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

Head and Neck Squamous Cell Carcinoma (Primary solid tumor)

16 April 2014 | analyses__2014_04_16

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/C1SQ8Z02

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 73 focal events and 10 molecular subtypes across 511 patients, 154 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_2q11.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_2q31.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_3q26.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
amp_5p15.33 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_5p12 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_6p12.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_6q12 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_7p11.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_7q21.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_8p11.23 cnv correlated to 'CN_CNMF'.
amp_8q11.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_8q24.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_9p24.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_9p23 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_9p13.3 cnv correlated to 'CN_CNMF'.
amp_9q34.3 cnv correlated to 'CN_CNMF'.
amp_11p13 cnv correlated to 'CN_CNMF'.
amp_11q13.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_12p13.33 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_12q15 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_13q22.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_13q34 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_17q12 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_18p11.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_18q11.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_20p12.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_20q11.22 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_xq28 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_1p36.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_1p13.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_2q21.2 cnv correlated to 'MIRSEQ_CNMF'.
del_2q22.1 cnv correlated to 'METHLYATION_CNMF'.
del_2q36.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_3p24.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_3p12.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_4p15.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_4q22.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_4q35.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.
del_5q11.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_5q15 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_5q35.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_6p25.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_7q36.1 cnv correlated to 'CN_CNMF'.
del_8p23.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p23 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_9p21.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_9q21.11 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_9q34.3 cnv correlated to 'CN_CNMF'.
del_10p15.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_10p11.21 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_10q23.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
del_11p15.5 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_11q23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_12q24.33 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_13q12.11 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_13q14.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_14q32.32 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_15q15.1 cnv correlated to 'CN_CNMF'.
del_16q23.3 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_17q25.3 cnv correlated to 'METHLYATION_CNMF'.
del_18q21.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_18q23 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_19p13.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_19q13.43 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_21q22.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_xp22.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_xp21.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_xq21.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 73 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, 154 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	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
amp 3q26 33	372 (73%)	139	1e-18 (7.09e-16)	3.52e-15 (2.44e-12)	0.129 (1.00)	0.317 (1.00)	2.26e-07 (0.000146)	2.71e-05 (0.0164)	0.000167 (0.0986)	0.413 (1.00)	0.0425 (1.00)	0.165 (1.00)
del 8p23 2	294 (58%)	217	1.44e-21 (1.03e-18)	1.26e-12 (8.55e-10)	0.282 (1.00)	0.122 (1.00)	0.00119 (0.676)	1.26e-05 (0.00775)	0.00202 (1.00)	0.00221 (1.00)	0.000218 (0.128)	6.2e-05 (0.0372)
del 11p15 5	156 (31%)	355	7.64e-11 (5.14e-08)	2.52e-10 (1.68e-07)	0.861 (1.00)	0.548 (1.00)	3.76e-05 (0.0227)	0.000207 (0.122)	2.09e-07 (0.000136)	0.112 (1.00)	0.161 (1.00)	0.00953 (1.00)
amp 8q11 21	305 (60%)	206	2.85e-11 (1.93e-08)	1.34e-07 (8.74e-05)	0.0983 (1.00)	0.429 (1.00)	0.00158 (0.888)	0.000208 (0.122)	0.0336 (1.00)	0.000267 (0.155)	0.0482 (1.00)	0.00151 (0.85)
del 1p36 21	94 (18%)	417	3.04e-10 (2.03e-07)	8.26e-19 (5.84e-16)	0.000846 (0.486)	0.607 (1.00)	4.19e-07 (0.000268)	5.54e-05 (0.0333)	0.000864 (0.494)	0.0953 (1.00)	0.0409 (1.00)	0.0135 (1.00)
del 4p15 2	201 (39%)	310	1.39e-17 (9.77e-15)	3.45e-15 (2.4e-12)	0.0116 (1.00)	0.782 (1.00)	9.53e-05 (0.0567)	7.12e-05 (0.0426)	0.0532 (1.00)	1 (1.00)	0.00382 (1.00)	0.0191 (1.00)
del 11q23 1	239 (47%)	272	2.16e-06 (0.00135)	2.45e-15 (1.7e-12)	0.0878 (1.00)	0.0422 (1.00)	3.09e-05 (0.0187)	4.22e-06 (0.00262)	0.00196 (1.00)	0.199 (1.00)	0.0228 (1.00)	0.109 (1.00)
del 13q14 2	209 (41%)	302	2.16e-14 (1.49e-11)	1.2e-09 (8.02e-07)	0.109 (1.00)	0.824 (1.00)	5.44e-06 (0.00336)	1.17e-08 (7.75e-06)	0.0035 (1.00)	0.305 (1.00)	0.196 (1.00)	0.00971 (1.00)
del 14q32 32	73 (14%)	438	0.000256 (0.149)	2.81e-12 (1.91e-09)	0.0191 (1.00)	0.15 (1.00)	8.89e-07 (0.000561)	1.02e-07 (6.61e-05)	0.00328 (1.00)	0.0183 (1.00)	0.0195 (1.00)	0.00266 (1.00)
amp 8q24 21	379 (74%)	132	3.59e-17 (2.52e-14)	2.18e-10 (1.46e-07)	0.31 (1.00)	0.467 (1.00)	0.0127 (1.00)	7.26e-05 (0.0434)	0.0646 (1.00)	0.0033 (1.00)	0.00186 (1.00)	0.015 (1.00)
amp 18p11 31	152 (30%)	359	6.77e-17 (4.74e-14)	2.2e-09 (1.46e-06)	0.519 (1.00)	0.818 (1.00)	0.0806 (1.00)	4.28e-05 (0.0258)	0.763 (1.00)	0.272 (1.00)	0.567 (1.00)	0.231 (1.00)
del 4q35 2	206 (40%)	305	1.05e-11 (7.13e-09)	1.27e-05 (0.00779)	0.84 (1.00)	0.000246 (0.144)	0.0122 (1.00)	0.0442 (1.00)	0.325 (1.00)	0.0501 (1.00)	0.407 (1.00)	0.11 (1.00)
del 5q35 3	195 (38%)	316	8.82e-25 (6.39e-22)	6.47e-21 (4.63e-18)	0.238 (1.00)	0.0275 (1.00)	0.0194 (1.00)	0.00028 (0.162)	0.335 (1.00)	0.187 (1.00)	0.457 (1.00)	0.329 (1.00)
del 10q23 31	134 (26%)	377	6.97e-06 (0.0043)	1.37e-06 (0.000863)	0.134 (1.00)	0.865 (1.00)	7.42e-05 (0.0442)	0.00169 (0.944)	0.00745 (1.00)	0.531 (1.00)	0.044 (1.00)	0.511 (1.00)
del 16q23 3	102 (20%)	409	0.00118 (0.669)	4.63e-07 (0.000296)	0.16 (1.00)	0.0681 (1.00)	4e-06 (0.00249)	2.37e-07 (0.000153)	0.00404 (1.00)	0.0506 (1.00)	0.006 (1.00)	0.0165 (1.00)
del xq21 33	74 (14%)	437	6.16e-06 (0.0038)	3.52e-07 (0.000225)	0.487 (1.00)	0.237 (1.00)	0.000858 (0.492)	0.00614 (1.00)	9.57e-05 (0.0569)	0.036 (1.00)	0.222 (1.00)	0.0126 (1.00)
amp 2q11 2	104 (20%)	407	6.82e-12 (4.62e-09)	3.55e-14 (2.43e-11)	0.499 (1.00)	0.31 (1.00)	0.0505 (1.00)	0.125 (1.00)	0.0648 (1.00)	0.361 (1.00)	0.148 (1.00)	0.521 (1.00)
amp 2q31 2	108 (21%)	403	5.01e-15 (3.47e-12)	1.32e-16 (9.27e-14)	0.241 (1.00)	0.615 (1.00)	0.189 (1.00)	0.145 (1.00)	0.191 (1.00)	0.736 (1.00)	0.331 (1.00)	0.872 (1.00)
amp 5p15 33	231 (45%)	280	5.01e-19 (3.55e-16)	2.31e-06 (0.00145)	0.847 (1.00)	0.451 (1.00)	0.155 (1.00)	0.173 (1.00)	0.687 (1.00)	1 (1.00)	0.963 (1.00)	1 (1.00)
amp 5p12	203 (40%)	308	1.54e-15 (1.08e-12)	6.51e-05 (0.039)	0.574 (1.00)	0.0684 (1.00)	0.311 (1.00)	0.435 (1.00)	0.581 (1.00)	0.708 (1.00)	0.989 (1.00)	0.953 (1.00)
amp 6p12 1	107 (21%)	404	3.23e-08 (2.12e-05)	1.31e-05 (0.00799)	0.45 (1.00)	0.787 (1.00)	0.847 (1.00)	0.625 (1.00)	0.448 (1.00)	0.0422 (1.00)	0.917 (1.00)	0.358 (1.00)
amp 6q12	92 (18%)	419	1.63e-08 (1.08e-05)	0.000328 (0.189)	0.279 (1.00)	0.667 (1.00)	0.85 (1.00)	0.983 (1.00)	0.301 (1.00)	0.188 (1.00)	0.796 (1.00)	0.775 (1.00)
