus 'METHLYATION_CNMF'

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

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

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

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

'3p' versus 'RPPA_CNMF'

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

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

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

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

'3p' versus 'RPPA_CHIERARCHICAL'

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

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

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

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

'3p' versus 'MRNASEQ_CNMF'

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

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

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

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

'3p' versus 'MRNASEQ_CHIERARCHICAL'

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

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

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

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

'3p' versus 'MIRSEQ_CNMF'

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

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

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

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

'3p' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

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

'3p' versus 'MIRSEQ_MATURE_CNMF'

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

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

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

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

'3p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

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

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

'3q' versus 'MRNA_CNMF'

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

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

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

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

'3q' versus 'MRNA_CHIERARCHICAL'

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

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

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

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

'3q' versus 'CN_CNMF'

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

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

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

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

'3q' versus 'METHLYATION_CNMF'

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

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

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

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

'3q' versus 'RPPA_CNMF'

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

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

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

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

'3q' versus 'MRNASEQ_CNMF'

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

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

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

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

'3q' versus 'MRNASEQ_CHIERARCHICAL'

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

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

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

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

'3q' versus 'MIRSEQ_CNMF'

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

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

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

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

'3q' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

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

'3q' versus 'MIRSEQ_MATURE_CNMF'

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

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

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

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

'3q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

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

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

'4p' versus 'MRNA_CNMF'

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

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

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

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

'4p' versus 'MRNA_CHIERARCHICAL'

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

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

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

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

'4p' versus 'CN_CNMF'

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

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

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

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

'4p' versus 'METHLYATION_CNMF'

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

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

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

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

'4p' versus 'RPPA_CNMF'

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

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

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

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

'4p' versus 'RPPA_CHIERARCHICAL'

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

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

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

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

'4p' versus 'MRNASEQ_CNMF'

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

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

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

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

'4p' versus 'MRNASEQ_CHIERARCHICAL'

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

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

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

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

'4p' versus 'MIRSEQ_CNMF'

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

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

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

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

'4p' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

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

'4p' versus 'MIRSEQ_MATURE_CNMF'

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

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

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

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

'4p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

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

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

'4q' versus 'MRNA_CNMF'

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

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

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

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

'4q' versus 'MRNA_CHIERARCHICAL'

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

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

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

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

'4q' versus 'CN_CNMF'

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

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

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

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

'4q' versus 'METHLYATION_CNMF'

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

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

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

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

'4q' versus 'MRNASEQ_CNMF'

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

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

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

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

'4q' versus 'MRNASEQ_CHIERARCHICAL'

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

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

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

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

'4q' versus 'MIRSEQ_CNMF'

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

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

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

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

'4q' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

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

'4q' versus 'MIRSEQ_MATURE_CNMF'

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

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

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

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

'4q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

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

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

'5p' versus 'MRNA_CNMF'

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

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

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

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

'5p' versus 'MRNA_CHIERARCHICAL'

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

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

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

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

'5p' versus 'CN_CNMF'

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

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

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

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

'5p' versus 'METHLYATION_CNMF'

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

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

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

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

'5p' versus 'RPPA_CNMF'

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

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

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

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

'5p' versus 'MRNASEQ_CNMF'

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

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

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

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

'5p' versus 'MRNASEQ_CHIERARCHICAL'

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

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

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

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

'5p' versus 'MIRSEQ_CNMF'

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

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

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

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

'5p' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

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

'5p' versus 'MIRSEQ_MATURE_CNMF'

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

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

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

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

'5p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

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

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

'5q' versus 'MRNA_CNMF'

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

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

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

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

'5q' versus 'MRNA_CHIERARCHICAL'

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

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

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

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

'5q' versus 'CN_CNMF'

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

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

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

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

'5q' versus 'METHLYATION_CNMF'

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

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

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

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

'5q' versus 'RPPA_CNMF'

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

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

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

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

'5q' versus 'RPPA_CHIERARCHICAL'

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

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

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

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

'5q' versus 'MRNASEQ_CNMF'

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

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

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

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

'5q' versus 'MRNASEQ_CHIERARCHICAL'

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

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

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

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

'5q' versus 'MIRSEQ_CNMF'

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

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

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

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

'5q' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

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

'5q' versus 'MIRSEQ_MATURE_CNMF'

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

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

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

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

'5q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

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

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

'6p' versus 'CN_CNMF'

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

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

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

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

'6p' versus 'METHLYATION_CNMF'

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

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

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

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

'6p' versus 'MRNASEQ_CNMF'

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

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

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

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

'6p' versus 'MRNASEQ_CHIERARCHICAL'

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

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

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

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

'6p' versus 'MIRSEQ_CNMF'

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

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

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

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

'6p' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

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

'6p' versus 'MIRSEQ_MATURE_CNMF'

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

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

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

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

'6p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

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

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

'6q' versus 'CN_CNMF'

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

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

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

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

'6q' versus 'METHLYATION_CNMF'

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

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

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

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

'6q' versus 'MRNASEQ_CHIERARCHICAL'

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

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

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

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

'6q' versus 'MIRSEQ_CNMF'

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

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

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

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

'6q' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

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

'6q' versus 'MIRSEQ_MATURE_CNMF'

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

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

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

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

'7p' versus 'MRNA_CNMF'

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

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

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

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

'7p' versus 'MRNA_CHIERARCHICAL'

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

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

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

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

'7p' versus 'CN_CNMF'

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

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

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

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

'7p' versus 'METHLYATION_CNMF'

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

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

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

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

'7p' versus 'MRNASEQ_CNMF'

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

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

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

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

'7p' versus 'MRNASEQ_CHIERARCHICAL'

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

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

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

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

'7p' versus 'MIRSEQ_CNMF'

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

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

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

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

'7p' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

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

'7p' versus 'MIRSEQ_MATURE_CNMF'

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

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

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

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

'7p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

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

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

'7q' versus 'CN_CNMF'

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

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

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

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

'7q' versus 'METHLYATION_CNMF'

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

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

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

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

'7q' versus 'MRNASEQ_CNMF'

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

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

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

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

'7q' versus 'MRNASEQ_CHIERARCHICAL'

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

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

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

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

'7q' versus 'MIRSEQ_CNMF'

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

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

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

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

'7q' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

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

'7q' versus 'MIRSEQ_MATURE_CNMF'

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

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

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

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

'7q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

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

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

'8p' versus 'MRNA_CNMF'

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

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

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

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

'8p' versus 'MRNA_CHIERARCHICAL'

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

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

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

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

'8p' versus 'CN_CNMF'

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

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

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

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

'8p' versus 'METHLYATION_CNMF'

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

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

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

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

'8p' versus 'MRNASEQ_CNMF'

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

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

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

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

'8p' versus 'MRNASEQ_CHIERARCHICAL'

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

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

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

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

'8p' versus 'MIRSEQ_CNMF'

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

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

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

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

'8p' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

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

'8p' versus 'MIRSEQ_MATURE_CNMF'

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

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

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

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

'8p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

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

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

'8q' versus 'MRNA_CNMF'

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

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

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

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

'8q' versus 'MRNA_CHIERARCHICAL'

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

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

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

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

'8q' versus 'CN_CNMF'

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

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

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

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

'8q' versus 'METHLYATION_CNMF'

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

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

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

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

'8q' versus 'MRNASEQ_CNMF'

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

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

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

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

'8q' versus 'MRNASEQ_CHIERARCHICAL'

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

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

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

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

'8q' versus 'MIRSEQ_CNMF'

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

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

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

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

'8q' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

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

'8q' versus 'MIRSEQ_MATURE_CNMF'

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

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

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

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

'8q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

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

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

'9p' versus 'MRNA_CNMF'

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

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

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

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

'9p' versus 'MRNA_CHIERARCHICAL'

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

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

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

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

'9p' versus 'CN_CNMF'

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

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

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

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

'9p' versus 'METHLYATION_CNMF'

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

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

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

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

'9p' versus 'RPPA_CNMF'

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

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

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

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

'9p' versus 'RPPA_CHIERARCHICAL'

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

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

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

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

'9p' versus 'MRNASEQ_CNMF'

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

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

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

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

'9p' versus 'MRNASEQ_CHIERARCHICAL'

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

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

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

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

'9p' versus 'MIRSEQ_CNMF'

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

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

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

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

'9p' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

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

'9p' versus 'MIRSEQ_MATURE_CNMF'

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

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

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

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

'9p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

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

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

'9q' versus 'MRNA_CNMF'

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

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

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

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

'9q' versus 'MRNA_CHIERARCHICAL'

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

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

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

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

'9q' versus 'CN_CNMF'

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

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

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

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

'9q' versus 'METHLYATION_CNMF'

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

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

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

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

'9q' versus 'RPPA_CNMF'

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

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

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

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

'9q' versus 'RPPA_CHIERARCHICAL'

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

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

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

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

'9q' versus 'MRNASEQ_CNMF'

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

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

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

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

'9q' versus 'MRNASEQ_CHIERARCHICAL'

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

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

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

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

'9q' versus 'MIRSEQ_CNMF'

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

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

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

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

'9q' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

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

'9q' versus 'MIRSEQ_MATURE_CNMF'

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

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

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

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

'9q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

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

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

'10p' versus 'MRNA_CNMF'

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

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

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

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

'10p' versus 'MRNA_CHIERARCHICAL'

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

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

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

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

'10p' versus 'CN_CNMF'

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

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

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

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

'10p' versus 'METHLYATION_CNMF'

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

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

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

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

'10p' versus 'RPPA_CNMF'

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

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

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

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

'10p' versus 'RPPA_CHIERARCHICAL'

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

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

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

Figure S189. Get High-res Image Gene #19: '10p' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10p' versus 'MRNASEQ_CNMF'

P value = 3.16e-21 (Fisher's exact test), Q value = 1.4e-18

Table S190. Gene #19: '10p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	186	542
10P MUTATED	156	28	173
10P WILD-TYPE	117	158	369

Figure S190. Get High-res Image Gene #19: '10p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.25e-18 (Fisher's exact test), Q value = 5.4e-16

