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

Thyroid Adenocarcinoma (Primary solid tumor)

15 January 2014 | analyses__2014_01_15

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1TT4PFD

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 10 molecular subtypes across 494 patients, 199 significant findings detected with P value < 0.05 and Q value < 0.25.

1p cnv correlated to 'CN_CNMF'.
1q cnv correlated to 'CN_CNMF'.
2p cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
2q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
3p cnv correlated to 'CN_CNMF'.
3q cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
4p cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
4q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
5p cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
5q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
6p cnv correlated to 'CN_CNMF'.
6q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
7p cnv correlated to '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', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
8p cnv correlated to 'CN_CNMF'.
8q cnv correlated to 'CN_CNMF'.
9p cnv correlated to 'CN_CNMF'.
9q cnv correlated to 'CN_CNMF'.
10p cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
10q cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 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 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
12p cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
12q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
13q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
14q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
15q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
16p cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
16q cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
17p cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
17q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
18p cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
18q cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
19p cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
19q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
20p cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
20q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
21q cnv correlated to 'CN_CNMF'.
22q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
xq cnv correlated to 'CN_CNMF' and 'METHLYATION_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 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 199 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
7q	20 (4%)	474	6.92e-25 (2.76e-22)	9.82e-06 (0.00311)	0.571 (1.00)	0.000676 (0.149)	6.01e-05 (0.0171)	1.13e-06 (0.000398)	0.000144 (0.0382)	1.15e-05 (0.00362)	4.38e-05 (0.0126)	9.06e-06 (0.00293)
17p	24 (5%)	470	5.12e-15 (1.99e-12)	2.14e-06 (0.000733)	0.689 (1.00)	0.000558 (0.127)	3.35e-05 (0.00989)	3.94e-07 (0.00014)	1.8e-05 (0.00557)	2.07e-06 (0.000711)	1.38e-05 (0.00433)	1.46e-06 (0.000507)
2p	12 (2%)	482	5.86e-14 (2.25e-11)	3.38e-05 (0.00995)	0.603 (1.00)	0.00943 (1.00)	0.000142 (0.0378)	1.54e-05 (0.00482)	2.57e-05 (0.00777)	2.21e-06 (0.000754)	3.13e-06 (0.00104)	2.71e-06 (0.000911)
2q	11 (2%)	483	2.99e-14 (1.15e-11)	0.000161 (0.0421)	0.562 (1.00)	0.068 (1.00)	0.000424 (0.0996)	7.22e-05 (0.0201)	6.45e-05 (0.0181)	7.03e-06 (0.00228)	0.000188 (0.0484)	7.44e-06 (0.00241)
5q	17 (3%)	477	1.76e-22 (7.01e-20)	3.39e-05 (0.00995)	0.85 (1.00)	0.00745 (1.00)	0.000338 (0.082)	9.22e-06 (0.00297)	0.000344 (0.0826)	4.11e-05 (0.012)	9.6e-05 (0.026)	3.18e-05 (0.00944)
7p	18 (4%)	476	6.29e-24 (2.5e-21)	7.19e-05 (0.0201)	0.66 (1.00)	0.00219 (0.401)	0.000338 (0.082)	9.22e-06 (0.00297)	0.00105 (0.217)	0.000121 (0.0327)	0.000259 (0.0644)	7.61e-05 (0.0211)
11p	13 (3%)	481	1.81e-11 (6.88e-09)	0.000186 (0.0479)	0.39 (1.00)	0.432 (1.00)	0.000259 (0.0644)	9.26e-05 (0.0253)	0.000157 (0.0412)	2.6e-05 (0.00786)	2.48e-05 (0.00754)	2.63e-05 (0.00792)
12p	15 (3%)	479	2.14e-16 (8.38e-14)	1.32e-06 (0.000461)	0.85 (1.00)	0.00745 (1.00)	9.29e-06 (0.00297)	3.61e-07 (0.00013)	2.24e-05 (0.00686)	2.87e-06 (0.000959)	3.63e-06 (0.0012)	2.66e-06 (0.000898)
12q	15 (3%)	479	2.14e-16 (8.38e-14)	1.32e-06 (0.000461)	0.85 (1.00)	0.00745 (1.00)	9.29e-06 (0.00297)	3.61e-07 (0.00013)	2.24e-05 (0.00686)	2.87e-06 (0.000959)	3.63e-06 (0.0012)	2.66e-06 (0.000898)
14q	12 (2%)	482	2.13e-11 (8.1e-09)	3.38e-05 (0.00995)	1 (1.00)	0.079 (1.00)	0.000235 (0.0591)	1.54e-05 (0.00482)	0.000146 (0.0386)	4.8e-05 (0.0137)	0.000508 (0.117)	4.25e-05 (0.0123)
15q	8 (2%)	486	5.63e-05 (0.0161)	0.000139 (0.0372)	0.193 (1.00)	0.126 (1.00)	0.000723 (0.158)	4.14e-05 (0.012)	6.43e-05 (0.0181)	1.99e-05 (0.00612)	0.000242 (0.0607)	1.75e-05 (0.00542)
16p	16 (3%)	478	3.09e-19 (1.22e-16)	0.000102 (0.0276)	0.432 (1.00)	0.0444 (1.00)	0.00049 (0.114)	3.11e-05 (0.00927)	0.000519 (0.118)	0.000129 (0.0347)	6.95e-05 (0.0195)	9.3e-05 (0.0253)
17q	22 (4%)	472	5.67e-15 (2.19e-12)	2.22e-06 (0.000759)	0.633 (1.00)	0.00271 (0.486)	2.92e-05 (0.00877)	3.64e-07 (0.00013)	2.05e-05 (0.0063)	2.03e-06 (0.000699)	1.06e-05 (0.00336)	1.64e-06 (0.000566)
19p	13 (3%)	481	1.08e-10 (4.08e-08)	3.34e-07 (0.00012)	1 (1.00)	0.0433 (1.00)	2.45e-06 (0.000831)	1.1e-07 (3.97e-05)	4.06e-07 (0.000144)	4.32e-08 (1.58e-05)	1.25e-06 (0.000436)	4.37e-08 (1.6e-05)
19q	11 (2%)	483	1.08e-12 (4.15e-10)	4.68e-06 (0.00153)	0.56 (1.00)	0.0521 (1.00)	2.99e-05 (0.00894)	1.05e-06 (0.000368)	2.82e-06 (0.000946)	3.1e-07 (0.000112)	7e-06 (0.00228)	4.37e-07 (0.000155)
22q	88 (18%)	406	1.9e-90 (7.58e-88)	1.13e-05 (0.00357)	0.123 (1.00)	0.15 (1.00)	6.03e-09 (2.23e-06)	3.33e-05 (0.00986)	0.000792 (0.169)	0.000262 (0.0647)	2.39e-06 (0.000813)	0.000155 (0.0408)
11q	14 (3%)	480	2.24e-10 (8.43e-08)	0.000746 (0.161)	0.446 (1.00)	0.257 (1.00)	0.00234 (0.426)	0.000248 (0.0621)	6.05e-05 (0.0171)	8.62e-05 (0.0237)	9.65e-06 (0.00307)	7.61e-05 (0.0211)
10p	9 (2%)	485	1.17e-11 (4.47e-09)	0.00199 (0.379)	1 (1.00)	0.25 (1.00)	0.0033 (0.567)	0.000679 (0.149)	0.000352 (0.0837)	0.000164 (0.0427)	0.00122 (0.246)	0.000171 (0.0442)
20p	12 (2%)	482	1.42e-15 (5.55e-13)	0.000376 (0.0892)	0.795 (1.00)	0.0193 (1.00)	0.00319 (0.557)	0.000202 (0.0513)	0.00466 (0.773)	0.00111 (0.226)	0.000508 (0.117)	0.000981 (0.205)
20q	12 (2%)	482	1.42e-15 (5.55e-13)	0.000376 (0.0892)	0.795 (1.00)	0.0193 (1.00)	0.00319 (0.557)	0.000202 (0.0513)	0.00466 (0.773)	0.00111 (0.226)	0.000508 (0.117)	0.000981 (0.205)
3q	6 (1%)	488	6.87e-08 (2.5e-05)	0.00139 (0.278)	1 (1.00)	0.25 (1.00)	0.0049 (0.804)	0.000909 (0.193)	0.000739 (0.16)	0.000308 (0.0755)	0.00237 (0.428)	0.00028 (0.069)
6q	8 (2%)	486	3.98e-06 (0.00131)	0.000975 (0.205)	0.0774 (1.00)	0.432 (1.00)	0.0119 (1.00)	0.00198 (0.379)	0.00106 (0.219)	0.000573 (0.13)	0.00344 (0.588)	0.000587 (0.131)
10q	8 (2%)	486	2.19e-10 (8.26e-08)	0.00369 (0.623)	1 (1.00)	0.284 (1.00)	0.00878 (1.00)	0.00198 (0.379)	0.00106 (0.219)	0.000573 (0.13)	0.00344 (0.588)	0.000587 (0.131)
13q	19 (4%)	475	5.97e-07 (0.000211)	0.000735 (0.16)	0.391 (1.00)	0.288 (1.00)	0.000309 (0.0755)	8.69e-05 (0.0238)	0.00702 (1.00)	0.00197 (0.379)	0.00508 (0.823)	0.00198 (0.379)
4p	7 (1%)	487	3.94e-09 (1.47e-06)	0.000343 (0.0826)	0.321 (1.00)	0.118 (1.00)	0.00165 (0.328)	0.00019 (0.0487)	0.00316 (0.557)	0.00196 (0.379)	0.00954 (1.00)	0.00199 (0.379)
4q	7 (1%)	487	3.94e-09 (1.47e-06)	0.000343 (0.0826)	0.321 (1.00)	0.118 (1.00)	0.00165 (0.328)	0.00019 (0.0487)	0.00316 (0.557)	0.00196 (0.379)	0.00954 (1.00)	0.00199 (0.379)
16q	15 (3%)	479	4.09e-17 (1.61e-14)	0.00165 (0.328)	0.633 (1.00)	0.374 (1.00)	0.00286 (0.506)	0.000772 (0.165)	0.00674 (1.00)	0.00181 (0.353)	0.000618 (0.137)	0.00167 (0.328)
5p	22 (4%)	472	3.27e-22 (1.29e-19)	0.00265 (0.478)	0.53 (1.00)	0.0969 (1.00)	0.0184 (1.00)	0.000768 (0.165)	0.0122 (1.00)	0.00206 (0.379)	0.0045 (0.751)	0.00137 (0.275)
18p	10 (2%)	484	3.56e-10 (1.34e-07)	0.0256 (1.00)	0.635 (1.00)	0.126 (1.00)	0.0115 (1.00)	0.00797 (1.00)	0.0465 (1.00)	0.0104 (1.00)	0.000426 (0.0998)	0.0079 (1.00)
18q	10 (2%)	484	3.56e-10 (1.34e-07)	0.0256 (1.00)	0.635 (1.00)	0.126 (1.00)	0.0115 (1.00)	0.00797 (1.00)	0.0465 (1.00)	0.0104 (1.00)	0.000426 (0.0998)	0.0079 (1.00)
xq	12 (2%)	482	4.08e-09 (1.51e-06)	0.000947 (0.2)	0.707 (1.00)	0.0425 (1.00)	0.00873 (1.00)	0.00185 (0.359)	0.0385 (1.00)	0.00969 (1.00)	0.0587 (1.00)	0.0106 (1.00)
1p	7 (1%)	487	4.62e-05 (0.0133)	0.242 (1.00)	0.78 (1.00)	0.284 (1.00)	0.417 (1.00)	0.264 (1.00)	0.0648 (1.00)	0.084 (1.00)	0.105 (1.00)	0.0705 (1.00)
1q	27 (5%)	467	1.64e-08 (6.01e-06)	0.314 (1.00)	0.00837 (1.00)	0.251 (1.00)	0.012 (1.00)	0.0219 (1.00)	0.235 (1.00)	0.179 (1.00)	0.191 (1.00)	0.139 (1.00)
3p	6 (1%)	488	6.87e-08 (2.5e-05)	0.0263 (1.00)	1 (1.00)	0.655 (1.00)	0.0524 (1.00)	0.0128 (1.00)	0.00929 (1.00)	0.00658 (1.00)	0.0259 (1.00)	0.00664 (1.00)
6p	6 (1%)	488	6.61e-06 (0.00216)	0.00505 (0.822)	0.457 (1.00)	0.655 (1.00)	0.0741 (1.00)	0.0128 (1.00)	0.00929 (1.00)	0.00658 (1.00)	0.0259 (1.00)	0.00664 (1.00)
8p	10 (2%)	484	1.58e-08 (5.8e-06)	0.0256 (1.00)	0.879 (1.00)	0.246 (1.00)	0.0866 (1.00)	0.0162 (1.00)	0.0465 (1.00)	0.0104 (1.00)	0.00771 (1.00)	0.0079 (1.00)
8q	11 (2%)	483	7.23e-10 (2.71e-07)	0.0243 (1.00)	0.879 (1.00)	0.246 (1.00)	0.187 (1.00)	0.033 (1.00)	0.0688 (1.00)	0.026 (1.00)	0.0304 (1.00)	0.0305 (1.00)
9p	22 (4%)	472	1.79e-14 (6.91e-12)	0.0134 (1.00)	0.629 (1.00)	0.492 (1.00)	0.0137 (1.00)	0.00274 (0.487)	0.015 (1.00)	0.00624 (1.00)	0.0203 (1.00)	0.00422 (0.709)
9q	28 (6%)	466	1.13e-16 (4.45e-14)	0.0476 (1.00)	0.432 (1.00)	0.102 (1.00)	0.0951 (1.00)	0.00622 (1.00)	0.0416 (1.00)	0.0284 (1.00)	0.0523 (1.00)	0.0182 (1.00)
21q	13 (3%)	481	3.8e-09 (1.42e-06)	0.0562 (1.00)	1 (1.00)	0.079 (1.00)	0.0868 (1.00)	0.069 (1.00)	0.0478 (1.00)	0.105 (1.00)	0.00715 (1.00)	0.0366 (1.00)