amp 7p11 2	215 (42%)	296	1.03e-12 (7.04e-10)	6.66e-12 (4.51e-09)	0.994 (1.00)	0.186 (1.00)	0.0486 (1.00)	0.06 (1.00)	0.716 (1.00)	0.164 (1.00)	0.263 (1.00)	0.377 (1.00)
amp 7q21 3	164 (32%)	347	8.91e-15 (6.15e-12)	1.65e-15 (1.15e-12)	0.329 (1.00)	1 (1.00)	0.305 (1.00)	0.735 (1.00)	0.0842 (1.00)	0.431 (1.00)	0.284 (1.00)	0.619 (1.00)
amp 9p24 1	122 (24%)	389	3.73e-21 (2.68e-18)	5.29e-06 (0.00328)	0.136 (1.00)	0.127 (1.00)	0.00286 (1.00)	0.00206 (1.00)	0.0349 (1.00)	0.593 (1.00)	0.16 (1.00)	0.481 (1.00)
amp 9p23	121 (24%)	390	2.17e-19 (1.54e-16)	1.3e-05 (0.00795)	0.385 (1.00)	0.407 (1.00)	0.00335 (1.00)	0.0053 (1.00)	0.0595 (1.00)	1 (1.00)	0.271 (1.00)	0.626 (1.00)
amp 11q13 3	223 (44%)	288	1.86e-26 (1.35e-23)	7.26e-11 (4.89e-08)	0.828 (1.00)	0.927 (1.00)	0.171 (1.00)	0.0687 (1.00)	0.415 (1.00)	0.139 (1.00)	0.249 (1.00)	0.394 (1.00)
amp 12p13 33	162 (32%)	349	2.82e-17 (1.98e-14)	1.68e-07 (0.000109)	0.0429 (1.00)	0.0966 (1.00)	0.00927 (1.00)	0.0106 (1.00)	0.0234 (1.00)	0.768 (1.00)	0.169 (1.00)	0.827 (1.00)
amp 12q15	101 (20%)	410	3.46e-07 (0.000222)	0.00039 (0.225)	0.0678 (1.00)	0.607 (1.00)	0.126 (1.00)	0.0931 (1.00)	0.907 (1.00)	0.909 (1.00)	1 (1.00)	0.327 (1.00)
amp 13q22 1	104 (20%)	407	1.92e-13 (1.31e-10)	4.36e-06 (0.0027)	0.15 (1.00)	0.374 (1.00)	0.326 (1.00)	0.356 (1.00)	0.436 (1.00)	0.137 (1.00)	0.827 (1.00)	0.408 (1.00)
amp 13q34	106 (21%)	405	1.33e-09 (8.84e-07)	7.39e-05 (0.0441)	0.252 (1.00)	0.661 (1.00)	0.198 (1.00)	0.268 (1.00)	0.345 (1.00)	0.053 (1.00)	0.334 (1.00)	0.164 (1.00)
amp 17q12	88 (17%)	423	1.97e-08 (1.29e-05)	1.46e-06 (0.000915)	0.187 (1.00)	0.544 (1.00)	0.0109 (1.00)	0.115 (1.00)	0.0101 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
amp 18q11 2	101 (20%)	410	5.78e-07 (0.000367)	0.000208 (0.122)	0.517 (1.00)	0.83 (1.00)	0.369 (1.00)	0.0141 (1.00)	0.0385 (1.00)	0.249 (1.00)	0.817 (1.00)	0.904 (1.00)
amp 20p12 2	189 (37%)	322	2.8e-05 (0.0169)	2.67e-05 (0.0162)	0.873 (1.00)	0.699 (1.00)	0.089 (1.00)	0.0559 (1.00)	0.149 (1.00)	0.00127 (0.715)	0.023 (1.00)	0.0309 (1.00)
amp 20q11 22	224 (44%)	287	4.77e-08 (3.12e-05)	8.54e-06 (0.00525)	0.499 (1.00)	0.126 (1.00)	0.106 (1.00)	0.338 (1.00)	0.476 (1.00)	0.0125 (1.00)	0.229 (1.00)	0.0246 (1.00)
amp xq28	145 (28%)	366	2.32e-10 (1.56e-07)	3.96e-06 (0.00247)	0.635 (1.00)	0.263 (1.00)	0.298 (1.00)	0.24 (1.00)	0.156 (1.00)	0.0658 (1.00)	0.955 (1.00)	0.695 (1.00)
del 1p13 2	127 (25%)	384	6.05e-16 (4.23e-13)	5.57e-15 (3.86e-12)	0.0256 (1.00)	0.38 (1.00)	0.0258 (1.00)	0.0418 (1.00)	0.018 (1.00)	0.915 (1.00)	0.0967 (1.00)	0.0123 (1.00)
del 2q36 2	152 (30%)	359	4.39e-08 (2.87e-05)	1.46e-07 (9.5e-05)	0.0915 (1.00)	0.514 (1.00)	0.0105 (1.00)	0.00322 (1.00)	0.0922 (1.00)	0.481 (1.00)	0.129 (1.00)	0.0789 (1.00)
del 3p24 1	357 (70%)	154	2.17e-31 (1.58e-28)	3.18e-24 (2.3e-21)	0.412 (1.00)	0.0826 (1.00)	0.00163 (0.916)	0.0107 (1.00)	0.00792 (1.00)	0.00504 (1.00)	0.111 (1.00)	0.0583 (1.00)
del 3p12 1	332 (65%)	179	1.63e-33 (1.19e-30)	1.38e-24 (1e-21)	0.827 (1.00)	0.343 (1.00)	0.0208 (1.00)	0.0602 (1.00)	0.0762 (1.00)	0.0681 (1.00)	0.341 (1.00)	0.679 (1.00)
del 4q22 1	164 (32%)	347	5.67e-15 (3.92e-12)	1.98e-10 (1.33e-07)	0.248 (1.00)	0.403 (1.00)	0.00878 (1.00)	0.00698 (1.00)	0.208 (1.00)	0.376 (1.00)	0.474 (1.00)	0.147 (1.00)
del 5q11 2	209 (41%)	302	9.49e-31 (6.91e-28)	2.47e-22 (1.78e-19)	0.132 (1.00)	0.177 (1.00)	0.101 (1.00)	0.00125 (0.706)	0.184 (1.00)	0.225 (1.00)	0.384 (1.00)	0.482 (1.00)
del 5q15	219 (43%)	292	3.01e-29 (2.19e-26)	6.14e-21 (4.39e-18)	0.143 (1.00)	0.654 (1.00)	0.109 (1.00)	0.00248 (1.00)	0.234 (1.00)	0.267 (1.00)	0.625 (1.00)	0.806 (1.00)
del 6p25 3	93 (18%)	418	0.000289 (0.167)	9.85e-06 (0.00605)	0.044 (1.00)	0.574 (1.00)	0.00229 (1.00)	0.135 (1.00)	0.195 (1.00)	0.813 (1.00)	0.677 (1.00)	0.324 (1.00)
del 9p23	233 (46%)	278	1.99e-28 (1.44e-25)	1.48e-19 (1.05e-16)	0.281 (1.00)	0.0874 (1.00)	0.823 (1.00)	0.876 (1.00)	0.762 (1.00)	1 (1.00)	0.254 (1.00)	0.928 (1.00)
del 9p21 3	292 (57%)	219	4.79e-18 (3.38e-15)	9.16e-20 (6.51e-17)	0.662 (1.00)	0.0886 (1.00)	0.144 (1.00)	0.181 (1.00)	1 (1.00)	0.354 (1.00)	0.108 (1.00)	0.0152 (1.00)
del 9q21 11	103 (20%)	408	1.4e-13 (9.59e-11)	2.25e-07 (0.000145)	0.97 (1.00)	0.541 (1.00)	0.852 (1.00)	0.924 (1.00)	0.725 (1.00)	0.302 (1.00)	0.484 (1.00)	0.122 (1.00)
del 10p15 3	165 (32%)	346	7.7e-07 (0.000488)	8.43e-07 (0.000533)	0.601 (1.00)	0.339 (1.00)	0.126 (1.00)	0.128 (1.00)	0.145 (1.00)	0.0618 (1.00)	0.0997 (1.00)	0.337 (1.00)
del 10p11 21	152 (30%)	359	2.34e-08 (1.54e-05)	2.29e-07 (0.000147)	0.453 (1.00)	0.0642 (1.00)	0.277 (1.00)	0.571 (1.00)	0.0176 (1.00)	0.482 (1.00)	0.132 (1.00)	0.791 (1.00)
del 12q24 33	60 (12%)	451	3.6e-06 (0.00225)	0.000169 (0.1)	0.612 (1.00)	0.718 (1.00)	0.851 (1.00)	0.686 (1.00)	0.492 (1.00)	0.562 (1.00)	0.0595 (1.00)	0.342 (1.00)
del 13q12 11	224 (44%)	287	8.6e-21 (6.14e-18)	4.06e-12 (2.76e-09)	0.148 (1.00)	0.677 (1.00)	0.0246 (1.00)	0.00166 (0.93)	0.826 (1.00)	0.712 (1.00)	0.592 (1.00)	0.0882 (1.00)
del 18q21 2	259 (51%)	252	2.44e-20 (1.74e-17)	1.3e-20 (9.27e-18)	0.894 (1.00)	0.117 (1.00)	0.00669 (1.00)	0.00831 (1.00)	0.0186 (1.00)	0.00246 (1.00)	0.192 (1.00)	0.0953 (1.00)
del 18q23	278 (54%)	233	6.42e-23 (4.63e-20)	4.7e-22 (3.38e-19)	0.255 (1.00)	0.00826 (1.00)	0.00513 (1.00)	0.00309 (1.00)	0.0243 (1.00)	0.00435 (1.00)	0.0751 (1.00)	0.18 (1.00)
del 19p13 3	165 (32%)	346	6.76e-08 (4.41e-05)	7.29e-07 (0.000463)	0.443 (1.00)	0.499 (1.00)	0.0201 (1.00)	0.247 (1.00)	0.221 (1.00)	0.0105 (1.00)	0.537 (1.00)	0.367 (1.00)
del 19q13 43	94 (18%)	417	7.74e-07 (0.00049)	5.67e-07 (0.000361)	0.327 (1.00)	1 (1.00)	0.865 (1.00)	0.654 (1.00)	0.621 (1.00)	0.407 (1.00)	0.602 (1.00)	0.781 (1.00)
del 21q22 3	195 (38%)	316	9.49e-15 (6.54e-12)	2.65e-10 (1.77e-07)	0.609 (1.00)	0.334 (1.00)	0.0456 (1.00)	0.143 (1.00)	0.611 (1.00)	0.073 (1.00)	0.914 (1.00)	0.27 (1.00)
del xp22 2	152 (30%)	359	3.93e-08 (2.58e-05)	1.27e-09 (8.43e-07)	0.316 (1.00)	0.163 (1.00)	0.0871 (1.00)	0.242 (1.00)	0.0176 (1.00)	0.546 (1.00)	0.388 (1.00)	0.868 (1.00)
del xp21 3	154 (30%)	357	6.12e-09 (4.05e-06)	2.74e-06 (0.00171)	0.556 (1.00)	0.607 (1.00)	0.469 (1.00)	0.106 (1.00)	0.21 (1.00)	0.422 (1.00)	0.738 (1.00)	0.865 (1.00)
amp 8p11 23	156 (31%)	355	2.53e-06 (0.00158)	0.0142 (1.00)	0.8 (1.00)	0.654 (1.00)	0.128 (1.00)	0.0799 (1.00)	0.00319 (1.00)	0.0217 (1.00)	0.287 (1.00)	0.129 (1.00)
amp 9p13 3	135 (26%)	376	2.19e-14 (1.51e-11)	0.00351 (1.00)	0.48 (1.00)	0.517 (1.00)	0.00086 (0.493)	0.00331 (1.00)	0.00297 (1.00)	0.0377 (1.00)	0.834 (1.00)	0.207 (1.00)
amp 9q34 3	174 (34%)	337	9.05e-14 (6.2e-11)	0.00298 (1.00)	0.239 (1.00)	0.148 (1.00)	0.95 (1.00)	0.209 (1.00)	0.71 (1.00)	0.699 (1.00)	0.92 (1.00)	0.847 (1.00)
amp 11p13	101 (20%)	410	0.000243 (0.142)	0.0026 (1.00)	0.456 (1.00)	0.321 (1.00)	0.957 (1.00)	0.498 (1.00)	0.805 (1.00)	0.246 (1.00)	0.315 (1.00)	0.495 (1.00)
del 2q21 2	73 (14%)	438	0.819 (1.00)	0.0216 (1.00)	0.702 (1.00)	0.77 (1.00)	0.0256 (1.00)	0.00173 (0.964)	0.000252 (0.147)	0.511 (1.00)	0.0667 (1.00)	0.524 (1.00)
del 2q22 1	114 (22%)	397	0.0684 (1.00)	1.91e-05 (0.0117)	0.35 (1.00)	0.883 (1.00)	0.283 (1.00)	0.135 (1.00)	0.176 (1.00)	0.443 (1.00)	0.894 (1.00)	0.445 (1.00)
del 7q36 1	127 (25%)	384	0.000104 (0.0615)	0.445 (1.00)	0.0449 (1.00)	0.926 (1.00)	0.767 (1.00)	0.925 (1.00)	0.629 (1.00)	0.915 (1.00)	0.75 (1.00)	0.417 (1.00)
del 9q34 3	76 (15%)	435	5.39e-07 (0.000344)	0.00108 (0.612)	0.606 (1.00)	0.273 (1.00)	0.446 (1.00)	0.588 (1.00)	0.716 (1.00)	0.898 (1.00)	0.196 (1.00)	0.4 (1.00)
del 15q15 1	119 (23%)	392	7.53e-09 (4.98e-06)	0.219 (1.00)	0.668 (1.00)	0.243 (1.00)	0.071 (1.00)	0.0139 (1.00)	0.8 (1.00)	0.516 (1.00)	0.69 (1.00)	0.535 (1.00)
del 17q25 3	68 (13%)	443	0.0391 (1.00)	0.000233 (0.137)	0.426 (1.00)	0.093 (1.00)	0.0124 (1.00)	0.00165 (0.928)	0.00375 (1.00)	0.0302 (1.00)	0.00489 (1.00)	0.0605 (1.00)
amp 15q26 3	102 (20%)	409	0.00195 (1.00)	0.0153 (1.00)	0.452 (1.00)	0.916 (1.00)	0.611 (1.00)	0.647 (1.00)	0.332 (1.00)	0.489 (1.00)	0.683 (1.00)	0.439 (1.00)
del 1q44	47 (9%)	464	0.000986 (0.563)	0.00518 (1.00)	0.712 (1.00)	0.828 (1.00)	0.0138 (1.00)	0.0195 (1.00)	0.000549 (0.317)	0.0375 (1.00)	0.0237 (1.00)	0.404 (1.00)
del 7q31 1	74 (14%)	437	0.00643 (1.00)	0.283 (1.00)	0.573 (1.00)	0.835 (1.00)	0.521 (1.00)	0.483 (1.00)	0.877 (1.00)	1 (1.00)	0.578 (1.00)	0.46 (1.00)
del 14q11 2	72 (14%)	439	0.00355 (1.00)	0.0197 (1.00)	0.314 (1.00)	0.713 (1.00)	0.114 (1.00)	0.324 (1.00)	0.0368 (1.00)	0.0224 (1.00)	0.158 (1.00)	0.0781 (1.00)
del 22q13 31	84 (16%)	427	0.00101 (0.577)	0.00948 (1.00)	0.684 (1.00)	0.948 (1.00)	0.0197 (1.00)	0.844 (1.00)	0.0116 (1.00)	0.319 (1.00)	0.13 (1.00)	0.726 (1.00)

