Correlation between copy number variation genes and molecular subtypes

Head and Neck Squamous Cell Carcinoma (Primary solid tumor)

23 May 2013 | analyses__2013_05_23

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 (2013): Correlation between copy number variation genes and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1H70CVW

Overview

Introduction

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

Summary

Testing the association between copy number variation of 71 peak regions and 10 molecular subtypes across 368 patients, 104 significant findings detected with Q value < 0.25.

Amp Peak 1(1q21.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 2(2q11.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 3(2q31.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 4(3q26.33) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 5(5p15.33) cnvs correlated to 'CN_CNMF'.
Amp Peak 6(6p12.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 7(6q12) cnvs correlated to 'CN_CNMF'.
Amp Peak 8(7p11.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 9(7q21.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 11(8q11.21) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 12(8q24.21) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 13(9p23) cnvs correlated to 'CN_CNMF'.
Amp Peak 14(9p13.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 16(11q13.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 17(12p13.33) cnvs correlated to 'CN_CNMF'.
Amp Peak 19(13q22.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 20(15q26.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 21(17q12) cnvs correlated to 'CN_CNMF'.
Amp Peak 22(18p11.31) cnvs correlated to 'CN_CNMF'.
Amp Peak 23(18q11.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 24(20q11.22) cnvs correlated to 'CN_CNMF'.
Del Peak 1(1p36.13) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 2(1p13.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 4(2q21.2) cnvs correlated to 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 6(2q36.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 7(3p25.3) cnvs correlated to 'CN_CNMF'.
Del Peak 8(3p14.2) cnvs correlated to 'CN_CNMF'.
Del Peak 9(3p14.2) cnvs correlated to 'CN_CNMF'.
Del Peak 10(3p12.2) cnvs correlated to 'CN_CNMF'.
Del Peak 11(4p15.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 12(4q22.1) cnvs correlated to 'CN_CNMF'.
Del Peak 13(4q35.2) cnvs correlated to 'CN_CNMF'.
Del Peak 14(5q11.2) cnvs correlated to 'CN_CNMF'.
Del Peak 15(5q15) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 16(5q35.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 21(8p23.2) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 22(9p23) cnvs correlated to 'CN_CNMF'.
Del Peak 23(9p21.3) cnvs correlated to 'CN_CNMF'.
Del Peak 24(9q21.11) cnvs correlated to 'CN_CNMF'.
Del Peak 28(10q23.31) cnvs correlated to 'METHLYATION_CNMF'.
Del Peak 29(11p15.4) cnvs correlated to 'CN_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 30(11q14.2) cnvs correlated to 'CN_CNMF'.
Del Peak 31(11q23.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 33(13q12.11) cnvs correlated to 'CN_CNMF'.
Del Peak 34(13q14.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 36(14q32.32) cnvs correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 37(15q15.1) cnvs correlated to 'CN_CNMF'.
Del Peak 38(16q12.1) cnvs correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 39(16q23.3) cnvs correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 41(18q21.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 42(18q23) cnvs correlated to 'CN_CNMF'.
Del Peak 43(19p13.3) cnvs correlated to 'CN_CNMF'.
Del Peak 44(19q13.43) cnvs correlated to 'CN_CNMF'.
Del Peak 45(Xp21.3) cnvs correlated to 'CN_CNMF'.
Del Peak 46(Xp11.3) cnvs correlated to 'CN_CNMF'.
Del Peak 47(Xq21.33) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 71 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 104 significant findings detected.


