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

Lung 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/C1MP51ZD

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 80 focal events and 12 molecular subtypes across 490 patients, 199 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1q21.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_2p16.1 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_2q31.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_3q26.33 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_4q12 cnv correlated to 'CN_CNMF'.
amp_5p15.33 cnv correlated to 'CN_CNMF'.
amp_5p12 cnv correlated to 'CN_CNMF'.
amp_6p12.1 cnv correlated to 'CN_CNMF'.
amp_6q12 cnv correlated to 'CN_CNMF'.
amp_7p11.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
amp_7q21.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_9p13.3 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
amp_11q13.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_12p13.33 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_12q15 cnv correlated to 'CN_CNMF'.
amp_15q26.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
amp_17q25.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_18p11.32 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_18q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19q12 cnv correlated to 'CN_CNMF'.
amp_19q13.2 cnv correlated to 'CN_CNMF'.
amp_20p12.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_20q11.21 cnv correlated to 'CN_CNMF'.
amp_22q11.21 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
del_1p36.32 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p13.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_2q37.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_3p13 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p12.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_4p15.2 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_4q22.1 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
del_4q32.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q35.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
del_5q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_6p25.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_6q22.31 cnv correlated to 'CN_CNMF'.
del_6q26 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_7q36.3 cnv correlated to 'MRNASEQ_CNMF'.
del_8p23.2 cnv correlated to 'CN_CNMF'.
del_9p23 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
del_9p21.3 cnv correlated to 'CN_CNMF'.
del_9q21.11 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_10p15.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_10p15.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_10q23.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_11p15.5 cnv correlated to 'CN_CNMF' and 'RPPA_CHIERARCHICAL'.
del_11q22.1 cnv correlated to 'CN_CNMF'.
del_14q11.2 cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_17q11.2 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_17q25.3 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
del_19p13.3 cnv correlated to 'CN_CNMF'.
del_19q13.32 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_21q11.2 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
del_21q22.3 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
del_22q13.32 cnv correlated to 'MRNA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_xp22.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xp21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xp11.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xq22.3 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 80 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, 199 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	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
del 1p36 32	213 (43%)	277	4.95e-07 (0.000439)	4.08e-08 (3.72e-05)	1.72e-35 (1.66e-32)	1.98e-19 (1.89e-16)	0.367 (1.00)	0.0128 (1.00)	6.31e-21 (6.05e-18)	1.05e-25 (1e-22)	1.18e-06 (0.00102)	2.94e-06 (0.00253)	0.00199 (1.00)	3.68e-07 (0.000328)
del 1p13 1	212 (43%)	278	0.000164 (0.13)	1.22e-05 (0.0103)	1.23e-20 (1.18e-17)	5.49e-12 (5.2e-09)	0.0399 (1.00)	0.0686 (1.00)	5.28e-12 (5e-09)	3.45e-14 (3.28e-11)	3.13e-08 (2.86e-05)	9.53e-07 (0.000836)	0.00987 (1.00)	1.06e-05 (0.00896)
amp 3q26 33	442 (90%)	48	0.000413 (0.312)	2.27e-05 (0.0188)	2.23e-14 (2.12e-11)	5.42e-09 (4.99e-06)	0.272 (1.00)	0.0403 (1.00)	2.09e-10 (1.96e-07)	5.2e-09 (4.8e-06)	3.57e-08 (3.26e-05)	3.11e-06 (0.00267)	0.00384 (1.00)	0.000161 (0.127)
del 9q21 11	248 (51%)	242	0.000244 (0.189)	5.96e-05 (0.0483)	4.48e-11 (4.22e-08)	2.74e-09 (2.54e-06)	0.55 (1.00)	0.155 (1.00)	1.1e-14 (1.05e-11)	1.02e-17 (9.77e-15)	4.01e-05 (0.0329)	6.57e-08 (5.95e-05)	0.00197 (1.00)	0.0461 (1.00)
amp 2p16 1	271 (55%)	219	0.00132 (0.944)	0.000163 (0.129)	5.71e-15 (5.45e-12)	1.68e-06 (0.00146)	0.941 (1.00)	0.41 (1.00)	2.01e-11 (1.89e-08)	2.28e-08 (2.08e-05)	2.21e-05 (0.0184)	0.000714 (0.526)	0.0019 (1.00)	0.000226 (0.176)
amp 17q25 1	233 (48%)	257	0.00872 (1.00)	0.021 (1.00)	9.19e-14 (8.72e-11)	4.77e-08 (4.34e-05)	0.383 (1.00)	0.314 (1.00)	5.42e-06 (0.00462)	9.27e-08 (8.37e-05)	0.000148 (0.118)	0.0223 (1.00)	1.04e-05 (0.00879)	3.09e-06 (0.00265)
del 10q23 31	259 (53%)	231	0.00335 (1.00)	0.00335 (1.00)	1.86e-08 (1.71e-05)	1.83e-08 (1.68e-05)	0.152 (1.00)	0.229 (1.00)	3.79e-09 (3.5e-06)	2.25e-10 (2.11e-07)	0.000305 (0.233)	5.85e-05 (0.0475)	2.54e-06 (0.00218)	0.00268 (1.00)
amp 18q11 2	148 (30%)	342	0.00036 (0.274)	0.0284 (1.00)	7.72e-09 (7.11e-06)	2.31e-05 (0.0192)	0.251 (1.00)	0.359 (1.00)	1.67e-06 (0.00145)	2.21e-09 (2.06e-06)	0.000821 (0.6)	0.0053 (1.00)	0.000167 (0.131)	0.000188 (0.148)
del 2q37 1	155 (32%)	335	0.00329 (1.00)	0.00206 (1.00)	5.65e-10 (5.27e-07)	6.31e-07 (0.000558)	0.38 (1.00)	0.368 (1.00)	1.28e-06 (0.00112)	1.96e-05 (0.0163)	1.33e-05 (0.0112)	0.65 (1.00)	1.09e-05 (0.00924)	0.000507 (0.379)
del 10p15 3	222 (45%)	268	0.323 (1.00)	0.487 (1.00)	8.47e-08 (7.65e-05)	1.59e-10 (1.49e-07)	0.168 (1.00)	0.373 (1.00)	4.08e-06 (0.00349)	1.16e-05 (0.00975)	8.19e-07 (0.000721)	5.51e-06 (0.00469)	0.00456 (1.00)	0.00533 (1.00)
del 10p15 1	210 (43%)	280	0.133 (1.00)	0.515 (1.00)	3.62e-06 (0.0031)	4.48e-11 (4.22e-08)	0.21 (1.00)	0.414 (1.00)	2.22e-07 (0.000199)	1.84e-05 (0.0153)	1.39e-07 (0.000125)	1.1e-06 (0.000959)	0.045 (1.00)	0.00343 (1.00)
amp 1q21 2	253 (52%)	237	0.0393 (1.00)	0.0421 (1.00)	1.28e-11 (1.21e-08)	7.11e-07 (0.000627)	0.186 (1.00)	0.0202 (1.00)	5.51e-08 (5.01e-05)	2.14e-08 (1.96e-05)	0.0014 (0.991)	0.000122 (0.0977)	0.0136 (1.00)	0.0146 (1.00)
amp 2q31 2	168 (34%)	322	0.0195 (1.00)	0.0273 (1.00)	3.07e-07 (0.000275)	3.13e-06 (0.00268)	0.706 (1.00)	0.499 (1.00)	1.77e-06 (0.00153)	3.32e-05 (0.0273)	0.0154 (1.00)	0.692 (1.00)	0.000165 (0.13)	0.000415 (0.312)
del 3p13	424 (87%)	66	0.261 (1.00)	0.8 (1.00)	1.33e-07 (0.00012)	0.000273 (0.209)	0.764 (1.00)	0.0216 (1.00)	0.00245 (1.00)	8.99e-05 (0.0724)	4.83e-05 (0.0395)	0.0169 (1.00)	0.00136 (0.964)	0.000284 (0.217)
del 4p15 2	307 (63%)	183	0.000196 (0.153)	0.00412 (1.00)	8.06e-10 (7.51e-07)	1.75e-06 (0.00151)	0.765 (1.00)	0.0268 (1.00)	0.00021 (0.164)	7.3e-07 (0.000644)	0.00153 (1.00)	0.777 (1.00)	0.00103 (0.745)	0.000857 (0.626)
del 4q32 3	322 (66%)	168	0.00658 (1.00)	0.0216 (1.00)	7.37e-11 (6.92e-08)	7.96e-05 (0.0642)	0.0659 (1.00)	0.572 (1.00)	7.43e-06 (0.00633)	0.000245 (0.19)	0.000638 (0.471)	0.00886 (1.00)	0.00151 (1.00)	0.000124 (0.099)
del 17q11 2	128 (26%)	362	0.00013 (0.104)	0.000486 (0.364)	1.01e-06 (0.000887)	1.03e-05 (0.00874)	0.37 (1.00)	0.299 (1.00)	9.63e-09 (8.86e-06)	1.61e-11 (1.52e-08)	0.175 (1.00)	0.00273 (1.00)	0.0153 (1.00)	0.000898 (0.654)
del xp21 1	149 (30%)	341	0.458 (1.00)	0.645 (1.00)	1.16e-06 (0.00101)	8.77e-07 (0.000772)	0.264 (1.00)	0.754 (1.00)	0.000397 (0.301)	0.0024 (1.00)	2.44e-05 (0.0203)	0.0199 (1.00)	0.00028 (0.215)	5.64e-10 (5.27e-07)
del xp11 3	145 (30%)	345	0.0982 (1.00)	0.645 (1.00)	3.79e-07 (0.000337)	6e-07 (0.000531)	0.105 (1.00)	0.086 (1.00)	0.000788 (0.579)	0.00144 (1.00)	4.96e-06 (0.00424)	0.0162 (1.00)	5.48e-05 (0.0446)	3.09e-09 (2.86e-06)
amp 7q21 2	258 (53%)	232	0.101 (1.00)	0.108 (1.00)	8.28e-15 (7.89e-12)	1.02e-06 (0.000893)	0.0731 (1.00)	0.333 (1.00)	4.41e-07 (0.000391)	1.68e-06 (0.00146)	0.000728 (0.536)	0.00496 (1.00)	0.00429 (1.00)	0.00127 (0.91)
del 2q22 1	124 (25%)	366	0.313 (1.00)	0.363 (1.00)	2.59e-07 (0.000232)	0.000288 (0.22)	0.391 (1.00)	0.0843 (1.00)	0.00211 (1.00)	0.00144 (1.00)	0.000126 (0.101)	0.0308 (1.00)	0.000209 (0.164)	0.0199 (1.00)
del 3p12 3	413 (84%)	77	0.16 (1.00)	0.89 (1.00)	1.17e-06 (0.00102)	0.000226 (0.176)	1 (1.00)	0.0377 (1.00)	0.00497 (1.00)	0.000188 (0.147)	0.000259 (0.199)	0.065 (1.00)	0.0121 (1.00)	0.00952 (1.00)
del 6p25 3	128 (26%)	362	0.321 (1.00)	0.0472 (1.00)	1.33e-05 (0.0112)	3.24e-05 (0.0267)	0.374 (1.00)	0.0135 (1.00)	3.39e-07 (0.000303)	1.02e-08 (9.36e-06)	0.0644 (1.00)	0.00566 (1.00)	0.0705 (1.00)	0.00856 (1.00)
amp 12p13 33	249 (51%)	241	0.00766 (1.00)	0.0441 (1.00)	1.83e-07 (0.000164)	0.00095 (0.69)	0.356 (1.00)	0.794 (1.00)	1.67e-07 (0.000151)	5.14e-05 (0.042)	0.0259 (1.00)	0.0227 (1.00)	0.204 (1.00)	0.0588 (1.00)
amp 20p12 2	273 (56%)	217	0.00104 (0.755)	0.00969 (1.00)	5.81e-10 (5.41e-07)	0.000249 (0.192)	0.914 (1.00)	0.378 (1.00)	0.00394 (1.00)	5.18e-05 (0.0423)	0.0096 (1.00)	0.344 (1.00)	0.0382 (1.00)	0.435 (1.00)
del 4q35 2	323 (66%)	167	0.0684 (1.00)	0.384 (1.00)	1.06e-09 (9.84e-07)	3.53e-05 (0.029)	0.361 (1.00)	0.584 (1.00)	9.45e-06 (0.00802)	0.00495 (1.00)	0.00305 (1.00)	0.0166 (1.00)	0.0403 (1.00)	0.00051 (0.38)
del 5q11 2	360 (73%)	130	0.482 (1.00)	0.416 (1.00)	3.64e-13 (3.45e-10)	1.95e-05 (0.0162)	1 (1.00)	0.299 (1.00)	0.00164 (1.00)	0.0127 (1.00)	0.0204 (1.00)	2.76e-05 (0.0228)	0.00139 (0.983)	0.00178 (1.00)
del 22q13 32	125 (26%)	365	0.000248 (0.192)	0.00237 (1.00)	0.114 (1.00)	0.0152 (1.00)	0.404 (1.00)	0.0763 (1.00)	0.000191 (0.15)	3.42e-05 (0.0281)	0.0539 (1.00)	0.000615 (0.456)	0.913 (1.00)	0.613 (1.00)