'1p' versus 'CN_CNMF'

P value = 4.62e-05 (Fisher's exact test), Q value = 0.013

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
1P MUTATED	5	2	0
1P WILD-TYPE	29	381	77

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

'1q' versus 'CN_CNMF'

P value = 1.64e-08 (Fisher's exact test), Q value = 6e-06

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
1Q MUTATED	12	14	1
1Q WILD-TYPE	22	369	76

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

'2p' versus 'CN_CNMF'

P value = 5.86e-14 (Fisher's exact test), Q value = 2.2e-11

Table S3. Gene #3: '2p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
2P MUTATED	11	0	1
2P WILD-TYPE	23	383	76

Figure S3. Get High-res Image Gene #3: '2p' versus Molecular Subtype #1: 'CN_CNMF'

'2p' versus 'METHLYATION_CNMF'

P value = 3.38e-05 (Fisher's exact test), Q value = 0.0099

Table S4. Gene #3: '2p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
2P MUTATED	11	0	1
2P WILD-TYPE	140	83	259

Figure S4. Get High-res Image Gene #3: '2p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p' versus 'MRNASEQ_CNMF'

P value = 0.000142 (Fisher's exact test), Q value = 0.038

Table S5. Gene #3: '2p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	152	53	118	163
2P MUTATED	11	0	1	0
2P WILD-TYPE	141	53	117	163

Figure S5. Get High-res Image Gene #3: '2p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.54e-05 (Fisher's exact test), Q value = 0.0048

Table S6. Gene #3: '2p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	288	64
2P MUTATED	11	1	0
2P WILD-TYPE	123	287	64

Figure S6. Get High-res Image Gene #3: '2p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p' versus 'MIRSEQ_CNMF'

P value = 2.57e-05 (Fisher's exact test), Q value = 0.0078

Table S7. Gene #3: '2p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
2P MUTATED	11	1	0
2P WILD-TYPE	139	172	170

Figure S7. Get High-res Image Gene #3: '2p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.21e-06 (Fisher's exact test), Q value = 0.00075

Table S8. Gene #3: '2p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
2P MUTATED	1	11	0
2P WILD-TYPE	154	119	208

Figure S8. Get High-res Image Gene #3: '2p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.13e-06 (Fisher's exact test), Q value = 0.001

Table S9. Gene #3: '2p' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
2P MUTATED	12	0	0
2P WILD-TYPE	151	169	161

Figure S9. Get High-res Image Gene #3: '2p' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.71e-06 (Fisher's exact test), Q value = 0.00091

Table S10. Gene #3: '2p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
2P MUTATED	0	11	1
2P WILD-TYPE	199	117	165

Figure S10. Get High-res Image Gene #3: '2p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q' versus 'CN_CNMF'

P value = 2.99e-14 (Fisher's exact test), Q value = 1.2e-11

Table S11. Gene #4: '2q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
2Q MUTATED	11	0	0
2Q WILD-TYPE	23	383	77

Figure S11. Get High-res Image Gene #4: '2q' versus Molecular Subtype #1: 'CN_CNMF'

'2q' versus 'METHLYATION_CNMF'

P value = 0.000161 (Fisher's exact test), Q value = 0.042

Table S12. Gene #4: '2q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
2Q MUTATED	10	0	1
2Q WILD-TYPE	141	83	259

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

'2q' versus 'MRNASEQ_CNMF'

