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 493 patients, 197 significant findings detected with P value < 0.05 and Q value < 0.25.

1p cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
1q cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
2p cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
2q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
3p cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
3q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
4p cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
4q cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
5p cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
5q cnv correlated to 'CN_CNMF'.
6p cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
6q cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
7p cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
7q cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
8p cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
8q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
9p cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
9q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
10p cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
10q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
11p cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
11q cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
12p cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
12q cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
13q cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
14q cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
15q cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
16p cnv correlated to 'CN_CNMF'.
16q cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
17p cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
17q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
18p cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
18q cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
20q cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
21q cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 197 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
8q	289 (59%)	204	0.0426 (1.00)	0.0548 (1.00)	2.39e-21 (1.14e-18)	6.91e-05 (0.0234)	0.444 (1.00)	0.103 (1.00)	7.57e-07 (0.000316)	1.47e-05 (0.00552)	2.06e-06 (0.000832)	2.96e-05 (0.0106)	0.000178 (0.0566)	2.03e-05 (0.00747)
19p	267 (54%)	226	0.514 (1.00)	0.619 (1.00)	3.24e-10 (1.49e-07)	2.89e-13 (1.36e-10)	0.363 (1.00)	0.551 (1.00)	8.46e-07 (0.000348)	1.13e-08 (5.06e-06)	7.25e-06 (0.00281)	1.97e-08 (8.74e-06)	6.34e-05 (0.0218)	3.28e-07 (0.00014)
19q	224 (45%)	269	0.0587 (1.00)	0.806 (1.00)	3.57e-10 (1.64e-07)	2.06e-10 (9.51e-08)	0.196 (1.00)	0.47 (1.00)	2.2e-06 (0.000884)	1.27e-07 (5.49e-05)	6.98e-05 (0.0236)	1.26e-07 (5.48e-05)	0.000194 (0.061)	3.41e-07 (0.000145)
20q	256 (52%)	237	0.0359 (1.00)	0.018 (1.00)	1.34e-08 (5.95e-06)	0.000155 (0.0499)	0.0601 (1.00)	0.0144 (1.00)	7.36e-05 (0.0248)	2.14e-06 (0.000864)	3.22e-05 (0.0115)	8.25e-07 (0.00034)	0.000515 (0.153)	2.73e-05 (0.0098)
22q	273 (55%)	220	0.179 (1.00)	0.187 (1.00)	3.96e-14 (1.88e-11)	0.000214 (0.0667)	0.176 (1.00)	0.00277 (0.695)	5.12e-06 (0.002)	4.2e-11 (1.96e-08)	1.88e-05 (0.00694)	2.48e-07 (0.000106)	3.72e-05 (0.0132)	5.7e-07 (0.000241)
2p	172 (35%)	321	0.316 (1.00)	0.182 (1.00)	8.25e-10 (3.77e-07)	0.000116 (0.0381)	0.311 (1.00)	0.33 (1.00)	0.000141 (0.046)	2.9e-06 (0.00115)	2.43e-05 (0.00879)	3.23e-05 (0.0115)	0.0503 (1.00)	0.000135 (0.0443)
4q	178 (36%)	315	0.0602 (1.00)	0.119 (1.00)	1.32e-07 (5.7e-05)	0.00766 (1.00)	0.0675 (1.00)	0.00725 (1.00)	1.77e-07 (7.58e-05)	3.61e-11 (1.69e-08)	1.72e-07 (7.38e-05)	7.97e-07 (0.00033)	0.000141 (0.046)	5.02e-05 (0.0175)
7p	284 (58%)	209	0.914 (1.00)	0.52 (1.00)	2.54e-17 (1.22e-14)	0.00203 (0.527)	0.00533 (1.00)	0.00189 (0.494)	3.93e-09 (1.78e-06)	4.58e-11 (2.13e-08)	2.22e-05 (0.00813)	0.000157 (0.0504)	0.000863 (0.245)	6.18e-06 (0.0024)
10p	213 (43%)	280	0.575 (1.00)	0.202 (1.00)	5.64e-11 (2.62e-08)	6.12e-07 (0.000257)	0.825 (1.00)	0.537 (1.00)	2.43e-06 (0.000972)	0.000368 (0.112)	6.16e-05 (0.0214)	0.000504 (0.15)	0.00127 (0.343)	0.00018 (0.0571)
11p	200 (41%)	293	0.0447 (1.00)	0.00524 (1.00)	2.65e-12 (1.24e-09)	0.00622 (1.00)	0.0269 (1.00)	0.0723 (1.00)	0.000138 (0.0452)	6.54e-09 (2.95e-06)	8.86e-06 (0.00341)	6.29e-05 (0.0218)	8.86e-05 (0.0295)	0.00036 (0.111)
11q	200 (41%)	293	0.0118 (1.00)	0.00313 (0.772)	3.68e-12 (1.72e-09)	0.000988 (0.277)	0.00174 (0.463)	0.223 (1.00)	1.29e-06 (0.000526)	1.01e-09 (4.59e-07)	1.25e-06 (0.00051)	9.31e-06 (0.00355)	1.45e-05 (0.00546)	0.00036 (0.111)
4p	196 (40%)	297	0.289 (1.00)	0.233 (1.00)	1.27e-10 (5.87e-08)	0.00302 (0.75)	0.0185 (1.00)	0.00561 (1.00)	2.67e-06 (0.00106)	5.49e-09 (2.48e-06)	1.6e-07 (6.87e-05)	1.48e-06 (0.000602)	0.00179 (0.474)	9.35e-05 (0.0309)
7q	246 (50%)	247	0.658 (1.00)	0.719 (1.00)	2.34e-10 (1.08e-07)	0.0156 (1.00)	0.0939 (1.00)	0.0827 (1.00)	2.25e-06 (0.000904)	1.65e-08 (7.34e-06)	0.000367 (0.112)	0.000283 (0.0875)	0.00254 (0.647)	0.000255 (0.0791)
8p	314 (64%)	179	0.00814 (1.00)	0.00836 (1.00)	1.01e-21 (4.83e-19)	0.00271 (0.683)	0.146 (1.00)	0.0757 (1.00)	8.75e-08 (3.81e-05)	1.1e-06 (0.000449)	6.7e-05 (0.0229)	0.000578 (0.169)	0.000894 (0.253)	0.000195 (0.0611)
10q	204 (41%)	289	0.438 (1.00)	0.118 (1.00)	6.73e-07 (0.000282)	4.56e-05 (0.016)	0.616 (1.00)	0.493 (1.00)	1.69e-05 (0.00629)	0.00296 (0.74)	0.000817 (0.234)	0.00254 (0.647)	0.000402 (0.122)	0.000806 (0.231)
17p	289 (59%)	204	0.0947 (1.00)	0.193 (1.00)	5.21e-17 (2.48e-14)	6.79e-05 (0.0232)	0.097 (1.00)	0.00969 (1.00)	3.82e-08 (1.67e-05)	4.65e-07 (0.000197)	2.37e-05 (0.00861)	0.0005 (0.15)	0.1 (1.00)	0.00533 (1.00)
17q	241 (49%)	252	0.0481 (1.00)	0.0778 (1.00)	5.63e-16 (2.68e-13)	4.55e-06 (0.00178)	0.0267 (1.00)	0.0149 (1.00)	3.14e-08 (1.38e-05)	1.22e-08 (5.45e-06)	1.88e-05 (0.00694)	6.3e-05 (0.0218)	0.00458 (1.00)	0.00203 (0.527)
18p	260 (53%)	233	0.227 (1.00)	0.322 (1.00)	3.34e-13 (1.57e-10)	0.000142 (0.0461)	0.274 (1.00)	0.0225 (1.00)	0.00425 (1.00)	8.86e-06 (0.00341)	8.62e-05 (0.0288)	0.003 (0.746)	0.000141 (0.046)	0.000177 (0.0565)
21q	251 (51%)	242	0.0333 (1.00)	0.00877 (1.00)	4.62e-05 (0.0162)	0.0725 (1.00)	0.1 (1.00)	0.0446 (1.00)	7.26e-06 (0.00281)	8.02e-06 (0.0031)	1.18e-05 (0.00448)	1.41e-05 (0.00536)	0.0249 (1.00)	0.00024 (0.0745)
9q	268 (54%)	225	0.499 (1.00)	1 (1.00)	7.78e-07 (0.000323)	0.000186 (0.0588)	0.282 (1.00)	0.0124 (1.00)	0.0192 (1.00)	2.9e-06 (0.00115)	0.00159 (0.425)	0.000525 (0.155)	0.0247 (1.00)	3.49e-06 (0.00138)
12p	237 (48%)	256	0.0959 (1.00)	0.135 (1.00)	4.34e-06 (0.00171)	0.0131 (1.00)	0.28 (1.00)	0.205 (1.00)	0.00841 (1.00)	2.34e-05 (0.00855)	0.000755 (0.219)	0.0149 (1.00)	0.000189 (0.0597)	0.000178 (0.0566)
14q	231 (47%)	262	0.606 (1.00)	0.186 (1.00)	1.12e-09 (5.11e-07)	0.00112 (0.307)	0.0175 (1.00)	0.00807 (1.00)	0.00218 (0.559)	2.3e-08 (1.02e-05)	3.21e-06 (0.00127)	9.1e-06 (0.00348)	0.000143 (0.0461)	0.000932 (0.262)
16q	231 (47%)	262	0.321 (1.00)	0.113 (1.00)	6.15e-10 (2.82e-07)	0.00478 (1.00)	0.00456 (1.00)	0.00538 (1.00)	0.000991 (0.277)	7.45e-05 (0.025)	8.32e-05 (0.0279)	0.000542 (0.16)	0.145 (1.00)	0.000566 (0.166)
20p	278 (56%)	215	0.0292 (1.00)	0.0219 (1.00)	2.89e-08 (1.27e-05)	0.00137 (0.371)	0.0012 (0.327)	0.00579 (1.00)	0.0014 (0.378)	5.9e-07 (0.000248)	4.89e-05 (0.0171)	1.06e-05 (0.00404)	0.00813 (1.00)	0.000763 (0.221)
5p	307 (62%)	186	1 (1.00)	1 (1.00)	3.91e-13 (1.84e-10)	0.117 (1.00)	0.464 (1.00)	0.284 (1.00)	0.00393 (0.938)	1.43e-05 (0.00541)	0.000794 (0.229)	0.00395 (0.939)	0.00118 (0.323)	6.43e-05 (0.0221)
12q	219 (44%)	274	0.364 (1.00)	0.0645 (1.00)	1.47e-05 (0.00552)	0.00209 (0.539)	0.648 (1.00)	0.528 (1.00)	0.000752 (0.219)	3.62e-05 (0.0128)	0.00179 (0.474)	0.0235 (1.00)	0.000307 (0.0945)	0.00222 (0.569)
13q	286 (58%)	207	0.799 (1.00)	0.597 (1.00)	4.26e-16 (2.03e-13)	0.00378 (0.908)	0.0219 (1.00)	0.000429 (0.13)	5.68e-05 (0.0198)	2.37e-05 (0.00861)	0.0186 (1.00)	0.00786 (1.00)	0.0845 (1.00)	0.0888 (1.00)
15q	268 (54%)	225	0.362 (1.00)	0.31 (1.00)	2.16e-05 (0.00792)	0.0376 (1.00)	0.18 (1.00)	0.168 (1.00)	7.69e-07 (0.00032)	1.59e-05 (0.00596)	6.84e-05 (0.0232)	0.00484 (1.00)	0.0346 (1.00)	0.00736 (1.00)
2q	158 (32%)	335	0.149 (1.00)	0.52 (1.00)	1.53e-07 (6.57e-05)	1.69e-05 (0.00627)	0.979 (1.00)	0.745 (1.00)	0.0385 (1.00)	0.00107 (0.299)	0.00264 (0.669)	0.0011 (0.305)	0.0938 (1.00)	0.000473 (0.142)
3p	245 (50%)	248	0.0936 (1.00)	0.0223 (1.00)	1.17e-08 (5.25e-06)	1.63e-06 (0.000661)	0.0433 (1.00)	0.0787 (1.00)	0.00158 (0.425)	3.99e-09 (1.8e-06)	0.00322 (0.79)	0.0504 (1.00)	0.0211 (1.00)	0.00316 (0.778)
3q	226 (46%)	267	0.0481 (1.00)	0.0423 (1.00)	8.03e-07 (0.000332)	3.69e-06 (0.00146)	0.193 (1.00)	0.524 (1.00)	0.0146 (1.00)	6e-06 (0.00234)	0.0687 (1.00)	0.091 (1.00)	0.0254 (1.00)	0.0109 (1.00)
18q	273 (55%)	220	0.123 (1.00)	0.103 (1.00)	7.58e-14 (3.59e-11)	0.00125 (0.34)	0.0204 (1.00)	0.0194 (1.00)	0.000618 (0.18)	0.000497 (0.149)	0.000904 (0.255)	0.041 (1.00)	0.0128 (1.00)	0.00731 (1.00)
1p	212 (43%)	281	0.0116 (1.00)	0.312 (1.00)	2.72e-05 (0.00979)	0.0127 (1.00)	0.081 (1.00)	0.356 (1.00)	0.00349 (0.845)	2.49e-05 (0.00898)	0.18 (1.00)	0.195 (1.00)	0.905 (1.00)	0.365 (1.00)
1q	325 (66%)	168	0.121 (1.00)	1 (1.00)	9.04e-05 (0.03)	6.86e-07 (0.000287)	0.0138 (1.00)	0.0902 (1.00)	0.0482 (1.00)	0.408 (1.00)	0.399 (1.00)	0.0572 (1.00)	0.0177 (1.00)	0.154 (1.00)
6p	242 (49%)	251	0.41 (1.00)	0.182 (1.00)	2.34e-08 (1.03e-05)	2.72e-07 (0.000116)	0.323 (1.00)	0.842 (1.00)	0.00522 (1.00)	0.456 (1.00)	0.0142 (1.00)	0.00722 (1.00)	0.0648 (1.00)	0.0671 (1.00)
6q	268 (54%)	225	0.227 (1.00)	0.322 (1.00)	4.05e-05 (0.0143)	2.19e-08 (9.66e-06)	0.246 (1.00)	0.585 (1.00)	0.00773 (1.00)	0.331 (1.00)	0.0572 (1.00)	0.00346 (0.844)	0.264 (1.00)	0.0791 (1.00)
9p	296 (60%)	197	0.0516 (1.00)	0.465 (1.00)	1.91e-06 (0.000775)	0.00188 (0.491)	0.454 (1.00)	0.15 (1.00)	0.0238 (1.00)	1.63e-05 (0.00609)	0.0362 (1.00)	0.0113 (1.00)	0.619 (1.00)	0.00369 (0.888)
xq	132 (27%)	361	0.498 (1.00)	0.426 (1.00)	4.89e-08 (2.13e-05)	0.00086 (0.245)	0.338 (1.00)	0.0442 (1.00)	0.0134 (1.00)	0.0512 (1.00)	0.255 (1.00)	0.625 (1.00)	0.16 (1.00)	0.171 (1.00)
5q	261 (53%)	232	0.733 (1.00)	0.719 (1.00)	3.09e-09 (1.4e-06)	0.0588 (1.00)	0.0829 (1.00)	0.0798 (1.00)	0.0582 (1.00)	0.00346 (0.844)	0.0061 (1.00)	0.0706 (1.00)	0.0874 (1.00)	0.0165 (1.00)
16p	235 (48%)	258	0.696 (1.00)	0.196 (1.00)	1.12e-08 (5.01e-06)	0.00783 (1.00)	0.0554 (1.00)	0.0367 (1.00)	0.0296 (1.00)	0.00637 (1.00)	0.00109 (0.301)	0.00179 (0.474)	0.433 (1.00)	0.008 (1.00)