del xp22 2	151 (31%)	339	0.72 (1.00)	0.778 (1.00)	5.98e-05 (0.0484)	0.000154 (0.122)	0.425 (1.00)	0.772 (1.00)	0.021 (1.00)	0.0768 (1.00)	0.00168 (1.00)	0.0408 (1.00)	0.000973 (0.705)	4.41e-07 (0.000391)
del xq22 3	110 (22%)	380	0.0224 (1.00)	0.00422 (1.00)	1.76e-05 (0.0147)	9.3e-07 (0.000818)	0.875 (1.00)	0.935 (1.00)	0.00134 (0.954)	0.0606 (1.00)	5.45e-05 (0.0445)	0.206 (1.00)	0.000387 (0.293)	0.00759 (1.00)
amp 7p11 2	249 (51%)	241	0.115 (1.00)	0.0661 (1.00)	1.85e-06 (0.00159)	0.00195 (1.00)	0.692 (1.00)	0.86 (1.00)	0.00223 (1.00)	0.000247 (0.191)	0.036 (1.00)	0.0709 (1.00)	0.0113 (1.00)	0.0468 (1.00)
amp 11q13 3	181 (37%)	309	0.0484 (1.00)	0.0672 (1.00)	9.49e-07 (0.000833)	0.00024 (0.186)	0.255 (1.00)	0.039 (1.00)	0.0147 (1.00)	0.0244 (1.00)	0.00165 (1.00)	0.104 (1.00)	0.025 (1.00)	0.425 (1.00)
amp 15q26 3	176 (36%)	314	0.358 (1.00)	0.0647 (1.00)	8.01e-06 (0.00681)	0.000407 (0.308)	0.439 (1.00)	0.037 (1.00)	1.57e-05 (0.0131)	0.000791 (0.581)	0.00865 (1.00)	0.00198 (1.00)	0.00761 (1.00)	0.0144 (1.00)
amp 18p11 32	175 (36%)	315	0.0429 (1.00)	0.0107 (1.00)	7.62e-08 (6.9e-05)	2.57e-05 (0.0213)	0.495 (1.00)	0.484 (1.00)	0.031 (1.00)	0.000468 (0.351)	0.00223 (1.00)	0.0455 (1.00)	0.00588 (1.00)	0.02 (1.00)
amp 22q11 21	253 (52%)	237	0.114 (1.00)	0.308 (1.00)	0.000135 (0.108)	0.00105 (0.76)	0.83 (1.00)	0.589 (1.00)	8.84e-05 (0.0712)	0.0285 (1.00)	0.0413 (1.00)	0.265 (1.00)	0.0048 (1.00)	0.376 (1.00)
del 4q22 1	278 (57%)	212	0.00326 (1.00)	0.0466 (1.00)	1.68e-07 (0.000151)	0.0015 (1.00)	0.11 (1.00)	0.407 (1.00)	0.000182 (0.143)	0.0041 (1.00)	0.0276 (1.00)	0.0542 (1.00)	0.104 (1.00)	0.12 (1.00)
del 6q26	130 (27%)	360	0.0424 (1.00)	0.0161 (1.00)	1.76e-05 (0.0147)	0.000147 (0.117)	0.905 (1.00)	0.684 (1.00)	0.000385 (0.292)	0.00061 (0.453)	0.0319 (1.00)	0.0316 (1.00)	0.028 (1.00)	0.0168 (1.00)
del 9p23	323 (66%)	167	0.0104 (1.00)	0.00706 (1.00)	3.58e-08 (3.27e-05)	0.0209 (1.00)	0.197 (1.00)	0.253 (1.00)	6.46e-05 (0.0523)	0.0201 (1.00)	0.00119 (0.856)	0.00422 (1.00)	0.0106 (1.00)	1 (1.00)
del 11p15 5	239 (49%)	251	0.000413 (0.312)	0.0538 (1.00)	6.14e-08 (5.56e-05)	0.00486 (1.00)	0.000348 (0.265)	1.48e-06 (0.00128)	0.0104 (1.00)	0.237 (1.00)	0.0402 (1.00)	0.4 (1.00)	0.00168 (1.00)	0.0459 (1.00)
del 14q11 2	171 (35%)	319	0.0381 (1.00)	0.159 (1.00)	0.577 (1.00)	0.993 (1.00)	0.257 (1.00)	0.263 (1.00)	1.58e-05 (0.0132)	3.93e-07 (0.00035)	0.00651 (1.00)	0.0664 (1.00)	0.444 (1.00)	0.301 (1.00)
del 19q13 32	143 (29%)	347	0.82 (1.00)	0.227 (1.00)	5.89e-08 (5.35e-05)	1.23e-05 (0.0103)	0.165 (1.00)	0.721 (1.00)	0.0064 (1.00)	0.00161 (1.00)	0.00484 (1.00)	0.827 (1.00)	0.209 (1.00)	0.0196 (1.00)
del 21q11 2	241 (49%)	249	0.558 (1.00)	0.473 (1.00)	4.86e-05 (0.0397)	0.147 (1.00)	0.98 (1.00)	0.972 (1.00)	0.104 (1.00)	0.0209 (1.00)	9.17e-05 (0.0737)	0.0558 (1.00)	0.0152 (1.00)	0.183 (1.00)
del 21q22 3	276 (56%)	214	0.764 (1.00)	0.142 (1.00)	1.84e-07 (0.000165)	0.0418 (1.00)	0.514 (1.00)	0.127 (1.00)	0.153 (1.00)	0.00319 (1.00)	0.000159 (0.126)	0.0826 (1.00)	0.215 (1.00)	0.0356 (1.00)
amp 4q12	114 (23%)	376	0.878 (1.00)	0.208 (1.00)	0.000256 (0.197)	0.0687 (1.00)	0.283 (1.00)	0.0755 (1.00)	0.0831 (1.00)	0.0786 (1.00)	0.00231 (1.00)	0.586 (1.00)	0.0447 (1.00)	1 (1.00)
amp 5p15 33	378 (77%)	112	0.843 (1.00)	0.964 (1.00)	2.77e-10 (2.59e-07)	0.0339 (1.00)	0.39 (1.00)	0.501 (1.00)	0.55 (1.00)	0.0569 (1.00)	0.645 (1.00)	0.0293 (1.00)	0.359 (1.00)	0.432 (1.00)
amp 5p12	346 (71%)	144	0.949 (1.00)	1 (1.00)	2.09e-09 (1.94e-06)	0.0104 (1.00)	0.206 (1.00)	0.987 (1.00)	0.303 (1.00)	0.675 (1.00)	0.944 (1.00)	0.144 (1.00)	0.672 (1.00)	0.905 (1.00)
amp 6p12 1	162 (33%)	328	0.649 (1.00)	0.731 (1.00)	3.15e-05 (0.026)	0.0527 (1.00)	0.93 (1.00)	0.231 (1.00)	0.00202 (1.00)	0.107 (1.00)	0.556 (1.00)	0.237 (1.00)	0.0233 (1.00)	0.00325 (1.00)
amp 6q12	147 (30%)	343	0.821 (1.00)	0.653 (1.00)	0.000235 (0.183)	0.0011 (0.79)	0.504 (1.00)	0.382 (1.00)	0.00156 (1.00)	0.00249 (1.00)	0.278 (1.00)	0.131 (1.00)	0.248 (1.00)	0.00777 (1.00)
amp 9p13 3	134 (27%)	356	0.124 (1.00)	0.824 (1.00)	0.00253 (1.00)	0.00221 (1.00)	0.0712 (1.00)	0.0096 (1.00)	0.000636 (0.47)	0.00016 (0.127)	0.0329 (1.00)	0.323 (1.00)	0.103 (1.00)	0.0811 (1.00)
amp 12q15	178 (36%)	312	0.136 (1.00)	0.199 (1.00)	7.45e-05 (0.0602)	0.0144 (1.00)	0.76 (1.00)	0.521 (1.00)	0.0109 (1.00)	0.00555 (1.00)	0.645 (1.00)	0.37 (1.00)	0.0831 (1.00)	0.168 (1.00)
amp 19q12	218 (44%)	272	0.37 (1.00)	0.565 (1.00)	1.71e-11 (1.61e-08)	0.00169 (1.00)	0.225 (1.00)	0.0522 (1.00)	0.00199 (1.00)	0.00259 (1.00)	0.141 (1.00)	0.44 (1.00)	0.022 (1.00)	0.0343 (1.00)
amp 19q13 2	229 (47%)	261	0.339 (1.00)	0.421 (1.00)	2.35e-09 (2.18e-06)	0.00306 (1.00)	0.368 (1.00)	0.279 (1.00)	0.00276 (1.00)	0.00117 (0.843)	0.345 (1.00)	0.498 (1.00)	0.0611 (1.00)	0.0766 (1.00)
amp 20q11 21	298 (61%)	192	0.811 (1.00)	0.872 (1.00)	3.58e-07 (0.000319)	0.00522 (1.00)	0.788 (1.00)	0.715 (1.00)	0.57 (1.00)	0.346 (1.00)	0.126 (1.00)	0.061 (1.00)	0.0507 (1.00)	0.734 (1.00)
del 6q22 31	118 (24%)	372	0.0405 (1.00)	0.0226 (1.00)	5.72e-05 (0.0465)	0.00171 (1.00)	0.466 (1.00)	0.245 (1.00)	0.000588 (0.437)	0.00149 (1.00)	0.0827 (1.00)	0.0496 (1.00)	0.072 (1.00)	0.0498 (1.00)
del 7q36 3	103 (21%)	387	0.176 (1.00)	0.134 (1.00)	0.00118 (0.844)	0.289 (1.00)	0.968 (1.00)	0.218 (1.00)	0.000295 (0.225)	0.00198 (1.00)	0.346 (1.00)	0.504 (1.00)	0.0644 (1.00)	0.892 (1.00)
del 8p23 2	335 (68%)	155	0.585 (1.00)	0.789 (1.00)	3.89e-05 (0.0319)	0.0136 (1.00)	0.233 (1.00)	0.09 (1.00)	0.112 (1.00)	0.0538 (1.00)	0.145 (1.00)	0.175 (1.00)	0.414 (1.00)	0.0577 (1.00)
del 9p21 3	378 (77%)	112	0.196 (1.00)	0.261 (1.00)	1.76e-06 (0.00152)	0.298 (1.00)	0.824 (1.00)	0.427 (1.00)	0.000615 (0.456)	0.376 (1.00)	0.165 (1.00)	0.261 (1.00)	0.042 (1.00)	1 (1.00)
del 11q22 1	158 (32%)	332	0.552 (1.00)	0.307 (1.00)	0.00022 (0.171)	0.000434 (0.326)	0.15 (1.00)	0.935 (1.00)	0.0243 (1.00)	0.00135 (0.961)	0.0014 (0.992)	0.573 (1.00)	0.0172 (1.00)	0.00506 (1.00)
del 17q25 3	100 (20%)	390	0.00504 (1.00)	0.016 (1.00)	0.00202 (1.00)	0.0294 (1.00)	0.611 (1.00)	0.988 (1.00)	0.00507 (1.00)	0.000264 (0.202)	0.891 (1.00)	0.0331 (1.00)	0.383 (1.00)	0.014 (1.00)
del 19p13 3	229 (47%)	261	0.439 (1.00)	0.00897 (1.00)	0.000103 (0.083)	0.777 (1.00)	0.091 (1.00)	0.124 (1.00)	0.147 (1.00)	0.00513 (1.00)	0.0475 (1.00)	0.0025 (1.00)	0.326 (1.00)	0.824 (1.00)
amp 3p11 1	96 (20%)	394	0.106 (1.00)	0.818 (1.00)	0.577 (1.00)	0.828 (1.00)	0.312 (1.00)	0.000813 (0.596)	0.215 (1.00)	0.908 (1.00)	0.14 (1.00)	0.714 (1.00)	0.744 (1.00)	0.117 (1.00)
amp 8p11 23	232 (47%)	258	0.0138 (1.00)	0.46 (1.00)	0.000624 (0.462)	0.019 (1.00)	0.189 (1.00)	0.1 (1.00)	0.0384 (1.00)	0.949 (1.00)	0.695 (1.00)	0.163 (1.00)	0.78 (1.00)	0.221 (1.00)
amp 8q24 21	342 (70%)	148	0.918 (1.00)	0.785 (1.00)	0.00636 (1.00)	0.33 (1.00)	0.826 (1.00)	0.754 (1.00)	0.828 (1.00)	0.936 (1.00)	0.511 (1.00)	0.672 (1.00)	0.348 (1.00)	1 (1.00)
amp 13q34	88 (18%)	402	0.977 (1.00)	0.0229 (1.00)	0.35 (1.00)	0.713 (1.00)	0.835 (1.00)	0.0864 (1.00)	0.836 (1.00)	0.703 (1.00)	0.383 (1.00)	0.149 (1.00)	0.638 (1.00)	0.567 (1.00)
amp 14q13 3	154 (31%)	336	0.313 (1.00)	0.194 (1.00)	0.145 (1.00)	0.137 (1.00)	0.698 (1.00)	0.00818 (1.00)	0.156 (1.00)	0.0323 (1.00)	0.00919 (1.00)	0.171 (1.00)	0.287 (1.00)	0.719 (1.00)
amp xq28	122 (25%)	368	0.873 (1.00)	0.767 (1.00)	0.0201 (1.00)	0.048 (1.00)	0.0377 (1.00)	0.0863 (1.00)	0.0857 (1.00)	0.216 (1.00)	0.00604 (1.00)	0.0314 (1.00)	0.08 (1.00)	0.0143 (1.00)
del 2p25 3	50 (10%)	440	0.123 (1.00)	0.0293 (1.00)	0.133 (1.00)	0.392 (1.00)	0.274 (1.00)	0.811 (1.00)	0.443 (1.00)	0.079 (1.00)	0.0227 (1.00)	0.428 (1.00)	0.0685 (1.00)	0.173 (1.00)
del 3p25 3	389 (79%)	101	0.384 (1.00)	0.253 (1.00)	0.00933 (1.00)	0.000937 (0.681)	0.868 (1.00)	0.181 (1.00)	0.00898 (1.00)	0.000554 (0.413)	0.000857 (0.626)	0.0142 (1.00)	0.102 (1.00)	0.0212 (1.00)
del 3q11 1	77 (16%)	413	0.76 (1.00)	0.626 (1.00)	0.212 (1.00)	0.937 (1.00)	0.764 (1.00)	0.291 (1.00)	0.703 (1.00)	0.0551 (1.00)	0.764 (1.00)	0.489 (1.00)	0.429 (1.00)	0.226 (1.00)
del 7q11 22	47 (10%)	443	0.802 (1.00)	0.108 (1.00)	0.000429 (0.322)	0.776 (1.00)	0.84 (1.00)	0.613 (1.00)	0.00183 (1.00)	0.0418 (1.00)	0.647 (1.00)	0.694 (1.00)	0.731 (1.00)	0.724 (1.00)
del 11q25	182 (37%)	308	0.787 (1.00)	0.596 (1.00)	0.00143 (1.00)	0.0497 (1.00)	0.172 (1.00)	0.842 (1.00)	0.0154 (1.00)	0.00123 (0.882)	0.0101 (1.00)	0.504 (1.00)	0.0526 (1.00)	0.0165 (1.00)
del 12q24 31	85 (17%)	405	0.88 (1.00)	0.594 (1.00)	0.369 (1.00)	0.257 (1.00)	0.197 (1.00)	0.267 (1.00)	0.721 (1.00)	0.536 (1.00)	0.447 (1.00)	0.045 (1.00)	0.436 (1.00)	1 (1.00)
del 13q12 11	326 (67%)	164	0.106 (1.00)	0.463 (1.00)	0.00222 (1.00)	0.119 (1.00)	0.875 (1.00)	0.18 (1.00)	0.778 (1.00)	0.62 (1.00)	0.765 (1.00)	0.281 (1.00)	0.0416 (1.00)	0.0986 (1.00)
del 13q14 2	337 (69%)	153	0.118 (1.00)	0.346 (1.00)	0.000816 (0.597)	0.0205 (1.00)	0.695 (1.00)	0.677 (1.00)	0.525 (1.00)	0.172 (1.00)	0.174 (1.00)	0.232 (1.00)	0.00494 (1.00)	0.012 (1.00)
del 15q12	169 (34%)	321	0.693 (1.00)	0.698 (1.00)	0.1 (1.00)	0.161 (1.00)	0.0387 (1.00)	0.0123 (1.00)	0.164 (1.00)	0.00321 (1.00)	0.00987 (1.00)	0.922 (1.00)	0.282 (1.00)	0.634 (1.00)
del 15q21 1	162 (33%)	328	0.447 (1.00)	0.524 (1.00)	0.0231 (1.00)	0.205 (1.00)	0.0932 (1.00)	0.00886 (1.00)	0.202 (1.00)	0.00109 (0.788)	0.00325 (1.00)	0.635 (1.00)	0.112 (1.00)	0.403 (1.00)
del 16p13 3	181 (37%)	309	0.253 (1.00)	0.339 (1.00)	0.00128 (0.914)	0.0496 (1.00)	0.21 (1.00)	0.474 (1.00)	0.615 (1.00)	0.0967 (1.00)	0.016 (1.00)	0.918 (1.00)	0.107 (1.00)	0.208 (1.00)
del 16q23 1	204 (42%)	286	0.911 (1.00)	0.311 (1.00)	0.00472 (1.00)	0.21 (1.00)	0.362 (1.00)	0.746 (1.00)	0.0614 (1.00)	0.1 (1.00)	0.025 (1.00)	0.258 (1.00)	0.000455 (0.341)	0.00239 (1.00)
del 18q23	227 (46%)	263	0.587 (1.00)	0.321 (1.00)	0.0158 (1.00)	0.201 (1.00)	0.894 (1.00)	0.258 (1.00)	0.899 (1.00)	0.262 (1.00)	0.18 (1.00)	0.633 (1.00)	0.0614 (1.00)	0.269 (1.00)
del 22q11 21	92 (19%)	398	0.0311 (1.00)	0.164 (1.00)	0.313 (1.00)	0.0673 (1.00)	0.131 (1.00)	0.128 (1.00)	0.153 (1.00)	0.0458 (1.00)	0.406 (1.00)	0.816 (1.00)	0.547 (1.00)	0.884 (1.00)