P value = 0.000424 (Fisher's exact test), Q value = 0.1

Table S13. Gene #4: '2q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	152	53	118	163
2Q MUTATED	10	0	1	0
2Q WILD-TYPE	142	53	117	163

Figure S13. Get High-res Image Gene #4: '2q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.22e-05 (Fisher's exact test), Q value = 0.02

Table S14. Gene #4: '2q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	288	64
2Q MUTATED	10	1	0
2Q WILD-TYPE	124	287	64

Figure S14. Get High-res Image Gene #4: '2q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q' versus 'MIRSEQ_CNMF'

P value = 6.45e-05 (Fisher's exact test), Q value = 0.018

Table S15. Gene #4: '2q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
2Q MUTATED	10	1	0
2Q WILD-TYPE	140	172	170

Figure S15. Get High-res Image Gene #4: '2q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.03e-06 (Fisher's exact test), Q value = 0.0023

Table S16. Gene #4: '2q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
2Q MUTATED	1	10	0
2Q WILD-TYPE	154	120	208

Figure S16. Get High-res Image Gene #4: '2q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000188 (Fisher's exact test), Q value = 0.048

Table S17. Gene #4: '2q' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
2Q MUTATED	10	1	0
2Q WILD-TYPE	153	168	161

Figure S17. Get High-res Image Gene #4: '2q' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.44e-06 (Fisher's exact test), Q value = 0.0024

Table S18. Gene #4: '2q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
2Q MUTATED	0	10	1
2Q WILD-TYPE	199	118	165

Figure S18. Get High-res Image Gene #4: '2q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p' versus 'CN_CNMF'

P value = 6.87e-08 (Fisher's exact test), Q value = 2.5e-05

Table S19. Gene #5: '3p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
3P MUTATED	6	0	0
3P WILD-TYPE	28	383	77

Figure S19. Get High-res Image Gene #5: '3p' versus Molecular Subtype #1: 'CN_CNMF'

'3q' versus 'CN_CNMF'

P value = 6.87e-08 (Fisher's exact test), Q value = 2.5e-05

Table S20. Gene #6: '3q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
3Q MUTATED	6	0	0
3Q WILD-TYPE	28	383	77

Figure S20. Get High-res Image Gene #6: '3q' versus Molecular Subtype #1: 'CN_CNMF'

'3q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000909 (Fisher's exact test), Q value = 0.19

Table S21. Gene #6: '3q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	288	64
3Q MUTATED	6	0	0
3Q WILD-TYPE	128	288	64

Figure S21. Get High-res Image Gene #6: '3q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3q' versus 'MIRSEQ_CNMF'

P value = 0.000739 (Fisher's exact test), Q value = 0.16

Table S22. Gene #6: '3q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
3Q MUTATED	6	0	0
3Q WILD-TYPE	144	173	170

Figure S22. Get High-res Image Gene #6: '3q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000308 (Fisher's exact test), Q value = 0.076

Table S23. Gene #6: '3q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
3Q MUTATED	0	6	0
3Q WILD-TYPE	155	124	208

Figure S23. Get High-res Image Gene #6: '3q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.069

Table S24. Gene #6: '3q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
3Q MUTATED	0	6	0
3Q WILD-TYPE	199	122	166

Figure S24. Get High-res Image Gene #6: '3q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p' versus 'CN_CNMF'

P value = 3.94e-09 (Fisher's exact test), Q value = 1.5e-06

Table S25. Gene #7: '4p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
4P MUTATED	7	0	0
4P WILD-TYPE	27	383	77

Figure S25. Get High-res Image Gene #7: '4p' versus Molecular Subtype #1: 'CN_CNMF'

'4p' versus 'METHLYATION_CNMF'

P value = 0.000343 (Fisher's exact test), Q value = 0.083

Table S26. Gene #7: '4p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
4P MUTATED	7	0	0
4P WILD-TYPE	144	83	260

Figure S26. Get High-res Image Gene #7: '4p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.049

Table S27. Gene #7: '4p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	288	64
4P MUTATED	7	0	0
4P WILD-TYPE	127	288	64

Figure S27. Get High-res Image Gene #7: '4p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q' versus 'CN_CNMF'

P value = 3.94e-09 (Fisher's exact test), Q value = 1.5e-06

Table S28. Gene #8: '4q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
4Q MUTATED	7	0	0
4Q WILD-TYPE	27	383	77

Figure S28. Get High-res Image Gene #8: '4q' versus Molecular Subtype #1: 'CN_CNMF'

'4q' versus 'METHLYATION_CNMF'

P value = 0.000343 (Fisher's exact test), Q value = 0.083

Table S29. Gene #8: '4q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
4Q MUTATED	7	0	0
4Q WILD-TYPE	144	83	260

Figure S29. Get High-res Image Gene #8: '4q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.049

Table S30. Gene #8: '4q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	288	64
4Q MUTATED	7	0	0
4Q WILD-TYPE	127	288	64

Figure S30. Get High-res Image Gene #8: '4q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p' versus 'CN_CNMF'

P value = 3.27e-22 (Fisher's exact test), Q value = 1.3e-19

Table S31. Gene #9: '5p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
5P MUTATED	19	3	0
5P WILD-TYPE	15	380	77

Figure S31. Get High-res Image Gene #9: '5p' versus Molecular Subtype #1: 'CN_CNMF'

'5p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000768 (Fisher's exact test), Q value = 0.17

Table S32. Gene #9: '5p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	288	64
5P MUTATED	14	8	0
5P WILD-TYPE	120	280	64

Figure S32. Get High-res Image Gene #9: '5p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q' versus 'CN_CNMF'

P value = 1.76e-22 (Fisher's exact test), Q value = 7e-20

Table S33. Gene #10: '5q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
5Q MUTATED	17	0	0
5Q WILD-TYPE	17	383	77

Figure S33. Get High-res Image Gene #10: '5q' versus Molecular Subtype #1: 'CN_CNMF'

'5q' versus 'METHLYATION_CNMF'

P value = 3.39e-05 (Fisher's exact test), Q value = 0.0099

Table S34. Gene #10: '5q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
5Q MUTATED	14	1	2
5Q WILD-TYPE	137	82	258

Figure S34. Get High-res Image Gene #10: '5q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q' versus 'MRNASEQ_CNMF'

P value = 0.000338 (Fisher's exact test), Q value = 0.082

Table S35. Gene #10: '5q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	152	53	118	163
5Q MUTATED	14	0	1	2
5Q WILD-TYPE	138	53	117	161

Figure S35. Get High-res Image Gene #10: '5q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.22e-06 (Fisher's exact test), Q value = 0.003

Table S36. Gene #10: '5q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	288	64
5Q MUTATED	14	3	0
5Q WILD-TYPE	120	285	64

Figure S36. Get High-res Image Gene #10: '5q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q' versus 'MIRSEQ_CNMF'

P value = 0.000344 (Fisher's exact test), Q value = 0.083

Table S37. Gene #10: '5q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
5Q MUTATED	13	2	2
5Q WILD-TYPE	137	171	168

Figure S37. Get High-res Image Gene #10: '5q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.11e-05 (Fisher's exact test), Q value = 0.012

Table S38. Gene #10: '5q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
5Q MUTATED	1	13	3
5Q WILD-TYPE	154	117	205

Figure S38. Get High-res Image Gene #10: '5q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.6e-05 (Fisher's exact test), Q value = 0.026

Table S39. Gene #10: '5q' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
5Q MUTATED	14	1	2
5Q WILD-TYPE	149	168	159

Figure S39. Get High-res Image Gene #10: '5q' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.18e-05 (Fisher's exact test), Q value = 0.0094

Table S40. Gene #10: '5q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
5Q MUTATED	3	13	1
5Q WILD-TYPE	196	115	165

Figure S40. Get High-res Image Gene #10: '5q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p' versus 'CN_CNMF'

P value = 6.61e-06 (Fisher's exact test), Q value = 0.0022

Table S41. Gene #11: '6p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
6P MUTATED	5	1	0
6P WILD-TYPE	29	382	77

Figure S41. Get High-res Image Gene #11: '6p' versus Molecular Subtype #1: 'CN_CNMF'

'6q' versus 'CN_CNMF'

P value = 3.98e-06 (Fisher's exact test), Q value = 0.0013

Table S42. Gene #12: '6q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
6Q MUTATED	6	2	0
6Q WILD-TYPE	28	381	77

Figure S42. Get High-res Image Gene #12: '6q' versus Molecular Subtype #1: 'CN_CNMF'

'6q' versus 'METHLYATION_CNMF'

P value = 0.000975 (Fisher's exact test), Q value = 0.2

Table S43. Gene #12: '6q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
6Q MUTATED	7	1	0
6Q WILD-TYPE	144	82	260

Figure S43. Get High-res Image Gene #12: '6q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q' versus 'MIRSEQ_CNMF'