		Molecular subtypes	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Chi-square test	Fisher's exact test	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 Peak 38(16q12 1)	0 (0%)	305	0.0522 (1.00)	4.05e-09 (2.75e-06)	0.746 (1.00)	0.0896 (1.00)	7.1e-08 (4.79e-05)	3.91e-07 (0.000263)	0.000157 (0.0983)	0.013 (1.00)	8.88e-06 (0.00583)	3.44e-05 (0.0221)
Amp Peak 1(1q21 2)	0 (0%)	283	1.19e-09 (8.15e-07)	2.12e-05 (0.0138)	0.473 (1.00)	0.718 (1.00)	0.000509 (0.307)	0.00316 (1.00)	0.00035 (0.214)	0.57 (1.00)	3.36e-05 (0.0217)	0.000316 (0.194)
Del Peak 34(13q14 2)	0 (0%)	210	8.8e-07 (0.000587)	0.000281 (0.174)	0.151 (1.00)	0.275 (1.00)	5.7e-05 (0.0364)	6.46e-05 (0.0412)	0.021 (1.00)	0.673 (1.00)	5.29e-05 (0.0339)	0.0181 (1.00)
Amp Peak 4(3q26 33)	0 (0%)	92	1.01e-16 (7.04e-14)	4.75e-05 (0.0305)	0.244 (1.00)	0.193 (1.00)	0.00128 (0.748)	0.000468 (0.283)	0.00152 (0.875)	0.0706 (1.00)	9.01e-05 (0.057)	6.81e-06 (0.00448)
Amp Peak 12(8q24 21)	0 (0%)	101	5.27e-09 (3.58e-06)	2.54e-05 (0.0165)	0.19 (1.00)	0.917 (1.00)	0.000102 (0.0645)	0.000135 (0.0851)	0.0313 (1.00)	0.000509 (0.307)	0.0435 (1.00)	0.00403 (1.00)
Del Peak 1(1p36 13)	0 (0%)	297	1.15e-13 (7.96e-11)	2.28e-07 (0.000154)	0.0225 (1.00)	0.739 (1.00)	3.03e-05 (0.0196)	0.000716 (0.427)	0.00468 (1.00)	0.103 (1.00)	2.14e-05 (0.0139)	0.00496 (1.00)
Del Peak 2(1p13 2)	0 (0%)	281	3.38e-11 (2.33e-08)	0.000147 (0.0921)	0.0124 (1.00)	0.118 (1.00)	0.00546 (1.00)	0.0927 (1.00)	0.000105 (0.066)	0.967 (1.00)	1.53e-05 (0.01)	0.00513 (1.00)
Del Peak 15(5q15)	0 (0%)	216	5.86e-16 (4.09e-13)	4.73e-05 (0.0304)	0.0337 (1.00)	0.598 (1.00)	0.0676 (1.00)	0.000402 (0.245)	0.119 (1.00)	0.441 (1.00)	0.000403 (0.245)	0.116 (1.00)
Del Peak 36(14q32 32)	0 (0%)	314	0.0418 (1.00)	6.74e-08 (4.55e-05)	0.0984 (1.00)	0.413 (1.00)	0.000242 (0.15)	9.8e-05 (0.0619)	0.00574 (1.00)	0.0785 (1.00)	0.000656 (0.393)	2.32e-06 (0.00154)
Del Peak 47(Xq21 33)	0 (0%)	309	7.56e-07 (0.000506)	0.000338 (0.207)	0.0255 (1.00)	0.444 (1.00)	0.00131 (0.763)	0.0123 (1.00)	2.36e-05 (0.0153)	0.00563 (1.00)	0.000164 (0.102)	0.00044 (0.267)
Del Peak 4(2q21 2)	0 (0%)	322	0.511 (1.00)	0.745 (1.00)	0.91 (1.00)	1 (1.00)	0.0154 (1.00)	0.00564 (1.00)	0.000297 (0.183)	0.29 (1.00)	0.000268 (0.166)	0.000159 (0.0992)
Del Peak 11(4p15 2)	0 (0%)	214	3.81e-13 (2.64e-10)	1.94e-05 (0.0127)	0.0483 (1.00)	0.13 (1.00)	0.0406 (1.00)	0.0129 (1.00)	0.0253 (1.00)	0.789 (1.00)	0.00039 (0.238)	0.0356 (1.00)
Del Peak 29(11p15 4)	0 (0%)	253	4.83e-11 (3.33e-08)	0.00668 (1.00)	0.471 (1.00)	0.458 (1.00)	0.00228 (1.00)	0.0071 (1.00)	0.00211 (1.00)	0.35 (1.00)	3.05e-09 (2.08e-06)	0.000321 (0.197)
Del Peak 31(11q23 1)	0 (0%)	193	1.28e-20 (8.98e-18)	3.94e-06 (0.0026)	0.169 (1.00)	0.254 (1.00)	0.000815 (0.483)	0.00023 (0.143)	0.175 (1.00)	0.277 (1.00)	0.00148 (0.859)	0.139 (1.00)
Amp Peak 11(8q11 21)	0 (0%)	148	1.93e-06 (0.00128)	0.000199 (0.123)	0.0323 (1.00)	0.518 (1.00)	0.00113 (0.664)	0.000664 (0.397)	0.00954 (1.00)	0.00141 (0.821)	0.0111 (1.00)	0.00172 (0.985)
Del Peak 6(2q36 2)	0 (0%)	261	1.28e-08 (8.66e-06)	7.6e-05 (0.0484)	0.114 (1.00)	0.531 (1.00)	0.000636 (0.382)	0.00125 (0.734)	0.00385 (1.00)	0.165 (1.00)	0.00334 (1.00)	0.0523 (1.00)
Del Peak 16(5q35 3)	0 (0%)	227	2.14e-14 (1.49e-11)	2.58e-06 (0.0017)	0.419 (1.00)	0.0645 (1.00)	0.0146 (1.00)	0.000477 (0.288)	0.223 (1.00)	0.657 (1.00)	0.00732 (1.00)	0.193 (1.00)
Del Peak 21(8p23 2)	0 (0%)	161	3.72e-16 (2.6e-13)	0.000934 (0.553)	0.134 (1.00)	0.188 (1.00)	0.0166 (1.00)	0.00353 (1.00)	0.234 (1.00)	0.025 (1.00)	0.0343 (1.00)	0.000335 (0.205)
Del Peak 39(16q23 3)	0 (0%)	295	0.0223 (1.00)	1.86e-05 (0.0122)	0.504 (1.00)	0.0196 (1.00)	0.000601 (0.361)	8.88e-05 (0.0563)	0.00687 (1.00)	0.142 (1.00)	0.00115 (0.675)	0.00171 (0.979)
Del Peak 41(18q21 2)	0 (0%)	177	3.89e-20 (2.73e-17)	0.00016 (0.0999)	0.603 (1.00)	0.642 (1.00)	0.00268 (1.00)	0.0073 (1.00)	0.00343 (1.00)	0.0033 (1.00)	0.0932 (1.00)	0.216 (1.00)
Amp Peak 2(2q11 2)	0 (0%)	292	1.01e-09 (6.91e-07)	0.00319 (1.00)	0.991 (1.00)	0.295 (1.00)	0.0119 (1.00)	0.0807 (1.00)	0.00184 (1.00)	0.168 (1.00)	0.00542 (1.00)	0.0377 (1.00)
Amp Peak 3(2q31 2)	0 (0%)	292	2.38e-12 (1.65e-09)	0.00152 (0.875)	0.814 (1.00)	0.498 (1.00)	0.308 (1.00)	0.134 (1.00)	0.212 (1.00)	0.274 (1.00)	0.0177 (1.00)	0.00832 (1.00)