'1p' versus 'CN_CNMF'

P value = 2.72e-05 (Fisher's exact test), Q value = 0.0098

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
1P MUTATED	96	68	48
1P WILD-TYPE	90	148	43

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

'1p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.49e-05 (Fisher's exact test), Q value = 0.009

Table S2. Gene #1: '1p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
1P MUTATED	65	66	77
1P WILD-TYPE	54	145	79

Figure S2. Get High-res Image Gene #1: '1p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q' versus 'CN_CNMF'

P value = 9.04e-05 (Fisher's exact test), Q value = 0.03

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
1Q MUTATED	132	121	72
1Q WILD-TYPE	54	95	19

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

'1q' versus 'METHLYATION_CNMF'

P value = 6.86e-07 (Fisher's exact test), Q value = 0.00029

Table S4. Gene #2: '1q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
1Q MUTATED	112	99	76
1Q WILD-TYPE	29	41	74

Figure S4. Get High-res Image Gene #2: '1q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p' versus 'CN_CNMF'

P value = 8.25e-10 (Fisher's exact test), Q value = 3.8e-07

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
2P MUTATED	87	42	43
2P WILD-TYPE	99	174	48

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

'2p' versus 'METHLYATION_CNMF'

P value = 0.000116 (Fisher's exact test), Q value = 0.038

Table S6. Gene #3: '2p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
2P MUTATED	64	49	33
2P WILD-TYPE	77	91	117

Figure S6. Get High-res Image Gene #3: '2p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p' versus 'MRNASEQ_CNMF'

P value = 0.000141 (Chi-square test), Q value = 0.046

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
2P MUTATED	46	24	29	55	18
2P WILD-TYPE	92	88	47	51	36

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

'2p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.9e-06 (Fisher's exact test), Q value = 0.0012