P value = 0.00106 (Fisher's exact test), Q value = 0.22

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
6Q MUTATED	7	0	1
6Q WILD-TYPE	143	173	169

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

'6q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000573 (Fisher's exact test), Q value = 0.13

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
6Q MUTATED	0	7	1
6Q WILD-TYPE	155	123	207

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

'6q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000587 (Fisher's exact test), Q value = 0.13

Table S46. Gene #12: '6q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
6Q MUTATED	1	7	0
6Q WILD-TYPE	198	121	166

Figure S46. Get High-res Image Gene #12: '6q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p' versus 'CN_CNMF'

P value = 6.29e-24 (Fisher's exact test), Q value = 2.5e-21

Table S47. Gene #13: '7p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
7P MUTATED	18	0	0
7P WILD-TYPE	16	383	77

Figure S47. Get High-res Image Gene #13: '7p' versus Molecular Subtype #1: 'CN_CNMF'

'7p' versus 'METHLYATION_CNMF'

P value = 7.19e-05 (Fisher's exact test), Q value = 0.02

Table S48. Gene #13: '7p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
7P MUTATED	14	2	2
7P WILD-TYPE	137	81	258

Figure S48. Get High-res Image Gene #13: '7p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p' versus 'MRNASEQ_CNMF'

P value = 0.000338 (Fisher's exact test), Q value = 0.082

Table S49. Gene #13: '7p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	152	53	118	163
7P MUTATED	14	0	1	2
7P WILD-TYPE	138	53	117	161

Figure S49. Get High-res Image Gene #13: '7p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.22e-06 (Fisher's exact test), Q value = 0.003

Table S50. Gene #13: '7p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	288	64
7P MUTATED	14	3	0
7P WILD-TYPE	120	285	64

Figure S50. Get High-res Image Gene #13: '7p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p' versus 'MIRSEQ_CNMF'

P value = 0.00105 (Fisher's exact test), Q value = 0.22

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
7P MUTATED	13	2	3
7P WILD-TYPE	137	171	167

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

'7p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000121 (Fisher's exact test), Q value = 0.033

Table S52. Gene #13: '7p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
7P MUTATED	1	13	4
7P WILD-TYPE	154	117	204

Figure S52. Get High-res Image Gene #13: '7p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000259 (Fisher's exact test), Q value = 0.064

Table S53. Gene #13: '7p' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
7P MUTATED	14	1	3
7P WILD-TYPE	149	168	158

Figure S53. Get High-res Image Gene #13: '7p' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.61e-05 (Fisher's exact test), Q value = 0.021

Table S54. Gene #13: '7p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
7P MUTATED	4	13	1
7P WILD-TYPE	195	115	165

Figure S54. Get High-res Image Gene #13: '7p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q' versus 'CN_CNMF'

P value = 6.92e-25 (Fisher's exact test), Q value = 2.8e-22

Table S55. Gene #14: '7q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
7Q MUTATED	19	0	1
7Q WILD-TYPE	15	383	76

Figure S55. Get High-res Image Gene #14: '7q' versus Molecular Subtype #1: 'CN_CNMF'

'7q' versus 'METHLYATION_CNMF'

P value = 9.82e-06 (Fisher's exact test), Q value = 0.0031

Table S56. Gene #14: '7q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
7Q MUTATED	16	2	2
7Q WILD-TYPE	135	81	258

Figure S56. Get High-res Image Gene #14: '7q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q' versus 'RPPA_CHIERARCHICAL'

P value = 0.000676 (Fisher's exact test), Q value = 0.15

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	94	96
7Q MUTATED	5	0	7
7Q WILD-TYPE	26	94	89

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

'7q' versus 'MRNASEQ_CNMF'

P value = 6.01e-05 (Fisher's exact test), Q value = 0.017

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	152	53	118	163
7Q MUTATED	16	0	1	2
7Q WILD-TYPE	136	53	117	161

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

'7q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.13e-06 (Fisher's exact test), Q value = 4e-04

Table S59. Gene #14: '7q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	288	64
7Q MUTATED	16	3	0
7Q WILD-TYPE	118	285	64

Figure S59. Get High-res Image Gene #14: '7q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7q' versus 'MIRSEQ_CNMF'

P value = 0.000144 (Fisher's exact test), Q value = 0.038

Table S60. Gene #14: '7q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
7Q MUTATED	15	2	3
7Q WILD-TYPE	135	171	167

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

'7q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.15e-05 (Fisher's exact test), Q value = 0.0036

Table S61. Gene #14: '7q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
7Q MUTATED	1	15	4
7Q WILD-TYPE	154	115	204

Figure S61. Get High-res Image Gene #14: '7q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7q' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.38e-05 (Fisher's exact test), Q value = 0.013

Table S62. Gene #14: '7q' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
7Q MUTATED	16	1	3
7Q WILD-TYPE	147	168	158

Figure S62. Get High-res Image Gene #14: '7q' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.06e-06 (Fisher's exact test), Q value = 0.0029

Table S63. Gene #14: '7q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
7Q MUTATED	4	15	1
7Q WILD-TYPE	195	113	165

Figure S63. Get High-res Image Gene #14: '7q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p' versus 'CN_CNMF'

P value = 1.58e-08 (Fisher's exact test), Q value = 5.8e-06

Table S64. Gene #15: '8p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
8P MUTATED	8	2	0
8P WILD-TYPE	26	381	77

Figure S64. Get High-res Image Gene #15: '8p' versus Molecular Subtype #1: 'CN_CNMF'

'8q' versus 'CN_CNMF'

P value = 7.23e-10 (Fisher's exact test), Q value = 2.7e-07

Table S65. Gene #16: '8q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
8Q MUTATED	9	2	0
8Q WILD-TYPE	25	381	77

Figure S65. Get High-res Image Gene #16: '8q' versus Molecular Subtype #1: 'CN_CNMF'

'9p' versus 'CN_CNMF'

P value = 1.79e-14 (Fisher's exact test), Q value = 6.9e-12

Table S66. Gene #17: '9p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
9P MUTATED	15	5	2
9P WILD-TYPE	19	378	75

Figure S66. Get High-res Image Gene #17: '9p' versus Molecular Subtype #1: 'CN_CNMF'

'9q' versus 'CN_CNMF'

P value = 1.13e-16 (Fisher's exact test), Q value = 4.4e-14

Table S67. Gene #18: '9q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
9Q MUTATED	18	8	2
9Q WILD-TYPE	16	375	75

Figure S67. Get High-res Image Gene #18: '9q' versus Molecular Subtype #1: 'CN_CNMF'

'10p' versus 'CN_CNMF'

P value = 1.17e-11 (Fisher's exact test), Q value = 4.5e-09

Table S68. Gene #19: '10p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
10P MUTATED	9	0	0
10P WILD-TYPE	25	383	77

Figure S68. Get High-res Image Gene #19: '10p' versus Molecular Subtype #1: 'CN_CNMF'

'10p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000679 (Fisher's exact test), Q value = 0.15

Table S69. Gene #19: '10p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	288	64
10P MUTATED	8	1	0
10P WILD-TYPE	126	287	64

Figure S69. Get High-res Image Gene #19: '10p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p' versus 'MIRSEQ_CNMF'

P value = 0.000352 (Fisher's exact test), Q value = 0.084

Table S70. Gene #19: '10p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
10P MUTATED	8	0	1
10P WILD-TYPE	142	173	169

Figure S70. Get High-res Image Gene #19: '10p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000164 (Fisher's exact test), Q value = 0.043

Table S71. Gene #19: '10p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
10P MUTATED	0	8	1
10P WILD-TYPE	155	122	207

Figure S71. Get High-res Image Gene #19: '10p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10p' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00122 (Fisher's exact test), Q value = 0.25

Table S72. Gene #19: '10p' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
10P MUTATED	8	0	1
10P WILD-TYPE	155	169	160

Figure S72. Get High-res Image Gene #19: '10p' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000171 (Fisher's exact test), Q value = 0.044

Table S73. Gene #19: '10p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
10P MUTATED	1	8	0
10P WILD-TYPE	198	120	166

Figure S73. Get High-res Image Gene #19: '10p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q' versus 'CN_CNMF'

P value = 2.19e-10 (Fisher's exact test), Q value = 8.3e-08

Table S74. Gene #20: '10q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
10Q MUTATED	8	0	0
10Q WILD-TYPE	26	383	77

Figure S74. Get High-res Image Gene #20: '10q' versus Molecular Subtype #1: 'CN_CNMF'

'10q' versus 'MIRSEQ_CNMF'

P value = 0.00106 (Fisher's exact test), Q value = 0.22

Table S75. Gene #20: '10q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
10Q MUTATED	7	0	1
10Q WILD-TYPE	143	173	169

Figure S75. Get High-res Image Gene #20: '10q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000573 (Fisher's exact test), Q value = 0.13