Table S191. Gene #19: '10p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	439	329
10P MUTATED	134	156	67
10P WILD-TYPE	99	283	262

Figure S191. Get High-res Image Gene #19: '10p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p' versus 'MIRSEQ_CNMF'

P value = 7.4e-15 (Fisher's exact test), Q value = 2.8e-12

Table S192. Gene #19: '10p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	398	287	292
10P MUTATED	126	65	157
10P WILD-TYPE	272	222	135

Figure S192. Get High-res Image Gene #19: '10p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.83e-21 (Fisher's exact test), Q value = 3e-18

Table S193. Gene #19: '10p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	252	299	426
10P MUTATED	149	104	95
10P WILD-TYPE	103	195	331

Figure S193. Get High-res Image Gene #19: '10p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.82e-12 (Fisher's exact test), Q value = 5.9e-10

Table S194. Gene #19: '10p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	219	198
10P MUTATED	76	46	108
10P WILD-TYPE	174	173	90

Figure S194. Get High-res Image Gene #19: '10p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.94e-11 (Fisher's exact test), Q value = 2.5e-08

Table S195. Gene #19: '10p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	177	345
10P MUTATED	84	41	105
10P WILD-TYPE	61	136	240

Figure S195. Get High-res Image Gene #19: '10p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q' versus 'MRNA_CNMF'

P value = 1.12e-05 (Chi-square test), Q value = 0.0017

Table S196. Gene #20: '10q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
10Q MUTATED	8	8	41	49	23	32	8	5
10Q WILD-TYPE	13	28	78	47	86	40	12	35

Figure S196. Get High-res Image Gene #20: '10q' versus Molecular Subtype #1: 'MRNA_CNMF'

'10q' versus 'MRNA_CHIERARCHICAL'

P value = 7.46e-06 (Fisher's exact test), Q value = 0.0012

Table S197. Gene #20: '10q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
10Q MUTATED	24	61	89
10Q WILD-TYPE	98	64	177

Figure S197. Get High-res Image Gene #20: '10q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10q' versus 'CN_CNMF'

P value = 2.16e-25 (Chi-square test), Q value = 9.7e-23

Table S198. Gene #20: '10q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	371	258	97	236	45
10Q MUTATED	47	97	37	127	19
10Q WILD-TYPE	324	161	60	109	26

Figure S198. Get High-res Image Gene #20: '10q' versus Molecular Subtype #3: 'CN_CNMF'

'10q' versus 'METHLYATION_CNMF'

P value = 6.12e-16 (Chi-square test), Q value = 2.4e-13

Table S199. Gene #20: '10q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	155	108	139	55	112
10Q MUTATED	68	24	41	57	10	19
10Q WILD-TYPE	48	131	67	82	45	93

Figure S199. Get High-res Image Gene #20: '10q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q' versus 'RPPA_CNMF'

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

Table S200. Gene #20: '10q' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
10Q MUTATED	76	36	31
10Q WILD-TYPE	71	97	86

Figure S200. Get High-res Image Gene #20: '10q' versus Molecular Subtype #5: 'RPPA_CNMF'

'10q' versus 'RPPA_CHIERARCHICAL'

P value = 0.000228 (Fisher's exact test), Q value = 0.025

Table S201. Gene #20: '10q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
10Q MUTATED	52	28	63
10Q WILD-TYPE	109	82	63

Figure S201. Get High-res Image Gene #20: '10q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10q' versus 'MRNASEQ_CNMF'

P value = 1.65e-14 (Fisher's exact test), Q value = 6.1e-12

Table S202. Gene #20: '10q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	186	542
10Q MUTATED	129	24	172
10Q WILD-TYPE	144	162	370

Figure S202. Get High-res Image Gene #20: '10q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.97e-14 (Fisher's exact test), Q value = 2.5e-11

Table S203. Gene #20: '10q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	439	329
10Q MUTATED	110	157	58
10Q WILD-TYPE	123	282	271

Figure S203. Get High-res Image Gene #20: '10q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q' versus 'MIRSEQ_CNMF'

P value = 8.09e-10 (Fisher's exact test), Q value = 2.1e-07

Table S204. Gene #20: '10q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	398	287	292
10Q MUTATED	118	63	136
10Q WILD-TYPE	280	224	156

Figure S204. Get High-res Image Gene #20: '10q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.92e-13 (Fisher's exact test), Q value = 2.3e-10

Table S205. Gene #20: '10q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	252	299	426
10Q MUTATED	127	95	95
10Q WILD-TYPE	125	204	331

Figure S205. Get High-res Image Gene #20: '10q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.42e-09 (Fisher's exact test), Q value = 3.7e-07

Table S206. Gene #20: '10q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	219	198
10Q MUTATED	74	45	98
10Q WILD-TYPE	176	174	100

Figure S206. Get High-res Image Gene #20: '10q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.57e-06 (Fisher's exact test), Q value = 0.0012

Table S207. Gene #20: '10q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	177	345
10Q MUTATED	71	43	103
10Q WILD-TYPE	74	134	242

Figure S207. Get High-res Image Gene #20: '10q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p' versus 'CN_CNMF'

P value = 9.86e-36 (Chi-square test), Q value = 4.7e-33

Table S208. Gene #21: '11p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	371	258	97	236	45
11P MUTATED	50	145	42	136	15
11P WILD-TYPE	321	113	55	100	30

Figure S208. Get High-res Image Gene #21: '11p' versus Molecular Subtype #3: 'CN_CNMF'

'11p' versus 'METHLYATION_CNMF'

P value = 4.78e-13 (Chi-square test), Q value = 1.6e-10

Table S209. Gene #21: '11p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	155	108	139	55	112
11P MUTATED	65	35	45	75	12	24
11P WILD-TYPE	51	120	63	64	43	88

Figure S209. Get High-res Image Gene #21: '11p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p' versus 'MRNASEQ_CNMF'

P value = 1.51e-11 (Fisher's exact test), Q value = 4.6e-09

Table S210. Gene #21: '11p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	186	542
11P MUTATED	140	36	212
11P WILD-TYPE	133	150	330

Figure S210. Get High-res Image Gene #21: '11p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.42e-12 (Fisher's exact test), Q value = 2.6e-09

Table S211. Gene #21: '11p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	439	329
11P MUTATED	117	193	78
11P WILD-TYPE	116	246	251

Figure S211. Get High-res Image Gene #21: '11p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p' versus 'MIRSEQ_CNMF'

P value = 8.21e-11 (Fisher's exact test), Q value = 2.3e-08

Table S212. Gene #21: '11p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	398	287	292
11P MUTATED	151	70	151
11P WILD-TYPE	247	217	141

Figure S212. Get High-res Image Gene #21: '11p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.54e-12 (Fisher's exact test), Q value = 5e-10

Table S213. Gene #21: '11p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	252	299	426
11P MUTATED	131	132	109
11P WILD-TYPE	121	167	317

Figure S213. Get High-res Image Gene #21: '11p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.19e-11 (Fisher's exact test), Q value = 1.8e-08

Table S214. Gene #21: '11p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	219	198
11P MUTATED	100	45	103
11P WILD-TYPE	150	174	95

Figure S214. Get High-res Image Gene #21: '11p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.72e-09 (Fisher's exact test), Q value = 1.4e-06

Table S215. Gene #21: '11p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	177	345
11P MUTATED	76	36	136
11P WILD-TYPE	69	141	209

Figure S215. Get High-res Image Gene #21: '11p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q' versus 'MRNA_CNMF'

P value = 0.000379 (Chi-square test), Q value = 0.039

Table S216. Gene #22: '11q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
11Q MUTATED	8	21	73	36	36	38	9	15
11Q WILD-TYPE	13	15	46	60	73	34	11	25

Figure S216. Get High-res Image Gene #22: '11q' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q' versus 'CN_CNMF'

P value = 5.97e-36 (Chi-square test), Q value = 2.8e-33

Table S217. Gene #22: '11q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	371	258	97	236	45
11Q MUTATED	71	179	46	127	17
11Q WILD-TYPE	300	79	51	109	28

Figure S217. Get High-res Image Gene #22: '11q' versus Molecular Subtype #3: 'CN_CNMF'

'11q' versus 'METHLYATION_CNMF'

P value = 2.16e-10 (Chi-square test), Q value = 6e-08

Table S218. Gene #22: '11q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	155	108	139	55	112
11Q MUTATED	60	49	55	86	16	28
11Q WILD-TYPE	56	106	53	53	39	84

Figure S218. Get High-res Image Gene #22: '11q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q' versus 'MRNASEQ_CNMF'

P value = 0.000257 (Fisher's exact test), Q value = 0.028

Table S219. Gene #22: '11q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	186	542
11Q MUTATED	128	57	254
11Q WILD-TYPE	145	129	288

Figure S219. Get High-res Image Gene #22: '11q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000429 (Fisher's exact test), Q value = 0.043

Table S220. Gene #22: '11q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	439	329
11Q MUTATED	107	216	116
11Q WILD-TYPE	126	223	213

Figure S220. Get High-res Image Gene #22: '11q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q' versus 'MIRSEQ_CNMF'

P value = 0.00158 (Fisher's exact test), Q value = 0.12

Table S221. Gene #22: '11q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	398	287	292
11Q MUTATED	172	103	148
11Q WILD-TYPE	226	184	144

Figure S221. Get High-res Image Gene #22: '11q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.2e-07 (Fisher's exact test), Q value = 0.00012

Table S222. Gene #22: '11q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	252	299	426
11Q MUTATED	123	156	144
11Q WILD-TYPE	129	143	282

Figure S222. Get High-res Image Gene #22: '11q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000768 (Fisher's exact test), Q value = 0.068

Table S223. Gene #22: '11q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	219	198
11Q MUTATED	114	69	95
11Q WILD-TYPE	136	150	103

Figure S223. Get High-res Image Gene #22: '11q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00064 (Fisher's exact test), Q value = 0.058