'amp_1q21.2' versus 'CN_CNMF'

P value = 1.28e-11 (Fisher's exact test), Q value = 1.2e-08

Table S1. Gene #1: 'amp_1q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
AMP PEAK 1(1Q21.2) MUTATED	79	120	54
AMP PEAK 1(1Q21.2) WILD-TYPE	114	42	81

Figure S1. Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q21.2' versus 'METHLYATION_CNMF'

P value = 7.11e-07 (Fisher's exact test), Q value = 0.00063

Table S2. Gene #1: 'amp_1q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
AMP PEAK 1(1Q21.2) MUTATED	50	78	51
AMP PEAK 1(1Q21.2) WILD-TYPE	92	36	49

Figure S2. Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q21.2' versus 'MRNASEQ_CNMF'

P value = 5.51e-08 (Fisher's exact test), Q value = 5e-05

Table S3. Gene #1: 'amp_1q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	110	145	153	78
AMP PEAK 1(1Q21.2) MUTATED	42	102	80	28
AMP PEAK 1(1Q21.2) WILD-TYPE	68	43	73	50

Figure S3. Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.14e-08 (Fisher's exact test), Q value = 2e-05

Table S4. Gene #1: 'amp_1q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	176	95
AMP PEAK 1(1Q21.2) MUTATED	80	117	55
AMP PEAK 1(1Q21.2) WILD-TYPE	135	59	40

Figure S4. Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000122 (Fisher's exact test), Q value = 0.098

Table S5. Gene #1: 'amp_1q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	163	230
AMP PEAK 1(1Q21.2) MUTATED	52	71	116
AMP PEAK 1(1Q21.2) WILD-TYPE	19	92	114

Figure S5. Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_2p16.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.000163 (Fisher's exact test), Q value = 0.13

Table S6. Gene #2: 'amp_2p16.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	22	56	23	53
AMP PEAK 2(2P16.1) MUTATED	7	42	15	21
AMP PEAK 2(2P16.1) WILD-TYPE	15	14	8	32

Figure S6. Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_2p16.1' versus 'CN_CNMF'

P value = 5.71e-15 (Fisher's exact test), Q value = 5.4e-12

Table S7. Gene #2: 'amp_2p16.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
AMP PEAK 2(2P16.1) MUTATED	70	127	74
AMP PEAK 2(2P16.1) WILD-TYPE	123	35	61

Figure S7. Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_2p16.1' versus 'METHLYATION_CNMF'

P value = 1.68e-06 (Fisher's exact test), Q value = 0.0015

Table S8. Gene #2: 'amp_2p16.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
AMP PEAK 2(2P16.1) MUTATED	61	85	54
AMP PEAK 2(2P16.1) WILD-TYPE	81	29	46

Figure S8. Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_2p16.1' versus 'MRNASEQ_CNMF'

P value = 2.01e-11 (Fisher's exact test), Q value = 1.9e-08

Table S9. Gene #2: 'amp_2p16.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	110	145	153	78
AMP PEAK 2(2P16.1) MUTATED	44	109	91	25
AMP PEAK 2(2P16.1) WILD-TYPE	66	36	62	53

Figure S9. Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_2p16.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.28e-08 (Fisher's exact test), Q value = 2.1e-05

Table S10. Gene #2: 'amp_2p16.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	176	95
AMP PEAK 2(2P16.1) MUTATED	89	125	55
AMP PEAK 2(2P16.1) WILD-TYPE	126	51	40

Figure S10. Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_2p16.1' versus 'MIRSEQ_CNMF'

P value = 2.21e-05 (Fisher's exact test), Q value = 0.018

Table S11. Gene #2: 'amp_2p16.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	130	125	64
AMP PEAK 2(2P16.1) MUTATED	81	90	49	39
AMP PEAK 2(2P16.1) WILD-TYPE	64	40	76	25

Figure S11. Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_2p16.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000226 (Fisher's exact test), Q value = 0.18

Table S12. Gene #2: 'amp_2p16.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	178	150
AMP PEAK 2(2P16.1) MUTATED	82	100
AMP PEAK 2(2P16.1) WILD-TYPE	96	50

Figure S12. Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_2q31.2' versus 'CN_CNMF'

P value = 3.07e-07 (Fisher's exact test), Q value = 0.00027

Table S13. Gene #3: 'amp_2q31.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
AMP PEAK 3(2Q31.2) MUTATED	42	80	46
AMP PEAK 3(2Q31.2) WILD-TYPE	151	82	89

Figure S13. Get High-res Image Gene #3: 'amp_2q31.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_2q31.2' versus 'METHLYATION_CNMF'

P value = 3.13e-06 (Fisher's exact test), Q value = 0.0027

Table S14. Gene #3: 'amp_2q31.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
AMP PEAK 3(2Q31.2) MUTATED	36	62	29
AMP PEAK 3(2Q31.2) WILD-TYPE	106	52	71

Figure S14. Get High-res Image Gene #3: 'amp_2q31.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_2q31.2' versus 'MRNASEQ_CNMF'

P value = 1.77e-06 (Fisher's exact test), Q value = 0.0015

Table S15. Gene #3: 'amp_2q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	110	145	153	78
AMP PEAK 3(2Q31.2) MUTATED	27	75	48	17
AMP PEAK 3(2Q31.2) WILD-TYPE	83	70	105	61

Figure S15. Get High-res Image Gene #3: 'amp_2q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_2q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.32e-05 (Fisher's exact test), Q value = 0.027

Table S16. Gene #3: 'amp_2q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	176	95
AMP PEAK 3(2Q31.2) MUTATED	53	82	32
AMP PEAK 3(2Q31.2) WILD-TYPE	162	94	63

Figure S16. Get High-res Image Gene #3: 'amp_2q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_2q31.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000165 (Fisher's exact test), Q value = 0.13

Table S17. Gene #3: 'amp_2q31.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	112	91
AMP PEAK 3(2Q31.2) MUTATED	59	28	22
AMP PEAK 3(2Q31.2) WILD-TYPE	66	84	69

Figure S17. Get High-res Image Gene #3: 'amp_2q31.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.33' versus 'MRNA_CHIERARCHICAL'

P value = 2.27e-05 (Fisher's exact test), Q value = 0.019

Table S18. Gene #5: 'amp_3q26.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	22	56	23	53
AMP PEAK 5(3Q26.33) MUTATED	14	56	20	50
AMP PEAK 5(3Q26.33) WILD-TYPE	8	0	3	3

Figure S18. Get High-res Image Gene #5: 'amp_3q26.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_3q26.33' versus 'CN_CNMF'

P value = 2.23e-14 (Fisher's exact test), Q value = 2.1e-11

Table S19. Gene #5: 'amp_3q26.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
AMP PEAK 5(3Q26.33) MUTATED	150	162	130
AMP PEAK 5(3Q26.33) WILD-TYPE	43	0	5

Figure S19. Get High-res Image Gene #5: 'amp_3q26.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3q26.33' versus 'METHLYATION_CNMF'

P value = 5.42e-09 (Fisher's exact test), Q value = 5e-06

Table S20. Gene #5: 'amp_3q26.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
AMP PEAK 5(3Q26.33) MUTATED	112	114	94
AMP PEAK 5(3Q26.33) WILD-TYPE	30	0	6