'amp_2q11.2' versus 'CN_CNMF'

P value = 6.82e-12 (Fisher's exact test), Q value = 4.6e-09

Table S1. Gene #1: 'amp_2q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 1(2Q11.2) MUTATED	54	35	12	3
AMP PEAK 1(2Q11.2) WILD-TYPE	124	67	177	39

Figure S1. Get High-res Image Gene #1: 'amp_2q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2q11.2' versus 'METHLYATION_CNMF'

P value = 3.55e-14 (Chi-square test), Q value = 2.4e-11

Table S2. Gene #1: 'amp_2q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
AMP PEAK 1(2Q11.2) MUTATED	28	20	39	2	4	6	5
AMP PEAK 1(2Q11.2) WILD-TYPE	45	75	53	77	67	73	17

Figure S2. Get High-res Image Gene #1: 'amp_2q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_2q31.2' versus 'CN_CNMF'

P value = 5.01e-15 (Fisher's exact test), Q value = 3.5e-12

Table S3. Gene #2: 'amp_2q31.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 2(2Q31.2) MUTATED	55	40	10	3
AMP PEAK 2(2Q31.2) WILD-TYPE	123	62	179	39

Figure S3. Get High-res Image Gene #2: 'amp_2q31.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2q31.2' versus 'METHLYATION_CNMF'

P value = 1.32e-16 (Chi-square test), Q value = 9.3e-14

Table S4. Gene #2: 'amp_2q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
AMP PEAK 2(2Q31.2) MUTATED	23	17	48	5	3	8	4
AMP PEAK 2(2Q31.2) WILD-TYPE	50	78	44	74	68	71	18

Figure S4. Get High-res Image Gene #2: 'amp_2q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q26.33' versus 'CN_CNMF'

P value = 1e-18 (Fisher's exact test), Q value = 7.1e-16

Table S5. Gene #3: 'amp_3q26.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 3(3Q26.33) MUTATED	149	97	96	30
AMP PEAK 3(3Q26.33) WILD-TYPE	29	5	93	12

Figure S5. Get High-res Image Gene #3: 'amp_3q26.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.33' versus 'METHLYATION_CNMF'

P value = 3.52e-15 (Chi-square test), Q value = 2.4e-12

Table S6. Gene #3: 'amp_3q26.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
AMP PEAK 3(3Q26.33) MUTATED	60	76	86	63	27	47	13
AMP PEAK 3(3Q26.33) WILD-TYPE	13	19	6	16	44	32	9

Figure S6. Get High-res Image Gene #3: 'amp_3q26.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q26.33' versus 'MRNASEQ_CNMF'

P value = 2.26e-07 (Fisher's exact test), Q value = 0.00015

Table S7. Gene #3: 'amp_3q26.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	207	134	152
AMP PEAK 3(3Q26.33) MUTATED	174	101	88
AMP PEAK 3(3Q26.33) WILD-TYPE	33	33	64

Figure S7. Get High-res Image Gene #3: 'amp_3q26.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_3q26.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.71e-05 (Fisher's exact test), Q value = 0.016

Table S8. Gene #3: 'amp_3q26.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	177	176
AMP PEAK 3(3Q26.33) MUTATED	104	111	148
AMP PEAK 3(3Q26.33) WILD-TYPE	36	66	28

Figure S8. Get High-res Image Gene #3: 'amp_3q26.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.33' versus 'MIRSEQ_CNMF'

P value = 0.000167 (Fisher's exact test), Q value = 0.099

Table S9. Gene #3: 'amp_3q26.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	216	146
AMP PEAK 3(3Q26.33) MUTATED	90	176	102
AMP PEAK 3(3Q26.33) WILD-TYPE	55	40	44

Figure S9. Get High-res Image Gene #3: 'amp_3q26.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5p15.33' versus 'CN_CNMF'

P value = 5.01e-19 (Fisher's exact test), Q value = 3.5e-16

Table S10. Gene #4: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 4(5P15.33) MUTATED	111	66	39	15
AMP PEAK 4(5P15.33) WILD-TYPE	67	36	150	27

Figure S10. Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

P value = 2.31e-06 (Chi-square test), Q value = 0.0014

Table S11. Gene #4: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
AMP PEAK 4(5P15.33) MUTATED	41	52	52	36	13	27	10
AMP PEAK 4(5P15.33) WILD-TYPE	32	43	40	43	58	52	12

Figure S11. Get High-res Image Gene #4: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5p12' versus 'CN_CNMF'

P value = 1.54e-15 (Fisher's exact test), Q value = 1.1e-12

Table S12. Gene #5: 'amp_5p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 5(5P12) MUTATED	97	58	33	15
AMP PEAK 5(5P12) WILD-TYPE	81	44	156	27

Figure S12. Get High-res Image Gene #5: 'amp_5p12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p12' versus 'METHLYATION_CNMF'

P value = 6.51e-05 (Chi-square test), Q value = 0.039

Table S13. Gene #5: 'amp_5p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
AMP PEAK 5(5P12) MUTATED	37	47	45	29	14	21	10
AMP PEAK 5(5P12) WILD-TYPE	36	48	47	50	57	58	12

Figure S13. Get High-res Image Gene #5: 'amp_5p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p12.1' versus 'CN_CNMF'

P value = 3.23e-08 (Fisher's exact test), Q value = 2.1e-05

Table S14. Gene #6: 'amp_6p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 6(6P12.1) MUTATED	52	29	14	12
AMP PEAK 6(6P12.1) WILD-TYPE	126	73	175	30

Figure S14. Get High-res Image Gene #6: 'amp_6p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p12.1' versus 'METHLYATION_CNMF'

P value = 1.31e-05 (Chi-square test), Q value = 0.008

Table S15. Gene #6: 'amp_6p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
AMP PEAK 6(6P12.1) MUTATED	24	31	25	7	7	10	3
AMP PEAK 6(6P12.1) WILD-TYPE	49	64	67	72	64	69	19

Figure S15. Get High-res Image Gene #6: 'amp_6p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q12' versus 'CN_CNMF'

P value = 1.63e-08 (Fisher's exact test), Q value = 1.1e-05

Table S16. Gene #7: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 7(6Q12) MUTATED	47	23	10	12
AMP PEAK 7(6Q12) WILD-TYPE	131	79	179	30