Table S224. Gene #22: '11q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	177	345
11Q MUTATED	71	53	154
11Q WILD-TYPE	74	124	191

Figure S224. Get High-res Image Gene #22: '11q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p' versus 'MRNA_CNMF'

P value = 1.36e-07 (Chi-square test), Q value = 2.9e-05

Table S225. Gene #23: '12p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
12P MUTATED	5	12	45	58	24	32	7	6
12P WILD-TYPE	16	24	74	38	85	40	13	34

Figure S225. Get High-res Image Gene #23: '12p' versus Molecular Subtype #1: 'MRNA_CNMF'

'12p' versus 'MRNA_CHIERARCHICAL'

P value = 3.82e-08 (Fisher's exact test), Q value = 8.7e-06

Table S226. Gene #23: '12p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
12P MUTATED	24	69	96
12P WILD-TYPE	98	56	170

Figure S226. Get High-res Image Gene #23: '12p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12p' versus 'CN_CNMF'

P value = 3.2e-31 (Chi-square test), Q value = 1.5e-28

Table S227. Gene #23: '12p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	371	258	97	236	45
12P MUTATED	50	120	40	138	12
12P WILD-TYPE	321	138	57	98	33

Figure S227. Get High-res Image Gene #23: '12p' versus Molecular Subtype #3: 'CN_CNMF'

'12p' versus 'METHLYATION_CNMF'

P value = 4.65e-18 (Chi-square test), Q value = 2e-15

Table S228. Gene #23: '12p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	155	108	139	55	112
12P MUTATED	75	27	35	66	13	22
12P WILD-TYPE	41	128	73	73	42	90

Figure S228. Get High-res Image Gene #23: '12p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p' versus 'RPPA_CNMF'

P value = 0.000954 (Fisher's exact test), Q value = 0.079

Table S229. Gene #23: '12p' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
12P MUTATED	75	46	35
12P WILD-TYPE	72	87	82

Figure S229. Get High-res Image Gene #23: '12p' versus Molecular Subtype #5: 'RPPA_CNMF'

'12p' versus 'RPPA_CHIERARCHICAL'

P value = 2.72e-05 (Fisher's exact test), Q value = 0.0039

Table S230. Gene #23: '12p' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
12P MUTATED	58	29	69
12P WILD-TYPE	103	81	57

Figure S230. Get High-res Image Gene #23: '12p' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'12p' versus 'MRNASEQ_CNMF'

P value = 2.31e-17 (Fisher's exact test), Q value = 9.6e-15

Table S231. Gene #23: '12p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	186	542
12P MUTATED	150	31	178
12P WILD-TYPE	123	155	364

Figure S231. Get High-res Image Gene #23: '12p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.27e-17 (Fisher's exact test), Q value = 3e-14

Table S232. Gene #23: '12p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	439	329
12P MUTATED	129	163	67
12P WILD-TYPE	104	276	262

Figure S232. Get High-res Image Gene #23: '12p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p' versus 'MIRSEQ_CNMF'

P value = 1.56e-15 (Fisher's exact test), Q value = 6e-13

Table S233. Gene #23: '12p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	398	287	292
12P MUTATED	122	65	158
12P WILD-TYPE	276	222	134

Figure S233. Get High-res Image Gene #23: '12p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.13e-17 (Fisher's exact test), Q value = 2.5e-14

Table S234. Gene #23: '12p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	252	299	426
12P MUTATED	141	106	98
12P WILD-TYPE	111	193	328

Figure S234. Get High-res Image Gene #23: '12p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.19e-11 (Fisher's exact test), Q value = 6.6e-09

Table S235. Gene #23: '12p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	219	198
12P MUTATED	78	48	107
12P WILD-TYPE	172	171	91

Figure S235. Get High-res Image Gene #23: '12p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.24e-07 (Fisher's exact test), Q value = 6.6e-05

Table S236. Gene #23: '12p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	177	345
12P MUTATED	77	43	113
12P WILD-TYPE	68	134	232

Figure S236. Get High-res Image Gene #23: '12p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q' versus 'MRNA_CNMF'

P value = 0.000294 (Chi-square test), Q value = 0.031

Table S237. Gene #24: '12q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
12Q MUTATED	3	10	40	44	22	28	4	6
12Q WILD-TYPE	18	26	79	52	87	44	16	34

Figure S237. Get High-res Image Gene #24: '12q' versus Molecular Subtype #1: 'MRNA_CNMF'

'12q' versus 'MRNA_CHIERARCHICAL'

P value = 3.31e-05 (Fisher's exact test), Q value = 0.0046

Table S238. Gene #24: '12q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
12Q MUTATED	20	53	84
12Q WILD-TYPE	102	72	182

Figure S238. Get High-res Image Gene #24: '12q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12q' versus 'CN_CNMF'

P value = 9.48e-23 (Chi-square test), Q value = 4.2e-20

Table S239. Gene #24: '12q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	371	258	97	236	45
12Q MUTATED	40	109	39	103	12
12Q WILD-TYPE	331	149	58	133	33

Figure S239. Get High-res Image Gene #24: '12q' versus Molecular Subtype #3: 'CN_CNMF'

'12q' versus 'METHLYATION_CNMF'

P value = 8.06e-16 (Chi-square test), Q value = 3.1e-13

Table S240. Gene #24: '12q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	155	108	139	55	112
12Q MUTATED	62	24	34	61	8	15
12Q WILD-TYPE	54	131	74	78	47	97

Figure S240. Get High-res Image Gene #24: '12q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q' versus 'RPPA_CHIERARCHICAL'

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

Table S241. Gene #24: '12q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
12Q MUTATED	50	24	54
12Q WILD-TYPE	111	86	72

Figure S241. Get High-res Image Gene #24: '12q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'12q' versus 'MRNASEQ_CNMF'

P value = 6.45e-11 (Fisher's exact test), Q value = 1.9e-08

Table S242. Gene #24: '12q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	186	542
12Q MUTATED	116	25	160
12Q WILD-TYPE	157	161	382

Figure S242. Get High-res Image Gene #24: '12q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.44e-11 (Fisher's exact test), Q value = 1.3e-08

Table S243. Gene #24: '12q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	439	329
12Q MUTATED	99	146	56
12Q WILD-TYPE	134	293	273

Figure S243. Get High-res Image Gene #24: '12q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q' versus 'MIRSEQ_CNMF'

P value = 2.37e-09 (Fisher's exact test), Q value = 6e-07

Table S244. Gene #24: '12q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	398	287	292
12Q MUTATED	106	57	126
12Q WILD-TYPE	292	230	166

Figure S244. Get High-res Image Gene #24: '12q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.11e-08 (Fisher's exact test), Q value = 2.6e-06

Table S245. Gene #24: '12q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	252	299	426
12Q MUTATED	108	92	89
12Q WILD-TYPE	144	207	337

Figure S245. Get High-res Image Gene #24: '12q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.69e-08 (Fisher's exact test), Q value = 1.5e-05

Table S246. Gene #24: '12q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	219	198
12Q MUTATED	71	42	89
12Q WILD-TYPE	179	177	109

Figure S246. Get High-res Image Gene #24: '12q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000426 (Fisher's exact test), Q value = 0.043

Table S247. Gene #24: '12q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	177	345
12Q MUTATED	62	40	100
12Q WILD-TYPE	83	137	245

Figure S247. Get High-res Image Gene #24: '12q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q' versus 'MRNA_CNMF'

P value = 8.48e-07 (Chi-square test), Q value = 0.00016

Table S248. Gene #25: '13q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
13Q MUTATED	10	17	73	65	42	44	10	8
13Q WILD-TYPE	11	19	46	31	67	28	10	32

Figure S248. Get High-res Image Gene #25: '13q' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q' versus 'MRNA_CHIERARCHICAL'

P value = 5.2e-08 (Fisher's exact test), Q value = 1.2e-05

Table S249. Gene #25: '13q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
13Q MUTATED	39	85	145
13Q WILD-TYPE	83	40	121

Figure S249. Get High-res Image Gene #25: '13q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q' versus 'CN_CNMF'

P value = 2.48e-35 (Chi-square test), Q value = 1.2e-32

Table S250. Gene #25: '13q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	371	258	97	236	45
13Q MUTATED	84	167	60	156	30
13Q WILD-TYPE	287	91	37	80	15

Figure S250. Get High-res Image Gene #25: '13q' versus Molecular Subtype #3: 'CN_CNMF'

'13q' versus 'METHLYATION_CNMF'

P value = 2.67e-14 (Chi-square test), Q value = 9.8e-12

Table S251. Gene #25: '13q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	155	108	139	55	112
13Q MUTATED	83	50	64	77	11	41
13Q WILD-TYPE	33	105	44	62	44	71

Figure S251. Get High-res Image Gene #25: '13q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q' versus 'MRNASEQ_CNMF'

P value = 3.23e-15 (Fisher's exact test), Q value = 1.2e-12

Table S252. Gene #25: '13q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	186	542
13Q MUTATED	178	50	266
13Q WILD-TYPE	95	136	276

Figure S252. Get High-res Image Gene #25: '13q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.67e-16 (Fisher's exact test), Q value = 6.7e-14

Table S253. Gene #25: '13q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	439	329
13Q MUTATED	156	233	105
13Q WILD-TYPE	77	206	224

Figure S253. Get High-res Image Gene #25: '13q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q' versus 'MIRSEQ_CNMF'

P value = 1.68e-13 (Fisher's exact test), Q value = 5.9e-11

Table S254. Gene #25: '13q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	398	287	292
13Q MUTATED	194	98	192
13Q WILD-TYPE	204	189	100

Figure S254. Get High-res Image Gene #25: '13q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.45e-14 (Fisher's exact test), Q value = 2.7e-11

Table S255. Gene #25: '13q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	252	299	426
13Q MUTATED	170	156	158
13Q WILD-TYPE	82	143	268

Figure S255. Get High-res Image Gene #25: '13q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-10 (Fisher's exact test), Q value = 5.6e-08

Table S256. Gene #25: '13q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	219	198
13Q MUTATED	107	76	131
13Q WILD-TYPE	143	143	67