Figure S20. Get High-res Image Gene #5: 'amp_3q26.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3q26.33' versus 'MRNASEQ_CNMF'

P value = 2.09e-10 (Fisher's exact test), Q value = 2e-07

Table S21. Gene #5: 'amp_3q26.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	110	145	153	78
AMP PEAK 5(3Q26.33) MUTATED	104	145	132	58
AMP PEAK 5(3Q26.33) WILD-TYPE	6	0	21	20

Figure S21. Get High-res Image Gene #5: 'amp_3q26.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3q26.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.2e-09 (Fisher's exact test), Q value = 4.8e-06

Table S22. Gene #5: 'amp_3q26.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	176	95
AMP PEAK 5(3Q26.33) MUTATED	178	175	86
AMP PEAK 5(3Q26.33) WILD-TYPE	37	1	9

Figure S22. Get High-res Image Gene #5: 'amp_3q26.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.33' versus 'MIRSEQ_CNMF'

P value = 3.57e-08 (Fisher's exact test), Q value = 3.3e-05

Table S23. Gene #5: 'amp_3q26.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	130	125	64
AMP PEAK 5(3Q26.33) MUTATED	131	128	97	63
AMP PEAK 5(3Q26.33) WILD-TYPE	14	2	28	1

Figure S23. Get High-res Image Gene #5: 'amp_3q26.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3q26.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.11e-06 (Fisher's exact test), Q value = 0.0027

Table S24. Gene #5: 'amp_3q26.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	163	230
AMP PEAK 5(3Q26.33) MUTATED	71	155	193
AMP PEAK 5(3Q26.33) WILD-TYPE	0	8	37

Figure S24. Get High-res Image Gene #5: 'amp_3q26.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000161 (Fisher's exact test), Q value = 0.13

Table S25. Gene #5: 'amp_3q26.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	178	150
AMP PEAK 5(3Q26.33) MUTATED	150	145
AMP PEAK 5(3Q26.33) WILD-TYPE	28	5

Figure S25. Get High-res Image Gene #5: 'amp_3q26.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4q12' versus 'CN_CNMF'

P value = 0.000256 (Fisher's exact test), Q value = 0.2

Table S26. Gene #6: 'amp_4q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
AMP PEAK 6(4Q12) MUTATED	28	41	45
AMP PEAK 6(4Q12) WILD-TYPE	165	121	90

Figure S26. Get High-res Image Gene #6: 'amp_4q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5p15.33' versus 'CN_CNMF'

P value = 2.77e-10 (Fisher's exact test), Q value = 2.6e-07

Table S27. Gene #7: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
AMP PEAK 7(5P15.33) MUTATED	134	115	129
AMP PEAK 7(5P15.33) WILD-TYPE	59	47	6

Figure S27. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5p12' versus 'CN_CNMF'

P value = 2.09e-09 (Fisher's exact test), Q value = 1.9e-06

Table S28. Gene #8: 'amp_5p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
AMP PEAK 8(5P12) MUTATED	114	111	121
AMP PEAK 8(5P12) WILD-TYPE	79	51	14

Figure S28. Get High-res Image Gene #8: 'amp_5p12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p12.1' versus 'CN_CNMF'

P value = 3.15e-05 (Fisher's exact test), Q value = 0.026

Table S29. Gene #9: 'amp_6p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
AMP PEAK 9(6P12.1) MUTATED	41	66	55
AMP PEAK 9(6P12.1) WILD-TYPE	152	96	80

Figure S29. Get High-res Image Gene #9: 'amp_6p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6q12' versus 'CN_CNMF'

P value = 0.000235 (Fisher's exact test), Q value = 0.18

Table S30. Gene #10: 'amp_6q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
AMP PEAK 10(6Q12) MUTATED	38	59	50
AMP PEAK 10(6Q12) WILD-TYPE	155	103	85

Figure S30. Get High-res Image Gene #10: 'amp_6q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7p11.2' versus 'CN_CNMF'

P value = 1.85e-06 (Fisher's exact test), Q value = 0.0016

Table S31. Gene #11: 'amp_7p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
AMP PEAK 11(7P11.2) MUTATED	75	107	67
AMP PEAK 11(7P11.2) WILD-TYPE	118	55	68

Figure S31. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000247 (Fisher's exact test), Q value = 0.19

Table S32. Gene #11: 'amp_7p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	176	95
AMP PEAK 11(7P11.2) MUTATED	100	110	37
AMP PEAK 11(7P11.2) WILD-TYPE	115	66	58

Figure S32. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7q21.2' versus 'CN_CNMF'

P value = 8.28e-15 (Fisher's exact test), Q value = 7.9e-12

Table S33. Gene #12: 'amp_7q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
AMP PEAK 12(7Q21.2) MUTATED	62	120	76
AMP PEAK 12(7Q21.2) WILD-TYPE	131	42	59

Figure S33. Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7q21.2' versus 'METHLYATION_CNMF'

P value = 1.02e-06 (Fisher's exact test), Q value = 0.00089

Table S34. Gene #12: 'amp_7q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
AMP PEAK 12(7Q21.2) MUTATED	49	76	55
AMP PEAK 12(7Q21.2) WILD-TYPE	93	38	45

Figure S34. Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7q21.2' versus 'MRNASEQ_CNMF'

P value = 4.41e-07 (Fisher's exact test), Q value = 0.00039

Table S35. Gene #12: 'amp_7q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	110	145	153	78
AMP PEAK 12(7Q21.2) MUTATED	52	104	70	30
AMP PEAK 12(7Q21.2) WILD-TYPE	58	41	83	48

Figure S35. Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.68e-06 (Fisher's exact test), Q value = 0.0015

Table S36. Gene #12: 'amp_7q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	176	95
AMP PEAK 12(7Q21.2) MUTATED	90	119	47
AMP PEAK 12(7Q21.2) WILD-TYPE	125	57	48

Figure S36. Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_9p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.13

Table S37. Gene #15: 'amp_9p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	176	95
AMP PEAK 15(9P13.3) MUTATED	41	67	26
AMP PEAK 15(9P13.3) WILD-TYPE	174	109	69

Figure S37. Get High-res Image Gene #15: 'amp_9p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'CN_CNMF'

P value = 9.49e-07 (Fisher's exact test), Q value = 0.00083

Table S38. Gene #16: 'amp_11q13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
AMP PEAK 16(11Q13.3) MUTATED	48	61	72
AMP PEAK 16(11Q13.3) WILD-TYPE	145	101	63

Figure S38. Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11q13.3' versus 'METHLYATION_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.19

Table S39. Gene #16: 'amp_11q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
AMP PEAK 16(11Q13.3) MUTATED	40	41	54
AMP PEAK 16(11Q13.3) WILD-TYPE	102	73	46

Figure S39. Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12p13.33' versus 'CN_CNMF'

P value = 1.83e-07 (Fisher's exact test), Q value = 0.00016

Table S40. Gene #17: 'amp_12p13.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
AMP PEAK 17(12P13.33) MUTATED	70	106	73
AMP PEAK 17(12P13.33) WILD-TYPE	123	56	62

Figure S40. Get High-res Image Gene #17: 'amp_12p13.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12p13.33' versus 'MRNASEQ_CNMF'

P value = 1.67e-07 (Fisher's exact test), Q value = 0.00015

Table S41. Gene #17: 'amp_12p13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	110	145	153	78
AMP PEAK 17(12P13.33) MUTATED	37	94	88	28
AMP PEAK 17(12P13.33) WILD-TYPE	73	51	65	50

Figure S41. Get High-res Image Gene #17: 'amp_12p13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12p13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.14e-05 (Fisher's exact test), Q value = 0.042

Table S42. Gene #17: 'amp_12p13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	176	95
AMP PEAK 17(12P13.33) MUTATED	85	106	56
AMP PEAK 17(12P13.33) WILD-TYPE	130	70	39

Figure S42. Get High-res Image Gene #17: 'amp_12p13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12q15' versus 'CN_CNMF'

P value = 7.45e-05 (Fisher's exact test), Q value = 0.06

Table S43. Gene #18: 'amp_12q15' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
AMP PEAK 18(12Q15) MUTATED	51	79	48
AMP PEAK 18(12Q15) WILD-TYPE	142	83	87

Figure S43. Get High-res Image Gene #18: 'amp_12q15' versus Molecular Subtype #3: 'CN_CNMF'

'amp_15q26.3' versus 'CN_CNMF'

P value = 8.01e-06 (Fisher's exact test), Q value = 0.0068

Table S44. Gene #21: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
AMP PEAK 21(15Q26.3) MUTATED	46	78	52
AMP PEAK 21(15Q26.3) WILD-TYPE	147	84	83

Figure S44. Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_15q26.3' versus 'MRNASEQ_CNMF'

P value = 1.57e-05 (Fisher's exact test), Q value = 0.013

Table S45. Gene #21: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	110	145	153	78
AMP PEAK 21(15Q26.3) MUTATED	26	75	49	23
AMP PEAK 21(15Q26.3) WILD-TYPE	84	70	104	55

Figure S45. Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q25.1' versus 'CN_CNMF'

P value = 9.19e-14 (Fisher's exact test), Q value = 8.7e-11

Table S46. Gene #22: 'amp_17q25.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
AMP PEAK 22(17Q25.1) MUTATED	54	111	68
AMP PEAK 22(17Q25.1) WILD-TYPE	139	51	67

Figure S46. Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q25.1' versus 'METHLYATION_CNMF'

P value = 4.77e-08 (Fisher's exact test), Q value = 4.3e-05

Table S47. Gene #22: 'amp_17q25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
AMP PEAK 22(17Q25.1) MUTATED	40	72	52
AMP PEAK 22(17Q25.1) WILD-TYPE	102	42	48

Figure S47. Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q25.1' versus 'MRNASEQ_CNMF'

P value = 5.42e-06 (Fisher's exact test), Q value = 0.0046

Table S48. Gene #22: 'amp_17q25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	110	145	153	78
AMP PEAK 22(17Q25.1) MUTATED	42	94	68	27
AMP PEAK 22(17Q25.1) WILD-TYPE	68	51	85	51

Figure S48. Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q25.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.27e-08 (Fisher's exact test), Q value = 8.4e-05

Table S49. Gene #22: 'amp_17q25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	176	95
AMP PEAK 22(17Q25.1) MUTATED	73	110	48
AMP PEAK 22(17Q25.1) WILD-TYPE	142	66	47

Figure S49. Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q25.1' versus 'MIRSEQ_CNMF'

P value = 0.000148 (Fisher's exact test), Q value = 0.12

Table S50. Gene #22: 'amp_17q25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	130	125	64
AMP PEAK 22(17Q25.1) MUTATED	74	77	40	29
AMP PEAK 22(17Q25.1) WILD-TYPE	71	53	85	35

Figure S50. Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q25.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.04e-05 (Fisher's exact test), Q value = 0.0088

Table S51. Gene #22: 'amp_17q25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	112	91
AMP PEAK 22(17Q25.1) MUTATED	79	38	36
AMP PEAK 22(17Q25.1) WILD-TYPE	46	74	55

Figure S51. Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_17q25.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.09e-06 (Fisher's exact test), Q value = 0.0027

Table S52. Gene #22: 'amp_17q25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	178	150
AMP PEAK 22(17Q25.1) MUTATED	62	91
AMP PEAK 22(17Q25.1) WILD-TYPE	116	59

Figure S52. Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_18p11.32' versus 'CN_CNMF'

P value = 7.62e-08 (Fisher's exact test), Q value = 6.9e-05

Table S53. Gene #23: 'amp_18p11.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
AMP PEAK 23(18P11.32) MUTATED	42	82	51
AMP PEAK 23(18P11.32) WILD-TYPE	151	80	84

Figure S53. Get High-res Image Gene #23: 'amp_18p11.32' versus Molecular Subtype #3: 'CN_CNMF'

'amp_18p11.32' versus 'METHLYATION_CNMF'

P value = 2.57e-05 (Fisher's exact test), Q value = 0.021

Table S54. Gene #23: 'amp_18p11.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
AMP PEAK 23(18P11.32) MUTATED	31	51	46
AMP PEAK 23(18P11.32) WILD-TYPE	111	63	54

Figure S54. Get High-res Image Gene #23: 'amp_18p11.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_18q11.2' versus 'CN_CNMF'

P value = 7.72e-09 (Fisher's exact test), Q value = 7.1e-06

Table S55. Gene #24: 'amp_18q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
AMP PEAK 24(18Q11.2) MUTATED	33	76	39
AMP PEAK 24(18Q11.2) WILD-TYPE	160	86	96

Figure S55. Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_18q11.2' versus 'METHLYATION_CNMF'

P value = 2.31e-05 (Fisher's exact test), Q value = 0.019

Table S56. Gene #24: 'amp_18q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
AMP PEAK 24(18Q11.2) MUTATED	24	49	31
AMP PEAK 24(18Q11.2) WILD-TYPE	118	65	69