Figure S16. Get High-res Image Gene #7: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q12' versus 'METHLYATION_CNMF'

P value = 0.000328 (Chi-square test), Q value = 0.19

Table S17. Gene #7: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
AMP PEAK 7(6Q12) MUTATED	17	27	23	4	7	10	4
AMP PEAK 7(6Q12) WILD-TYPE	56	68	69	75	64	69	18

Figure S17. Get High-res Image Gene #7: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7p11.2' versus 'CN_CNMF'

P value = 1.03e-12 (Fisher's exact test), Q value = 7e-10

Table S18. Gene #8: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 8(7P11.2) MUTATED	106	50	41	18
AMP PEAK 8(7P11.2) WILD-TYPE	72	52	148	24

Figure S18. Get High-res Image Gene #8: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p11.2' versus 'METHLYATION_CNMF'

P value = 6.66e-12 (Chi-square test), Q value = 4.5e-09

Table S19. Gene #8: 'amp_7p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
AMP PEAK 8(7P11.2) MUTATED	41	50	54	6	24	28	12
AMP PEAK 8(7P11.2) WILD-TYPE	32	45	38	73	47	51	10

Figure S19. Get High-res Image Gene #8: 'amp_7p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q21.3' versus 'CN_CNMF'

P value = 8.91e-15 (Fisher's exact test), Q value = 6.2e-12

Table S20. Gene #9: 'amp_7q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 9(7Q21.3) MUTATED	84	46	22	12
AMP PEAK 9(7Q21.3) WILD-TYPE	94	56	167	30

Figure S20. Get High-res Image Gene #9: 'amp_7q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q21.3' versus 'METHLYATION_CNMF'

P value = 1.65e-15 (Chi-square test), Q value = 1.1e-12

Table S21. Gene #9: 'amp_7q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
AMP PEAK 9(7Q21.3) MUTATED	33	29	60	9	13	14	6
AMP PEAK 9(7Q21.3) WILD-TYPE	40	66	32	70	58	65	16

Figure S21. Get High-res Image Gene #9: 'amp_7q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8p11.23' versus 'CN_CNMF'

P value = 2.53e-06 (Fisher's exact test), Q value = 0.0016

Table S22. Gene #10: 'amp_8p11.23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 10(8P11.23) MUTATED	45	54	45	12
AMP PEAK 10(8P11.23) WILD-TYPE	133	48	144	30

Figure S22. Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q11.21' versus 'CN_CNMF'

P value = 2.85e-11 (Fisher's exact test), Q value = 1.9e-08

Table S23. Gene #11: 'amp_8q11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 11(8Q11.21) MUTATED	135	55	81	34
AMP PEAK 11(8Q11.21) WILD-TYPE	43	47	108	8

Figure S23. Get High-res Image Gene #11: 'amp_8q11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q11.21' versus 'METHLYATION_CNMF'

P value = 1.34e-07 (Chi-square test), Q value = 8.7e-05

Table S24. Gene #11: 'amp_8q11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
AMP PEAK 11(8Q11.21) MUTATED	41	79	52	30	37	49	17
AMP PEAK 11(8Q11.21) WILD-TYPE	32	16	40	49	34	30	5

Figure S24. Get High-res Image Gene #11: 'amp_8q11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000208 (Fisher's exact test), Q value = 0.12

Table S25. Gene #11: 'amp_8q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	177	176
AMP PEAK 11(8Q11.21) MUTATED	97	113	84
AMP PEAK 11(8Q11.21) WILD-TYPE	43	64	92

Figure S25. Get High-res Image Gene #11: 'amp_8q11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8q11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000267 (Fisher's exact test), Q value = 0.16

Table S26. Gene #11: 'amp_8q11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	190	317
AMP PEAK 11(8Q11.21) MUTATED	133	170
AMP PEAK 11(8Q11.21) WILD-TYPE	57	147

Figure S26. Get High-res Image Gene #11: 'amp_8q11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 3.59e-17 (Fisher's exact test), Q value = 2.5e-14

Table S27. Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 12(8Q24.21) MUTATED	167	72	105	35
AMP PEAK 12(8Q24.21) WILD-TYPE	11	30	84	7

Figure S27. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 2.18e-10 (Chi-square test), Q value = 1.5e-07

Table S28. Gene #12: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
AMP PEAK 12(8Q24.21) MUTATED	55	86	74	36	47	60	21
AMP PEAK 12(8Q24.21) WILD-TYPE	18	9	18	43	24	19	1

Figure S28. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.26e-05 (Fisher's exact test), Q value = 0.043

Table S29. Gene #12: 'amp_8q24.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	177	176
AMP PEAK 12(8Q24.21) MUTATED	113	143	110
AMP PEAK 12(8Q24.21) WILD-TYPE	27	34	66

Figure S29. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_9p24.1' versus 'CN_CNMF'

P value = 3.73e-21 (Fisher's exact test), Q value = 2.7e-18

Table S30. Gene #13: 'amp_9p24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 13(9P24.1) MUTATED	29	13	42	38
AMP PEAK 13(9P24.1) WILD-TYPE	149	89	147	4

Figure S30. Get High-res Image Gene #13: 'amp_9p24.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9p24.1' versus 'METHLYATION_CNMF'

P value = 5.29e-06 (Chi-square test), Q value = 0.0033

Table S31. Gene #13: 'amp_9p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
AMP PEAK 13(9P24.1) MUTATED	8	20	19	20	34	13	8
AMP PEAK 13(9P24.1) WILD-TYPE	65	75	73	59	37	66	14

Figure S31. Get High-res Image Gene #13: 'amp_9p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_9p23' versus 'CN_CNMF'

P value = 2.17e-19 (Fisher's exact test), Q value = 1.5e-16

Table S32. Gene #14: 'amp_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 14(9P23) MUTATED	30	14	40	37
AMP PEAK 14(9P23) WILD-TYPE	148	88	149	5

Figure S32. Get High-res Image Gene #14: 'amp_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9p23' versus 'METHLYATION_CNMF'

P value = 1.3e-05 (Chi-square test), Q value = 0.008

Table S33. Gene #14: 'amp_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
AMP PEAK 14(9P23) MUTATED	7	20	20	19	33	14	8
AMP PEAK 14(9P23) WILD-TYPE	66	75	72	60	38	65	14

Figure S33. Get High-res Image Gene #14: 'amp_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_9p13.3' versus 'CN_CNMF'

P value = 2.19e-14 (Fisher's exact test), Q value = 1.5e-11

Table S34. Gene #15: 'amp_9p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 15(9P13.3) MUTATED	39	24	37	35
AMP PEAK 15(9P13.3) WILD-TYPE	139	78	152	7

Figure S34. Get High-res Image Gene #15: 'amp_9p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9q34.3' versus 'CN_CNMF'

P value = 9.05e-14 (Fisher's exact test), Q value = 6.2e-11

Table S35. Gene #16: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 16(9Q34.3) MUTATED	55	47	38	34
AMP PEAK 16(9Q34.3) WILD-TYPE	123	55	151	8

Figure S35. Get High-res Image Gene #16: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11p13' versus 'CN_CNMF'

P value = 0.000243 (Fisher's exact test), Q value = 0.14

Table S36. Gene #17: 'amp_11p13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 17(11P13) MUTATED	50	13	25	13
AMP PEAK 17(11P13) WILD-TYPE	128	89	164	29

Figure S36. Get High-res Image Gene #17: 'amp_11p13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q13.3' versus 'CN_CNMF'

P value = 1.86e-26 (Fisher's exact test), Q value = 1.3e-23

Table S37. Gene #18: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 18(11Q13.3) MUTATED	133	39	37	14
AMP PEAK 18(11Q13.3) WILD-TYPE	45	63	152	28

Figure S37. Get High-res Image Gene #18: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q13.3' versus 'METHLYATION_CNMF'

P value = 7.26e-11 (Chi-square test), Q value = 4.9e-08

Table S38. Gene #18: 'amp_11q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
AMP PEAK 18(11Q13.3) MUTATED	27	60	57	16	19	30	14
AMP PEAK 18(11Q13.3) WILD-TYPE	46	35	35	63	52	49	8

Figure S38. Get High-res Image Gene #18: 'amp_11q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12p13.33' versus 'CN_CNMF'

P value = 2.82e-17 (Fisher's exact test), Q value = 2e-14

Table S39. Gene #19: 'amp_12p13.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 19(12P13.33) MUTATED	73	56	19	14
AMP PEAK 19(12P13.33) WILD-TYPE	105	46	170	28

Figure S39. Get High-res Image Gene #19: 'amp_12p13.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12p13.33' versus 'METHLYATION_CNMF'

P value = 1.68e-07 (Chi-square test), Q value = 0.00011

Table S40. Gene #19: 'amp_12p13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
AMP PEAK 19(12P13.33) MUTATED	33	33	46	23	9	13	5
AMP PEAK 19(12P13.33) WILD-TYPE	40	62	46	56	62	66	17

Figure S40. Get High-res Image Gene #19: 'amp_12p13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12q15' versus 'CN_CNMF'

P value = 3.46e-07 (Fisher's exact test), Q value = 0.00022

Table S41. Gene #20: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 20(12Q15) MUTATED	47	28	14	12
AMP PEAK 20(12Q15) WILD-TYPE	131	74	175	30

Figure S41. Get High-res Image Gene #20: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

P value = 0.00039 (Chi-square test), Q value = 0.22

Table S42. Gene #20: 'amp_12q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
AMP PEAK 20(12Q15) MUTATED	22	22	28	13	7	7	2
AMP PEAK 20(12Q15) WILD-TYPE	51	73	64	66	64	72	20

Figure S42. Get High-res Image Gene #20: 'amp_12q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q22.1' versus 'CN_CNMF'

P value = 1.92e-13 (Fisher's exact test), Q value = 1.3e-10

Table S43. Gene #21: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 21(13Q22.1) MUTATED	71	13	17	3
AMP PEAK 21(13Q22.1) WILD-TYPE	107	89	172	39

Figure S43. Get High-res Image Gene #21: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q22.1' versus 'METHLYATION_CNMF'

P value = 4.36e-06 (Chi-square test), Q value = 0.0027

Table S44. Gene #21: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
AMP PEAK 21(13Q22.1) MUTATED	16	36	20	13	5	7	7
AMP PEAK 21(13Q22.1) WILD-TYPE	57	59	72	66	66	72	15

Figure S44. Get High-res Image Gene #21: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q34' versus 'CN_CNMF'