Table S76. Gene #20: '10q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
10Q MUTATED	0	7	1
10Q WILD-TYPE	155	123	207

Figure S76. Get High-res Image Gene #20: '10q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000587 (Fisher's exact test), Q value = 0.13

Table S77. Gene #20: '10q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
10Q MUTATED	1	7	0
10Q WILD-TYPE	198	121	166

Figure S77. Get High-res Image Gene #20: '10q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p' versus 'CN_CNMF'

P value = 1.81e-11 (Fisher's exact test), Q value = 6.9e-09

Table S78. Gene #21: '11p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
11P MUTATED	10	1	2
11P WILD-TYPE	24	382	75

Figure S78. Get High-res Image Gene #21: '11p' versus Molecular Subtype #1: 'CN_CNMF'

'11p' versus 'METHLYATION_CNMF'

P value = 0.000186 (Fisher's exact test), Q value = 0.048

Table S79. Gene #21: '11p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
11P MUTATED	11	0	2
11P WILD-TYPE	140	83	258

Figure S79. Get High-res Image Gene #21: '11p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p' versus 'MRNASEQ_CNMF'

P value = 0.000259 (Fisher's exact test), Q value = 0.064

Table S80. Gene #21: '11p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	152	53	118	163
11P MUTATED	11	1	1	0
11P WILD-TYPE	141	52	117	163

Figure S80. Get High-res Image Gene #21: '11p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.26e-05 (Fisher's exact test), Q value = 0.025

Table S81. Gene #21: '11p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	288	64
11P MUTATED	11	2	0
11P WILD-TYPE	123	286	64

Figure S81. Get High-res Image Gene #21: '11p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p' versus 'MIRSEQ_CNMF'

P value = 0.000157 (Fisher's exact test), Q value = 0.041

Table S82. Gene #21: '11p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
11P MUTATED	11	1	1
11P WILD-TYPE	139	172	169

Figure S82. Get High-res Image Gene #21: '11p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.6e-05 (Fisher's exact test), Q value = 0.0079

Table S83. Gene #21: '11p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
11P MUTATED	1	11	1
11P WILD-TYPE	154	119	207

Figure S83. Get High-res Image Gene #21: '11p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11p' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.48e-05 (Fisher's exact test), Q value = 0.0075

Table S84. Gene #21: '11p' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
11P MUTATED	12	0	1
11P WILD-TYPE	151	169	160

Figure S84. Get High-res Image Gene #21: '11p' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.63e-05 (Fisher's exact test), Q value = 0.0079

Table S85. Gene #21: '11p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
11P MUTATED	1	11	1
11P WILD-TYPE	198	117	165

Figure S85. Get High-res Image Gene #21: '11p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q' versus 'CN_CNMF'

P value = 2.24e-10 (Fisher's exact test), Q value = 8.4e-08

Table S86. Gene #22: '11q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
11Q MUTATED	10	2	2
11Q WILD-TYPE	24	381	75

Figure S86. Get High-res Image Gene #22: '11q' versus Molecular Subtype #1: 'CN_CNMF'

'11q' versus 'METHLYATION_CNMF'

P value = 0.000746 (Fisher's exact test), Q value = 0.16

Table S87. Gene #22: '11q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
11Q MUTATED	11	0	3
11Q WILD-TYPE	140	83	257

Figure S87. Get High-res Image Gene #22: '11q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000248 (Fisher's exact test), Q value = 0.062

Table S88. Gene #22: '11q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	288	64
11Q MUTATED	11	3	0
11Q WILD-TYPE	123	285	64

Figure S88. Get High-res Image Gene #22: '11q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11q' versus 'MIRSEQ_CNMF'

P value = 6.05e-05 (Fisher's exact test), Q value = 0.017

Table S89. Gene #22: '11q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
11Q MUTATED	12	1	1
11Q WILD-TYPE	138	172	169

Figure S89. Get High-res Image Gene #22: '11q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.62e-05 (Fisher's exact test), Q value = 0.024

Table S90. Gene #22: '11q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
11Q MUTATED	2	11	1
11Q WILD-TYPE	153	119	207

Figure S90. Get High-res Image Gene #22: '11q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11q' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.65e-06 (Fisher's exact test), Q value = 0.0031

Table S91. Gene #22: '11q' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
11Q MUTATED	13	0	1
11Q WILD-TYPE	150	169	160

Figure S91. Get High-res Image Gene #22: '11q' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.61e-05 (Fisher's exact test), Q value = 0.021

Table S92. Gene #22: '11q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
11Q MUTATED	1	11	2
11Q WILD-TYPE	198	117	164

Figure S92. Get High-res Image Gene #22: '11q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p' versus 'CN_CNMF'

P value = 2.14e-16 (Fisher's exact test), Q value = 8.4e-14

Table S93. Gene #23: '12p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
12P MUTATED	13	0	2
12P WILD-TYPE	21	383	75

Figure S93. Get High-res Image Gene #23: '12p' versus Molecular Subtype #1: 'CN_CNMF'

'12p' versus 'METHLYATION_CNMF'

P value = 1.32e-06 (Fisher's exact test), Q value = 0.00046

Table S94. Gene #23: '12p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
12P MUTATED	14	0	1
12P WILD-TYPE	137	83	259

Figure S94. Get High-res Image Gene #23: '12p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p' versus 'MRNASEQ_CNMF'

P value = 9.29e-06 (Fisher's exact test), Q value = 0.003

Table S95. Gene #23: '12p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	152	53	118	163
12P MUTATED	14	0	1	0
12P WILD-TYPE	138	53	117	163

Figure S95. Get High-res Image Gene #23: '12p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.61e-07 (Fisher's exact test), Q value = 0.00013

Table S96. Gene #23: '12p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	288	64
12P MUTATED	14	1	0
12P WILD-TYPE	120	287	64

Figure S96. Get High-res Image Gene #23: '12p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p' versus 'MIRSEQ_CNMF'

P value = 2.24e-05 (Fisher's exact test), Q value = 0.0069

Table S97. Gene #23: '12p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
12P MUTATED	13	1	1
12P WILD-TYPE	137	172	169

Figure S97. Get High-res Image Gene #23: '12p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.87e-06 (Fisher's exact test), Q value = 0.00096

Table S98. Gene #23: '12p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
12P MUTATED	1	13	1
12P WILD-TYPE	154	117	207

Figure S98. Get High-res Image Gene #23: '12p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.63e-06 (Fisher's exact test), Q value = 0.0012

Table S99. Gene #23: '12p' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
12P MUTATED	14	0	1
12P WILD-TYPE	149	169	160

Figure S99. Get High-res Image Gene #23: '12p' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.66e-06 (Fisher's exact test), Q value = 9e-04

Table S100. Gene #23: '12p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
12P MUTATED	1	13	1
12P WILD-TYPE	198	115	165

Figure S100. Get High-res Image Gene #23: '12p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q' versus 'CN_CNMF'

P value = 2.14e-16 (Fisher's exact test), Q value = 8.4e-14

Table S101. Gene #24: '12q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
12Q MUTATED	13	0	2
12Q WILD-TYPE	21	383	75

Figure S101. Get High-res Image Gene #24: '12q' versus Molecular Subtype #1: 'CN_CNMF'

'12q' versus 'METHLYATION_CNMF'

P value = 1.32e-06 (Fisher's exact test), Q value = 0.00046

Table S102. Gene #24: '12q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
12Q MUTATED	14	0	1
12Q WILD-TYPE	137	83	259

Figure S102. Get High-res Image Gene #24: '12q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q' versus 'MRNASEQ_CNMF'

P value = 9.29e-06 (Fisher's exact test), Q value = 0.003

Table S103. Gene #24: '12q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	152	53	118	163
12Q MUTATED	14	0	1	0
12Q WILD-TYPE	138	53	117	163

Figure S103. Get High-res Image Gene #24: '12q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.61e-07 (Fisher's exact test), Q value = 0.00013

Table S104. Gene #24: '12q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	288	64
12Q MUTATED	14	1	0
12Q WILD-TYPE	120	287	64

Figure S104. Get High-res Image Gene #24: '12q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q' versus 'MIRSEQ_CNMF'

P value = 2.24e-05 (Fisher's exact test), Q value = 0.0069

Table S105. Gene #24: '12q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
12Q MUTATED	13	1	1
12Q WILD-TYPE	137	172	169

Figure S105. Get High-res Image Gene #24: '12q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.87e-06 (Fisher's exact test), Q value = 0.00096

Table S106. Gene #24: '12q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
12Q MUTATED	1	13	1
12Q WILD-TYPE	154	117	207

Figure S106. Get High-res Image Gene #24: '12q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12q' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.63e-06 (Fisher's exact test), Q value = 0.0012

Table S107. Gene #24: '12q' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
12Q MUTATED	14	0	1
12Q WILD-TYPE	149	169	160