Figure S56. Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CNMF'

P value = 1.67e-06 (Fisher's exact test), Q value = 0.0015

Table S57. Gene #24: 'amp_18q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	110	145	153	78
AMP PEAK 24(18Q11.2) MUTATED	25	63	50	9
AMP PEAK 24(18Q11.2) WILD-TYPE	85	82	103	69

Figure S57. Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.21e-09 (Fisher's exact test), Q value = 2.1e-06

Table S58. Gene #24: 'amp_18q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	176	95
AMP PEAK 24(18Q11.2) MUTATED	34	74	39
AMP PEAK 24(18Q11.2) WILD-TYPE	181	102	56

Figure S58. Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000167 (Fisher's exact test), Q value = 0.13

Table S59. Gene #24: 'amp_18q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	112	91
AMP PEAK 24(18Q11.2) MUTATED	49	17	25
AMP PEAK 24(18Q11.2) WILD-TYPE	76	95	66

Figure S59. Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000188 (Fisher's exact test), Q value = 0.15

Table S60. Gene #24: 'amp_18q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	178	150
AMP PEAK 24(18Q11.2) MUTATED	34	57
AMP PEAK 24(18Q11.2) WILD-TYPE	144	93

Figure S60. Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 1.71e-11 (Fisher's exact test), Q value = 1.6e-08

Table S61. Gene #25: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
AMP PEAK 25(19Q12) MUTATED	57	107	54
AMP PEAK 25(19Q12) WILD-TYPE	136	55	81

Figure S61. Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q13.2' versus 'CN_CNMF'

P value = 2.35e-09 (Fisher's exact test), Q value = 2.2e-06

Table S62. Gene #26: 'amp_19q13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
AMP PEAK 26(19Q13.2) MUTATED	64	107	58
AMP PEAK 26(19Q13.2) WILD-TYPE	129	55	77

Figure S62. Get High-res Image Gene #26: 'amp_19q13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20p12.2' versus 'CN_CNMF'

P value = 5.81e-10 (Fisher's exact test), Q value = 5.4e-07

Table S63. Gene #27: 'amp_20p12.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
AMP PEAK 27(20P12.2) MUTATED	76	119	78
AMP PEAK 27(20P12.2) WILD-TYPE	117	43	57

Figure S63. Get High-res Image Gene #27: 'amp_20p12.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20p12.2' versus 'METHLYATION_CNMF'

P value = 0.000249 (Fisher's exact test), Q value = 0.19

Table S64. Gene #27: 'amp_20p12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
AMP PEAK 27(20P12.2) MUTATED	67	82	54
AMP PEAK 27(20P12.2) WILD-TYPE	75	32	46

Figure S64. Get High-res Image Gene #27: 'amp_20p12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20p12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.18e-05 (Fisher's exact test), Q value = 0.042

Table S65. Gene #27: 'amp_20p12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	176	95
AMP PEAK 27(20P12.2) MUTATED	97	118	57
AMP PEAK 27(20P12.2) WILD-TYPE	118	58	38

Figure S65. Get High-res Image Gene #27: 'amp_20p12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'CN_CNMF'

P value = 3.58e-07 (Fisher's exact test), Q value = 0.00032

Table S66. Gene #28: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
AMP PEAK 28(20Q11.21) MUTATED	89	110	99
AMP PEAK 28(20Q11.21) WILD-TYPE	104	52	36

Figure S66. Get High-res Image Gene #28: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_22q11.21' versus 'CN_CNMF'

P value = 0.000135 (Fisher's exact test), Q value = 0.11

Table S67. Gene #29: 'amp_22q11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
AMP PEAK 29(22Q11.21) MUTATED	77	98	78
AMP PEAK 29(22Q11.21) WILD-TYPE	116	64	57

Figure S67. Get High-res Image Gene #29: 'amp_22q11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_22q11.21' versus 'MRNASEQ_CNMF'

P value = 8.84e-05 (Fisher's exact test), Q value = 0.071

Table S68. Gene #29: 'amp_22q11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	110	145	153	78
AMP PEAK 29(22Q11.21) MUTATED	53	97	71	30
AMP PEAK 29(22Q11.21) WILD-TYPE	57	48	82	48

Figure S68. Get High-res Image Gene #29: 'amp_22q11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.32' versus 'MRNA_CNMF'

P value = 4.95e-07 (Fisher's exact test), Q value = 0.00044

Table S69. Gene #31: 'del_1p36.32' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	52	32	28
DEL PEAK 1(1P36.32) MUTATED	9	39	14	8
DEL PEAK 1(1P36.32) WILD-TYPE	33	13	18	20

Figure S69. Get High-res Image Gene #31: 'del_1p36.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p36.32' versus 'MRNA_CHIERARCHICAL'

P value = 4.08e-08 (Fisher's exact test), Q value = 3.7e-05

Table S70. Gene #31: 'del_1p36.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	22	56	23	53
DEL PEAK 1(1P36.32) MUTATED	8	43	7	12
DEL PEAK 1(1P36.32) WILD-TYPE	14	13	16	41

Figure S70. Get High-res Image Gene #31: 'del_1p36.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p36.32' versus 'CN_CNMF'

P value = 1.72e-35 (Fisher's exact test), Q value = 1.7e-32

Table S71. Gene #31: 'del_1p36.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
DEL PEAK 1(1P36.32) MUTATED	51	134	28
DEL PEAK 1(1P36.32) WILD-TYPE	142	28	107

Figure S71. Get High-res Image Gene #31: 'del_1p36.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.32' versus 'METHLYATION_CNMF'

P value = 1.98e-19 (Fisher's exact test), Q value = 1.9e-16

Table S72. Gene #31: 'del_1p36.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 1(1P36.32) MUTATED	26	85	38
DEL PEAK 1(1P36.32) WILD-TYPE	116	29	62

Figure S72. Get High-res Image Gene #31: 'del_1p36.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.32' versus 'MRNASEQ_CNMF'

P value = 6.31e-21 (Fisher's exact test), Q value = 6e-18

Table S73. Gene #31: 'del_1p36.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	110	145	153	78
DEL PEAK 1(1P36.32) MUTATED	31	112	45	24
DEL PEAK 1(1P36.32) WILD-TYPE	79	33	108	54

Figure S73. Get High-res Image Gene #31: 'del_1p36.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.05e-25 (Fisher's exact test), Q value = 1e-22

Table S74. Gene #31: 'del_1p36.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	176	95
DEL PEAK 1(1P36.32) MUTATED	51	132	29
DEL PEAK 1(1P36.32) WILD-TYPE	164	44	66

Figure S74. Get High-res Image Gene #31: 'del_1p36.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.32' versus 'MIRSEQ_CNMF'

P value = 1.18e-06 (Fisher's exact test), Q value = 0.001

Table S75. Gene #31: 'del_1p36.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	130	125	64
DEL PEAK 1(1P36.32) MUTATED	60	62	35	44
DEL PEAK 1(1P36.32) WILD-TYPE	85	68	90	20

Figure S75. Get High-res Image Gene #31: 'del_1p36.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p36.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.94e-06 (Fisher's exact test), Q value = 0.0025

Table S76. Gene #31: 'del_1p36.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	163	230
DEL PEAK 1(1P36.32) MUTATED	50	66	85
DEL PEAK 1(1P36.32) WILD-TYPE	21	97	145

Figure S76. Get High-res Image Gene #31: 'del_1p36.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.68e-07 (Fisher's exact test), Q value = 0.00033

Table S77. Gene #31: 'del_1p36.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	178	150
DEL PEAK 1(1P36.32) MUTATED	52	86
DEL PEAK 1(1P36.32) WILD-TYPE	126	64

Figure S77. Get High-res Image Gene #31: 'del_1p36.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p13.1' versus 'MRNA_CNMF'

P value = 0.000164 (Fisher's exact test), Q value = 0.13

Table S78. Gene #32: 'del_1p13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	52	32	28
DEL PEAK 2(1P13.1) MUTATED	17	37	9	9
DEL PEAK 2(1P13.1) WILD-TYPE	25	15	23	19

Figure S78. Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p13.1' versus 'MRNA_CHIERARCHICAL'

P value = 1.22e-05 (Fisher's exact test), Q value = 0.01

Table S79. Gene #32: 'del_1p13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	22	56	23	53
DEL PEAK 2(1P13.1) MUTATED	9	39	12	12
DEL PEAK 2(1P13.1) WILD-TYPE	13	17	11	41

Figure S79. Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p13.1' versus 'CN_CNMF'

P value = 1.23e-20 (Fisher's exact test), Q value = 1.2e-17

Table S80. Gene #32: 'del_1p13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
DEL PEAK 2(1P13.1) MUTATED	52	119	41
DEL PEAK 2(1P13.1) WILD-TYPE	141	43	94

Figure S80. Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p13.1' versus 'METHLYATION_CNMF'

P value = 5.49e-12 (Fisher's exact test), Q value = 5.2e-09

Table S81. Gene #32: 'del_1p13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 2(1P13.1) MUTATED	36	78	34
DEL PEAK 2(1P13.1) WILD-TYPE	106	36	66

Figure S81. Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p13.1' versus 'MRNASEQ_CNMF'

P value = 5.28e-12 (Fisher's exact test), Q value = 5e-09

Table S82. Gene #32: 'del_1p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	110	145	153	78
DEL PEAK 2(1P13.1) MUTATED	34	100	53	24
DEL PEAK 2(1P13.1) WILD-TYPE	76	45	100	54

Figure S82. Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.45e-14 (Fisher's exact test), Q value = 3.3e-11

Table S83. Gene #32: 'del_1p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	176	95
DEL PEAK 2(1P13.1) MUTATED	56	115	40
DEL PEAK 2(1P13.1) WILD-TYPE	159	61	55

Figure S83. Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p13.1' versus 'MIRSEQ_CNMF'

P value = 3.13e-08 (Fisher's exact test), Q value = 2.9e-05

Table S84. Gene #32: 'del_1p13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	130	125	64
DEL PEAK 2(1P13.1) MUTATED	66	61	30	44
DEL PEAK 2(1P13.1) WILD-TYPE	79	69	95	20

Figure S84. Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.53e-07 (Fisher's exact test), Q value = 0.00084

Table S85. Gene #32: 'del_1p13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	163	230
DEL PEAK 2(1P13.1) MUTATED	51	63	87
DEL PEAK 2(1P13.1) WILD-TYPE	20	100	143

Figure S85. Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.06e-05 (Fisher's exact test), Q value = 0.009

Table S86. Gene #32: 'del_1p13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	178	150
DEL PEAK 2(1P13.1) MUTATED	54	82
DEL PEAK 2(1P13.1) WILD-TYPE	124	68

Figure S86. Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q22.1' versus 'CN_CNMF'

P value = 2.59e-07 (Fisher's exact test), Q value = 0.00023

Table S87. Gene #34: 'del_2q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
DEL PEAK 4(2Q22.1) MUTATED	25	61	38
DEL PEAK 4(2Q22.1) WILD-TYPE	168	101	97

Figure S87. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 0.000288 (Fisher's exact test), Q value = 0.22

Table S88. Gene #34: 'del_2q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 4(2Q22.1) MUTATED	19	39	27
DEL PEAK 4(2Q22.1) WILD-TYPE	123	75	73

Figure S88. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q22.1' versus 'MIRSEQ_CNMF'

P value = 0.000126 (Fisher's exact test), Q value = 0.1

Table S89. Gene #34: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	130	125	64
DEL PEAK 4(2Q22.1) MUTATED	48	35	15	22
DEL PEAK 4(2Q22.1) WILD-TYPE	97	95	110	42

Figure S89. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000209 (Fisher's exact test), Q value = 0.16

Table S90. Gene #34: 'del_2q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	112	91
DEL PEAK 4(2Q22.1) MUTATED	46	21	13
DEL PEAK 4(2Q22.1) WILD-TYPE	79	91	78

Figure S90. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_2q37.1' versus 'CN_CNMF'

P value = 5.65e-10 (Fisher's exact test), Q value = 5.3e-07

Table S91. Gene #35: 'del_2q37.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
DEL PEAK 5(2Q37.1) MUTATED	36	82	37
DEL PEAK 5(2Q37.1) WILD-TYPE	157	80	98

Figure S91. Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q37.1' versus 'METHLYATION_CNMF'

P value = 6.31e-07 (Fisher's exact test), Q value = 0.00056

Table S92. Gene #35: 'del_2q37.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 5(2Q37.1) MUTATED	25	55	36
DEL PEAK 5(2Q37.1) WILD-TYPE	117	59	64

Figure S92. Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q37.1' versus 'MRNASEQ_CNMF'

P value = 1.28e-06 (Fisher's exact test), Q value = 0.0011

Table S93. Gene #35: 'del_2q37.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	110	145	153	78
DEL PEAK 5(2Q37.1) MUTATED	33	68	43	10
DEL PEAK 5(2Q37.1) WILD-TYPE	77	77	110	68