P value = 1.33e-09 (Fisher's exact test), Q value = 8.8e-07

Table S45. Gene #22: 'amp_13q34' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 22(13Q34) MUTATED	66	11	21	8
AMP PEAK 22(13Q34) WILD-TYPE	112	91	168	34

Figure S45. Get High-res Image Gene #22: 'amp_13q34' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q34' versus 'METHLYATION_CNMF'

P value = 7.39e-05 (Chi-square test), Q value = 0.044

Table S46. Gene #22: 'amp_13q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
AMP PEAK 22(13Q34) MUTATED	16	34	21	11	6	10	8
AMP PEAK 22(13Q34) WILD-TYPE	57	61	71	68	65	69	14

Figure S46. Get High-res Image Gene #22: 'amp_13q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q12' versus 'CN_CNMF'

P value = 1.97e-08 (Fisher's exact test), Q value = 1.3e-05

Table S47. Gene #24: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 24(17Q12) MUTATED	42	27	9	10
AMP PEAK 24(17Q12) WILD-TYPE	136	75	180	32

Figure S47. Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 1.46e-06 (Chi-square test), Q value = 0.00092

Table S48. Gene #24: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
AMP PEAK 24(17Q12) MUTATED	17	19	32	6	6	6	2
AMP PEAK 24(17Q12) WILD-TYPE	56	76	60	73	65	73	20

Figure S48. Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_18p11.31' versus 'CN_CNMF'

P value = 6.77e-17 (Fisher's exact test), Q value = 4.7e-14

Table S49. Gene #25: 'amp_18p11.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 25(18P11.31) MUTATED	73	53	19	7
AMP PEAK 25(18P11.31) WILD-TYPE	105	49	170	35

Figure S49. Get High-res Image Gene #25: 'amp_18p11.31' versus Molecular Subtype #1: 'CN_CNMF'

'amp_18p11.31' versus 'METHLYATION_CNMF'

P value = 2.2e-09 (Chi-square test), Q value = 1.5e-06

Table S50. Gene #25: 'amp_18p11.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
AMP PEAK 25(18P11.31) MUTATED	41	32	35	21	9	9	5
AMP PEAK 25(18P11.31) WILD-TYPE	32	63	57	58	62	70	17

Figure S50. Get High-res Image Gene #25: 'amp_18p11.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_18p11.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.28e-05 (Fisher's exact test), Q value = 0.026

Table S51. Gene #25: 'amp_18p11.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	177	176
AMP PEAK 25(18P11.31) MUTATED	39	36	74
AMP PEAK 25(18P11.31) WILD-TYPE	101	141	102

Figure S51. Get High-res Image Gene #25: 'amp_18p11.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'CN_CNMF'

P value = 5.78e-07 (Fisher's exact test), Q value = 0.00037

Table S52. Gene #26: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 26(18Q11.2) MUTATED	45	34	17	5
AMP PEAK 26(18Q11.2) WILD-TYPE	133	68	172	37

Figure S52. Get High-res Image Gene #26: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_18q11.2' versus 'METHLYATION_CNMF'

P value = 0.000208 (Chi-square test), Q value = 0.12

Table S53. Gene #26: 'amp_18q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
AMP PEAK 26(18Q11.2) MUTATED	19	25	27	17	6	5	2
AMP PEAK 26(18Q11.2) WILD-TYPE	54	70	65	62	65	74	20

Figure S53. Get High-res Image Gene #26: 'amp_18q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20p12.2' versus 'CN_CNMF'

P value = 2.8e-05 (Fisher's exact test), Q value = 0.017

Table S54. Gene #27: 'amp_20p12.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 27(20P12.2) MUTATED	83	39	46	21
AMP PEAK 27(20P12.2) WILD-TYPE	95	63	143	21

Figure S54. Get High-res Image Gene #27: 'amp_20p12.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20p12.2' versus 'METHLYATION_CNMF'

P value = 2.67e-05 (Chi-square test), Q value = 0.016

Table S55. Gene #27: 'amp_20p12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
AMP PEAK 27(20P12.2) MUTATED	22	55	39	21	16	27	9
AMP PEAK 27(20P12.2) WILD-TYPE	51	40	53	58	55	52	13

Figure S55. Get High-res Image Gene #27: 'amp_20p12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q11.22' versus 'CN_CNMF'

P value = 4.77e-08 (Fisher's exact test), Q value = 3.1e-05

Table S56. Gene #28: 'amp_20q11.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 28(20Q11.22) MUTATED	99	50	51	24
AMP PEAK 28(20Q11.22) WILD-TYPE	79	52	138	18

Figure S56. Get High-res Image Gene #28: 'amp_20q11.22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q11.22' versus 'METHLYATION_CNMF'

P value = 8.54e-06 (Chi-square test), Q value = 0.0053

Table S57. Gene #28: 'amp_20q11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
AMP PEAK 28(20Q11.22) MUTATED	36	60	45	27	16	30	10
AMP PEAK 28(20Q11.22) WILD-TYPE	37	35	47	52	55	49	12

Figure S57. Get High-res Image Gene #28: 'amp_20q11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_xq28' versus 'CN_CNMF'

P value = 2.32e-10 (Fisher's exact test), Q value = 1.6e-07

Table S58. Gene #29: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
AMP PEAK 29(XQ28) MUTATED	83	23	28	11
AMP PEAK 29(XQ28) WILD-TYPE	95	79	161	31

Figure S58. Get High-res Image Gene #29: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq28' versus 'METHLYATION_CNMF'

P value = 3.96e-06 (Chi-square test), Q value = 0.0025

Table S59. Gene #29: 'amp_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
AMP PEAK 29(XQ28) MUTATED	17	43	37	20	12	10	6
AMP PEAK 29(XQ28) WILD-TYPE	56	52	55	59	59	69	16

Figure S59. Get High-res Image Gene #29: 'amp_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.21' versus 'CN_CNMF'

P value = 3.04e-10 (Fisher's exact test), Q value = 2e-07

Table S60. Gene #30: 'del_1p36.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 1(1P36.21) MUTATED	33	41	13	7
DEL PEAK 1(1P36.21) WILD-TYPE	145	61	176	35

Figure S60. Get High-res Image Gene #30: 'del_1p36.21' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.21' versus 'METHLYATION_CNMF'

P value = 8.26e-19 (Chi-square test), Q value = 5.8e-16

Table S61. Gene #30: 'del_1p36.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
DEL PEAK 1(1P36.21) MUTATED	14	8	49	8	9	3	3
DEL PEAK 1(1P36.21) WILD-TYPE	59	87	43	71	62	76	19

Figure S61. Get High-res Image Gene #30: 'del_1p36.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.21' versus 'MRNASEQ_CNMF'

P value = 4.19e-07 (Fisher's exact test), Q value = 0.00027

Table S62. Gene #30: 'del_1p36.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	207	134	152
DEL PEAK 1(1P36.21) MUTATED	60	21	11
DEL PEAK 1(1P36.21) WILD-TYPE	147	113	141

Figure S62. Get High-res Image Gene #30: 'del_1p36.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p36.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.54e-05 (Fisher's exact test), Q value = 0.033

Table S63. Gene #30: 'del_1p36.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	177	176
DEL PEAK 1(1P36.21) MUTATED	24	18	50
DEL PEAK 1(1P36.21) WILD-TYPE	116	159	126

Figure S63. Get High-res Image Gene #30: 'del_1p36.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p13.2' versus 'CN_CNMF'

P value = 6.05e-16 (Fisher's exact test), Q value = 4.2e-13

Table S64. Gene #31: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 2(1P13.2) MUTATED	55	49	12	11
DEL PEAK 2(1P13.2) WILD-TYPE	123	53	177	31

Figure S64. Get High-res Image Gene #31: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p13.2' versus 'METHLYATION_CNMF'

P value = 5.57e-15 (Chi-square test), Q value = 3.9e-12

Table S65. Gene #31: 'del_1p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
DEL PEAK 2(1P13.2) MUTATED	22	21	53	6	8	11	6
DEL PEAK 2(1P13.2) WILD-TYPE	51	74	39	73	63	68	16

Figure S65. Get High-res Image Gene #31: 'del_1p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q21.2' versus 'MIRSEQ_CNMF'

P value = 0.000252 (Fisher's exact test), Q value = 0.15

Table S66. Gene #33: 'del_2q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	216	146
DEL PEAK 4(2Q21.2) MUTATED	34	28	10
DEL PEAK 4(2Q21.2) WILD-TYPE	111	188	136

Figure S66. Get High-res Image Gene #33: 'del_2q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 1.91e-05 (Chi-square test), Q value = 0.012

Table S67. Gene #34: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
DEL PEAK 5(2Q22.1) MUTATED	13	22	36	11	22	9	1
DEL PEAK 5(2Q22.1) WILD-TYPE	60	73	56	68	49	70	21

Figure S67. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q36.2' versus 'CN_CNMF'

P value = 4.39e-08 (Fisher's exact test), Q value = 2.9e-05

Table S68. Gene #35: 'del_2q36.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 6(2Q36.2) MUTATED	58	51	31	12
DEL PEAK 6(2Q36.2) WILD-TYPE	120	51	158	30

Figure S68. Get High-res Image Gene #35: 'del_2q36.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q36.2' versus 'METHLYATION_CNMF'

P value = 1.46e-07 (Chi-square test), Q value = 9.5e-05

Table S69. Gene #35: 'del_2q36.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
DEL PEAK 6(2Q36.2) MUTATED	22	26	48	25	21	6	4
DEL PEAK 6(2Q36.2) WILD-TYPE	51	69	44	54	50	73	18

Figure S69. Get High-res Image Gene #35: 'del_2q36.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p24.1' versus 'CN_CNMF'

P value = 2.17e-31 (Fisher's exact test), Q value = 1.6e-28

Table S70. Gene #36: 'del_3p24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 7(3P24.1) MUTATED	164	89	74	30
DEL PEAK 7(3P24.1) WILD-TYPE	14	13	115	12

Figure S70. Get High-res Image Gene #36: 'del_3p24.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p24.1' versus 'METHLYATION_CNMF'

P value = 3.18e-24 (Chi-square test), Q value = 2.3e-21

Table S71. Gene #36: 'del_3p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
DEL PEAK 7(3P24.1) MUTATED	65	87	82	30	29	46	18
DEL PEAK 7(3P24.1) WILD-TYPE	8	8	10	49	42	33	4

Figure S71. Get High-res Image Gene #36: 'del_3p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p12.1' versus 'CN_CNMF'