Amp Peak 5(5p15 33)	0 (0%)	202	1.41e-09 (9.59e-07)	0.158 (1.00)	0.624 (1.00)	0.282 (1.00)	0.683 (1.00)	0.32 (1.00)	0.682 (1.00)	0.337 (1.00)	0.653 (1.00)	0.469 (1.00)
Amp Peak 6(6p12 1)	0 (0%)	295	1.87e-05 (0.0122)	0.328 (1.00)	0.303 (1.00)	0.47 (1.00)	0.983 (1.00)	0.802 (1.00)	1 (1.00)	0.0781 (1.00)	0.834 (1.00)	0.246 (1.00)
Amp Peak 7(6q12)	0 (0%)	301	7.89e-05 (0.0501)	0.396 (1.00)	0.811 (1.00)	0.373 (1.00)	1 (1.00)	0.822 (1.00)	0.795 (1.00)	0.27 (1.00)	1 (1.00)	0.985 (1.00)
Amp Peak 8(7p11 2)	0 (0%)	214	9.14e-07 (0.000609)	0.0109 (1.00)	0.26 (1.00)	0.832 (1.00)	0.5 (1.00)	0.923 (1.00)	0.99 (1.00)	0.282 (1.00)	0.485 (1.00)	0.862 (1.00)
Amp Peak 9(7q21 3)	0 (0%)	244	3.49e-15 (2.44e-12)	0.115 (1.00)	0.238 (1.00)	0.468 (1.00)	0.154 (1.00)	0.128 (1.00)	0.0472 (1.00)	0.0724 (1.00)	0.0738 (1.00)	0.264 (1.00)
Amp Peak 13(9p23)	0 (0%)	281	6.75e-06 (0.00445)	0.406 (1.00)	0.655 (1.00)	0.888 (1.00)	0.0993 (1.00)	0.227 (1.00)	0.402 (1.00)	1 (1.00)	0.0311 (1.00)	0.0242 (1.00)
Amp Peak 14(9p13 3)	0 (0%)	266	0.000371 (0.226)	0.356 (1.00)	0.39 (1.00)	0.254 (1.00)	0.00708 (1.00)	0.0379 (1.00)	0.0126 (1.00)	0.0497 (1.00)	0.0281 (1.00)	0.0328 (1.00)
Amp Peak 16(11q13 3)	0 (0%)	198	3.83e-30 (2.71e-27)	0.0812 (1.00)	0.901 (1.00)	0.284 (1.00)	0.361 (1.00)	0.504 (1.00)	0.781 (1.00)	0.17 (1.00)	0.919 (1.00)	0.495 (1.00)
Amp Peak 17(12p13 33)	0 (0%)	243	1.99e-12 (1.38e-09)	0.00308 (1.00)	0.276 (1.00)	0.352 (1.00)	0.00912 (1.00)	0.00101 (0.596)	0.00302 (1.00)	0.864 (1.00)	0.00251 (1.00)	0.0105 (1.00)
Amp Peak 19(13q22 1)	0 (0%)	291	1.18e-06 (0.000783)	0.186 (1.00)	0.0181 (1.00)	0.205 (1.00)	0.233 (1.00)	0.0924 (1.00)	0.138 (1.00)	0.132 (1.00)	0.821 (1.00)	0.381 (1.00)
Amp Peak 20(15q26 3)	0 (0%)	292	5.54e-05 (0.0355)	0.438 (1.00)	0.263 (1.00)	0.624 (1.00)	0.923 (1.00)	0.416 (1.00)	0.88 (1.00)	0.242 (1.00)	0.264 (1.00)	0.0521 (1.00)
Amp Peak 21(17q12)	0 (0%)	302	8.18e-07 (0.000546)	0.031 (1.00)	0.623 (1.00)	0.73 (1.00)	0.0168 (1.00)	0.0308 (1.00)	0.0196 (1.00)	0.448 (1.00)	0.0285 (1.00)	0.0128 (1.00)
Amp Peak 22(18p11 31)	0 (0%)	257	7.52e-07 (0.000504)	0.000945 (0.558)	0.962 (1.00)	0.766 (1.00)	0.262 (1.00)	0.206 (1.00)	0.579 (1.00)	0.741 (1.00)	0.0202 (1.00)	0.0374 (1.00)
Amp Peak 23(18q11 2)	0 (0%)	289	7.62e-05 (0.0484)	0.0304 (1.00)	0.157 (1.00)	0.462 (1.00)	1 (1.00)	0.689 (1.00)	0.191 (1.00)	0.489 (1.00)	0.00157 (0.9)	0.0316 (1.00)
Amp Peak 24(20q11 22)	0 (0%)	206	5.45e-07 (0.000365)	0.0804 (1.00)	0.845 (1.00)	0.442 (1.00)	0.0128 (1.00)	0.0854 (1.00)	0.298 (1.00)	0.009 (1.00)	0.339 (1.00)	0.0304 (1.00)
Del Peak 7(3p25 3)	0 (0%)	111	7.39e-27 (5.21e-24)	0.00975 (1.00)	0.213 (1.00)	0.39 (1.00)	0.0134 (1.00)	0.0632 (1.00)	0.176 (1.00)	0.00314 (1.00)	0.0281 (1.00)	0.258 (1.00)
Del Peak 8(3p14 2)	0 (0%)	96	1.1e-39 (7.84e-37)	0.00151 (0.875)	0.259 (1.00)	0.5 (1.00)	0.115 (1.00)	0.161 (1.00)	0.522 (1.00)	0.127 (1.00)	0.0541 (1.00)	0.154 (1.00)
Del Peak 9(3p14 2)	0 (0%)	96	1.1e-39 (7.84e-37)	0.00151 (0.875)	0.216 (1.00)	0.386 (1.00)	0.115 (1.00)	0.161 (1.00)	0.522 (1.00)	0.127 (1.00)	0.0393 (1.00)	0.118 (1.00)
Del Peak 10(3p12 2)	0 (0%)	110	1.31e-31 (9.27e-29)	0.00359 (1.00)	0.853 (1.00)	0.684 (1.00)	0.241 (1.00)	0.463 (1.00)	0.229 (1.00)	0.432 (1.00)	0.0143 (1.00)	0.446 (1.00)
Del Peak 12(4q22 1)	0 (0%)	247	1.21e-13 (8.41e-11)	0.0231 (1.00)	0.13 (1.00)	0.651 (1.00)	0.371 (1.00)	0.205 (1.00)	0.383 (1.00)	0.341 (1.00)	0.0048 (1.00)	0.0695 (1.00)
Del Peak 13(4q35 2)	0 (0%)	219	2.03e-10 (1.39e-07)	0.647 (1.00)	0.0962 (1.00)	0.534 (1.00)	0.275 (1.00)	0.353 (1.00)	0.209 (1.00)	0.32 (1.00)	0.0399 (1.00)	0.351 (1.00)
Del Peak 14(5q11 2)	0 (0%)	220	7.05e-17 (4.94e-14)	0.000751 (0.448)	0.0186 (1.00)	0.615 (1.00)	0.0401 (1.00)	0.000767 (0.457)	0.0809 (1.00)	0.325 (1.00)	0.00377 (1.00)	0.0109 (1.00)
Del Peak 22(9p23)	0 (0%)	199	9.87e-14 (6.86e-11)	0.0581 (1.00)	0.538 (1.00)	0.851 (1.00)	0.74 (1.00)	0.493 (1.00)	0.677 (1.00)	0.385 (1.00)	0.0341 (1.00)	0.333 (1.00)
Del Peak 23(9p21 3)	0 (0%)	156	3.41e-10 (2.33e-07)	0.0126 (1.00)	0.707 (1.00)	0.423 (1.00)	0.39 (1.00)	0.462 (1.00)	0.824 (1.00)	0.2 (1.00)	0.573 (1.00)	0.666 (1.00)