Figure S256. Get High-res Image Gene #25: '13q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'13q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.14e-06 (Fisher's exact test), Q value = 0.00039

Table S257. Gene #25: '13q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	177	345
13Q MUTATED	94	66	154
13Q WILD-TYPE	51	111	191

Figure S257. Get High-res Image Gene #25: '13q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q' versus 'MRNA_CNMF'

P value = 6.95e-08 (Chi-square test), Q value = 1.5e-05

Table S258. Gene #26: '14q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
14Q MUTATED	6	9	46	56	25	34	12	6
14Q WILD-TYPE	15	27	73	40	84	38	8	34

Figure S258. Get High-res Image Gene #26: '14q' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q' versus 'MRNA_CHIERARCHICAL'

P value = 9.07e-07 (Fisher's exact test), Q value = 0.00017

Table S259. Gene #26: '14q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
14Q MUTATED	28	69	97
14Q WILD-TYPE	94	56	169

Figure S259. Get High-res Image Gene #26: '14q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q' versus 'CN_CNMF'

P value = 9.33e-32 (Chi-square test), Q value = 4.3e-29

Table S260. Gene #26: '14q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	371	258	97	236	45
14Q MUTATED	57	114	41	150	17
14Q WILD-TYPE	314	144	56	86	28

Figure S260. Get High-res Image Gene #26: '14q' versus Molecular Subtype #3: 'CN_CNMF'

'14q' versus 'METHLYATION_CNMF'

P value = 3.24e-17 (Chi-square test), Q value = 1.3e-14

Table S261. Gene #26: '14q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	155	108	139	55	112
14Q MUTATED	79	30	46	58	11	27
14Q WILD-TYPE	37	125	62	81	44	85

Figure S261. Get High-res Image Gene #26: '14q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q' versus 'RPPA_CNMF'

P value = 2.84e-06 (Fisher's exact test), Q value = 5e-04

Table S262. Gene #26: '14q' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
14Q MUTATED	79	34	38
14Q WILD-TYPE	68	99	79

Figure S262. Get High-res Image Gene #26: '14q' versus Molecular Subtype #5: 'RPPA_CNMF'

'14q' versus 'RPPA_CHIERARCHICAL'

P value = 0.000749 (Fisher's exact test), Q value = 0.067

Table S263. Gene #26: '14q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
14Q MUTATED	53	33	65
14Q WILD-TYPE	108	77	61

Figure S263. Get High-res Image Gene #26: '14q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'14q' versus 'MRNASEQ_CNMF'

P value = 8.2e-19 (Fisher's exact test), Q value = 3.5e-16

Table S264. Gene #26: '14q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	186	542
14Q MUTATED	155	30	192
14Q WILD-TYPE	118	156	350

Figure S264. Get High-res Image Gene #26: '14q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.47e-20 (Fisher's exact test), Q value = 1.1e-17

Table S265. Gene #26: '14q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	439	329
14Q MUTATED	140	168	69
14Q WILD-TYPE	93	271	260

Figure S265. Get High-res Image Gene #26: '14q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q' versus 'MIRSEQ_CNMF'

P value = 2.75e-16 (Fisher's exact test), Q value = 1.1e-13

Table S266. Gene #26: '14q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	398	287	292
14Q MUTATED	139	64	163
14Q WILD-TYPE	259	223	129

Figure S266. Get High-res Image Gene #26: '14q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.55e-17 (Fisher's exact test), Q value = 1.1e-14

Table S267. Gene #26: '14q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	252	299	426
14Q MUTATED	152	98	116
14Q WILD-TYPE	100	201	310

Figure S267. Get High-res Image Gene #26: '14q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.42e-12 (Fisher's exact test), Q value = 4.6e-10

Table S268. Gene #26: '14q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	219	198
14Q MUTATED	91	53	117
14Q WILD-TYPE	159	166	81

Figure S268. Get High-res Image Gene #26: '14q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.69e-13 (Fisher's exact test), Q value = 1.3e-10

Table S269. Gene #26: '14q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	177	345
14Q MUTATED	95	46	120
14Q WILD-TYPE	50	131	225

Figure S269. Get High-res Image Gene #26: '14q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q' versus 'MRNA_CNMF'

P value = 8.63e-09 (Chi-square test), Q value = 2.1e-06

Table S270. Gene #27: '15q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
15Q MUTATED	6	13	42	56	25	42	12	7
15Q WILD-TYPE	15	23	77	40	84	30	8	33

Figure S270. Get High-res Image Gene #27: '15q' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q' versus 'MRNA_CHIERARCHICAL'

P value = 5.92e-07 (Fisher's exact test), Q value = 0.00012

Table S271. Gene #27: '15q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
15Q MUTATED	28	70	105
15Q WILD-TYPE	94	55	161

Figure S271. Get High-res Image Gene #27: '15q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'15q' versus 'CN_CNMF'

P value = 8.57e-37 (Chi-square test), Q value = 4.1e-34

Table S272. Gene #27: '15q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	371	258	97	236	45
15Q MUTATED	56	107	52	157	15
15Q WILD-TYPE	315	151	45	79	30

Figure S272. Get High-res Image Gene #27: '15q' versus Molecular Subtype #3: 'CN_CNMF'

'15q' versus 'METHLYATION_CNMF'

P value = 2.24e-17 (Chi-square test), Q value = 9.3e-15

Table S273. Gene #27: '15q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	155	108	139	55	112
15Q MUTATED	82	29	45	58	16	29
15Q WILD-TYPE	34	126	63	81	39	83

Figure S273. Get High-res Image Gene #27: '15q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q' versus 'RPPA_CNMF'

P value = 0.000514 (Fisher's exact test), Q value = 0.05

Table S274. Gene #27: '15q' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
15Q MUTATED	80	46	40
15Q WILD-TYPE	67	87	77

Figure S274. Get High-res Image Gene #27: '15q' versus Molecular Subtype #5: 'RPPA_CNMF'

'15q' versus 'RPPA_CHIERARCHICAL'

P value = 0.000127 (Fisher's exact test), Q value = 0.016

Table S275. Gene #27: '15q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
15Q MUTATED	58	36	72
15Q WILD-TYPE	103	74	54

Figure S275. Get High-res Image Gene #27: '15q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'15q' versus 'MRNASEQ_CNMF'

P value = 5.19e-21 (Fisher's exact test), Q value = 2.3e-18

Table S276. Gene #27: '15q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	186	542
15Q MUTATED	159	28	197
15Q WILD-TYPE	114	158	345

Figure S276. Get High-res Image Gene #27: '15q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.5e-19 (Fisher's exact test), Q value = 6.5e-17

Table S277. Gene #27: '15q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	439	329
15Q MUTATED	136	180	68
15Q WILD-TYPE	97	259	261

Figure S277. Get High-res Image Gene #27: '15q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q' versus 'MIRSEQ_CNMF'

P value = 1.78e-15 (Fisher's exact test), Q value = 6.8e-13

Table S278. Gene #27: '15q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	398	287	292
15Q MUTATED	143	66	163
15Q WILD-TYPE	255	221	129

Figure S278. Get High-res Image Gene #27: '15q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.79e-18 (Fisher's exact test), Q value = 2.4e-15

Table S279. Gene #27: '15q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	252	299	426
15Q MUTATED	154	103	115
15Q WILD-TYPE	98	196	311

Figure S279. Get High-res Image Gene #27: '15q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.78e-11 (Fisher's exact test), Q value = 1.1e-08

Table S280. Gene #27: '15q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	219	198
15Q MUTATED	94	48	108
15Q WILD-TYPE	156	171	90

Figure S280. Get High-res Image Gene #27: '15q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.07e-10 (Fisher's exact test), Q value = 1.9e-07

Table S281. Gene #27: '15q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	177	345
15Q MUTATED	85	42	123
15Q WILD-TYPE	60	135	222

Figure S281. Get High-res Image Gene #27: '15q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p' versus 'MRNA_CHIERARCHICAL'

P value = 0.0031 (Fisher's exact test), Q value = 0.21

Table S282. Gene #28: '16p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
16P MUTATED	68	68	185
16P WILD-TYPE	54	57	81

Figure S282. Get High-res Image Gene #28: '16p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16p' versus 'CN_CNMF'

P value = 6.64e-08 (Chi-square test), Q value = 1.5e-05

Table S283. Gene #28: '16p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	371	258	97	236	45
16P MUTATED	188	164	82	142	27
16P WILD-TYPE	183	94	15	94	18

Figure S283. Get High-res Image Gene #28: '16p' versus Molecular Subtype #3: 'CN_CNMF'

'16p' versus 'METHLYATION_CNMF'

P value = 4.9e-05 (Chi-square test), Q value = 0.0064

Table S284. Gene #28: '16p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	155	108	139	55	112
16P MUTATED	66	102	74	73	19	53
16P WILD-TYPE	50	53	34	66	36	59

Figure S284. Get High-res Image Gene #28: '16p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p' versus 'MRNASEQ_CNMF'

P value = 0.000913 (Fisher's exact test), Q value = 0.078

Table S285. Gene #28: '16p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	186	542
16P MUTATED	144	102	353
16P WILD-TYPE	129	84	189

Figure S285. Get High-res Image Gene #28: '16p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000542 (Fisher's exact test), Q value = 0.052

Table S286. Gene #28: '16p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	439	329
16P MUTATED	118	289	192
16P WILD-TYPE	115	150	137

Figure S286. Get High-res Image Gene #28: '16p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q' versus 'MRNA_CNMF'

P value = 1.96e-07 (Chi-square test), Q value = 4.1e-05

Table S287. Gene #29: '16q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
16Q MUTATED	14	25	80	44	94	48	16	33
16Q WILD-TYPE	7	11	39	52	15	24	4	7

Figure S287. Get High-res Image Gene #29: '16q' versus Molecular Subtype #1: 'MRNA_CNMF'

'16q' versus 'MRNA_CHIERARCHICAL'