Figure S93. Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2q37.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.96e-05 (Fisher's exact test), Q value = 0.016

Table S94. Gene #35: 'del_2q37.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	176	95
DEL PEAK 5(2Q37.1) MUTATED	48	78	28
DEL PEAK 5(2Q37.1) WILD-TYPE	167	98	67

Figure S94. Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.1' versus 'MIRSEQ_CNMF'

P value = 1.33e-05 (Fisher's exact test), Q value = 0.011

Table S95. Gene #35: 'del_2q37.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	130	125	64
DEL PEAK 5(2Q37.1) MUTATED	53	54	19	23
DEL PEAK 5(2Q37.1) WILD-TYPE	92	76	106	41

Figure S95. Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2q37.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.09e-05 (Fisher's exact test), Q value = 0.0092

Table S96. Gene #35: 'del_2q37.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	112	91
DEL PEAK 5(2Q37.1) MUTATED	59	25	19
DEL PEAK 5(2Q37.1) WILD-TYPE	66	87	72

Figure S96. Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p13' versus 'CN_CNMF'

P value = 1.33e-07 (Fisher's exact test), Q value = 0.00012

Table S97. Gene #37: 'del_3p13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
DEL PEAK 7(3P13) MUTATED	146	153	125
DEL PEAK 7(3P13) WILD-TYPE	47	9	10

Figure S97. Get High-res Image Gene #37: 'del_3p13' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p13' versus 'METHLYATION_CNMF'

P value = 0.000273 (Fisher's exact test), Q value = 0.21

Table S98. Gene #37: 'del_3p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 7(3P13) MUTATED	110	107	91
DEL PEAK 7(3P13) WILD-TYPE	32	7	9

Figure S98. Get High-res Image Gene #37: 'del_3p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.99e-05 (Fisher's exact test), Q value = 0.072

Table S99. Gene #37: 'del_3p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	176	95
DEL PEAK 7(3P13) MUTATED	170	163	88
DEL PEAK 7(3P13) WILD-TYPE	45	13	7

Figure S99. Get High-res Image Gene #37: 'del_3p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p13' versus 'MIRSEQ_CNMF'

P value = 4.83e-05 (Fisher's exact test), Q value = 0.04

Table S100. Gene #37: 'del_3p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	130	125	64
DEL PEAK 7(3P13) MUTATED	129	120	92	60
DEL PEAK 7(3P13) WILD-TYPE	16	10	33	4

Figure S100. Get High-res Image Gene #37: 'del_3p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000284 (Fisher's exact test), Q value = 0.22

Table S101. Gene #37: 'del_3p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	178	150
DEL PEAK 7(3P13) MUTATED	143	141
DEL PEAK 7(3P13) WILD-TYPE	35	9

Figure S101. Get High-res Image Gene #37: 'del_3p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p12.3' versus 'CN_CNMF'

P value = 1.17e-06 (Fisher's exact test), Q value = 0.001

Table S102. Gene #38: 'del_3p12.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
DEL PEAK 8(3P12.3) MUTATED	142	150	121
DEL PEAK 8(3P12.3) WILD-TYPE	51	12	14

Figure S102. Get High-res Image Gene #38: 'del_3p12.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p12.3' versus 'METHLYATION_CNMF'

P value = 0.000226 (Fisher's exact test), Q value = 0.18

Table S103. Gene #38: 'del_3p12.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 8(3P12.3) MUTATED	106	106	87
DEL PEAK 8(3P12.3) WILD-TYPE	36	8	13

Figure S103. Get High-res Image Gene #38: 'del_3p12.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p12.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000188 (Fisher's exact test), Q value = 0.15

Table S104. Gene #38: 'del_3p12.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	176	95
DEL PEAK 8(3P12.3) MUTATED	165	157	88
DEL PEAK 8(3P12.3) WILD-TYPE	50	19	7

Figure S104. Get High-res Image Gene #38: 'del_3p12.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p12.3' versus 'MIRSEQ_CNMF'

P value = 0.000259 (Fisher's exact test), Q value = 0.2

Table S105. Gene #38: 'del_3p12.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	130	125	64
DEL PEAK 8(3P12.3) MUTATED	125	115	90	60
DEL PEAK 8(3P12.3) WILD-TYPE	20	15	35	4

Figure S105. Get High-res Image Gene #38: 'del_3p12.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4p15.2' versus 'MRNA_CNMF'

P value = 0.000196 (Fisher's exact test), Q value = 0.15

Table S106. Gene #40: 'del_4p15.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	52	32	28
DEL PEAK 10(4P15.2) MUTATED	31	41	12	13
DEL PEAK 10(4P15.2) WILD-TYPE	11	11	20	15

Figure S106. Get High-res Image Gene #40: 'del_4p15.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4p15.2' versus 'CN_CNMF'

P value = 8.06e-10 (Fisher's exact test), Q value = 7.5e-07

Table S107. Gene #40: 'del_4p15.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
DEL PEAK 10(4P15.2) MUTATED	93	131	83
DEL PEAK 10(4P15.2) WILD-TYPE	100	31	52

Figure S107. Get High-res Image Gene #40: 'del_4p15.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p15.2' versus 'METHLYATION_CNMF'

P value = 1.75e-06 (Fisher's exact test), Q value = 0.0015

Table S108. Gene #40: 'del_4p15.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 10(4P15.2) MUTATED	66	87	69
DEL PEAK 10(4P15.2) WILD-TYPE	76	27	31

Figure S108. Get High-res Image Gene #40: 'del_4p15.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4p15.2' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.16

Table S109. Gene #40: 'del_4p15.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	110	145	153	78
DEL PEAK 10(4P15.2) MUTATED	72	110	82	42
DEL PEAK 10(4P15.2) WILD-TYPE	38	35	71	36

Figure S109. Get High-res Image Gene #40: 'del_4p15.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4p15.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.3e-07 (Fisher's exact test), Q value = 0.00064

Table S110. Gene #40: 'del_4p15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	176	95
DEL PEAK 10(4P15.2) MUTATED	113	137	56
DEL PEAK 10(4P15.2) WILD-TYPE	102	39	39

Figure S110. Get High-res Image Gene #40: 'del_4p15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

P value = 1.68e-07 (Fisher's exact test), Q value = 0.00015

Table S111. Gene #41: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
DEL PEAK 11(4Q22.1) MUTATED	86	119	73
DEL PEAK 11(4Q22.1) WILD-TYPE	107	43	62

Figure S111. Get High-res Image Gene #41: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q22.1' versus 'MRNASEQ_CNMF'

P value = 0.000182 (Fisher's exact test), Q value = 0.14

Table S112. Gene #41: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	110	145	153	78
DEL PEAK 11(4Q22.1) MUTATED	60	102	82	32
DEL PEAK 11(4Q22.1) WILD-TYPE	50	43	71	46

Figure S112. Get High-res Image Gene #41: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q32.3' versus 'CN_CNMF'

P value = 7.37e-11 (Fisher's exact test), Q value = 6.9e-08

Table S113. Gene #42: 'del_4q32.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
DEL PEAK 12(4Q32.3) MUTATED	101	138	83
DEL PEAK 12(4Q32.3) WILD-TYPE	92	24	52

Figure S113. Get High-res Image Gene #42: 'del_4q32.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q32.3' versus 'METHLYATION_CNMF'

P value = 7.96e-05 (Fisher's exact test), Q value = 0.064

Table S114. Gene #42: 'del_4q32.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 12(4Q32.3) MUTATED	74	88	70
DEL PEAK 12(4Q32.3) WILD-TYPE	68	26	30

Figure S114. Get High-res Image Gene #42: 'del_4q32.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q32.3' versus 'MRNASEQ_CNMF'

P value = 7.43e-06 (Fisher's exact test), Q value = 0.0063

Table S115. Gene #42: 'del_4q32.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	110	145	153	78
DEL PEAK 12(4Q32.3) MUTATED	71	117	94	38
DEL PEAK 12(4Q32.3) WILD-TYPE	39	28	59	40

Figure S115. Get High-res Image Gene #42: 'del_4q32.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q32.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000245 (Fisher's exact test), Q value = 0.19

Table S116. Gene #42: 'del_4q32.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	176	95
DEL PEAK 12(4Q32.3) MUTATED	123	135	62
DEL PEAK 12(4Q32.3) WILD-TYPE	92	41	33

Figure S116. Get High-res Image Gene #42: 'del_4q32.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q32.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000124 (Fisher's exact test), Q value = 0.099

Table S117. Gene #42: 'del_4q32.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	178	150
DEL PEAK 12(4Q32.3) MUTATED	99	114
DEL PEAK 12(4Q32.3) WILD-TYPE	79	36

Figure S117. Get High-res Image Gene #42: 'del_4q32.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q35.2' versus 'CN_CNMF'

P value = 1.06e-09 (Fisher's exact test), Q value = 9.8e-07

Table S118. Gene #43: 'del_4q35.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
DEL PEAK 13(4Q35.2) MUTATED	105	137	81
DEL PEAK 13(4Q35.2) WILD-TYPE	88	25	54

Figure S118. Get High-res Image Gene #43: 'del_4q35.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q35.2' versus 'METHLYATION_CNMF'

P value = 3.53e-05 (Fisher's exact test), Q value = 0.029

Table S119. Gene #43: 'del_4q35.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 13(4Q35.2) MUTATED	74	90	67
DEL PEAK 13(4Q35.2) WILD-TYPE	68	24	33

Figure S119. Get High-res Image Gene #43: 'del_4q35.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q35.2' versus 'MRNASEQ_CNMF'

P value = 9.45e-06 (Fisher's exact test), Q value = 0.008

Table S120. Gene #43: 'del_4q35.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	110	145	153	78
DEL PEAK 13(4Q35.2) MUTATED	69	117	97	38
DEL PEAK 13(4Q35.2) WILD-TYPE	41	28	56	40

Figure S120. Get High-res Image Gene #43: 'del_4q35.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q11.2' versus 'CN_CNMF'

P value = 3.64e-13 (Fisher's exact test), Q value = 3.4e-10

Table S121. Gene #44: 'del_5q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
DEL PEAK 14(5Q11.2) MUTATED	106	134	120
DEL PEAK 14(5Q11.2) WILD-TYPE	87	28	15

Figure S121. Get High-res Image Gene #44: 'del_5q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q11.2' versus 'METHLYATION_CNMF'

P value = 1.95e-05 (Fisher's exact test), Q value = 0.016

Table S122. Gene #44: 'del_5q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 14(5Q11.2) MUTATED	84	92	83
DEL PEAK 14(5Q11.2) WILD-TYPE	58	22	17

Figure S122. Get High-res Image Gene #44: 'del_5q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.76e-05 (Fisher's exact test), Q value = 0.023

Table S123. Gene #44: 'del_5q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	163	230
DEL PEAK 14(5Q11.2) MUTATED	55	139	150
DEL PEAK 14(5Q11.2) WILD-TYPE	16	24	80

Figure S123. Get High-res Image Gene #44: 'del_5q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_6p25.3' versus 'CN_CNMF'

P value = 1.33e-05 (Fisher's exact test), Q value = 0.011

Table S124. Gene #45: 'del_6p25.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
DEL PEAK 15(6P25.3) MUTATED	41	64	23
DEL PEAK 15(6P25.3) WILD-TYPE	152	98	112

Figure S124. Get High-res Image Gene #45: 'del_6p25.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_6p25.3' versus 'METHLYATION_CNMF'

P value = 3.24e-05 (Fisher's exact test), Q value = 0.027

Table S125. Gene #45: 'del_6p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 15(6P25.3) MUTATED	25	49	24
DEL PEAK 15(6P25.3) WILD-TYPE	117	65	76

Figure S125. Get High-res Image Gene #45: 'del_6p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6p25.3' versus 'MRNASEQ_CNMF'

P value = 3.39e-07 (Fisher's exact test), Q value = 3e-04

Table S126. Gene #45: 'del_6p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	110	145	153	78
DEL PEAK 15(6P25.3) MUTATED	28	62	22	15
DEL PEAK 15(6P25.3) WILD-TYPE	82	83	131	63

Figure S126. Get High-res Image Gene #45: 'del_6p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6p25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.02e-08 (Fisher's exact test), Q value = 9.4e-06

Table S127. Gene #45: 'del_6p25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	176	95
DEL PEAK 15(6P25.3) MUTATED	41	74	12
DEL PEAK 15(6P25.3) WILD-TYPE	174	102	83

Figure S127. Get High-res Image Gene #45: 'del_6p25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q22.31' versus 'CN_CNMF'

P value = 5.72e-05 (Fisher's exact test), Q value = 0.047

Table S128. Gene #46: 'del_6q22.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
DEL PEAK 16(6Q22.31) MUTATED	33	59	26
DEL PEAK 16(6Q22.31) WILD-TYPE	160	103	109

Figure S128. Get High-res Image Gene #46: 'del_6q22.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q26' versus 'CN_CNMF'