P value = 1.63e-33 (Fisher's exact test), Q value = 1.2e-30

Table S72. Gene #37: 'del_3p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 8(3P12.1) MUTATED	157	86	60	29
DEL PEAK 8(3P12.1) WILD-TYPE	21	16	129	13

Figure S72. Get High-res Image Gene #37: 'del_3p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p12.1' versus 'METHLYATION_CNMF'

P value = 1.38e-24 (Chi-square test), Q value = 1e-21

Table S73. Gene #37: 'del_3p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
DEL PEAK 8(3P12.1) MUTATED	64	77	82	25	24	43	17
DEL PEAK 8(3P12.1) WILD-TYPE	9	18	10	54	47	36	5

Figure S73. Get High-res Image Gene #37: 'del_3p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4p15.2' versus 'CN_CNMF'

P value = 1.39e-17 (Fisher's exact test), Q value = 9.8e-15

Table S74. Gene #38: 'del_4p15.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 9(4P15.2) MUTATED	88	67	32	14
DEL PEAK 9(4P15.2) WILD-TYPE	90	35	157	28

Figure S74. Get High-res Image Gene #38: 'del_4p15.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_4p15.2' versus 'METHLYATION_CNMF'

P value = 3.45e-15 (Chi-square test), Q value = 2.4e-12

Table S75. Gene #38: 'del_4p15.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
DEL PEAK 9(4P15.2) MUTATED	40	29	68	22	14	19	9
DEL PEAK 9(4P15.2) WILD-TYPE	33	66	24	57	57	60	13

Figure S75. Get High-res Image Gene #38: 'del_4p15.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4p15.2' versus 'MRNASEQ_CNMF'

P value = 9.53e-05 (Fisher's exact test), Q value = 0.057

Table S76. Gene #38: 'del_4p15.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	207	134	152
DEL PEAK 9(4P15.2) MUTATED	97	59	39
DEL PEAK 9(4P15.2) WILD-TYPE	110	75	113

Figure S76. Get High-res Image Gene #38: 'del_4p15.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4p15.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.12e-05 (Fisher's exact test), Q value = 0.043

Table S77. Gene #38: 'del_4p15.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	177	176
DEL PEAK 9(4P15.2) MUTATED	61	48	86
DEL PEAK 9(4P15.2) WILD-TYPE	79	129	90

Figure S77. Get High-res Image Gene #38: 'del_4p15.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

P value = 5.67e-15 (Fisher's exact test), Q value = 3.9e-12

Table S78. Gene #39: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 10(4Q22.1) MUTATED	70	57	23	14
DEL PEAK 10(4Q22.1) WILD-TYPE	108	45	166	28

Figure S78. Get High-res Image Gene #39: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q22.1' versus 'METHLYATION_CNMF'

P value = 1.98e-10 (Chi-square test), Q value = 1.3e-07

Table S79. Gene #39: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
DEL PEAK 10(4Q22.1) MUTATED	29	30	56	18	15	11	5
DEL PEAK 10(4Q22.1) WILD-TYPE	44	65	36	61	56	68	17

Figure S79. Get High-res Image Gene #39: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q35.2' versus 'CN_CNMF'

P value = 1.05e-11 (Fisher's exact test), Q value = 7.1e-09

Table S80. Gene #40: 'del_4q35.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 11(4Q35.2) MUTATED	90	56	38	22
DEL PEAK 11(4Q35.2) WILD-TYPE	88	46	151	20

Figure S80. Get High-res Image Gene #40: 'del_4q35.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q35.2' versus 'METHLYATION_CNMF'

P value = 1.27e-05 (Chi-square test), Q value = 0.0078

Table S81. Gene #40: 'del_4q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
DEL PEAK 11(4Q35.2) MUTATED	34	47	53	20	23	20	9
DEL PEAK 11(4Q35.2) WILD-TYPE	39	48	39	59	48	59	13

Figure S81. Get High-res Image Gene #40: 'del_4q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q35.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.000246 (Fisher's exact test), Q value = 0.14

Table S82. Gene #40: 'del_4q35.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	16	72	118
DEL PEAK 11(4Q35.2) MUTATED	0	34	57
DEL PEAK 11(4Q35.2) WILD-TYPE	16	38	61

Figure S82. Get High-res Image Gene #40: 'del_4q35.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_5q11.2' versus 'CN_CNMF'

P value = 9.49e-31 (Fisher's exact test), Q value = 6.9e-28

Table S83. Gene #41: 'del_5q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 12(5Q11.2) MUTATED	112	65	21	11
DEL PEAK 12(5Q11.2) WILD-TYPE	66	37	168	31

Figure S83. Get High-res Image Gene #41: 'del_5q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q11.2' versus 'METHLYATION_CNMF'

P value = 2.47e-22 (Chi-square test), Q value = 1.8e-19

Table S84. Gene #41: 'del_5q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
DEL PEAK 12(5Q11.2) MUTATED	48	53	62	11	8	18	9
DEL PEAK 12(5Q11.2) WILD-TYPE	25	42	30	68	63	61	13

Figure S84. Get High-res Image Gene #41: 'del_5q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q15' versus 'CN_CNMF'

P value = 3.01e-29 (Fisher's exact test), Q value = 2.2e-26

Table S85. Gene #42: 'del_5q15' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 13(5Q15) MUTATED	114	68	26	11
DEL PEAK 13(5Q15) WILD-TYPE	64	34	163	31

Figure S85. Get High-res Image Gene #42: 'del_5q15' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q15' versus 'METHLYATION_CNMF'

P value = 6.14e-21 (Chi-square test), Q value = 4.4e-18

Table S86. Gene #42: 'del_5q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
DEL PEAK 13(5Q15) MUTATED	49	52	65	13	11	19	10
DEL PEAK 13(5Q15) WILD-TYPE	24	43	27	66	60	60	12

Figure S86. Get High-res Image Gene #42: 'del_5q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q35.3' versus 'CN_CNMF'

P value = 8.82e-25 (Fisher's exact test), Q value = 6.4e-22

Table S87. Gene #43: 'del_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 14(5Q35.3) MUTATED	92	68	22	13
DEL PEAK 14(5Q35.3) WILD-TYPE	86	34	167	29

Figure S87. Get High-res Image Gene #43: 'del_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q35.3' versus 'METHLYATION_CNMF'

P value = 6.47e-21 (Chi-square test), Q value = 4.6e-18

Table S88. Gene #43: 'del_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
DEL PEAK 14(5Q35.3) MUTATED	52	46	53	12	5	18	9
DEL PEAK 14(5Q35.3) WILD-TYPE	21	49	39	67	66	61	13

Figure S88. Get High-res Image Gene #43: 'del_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q35.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.16

Table S89. Gene #43: 'del_5q35.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	177	176
DEL PEAK 14(5Q35.3) MUTATED	61	48	82
DEL PEAK 14(5Q35.3) WILD-TYPE	79	129	94

Figure S89. Get High-res Image Gene #43: 'del_5q35.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6p25.3' versus 'CN_CNMF'

P value = 0.000289 (Fisher's exact test), Q value = 0.17

Table S90. Gene #44: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 15(6P25.3) MUTATED	38	30	19	6
DEL PEAK 15(6P25.3) WILD-TYPE	140	72	170	36

Figure S90. Get High-res Image Gene #44: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p25.3' versus 'METHLYATION_CNMF'

P value = 9.85e-06 (Chi-square test), Q value = 0.006

Table S91. Gene #44: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
DEL PEAK 15(6P25.3) MUTATED	12	16	35	11	5	10	4
DEL PEAK 15(6P25.3) WILD-TYPE	61	79	57	68	66	69	18

Figure S91. Get High-res Image Gene #44: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q36.1' versus 'CN_CNMF'

P value = 0.000104 (Fisher's exact test), Q value = 0.062

Table S92. Gene #46: 'del_7q36.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 17(7Q36.1) MUTATED	60	24	28	15
DEL PEAK 17(7Q36.1) WILD-TYPE	118	78	161	27

Figure S92. Get High-res Image Gene #46: 'del_7q36.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.2' versus 'CN_CNMF'

P value = 1.44e-21 (Fisher's exact test), Q value = 1e-18

Table S93. Gene #47: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 18(8P23.2) MUTATED	152	43	74	25
DEL PEAK 18(8P23.2) WILD-TYPE	26	59	115	17

Figure S93. Get High-res Image Gene #47: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 1.26e-12 (Chi-square test), Q value = 8.6e-10

Table S94. Gene #47: 'del_8p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
DEL PEAK 18(8P23.2) MUTATED	34	73	63	17	45	46	16
DEL PEAK 18(8P23.2) WILD-TYPE	39	22	29	62	26	33	6

Figure S94. Get High-res Image Gene #47: 'del_8p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.26e-05 (Fisher's exact test), Q value = 0.0077

Table S95. Gene #47: 'del_8p23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	177	176
DEL PEAK 18(8P23.2) MUTATED	95	113	77
DEL PEAK 18(8P23.2) WILD-TYPE	45	64	99

Figure S95. Get High-res Image Gene #47: 'del_8p23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000218 (Fisher's exact test), Q value = 0.13

Table S96. Gene #47: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	174	159	138
DEL PEAK 18(8P23.2) MUTATED	108	71	92
DEL PEAK 18(8P23.2) WILD-TYPE	66	88	46

Figure S96. Get High-res Image Gene #47: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.2e-05 (Fisher's exact test), Q value = 0.037

Table S97. Gene #47: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	230	74
DEL PEAK 18(8P23.2) MUTATED	110	109	52
DEL PEAK 18(8P23.2) WILD-TYPE	57	121	22

Figure S97. Get High-res Image Gene #47: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1.99e-28 (Fisher's exact test), Q value = 1.4e-25

Table S98. Gene #48: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 19(9P23) MUTATED	125	63	43	2
DEL PEAK 19(9P23) WILD-TYPE	53	39	146	40

Figure S98. Get High-res Image Gene #48: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 1.48e-19 (Chi-square test), Q value = 1e-16

Table S99. Gene #48: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
DEL PEAK 19(9P23) MUTATED	51	53	65	9	17	26	12
DEL PEAK 19(9P23) WILD-TYPE	22	42	27	70	54	53	10

Figure S99. Get High-res Image Gene #48: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 4.79e-18 (Fisher's exact test), Q value = 3.4e-15

Table S100. Gene #49: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 20(9P21.3) MUTATED	137	72	73	10
DEL PEAK 20(9P21.3) WILD-TYPE	41	30	116	32