P value = 8.93e-08 (Fisher's exact test), Q value = 2e-05

Table S288. Gene #29: '16q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
16Q MUTATED	91	60	203
16Q WILD-TYPE	31	65	63

Figure S288. Get High-res Image Gene #29: '16q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16q' versus 'CN_CNMF'

P value = 3.33e-07 (Chi-square test), Q value = 6.8e-05

Table S289. Gene #29: '16q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	371	258	97	236	45
16Q MUTATED	253	180	87	134	33
16Q WILD-TYPE	118	78	10	102	12

Figure S289. Get High-res Image Gene #29: '16q' versus Molecular Subtype #3: 'CN_CNMF'

'16q' versus 'METHLYATION_CNMF'

P value = 5.06e-11 (Chi-square test), Q value = 1.5e-08

Table S290. Gene #29: '16q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	155	108	139	55	112
16Q MUTATED	63	132	88	87	27	63
16Q WILD-TYPE	53	23	20	52	28	49

Figure S290. Get High-res Image Gene #29: '16q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q' versus 'RPPA_CNMF'

P value = 0.000897 (Fisher's exact test), Q value = 0.078

Table S291. Gene #29: '16q' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
16Q MUTATED	83	103	80
16Q WILD-TYPE	64	30	37

Figure S291. Get High-res Image Gene #29: '16q' versus Molecular Subtype #5: 'RPPA_CNMF'

'16q' versus 'RPPA_CHIERARCHICAL'

P value = 6.47e-06 (Fisher's exact test), Q value = 0.0011

Table S292. Gene #29: '16q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
16Q MUTATED	123	80	63
16Q WILD-TYPE	38	30	63

Figure S292. Get High-res Image Gene #29: '16q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16q' versus 'MRNASEQ_CNMF'

P value = 7.27e-12 (Fisher's exact test), Q value = 2.2e-09

Table S293. Gene #29: '16q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	186	542
16Q MUTATED	139	145	399
16Q WILD-TYPE	134	41	143

Figure S293. Get High-res Image Gene #29: '16q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.36e-12 (Fisher's exact test), Q value = 4.4e-10

Table S294. Gene #29: '16q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	439	329
16Q MUTATED	113	316	254
16Q WILD-TYPE	120	123	75

Figure S294. Get High-res Image Gene #29: '16q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q' versus 'MIRSEQ_CNMF'

P value = 1.98e-07 (Fisher's exact test), Q value = 4.1e-05

Table S295. Gene #29: '16q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	398	287	292
16Q MUTATED	290	215	162
16Q WILD-TYPE	108	72	130

Figure S295. Get High-res Image Gene #29: '16q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.18e-11 (Fisher's exact test), Q value = 1.2e-08

Table S296. Gene #29: '16q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	252	299	426
16Q MUTATED	142	186	339
16Q WILD-TYPE	110	113	87

Figure S296. Get High-res Image Gene #29: '16q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000135 (Fisher's exact test), Q value = 0.016

Table S297. Gene #29: '16q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	219	198
16Q MUTATED	174	167	113
16Q WILD-TYPE	76	52	85

Figure S297. Get High-res Image Gene #29: '16q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.32e-05 (Fisher's exact test), Q value = 0.0069

Table S298. Gene #29: '16q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	177	345
16Q MUTATED	78	136	240
16Q WILD-TYPE	67	41	105

Figure S298. Get High-res Image Gene #29: '16q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p' versus 'MRNA_CNMF'

P value = 4.91e-13 (Chi-square test), Q value = 1.7e-10

Table S299. Gene #30: '17p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
17P MUTATED	14	28	89	69	37	62	15	23
17P WILD-TYPE	7	8	30	27	72	10	5	17

Figure S299. Get High-res Image Gene #30: '17p' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p' versus 'CN_CNMF'

P value = 4.02e-34 (Chi-square test), Q value = 1.9e-31

Table S300. Gene #30: '17p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	371	258	97	236	45
17P MUTATED	150	212	58	195	29
17P WILD-TYPE	221	46	39	41	16

Figure S300. Get High-res Image Gene #30: '17p' versus Molecular Subtype #3: 'CN_CNMF'

'17p' versus 'METHLYATION_CNMF'

P value = 2.51e-12 (Chi-square test), Q value = 8e-10

Table S301. Gene #30: '17p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	155	108	139	55	112
17P MUTATED	88	71	75	113	27	55
17P WILD-TYPE	28	84	33	26	28	57

Figure S301. Get High-res Image Gene #30: '17p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p' versus 'RPPA_CNMF'

P value = 7.42e-07 (Fisher's exact test), Q value = 0.00014

Table S302. Gene #30: '17p' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
17P MUTATED	121	73	70
17P WILD-TYPE	26	60	47

Figure S302. Get High-res Image Gene #30: '17p' versus Molecular Subtype #5: 'RPPA_CNMF'

'17p' versus 'RPPA_CHIERARCHICAL'

P value = 0.00231 (Fisher's exact test), Q value = 0.17

Table S303. Gene #30: '17p' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
17P MUTATED	103	63	98
17P WILD-TYPE	58	47	28

Figure S303. Get High-res Image Gene #30: '17p' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17p' versus 'MRNASEQ_CNMF'

P value = 1.07e-07 (Fisher's exact test), Q value = 2.3e-05

Table S304. Gene #30: '17p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	186	542
17P MUTATED	207	94	339
17P WILD-TYPE	66	92	203

Figure S304. Get High-res Image Gene #30: '17p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.59e-05 (Fisher's exact test), Q value = 0.0037

Table S305. Gene #30: '17p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	439	329
17P MUTATED	170	290	180
17P WILD-TYPE	63	149	149

Figure S305. Get High-res Image Gene #30: '17p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p' versus 'MIRSEQ_CNMF'

P value = 6e-09 (Fisher's exact test), Q value = 1.5e-06

Table S306. Gene #30: '17p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	398	287	292
17P MUTATED	248	151	224
17P WILD-TYPE	150	136	68

Figure S306. Get High-res Image Gene #30: '17p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.61e-08 (Fisher's exact test), Q value = 1.3e-05

Table S307. Gene #30: '17p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	252	299	426
17P MUTATED	191	200	232
17P WILD-TYPE	61	99	194

Figure S307. Get High-res Image Gene #30: '17p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.77e-07 (Fisher's exact test), Q value = 3.7e-05

Table S308. Gene #30: '17p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	219	198
17P MUTATED	153	114	154
17P WILD-TYPE	97	105	44

Figure S308. Get High-res Image Gene #30: '17p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00327 (Fisher's exact test), Q value = 0.22

Table S309. Gene #30: '17p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	177	345
17P MUTATED	105	96	220
17P WILD-TYPE	40	81	125

Figure S309. Get High-res Image Gene #30: '17p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q' versus 'MRNA_CNMF'

P value = 6.31e-10 (Chi-square test), Q value = 1.7e-07

Table S310. Gene #31: '17q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
17Q MUTATED	7	12	69	59	22	45	9	17
17Q WILD-TYPE	14	24	50	37	87	27	11	23

Figure S310. Get High-res Image Gene #31: '17q' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q' versus 'MRNA_CHIERARCHICAL'

P value = 1.68e-05 (Fisher's exact test), Q value = 0.0025

Table S311. Gene #31: '17q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
17Q MUTATED	39	77	124
17Q WILD-TYPE	83	48	142

Figure S311. Get High-res Image Gene #31: '17q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q' versus 'CN_CNMF'

P value = 3.62e-29 (Chi-square test), Q value = 1.7e-26

Table S312. Gene #31: '17q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	371	258	97	236	45
17Q MUTATED	86	164	42	150	20
17Q WILD-TYPE	285	94	55	86	25

Figure S312. Get High-res Image Gene #31: '17q' versus Molecular Subtype #3: 'CN_CNMF'

'17q' versus 'METHLYATION_CNMF'

P value = 2.99e-12 (Chi-square test), Q value = 9.5e-10

Table S313. Gene #31: '17q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	155	108	139	55	112
17Q MUTATED	71	39	46	85	13	45
17Q WILD-TYPE	45	116	62	54	42	67

Figure S313. Get High-res Image Gene #31: '17q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q' versus 'RPPA_CNMF'

P value = 7.27e-07 (Fisher's exact test), Q value = 0.00014

Table S314. Gene #31: '17q' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
17Q MUTATED	96	46	51
17Q WILD-TYPE	51	87	66

Figure S314. Get High-res Image Gene #31: '17q' versus Molecular Subtype #5: 'RPPA_CNMF'

'17q' versus 'RPPA_CHIERARCHICAL'

P value = 0.000237 (Fisher's exact test), Q value = 0.026

Table S315. Gene #31: '17q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
17Q MUTATED	65	48	80
17Q WILD-TYPE	96	62	46

Figure S315. Get High-res Image Gene #31: '17q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17q' versus 'MRNASEQ_CNMF'

P value = 1.34e-09 (Fisher's exact test), Q value = 3.5e-07

Table S316. Gene #31: '17q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	186	542
17Q MUTATED	162	55	241
17Q WILD-TYPE	111	131	301

Figure S316. Get High-res Image Gene #31: '17q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.91e-09 (Fisher's exact test), Q value = 1.2e-06

Table S317. Gene #31: '17q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	439	329
17Q MUTATED	138	210	110
17Q WILD-TYPE	95	229	219

Figure S317. Get High-res Image Gene #31: '17q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q' versus 'MIRSEQ_CNMF'

P value = 1.15e-08 (Fisher's exact test), Q value = 2.7e-06

Table S318. Gene #31: '17q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	398	287	292
17Q MUTATED	172	101	174
17Q WILD-TYPE	226	186	118

Figure S318. Get High-res Image Gene #31: '17q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.52e-13 (Fisher's exact test), Q value = 5.3e-11

Table S319. Gene #31: '17q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	252	299	426
17Q MUTATED	153	156	138
17Q WILD-TYPE	99	143	288

Figure S319. Get High-res Image Gene #31: '17q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.38e-08 (Fisher's exact test), Q value = 2e-05