Del Peak 24(9q21 11)	0 (0%)	301	1.33e-05 (0.00871)	0.00187 (1.00)	0.96 (1.00)	0.926 (1.00)	0.882 (1.00)	0.673 (1.00)	0.588 (1.00)	0.00252 (1.00)	0.582 (1.00)	0.0693 (1.00)
Del Peak 28(10q23 31)	0 (0%)	277	0.00565 (1.00)	0.000159 (0.0992)	0.179 (1.00)	0.548 (1.00)	0.0249 (1.00)	0.0128 (1.00)	0.0843 (1.00)	0.905 (1.00)	0.00143 (0.828)	0.0601 (1.00)
Del Peak 30(11q14 2)	0 (0%)	232	2.56e-20 (1.8e-17)	0.0012 (0.701)	0.232 (1.00)	0.803 (1.00)	0.00101 (0.596)	0.0121 (1.00)	0.632 (1.00)	0.457 (1.00)	0.0137 (1.00)	0.425 (1.00)
Del Peak 33(13q12 11)	0 (0%)	200	7.7e-11 (5.29e-08)	0.00693 (1.00)	0.272 (1.00)	0.371 (1.00)	0.053 (1.00)	0.0289 (1.00)	0.498 (1.00)	0.624 (1.00)	0.00224 (1.00)	0.214 (1.00)
Del Peak 37(15q15 1)	0 (0%)	286	1.19e-06 (0.000792)	0.723 (1.00)	0.293 (1.00)	0.161 (1.00)	0.0226 (1.00)	0.0628 (1.00)	0.179 (1.00)	0.183 (1.00)	0.266 (1.00)	0.411 (1.00)
Del Peak 42(18q23)	0 (0%)	161	1.08e-22 (7.63e-20)	0.00193 (1.00)	0.183 (1.00)	0.385 (1.00)	0.00216 (1.00)	0.00333 (1.00)	0.0145 (1.00)	0.0191 (1.00)	0.252 (1.00)	0.362 (1.00)
Del Peak 43(19p13 3)	0 (0%)	249	0.000105 (0.0658)	0.528 (1.00)	0.31 (1.00)	0.0817 (1.00)	0.0853 (1.00)	0.679 (1.00)	0.441 (1.00)	0.11 (1.00)	0.581 (1.00)	0.406 (1.00)
Del Peak 44(19q13 43)	0 (0%)	297	8.73e-06 (0.00573)	0.0423 (1.00)	0.256 (1.00)	0.0841 (1.00)	0.584 (1.00)	0.262 (1.00)	0.0674 (1.00)	0.839 (1.00)	0.0563 (1.00)	0.87 (1.00)
Del Peak 45(Xp21 3)	0 (0%)	247	2.14e-07 (0.000144)	0.0609 (1.00)	0.424 (1.00)	0.0649 (1.00)	0.275 (1.00)	0.0415 (1.00)	0.199 (1.00)	0.52 (1.00)	0.568 (1.00)	0.664 (1.00)
Del Peak 46(Xp11 3)	0 (0%)	249	1.29e-08 (8.7e-06)	0.0276 (1.00)	0.346 (1.00)	0.00914 (1.00)	0.211 (1.00)	0.0598 (1.00)	0.102 (1.00)	0.79 (1.00)	0.0478 (1.00)	0.714 (1.00)
Amp Peak 10(8p11 23)	0 (0%)	249	0.00368 (1.00)	0.0827 (1.00)	0.897 (1.00)	0.629 (1.00)	0.15 (1.00)	0.0182 (1.00)	0.0102 (1.00)	0.0711 (1.00)	0.0437 (1.00)	0.191 (1.00)
Amp Peak 15(11p13)	0 (0%)	296	0.0134 (1.00)	0.331 (1.00)	0.187 (1.00)	0.0539 (1.00)	0.631 (1.00)	0.163 (1.00)	0.523 (1.00)	0.134 (1.00)	0.781 (1.00)	0.783 (1.00)
Amp Peak 18(12q15)	0 (0%)	293	0.00193 (1.00)	0.486 (1.00)	0.0609 (1.00)	0.193 (1.00)	0.09 (1.00)	0.0459 (1.00)	0.471 (1.00)	0.695 (1.00)	0.326 (1.00)	0.752 (1.00)
Del Peak 3(1q44)	0 (0%)	337	0.568 (1.00)	0.0115 (1.00)	0.859 (1.00)	0.931 (1.00)	0.0628 (1.00)	0.0133 (1.00)	0.00659 (1.00)	0.213 (1.00)	0.0906 (1.00)	0.0169 (1.00)
Del Peak 5(2q22 1)	0 (0%)	289	0.0342 (1.00)	0.165 (1.00)	0.29 (1.00)	0.522 (1.00)	0.0513 (1.00)	0.0292 (1.00)	0.0573 (1.00)	0.0192 (1.00)	0.0538 (1.00)	0.0476 (1.00)
Del Peak 17(6p25 3)	0 (0%)	299	0.00185 (1.00)	0.00731 (1.00)	0.0727 (1.00)	0.133 (1.00)	0.00752 (1.00)	0.38 (1.00)	0.099 (1.00)	0.842 (1.00)	0.101 (1.00)	0.474 (1.00)
Del Peak 18(6q12)	0 (0%)	305	0.0132 (1.00)	0.0233 (1.00)	0.052 (1.00)	0.153 (1.00)	0.949 (1.00)	0.949 (1.00)	0.206 (1.00)	0.464 (1.00)	0.338 (1.00)	0.222 (1.00)
Del Peak 19(7q31 1)	0 (0%)	312	0.0487 (1.00)	0.213 (1.00)	0.17 (1.00)	0.581 (1.00)	0.363 (1.00)	0.609 (1.00)	0.571 (1.00)	0.273 (1.00)	0.901 (1.00)	0.194 (1.00)
Del Peak 20(7q36 1)	0 (0%)	278	0.0257 (1.00)	0.693 (1.00)	0.00511 (1.00)	0.277 (1.00)	0.957 (1.00)	0.674 (1.00)	0.815 (1.00)	0.254 (1.00)	0.781 (1.00)	0.397 (1.00)
Del Peak 25(9q34 3)	0 (0%)	310	0.00081 (0.481)	0.0206 (1.00)	0.712 (1.00)	0.108 (1.00)	0.851 (1.00)	0.409 (1.00)	0.276 (1.00)	0.0275 (1.00)	0.583 (1.00)	0.326 (1.00)
Del Peak 26(10p15 3)	0 (0%)	251	0.00337 (1.00)	0.227 (1.00)	0.504 (1.00)	0.155 (1.00)	0.327 (1.00)	0.307 (1.00)	0.271 (1.00)	0.703 (1.00)	0.0166 (1.00)	0.332 (1.00)
Del Peak 27(10p11 21)	0 (0%)	258	0.00132 (0.767)	0.0495 (1.00)	0.225 (1.00)	0.0652 (1.00)	0.702 (1.00)	0.975 (1.00)	0.542 (1.00)	0.831 (1.00)	0.0675 (1.00)	0.458 (1.00)
Del Peak 32(12q24 33)	0 (0%)	327	0.0202 (1.00)	0.208 (1.00)	0.082 (1.00)	0.748 (1.00)	0.859 (1.00)	0.775 (1.00)	0.931 (1.00)	0.358 (1.00)	0.366 (1.00)	0.509 (1.00)
Del Peak 35(14q11 2)	0 (0%)	316	0.0288 (1.00)	0.113 (1.00)	0.38 (1.00)	0.515 (1.00)	0.463 (1.00)	0.329 (1.00)	0.111 (1.00)	0.154 (1.00)	0.0401 (1.00)	0.0328 (1.00)
Del Peak 40(17q25 3)	0 (0%)	324	0.321 (1.00)	0.0923 (1.00)	0.474 (1.00)	1 (1.00)	0.037 (1.00)	0.0612 (1.00)	0.0204 (1.00)	0.0941 (1.00)	0.00228 (1.00)	0.0789 (1.00)