P value = 1.76e-05 (Fisher's exact test), Q value = 0.015

Table S129. Gene #47: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
DEL PEAK 17(6Q26) MUTATED	34	64	32
DEL PEAK 17(6Q26) WILD-TYPE	159	98	103

Figure S129. Get High-res Image Gene #47: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 0.000147 (Fisher's exact test), Q value = 0.12

Table S130. Gene #47: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 17(6Q26) MUTATED	27	48	23
DEL PEAK 17(6Q26) WILD-TYPE	115	66	77

Figure S130. Get High-res Image Gene #47: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_7q36.3' versus 'MRNASEQ_CNMF'

P value = 0.000295 (Fisher's exact test), Q value = 0.23

Table S131. Gene #49: 'del_7q36.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	110	145	153	78
DEL PEAK 19(7Q36.3) MUTATED	26	18	48	11
DEL PEAK 19(7Q36.3) WILD-TYPE	84	127	105	67

Figure S131. Get High-res Image Gene #49: 'del_7q36.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'CN_CNMF'

P value = 3.89e-05 (Fisher's exact test), Q value = 0.032

Table S132. Gene #50: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
DEL PEAK 20(8P23.2) MUTATED	110	118	107
DEL PEAK 20(8P23.2) WILD-TYPE	83	44	28

Figure S132. Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p23' versus 'CN_CNMF'

P value = 3.58e-08 (Fisher's exact test), Q value = 3.3e-05

Table S133. Gene #51: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
DEL PEAK 21(9P23) MUTATED	109	99	115
DEL PEAK 21(9P23) WILD-TYPE	84	63	20

Figure S133. Get High-res Image Gene #51: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 6.46e-05 (Fisher's exact test), Q value = 0.052

Table S134. Gene #51: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	110	145	153	78
DEL PEAK 21(9P23) MUTATED	86	81	111	42
DEL PEAK 21(9P23) WILD-TYPE	24	64	42	36

Figure S134. Get High-res Image Gene #51: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 1.76e-06 (Fisher's exact test), Q value = 0.0015

Table S135. Gene #52: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
DEL PEAK 22(9P21.3) MUTATED	129	127	122
DEL PEAK 22(9P21.3) WILD-TYPE	64	35	13

Figure S135. Get High-res Image Gene #52: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_9q21.11' versus 'MRNA_CNMF'

P value = 0.000244 (Fisher's exact test), Q value = 0.19

Table S136. Gene #53: 'del_9q21.11' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	52	32	28
DEL PEAK 23(9Q21.11) MUTATED	28	13	19	15
DEL PEAK 23(9Q21.11) WILD-TYPE	14	39	13	13

Figure S136. Get High-res Image Gene #53: 'del_9q21.11' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9q21.11' versus 'MRNA_CHIERARCHICAL'

P value = 5.96e-05 (Fisher's exact test), Q value = 0.048

Table S137. Gene #53: 'del_9q21.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	22	56	23	53
DEL PEAK 23(9Q21.11) MUTATED	14	14	17	30
DEL PEAK 23(9Q21.11) WILD-TYPE	8	42	6	23

Figure S137. Get High-res Image Gene #53: 'del_9q21.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9q21.11' versus 'CN_CNMF'

P value = 4.48e-11 (Fisher's exact test), Q value = 4.2e-08

Table S138. Gene #53: 'del_9q21.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
DEL PEAK 23(9Q21.11) MUTATED	101	51	96
DEL PEAK 23(9Q21.11) WILD-TYPE	92	111	39

Figure S138. Get High-res Image Gene #53: 'del_9q21.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_9q21.11' versus 'METHLYATION_CNMF'

P value = 2.74e-09 (Fisher's exact test), Q value = 2.5e-06

Table S139. Gene #53: 'del_9q21.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 23(9Q21.11) MUTATED	84	31	66
DEL PEAK 23(9Q21.11) WILD-TYPE	58	83	34

Figure S139. Get High-res Image Gene #53: 'del_9q21.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9q21.11' versus 'MRNASEQ_CNMF'

P value = 1.1e-14 (Fisher's exact test), Q value = 1e-11

Table S140. Gene #53: 'del_9q21.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	110	145	153	78
DEL PEAK 23(9Q21.11) MUTATED	71	34	101	40
DEL PEAK 23(9Q21.11) WILD-TYPE	39	111	52	38

Figure S140. Get High-res Image Gene #53: 'del_9q21.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9q21.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.02e-17 (Fisher's exact test), Q value = 9.8e-15

Table S141. Gene #53: 'del_9q21.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	176	95
DEL PEAK 23(9Q21.11) MUTATED	139	43	64
DEL PEAK 23(9Q21.11) WILD-TYPE	76	133	31

Figure S141. Get High-res Image Gene #53: 'del_9q21.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_CNMF'

P value = 4.01e-05 (Fisher's exact test), Q value = 0.033

Table S142. Gene #53: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	130	125	64
DEL PEAK 23(9Q21.11) MUTATED	63	80	72	19
DEL PEAK 23(9Q21.11) WILD-TYPE	82	50	53	45

Figure S142. Get High-res Image Gene #53: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9q21.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.57e-08 (Fisher's exact test), Q value = 6e-05

Table S143. Gene #53: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	163	230
DEL PEAK 23(9Q21.11) MUTATED	18	106	110
DEL PEAK 23(9Q21.11) WILD-TYPE	53	57	120

Figure S143. Get High-res Image Gene #53: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

P value = 8.47e-08 (Fisher's exact test), Q value = 7.7e-05

Table S144. Gene #54: 'del_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
DEL PEAK 24(10P15.3) MUTATED	61	100	61
DEL PEAK 24(10P15.3) WILD-TYPE	132	62	74

Figure S144. Get High-res Image Gene #54: 'del_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 1.59e-10 (Fisher's exact test), Q value = 1.5e-07

Table S145. Gene #54: 'del_10p15.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 24(10P15.3) MUTATED	45	82	39
DEL PEAK 24(10P15.3) WILD-TYPE	97	32	61

Figure S145. Get High-res Image Gene #54: 'del_10p15.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10p15.3' versus 'MRNASEQ_CNMF'

P value = 4.08e-06 (Fisher's exact test), Q value = 0.0035

Table S146. Gene #54: 'del_10p15.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	110	145	153	78
DEL PEAK 24(10P15.3) MUTATED	38	91	66	26
DEL PEAK 24(10P15.3) WILD-TYPE	72	54	87	52

Figure S146. Get High-res Image Gene #54: 'del_10p15.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.16e-05 (Fisher's exact test), Q value = 0.0098

Table S147. Gene #54: 'del_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	176	95
DEL PEAK 24(10P15.3) MUTATED	78	105	38
DEL PEAK 24(10P15.3) WILD-TYPE	137	71	57

Figure S147. Get High-res Image Gene #54: 'del_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_CNMF'

P value = 8.19e-07 (Fisher's exact test), Q value = 0.00072

Table S148. Gene #54: 'del_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	130	125	64
DEL PEAK 24(10P15.3) MUTATED	68	69	35	43
DEL PEAK 24(10P15.3) WILD-TYPE	77	61	90	21

Figure S148. Get High-res Image Gene #54: 'del_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10p15.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.51e-06 (Fisher's exact test), Q value = 0.0047

Table S149. Gene #54: 'del_10p15.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	163	230
DEL PEAK 24(10P15.3) MUTATED	51	75	89
DEL PEAK 24(10P15.3) WILD-TYPE	20	88	141

Figure S149. Get High-res Image Gene #54: 'del_10p15.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10p15.1' versus 'CN_CNMF'

P value = 3.62e-06 (Fisher's exact test), Q value = 0.0031

Table S150. Gene #55: 'del_10p15.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
DEL PEAK 25(10P15.1) MUTATED	60	93	57
DEL PEAK 25(10P15.1) WILD-TYPE	133	69	78

Figure S150. Get High-res Image Gene #55: 'del_10p15.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_10p15.1' versus 'METHLYATION_CNMF'

P value = 4.48e-11 (Fisher's exact test), Q value = 4.2e-08

Table S151. Gene #55: 'del_10p15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 25(10P15.1) MUTATED	44	80	32
DEL PEAK 25(10P15.1) WILD-TYPE	98	34	68

Figure S151. Get High-res Image Gene #55: 'del_10p15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10p15.1' versus 'MRNASEQ_CNMF'

P value = 2.22e-07 (Fisher's exact test), Q value = 2e-04

Table S152. Gene #55: 'del_10p15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	110	145	153	78
DEL PEAK 25(10P15.1) MUTATED	36	90	61	22
DEL PEAK 25(10P15.1) WILD-TYPE	74	55	92	56

Figure S152. Get High-res Image Gene #55: 'del_10p15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10p15.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.84e-05 (Fisher's exact test), Q value = 0.015

Table S153. Gene #55: 'del_10p15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	176	95
DEL PEAK 25(10P15.1) MUTATED	73	100	36
DEL PEAK 25(10P15.1) WILD-TYPE	142	76	59

Figure S153. Get High-res Image Gene #55: 'del_10p15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.1' versus 'MIRSEQ_CNMF'

P value = 1.39e-07 (Fisher's exact test), Q value = 0.00012

Table S154. Gene #55: 'del_10p15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	130	125	64
DEL PEAK 25(10P15.1) MUTATED	66	63	31	43
DEL PEAK 25(10P15.1) WILD-TYPE	79	67	94	21

Figure S154. Get High-res Image Gene #55: 'del_10p15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10p15.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.1e-06 (Fisher's exact test), Q value = 0.00096

Table S155. Gene #55: 'del_10p15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	163	230
DEL PEAK 25(10P15.1) MUTATED	50	72	81
DEL PEAK 25(10P15.1) WILD-TYPE	21	91	149

Figure S155. Get High-res Image Gene #55: 'del_10p15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1.86e-08 (Fisher's exact test), Q value = 1.7e-05

Table S156. Gene #56: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
DEL PEAK 26(10Q23.31) MUTATED	77	115	67
DEL PEAK 26(10Q23.31) WILD-TYPE	116	47	68

Figure S156. Get High-res Image Gene #56: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 1.83e-08 (Fisher's exact test), Q value = 1.7e-05

Table S157. Gene #56: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 26(10Q23.31) MUTATED	52	84	53
DEL PEAK 26(10Q23.31) WILD-TYPE	90	30	47

Figure S157. Get High-res Image Gene #56: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 3.79e-09 (Fisher's exact test), Q value = 3.5e-06

Table S158. Gene #56: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	110	145	153	78
DEL PEAK 26(10Q23.31) MUTATED	46	109	69	34
DEL PEAK 26(10Q23.31) WILD-TYPE	64	36	84	44

Figure S158. Get High-res Image Gene #56: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.25e-10 (Fisher's exact test), Q value = 2.1e-07

Table S159. Gene #56: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	176	95
DEL PEAK 26(10Q23.31) MUTATED	82	126	50
DEL PEAK 26(10Q23.31) WILD-TYPE	133	50	45

Figure S159. Get High-res Image Gene #56: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 0.000305 (Fisher's exact test), Q value = 0.23

Table S160. Gene #56: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	130	125	64
DEL PEAK 26(10Q23.31) MUTATED	68	79	53	45
DEL PEAK 26(10Q23.31) WILD-TYPE	77	51	72	19

Figure S160. Get High-res Image Gene #56: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.85e-05 (Fisher's exact test), Q value = 0.048

Table S161. Gene #56: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	163	230
DEL PEAK 26(10Q23.31) MUTATED	52	91	102
DEL PEAK 26(10Q23.31) WILD-TYPE	19	72	128

Figure S161. Get High-res Image Gene #56: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.54e-06 (Fisher's exact test), Q value = 0.0022

Table S162. Gene #56: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	112	91
DEL PEAK 26(10Q23.31) MUTATED	88	46	39
DEL PEAK 26(10Q23.31) WILD-TYPE	37	66	52

Figure S162. Get High-res Image Gene #56: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11p15.5' versus 'CN_CNMF'

P value = 6.14e-08 (Fisher's exact test), Q value = 5.6e-05

Table S163. Gene #57: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
DEL PEAK 27(11P15.5) MUTATED	67	82	90
DEL PEAK 27(11P15.5) WILD-TYPE	126	80	45

Figure S163. Get High-res Image Gene #57: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

'del_11p15.5' versus 'RPPA_CHIERARCHICAL'

P value = 1.48e-06 (Fisher's exact test), Q value = 0.0013

Table S164. Gene #57: 'del_11p15.5' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	47	49	40
DEL PEAK 27(11P15.5) MUTATED	30	17	39	11
DEL PEAK 27(11P15.5) WILD-TYPE	28	30	10	29

Figure S164. Get High-res Image Gene #57: 'del_11p15.5' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_11q22.1' versus 'CN_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.17

Table S165. Gene #58: 'del_11q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
DEL PEAK 28(11Q22.1) MUTATED	42	66	50
DEL PEAK 28(11Q22.1) WILD-TYPE	151	96	85