Table S320. Gene #31: '17q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	219	198
17Q MUTATED	108	78	124
17Q WILD-TYPE	142	141	74

Figure S320. Get High-res Image Gene #31: '17q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000219 (Fisher's exact test), Q value = 0.025

Table S321. Gene #31: '17q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	177	345
17Q MUTATED	82	61	167
17Q WILD-TYPE	63	116	178

Figure S321. Get High-res Image Gene #31: '17q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p' versus 'MRNA_CNMF'

P value = 5.82e-07 (Chi-square test), Q value = 0.00011

Table S322. Gene #32: '18p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
18P MUTATED	7	12	55	62	35	48	13	14
18P WILD-TYPE	14	24	64	34	74	24	7	26

Figure S322. Get High-res Image Gene #32: '18p' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p' versus 'MRNA_CHIERARCHICAL'

P value = 2.67e-06 (Fisher's exact test), Q value = 0.00047

Table S323. Gene #32: '18p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
18P MUTATED	39	80	127
18P WILD-TYPE	83	45	139

Figure S323. Get High-res Image Gene #32: '18p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p' versus 'CN_CNMF'

P value = 1.85e-33 (Chi-square test), Q value = 8.7e-31

Table S324. Gene #32: '18p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	371	258	97	236	45
18P MUTATED	78	145	59	161	20
18P WILD-TYPE	293	113	38	75	25

Figure S324. Get High-res Image Gene #32: '18p' versus Molecular Subtype #3: 'CN_CNMF'

'18p' versus 'METHLYATION_CNMF'

P value = 1.99e-13 (Chi-square test), Q value = 6.9e-11

Table S325. Gene #32: '18p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	155	108	139	55	112
18P MUTATED	76	38	59	74	13	39
18P WILD-TYPE	40	117	49	65	42	73

Figure S325. Get High-res Image Gene #32: '18p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p' versus 'RPPA_CNMF'

P value = 0.000148 (Fisher's exact test), Q value = 0.018

Table S326. Gene #32: '18p' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
18P MUTATED	92	54	48
18P WILD-TYPE	55	79	69

Figure S326. Get High-res Image Gene #32: '18p' versus Molecular Subtype #5: 'RPPA_CNMF'

'18p' versus 'RPPA_CHIERARCHICAL'

P value = 0.000204 (Fisher's exact test), Q value = 0.023

Table S327. Gene #32: '18p' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
18P MUTATED	72	42	80
18P WILD-TYPE	89	68	46

Figure S327. Get High-res Image Gene #32: '18p' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18p' versus 'MRNASEQ_CNMF'

P value = 5.27e-17 (Fisher's exact test), Q value = 2.2e-14

Table S328. Gene #32: '18p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	186	542
18P MUTATED	173	43	244
18P WILD-TYPE	100	143	298

Figure S328. Get High-res Image Gene #32: '18p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.93e-16 (Fisher's exact test), Q value = 7.7e-14

Table S329. Gene #32: '18p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	439	329
18P MUTATED	149	216	95
18P WILD-TYPE	84	223	234

Figure S329. Get High-res Image Gene #32: '18p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p' versus 'MIRSEQ_CNMF'

P value = 3.31e-14 (Fisher's exact test), Q value = 1.2e-11

Table S330. Gene #32: '18p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	398	287	292
18P MUTATED	172	90	185
18P WILD-TYPE	226	197	107

Figure S330. Get High-res Image Gene #32: '18p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.48e-13 (Fisher's exact test), Q value = 5.2e-11

Table S331. Gene #32: '18p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	252	299	426
18P MUTATED	162	140	145
18P WILD-TYPE	90	159	281

Figure S331. Get High-res Image Gene #32: '18p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.61e-13 (Fisher's exact test), Q value = 9e-11

Table S332. Gene #32: '18p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	219	198
18P MUTATED	110	61	128
18P WILD-TYPE	140	158	70

Figure S332. Get High-res Image Gene #32: '18p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.1e-09 (Fisher's exact test), Q value = 1.7e-06

Table S333. Gene #32: '18p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	177	345
18P MUTATED	94	55	150
18P WILD-TYPE	51	122	195

Figure S333. Get High-res Image Gene #32: '18p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q' versus 'MRNA_CNMF'

P value = 9.47e-05 (Chi-square test), Q value = 0.012

Table S334. Gene #33: '18q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
18Q MUTATED	7	12	55	56	36	43	11	10
18Q WILD-TYPE	14	24	64	40	73	29	9	30

Figure S334. Get High-res Image Gene #33: '18q' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q' versus 'MRNA_CHIERARCHICAL'

P value = 0.000137 (Fisher's exact test), Q value = 0.016

Table S335. Gene #33: '18q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
18Q MUTATED	36	69	125
18Q WILD-TYPE	86	56	141

Figure S335. Get High-res Image Gene #33: '18q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q' versus 'CN_CNMF'

P value = 1.44e-34 (Chi-square test), Q value = 6.8e-32

Table S336. Gene #33: '18q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	371	258	97	236	45
18Q MUTATED	69	141	61	153	19
18Q WILD-TYPE	302	117	36	83	26

Figure S336. Get High-res Image Gene #33: '18q' versus Molecular Subtype #3: 'CN_CNMF'

'18q' versus 'METHLYATION_CNMF'

P value = 4.2e-13 (Chi-square test), Q value = 1.4e-10

Table S337. Gene #33: '18q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	155	108	139	55	112
18Q MUTATED	69	38	60	77	13	33
18Q WILD-TYPE	47	117	48	62	42	79

Figure S337. Get High-res Image Gene #33: '18q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q' versus 'RPPA_CNMF'

P value = 0.000616 (Fisher's exact test), Q value = 0.058

Table S338. Gene #33: '18q' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
18Q MUTATED	85	52	43
18Q WILD-TYPE	62	81	74

Figure S338. Get High-res Image Gene #33: '18q' versus Molecular Subtype #5: 'RPPA_CNMF'

'18q' versus 'MRNASEQ_CNMF'

P value = 8.86e-14 (Fisher's exact test), Q value = 3.2e-11

Table S339. Gene #33: '18q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	186	542
18Q MUTATED	156	40	243
18Q WILD-TYPE	117	146	299

Figure S339. Get High-res Image Gene #33: '18q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.93e-11 (Fisher's exact test), Q value = 5.8e-09

Table S340. Gene #33: '18q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	439	329
18Q MUTATED	131	213	95
18Q WILD-TYPE	102	226	234

Figure S340. Get High-res Image Gene #33: '18q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q' versus 'MIRSEQ_CNMF'

P value = 2.48e-11 (Fisher's exact test), Q value = 7.5e-09

Table S341. Gene #33: '18q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	398	287	292
18Q MUTATED	170	85	170
18Q WILD-TYPE	228	202	122

Figure S341. Get High-res Image Gene #33: '18q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.44e-10 (Fisher's exact test), Q value = 6.7e-08

Table S342. Gene #33: '18q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	252	299	426
18Q MUTATED	149	135	141
18Q WILD-TYPE	103	164	285

Figure S342. Get High-res Image Gene #33: '18q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.14e-11 (Fisher's exact test), Q value = 3.5e-09

Table S343. Gene #33: '18q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	219	198
18Q MUTATED	104	59	121
18Q WILD-TYPE	146	160	77

Figure S343. Get High-res Image Gene #33: '18q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.22e-06 (Fisher's exact test), Q value = 0.0013

Table S344. Gene #33: '18q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	177	345
18Q MUTATED	83	54	147
18Q WILD-TYPE	62	123	198

Figure S344. Get High-res Image Gene #33: '18q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p' versus 'MRNA_CNMF'

P value = 8.91e-06 (Chi-square test), Q value = 0.0014

Table S345. Gene #34: '19p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
19P MUTATED	8	9	46	49	23	35	9	6
19P WILD-TYPE	13	27	73	47	86	37	11	34

Figure S345. Get High-res Image Gene #34: '19p' versus Molecular Subtype #1: 'MRNA_CNMF'

'19p' versus 'MRNA_CHIERARCHICAL'

P value = 2.33e-06 (Fisher's exact test), Q value = 0.00041

Table S346. Gene #34: '19p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
19P MUTATED	23	61	101
19P WILD-TYPE	99	64	165

Figure S346. Get High-res Image Gene #34: '19p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19p' versus 'CN_CNMF'

P value = 1.93e-28 (Chi-square test), Q value = 8.9e-26

Table S347. Gene #34: '19p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	371	258	97	236	45
19P MUTATED	48	124	36	127	15
19P WILD-TYPE	323	134	61	109	30

Figure S347. Get High-res Image Gene #34: '19p' versus Molecular Subtype #3: 'CN_CNMF'

'19p' versus 'METHLYATION_CNMF'

P value = 7.21e-13 (Chi-square test), Q value = 2.4e-10

Table S348. Gene #34: '19p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	155	108	139	55	112
19P MUTATED	60	21	36	66	10	30
19P WILD-TYPE	56	134	72	73	45	82

Figure S348. Get High-res Image Gene #34: '19p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p' versus 'RPPA_CNMF'

P value = 1.53e-05 (Fisher's exact test), Q value = 0.0023

Table S349. Gene #34: '19p' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
19P MUTATED	77	43	30
19P WILD-TYPE	70	90	87

Figure S349. Get High-res Image Gene #34: '19p' versus Molecular Subtype #5: 'RPPA_CNMF'

'19p' versus 'RPPA_CHIERARCHICAL'

P value = 5.02e-05 (Fisher's exact test), Q value = 0.0065

Table S350. Gene #34: '19p' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
19P MUTATED	54	29	67
19P WILD-TYPE	107	81	59

Figure S350. Get High-res Image Gene #34: '19p' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'19p' versus 'MRNASEQ_CNMF'

P value = 6.71e-13 (Fisher's exact test), Q value = 2.2e-10

Table S351. Gene #34: '19p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	186	542
19P MUTATED	138	33	176
19P WILD-TYPE	135	153	366