'Amp Peak 1(1q21.2)' versus 'CN_CNMF'

P value = 1.19e-09 (Chi-square test), Q value = 8.2e-07

Table S1. Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
AMP PEAK 1(1Q21.2) CNV	31	24	5	2	8	4	2	9
AMP PEAK 1(1Q21.2) WILD-TYPE	55	32	72	29	68	14	7	6

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 1(1q21.2)' versus 'METHLYATION_CNMF'

P value = 2.12e-05 (Fisher's exact test), Q value = 0.014

Table S2. Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	106	101
AMP PEAK 1(1Q21.2) CNV	20	40	11
AMP PEAK 1(1Q21.2) WILD-TYPE	79	66	90

Figure S2. Get High-res Image Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 1(1q21.2)' versus 'MIRSEQ_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.21

Table S3. Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	134	104
AMP PEAK 1(1Q21.2) CNV	15	46	21
AMP PEAK 1(1Q21.2) WILD-TYPE	98	88	83

Figure S3. Get High-res Image Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Amp Peak 1(1q21.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.36e-05 (Fisher's exact test), Q value = 0.022

Table S4. Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	117	96
AMP PEAK 1(1Q21.2) CNV	14	46	19
AMP PEAK 1(1Q21.2) WILD-TYPE	88	71	77

Figure S4. Get High-res Image Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 1(1q21.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000316 (Fisher's exact test), Q value = 0.19

Table S5. Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	5	93	92	125
AMP PEAK 1(1Q21.2) CNV	1	37	12	29
AMP PEAK 1(1Q21.2) WILD-TYPE	4	56	80	96

Figure S5. Get High-res Image Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 2(2q11.2)' versus 'CN_CNMF'

P value = 1.01e-09 (Chi-square test), Q value = 6.9e-07

Table S6. Gene #2: 'Amp Peak 2(2q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
AMP PEAK 2(2Q11.2) CNV	25	23	1	2	11	4	1	9
AMP PEAK 2(2Q11.2) WILD-TYPE	61	33	76	29	65	14	8	6

Figure S6. Get High-res Image Gene #2: 'Amp Peak 2(2q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 3(2q31.2)' versus 'CN_CNMF'

P value = 2.38e-12 (Chi-square test), Q value = 1.6e-09

Table S7. Gene #3: 'Amp Peak 3(2q31.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
AMP PEAK 3(2Q31.2) CNV	28	26	2	2	6	4	0	8
AMP PEAK 3(2Q31.2) WILD-TYPE	58	30	75	29	70	14	9	7

Figure S7. Get High-res Image Gene #3: 'Amp Peak 3(2q31.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 4(3q26.33)' versus 'CN_CNMF'

P value = 1.01e-16 (Chi-square test), Q value = 7e-14

Table S8. Gene #4: 'Amp Peak 4(3q26.33)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
AMP PEAK 4(3Q26.33) CNV	76	53	27	23	60	16	7	14
AMP PEAK 4(3Q26.33) WILD-TYPE	10	3	50	8	16	2	2	1

Figure S8. Get High-res Image Gene #4: 'Amp Peak 4(3q26.33)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 4(3q26.33)' versus 'METHLYATION_CNMF'

P value = 4.75e-05 (Fisher's exact test), Q value = 0.031

Table S9. Gene #4: 'Amp Peak 4(3q26.33)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	106	101
AMP PEAK 4(3Q26.33) CNV	70	94	64
AMP PEAK 4(3Q26.33) WILD-TYPE	29	12	37

Figure S9. Get High-res Image Gene #4: 'Amp Peak 4(3q26.33)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 4(3q26.33)' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.01e-05 (Fisher's exact test), Q value = 0.057