Figure S107. Get High-res Image Gene #24: '12q' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.66e-06 (Fisher's exact test), Q value = 9e-04

Table S108. Gene #24: '12q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
12Q MUTATED	1	13	1
12Q WILD-TYPE	198	115	165

Figure S108. Get High-res Image Gene #24: '12q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q' versus 'CN_CNMF'

P value = 5.97e-07 (Fisher's exact test), Q value = 0.00021

Table S109. Gene #25: '13q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
13Q MUTATED	9	7	3
13Q WILD-TYPE	25	376	74

Figure S109. Get High-res Image Gene #25: '13q' versus Molecular Subtype #1: 'CN_CNMF'

'13q' versus 'METHLYATION_CNMF'

P value = 0.000735 (Fisher's exact test), Q value = 0.16

Table S110. Gene #25: '13q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
13Q MUTATED	13	3	3
13Q WILD-TYPE	138	80	257

Figure S110. Get High-res Image Gene #25: '13q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q' versus 'MRNASEQ_CNMF'

P value = 0.000309 (Fisher's exact test), Q value = 0.076

Table S111. Gene #25: '13q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	152	53	118	163
13Q MUTATED	13	1	3	0
13Q WILD-TYPE	139	52	115	163

Figure S111. Get High-res Image Gene #25: '13q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.69e-05 (Fisher's exact test), Q value = 0.024

Table S112. Gene #25: '13q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	288	64
13Q MUTATED	13	4	0
13Q WILD-TYPE	121	284	64

Figure S112. Get High-res Image Gene #25: '13q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q' versus 'CN_CNMF'

P value = 2.13e-11 (Fisher's exact test), Q value = 8.1e-09

Table S113. Gene #26: '14q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
14Q MUTATED	10	1	1
14Q WILD-TYPE	24	382	76

Figure S113. Get High-res Image Gene #26: '14q' versus Molecular Subtype #1: 'CN_CNMF'

'14q' versus 'METHLYATION_CNMF'

P value = 3.38e-05 (Fisher's exact test), Q value = 0.0099

Table S114. Gene #26: '14q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
14Q MUTATED	11	0	1
14Q WILD-TYPE	140	83	259

Figure S114. Get High-res Image Gene #26: '14q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q' versus 'MRNASEQ_CNMF'

P value = 0.000235 (Fisher's exact test), Q value = 0.059

Table S115. Gene #26: '14q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	152	53	118	163
14Q MUTATED	11	0	0	1
14Q WILD-TYPE	141	53	118	162

Figure S115. Get High-res Image Gene #26: '14q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.54e-05 (Fisher's exact test), Q value = 0.0048

Table S116. Gene #26: '14q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	288	64
14Q MUTATED	11	1	0
14Q WILD-TYPE	123	287	64

Figure S116. Get High-res Image Gene #26: '14q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q' versus 'MIRSEQ_CNMF'

P value = 0.000146 (Fisher's exact test), Q value = 0.039

Table S117. Gene #26: '14q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
14Q MUTATED	10	0	2
14Q WILD-TYPE	140	173	168

Figure S117. Get High-res Image Gene #26: '14q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.8e-05 (Fisher's exact test), Q value = 0.014

Table S118. Gene #26: '14q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
14Q MUTATED	0	10	2
14Q WILD-TYPE	155	120	206

Figure S118. Get High-res Image Gene #26: '14q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000508 (Fisher's exact test), Q value = 0.12

Table S119. Gene #26: '14q' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
14Q MUTATED	10	0	2
14Q WILD-TYPE	153	169	159

Figure S119. Get High-res Image Gene #26: '14q' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.25e-05 (Fisher's exact test), Q value = 0.012

Table S120. Gene #26: '14q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
14Q MUTATED	2	10	0
14Q WILD-TYPE	197	118	166

Figure S120. Get High-res Image Gene #26: '14q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q' versus 'CN_CNMF'

P value = 5.63e-05 (Fisher's exact test), Q value = 0.016

Table S121. Gene #27: '15q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
15Q MUTATED	5	2	1
15Q WILD-TYPE	29	381	76

Figure S121. Get High-res Image Gene #27: '15q' versus Molecular Subtype #1: 'CN_CNMF'

'15q' versus 'METHLYATION_CNMF'

P value = 0.000139 (Fisher's exact test), Q value = 0.037

Table S122. Gene #27: '15q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
15Q MUTATED	8	0	0
15Q WILD-TYPE	143	83	260

Figure S122. Get High-res Image Gene #27: '15q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q' versus 'MRNASEQ_CNMF'

P value = 0.000723 (Fisher's exact test), Q value = 0.16

Table S123. Gene #27: '15q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	152	53	118	163
15Q MUTATED	8	0	0	0
15Q WILD-TYPE	144	53	118	163

Figure S123. Get High-res Image Gene #27: '15q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.14e-05 (Fisher's exact test), Q value = 0.012

Table S124. Gene #27: '15q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	288	64
15Q MUTATED	8	0	0
15Q WILD-TYPE	126	288	64

Figure S124. Get High-res Image Gene #27: '15q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q' versus 'MIRSEQ_CNMF'

P value = 6.43e-05 (Fisher's exact test), Q value = 0.018

Table S125. Gene #27: '15q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
15Q MUTATED	8	0	0
15Q WILD-TYPE	142	173	170

Figure S125. Get High-res Image Gene #27: '15q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.99e-05 (Fisher's exact test), Q value = 0.0061

Table S126. Gene #27: '15q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
15Q MUTATED	0	8	0
15Q WILD-TYPE	155	122	208

Figure S126. Get High-res Image Gene #27: '15q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000242 (Fisher's exact test), Q value = 0.061

Table S127. Gene #27: '15q' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
15Q MUTATED	8	0	0
15Q WILD-TYPE	155	169	161

Figure S127. Get High-res Image Gene #27: '15q' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'15q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.75e-05 (Fisher's exact test), Q value = 0.0054

Table S128. Gene #27: '15q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
15Q MUTATED	0	8	0
15Q WILD-TYPE	199	120	166

Figure S128. Get High-res Image Gene #27: '15q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p' versus 'CN_CNMF'

P value = 3.09e-19 (Fisher's exact test), Q value = 1.2e-16

Table S129. Gene #28: '16p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
16P MUTATED	15	0	1
16P WILD-TYPE	19	383	76

Figure S129. Get High-res Image Gene #28: '16p' versus Molecular Subtype #1: 'CN_CNMF'

'16p' versus 'METHLYATION_CNMF'

P value = 0.000102 (Fisher's exact test), Q value = 0.028

Table S130. Gene #28: '16p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
16P MUTATED	13	1	2
16P WILD-TYPE	138	82	258

Figure S130. Get High-res Image Gene #28: '16p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p' versus 'MRNASEQ_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.11

Table S131. Gene #28: '16p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	152	53	118	163
16P MUTATED	13	1	1	1
16P WILD-TYPE	139	52	117	162

Figure S131. Get High-res Image Gene #28: '16p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.11e-05 (Fisher's exact test), Q value = 0.0093

Table S132. Gene #28: '16p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	288	64
16P MUTATED	13	3	0
16P WILD-TYPE	121	285	64

Figure S132. Get High-res Image Gene #28: '16p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p' versus 'MIRSEQ_CNMF'

P value = 0.000519 (Fisher's exact test), Q value = 0.12

Table S133. Gene #28: '16p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
16P MUTATED	12	1	3
16P WILD-TYPE	138	172	167

Figure S133. Get High-res Image Gene #28: '16p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000129 (Fisher's exact test), Q value = 0.035

Table S134. Gene #28: '16p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
16P MUTATED	1	12	3
16P WILD-TYPE	154	118	205

Figure S134. Get High-res Image Gene #28: '16p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.95e-05 (Fisher's exact test), Q value = 0.019

Table S135. Gene #28: '16p' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
16P MUTATED	13	0	3
16P WILD-TYPE	150	169	158

Figure S135. Get High-res Image Gene #28: '16p' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.3e-05 (Fisher's exact test), Q value = 0.025

Table S136. Gene #28: '16p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
16P MUTATED	3	12	1
16P WILD-TYPE	196	116	165

Figure S136. Get High-res Image Gene #28: '16p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q' versus 'CN_CNMF'

P value = 4.09e-17 (Fisher's exact test), Q value = 1.6e-14

Table S137. Gene #29: '16q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
16Q MUTATED	14	1	0
16Q WILD-TYPE	20	382	77

Figure S137. Get High-res Image Gene #29: '16q' versus Molecular Subtype #1: 'CN_CNMF'

'16q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000772 (Fisher's exact test), Q value = 0.17

Table S138. Gene #29: '16q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	288	64
16Q MUTATED	11	4	0
16Q WILD-TYPE	123	284	64