Figure S100. Get High-res Image Gene #49: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 9.16e-20 (Chi-square test), Q value = 6.5e-17

Table S101. Gene #49: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
DEL PEAK 20(9P21.3) MUTATED	60	67	68	11	33	39	14
DEL PEAK 20(9P21.3) WILD-TYPE	13	28	24	68	38	40	8

Figure S101. Get High-res Image Gene #49: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9q21.11' versus 'CN_CNMF'

P value = 1.4e-13 (Fisher's exact test), Q value = 9.6e-11

Table S102. Gene #50: 'del_9q21.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 21(9Q21.11) MUTATED	68	19	15	1
DEL PEAK 21(9Q21.11) WILD-TYPE	110	83	174	41

Figure S102. Get High-res Image Gene #50: 'del_9q21.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q21.11' versus 'METHLYATION_CNMF'

P value = 2.25e-07 (Chi-square test), Q value = 0.00015

Table S103. Gene #50: 'del_9q21.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
DEL PEAK 21(9Q21.11) MUTATED	28	21	25	5	4	12	8
DEL PEAK 21(9Q21.11) WILD-TYPE	45	74	67	74	67	67	14

Figure S103. Get High-res Image Gene #50: 'del_9q21.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9q34.3' versus 'CN_CNMF'

P value = 5.39e-07 (Fisher's exact test), Q value = 0.00034

Table S104. Gene #51: 'del_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 22(9Q34.3) MUTATED	46	14	16	0
DEL PEAK 22(9Q34.3) WILD-TYPE	132	88	173	42

Figure S104. Get High-res Image Gene #51: 'del_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p15.3' versus 'CN_CNMF'

P value = 7.7e-07 (Fisher's exact test), Q value = 0.00049

Table S105. Gene #52: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 23(10P15.3) MUTATED	83	31	37	14
DEL PEAK 23(10P15.3) WILD-TYPE	95	71	152	28

Figure S105. Get High-res Image Gene #52: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 8.43e-07 (Chi-square test), Q value = 0.00053

Table S106. Gene #52: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
DEL PEAK 23(10P15.3) MUTATED	20	44	42	12	19	16	12
DEL PEAK 23(10P15.3) WILD-TYPE	53	51	50	67	52	63	10

Figure S106. Get High-res Image Gene #52: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p11.21' versus 'CN_CNMF'

P value = 2.34e-08 (Fisher's exact test), Q value = 1.5e-05

Table S107. Gene #53: 'del_10p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 24(10P11.21) MUTATED	79	32	29	12
DEL PEAK 24(10P11.21) WILD-TYPE	99	70	160	30

Figure S107. Get High-res Image Gene #53: 'del_10p11.21' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p11.21' versus 'METHLYATION_CNMF'

P value = 2.29e-07 (Chi-square test), Q value = 0.00015

Table S108. Gene #53: 'del_10p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
DEL PEAK 24(10P11.21) MUTATED	20	43	40	13	16	10	10
DEL PEAK 24(10P11.21) WILD-TYPE	53	52	52	66	55	69	12

Figure S108. Get High-res Image Gene #53: 'del_10p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'CN_CNMF'

P value = 6.97e-06 (Fisher's exact test), Q value = 0.0043

Table S109. Gene #54: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 25(10Q23.31) MUTATED	58	40	29	7
DEL PEAK 25(10Q23.31) WILD-TYPE	120	62	160	35

Figure S109. Get High-res Image Gene #54: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 1.37e-06 (Chi-square test), Q value = 0.00086

Table S110. Gene #54: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
DEL PEAK 25(10Q23.31) MUTATED	21	30	39	25	7	7	5
DEL PEAK 25(10Q23.31) WILD-TYPE	52	65	53	54	64	72	17

Figure S110. Get High-res Image Gene #54: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 7.42e-05 (Fisher's exact test), Q value = 0.044

Table S111. Gene #54: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	207	134	152
DEL PEAK 25(10Q23.31) MUTATED	73	33	23
DEL PEAK 25(10Q23.31) WILD-TYPE	134	101	129

Figure S111. Get High-res Image Gene #54: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11p15.5' versus 'CN_CNMF'

P value = 7.64e-11 (Fisher's exact test), Q value = 5.1e-08

Table S112. Gene #55: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 26(11P15.5) MUTATED	64	54	34	4
DEL PEAK 26(11P15.5) WILD-TYPE	114	48	155	38

Figure S112. Get High-res Image Gene #55: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 2.52e-10 (Chi-square test), Q value = 1.7e-07

Table S113. Gene #55: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
DEL PEAK 26(11P15.5) MUTATED	26	23	53	26	5	19	4
DEL PEAK 26(11P15.5) WILD-TYPE	47	72	39	53	66	60	18

Figure S113. Get High-res Image Gene #55: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p15.5' versus 'MRNASEQ_CNMF'

P value = 3.76e-05 (Fisher's exact test), Q value = 0.023

Table S114. Gene #55: 'del_11p15.5' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	207	134	152
DEL PEAK 26(11P15.5) MUTATED	85	35	30
DEL PEAK 26(11P15.5) WILD-TYPE	122	99	122

Figure S114. Get High-res Image Gene #55: 'del_11p15.5' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000207 (Fisher's exact test), Q value = 0.12

Table S115. Gene #55: 'del_11p15.5' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	177	176
DEL PEAK 26(11P15.5) MUTATED	33	43	74
DEL PEAK 26(11P15.5) WILD-TYPE	107	134	102

Figure S115. Get High-res Image Gene #55: 'del_11p15.5' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 2.09e-07 (Fisher's exact test), Q value = 0.00014

Table S116. Gene #55: 'del_11p15.5' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	216	146
DEL PEAK 26(11P15.5) MUTATED	24	93	39
DEL PEAK 26(11P15.5) WILD-TYPE	121	123	107

Figure S116. Get High-res Image Gene #55: 'del_11p15.5' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11q23.1' versus 'CN_CNMF'

P value = 2.16e-06 (Fisher's exact test), Q value = 0.0014

Table S117. Gene #56: 'del_11q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 27(11Q23.1) MUTATED	107	53	63	16
DEL PEAK 27(11Q23.1) WILD-TYPE	71	49	126	26

Figure S117. Get High-res Image Gene #56: 'del_11q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q23.1' versus 'METHLYATION_CNMF'

P value = 2.45e-15 (Chi-square test), Q value = 1.7e-12

Table S118. Gene #56: 'del_11q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
DEL PEAK 27(11Q23.1) MUTATED	28	48	51	66	12	26	8
DEL PEAK 27(11Q23.1) WILD-TYPE	45	47	41	13	59	53	14

Figure S118. Get High-res Image Gene #56: 'del_11q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q23.1' versus 'MRNASEQ_CNMF'

P value = 3.09e-05 (Fisher's exact test), Q value = 0.019

Table S119. Gene #56: 'del_11q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	207	134	152
DEL PEAK 27(11Q23.1) MUTATED	120	58	52
DEL PEAK 27(11Q23.1) WILD-TYPE	87	76	100

Figure S119. Get High-res Image Gene #56: 'del_11q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.22e-06 (Fisher's exact test), Q value = 0.0026

Table S120. Gene #56: 'del_11q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	177	176
DEL PEAK 27(11Q23.1) MUTATED	58	64	108
DEL PEAK 27(11Q23.1) WILD-TYPE	82	113	68

Figure S120. Get High-res Image Gene #56: 'del_11q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_12q24.33' versus 'CN_CNMF'

P value = 3.6e-06 (Fisher's exact test), Q value = 0.0022

Table S121. Gene #57: 'del_12q24.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 28(12Q24.33) MUTATED	37	13	7	3
DEL PEAK 28(12Q24.33) WILD-TYPE	141	89	182	39

Figure S121. Get High-res Image Gene #57: 'del_12q24.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q24.33' versus 'METHLYATION_CNMF'

P value = 0.000169 (Chi-square test), Q value = 0.1

Table S122. Gene #57: 'del_12q24.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
DEL PEAK 28(12Q24.33) MUTATED	12	13	21	4	1	5	4
DEL PEAK 28(12Q24.33) WILD-TYPE	61	82	71	75	70	74	18

Figure S122. Get High-res Image Gene #57: 'del_12q24.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q12.11' versus 'CN_CNMF'

P value = 8.6e-21 (Fisher's exact test), Q value = 6.1e-18

Table S123. Gene #58: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 29(13Q12.11) MUTATED	99	73	35	17
DEL PEAK 29(13Q12.11) WILD-TYPE	79	29	154	25

Figure S123. Get High-res Image Gene #58: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q12.11' versus 'METHLYATION_CNMF'

P value = 4.06e-12 (Chi-square test), Q value = 2.8e-09

Table S124. Gene #58: 'del_13q12.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
DEL PEAK 29(13Q12.11) MUTATED	50	47	59	25	15	21	7
DEL PEAK 29(13Q12.11) WILD-TYPE	23	48	33	54	56	58	15

Figure S124. Get High-res Image Gene #58: 'del_13q12.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q14.2' versus 'CN_CNMF'

P value = 2.16e-14 (Fisher's exact test), Q value = 1.5e-11

Table S125. Gene #59: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 30(13Q14.2) MUTATED	69	76	49	15
DEL PEAK 30(13Q14.2) WILD-TYPE	109	26	140	27

Figure S125. Get High-res Image Gene #59: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 1.2e-09 (Chi-square test), Q value = 8e-07

Table S126. Gene #59: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
DEL PEAK 30(13Q14.2) MUTATED	43	38	49	44	14	17	4
DEL PEAK 30(13Q14.2) WILD-TYPE	30	57	43	35	57	62	18

Figure S126. Get High-res Image Gene #59: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 5.44e-06 (Fisher's exact test), Q value = 0.0034

Table S127. Gene #59: 'del_13q14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	207	134	152
DEL PEAK 30(13Q14.2) MUTATED	110	52	42
DEL PEAK 30(13Q14.2) WILD-TYPE	97	82	110

Figure S127. Get High-res Image Gene #59: 'del_13q14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.17e-08 (Fisher's exact test), Q value = 7.7e-06

Table S128. Gene #59: 'del_13q14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	177	176
DEL PEAK 30(13Q14.2) MUTATED	55	47	102
DEL PEAK 30(13Q14.2) WILD-TYPE	85	130	74

Figure S128. Get High-res Image Gene #59: 'del_13q14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q32.32' versus 'CN_CNMF'