Figure S351. Get High-res Image Gene #34: '19p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.96e-14 (Fisher's exact test), Q value = 2.5e-11

Table S352. Gene #34: '19p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	439	329
19P MUTATED	117	165	65
19P WILD-TYPE	116	274	264

Figure S352. Get High-res Image Gene #34: '19p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p' versus 'MIRSEQ_CNMF'

P value = 2.48e-16 (Fisher's exact test), Q value = 9.9e-14

Table S353. Gene #34: '19p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	398	287	292
19P MUTATED	121	59	155
19P WILD-TYPE	277	228	137

Figure S353. Get High-res Image Gene #34: '19p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.16e-13 (Fisher's exact test), Q value = 4.1e-11

Table S354. Gene #34: '19p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	252	299	426
19P MUTATED	125	117	93
19P WILD-TYPE	127	182	333

Figure S354. Get High-res Image Gene #34: '19p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.3e-14 (Fisher's exact test), Q value = 3.3e-11

Table S355. Gene #34: '19p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	219	198
19P MUTATED	76	43	109
19P WILD-TYPE	174	176	89

Figure S355. Get High-res Image Gene #34: '19p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.26e-06 (Fisher's exact test), Q value = 0.00057

Table S356. Gene #34: '19p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	177	345
19P MUTATED	74	44	110
19P WILD-TYPE	71	133	235

Figure S356. Get High-res Image Gene #34: '19p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q' versus 'MRNA_CNMF'

P value = 2.49e-05 (Chi-square test), Q value = 0.0036

Table S357. Gene #35: '19q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
19Q MUTATED	8	9	48	46	23	37	9	7
19Q WILD-TYPE	13	27	71	50	86	35	11	33

Figure S357. Get High-res Image Gene #35: '19q' versus Molecular Subtype #1: 'MRNA_CNMF'

'19q' versus 'MRNA_CHIERARCHICAL'

P value = 1.06e-05 (Fisher's exact test), Q value = 0.0017

Table S358. Gene #35: '19q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
19Q MUTATED	24	59	104
19Q WILD-TYPE	98	66	162

Figure S358. Get High-res Image Gene #35: '19q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19q' versus 'CN_CNMF'

P value = 2.11e-27 (Chi-square test), Q value = 9.6e-25

Table S359. Gene #35: '19q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	371	258	97	236	45
19Q MUTATED	49	126	36	123	20
19Q WILD-TYPE	322	132	61	113	25

Figure S359. Get High-res Image Gene #35: '19q' versus Molecular Subtype #3: 'CN_CNMF'

'19q' versus 'METHLYATION_CNMF'

P value = 1.09e-10 (Chi-square test), Q value = 3.1e-08

Table S360. Gene #35: '19q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	155	108	139	55	112
19Q MUTATED	56	24	37	67	10	31
19Q WILD-TYPE	60	131	71	72	45	81

Figure S360. Get High-res Image Gene #35: '19q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q' versus 'RPPA_CNMF'

P value = 0.000631 (Fisher's exact test), Q value = 0.058

Table S361. Gene #35: '19q' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
19Q MUTATED	70	43	30
19Q WILD-TYPE	77	90	87

Figure S361. Get High-res Image Gene #35: '19q' versus Molecular Subtype #5: 'RPPA_CNMF'

'19q' versus 'MRNASEQ_CNMF'

P value = 8.6e-11 (Fisher's exact test), Q value = 2.5e-08

Table S362. Gene #35: '19q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	186	542
19Q MUTATED	135	36	181
19Q WILD-TYPE	138	150	361

Figure S362. Get High-res Image Gene #35: '19q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.52e-14 (Fisher's exact test), Q value = 2e-11

Table S363. Gene #35: '19q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	439	329
19Q MUTATED	116	171	65
19Q WILD-TYPE	117	268	264

Figure S363. Get High-res Image Gene #35: '19q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q' versus 'MIRSEQ_CNMF'

P value = 5.27e-13 (Fisher's exact test), Q value = 1.8e-10

Table S364. Gene #35: '19q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	398	287	292
19Q MUTATED	126	65	151
19Q WILD-TYPE	272	222	141

Figure S364. Get High-res Image Gene #35: '19q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.31e-12 (Fisher's exact test), Q value = 1e-09

Table S365. Gene #35: '19q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	252	299	426
19Q MUTATED	123	121	98
19Q WILD-TYPE	129	178	328

Figure S365. Get High-res Image Gene #35: '19q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-10 (Fisher's exact test), Q value = 1.1e-07

Table S366. Gene #35: '19q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	219	198
19Q MUTATED	78	49	104
19Q WILD-TYPE	172	170	94

Figure S366. Get High-res Image Gene #35: '19q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.68e-05 (Fisher's exact test), Q value = 0.0038

Table S367. Gene #35: '19q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	177	345
19Q MUTATED	72	45	114
19Q WILD-TYPE	73	132	231

Figure S367. Get High-res Image Gene #35: '19q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p' versus 'MRNA_CNMF'

P value = 3.96e-09 (Chi-square test), Q value = 9.9e-07

Table S368. Gene #36: '20p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
20P MUTATED	9	15	59	58	36	50	16	7
20P WILD-TYPE	12	21	60	38	73	22	4	33

Figure S368. Get High-res Image Gene #36: '20p' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p' versus 'MRNA_CHIERARCHICAL'

P value = 8.63e-06 (Fisher's exact test), Q value = 0.0014

Table S369. Gene #36: '20p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
20P MUTATED	38	76	136
20P WILD-TYPE	84	49	130

Figure S369. Get High-res Image Gene #36: '20p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p' versus 'CN_CNMF'

P value = 6.94e-48 (Chi-square test), Q value = 3.3e-45

Table S370. Gene #36: '20p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	371	258	97	236	45
20P MUTATED	62	168	61	163	23
20P WILD-TYPE	309	90	36	73	22

Figure S370. Get High-res Image Gene #36: '20p' versus Molecular Subtype #3: 'CN_CNMF'

'20p' versus 'METHLYATION_CNMF'

P value = 6.63e-17 (Chi-square test), Q value = 2.7e-14

Table S371. Gene #36: '20p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	155	108	139	55	112
20P MUTATED	79	40	58	90	16	36
20P WILD-TYPE	37	115	50	49	39	76

Figure S371. Get High-res Image Gene #36: '20p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p' versus 'RPPA_CNMF'

P value = 0.000234 (Fisher's exact test), Q value = 0.025

Table S372. Gene #36: '20p' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
20P MUTATED	92	53	51
20P WILD-TYPE	55	80	66

Figure S372. Get High-res Image Gene #36: '20p' versus Molecular Subtype #5: 'RPPA_CNMF'

'20p' versus 'MRNASEQ_CNMF'

P value = 6.76e-16 (Fisher's exact test), Q value = 2.6e-13

Table S373. Gene #36: '20p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	186	542
20P MUTATED	169	43	263
20P WILD-TYPE	104	143	279

Figure S373. Get High-res Image Gene #36: '20p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.65e-14 (Fisher's exact test), Q value = 6.1e-12

Table S374. Gene #36: '20p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	439	329
20P MUTATED	141	235	99
20P WILD-TYPE	92	204	230

Figure S374. Get High-res Image Gene #36: '20p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p' versus 'MIRSEQ_CNMF'

P value = 1.44e-13 (Fisher's exact test), Q value = 5.1e-11

Table S375. Gene #36: '20p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	398	287	292
20P MUTATED	185	90	184
20P WILD-TYPE	213	197	108

Figure S375. Get High-res Image Gene #36: '20p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.18e-13 (Fisher's exact test), Q value = 1.7e-10

Table S376. Gene #36: '20p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	252	299	426
20P MUTATED	160	152	147
20P WILD-TYPE	92	147	279

Figure S376. Get High-res Image Gene #36: '20p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.45e-08 (Fisher's exact test), Q value = 3.3e-06

Table S377. Gene #36: '20p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	219	198
20P MUTATED	115	72	123
20P WILD-TYPE	135	147	75

Figure S377. Get High-res Image Gene #36: '20p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.81e-09 (Fisher's exact test), Q value = 2.1e-06

Table S378. Gene #36: '20p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	177	345
20P MUTATED	92	53	165
20P WILD-TYPE	53	124	180

Figure S378. Get High-res Image Gene #36: '20p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q' versus 'MRNA_CNMF'

P value = 5.28e-06 (Chi-square test), Q value = 0.00089

Table S379. Gene #37: '20q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
20Q MUTATED	8	15	64	51	36	47	15	10
20Q WILD-TYPE	13	21	55	45	73	25	5	30

Figure S379. Get High-res Image Gene #37: '20q' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q' versus 'MRNA_CHIERARCHICAL'

P value = 0.00129 (Fisher's exact test), Q value = 0.1

Table S380. Gene #37: '20q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
20Q MUTATED	41	66	139
20Q WILD-TYPE	81	59	127

Figure S380. Get High-res Image Gene #37: '20q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q' versus 'CN_CNMF'

P value = 1.03e-45 (Chi-square test), Q value = 5e-43

Table S381. Gene #37: '20q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	371	258	97	236	45
20Q MUTATED	63	177	60	149	24
20Q WILD-TYPE	308	81	37	87	21

Figure S381. Get High-res Image Gene #37: '20q' versus Molecular Subtype #3: 'CN_CNMF'

'20q' versus 'METHLYATION_CNMF'

P value = 1.31e-18 (Chi-square test), Q value = 5.6e-16

Table S382. Gene #37: '20q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	155	108	139	55	112
20Q MUTATED	74	39	57	96	13	36
20Q WILD-TYPE	42	116	51	43	42	76

Figure S382. Get High-res Image Gene #37: '20q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q' versus 'MRNASEQ_CNMF'

P value = 2.96e-12 (Fisher's exact test), Q value = 9.4e-10

Table S383. Gene #37: '20q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	186	542
20Q MUTATED	155	45	270
20Q WILD-TYPE	118	141	272

Figure S383. Get High-res Image Gene #37: '20q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.89e-11 (Fisher's exact test), Q value = 5.7e-09