Figure S138. Get High-res Image Gene #29: '16q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000618 (Fisher's exact test), Q value = 0.14

Table S139. Gene #29: '16q' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
16Q MUTATED	11	0	4
16Q WILD-TYPE	152	169	157

Figure S139. Get High-res Image Gene #29: '16q' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p' versus 'CN_CNMF'

P value = 5.12e-15 (Fisher's exact test), Q value = 2e-12

Table S140. Gene #30: '17p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
17P MUTATED	16	6	2
17P WILD-TYPE	18	377	75

Figure S140. Get High-res Image Gene #30: '17p' versus Molecular Subtype #1: 'CN_CNMF'

'17p' versus 'METHLYATION_CNMF'

P value = 2.14e-06 (Fisher's exact test), Q value = 0.00073

Table S141. Gene #30: '17p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
17P MUTATED	19	0	5
17P WILD-TYPE	132	83	255

Figure S141. Get High-res Image Gene #30: '17p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p' versus 'RPPA_CHIERARCHICAL'

P value = 0.000558 (Fisher's exact test), Q value = 0.13

Table S142. Gene #30: '17p' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	94	96
17P MUTATED	5	0	6
17P WILD-TYPE	26	94	90

Figure S142. Get High-res Image Gene #30: '17p' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'17p' versus 'MRNASEQ_CNMF'

P value = 3.35e-05 (Fisher's exact test), Q value = 0.0099

Table S143. Gene #30: '17p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	152	53	118	163
17P MUTATED	19	0	2	3
17P WILD-TYPE	133	53	116	160

Figure S143. Get High-res Image Gene #30: '17p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.94e-07 (Fisher's exact test), Q value = 0.00014

Table S144. Gene #30: '17p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	288	64
17P MUTATED	19	5	0
17P WILD-TYPE	115	283	64

Figure S144. Get High-res Image Gene #30: '17p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p' versus 'MIRSEQ_CNMF'

P value = 1.8e-05 (Fisher's exact test), Q value = 0.0056

Table S145. Gene #30: '17p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
17P MUTATED	18	2	4
17P WILD-TYPE	132	171	166

Figure S145. Get High-res Image Gene #30: '17p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.07e-06 (Fisher's exact test), Q value = 0.00071

Table S146. Gene #30: '17p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
17P MUTATED	2	18	4
17P WILD-TYPE	153	112	204

Figure S146. Get High-res Image Gene #30: '17p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.38e-05 (Fisher's exact test), Q value = 0.0043

Table S147. Gene #30: '17p' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
17P MUTATED	19	2	3
17P WILD-TYPE	144	167	158

Figure S147. Get High-res Image Gene #30: '17p' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.46e-06 (Fisher's exact test), Q value = 0.00051

Table S148. Gene #30: '17p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
17P MUTATED	4	18	2
17P WILD-TYPE	195	110	164

Figure S148. Get High-res Image Gene #30: '17p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q' versus 'CN_CNMF'

P value = 5.67e-15 (Fisher's exact test), Q value = 2.2e-12

Table S149. Gene #31: '17q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
17Q MUTATED	15	4	3
17Q WILD-TYPE	19	379	74

Figure S149. Get High-res Image Gene #31: '17q' versus Molecular Subtype #1: 'CN_CNMF'

'17q' versus 'METHLYATION_CNMF'

P value = 2.22e-06 (Fisher's exact test), Q value = 0.00076

Table S150. Gene #31: '17q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
17Q MUTATED	18	0	4
17Q WILD-TYPE	133	83	256

Figure S150. Get High-res Image Gene #31: '17q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q' versus 'MRNASEQ_CNMF'

P value = 2.92e-05 (Fisher's exact test), Q value = 0.0088

Table S151. Gene #31: '17q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	152	53	118	163
17Q MUTATED	18	0	2	2
17Q WILD-TYPE	134	53	116	161

Figure S151. Get High-res Image Gene #31: '17q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.64e-07 (Fisher's exact test), Q value = 0.00013

Table S152. Gene #31: '17q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	288	64
17Q MUTATED	18	4	0
17Q WILD-TYPE	116	284	64

Figure S152. Get High-res Image Gene #31: '17q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q' versus 'MIRSEQ_CNMF'

P value = 2.05e-05 (Fisher's exact test), Q value = 0.0063

Table S153. Gene #31: '17q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
17Q MUTATED	17	2	3
17Q WILD-TYPE	133	171	167

Figure S153. Get High-res Image Gene #31: '17q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.03e-06 (Fisher's exact test), Q value = 7e-04

Table S154. Gene #31: '17q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
17Q MUTATED	2	17	3
17Q WILD-TYPE	153	113	205

Figure S154. Get High-res Image Gene #31: '17q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.06e-05 (Fisher's exact test), Q value = 0.0034

Table S155. Gene #31: '17q' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
17Q MUTATED	18	2	2
17Q WILD-TYPE	145	167	159

Figure S155. Get High-res Image Gene #31: '17q' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.64e-06 (Fisher's exact test), Q value = 0.00057

Table S156. Gene #31: '17q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
17Q MUTATED	3	17	2
17Q WILD-TYPE	196	111	164

Figure S156. Get High-res Image Gene #31: '17q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p' versus 'CN_CNMF'

P value = 3.56e-10 (Fisher's exact test), Q value = 1.3e-07

Table S157. Gene #32: '18p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
18P MUTATED	8	0	2
18P WILD-TYPE	26	383	75

Figure S157. Get High-res Image Gene #32: '18p' versus Molecular Subtype #1: 'CN_CNMF'

'18p' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000426 (Fisher's exact test), Q value = 0.1

Table S158. Gene #32: '18p' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
18P MUTATED	9	0	1
18P WILD-TYPE	154	169	160

Figure S158. Get High-res Image Gene #32: '18p' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18q' versus 'CN_CNMF'

P value = 3.56e-10 (Fisher's exact test), Q value = 1.3e-07

Table S159. Gene #33: '18q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
18Q MUTATED	8	0	2
18Q WILD-TYPE	26	383	75

Figure S159. Get High-res Image Gene #33: '18q' versus Molecular Subtype #1: 'CN_CNMF'

'18q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000426 (Fisher's exact test), Q value = 0.1

Table S160. Gene #33: '18q' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
18Q MUTATED	9	0	1
18Q WILD-TYPE	154	169	160

Figure S160. Get High-res Image Gene #33: '18q' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19p' versus 'CN_CNMF'

P value = 1.08e-10 (Fisher's exact test), Q value = 4.1e-08

Table S161. Gene #34: '19p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
19P MUTATED	10	2	1
19P WILD-TYPE	24	381	76

Figure S161. Get High-res Image Gene #34: '19p' versus Molecular Subtype #1: 'CN_CNMF'

'19p' versus 'METHLYATION_CNMF'

P value = 3.34e-07 (Fisher's exact test), Q value = 0.00012

Table S162. Gene #34: '19p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
19P MUTATED	13	0	0
19P WILD-TYPE	138	83	260

Figure S162. Get High-res Image Gene #34: '19p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p' versus 'MRNASEQ_CNMF'

P value = 2.45e-06 (Fisher's exact test), Q value = 0.00083

Table S163. Gene #34: '19p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	152	53	118	163
19P MUTATED	13	0	0	0
19P WILD-TYPE	139	53	118	163

Figure S163. Get High-res Image Gene #34: '19p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.1e-07 (Fisher's exact test), Q value = 4e-05

Table S164. Gene #34: '19p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	288	64
19P MUTATED	13	0	0
19P WILD-TYPE	121	288	64

Figure S164. Get High-res Image Gene #34: '19p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p' versus 'MIRSEQ_CNMF'

P value = 4.06e-07 (Fisher's exact test), Q value = 0.00014

Table S165. Gene #34: '19p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
19P MUTATED	13	0	0
19P WILD-TYPE	137	173	170

Figure S165. Get High-res Image Gene #34: '19p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.32e-08 (Fisher's exact test), Q value = 1.6e-05

Table S166. Gene #34: '19p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
19P MUTATED	0	13	0
19P WILD-TYPE	155	117	208

Figure S166. Get High-res Image Gene #34: '19p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.25e-06 (Fisher's exact test), Q value = 0.00044

Table S167. Gene #34: '19p' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
19P MUTATED	13	0	0
19P WILD-TYPE	150	169	161

Figure S167. Get High-res Image Gene #34: '19p' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.37e-08 (Fisher's exact test), Q value = 1.6e-05

Table S168. Gene #34: '19p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
19P MUTATED	0	13	0
19P WILD-TYPE	199	115	166

Figure S168. Get High-res Image Gene #34: '19p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q' versus 'CN_CNMF'

P value = 1.08e-12 (Fisher's exact test), Q value = 4.2e-10

Table S169. Gene #35: '19q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
19Q MUTATED	10	0	1
19Q WILD-TYPE	24	383	76