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
2P MUTATED	40	53	79
2P WILD-TYPE	79	158	77

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

'2p' versus 'MIRSEQ_CNMF'

P value = 2.43e-05 (Fisher's exact test), Q value = 0.0088

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
2P MUTATED	44	105	22
2P WILD-TYPE	135	126	56

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

'2p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.23e-05 (Fisher's exact test), Q value = 0.012

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
2P MUTATED	11	111	49
2P WILD-TYPE	40	138	139

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

'2p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000135 (Fisher's exact test), Q value = 0.044

Table S11. Gene #3: '2p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
2P MUTATED	14	84	46
2P WILD-TYPE	35	104	142

Figure S11. Get High-res Image Gene #3: '2p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q' versus 'CN_CNMF'

P value = 1.53e-07 (Fisher's exact test), Q value = 6.6e-05

Table S12. Gene #4: '2q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
2Q MUTATED	77	41	40
2Q WILD-TYPE	109	175	51

Figure S12. Get High-res Image Gene #4: '2q' versus Molecular Subtype #3: 'CN_CNMF'

'2q' versus 'METHLYATION_CNMF'

P value = 1.69e-05 (Fisher's exact test), Q value = 0.0063

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
2Q MUTATED	60	48	27
2Q WILD-TYPE	81	92	123

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

'2q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000473 (Fisher's exact test), Q value = 0.14

Table S14. Gene #4: '2q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
2Q MUTATED	11	78	45
2Q WILD-TYPE	38	110	143

Figure S14. Get High-res Image Gene #4: '2q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p' versus 'CN_CNMF'

P value = 1.17e-08 (Fisher's exact test), Q value = 5.2e-06

Table S15. Gene #5: '3p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
3P MUTATED	106	76	63
3P WILD-TYPE	80	140	28

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

'3p' versus 'METHLYATION_CNMF'

P value = 1.63e-06 (Fisher's exact test), Q value = 0.00066

Table S16. Gene #5: '3p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
3P MUTATED	93	67	54
3P WILD-TYPE	48	73	96

Figure S16. Get High-res Image Gene #5: '3p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.99e-09 (Fisher's exact test), Q value = 1.8e-06

Table S17. Gene #5: '3p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
3P MUTATED	60	76	107
3P WILD-TYPE	59	135	49

Figure S17. Get High-res Image Gene #5: '3p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q' versus 'CN_CNMF'

P value = 8.03e-07 (Fisher's exact test), Q value = 0.00033

Table S18. Gene #6: '3q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
3Q MUTATED	99	71	56
3Q WILD-TYPE	87	145	35

Figure S18. Get High-res Image Gene #6: '3q' versus Molecular Subtype #3: 'CN_CNMF'

'3q' versus 'METHLYATION_CNMF'

P value = 3.69e-06 (Fisher's exact test), Q value = 0.0015

Table S19. Gene #6: '3q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
3Q MUTATED	85	67	47
3Q WILD-TYPE	56	73	103

Figure S19. Get High-res Image Gene #6: '3q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-06 (Fisher's exact test), Q value = 0.0023

Table S20. Gene #6: '3q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
3Q MUTATED	61	71	91
3Q WILD-TYPE	58	140	65

Figure S20. Get High-res Image Gene #6: '3q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p' versus 'CN_CNMF'

P value = 1.27e-10 (Fisher's exact test), Q value = 5.9e-08

Table S21. Gene #7: '4p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
4P MUTATED	98	50	48
4P WILD-TYPE	88	166	43

Figure S21. Get High-res Image Gene #7: '4p' versus Molecular Subtype #3: 'CN_CNMF'

'4p' versus 'MRNASEQ_CNMF'

P value = 2.67e-06 (Chi-square test), Q value = 0.0011

Table S22. Gene #7: '4p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
4P MUTATED	62	22	35	57	18
4P WILD-TYPE	76	90	41	49	36

Figure S22. Get High-res Image Gene #7: '4p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.49e-09 (Fisher's exact test), Q value = 2.5e-06

Table S23. Gene #7: '4p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
4P MUTATED	51	54	89
4P WILD-TYPE	68	157	67

Figure S23. Get High-res Image Gene #7: '4p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p' versus 'MIRSEQ_CNMF'

P value = 1.6e-07 (Fisher's exact test), Q value = 6.9e-05

Table S24. Gene #7: '4p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
4P MUTATED	44	119	32
4P WILD-TYPE	135	112	46

Figure S24. Get High-res Image Gene #7: '4p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.48e-06 (Fisher's exact test), Q value = 6e-04

Table S25. Gene #7: '4p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
4P MUTATED	17	127	51
4P WILD-TYPE	34	122	137

Figure S25. Get High-res Image Gene #7: '4p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.35e-05 (Fisher's exact test), Q value = 0.031

Table S26. Gene #7: '4p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
4P MUTATED	14	95	57
4P WILD-TYPE	35	93	131

Figure S26. Get High-res Image Gene #7: '4p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q' versus 'CN_CNMF'

P value = 1.32e-07 (Fisher's exact test), Q value = 5.7e-05

Table S27. Gene #8: '4q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
4Q MUTATED	83	49	46
4Q WILD-TYPE	103	167	45

Figure S27. Get High-res Image Gene #8: '4q' versus Molecular Subtype #3: 'CN_CNMF'

'4q' versus 'MRNASEQ_CNMF'

P value = 1.77e-07 (Chi-square test), Q value = 7.6e-05

Table S28. Gene #8: '4q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
4Q MUTATED	57	17	30	56	16
4Q WILD-TYPE	81	95	46	50	38

Figure S28. Get High-res Image Gene #8: '4q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.61e-11 (Fisher's exact test), Q value = 1.7e-08

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
4Q MUTATED	43	45	88
4Q WILD-TYPE	76	166	68

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

'4q' versus 'MIRSEQ_CNMF'

P value = 1.72e-07 (Fisher's exact test), Q value = 7.4e-05

Table S30. Gene #8: '4q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
4Q MUTATED	37	106	34
4Q WILD-TYPE	142	125	44

Figure S30. Get High-res Image Gene #8: '4q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.97e-07 (Fisher's exact test), Q value = 0.00033

Table S31. Gene #8: '4q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
4Q MUTATED	19	116	42
4Q WILD-TYPE	32	133	146

Figure S31. Get High-res Image Gene #8: '4q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000141 (Fisher's exact test), Q value = 0.046

Table S32. Gene #8: '4q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
4Q MUTATED	36	86	28
4Q WILD-TYPE	119	106	50

Figure S32. Get High-res Image Gene #8: '4q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.02e-05 (Fisher's exact test), Q value = 0.018

Table S33. Gene #8: '4q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
4Q MUTATED	17	87	46
4Q WILD-TYPE	32	101	142

Figure S33. Get High-res Image Gene #8: '4q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p' versus 'CN_CNMF'

P value = 3.91e-13 (Fisher's exact test), Q value = 1.8e-10

Table S34. Gene #9: '5p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
5P MUTATED	152	99	56
5P WILD-TYPE	34	117	35

Figure S34. Get High-res Image Gene #9: '5p' versus Molecular Subtype #3: 'CN_CNMF'

'5p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.43e-05 (Fisher's exact test), Q value = 0.0054

Table S35. Gene #9: '5p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
5P MUTATED	81	106	114
5P WILD-TYPE	38	105	42

Figure S35. Get High-res Image Gene #9: '5p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p' versus 'MIRSEQ_CNMF'

P value = 0.000794 (Fisher's exact test), Q value = 0.23

Table S36. Gene #9: '5p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
5P MUTATED	92	160	52
5P WILD-TYPE	87	71	26

Figure S36. Get High-res Image Gene #9: '5p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.43e-05 (Fisher's exact test), Q value = 0.022

Table S37. Gene #9: '5p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
5P MUTATED	30	138	97
5P WILD-TYPE	19	50	91

Figure S37. Get High-res Image Gene #9: '5p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q' versus 'CN_CNMF'

P value = 3.09e-09 (Fisher's exact test), Q value = 1.4e-06

Table S38. Gene #10: '5q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
5Q MUTATED	128	82	51
5Q WILD-TYPE	58	134	40

Figure S38. Get High-res Image Gene #10: '5q' versus Molecular Subtype #3: 'CN_CNMF'

'6p' versus 'CN_CNMF'

P value = 2.34e-08 (Fisher's exact test), Q value = 1e-05

Table S39. Gene #11: '6p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
6P MUTATED	109	74	59
6P WILD-TYPE	77	142	32

Figure S39. Get High-res Image Gene #11: '6p' versus Molecular Subtype #3: 'CN_CNMF'

'6p' versus 'METHLYATION_CNMF'

P value = 2.72e-07 (Fisher's exact test), Q value = 0.00012

Table S40. Gene #11: '6p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
6P MUTATED	87	77	47
6P WILD-TYPE	54	63	103