Table S384. Gene #37: '20q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	439	329
20Q MUTATED	131	236	103
20Q WILD-TYPE	102	203	226

Figure S384. Get High-res Image Gene #37: '20q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q' versus 'MIRSEQ_CNMF'

P value = 4.24e-10 (Fisher's exact test), Q value = 1.1e-07

Table S385. Gene #37: '20q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	398	287	292
20Q MUTATED	194	93	173
20Q WILD-TYPE	204	194	119

Figure S385. Get High-res Image Gene #37: '20q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.58e-10 (Fisher's exact test), Q value = 7.1e-08

Table S386. Gene #37: '20q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	252	299	426
20Q MUTATED	151	158	151
20Q WILD-TYPE	101	141	275

Figure S386. Get High-res Image Gene #37: '20q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.93e-08 (Fisher's exact test), Q value = 1.5e-05

Table S387. Gene #37: '20q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	219	198
20Q MUTATED	123	73	121
20Q WILD-TYPE	127	146	77

Figure S387. Get High-res Image Gene #37: '20q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.21e-07 (Fisher's exact test), Q value = 8.4e-05

Table S388. Gene #37: '20q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	177	345
20Q MUTATED	88	56	173
20Q WILD-TYPE	57	121	172

Figure S388. Get High-res Image Gene #37: '20q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q' versus 'MRNA_CNMF'

P value = 1.47e-09 (Chi-square test), Q value = 3.8e-07

Table S389. Gene #38: '21q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
21Q MUTATED	4	11	44	44	21	48	10	8
21Q WILD-TYPE	17	25	75	52	88	24	10	32

Figure S389. Get High-res Image Gene #38: '21q' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q' versus 'MRNA_CHIERARCHICAL'

P value = 2.31e-05 (Fisher's exact test), Q value = 0.0034

Table S390. Gene #38: '21q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
21Q MUTATED	26	61	103
21Q WILD-TYPE	96	64	163

Figure S390. Get High-res Image Gene #38: '21q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'21q' versus 'CN_CNMF'

P value = 5.6e-27 (Chi-square test), Q value = 2.5e-24

Table S391. Gene #38: '21q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	371	258	97	236	45
21Q MUTATED	50	107	41	131	21
21Q WILD-TYPE	321	151	56	105	24

Figure S391. Get High-res Image Gene #38: '21q' versus Molecular Subtype #3: 'CN_CNMF'

'21q' versus 'METHLYATION_CNMF'

P value = 2.06e-10 (Chi-square test), Q value = 5.7e-08

Table S392. Gene #38: '21q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	155	108	139	55	112
21Q MUTATED	64	31	40	55	9	25
21Q WILD-TYPE	52	124	68	84	46	87

Figure S392. Get High-res Image Gene #38: '21q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q' versus 'RPPA_CNMF'

P value = 0.000275 (Fisher's exact test), Q value = 0.029

Table S393. Gene #38: '21q' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
21Q MUTATED	75	37	42
21Q WILD-TYPE	72	96	75

Figure S393. Get High-res Image Gene #38: '21q' versus Molecular Subtype #5: 'RPPA_CNMF'

'21q' versus 'RPPA_CHIERARCHICAL'

P value = 0.00189 (Fisher's exact test), Q value = 0.15

Table S394. Gene #38: '21q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
21Q MUTATED	53	36	65
21Q WILD-TYPE	108	74	61

Figure S394. Get High-res Image Gene #38: '21q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'21q' versus 'MRNASEQ_CNMF'

P value = 2.28e-15 (Fisher's exact test), Q value = 8.6e-13

Table S395. Gene #38: '21q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	186	542
21Q MUTATED	142	30	175
21Q WILD-TYPE	131	156	367

Figure S395. Get High-res Image Gene #38: '21q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.25e-17 (Fisher's exact test), Q value = 2.9e-14

Table S396. Gene #38: '21q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	439	329
21Q MUTATED	121	166	60
21Q WILD-TYPE	112	273	269

Figure S396. Get High-res Image Gene #38: '21q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q' versus 'MIRSEQ_CNMF'

P value = 7.97e-13 (Fisher's exact test), Q value = 2.6e-10

Table S397. Gene #38: '21q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	398	287	292
21Q MUTATED	128	61	147
21Q WILD-TYPE	270	226	145

Figure S397. Get High-res Image Gene #38: '21q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.78e-12 (Fisher's exact test), Q value = 1.2e-09

Table S398. Gene #38: '21q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	252	299	426
21Q MUTATED	131	101	104
21Q WILD-TYPE	121	198	322

Figure S398. Get High-res Image Gene #38: '21q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.46e-10 (Fisher's exact test), Q value = 6.8e-08

Table S399. Gene #38: '21q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	219	198
21Q MUTATED	77	45	101
21Q WILD-TYPE	173	174	97

Figure S399. Get High-res Image Gene #38: '21q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.63e-09 (Fisher's exact test), Q value = 1.8e-06

Table S400. Gene #38: '21q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	177	345
21Q MUTATED	78	39	106
21Q WILD-TYPE	67	138	239

Figure S400. Get High-res Image Gene #38: '21q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q' versus 'CN_CNMF'

P value = 1.1e-17 (Chi-square test), Q value = 4.6e-15

Table S401. Gene #39: '22q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	371	258	97	236	45
22Q MUTATED	131	168	69	149	28
22Q WILD-TYPE	240	90	28	87	17

Figure S401. Get High-res Image Gene #39: '22q' versus Molecular Subtype #3: 'CN_CNMF'

'22q' versus 'METHLYATION_CNMF'

P value = 1.12e-09 (Chi-square test), Q value = 2.9e-07

Table S402. Gene #39: '22q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	155	108	139	55	112
22Q MUTATED	71	63	66	99	18	45
22Q WILD-TYPE	45	92	42	40	37	67

Figure S402. Get High-res Image Gene #39: '22q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q' versus 'MRNASEQ_CNMF'

P value = 0.000227 (Fisher's exact test), Q value = 0.025

Table S403. Gene #39: '22q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	186	542
22Q MUTATED	151	76	315
22Q WILD-TYPE	122	110	227

Figure S403. Get High-res Image Gene #39: '22q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q' versus 'MIRSEQ_CNMF'

P value = 0.00127 (Fisher's exact test), Q value = 0.1

Table S404. Gene #39: '22q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	398	287	292
22Q MUTATED	227	128	169
22Q WILD-TYPE	171	159	123

Figure S404. Get High-res Image Gene #39: '22q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq' versus 'MRNA_CNMF'

P value = 3.38e-05 (Chi-square test), Q value = 0.0047

Table S405. Gene #40: 'xq' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
XQ MUTATED	4	7	45	44	25	34	6	5
XQ WILD-TYPE	17	29	74	52	84	38	14	35

Figure S405. Get High-res Image Gene #40: 'xq' versus Molecular Subtype #1: 'MRNA_CNMF'

'xq' versus 'MRNA_CHIERARCHICAL'

P value = 8.93e-07 (Fisher's exact test), Q value = 0.00017

Table S406. Gene #40: 'xq' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	125	266
XQ MUTATED	20	59	91
XQ WILD-TYPE	102	66	175

Figure S406. Get High-res Image Gene #40: 'xq' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'xq' versus 'CN_CNMF'

P value = 4.84e-23 (Chi-square test), Q value = 2.2e-20

Table S407. Gene #40: 'xq' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	371	258	97	236	45
XQ MUTATED	40	101	32	112	14
XQ WILD-TYPE	331	157	65	124	31

Figure S407. Get High-res Image Gene #40: 'xq' versus Molecular Subtype #3: 'CN_CNMF'

'xq' versus 'METHLYATION_CNMF'

P value = 2.26e-09 (Chi-square test), Q value = 5.8e-07

Table S408. Gene #40: 'xq' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	116	155	108	139	55	112
XQ MUTATED	49	29	36	50	9	10
XQ WILD-TYPE	67	126	72	89	46	102

Figure S408. Get High-res Image Gene #40: 'xq' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq' versus 'RPPA_CHIERARCHICAL'

P value = 0.000598 (Fisher's exact test), Q value = 0.057

Table S409. Gene #40: 'xq' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
XQ MUTATED	55	23	56
XQ WILD-TYPE	106	87	70

Figure S409. Get High-res Image Gene #40: 'xq' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'xq' versus 'MRNASEQ_CNMF'

P value = 1.49e-11 (Fisher's exact test), Q value = 4.6e-09

Table S410. Gene #40: 'xq' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	186	542
XQ MUTATED	110	21	167
XQ WILD-TYPE	163	165	375

Figure S410. Get High-res Image Gene #40: 'xq' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.6e-13 (Fisher's exact test), Q value = 2.5e-10

Table S411. Gene #40: 'xq' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	439	329
XQ MUTATED	95	153	50
XQ WILD-TYPE	138	286	279

Figure S411. Get High-res Image Gene #40: 'xq' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq' versus 'MIRSEQ_CNMF'

P value = 9.05e-14 (Fisher's exact test), Q value = 3.2e-11

Table S412. Gene #40: 'xq' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	398	287	292
XQ MUTATED	127	39	121
XQ WILD-TYPE	271	248	171

Figure S412. Get High-res Image Gene #40: 'xq' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.95e-09 (Fisher's exact test), Q value = 2.1e-06

Table S413. Gene #40: 'xq' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	252	299	426
XQ MUTATED	97	107	83
XQ WILD-TYPE	155	192	343

Figure S413. Get High-res Image Gene #40: 'xq' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xq' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.19e-06 (Fisher's exact test), Q value = 0.00056

Table S414. Gene #40: 'xq' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	250	219	198
XQ MUTATED	69	34	73
XQ WILD-TYPE	181	185	125

Figure S414. Get High-res Image Gene #40: 'xq' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = BRCA-TP.transferedmergedcluster.txt
Number of patients = 1007
Number of significantly focal cnvs = 40
Number of molecular subtypes = 12
Exclude genes that fewer than K tumors have alterations, K = 3

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References

[1] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[2] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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