Figure S169. Get High-res Image Gene #35: '19q' versus Molecular Subtype #1: 'CN_CNMF'

'19q' versus 'METHLYATION_CNMF'

P value = 4.68e-06 (Fisher's exact test), Q value = 0.0015

Table S170. Gene #35: '19q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
19Q MUTATED	11	0	0
19Q WILD-TYPE	140	83	260

Figure S170. Get High-res Image Gene #35: '19q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q' versus 'MRNASEQ_CNMF'

P value = 2.99e-05 (Fisher's exact test), Q value = 0.0089

Table S171. Gene #35: '19q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	152	53	118	163
19Q MUTATED	11	0	0	0
19Q WILD-TYPE	141	53	118	163

Figure S171. Get High-res Image Gene #35: '19q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.05e-06 (Fisher's exact test), Q value = 0.00037

Table S172. Gene #35: '19q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	288	64
19Q MUTATED	11	0	0
19Q WILD-TYPE	123	288	64

Figure S172. Get High-res Image Gene #35: '19q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q' versus 'MIRSEQ_CNMF'

P value = 2.82e-06 (Fisher's exact test), Q value = 0.00095

Table S173. Gene #35: '19q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
19Q MUTATED	11	0	0
19Q WILD-TYPE	139	173	170

Figure S173. Get High-res Image Gene #35: '19q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.1e-07 (Fisher's exact test), Q value = 0.00011

Table S174. Gene #35: '19q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
19Q MUTATED	0	11	0
19Q WILD-TYPE	155	119	208

Figure S174. Get High-res Image Gene #35: '19q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19q' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-06 (Fisher's exact test), Q value = 0.0023

Table S175. Gene #35: '19q' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
19Q MUTATED	11	0	0
19Q WILD-TYPE	152	169	161

Figure S175. Get High-res Image Gene #35: '19q' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.37e-07 (Fisher's exact test), Q value = 0.00015

Table S176. Gene #35: '19q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
19Q MUTATED	0	11	0
19Q WILD-TYPE	199	117	166

Figure S176. Get High-res Image Gene #35: '19q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p' versus 'CN_CNMF'

P value = 1.42e-15 (Fisher's exact test), Q value = 5.5e-13

Table S177. Gene #36: '20p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
20P MUTATED	12	0	0
20P WILD-TYPE	22	383	77

Figure S177. Get High-res Image Gene #36: '20p' versus Molecular Subtype #1: 'CN_CNMF'

'20p' versus 'METHLYATION_CNMF'

P value = 0.000376 (Fisher's exact test), Q value = 0.089

Table S178. Gene #36: '20p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
20P MUTATED	10	1	1
20P WILD-TYPE	141	82	259

Figure S178. Get High-res Image Gene #36: '20p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000202 (Fisher's exact test), Q value = 0.051

Table S179. Gene #36: '20p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	288	64
20P MUTATED	10	2	0
20P WILD-TYPE	124	286	64

Figure S179. Get High-res Image Gene #36: '20p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00111 (Fisher's exact test), Q value = 0.23

Table S180. Gene #36: '20p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
20P MUTATED	1	9	2
20P WILD-TYPE	154	121	206

Figure S180. Get High-res Image Gene #36: '20p' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000508 (Fisher's exact test), Q value = 0.12

Table S181. Gene #36: '20p' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
20P MUTATED	10	0	2
20P WILD-TYPE	153	169	159

Figure S181. Get High-res Image Gene #36: '20p' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000981 (Fisher's exact test), Q value = 0.21

Table S182. Gene #36: '20p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
20P MUTATED	2	9	1
20P WILD-TYPE	197	119	165

Figure S182. Get High-res Image Gene #36: '20p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q' versus 'CN_CNMF'

P value = 1.42e-15 (Fisher's exact test), Q value = 5.5e-13

Table S183. Gene #37: '20q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
20Q MUTATED	12	0	0
20Q WILD-TYPE	22	383	77

Figure S183. Get High-res Image Gene #37: '20q' versus Molecular Subtype #1: 'CN_CNMF'

'20q' versus 'METHLYATION_CNMF'

P value = 0.000376 (Fisher's exact test), Q value = 0.089

Table S184. Gene #37: '20q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
20Q MUTATED	10	1	1
20Q WILD-TYPE	141	82	259

Figure S184. Get High-res Image Gene #37: '20q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000202 (Fisher's exact test), Q value = 0.051

Table S185. Gene #37: '20q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	288	64
20Q MUTATED	10	2	0
20Q WILD-TYPE	124	286	64

Figure S185. Get High-res Image Gene #37: '20q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00111 (Fisher's exact test), Q value = 0.23

Table S186. Gene #37: '20q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
20Q MUTATED	1	9	2
20Q WILD-TYPE	154	121	206

Figure S186. Get High-res Image Gene #37: '20q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000508 (Fisher's exact test), Q value = 0.12

Table S187. Gene #37: '20q' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
20Q MUTATED	10	0	2
20Q WILD-TYPE	153	169	159

Figure S187. Get High-res Image Gene #37: '20q' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000981 (Fisher's exact test), Q value = 0.21

Table S188. Gene #37: '20q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
20Q MUTATED	2	9	1
20Q WILD-TYPE	197	119	165

Figure S188. Get High-res Image Gene #37: '20q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q' versus 'CN_CNMF'

P value = 3.8e-09 (Fisher's exact test), Q value = 1.4e-06

Table S189. Gene #38: '21q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
21Q MUTATED	9	2	2
21Q WILD-TYPE	25	381	75

Figure S189. Get High-res Image Gene #38: '21q' versus Molecular Subtype #1: 'CN_CNMF'

'22q' versus 'CN_CNMF'

P value = 1.9e-90 (Fisher's exact test), Q value = 7.6e-88

Table S190. Gene #39: '22q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
22Q MUTATED	11	0	77
22Q WILD-TYPE	23	383	0

Figure S190. Get High-res Image Gene #39: '22q' versus Molecular Subtype #1: 'CN_CNMF'

'22q' versus 'METHLYATION_CNMF'

P value = 1.13e-05 (Fisher's exact test), Q value = 0.0036

Table S191. Gene #39: '22q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
22Q MUTATED	46	8	34
22Q WILD-TYPE	105	75	226

Figure S191. Get High-res Image Gene #39: '22q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q' versus 'MRNASEQ_CNMF'

P value = 6.03e-09 (Fisher's exact test), Q value = 2.2e-06

Table S192. Gene #39: '22q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	152	53	118	163
22Q MUTATED	44	7	27	7
22Q WILD-TYPE	108	46	91	156

Figure S192. Get High-res Image Gene #39: '22q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.33e-05 (Fisher's exact test), Q value = 0.0099

Table S193. Gene #39: '22q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	288	64
22Q MUTATED	41	35	9
22Q WILD-TYPE	93	253	55

Figure S193. Get High-res Image Gene #39: '22q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q' versus 'MIRSEQ_CNMF'

P value = 0.000792 (Fisher's exact test), Q value = 0.17

Table S194. Gene #39: '22q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	173	170
22Q MUTATED	42	24	22
22Q WILD-TYPE	108	149	148

Figure S194. Get High-res Image Gene #39: '22q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000262 (Fisher's exact test), Q value = 0.065

Table S195. Gene #39: '22q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	130	208
22Q MUTATED	22	39	27
22Q WILD-TYPE	133	91	181

Figure S195. Get High-res Image Gene #39: '22q' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.39e-06 (Fisher's exact test), Q value = 0.00081

Table S196. Gene #39: '22q' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	169	161
22Q MUTATED	50	18	20
22Q WILD-TYPE	113	151	141

Figure S196. Get High-res Image Gene #39: '22q' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000155 (Fisher's exact test), Q value = 0.041

Table S197. Gene #39: '22q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	199	128	166
22Q MUTATED	25	39	24
22Q WILD-TYPE	174	89	142

Figure S197. Get High-res Image Gene #39: '22q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq' versus 'CN_CNMF'

P value = 4.08e-09 (Fisher's exact test), Q value = 1.5e-06

Table S198. Gene #40: 'xq' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	383	77
XQ MUTATED	9	3	0
XQ WILD-TYPE	25	380	77

Figure S198. Get High-res Image Gene #40: 'xq' versus Molecular Subtype #1: 'CN_CNMF'

'xq' versus 'METHLYATION_CNMF'

P value = 0.000947 (Fisher's exact test), Q value = 0.2

Table S199. Gene #40: 'xq' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	83	260
XQ MUTATED	9	2	1
XQ WILD-TYPE	142	81	259

Figure S199. Get High-res Image Gene #40: 'xq' versus Molecular Subtype #2: 'METHLYATION_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = THCA-TP.transferedmergedcluster.txt
Number of patients = 494
Number of significantly focal cnvs = 40
Number of molecular subtypes = 10
Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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