Figure S40. Get High-res Image Gene #11: '6p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q' versus 'CN_CNMF'

P value = 4.05e-05 (Fisher's exact test), Q value = 0.014

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
6Q MUTATED	115	93	60
6Q WILD-TYPE	71	123	31

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

'6q' versus 'METHLYATION_CNMF'

P value = 2.19e-08 (Fisher's exact test), Q value = 9.7e-06

Table S42. Gene #12: '6q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
6Q MUTATED	90	93	53
6Q WILD-TYPE	51	47	97

Figure S42. Get High-res Image Gene #12: '6q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p' versus 'CN_CNMF'

P value = 2.54e-17 (Fisher's exact test), Q value = 1.2e-14

Table S43. Gene #13: '7p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
7P MUTATED	150	83	51
7P WILD-TYPE	36	133	40

Figure S43. Get High-res Image Gene #13: '7p' versus Molecular Subtype #3: 'CN_CNMF'

'7p' versus 'MRNASEQ_CNMF'

P value = 3.93e-09 (Chi-square test), Q value = 1.8e-06

Table S44. Gene #13: '7p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
7P MUTATED	106	39	44	62	29
7P WILD-TYPE	32	73	32	44	25

Figure S44. Get High-res Image Gene #13: '7p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.58e-11 (Fisher's exact test), Q value = 2.1e-08

Table S45. Gene #13: '7p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
7P MUTATED	96	90	94
7P WILD-TYPE	23	121	62

Figure S45. Get High-res Image Gene #13: '7p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p' versus 'MIRSEQ_CNMF'

P value = 2.22e-05 (Fisher's exact test), Q value = 0.0081

Table S46. Gene #13: '7p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
7P MUTATED	79	148	54
7P WILD-TYPE	100	83	24

Figure S46. Get High-res Image Gene #13: '7p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000157 (Fisher's exact test), Q value = 0.05

Table S47. Gene #13: '7p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
7P MUTATED	34	161	86
7P WILD-TYPE	17	88	102

Figure S47. Get High-res Image Gene #13: '7p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000863 (Fisher's exact test), Q value = 0.25

Table S48. Gene #13: '7p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
7P MUTATED	70	118	53
7P WILD-TYPE	85	74	25

Figure S48. Get High-res Image Gene #13: '7p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.18e-06 (Fisher's exact test), Q value = 0.0024

Table S49. Gene #13: '7p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
7P MUTATED	35	124	82
7P WILD-TYPE	14	64	106

Figure S49. Get High-res Image Gene #13: '7p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q' versus 'CN_CNMF'

P value = 2.34e-10 (Fisher's exact test), Q value = 1.1e-07

Table S50. Gene #14: '7q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
7Q MUTATED	126	75	45
7Q WILD-TYPE	60	141	46

Figure S50. Get High-res Image Gene #14: '7q' versus Molecular Subtype #3: 'CN_CNMF'

'7q' versus 'MRNASEQ_CNMF'

P value = 2.25e-06 (Chi-square test), Q value = 9e-04

Table S51. Gene #14: '7q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
7Q MUTATED	93	36	38	49	26
7Q WILD-TYPE	45	76	38	57	28

Figure S51. Get High-res Image Gene #14: '7q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.65e-08 (Fisher's exact test), Q value = 7.3e-06

Table S52. Gene #14: '7q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
7Q MUTATED	85	79	78
7Q WILD-TYPE	34	132	78

Figure S52. Get High-res Image Gene #14: '7q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q' versus 'MIRSEQ_CNMF'

P value = 0.000367 (Fisher's exact test), Q value = 0.11

Table S53. Gene #14: '7q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
7Q MUTATED	68	131	44
7Q WILD-TYPE	111	100	34

Figure S53. Get High-res Image Gene #14: '7q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000283 (Fisher's exact test), Q value = 0.087

Table S54. Gene #14: '7q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
7Q MUTATED	28	143	72
7Q WILD-TYPE	23	106	116

Figure S54. Get High-res Image Gene #14: '7q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000255 (Fisher's exact test), Q value = 0.079

Table S55. Gene #14: '7q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
7Q MUTATED	29	106	70
7Q WILD-TYPE	20	82	118

Figure S55. Get High-res Image Gene #14: '7q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p' versus 'CN_CNMF'

P value = 1.01e-21 (Fisher's exact test), Q value = 4.8e-19

Table S56. Gene #15: '8p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
8P MUTATED	152	86	76
8P WILD-TYPE	34	130	15

Figure S56. Get High-res Image Gene #15: '8p' versus Molecular Subtype #3: 'CN_CNMF'

'8p' versus 'MRNASEQ_CNMF'

P value = 8.75e-08 (Chi-square test), Q value = 3.8e-05

Table S57. Gene #15: '8p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
8P MUTATED	105	53	42	82	26
8P WILD-TYPE	33	59	34	24	28

Figure S57. Get High-res Image Gene #15: '8p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.1e-06 (Fisher's exact test), Q value = 0.00045

Table S58. Gene #15: '8p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
8P MUTATED	92	107	109
8P WILD-TYPE	27	104	47

Figure S58. Get High-res Image Gene #15: '8p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p' versus 'MIRSEQ_CNMF'

P value = 6.7e-05 (Fisher's exact test), Q value = 0.023

Table S59. Gene #15: '8p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
8P MUTATED	92	167	52
8P WILD-TYPE	87	64	26

Figure S59. Get High-res Image Gene #15: '8p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000578 (Fisher's exact test), Q value = 0.17

Table S60. Gene #15: '8p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
8P MUTATED	29	179	103
8P WILD-TYPE	22	70	85

Figure S60. Get High-res Image Gene #15: '8p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000195 (Fisher's exact test), Q value = 0.061

Table S61. Gene #15: '8p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
8P MUTATED	30	140	102
8P WILD-TYPE	19	48	86

Figure S61. Get High-res Image Gene #15: '8p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q' versus 'CN_CNMF'

P value = 2.39e-21 (Fisher's exact test), Q value = 1.1e-18

Table S62. Gene #16: '8q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
8Q MUTATED	126	80	83
8Q WILD-TYPE	60	136	8

Figure S62. Get High-res Image Gene #16: '8q' versus Molecular Subtype #3: 'CN_CNMF'

'8q' versus 'METHLYATION_CNMF'

P value = 6.91e-05 (Fisher's exact test), Q value = 0.023

Table S63. Gene #16: '8q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
8Q MUTATED	94	93	67
8Q WILD-TYPE	47	47	83

Figure S63. Get High-res Image Gene #16: '8q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q' versus 'MRNASEQ_CNMF'

P value = 7.57e-07 (Chi-square test), Q value = 0.00032

Table S64. Gene #16: '8q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
8Q MUTATED	90	47	39	81	25
8Q WILD-TYPE	48	65	37	25	29

Figure S64. Get High-res Image Gene #16: '8q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.47e-05 (Fisher's exact test), Q value = 0.0055

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
8Q MUTATED	79	97	106
8Q WILD-TYPE	40	114	50

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

'8q' versus 'MIRSEQ_CNMF'

P value = 2.06e-06 (Fisher's exact test), Q value = 0.00083

Table S66. Gene #16: '8q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
8Q MUTATED	78	156	52
8Q WILD-TYPE	101	75	26

Figure S66. Get High-res Image Gene #16: '8q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.96e-05 (Fisher's exact test), Q value = 0.011

Table S67. Gene #16: '8q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
8Q MUTATED	28	170	88
8Q WILD-TYPE	23	79	100

Figure S67. Get High-res Image Gene #16: '8q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000178 (Fisher's exact test), Q value = 0.057

Table S68. Gene #16: '8q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
8Q MUTATED	72	131	49
8Q WILD-TYPE	83	61	29

Figure S68. Get High-res Image Gene #16: '8q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.03e-05 (Fisher's exact test), Q value = 0.0075

Table S69. Gene #16: '8q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
8Q MUTATED	30	133	89
8Q WILD-TYPE	19	55	99

Figure S69. Get High-res Image Gene #16: '8q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p' versus 'CN_CNMF'

P value = 1.91e-06 (Fisher's exact test), Q value = 0.00078

Table S70. Gene #17: '9p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
9P MUTATED	131	102	63
9P WILD-TYPE	55	114	28

Figure S70. Get High-res Image Gene #17: '9p' versus Molecular Subtype #3: 'CN_CNMF'

'9p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.63e-05 (Fisher's exact test), Q value = 0.0061

Table S71. Gene #17: '9p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
9P MUTATED	64	111	117
9P WILD-TYPE	55	100	39

Figure S71. Get High-res Image Gene #17: '9p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q' versus 'CN_CNMF'

P value = 7.78e-07 (Fisher's exact test), Q value = 0.00032

Table S72. Gene #18: '9q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
9Q MUTATED	116	89	63
9Q WILD-TYPE	70	127	28