Table S10. Gene #4: 'Amp Peak 4(3q26.33)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	117	96
AMP PEAK 4(3Q26.33) CNV	61	100	70
AMP PEAK 4(3Q26.33) WILD-TYPE	41	17	26

Figure S10. Get High-res Image Gene #4: 'Amp Peak 4(3q26.33)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 4(3q26.33)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.81e-06 (Fisher's exact test), Q value = 0.0045

Table S11. Gene #4: 'Amp Peak 4(3q26.33)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	5	93	92	125
AMP PEAK 4(3Q26.33) CNV	2	82	53	94
AMP PEAK 4(3Q26.33) WILD-TYPE	3	11	39	31

Figure S11. Get High-res Image Gene #4: 'Amp Peak 4(3q26.33)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 5(5p15.33)' versus 'CN_CNMF'

P value = 1.41e-09 (Chi-square test), Q value = 9.6e-07

Table S12. Gene #5: 'Amp Peak 5(5p15.33)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
AMP PEAK 5(5P15.33) CNV	52	29	19	10	25	16	2	13
AMP PEAK 5(5P15.33) WILD-TYPE	34	27	58	21	51	2	7	2

Figure S12. Get High-res Image Gene #5: 'Amp Peak 5(5p15.33)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 6(6p12.1)' versus 'CN_CNMF'

P value = 1.87e-05 (Chi-square test), Q value = 0.012

Table S13. Gene #6: 'Amp Peak 6(6p12.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
AMP PEAK 6(6P12.1) CNV	27	13	4	1	14	9	2	3
AMP PEAK 6(6P12.1) WILD-TYPE	59	43	73	30	62	9	7	12

Figure S13. Get High-res Image Gene #6: 'Amp Peak 6(6p12.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 7(6q12)' versus 'CN_CNMF'

P value = 7.89e-05 (Chi-square test), Q value = 0.05

Table S14. Gene #7: 'Amp Peak 7(6q12)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
AMP PEAK 7(6Q12) CNV	20	13	3	1	16	9	2	3
AMP PEAK 7(6Q12) WILD-TYPE	66	43	74	30	60	9	7	12

Figure S14. Get High-res Image Gene #7: 'Amp Peak 7(6q12)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 8(7p11.2)' versus 'CN_CNMF'

P value = 9.14e-07 (Chi-square test), Q value = 0.00061

Table S15. Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
AMP PEAK 8(7P11.2) CNV	49	28	17	5	31	11	2	11
AMP PEAK 8(7P11.2) WILD-TYPE	37	28	60	26	45	7	7	4

Figure S15. Get High-res Image Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 9(7q21.3)' versus 'CN_CNMF'

P value = 3.49e-15 (Chi-square test), Q value = 2.4e-12

Table S16. Gene #9: 'Amp Peak 9(7q21.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
AMP PEAK 9(7Q21.3) CNV	48	31	11	3	12	4	2	13
AMP PEAK 9(7Q21.3) WILD-TYPE	38	25	66	28	64	14	7	2

Figure S16. Get High-res Image Gene #9: 'Amp Peak 9(7q21.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 11(8q11.21)' versus 'CN_CNMF'

P value = 1.93e-06 (Chi-square test), Q value = 0.0013

Table S17. Gene #11: 'Amp Peak 11(8q11.21)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
AMP PEAK 11(8Q11.21) CNV	56	29	30	14	54	18	7	12
AMP PEAK 11(8Q11.21) WILD-TYPE	30	27	47	17	22	0	2	3

Figure S17. Get High-res Image Gene #11: 'Amp Peak 11(8q11.21)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 11(8q11.21)' versus 'METHLYATION_CNMF'

P value = 0.000199 (Fisher's exact test), Q value = 0.12

Table S18. Gene #11: 'Amp Peak 11(8q11.21)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	106	101
AMP PEAK 11(8Q11.21) CNV	68	44	63
AMP PEAK 11(8Q11.21) WILD-TYPE	31	62	38

Figure S18. Get High-res Image Gene #11: 'Amp Peak 11(8q11.21)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 12(8q24.21)' versus 'CN_CNMF'

P value = 5.27e-09 (Chi-square test), Q value = 3.6e-06

Table S19. Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
AMP PEAK 12(8Q24.21) CNV	74	36	37	18	61	18	8	15
AMP PEAK 12(8Q24.21) WILD-TYPE	12	20	40	13	15	0	1	0

Figure S19. Get High-res Image Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 12(8q24.21)' versus 'METHLYATION_CNMF'

P value = 2.54e-05 (Fisher's exact test), Q value = 0.016

Table S20. Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	106	101
AMP PEAK 12(8Q24.21) CNV	82	58	77
AMP PEAK 12(8Q24.21) WILD-TYPE	17	48	24

Figure S20. Get High-res Image Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 12(8q24.21)' versus 'MRNASEQ_CNMF'

P value = 0.000102 (Fisher's exact test), Q value = 0.065

Table S21. Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	91	90
AMP PEAK 12(8Q24.21) CNV	69	77	68
AMP PEAK 12(8Q24.21) WILD-TYPE	49	14	22

Figure S21. Get High-res Image Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Amp Peak 12(8q24.21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000135 (Fisher's exact test), Q value = 0.085

Table S22. Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	84	120
AMP PEAK 12(8Q24.21) CNV	79	65	70
AMP PEAK 12(8Q24.21) WILD-TYPE	16	19	50

Figure S22. Get High-res Image Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 13(9p23)' versus 'CN_CNMF'

P value = 6.75e-06 (Chi-square test), Q value = 0.0044

Table S23. Gene #13: 'Amp Peak 13(9p23)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
AMP PEAK 13(9P23) CNV	19	14	17	8	11	7	9	2
AMP PEAK 13(9P23) WILD-TYPE	67	42	60	23	65	11	0	13

Figure S23. Get High-res Image Gene #13: 'Amp Peak 13(9p23)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 14(9p13.3)' versus 'CN_CNMF'