P value = 0.000256 (Fisher's exact test), Q value = 0.15

Table S129. Gene #61: 'del_14q32.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 32(14Q32.32) MUTATED	12	26	29	6
DEL PEAK 32(14Q32.32) WILD-TYPE	166	76	160	36

Figure S129. Get High-res Image Gene #61: 'del_14q32.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q32.32' versus 'METHLYATION_CNMF'

P value = 2.81e-12 (Chi-square test), Q value = 1.9e-09

Table S130. Gene #61: 'del_14q32.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
DEL PEAK 32(14Q32.32) MUTATED	11	7	17	32	3	2	1
DEL PEAK 32(14Q32.32) WILD-TYPE	62	88	75	47	68	77	21

Figure S130. Get High-res Image Gene #61: 'del_14q32.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q32.32' versus 'MRNASEQ_CNMF'

P value = 8.89e-07 (Fisher's exact test), Q value = 0.00056

Table S131. Gene #61: 'del_14q32.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	207	134	152
DEL PEAK 32(14Q32.32) MUTATED	48	14	7
DEL PEAK 32(14Q32.32) WILD-TYPE	159	120	145

Figure S131. Get High-res Image Gene #61: 'del_14q32.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q32.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.02e-07 (Fisher's exact test), Q value = 6.6e-05

Table S132. Gene #61: 'del_14q32.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	177	176
DEL PEAK 32(14Q32.32) MUTATED	15	9	45
DEL PEAK 32(14Q32.32) WILD-TYPE	125	168	131

Figure S132. Get High-res Image Gene #61: 'del_14q32.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q15.1' versus 'CN_CNMF'

P value = 7.53e-09 (Fisher's exact test), Q value = 5e-06

Table S133. Gene #62: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 33(15Q15.1) MUTATED	56	26	18	19
DEL PEAK 33(15Q15.1) WILD-TYPE	122	76	171	23

Figure S133. Get High-res Image Gene #62: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.3' versus 'METHLYATION_CNMF'

P value = 4.63e-07 (Chi-square test), Q value = 3e-04

Table S134. Gene #63: 'del_16q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
DEL PEAK 34(16Q23.3) MUTATED	15	9	32	27	10	5	4
DEL PEAK 34(16Q23.3) WILD-TYPE	58	86	60	52	61	74	18

Figure S134. Get High-res Image Gene #63: 'del_16q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.3' versus 'MRNASEQ_CNMF'

P value = 4e-06 (Fisher's exact test), Q value = 0.0025

Table S135. Gene #63: 'del_16q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	207	134	152
DEL PEAK 34(16Q23.3) MUTATED	63	22	15
DEL PEAK 34(16Q23.3) WILD-TYPE	144	112	137

Figure S135. Get High-res Image Gene #63: 'del_16q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.37e-07 (Fisher's exact test), Q value = 0.00015

Table S136. Gene #63: 'del_16q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	177	176
DEL PEAK 34(16Q23.3) MUTATED	25	17	58
DEL PEAK 34(16Q23.3) WILD-TYPE	115	160	118

Figure S136. Get High-res Image Gene #63: 'del_16q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17q25.3' versus 'METHLYATION_CNMF'

P value = 0.000233 (Chi-square test), Q value = 0.14

Table S137. Gene #64: 'del_17q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
DEL PEAK 35(17Q25.3) MUTATED	8	11	20	19	3	3	4
DEL PEAK 35(17Q25.3) WILD-TYPE	65	84	72	60	68	76	18

Figure S137. Get High-res Image Gene #64: 'del_17q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q21.2' versus 'CN_CNMF'

P value = 2.44e-20 (Fisher's exact test), Q value = 1.7e-17

Table S138. Gene #65: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 36(18Q21.2) MUTATED	133	56	48	22
DEL PEAK 36(18Q21.2) WILD-TYPE	45	46	141	20

Figure S138. Get High-res Image Gene #65: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q21.2' versus 'METHLYATION_CNMF'

P value = 1.3e-20 (Chi-square test), Q value = 9.3e-18

Table S139. Gene #65: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
DEL PEAK 36(18Q21.2) MUTATED	51	65	64	5	24	39	11
DEL PEAK 36(18Q21.2) WILD-TYPE	22	30	28	74	47	40	11

Figure S139. Get High-res Image Gene #65: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q23' versus 'CN_CNMF'

P value = 6.42e-23 (Fisher's exact test), Q value = 4.6e-20

Table S140. Gene #66: 'del_18q23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 37(18Q23) MUTATED	141	63	52	22
DEL PEAK 37(18Q23) WILD-TYPE	37	39	137	20

Figure S140. Get High-res Image Gene #66: 'del_18q23' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q23' versus 'METHLYATION_CNMF'

P value = 4.7e-22 (Chi-square test), Q value = 3.4e-19

Table S141. Gene #66: 'del_18q23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
DEL PEAK 37(18Q23) MUTATED	52	71	70	9	24	41	11
DEL PEAK 37(18Q23) WILD-TYPE	21	24	22	70	47	38	11

Figure S141. Get High-res Image Gene #66: 'del_18q23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.3' versus 'CN_CNMF'

P value = 6.76e-08 (Fisher's exact test), Q value = 4.4e-05

Table S142. Gene #67: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 38(19P13.3) MUTATED	79	37	32	17
DEL PEAK 38(19P13.3) WILD-TYPE	99	65	157	25

Figure S142. Get High-res Image Gene #67: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 7.29e-07 (Chi-square test), Q value = 0.00046

Table S143. Gene #67: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
DEL PEAK 38(19P13.3) MUTATED	25	48	40	13	19	13	7
DEL PEAK 38(19P13.3) WILD-TYPE	48	47	52	66	52	66	15

Figure S143. Get High-res Image Gene #67: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19q13.43' versus 'CN_CNMF'

P value = 7.74e-07 (Fisher's exact test), Q value = 0.00049

Table S144. Gene #68: 'del_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 39(19Q13.43) MUTATED	48	25	13	8
DEL PEAK 39(19Q13.43) WILD-TYPE	130	77	176	34

Figure S144. Get High-res Image Gene #68: 'del_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

'del_19q13.43' versus 'METHLYATION_CNMF'

P value = 5.67e-07 (Chi-square test), Q value = 0.00036

Table S145. Gene #68: 'del_19q13.43' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
DEL PEAK 39(19Q13.43) MUTATED	16	27	30	5	5	6	5
DEL PEAK 39(19Q13.43) WILD-TYPE	57	68	62	74	66	73	17

Figure S145. Get High-res Image Gene #68: 'del_19q13.43' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q22.3' versus 'CN_CNMF'

P value = 9.49e-15 (Fisher's exact test), Q value = 6.5e-12

Table S146. Gene #69: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 40(21Q22.3) MUTATED	89	55	30	21
DEL PEAK 40(21Q22.3) WILD-TYPE	89	47	159	21

Figure S146. Get High-res Image Gene #69: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q22.3' versus 'METHLYATION_CNMF'

P value = 2.65e-10 (Chi-square test), Q value = 1.8e-07

Table S147. Gene #69: 'del_21q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
DEL PEAK 40(21Q22.3) MUTATED	32	53	50	13	18	17	12
DEL PEAK 40(21Q22.3) WILD-TYPE	41	42	42	66	53	62	10

Figure S147. Get High-res Image Gene #69: 'del_21q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp22.2' versus 'CN_CNMF'

P value = 3.93e-08 (Fisher's exact test), Q value = 2.6e-05

Table S148. Gene #71: 'del_xp22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 42(XP22.2) MUTATED	76	37	29	10
DEL PEAK 42(XP22.2) WILD-TYPE	102	65	160	32

Figure S148. Get High-res Image Gene #71: 'del_xp22.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp22.2' versus 'METHLYATION_CNMF'

P value = 1.27e-09 (Chi-square test), Q value = 8.4e-07

Table S149. Gene #71: 'del_xp22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
DEL PEAK 42(XP22.2) MUTATED	20	35	51	17	8	13	8
DEL PEAK 42(XP22.2) WILD-TYPE	53	60	41	62	63	66	14

Figure S149. Get High-res Image Gene #71: 'del_xp22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp21.3' versus 'CN_CNMF'

P value = 6.12e-09 (Fisher's exact test), Q value = 4.1e-06

Table S150. Gene #72: 'del_xp21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 43(XP21.3) MUTATED	81	34	30	9
DEL PEAK 43(XP21.3) WILD-TYPE	97	68	159	33

Figure S150. Get High-res Image Gene #72: 'del_xp21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp21.3' versus 'METHLYATION_CNMF'

P value = 2.74e-06 (Chi-square test), Q value = 0.0017

Table S151. Gene #72: 'del_xp21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
DEL PEAK 43(XP21.3) MUTATED	22	39	44	15	11	15	8
DEL PEAK 43(XP21.3) WILD-TYPE	51	56	48	64	60	64	14

Figure S151. Get High-res Image Gene #72: 'del_xp21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq21.33' versus 'CN_CNMF'

P value = 6.16e-06 (Fisher's exact test), Q value = 0.0038

Table S152. Gene #73: 'del_xq21.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	178	102	189	42
DEL PEAK 44(XQ21.33) MUTATED	36	24	13	1
DEL PEAK 44(XQ21.33) WILD-TYPE	142	78	176	41

Figure S152. Get High-res Image Gene #73: 'del_xq21.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq21.33' versus 'METHLYATION_CNMF'

P value = 3.52e-07 (Chi-square test), Q value = 0.00023

Table S153. Gene #73: 'del_xq21.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	73	95	92	79	71	79	22
DEL PEAK 44(XQ21.33) MUTATED	13	15	29	11	0	4	2
DEL PEAK 44(XQ21.33) WILD-TYPE	60	80	63	68	71	75	20

Figure S153. Get High-res Image Gene #73: 'del_xq21.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq21.33' versus 'MIRSEQ_CNMF'

P value = 9.57e-05 (Fisher's exact test), Q value = 0.057

Table S154. Gene #73: 'del_xq21.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	145	216	146
DEL PEAK 44(XQ21.33) MUTATED	14	48	11
DEL PEAK 44(XQ21.33) WILD-TYPE	131	168	135

Figure S154. Get High-res Image Gene #73: 'del_xq21.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = HNSC-TP.transferedmergedcluster.txt
Number of patients = 511
Number of significantly focal cnvs = 73
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

Chi-square test

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

Q value calculation

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

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

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

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

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

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