Figure S72. Get High-res Image Gene #18: '9q' versus Molecular Subtype #3: 'CN_CNMF'

'9q' versus 'METHLYATION_CNMF'

P value = 0.000186 (Fisher's exact test), Q value = 0.059

Table S73. Gene #18: '9q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
9Q MUTATED	95	68	67
9Q WILD-TYPE	46	72	83

Figure S73. Get High-res Image Gene #18: '9q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.9e-06 (Fisher's exact test), Q value = 0.0012

Table S74. Gene #18: '9q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
9Q MUTATED	61	94	110
9Q WILD-TYPE	58	117	46

Figure S74. Get High-res Image Gene #18: '9q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000525 (Fisher's exact test), Q value = 0.16

Table S75. Gene #18: '9q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
9Q MUTATED	23	156	85
9Q WILD-TYPE	28	93	103

Figure S75. Get High-res Image Gene #18: '9q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.49e-06 (Fisher's exact test), Q value = 0.0014

Table S76. Gene #18: '9q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
9Q MUTATED	25	126	78
9Q WILD-TYPE	24	62	110

Figure S76. Get High-res Image Gene #18: '9q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p' versus 'CN_CNMF'

P value = 5.64e-11 (Fisher's exact test), Q value = 2.6e-08

Table S77. Gene #19: '10p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
10P MUTATED	110	57	46
10P WILD-TYPE	76	159	45

Figure S77. Get High-res Image Gene #19: '10p' versus Molecular Subtype #3: 'CN_CNMF'

'10p' versus 'METHLYATION_CNMF'

P value = 6.12e-07 (Fisher's exact test), Q value = 0.00026

Table S78. Gene #19: '10p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
10P MUTATED	71	74	38
10P WILD-TYPE	70	66	112

Figure S78. Get High-res Image Gene #19: '10p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p' versus 'MRNASEQ_CNMF'

P value = 2.43e-06 (Chi-square test), Q value = 0.00097

Table S79. Gene #19: '10p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
10P MUTATED	73	28	25	60	24
10P WILD-TYPE	65	84	51	46	30

Figure S79. Get High-res Image Gene #19: '10p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000368 (Fisher's exact test), Q value = 0.11

Table S80. Gene #19: '10p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
10P MUTATED	58	70	82
10P WILD-TYPE	61	141	74

Figure S80. Get High-res Image Gene #19: '10p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p' versus 'MIRSEQ_CNMF'

P value = 6.16e-05 (Fisher's exact test), Q value = 0.021

Table S81. Gene #19: '10p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
10P MUTATED	54	113	42
10P WILD-TYPE	125	118	36

Figure S81. Get High-res Image Gene #19: '10p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000504 (Fisher's exact test), Q value = 0.15

Table S82. Gene #19: '10p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
10P MUTATED	24	125	60
10P WILD-TYPE	27	124	128

Figure S82. Get High-res Image Gene #19: '10p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.057

Table S83. Gene #19: '10p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
10P MUTATED	25	98	60
10P WILD-TYPE	24	90	128

Figure S83. Get High-res Image Gene #19: '10p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q' versus 'CN_CNMF'

P value = 6.73e-07 (Fisher's exact test), Q value = 0.00028

Table S84. Gene #20: '10q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
10Q MUTATED	99	61	44
10Q WILD-TYPE	87	155	47

Figure S84. Get High-res Image Gene #20: '10q' versus Molecular Subtype #3: 'CN_CNMF'

'10q' versus 'METHLYATION_CNMF'

P value = 4.56e-05 (Fisher's exact test), Q value = 0.016

Table S85. Gene #20: '10q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
10Q MUTATED	71	65	40
10Q WILD-TYPE	70	75	110

Figure S85. Get High-res Image Gene #20: '10q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q' versus 'MRNASEQ_CNMF'

P value = 1.69e-05 (Chi-square test), Q value = 0.0063

Table S86. Gene #20: '10q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
10Q MUTATED	68	26	28	58	21
10Q WILD-TYPE	70	86	48	48	33

Figure S86. Get High-res Image Gene #20: '10q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q' versus 'MIRSEQ_CNMF'

P value = 0.000817 (Fisher's exact test), Q value = 0.23

Table S87. Gene #20: '10q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
10Q MUTATED	54	107	39
10Q WILD-TYPE	125	124	39

Figure S87. Get High-res Image Gene #20: '10q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000402 (Fisher's exact test), Q value = 0.12

Table S88. Gene #20: '10q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
10Q MUTATED	45	93	38
10Q WILD-TYPE	110	99	40

Figure S88. Get High-res Image Gene #20: '10q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000806 (Fisher's exact test), Q value = 0.23

Table S89. Gene #20: '10q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
10Q MUTATED	25	92	59
10Q WILD-TYPE	24	96	129

Figure S89. Get High-res Image Gene #20: '10q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p' versus 'CN_CNMF'

P value = 2.65e-12 (Fisher's exact test), Q value = 1.2e-09

Table S90. Gene #21: '11p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
11P MUTATED	98	49	53
11P WILD-TYPE	88	167	38

Figure S90. Get High-res Image Gene #21: '11p' versus Molecular Subtype #3: 'CN_CNMF'

'11p' versus 'MRNASEQ_CNMF'

P value = 0.000138 (Chi-square test), Q value = 0.045

Table S91. Gene #21: '11p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
11P MUTATED	63	27	33	56	17
11P WILD-TYPE	75	85	43	50	37

Figure S91. Get High-res Image Gene #21: '11p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.54e-09 (Fisher's exact test), Q value = 2.9e-06

Table S92. Gene #21: '11p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
11P MUTATED	54	54	88
11P WILD-TYPE	65	157	68

Figure S92. Get High-res Image Gene #21: '11p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p' versus 'MIRSEQ_CNMF'

P value = 8.86e-06 (Fisher's exact test), Q value = 0.0034

Table S93. Gene #21: '11p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
11P MUTATED	48	115	35
11P WILD-TYPE	131	116	43

Figure S93. Get High-res Image Gene #21: '11p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.29e-05 (Fisher's exact test), Q value = 0.022

Table S94. Gene #21: '11p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
11P MUTATED	21	123	54
11P WILD-TYPE	30	126	134

Figure S94. Get High-res Image Gene #21: '11p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.86e-05 (Fisher's exact test), Q value = 0.03

Table S95. Gene #21: '11p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
11P MUTATED	42	95	34
11P WILD-TYPE	113	97	44

Figure S95. Get High-res Image Gene #21: '11p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.11

Table S96. Gene #21: '11p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
11P MUTATED	22	93	56
11P WILD-TYPE	27	95	132

Figure S96. Get High-res Image Gene #21: '11p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q' versus 'CN_CNMF'

P value = 3.68e-12 (Fisher's exact test), Q value = 1.7e-09

Table S97. Gene #22: '11q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
11Q MUTATED	102	49	49
11Q WILD-TYPE	84	167	42

Figure S97. Get High-res Image Gene #22: '11q' versus Molecular Subtype #3: 'CN_CNMF'

'11q' versus 'MRNASEQ_CNMF'

P value = 1.29e-06 (Chi-square test), Q value = 0.00053

Table S98. Gene #22: '11q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
11Q MUTATED	64	25	30	61	16
11Q WILD-TYPE	74	87	46	45	38

Figure S98. Get High-res Image Gene #22: '11q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.01e-09 (Fisher's exact test), Q value = 4.6e-07

Table S99. Gene #22: '11q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
11Q MUTATED	56	52	88
11Q WILD-TYPE	63	159	68

Figure S99. Get High-res Image Gene #22: '11q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q' versus 'MIRSEQ_CNMF'

P value = 1.25e-06 (Fisher's exact test), Q value = 0.00051

Table S100. Gene #22: '11q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
11Q MUTATED	46	117	34
11Q WILD-TYPE	133	114	44

Figure S100. Get High-res Image Gene #22: '11q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.31e-06 (Fisher's exact test), Q value = 0.0036

Table S101. Gene #22: '11q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
11Q MUTATED	23	123	51
11Q WILD-TYPE	28	126	137

Figure S101. Get High-res Image Gene #22: '11q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.45e-05 (Fisher's exact test), Q value = 0.0055

Table S102. Gene #22: '11q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
11Q MUTATED	40	96	35
11Q WILD-TYPE	115	96	43

Figure S102. Get High-res Image Gene #22: '11q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.11

Table S103. Gene #22: '11q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
11Q MUTATED	22	93	56
11Q WILD-TYPE	27	95	132

Figure S103. Get High-res Image Gene #22: '11q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p' versus 'CN_CNMF'

P value = 4.34e-06 (Fisher's exact test), Q value = 0.0017

Table S104. Gene #23: '12p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
12P MUTATED	104	77	56
12P WILD-TYPE	82	139	35