P value = 0.000371 (Chi-square test), Q value = 0.23

Table S24. Gene #14: 'Amp Peak 14(9p13.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
AMP PEAK 14(9P13.3) CNV	21	17	16	7	22	6	9	4
AMP PEAK 14(9P13.3) WILD-TYPE	65	39	61	24	54	12	0	11

Figure S24. Get High-res Image Gene #14: 'Amp Peak 14(9p13.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 16(11q13.3)' versus 'CN_CNMF'

P value = 3.83e-30 (Chi-square test), Q value = 2.7e-27

Table S25. Gene #16: 'Amp Peak 16(11q13.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
AMP PEAK 16(11Q13.3) CNV	86	19	8	5	34	8	4	6
AMP PEAK 16(11Q13.3) WILD-TYPE	0	37	69	26	42	10	5	9

Figure S25. Get High-res Image Gene #16: 'Amp Peak 16(11q13.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 17(12p13.33)' versus 'CN_CNMF'

P value = 1.99e-12 (Chi-square test), Q value = 1.4e-09

Table S26. Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
AMP PEAK 17(12P13.33) CNV	33	36	8	4	20	14	2	8
AMP PEAK 17(12P13.33) WILD-TYPE	53	20	69	27	56	4	7	7

Figure S26. Get High-res Image Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 19(13q22.1)' versus 'CN_CNMF'

P value = 1.18e-06 (Chi-square test), Q value = 0.00078

Table S27. Gene #19: 'Amp Peak 19(13q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
AMP PEAK 19(13Q22.1) CNV	24	8	3	6	17	7	2	10
AMP PEAK 19(13Q22.1) WILD-TYPE	62	48	74	25	59	11	7	5

Figure S27. Get High-res Image Gene #19: 'Amp Peak 19(13q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 20(15q26.3)' versus 'CN_CNMF'

P value = 5.54e-05 (Chi-square test), Q value = 0.035

Table S28. Gene #20: 'Amp Peak 20(15q26.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
AMP PEAK 20(15Q26.3) CNV	29	13	5	2	17	3	0	7
AMP PEAK 20(15Q26.3) WILD-TYPE	57	43	72	29	59	15	9	8

Figure S28. Get High-res Image Gene #20: 'Amp Peak 20(15q26.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 21(17q12)' versus 'CN_CNMF'

P value = 8.18e-07 (Chi-square test), Q value = 0.00055

Table S29. Gene #21: 'Amp Peak 21(17q12)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
AMP PEAK 21(17Q12) CNV	25	20	1	2	10	2	1	5
AMP PEAK 21(17Q12) WILD-TYPE	61	36	76	29	66	16	8	10

Figure S29. Get High-res Image Gene #21: 'Amp Peak 21(17q12)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 22(18p11.31)' versus 'CN_CNMF'

P value = 7.52e-07 (Chi-square test), Q value = 5e-04

Table S30. Gene #22: 'Amp Peak 22(18p11.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
AMP PEAK 22(18P11.31) CNV	32	29	9	5	17	11	4	4
AMP PEAK 22(18P11.31) WILD-TYPE	54	27	68	26	59	7	5	11

Figure S30. Get High-res Image Gene #22: 'Amp Peak 22(18p11.31)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 23(18q11.2)' versus 'CN_CNMF'

P value = 7.62e-05 (Chi-square test), Q value = 0.048

Table S31. Gene #23: 'Amp Peak 23(18q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
AMP PEAK 23(18Q11.2) CNV	16	26	8	3	16	5	1	4
AMP PEAK 23(18Q11.2) WILD-TYPE	70	30	69	28	60	13	8	11

Figure S31. Get High-res Image Gene #23: 'Amp Peak 23(18q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 24(20q11.22)' versus 'CN_CNMF'

P value = 5.45e-07 (Chi-square test), Q value = 0.00037

Table S32. Gene #24: 'Amp Peak 24(20q11.22)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
AMP PEAK 24(20Q11.22) CNV	39	22	18	12	39	18	4	10
AMP PEAK 24(20Q11.22) WILD-TYPE	47	34	59	19	37	0	5	5

Figure S32. Get High-res Image Gene #24: 'Amp Peak 24(20q11.22)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 1(1p36.13)' versus 'CN_CNMF'

P value = 1.15e-13 (Chi-square test), Q value = 8e-11

Table S33. Gene #25: 'Del Peak 1(1p36.13)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
DEL PEAK 1(1P36.13) CNV	17	29	5	1	10	0	0	9
DEL PEAK 1(1P36.13) WILD-TYPE	69	27	72	30	66	18	9	6

Figure S33. Get High-res Image Gene #25: 'Del Peak 1(1p36.13)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 1(1p36.13)' versus 'METHLYATION_CNMF'

P value = 2.28e-07 (Fisher's exact test), Q value = 0.00015

Table S34. Gene #25: 'Del Peak 1(1p36.13)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	106	101
DEL PEAK 1(1P36.13) CNV	14	41	9
DEL PEAK 1(1P36.13) WILD-TYPE	85	65	92

Figure S34. Get High-res Image Gene #25: 'Del Peak 1(1p36.13)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 1(1p36.13)' versus 'MRNASEQ_CNMF'

P value = 3.03e-05 (Fisher's exact test), Q value = 0.02

Table S35. Gene #25: 'Del Peak 1(1p36.13)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	91	90
DEL PEAK 1(1P36.13) CNV	39	17	7
DEL PEAK 1(1P36.13) WILD-TYPE	79	74	83

Figure S35. Get High-res Image Gene #25: 'Del Peak 1(1p36.13)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 1(1p36.13)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.14e-05 (Fisher's exact test), Q value = 0.014

Table S36. Gene #25: 'Del Peak 1(1p36.13)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	117	96
DEL PEAK 1(1P36.13) CNV	10	39	13
DEL PEAK 1(1P36.13) WILD-TYPE	92	78	83

Figure S36. Get High-res Image Gene #25: 'Del Peak 1(1p36.13)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'Del Peak 2(1p13.2)' versus 'CN_CNMF'

P value = 3.38e-11 (Chi-square test), Q value = 2.3e-08

Table S37. Gene #26: 'Del Peak 2(1p13.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
DEL PEAK 2(1P13.2) CNV	21	31	4	2	15	4	1	9
DEL PEAK 2(1P13.2) WILD-TYPE	65	25	73	29	61	14	8	6