Figure S165. Get High-res Image Gene #58: 'del_11q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q11.2' versus 'MRNASEQ_CNMF'

P value = 1.58e-05 (Fisher's exact test), Q value = 0.013

Table S166. Gene #63: 'del_14q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	110	145	153	78
DEL PEAK 33(14Q11.2) MUTATED	23	54	73	19
DEL PEAK 33(14Q11.2) WILD-TYPE	87	91	80	59

Figure S166. Get High-res Image Gene #63: 'del_14q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.93e-07 (Fisher's exact test), Q value = 0.00035

Table S167. Gene #63: 'del_14q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	176	95
DEL PEAK 33(14Q11.2) MUTATED	53	62	54
DEL PEAK 33(14Q11.2) WILD-TYPE	162	114	41

Figure S167. Get High-res Image Gene #63: 'del_14q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17q11.2' versus 'MRNA_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.1

Table S168. Gene #68: 'del_17q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	52	32	28
DEL PEAK 38(17Q11.2) MUTATED	21	5	11	6
DEL PEAK 38(17Q11.2) WILD-TYPE	21	47	21	22

Figure S168. Get High-res Image Gene #68: 'del_17q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17q11.2' versus 'CN_CNMF'

P value = 1.01e-06 (Fisher's exact test), Q value = 0.00089

Table S169. Gene #68: 'del_17q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
DEL PEAK 38(17Q11.2) MUTATED	58	20	50
DEL PEAK 38(17Q11.2) WILD-TYPE	135	142	85

Figure S169. Get High-res Image Gene #68: 'del_17q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_17q11.2' versus 'METHLYATION_CNMF'

P value = 1.03e-05 (Fisher's exact test), Q value = 0.0087

Table S170. Gene #68: 'del_17q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 38(17Q11.2) MUTATED	47	11	30
DEL PEAK 38(17Q11.2) WILD-TYPE	95	103	70

Figure S170. Get High-res Image Gene #68: 'del_17q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17q11.2' versus 'MRNASEQ_CNMF'

P value = 9.63e-09 (Fisher's exact test), Q value = 8.9e-06

Table S171. Gene #68: 'del_17q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	110	145	153	78
DEL PEAK 38(17Q11.2) MUTATED	41	12	49	25
DEL PEAK 38(17Q11.2) WILD-TYPE	69	133	104	53

Figure S171. Get High-res Image Gene #68: 'del_17q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.61e-11 (Fisher's exact test), Q value = 1.5e-08

Table S172. Gene #68: 'del_17q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	176	95
DEL PEAK 38(17Q11.2) MUTATED	84	16	27
DEL PEAK 38(17Q11.2) WILD-TYPE	131	160	68

Figure S172. Get High-res Image Gene #68: 'del_17q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17q25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000264 (Fisher's exact test), Q value = 0.2

Table S173. Gene #69: 'del_17q25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	176	95
DEL PEAK 39(17Q25.3) MUTATED	61	21	18
DEL PEAK 39(17Q25.3) WILD-TYPE	154	155	77

Figure S173. Get High-res Image Gene #69: 'del_17q25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 0.000103 (Fisher's exact test), Q value = 0.083

Table S174. Gene #71: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
DEL PEAK 41(19P13.3) MUTATED	71	76	82
DEL PEAK 41(19P13.3) WILD-TYPE	122	86	53

Figure S174. Get High-res Image Gene #71: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_19q13.32' versus 'CN_CNMF'

P value = 5.89e-08 (Fisher's exact test), Q value = 5.3e-05

Table S175. Gene #72: 'del_19q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
DEL PEAK 42(19Q13.32) MUTATED	32	72	39
DEL PEAK 42(19Q13.32) WILD-TYPE	161	90	96

Figure S175. Get High-res Image Gene #72: 'del_19q13.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_19q13.32' versus 'METHLYATION_CNMF'

P value = 1.23e-05 (Fisher's exact test), Q value = 0.01

Table S176. Gene #72: 'del_19q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 42(19Q13.32) MUTATED	21	43	37
DEL PEAK 42(19Q13.32) WILD-TYPE	121	71	63

Figure S176. Get High-res Image Gene #72: 'del_19q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_21q11.2' versus 'CN_CNMF'

P value = 4.86e-05 (Fisher's exact test), Q value = 0.04

Table S177. Gene #73: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
DEL PEAK 43(21Q11.2) MUTATED	71	91	79
DEL PEAK 43(21Q11.2) WILD-TYPE	122	71	56

Figure S177. Get High-res Image Gene #73: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_21q11.2' versus 'MIRSEQ_CNMF'

P value = 9.17e-05 (Fisher's exact test), Q value = 0.074

Table S178. Gene #73: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	130	125	64
DEL PEAK 43(21Q11.2) MUTATED	77	82	46	25
DEL PEAK 43(21Q11.2) WILD-TYPE	68	48	79	39

Figure S178. Get High-res Image Gene #73: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_21q22.3' versus 'CN_CNMF'

P value = 1.84e-07 (Fisher's exact test), Q value = 0.00016

Table S179. Gene #74: 'del_21q22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
DEL PEAK 44(21Q22.3) MUTATED	79	110	87
DEL PEAK 44(21Q22.3) WILD-TYPE	114	52	48

Figure S179. Get High-res Image Gene #74: 'del_21q22.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_21q22.3' versus 'MIRSEQ_CNMF'

P value = 0.000159 (Fisher's exact test), Q value = 0.13

Table S180. Gene #74: 'del_21q22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	130	125	64
DEL PEAK 44(21Q22.3) MUTATED	95	84	52	33
DEL PEAK 44(21Q22.3) WILD-TYPE	50	46	73	31

Figure S180. Get High-res Image Gene #74: 'del_21q22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_22q13.32' versus 'MRNA_CNMF'

P value = 0.000248 (Fisher's exact test), Q value = 0.19

Table S181. Gene #76: 'del_22q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	52	32	28
DEL PEAK 46(22Q13.32) MUTATED	8	8	8	17
DEL PEAK 46(22Q13.32) WILD-TYPE	34	44	24	11

Figure S181. Get High-res Image Gene #76: 'del_22q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 0.000191 (Fisher's exact test), Q value = 0.15

Table S182. Gene #76: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	110	145	153	78
DEL PEAK 46(22Q13.32) MUTATED	29	22	57	17
DEL PEAK 46(22Q13.32) WILD-TYPE	81	123	96	61

Figure S182. Get High-res Image Gene #76: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.42e-05 (Fisher's exact test), Q value = 0.028

Table S183. Gene #76: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	176	95
DEL PEAK 46(22Q13.32) MUTATED	63	26	36
DEL PEAK 46(22Q13.32) WILD-TYPE	152	150	59

Figure S183. Get High-res Image Gene #76: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_xp22.2' versus 'CN_CNMF'

P value = 5.98e-05 (Fisher's exact test), Q value = 0.048

Table S184. Gene #77: 'del_xp22.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
DEL PEAK 47(XP22.2) MUTATED	38	64	49
DEL PEAK 47(XP22.2) WILD-TYPE	155	98	86

Figure S184. Get High-res Image Gene #77: 'del_xp22.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_xp22.2' versus 'METHLYATION_CNMF'

P value = 0.000154 (Fisher's exact test), Q value = 0.12

Table S185. Gene #77: 'del_xp22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 47(XP22.2) MUTATED	26	44	39
DEL PEAK 47(XP22.2) WILD-TYPE	116	70	61

Figure S185. Get High-res Image Gene #77: 'del_xp22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_xp22.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.41e-07 (Fisher's exact test), Q value = 0.00039

Table S186. Gene #77: 'del_xp22.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	178	150
DEL PEAK 47(XP22.2) MUTATED	35	69
DEL PEAK 47(XP22.2) WILD-TYPE	143	81

Figure S186. Get High-res Image Gene #77: 'del_xp22.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp21.1' versus 'CN_CNMF'

P value = 1.16e-06 (Fisher's exact test), Q value = 0.001

Table S187. Gene #78: 'del_xp21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
DEL PEAK 48(XP21.1) MUTATED	34	68	47
DEL PEAK 48(XP21.1) WILD-TYPE	159	94	88

Figure S187. Get High-res Image Gene #78: 'del_xp21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_xp21.1' versus 'METHLYATION_CNMF'

P value = 8.77e-07 (Fisher's exact test), Q value = 0.00077

Table S188. Gene #78: 'del_xp21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 48(XP21.1) MUTATED	21	47	39
DEL PEAK 48(XP21.1) WILD-TYPE	121	67	61

Figure S188. Get High-res Image Gene #78: 'del_xp21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_xp21.1' versus 'MIRSEQ_CNMF'

P value = 2.44e-05 (Fisher's exact test), Q value = 0.02

Table S189. Gene #78: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	130	125	64
DEL PEAK 48(XP21.1) MUTATED	44	52	20	28
DEL PEAK 48(XP21.1) WILD-TYPE	101	78	105	36

Figure S189. Get High-res Image Gene #78: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_xp21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.21

Table S190. Gene #78: 'del_xp21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	112	91
DEL PEAK 48(XP21.1) MUTATED	55	24	22
DEL PEAK 48(XP21.1) WILD-TYPE	70	88	69

Figure S190. Get High-res Image Gene #78: 'del_xp21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_xp21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.64e-10 (Fisher's exact test), Q value = 5.3e-07

Table S191. Gene #78: 'del_xp21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	178	150
DEL PEAK 48(XP21.1) MUTATED	29	72
DEL PEAK 48(XP21.1) WILD-TYPE	149	78

Figure S191. Get High-res Image Gene #78: 'del_xp21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp11.3' versus 'CN_CNMF'

P value = 3.79e-07 (Fisher's exact test), Q value = 0.00034

Table S192. Gene #79: 'del_xp11.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
DEL PEAK 49(XP11.3) MUTATED	33	70	42
DEL PEAK 49(XP11.3) WILD-TYPE	160	92	93

Figure S192. Get High-res Image Gene #79: 'del_xp11.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_xp11.3' versus 'METHLYATION_CNMF'

P value = 6e-07 (Fisher's exact test), Q value = 0.00053

Table S193. Gene #79: 'del_xp11.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 49(XP11.3) MUTATED	20	48	36
DEL PEAK 49(XP11.3) WILD-TYPE	122	66	64

Figure S193. Get High-res Image Gene #79: 'del_xp11.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_xp11.3' versus 'MIRSEQ_CNMF'

P value = 4.96e-06 (Fisher's exact test), Q value = 0.0042

Table S194. Gene #79: 'del_xp11.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	130	125	64
DEL PEAK 49(XP11.3) MUTATED	40	50	19	30
DEL PEAK 49(XP11.3) WILD-TYPE	105	80	106	34

Figure S194. Get High-res Image Gene #79: 'del_xp11.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_xp11.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.48e-05 (Fisher's exact test), Q value = 0.045

Table S195. Gene #79: 'del_xp11.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	112	91
DEL PEAK 49(XP11.3) MUTATED	55	23	19
DEL PEAK 49(XP11.3) WILD-TYPE	70	89	72

Figure S195. Get High-res Image Gene #79: 'del_xp11.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_xp11.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.09e-09 (Fisher's exact test), Q value = 2.9e-06

Table S196. Gene #79: 'del_xp11.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	178	150
DEL PEAK 49(XP11.3) MUTATED	28	69
DEL PEAK 49(XP11.3) WILD-TYPE	150	81

Figure S196. Get High-res Image Gene #79: 'del_xp11.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xq22.3' versus 'CN_CNMF'

P value = 1.76e-05 (Fisher's exact test), Q value = 0.015

Table S197. Gene #80: 'del_xq22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	193	162	135
DEL PEAK 50(XQ22.3) MUTATED	26	36	48
DEL PEAK 50(XQ22.3) WILD-TYPE	167	126	87

Figure S197. Get High-res Image Gene #80: 'del_xq22.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_xq22.3' versus 'METHLYATION_CNMF'

P value = 9.3e-07 (Fisher's exact test), Q value = 0.00082

Table S198. Gene #80: 'del_xq22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	100
DEL PEAK 50(XQ22.3) MUTATED	13	25	37
DEL PEAK 50(XQ22.3) WILD-TYPE	129	89	63

Figure S198. Get High-res Image Gene #80: 'del_xq22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_xq22.3' versus 'MIRSEQ_CNMF'

P value = 5.45e-05 (Fisher's exact test), Q value = 0.044

Table S199. Gene #80: 'del_xq22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	130	125	64
DEL PEAK 50(XQ22.3) MUTATED	37	43	12	14
DEL PEAK 50(XQ22.3) WILD-TYPE	108	87	113	50

Figure S199. Get High-res Image Gene #80: 'del_xq22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = LUSC-TP.transferedmergedcluster.txt
Number of patients = 490
Number of significantly focal cnvs = 80
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

Q value calculation

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

Download Results

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

References

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

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

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