Figure S104. Get High-res Image Gene #23: '12p' versus Molecular Subtype #3: 'CN_CNMF'

'12p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.34e-05 (Fisher's exact test), Q value = 0.0085

Table S105. Gene #23: '12p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
12P MUTATED	61	78	95
12P WILD-TYPE	58	133	61

Figure S105. Get High-res Image Gene #23: '12p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p' versus 'MIRSEQ_CNMF'

P value = 0.000755 (Fisher's exact test), Q value = 0.22

Table S106. Gene #23: '12p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
12P MUTATED	66	128	40
12P WILD-TYPE	113	103	38

Figure S106. Get High-res Image Gene #23: '12p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000189 (Fisher's exact test), Q value = 0.06

Table S107. Gene #23: '12p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
12P MUTATED	56	112	39
12P WILD-TYPE	99	80	39

Figure S107. Get High-res Image Gene #23: '12p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000178 (Fisher's exact test), Q value = 0.057

Table S108. Gene #23: '12p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
12P MUTATED	23	112	72
12P WILD-TYPE	26	76	116

Figure S108. Get High-res Image Gene #23: '12p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q' versus 'CN_CNMF'

P value = 1.47e-05 (Fisher's exact test), Q value = 0.0055

Table S109. Gene #24: '12q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
12Q MUTATED	95	71	53
12Q WILD-TYPE	91	145	38

Figure S109. Get High-res Image Gene #24: '12q' versus Molecular Subtype #3: 'CN_CNMF'

'12q' versus 'MRNASEQ_CNMF'

P value = 0.000752 (Chi-square test), Q value = 0.22

Table S110. Gene #24: '12q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
12Q MUTATED	67	32	35	60	22
12Q WILD-TYPE	71	80	41	46	32

Figure S110. Get High-res Image Gene #24: '12q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.62e-05 (Fisher's exact test), Q value = 0.013

Table S111. Gene #24: '12q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
12Q MUTATED	56	71	89
12Q WILD-TYPE	63	140	67

Figure S111. Get High-res Image Gene #24: '12q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000307 (Fisher's exact test), Q value = 0.095

Table S112. Gene #24: '12q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
12Q MUTATED	51	102	41
12Q WILD-TYPE	104	90	37

Figure S112. Get High-res Image Gene #24: '12q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'13q' versus 'CN_CNMF'

P value = 4.26e-16 (Fisher's exact test), Q value = 2e-13

Table S113. Gene #25: '13q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
13Q MUTATED	136	80	70
13Q WILD-TYPE	50	136	21

Figure S113. Get High-res Image Gene #25: '13q' versus Molecular Subtype #3: 'CN_CNMF'

'13q' versus 'RPPA_CHIERARCHICAL'

P value = 0.000429 (Fisher's exact test), Q value = 0.13

Table S114. Gene #25: '13q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	106	70	59
13Q MUTATED	68	25	37
13Q WILD-TYPE	38	45	22

Figure S114. Get High-res Image Gene #25: '13q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'13q' versus 'MRNASEQ_CNMF'

P value = 5.68e-05 (Chi-square test), Q value = 0.02

Table S115. Gene #25: '13q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
13Q MUTATED	94	52	36	75	26
13Q WILD-TYPE	44	60	40	31	28

Figure S115. Get High-res Image Gene #25: '13q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.37e-05 (Fisher's exact test), Q value = 0.0086

Table S116. Gene #25: '13q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
13Q MUTATED	81	98	104
13Q WILD-TYPE	38	113	52

Figure S116. Get High-res Image Gene #25: '13q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q' versus 'CN_CNMF'

P value = 1.12e-09 (Fisher's exact test), Q value = 5.1e-07

Table S117. Gene #26: '14q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
14Q MUTATED	99	69	63
14Q WILD-TYPE	87	147	28

Figure S117. Get High-res Image Gene #26: '14q' versus Molecular Subtype #3: 'CN_CNMF'

'14q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.3e-08 (Fisher's exact test), Q value = 1e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
14Q MUTATED	56	71	101
14Q WILD-TYPE	63	140	55

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

'14q' versus 'MIRSEQ_CNMF'

P value = 3.21e-06 (Fisher's exact test), Q value = 0.0013

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
14Q MUTATED	58	132	38
14Q WILD-TYPE	121	99	40

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

'14q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.1e-06 (Fisher's exact test), Q value = 0.0035

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
14Q MUTATED	24	141	63
14Q WILD-TYPE	27	108	125

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

'14q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000143 (Fisher's exact test), Q value = 0.046

Table S121. Gene #26: '14q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
14Q MUTATED	55	111	34
14Q WILD-TYPE	100	81	44

Figure S121. Get High-res Image Gene #26: '14q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q' versus 'CN_CNMF'

P value = 2.16e-05 (Fisher's exact test), Q value = 0.0079

Table S122. Gene #27: '15q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
15Q MUTATED	119	92	57
15Q WILD-TYPE	67	124	34

Figure S122. Get High-res Image Gene #27: '15q' versus Molecular Subtype #3: 'CN_CNMF'

'15q' versus 'MRNASEQ_CNMF'

P value = 7.69e-07 (Chi-square test), Q value = 0.00032

Table S123. Gene #27: '15q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
15Q MUTATED	95	41	32	67	28
15Q WILD-TYPE	43	71	44	39	26

Figure S123. Get High-res Image Gene #27: '15q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.59e-05 (Fisher's exact test), Q value = 0.006

Table S124. Gene #27: '15q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
15Q MUTATED	81	90	92
15Q WILD-TYPE	38	121	64

Figure S124. Get High-res Image Gene #27: '15q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q' versus 'MIRSEQ_CNMF'

P value = 6.84e-05 (Fisher's exact test), Q value = 0.023

Table S125. Gene #27: '15q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
15Q MUTATED	74	142	49
15Q WILD-TYPE	105	89	29

Figure S125. Get High-res Image Gene #27: '15q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p' versus 'CN_CNMF'

P value = 1.12e-08 (Fisher's exact test), Q value = 5e-06

Table S126. Gene #28: '16p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
16P MUTATED	113	70	52
16P WILD-TYPE	73	146	39

Figure S126. Get High-res Image Gene #28: '16p' versus Molecular Subtype #3: 'CN_CNMF'

'16q' versus 'CN_CNMF'

P value = 6.15e-10 (Fisher's exact test), Q value = 2.8e-07

Table S127. Gene #29: '16q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
16Q MUTATED	114	66	51
16Q WILD-TYPE	72	150	40

Figure S127. Get High-res Image Gene #29: '16q' versus Molecular Subtype #3: 'CN_CNMF'

'16q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.45e-05 (Fisher's exact test), Q value = 0.025

Table S128. Gene #29: '16q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
16Q MUTATED	73	78	78
16Q WILD-TYPE	46	133	78

Figure S128. Get High-res Image Gene #29: '16q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q' versus 'MIRSEQ_CNMF'

P value = 8.32e-05 (Fisher's exact test), Q value = 0.028

Table S129. Gene #29: '16q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
16Q MUTATED	62	122	46
16Q WILD-TYPE	117	109	32

Figure S129. Get High-res Image Gene #29: '16q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000542 (Fisher's exact test), Q value = 0.16

Table S130. Gene #29: '16q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
16Q MUTATED	29	133	68
16Q WILD-TYPE	22	116	120

Figure S130. Get High-res Image Gene #29: '16q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000566 (Fisher's exact test), Q value = 0.17

Table S131. Gene #29: '16q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
16Q MUTATED	21	106	69
16Q WILD-TYPE	28	82	119

Figure S131. Get High-res Image Gene #29: '16q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p' versus 'CN_CNMF'

P value = 5.21e-17 (Fisher's exact test), Q value = 2.5e-14

Table S132. Gene #30: '17p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
17P MUTATED	139	80	70
17P WILD-TYPE	47	136	21

Figure S132. Get High-res Image Gene #30: '17p' versus Molecular Subtype #3: 'CN_CNMF'

'17p' versus 'METHLYATION_CNMF'

P value = 6.79e-05 (Fisher's exact test), Q value = 0.023

Table S133. Gene #30: '17p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
17P MUTATED	87	96	66
17P WILD-TYPE	54	44	84

Figure S133. Get High-res Image Gene #30: '17p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p' versus 'MRNASEQ_CNMF'

P value = 3.82e-08 (Chi-square test), Q value = 1.7e-05

Table S134. Gene #30: '17p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
17P MUTATED	103	42	42	71	27
17P WILD-TYPE	35	70	34	35	27

Figure S134. Get High-res Image Gene #30: '17p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.65e-07 (Fisher's exact test), Q value = 2e-04

Table S135. Gene #30: '17p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
17P MUTATED	88	96	101
17P WILD-TYPE	31	115	55

Figure S135. Get High-res Image Gene #30: '17p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p' versus 'MIRSEQ_CNMF'

P value = 2.37e-05 (Fisher's exact test), Q value = 0.0086

Table S136. Gene #30: '17p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
17P MUTATED	85	160	41
17P WILD-TYPE	94	71	37

Figure S136. Get High-res Image Gene #30: '17p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-04 (Fisher's exact test), Q value = 0.15

Table S137. Gene #30: '17p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
17P MUTATED	26	167	93
17P WILD-TYPE	25	82	95

Figure S137. Get High-res Image Gene #30: '17p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q' versus 'CN_CNMF'

P value = 5.63e-16 (Fisher's exact test), Q value = 2.7e-13

Table S138. Gene #31: '17q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
17Q MUTATED	121	60	60
17Q WILD-TYPE	65	156	31

Figure S138. Get High-res Image Gene #31: '17q' versus Molecular Subtype #3: 'CN_CNMF'

'17q' versus 'METHLYATION_CNMF'

P value = 4.55e-06 (Fisher's exact test), Q value = 0.0018

Table S139. Gene #31: '17q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
17Q MUTATED	71	88	51
17Q WILD-TYPE	70	52	99

Figure S139. Get High-res Image Gene #31: '17q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q' versus 'MRNASEQ_CNMF'

P value = 3.14e-08 (Chi-square test), Q value = 1.4e-05

Table S140. Gene #31: '17q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
17Q MUTATED	95	35	29	55	23
17Q WILD-TYPE	43	77	47	51	31

Figure S140. Get High-res Image Gene #31: '17q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.22e-08 (Fisher's exact test), Q value = 5.4e-06

Table S141. Gene #31: '17q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
17Q MUTATED	81	73	83
17Q WILD-TYPE	38	138	73

Figure S141. Get High-res Image Gene #31: '17q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q' versus 'MIRSEQ_CNMF'

P value = 1.88e-05 (Fisher's exact test), Q value = 0.0069

Table S142. Gene #31: '17q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
17Q MUTATED	64	136	38
17Q WILD-TYPE	115	95	40

Figure S142. Get High-res Image Gene #31: '17q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.3e-05 (Fisher's exact test), Q value = 0.022

Table S143. Gene #31: '17q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
17Q MUTATED	25	144	69
17Q WILD-TYPE	26	105	119

Figure S143. Get High-res Image Gene #31: '17q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p' versus 'CN_CNMF'

P value = 3.34e-13 (Fisher's exact test), Q value = 1.6e-10

Table S144. Gene #32: '18p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
18P MUTATED	135	76	49
18P WILD-TYPE	51	140	42

Figure S144. Get High-res Image Gene #32: '18p' versus Molecular Subtype #3: 'CN_CNMF'

'18p' versus 'METHLYATION_CNMF'

P value = 0.000142 (Fisher's exact test), Q value = 0.046

Table S145. Gene #32: '18p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
18P MUTATED	91	75	60
18P WILD-TYPE	50	65	90

Figure S145. Get High-res Image Gene #32: '18p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.86e-06 (Fisher's exact test), Q value = 0.0034

Table S146. Gene #32: '18p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
18P MUTATED	76	85	95
18P WILD-TYPE	43	126	61

Figure S146. Get High-res Image Gene #32: '18p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p' versus 'MIRSEQ_CNMF'

P value = 8.62e-05 (Fisher's exact test), Q value = 0.029

Table S147. Gene #32: '18p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
18P MUTATED	71	137	48
18P WILD-TYPE	108	94	30

Figure S147. Get High-res Image Gene #32: '18p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000141 (Fisher's exact test), Q value = 0.046

Table S148. Gene #32: '18p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
18P MUTATED	61	119	42
18P WILD-TYPE	94	73	36

Figure S148. Get High-res Image Gene #32: '18p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000177 (Fisher's exact test), Q value = 0.057

Table S149. Gene #32: '18p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
18P MUTATED	24	119	79
18P WILD-TYPE	25	69	109

Figure S149. Get High-res Image Gene #32: '18p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q' versus 'CN_CNMF'

P value = 7.58e-14 (Fisher's exact test), Q value = 3.6e-11

Table S150. Gene #33: '18q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
18Q MUTATED	142	83	48
18Q WILD-TYPE	44	133	43

Figure S150. Get High-res Image Gene #33: '18q' versus Molecular Subtype #3: 'CN_CNMF'

'18q' versus 'MRNASEQ_CNMF'

P value = 0.000618 (Chi-square test), Q value = 0.18

Table S151. Gene #33: '18q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
18Q MUTATED	93	47	42	63	24
18Q WILD-TYPE	45	65	34	43	30

Figure S151. Get High-res Image Gene #33: '18q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000497 (Fisher's exact test), Q value = 0.15

Table S152. Gene #33: '18q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
18Q MUTATED	78	96	95
18Q WILD-TYPE	41	115	61

Figure S152. Get High-res Image Gene #33: '18q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p' versus 'CN_CNMF'

P value = 3.24e-10 (Fisher's exact test), Q value = 1.5e-07

Table S153. Gene #34: '19p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
19P MUTATED	109	86	72
19P WILD-TYPE	77	130	19

Figure S153. Get High-res Image Gene #34: '19p' versus Molecular Subtype #3: 'CN_CNMF'

'19p' versus 'METHLYATION_CNMF'

P value = 2.89e-13 (Fisher's exact test), Q value = 1.4e-10

Table S154. Gene #34: '19p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
19P MUTATED	109	70	51
19P WILD-TYPE	32	70	99

Figure S154. Get High-res Image Gene #34: '19p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p' versus 'MRNASEQ_CNMF'

P value = 8.46e-07 (Chi-square test), Q value = 0.00035

Table S155. Gene #34: '19p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
19P MUTATED	73	46	47	79	20
19P WILD-TYPE	65	66	29	27	34

Figure S155. Get High-res Image Gene #34: '19p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.13e-08 (Fisher's exact test), Q value = 5.1e-06

Table S156. Gene #34: '19p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
19P MUTATED	63	88	114
19P WILD-TYPE	56	123	42

Figure S156. Get High-res Image Gene #34: '19p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p' versus 'MIRSEQ_CNMF'

P value = 7.25e-06 (Fisher's exact test), Q value = 0.0028

Table S157. Gene #34: '19p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
19P MUTATED	74	150	38
19P WILD-TYPE	105	81	40

Figure S157. Get High-res Image Gene #34: '19p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.97e-08 (Fisher's exact test), Q value = 8.7e-06

Table S158. Gene #34: '19p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
19P MUTATED	18	166	78
19P WILD-TYPE	33	83	110

Figure S158. Get High-res Image Gene #34: '19p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.34e-05 (Fisher's exact test), Q value = 0.022

Table S159. Gene #34: '19p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
19P MUTATED	68	125	34
19P WILD-TYPE	87	67	44

Figure S159. Get High-res Image Gene #34: '19p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.28e-07 (Fisher's exact test), Q value = 0.00014

Table S160. Gene #34: '19p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
19P MUTATED	19	128	80
19P WILD-TYPE	30	60	108

Figure S160. Get High-res Image Gene #34: '19p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q' versus 'CN_CNMF'

P value = 3.57e-10 (Fisher's exact test), Q value = 1.6e-07

Table S161. Gene #35: '19q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
19Q MUTATED	97	65	62
19Q WILD-TYPE	89	151	29

Figure S161. Get High-res Image Gene #35: '19q' versus Molecular Subtype #3: 'CN_CNMF'

'19q' versus 'METHLYATION_CNMF'

P value = 2.06e-10 (Fisher's exact test), Q value = 9.5e-08

Table S162. Gene #35: '19q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
19Q MUTATED	93	62	41
19Q WILD-TYPE	48	78	109

Figure S162. Get High-res Image Gene #35: '19q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q' versus 'MRNASEQ_CNMF'

P value = 2.2e-06 (Chi-square test), Q value = 0.00088

Table S163. Gene #35: '19q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
19Q MUTATED	64	35	38	69	16
19Q WILD-TYPE	74	77	38	37	38

Figure S163. Get High-res Image Gene #35: '19q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.27e-07 (Fisher's exact test), Q value = 5.5e-05

Table S164. Gene #35: '19q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
19Q MUTATED	56	69	97
19Q WILD-TYPE	63	142	59

Figure S164. Get High-res Image Gene #35: '19q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q' versus 'MIRSEQ_CNMF'

P value = 6.98e-05 (Fisher's exact test), Q value = 0.024

Table S165. Gene #35: '19q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
19Q MUTATED	59	126	35
19Q WILD-TYPE	120	105	43

Figure S165. Get High-res Image Gene #35: '19q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.26e-07 (Fisher's exact test), Q value = 5.5e-05

Table S166. Gene #35: '19q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
19Q MUTATED	15	143	62
19Q WILD-TYPE	36	106	126

Figure S166. Get High-res Image Gene #35: '19q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000194 (Fisher's exact test), Q value = 0.061

Table S167. Gene #35: '19q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
19Q MUTATED	54	108	31
19Q WILD-TYPE	101	84	47

Figure S167. Get High-res Image Gene #35: '19q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.41e-07 (Fisher's exact test), Q value = 0.00014

Table S168. Gene #35: '19q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
19Q MUTATED	18	113	62
19Q WILD-TYPE	31	75	126

Figure S168. Get High-res Image Gene #35: '19q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p' versus 'CN_CNMF'

P value = 2.89e-08 (Fisher's exact test), Q value = 1.3e-05

Table S169. Gene #36: '20p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
20P MUTATED	123	90	65
20P WILD-TYPE	63	126	26

Figure S169. Get High-res Image Gene #36: '20p' versus Molecular Subtype #3: 'CN_CNMF'

'20p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.9e-07 (Fisher's exact test), Q value = 0.00025

Table S170. Gene #36: '20p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
20P MUTATED	81	90	103
20P WILD-TYPE	38	121	53

Figure S170. Get High-res Image Gene #36: '20p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p' versus 'MIRSEQ_CNMF'

P value = 4.89e-05 (Fisher's exact test), Q value = 0.017

Table S171. Gene #36: '20p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
20P MUTATED	77	146	51
20P WILD-TYPE	102	85	27

Figure S171. Get High-res Image Gene #36: '20p' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.06e-05 (Fisher's exact test), Q value = 0.004

Table S172. Gene #36: '20p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
20P MUTATED	33	161	80
20P WILD-TYPE	18	88	108

Figure S172. Get High-res Image Gene #36: '20p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000763 (Fisher's exact test), Q value = 0.22

Table S173. Gene #36: '20p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
20P MUTATED	31	121	86
20P WILD-TYPE	18	67	102

Figure S173. Get High-res Image Gene #36: '20p' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q' versus 'CN_CNMF'

P value = 1.34e-08 (Fisher's exact test), Q value = 6e-06

Table S174. Gene #37: '20q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
20Q MUTATED	110	81	65
20Q WILD-TYPE	76	135	26

Figure S174. Get High-res Image Gene #37: '20q' versus Molecular Subtype #3: 'CN_CNMF'

'20q' versus 'METHLYATION_CNMF'

P value = 0.000155 (Fisher's exact test), Q value = 0.05

Table S175. Gene #37: '20q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
20Q MUTATED	89	73	58
20Q WILD-TYPE	52	67	92

Figure S175. Get High-res Image Gene #37: '20q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q' versus 'MRNASEQ_CNMF'

P value = 7.36e-05 (Chi-square test), Q value = 0.025

Table S176. Gene #37: '20q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
20Q MUTATED	77	44	37	73	21
20Q WILD-TYPE	61	68	39	33	33

Figure S176. Get High-res Image Gene #37: '20q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.14e-06 (Fisher's exact test), Q value = 0.00086

Table S177. Gene #37: '20q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
20Q MUTATED	70	82	100
20Q WILD-TYPE	49	129	56

Figure S177. Get High-res Image Gene #37: '20q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q' versus 'MIRSEQ_CNMF'

P value = 3.22e-05 (Fisher's exact test), Q value = 0.012

Table S178. Gene #37: '20q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
20Q MUTATED	69	141	42
20Q WILD-TYPE	110	90	36

Figure S178. Get High-res Image Gene #37: '20q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.25e-07 (Fisher's exact test), Q value = 0.00034

Table S179. Gene #37: '20q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
20Q MUTATED	29	154	69
20Q WILD-TYPE	22	95	119

Figure S179. Get High-res Image Gene #37: '20q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000515 (Fisher's exact test), Q value = 0.15

Table S180. Gene #37: '20q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
20Q MUTATED	62	117	40
20Q WILD-TYPE	93	75	38

Figure S180. Get High-res Image Gene #37: '20q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.73e-05 (Fisher's exact test), Q value = 0.0098

Table S181. Gene #37: '20q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
20Q MUTATED	27	118	74
20Q WILD-TYPE	22	70	114

Figure S181. Get High-res Image Gene #37: '20q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q' versus 'CN_CNMF'

P value = 4.62e-05 (Fisher's exact test), Q value = 0.016

Table S182. Gene #38: '21q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
21Q MUTATED	104	87	60
21Q WILD-TYPE	82	129	31

Figure S182. Get High-res Image Gene #38: '21q' versus Molecular Subtype #3: 'CN_CNMF'

'21q' versus 'MRNASEQ_CNMF'

P value = 7.26e-06 (Chi-square test), Q value = 0.0028

Table S183. Gene #38: '21q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
21Q MUTATED	74	42	41	72	17
21Q WILD-TYPE	64	70	35	34	37

Figure S183. Get High-res Image Gene #38: '21q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.02e-06 (Fisher's exact test), Q value = 0.0031

Table S184. Gene #38: '21q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
21Q MUTATED	62	83	101
21Q WILD-TYPE	57	128	55

Figure S184. Get High-res Image Gene #38: '21q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q' versus 'MIRSEQ_CNMF'

P value = 1.18e-05 (Fisher's exact test), Q value = 0.0045

Table S185. Gene #38: '21q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
21Q MUTATED	67	141	39
21Q WILD-TYPE	112	90	39

Figure S185. Get High-res Image Gene #38: '21q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.41e-05 (Fisher's exact test), Q value = 0.0054

Table S186. Gene #38: '21q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
21Q MUTATED	21	152	74
21Q WILD-TYPE	30	97	114

Figure S186. Get High-res Image Gene #38: '21q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.075

Table S187. Gene #38: '21q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
21Q MUTATED	16	113	82
21Q WILD-TYPE	33	75	106

Figure S187. Get High-res Image Gene #38: '21q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q' versus 'CN_CNMF'

P value = 3.96e-14 (Fisher's exact test), Q value = 1.9e-11

Table S188. Gene #39: '22q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
22Q MUTATED	129	77	67
22Q WILD-TYPE	57	139	24

Figure S188. Get High-res Image Gene #39: '22q' versus Molecular Subtype #3: 'CN_CNMF'

'22q' versus 'METHLYATION_CNMF'

P value = 0.000214 (Fisher's exact test), Q value = 0.067

Table S189. Gene #39: '22q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
22Q MUTATED	87	89	63
22Q WILD-TYPE	54	51	87

Figure S189. Get High-res Image Gene #39: '22q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q' versus 'MRNASEQ_CNMF'

P value = 5.12e-06 (Chi-square test), Q value = 0.002

Table S190. Gene #39: '22q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	138	112	76	106	54
22Q MUTATED	84	42	47	73	22
22Q WILD-TYPE	54	70	29	33	32

Figure S190. Get High-res Image Gene #39: '22q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.2e-11 (Fisher's exact test), Q value = 2e-08

Table S191. Gene #39: '22q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	119	211	156
22Q MUTATED	75	80	113
22Q WILD-TYPE	44	131	43

Figure S191. Get High-res Image Gene #39: '22q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q' versus 'MIRSEQ_CNMF'

P value = 1.88e-05 (Fisher's exact test), Q value = 0.0069

Table S192. Gene #39: '22q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
22Q MUTATED	75	150	44
22Q WILD-TYPE	104	81	34

Figure S192. Get High-res Image Gene #39: '22q' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.48e-07 (Fisher's exact test), Q value = 0.00011

Table S193. Gene #39: '22q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
22Q MUTATED	19	167	83
22Q WILD-TYPE	32	82	105

Figure S193. Get High-res Image Gene #39: '22q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.72e-05 (Fisher's exact test), Q value = 0.013

Table S194. Gene #39: '22q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
22Q MUTATED	69	129	37
22Q WILD-TYPE	86	63	41

Figure S194. Get High-res Image Gene #39: '22q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.7e-07 (Fisher's exact test), Q value = 0.00024

Table S195. Gene #39: '22q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
22Q MUTATED	21	131	83
22Q WILD-TYPE	28	57	105

Figure S195. Get High-res Image Gene #39: '22q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq' versus 'CN_CNMF'

P value = 4.89e-08 (Fisher's exact test), Q value = 2.1e-05

Table S196. Gene #40: 'xq' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	216	91
XQ MUTATED	73	31	28
XQ WILD-TYPE	113	185	63

Figure S196. Get High-res Image Gene #40: 'xq' versus Molecular Subtype #3: 'CN_CNMF'

'xq' versus 'METHLYATION_CNMF'

P value = 0.00086 (Fisher's exact test), Q value = 0.25

Table S197. Gene #40: 'xq' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
XQ MUTATED	46	45	24
XQ WILD-TYPE	95	95	126

Figure S197. Get High-res Image Gene #40: 'xq' versus Molecular Subtype #4: 'METHLYATION_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = LUAD-TP.transferedmergedcluster.txt
Number of patients = 493
Number of significantly focal cnvs = 40
Number of molecular subtypes = 12
Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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