Figure S37. Get High-res Image Gene #26: 'Del Peak 2(1p13.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 2(1p13.2)' versus 'METHLYATION_CNMF'

P value = 0.000147 (Fisher's exact test), Q value = 0.092

Table S38. Gene #26: 'Del Peak 2(1p13.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	106	101
DEL PEAK 2(1P13.2) CNV	22	40	13
DEL PEAK 2(1P13.2) WILD-TYPE	77	66	88

Figure S38. Get High-res Image Gene #26: 'Del Peak 2(1p13.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 2(1p13.2)' versus 'MIRSEQ_CNMF'

P value = 0.000105 (Fisher's exact test), Q value = 0.066

Table S39. Gene #26: 'Del Peak 2(1p13.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	134	104
DEL PEAK 2(1P13.2) CNV	16	49	20
DEL PEAK 2(1P13.2) WILD-TYPE	97	85	84

Figure S39. Get High-res Image Gene #26: 'Del Peak 2(1p13.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 2(1p13.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.53e-05 (Fisher's exact test), Q value = 0.01

Table S40. Gene #26: 'Del Peak 2(1p13.2)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	117	96
DEL PEAK 2(1P13.2) CNV	13	46	19
DEL PEAK 2(1P13.2) WILD-TYPE	89	71	77

Figure S40. Get High-res Image Gene #26: 'Del Peak 2(1p13.2)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'Del Peak 4(2q21.2)' versus 'MIRSEQ_CNMF'

P value = 0.000297 (Fisher's exact test), Q value = 0.18

Table S41. Gene #28: 'Del Peak 4(2q21.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	134	104
DEL PEAK 4(2Q21.2) CNV	26	15	5
DEL PEAK 4(2Q21.2) WILD-TYPE	87	119	99

Figure S41. Get High-res Image Gene #28: 'Del Peak 4(2q21.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 4(2q21.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000268 (Fisher's exact test), Q value = 0.17

Table S42. Gene #28: 'Del Peak 4(2q21.2)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	117	96
DEL PEAK 4(2Q21.2) CNV	23	11	4
DEL PEAK 4(2Q21.2) WILD-TYPE	79	106	92

Figure S42. Get High-res Image Gene #28: 'Del Peak 4(2q21.2)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'Del Peak 4(2q21.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000159 (Fisher's exact test), Q value = 0.099

Table S43. Gene #28: 'Del Peak 4(2q21.2)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	5	93	92	125
DEL PEAK 4(2Q21.2) CNV	1	6	23	8
DEL PEAK 4(2Q21.2) WILD-TYPE	4	87	69	117

Figure S43. Get High-res Image Gene #28: 'Del Peak 4(2q21.2)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 6(2q36.2)' versus 'CN_CNMF'

P value = 1.28e-08 (Chi-square test), Q value = 8.7e-06

Table S44. Gene #30: 'Del Peak 6(2q36.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
DEL PEAK 6(2Q36.2) CNV	25	34	11	4	17	3	4	9
DEL PEAK 6(2Q36.2) WILD-TYPE	61	22	66	27	59	15	5	6

Figure S44. Get High-res Image Gene #30: 'Del Peak 6(2q36.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 6(2q36.2)' versus 'METHLYATION_CNMF'

P value = 7.6e-05 (Fisher's exact test), Q value = 0.048

Table S45. Gene #30: 'Del Peak 6(2q36.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	106	101
DEL PEAK 6(2Q36.2) CNV	27	48	18
DEL PEAK 6(2Q36.2) WILD-TYPE	72	58	83

Figure S45. Get High-res Image Gene #30: 'Del Peak 6(2q36.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 7(3p25.3)' versus 'CN_CNMF'

P value = 7.39e-27 (Chi-square test), Q value = 5.2e-24

Table S46. Gene #31: 'Del Peak 7(3p25.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
DEL PEAK 7(3P25.3) CNV	76	44	12	24	63	16	8	14
DEL PEAK 7(3P25.3) WILD-TYPE	10	12	65	7	13	2	1	1

Figure S46. Get High-res Image Gene #31: 'Del Peak 7(3p25.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 8(3p14.2)' versus 'CN_CNMF'

P value = 1.1e-39 (Chi-square test), Q value = 7.8e-37

Table S47. Gene #32: 'Del Peak 8(3p14.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
DEL PEAK 8(3P14.2) CNV	83	49	9	29	64	15	9	14
DEL PEAK 8(3P14.2) WILD-TYPE	3	7	68	2	12	3	0	1

Figure S47. Get High-res Image Gene #32: 'Del Peak 8(3p14.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 9(3p14.2)' versus 'CN_CNMF'

P value = 1.1e-39 (Chi-square test), Q value = 7.8e-37

Table S48. Gene #33: 'Del Peak 9(3p14.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
DEL PEAK 9(3P14.2) CNV	83	49	9	29	64	15	9	14
DEL PEAK 9(3P14.2) WILD-TYPE	3	7	68	2	12	3	0	1

Figure S48. Get High-res Image Gene #33: 'Del Peak 9(3p14.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 10(3p12.2)' versus 'CN_CNMF'

P value = 1.31e-31 (Chi-square test), Q value = 9.3e-29

Table S49. Gene #34: 'Del Peak 10(3p12.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
DEL PEAK 10(3P12.2) CNV	79	48	9	26	61	14	8	13
DEL PEAK 10(3P12.2) WILD-TYPE	7	8	68	5	15	4	1	2

Figure S49. Get High-res Image Gene #34: 'Del Peak 10(3p12.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 11(4p15.2)' versus 'CN_CNMF'

P value = 3.81e-13 (Chi-square test), Q value = 2.6e-10

Table S50. Gene #35: 'Del Peak 11(4p15.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
DEL PEAK 11(4P15.2) CNV	51	40	9	8	31	3	2	10
DEL PEAK 11(4P15.2) WILD-TYPE	35	16	68	23	45	15	7	5

Figure S50. Get High-res Image Gene #35: 'Del Peak 11(4p15.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 11(4p15.2)' versus 'METHLYATION_CNMF'

P value = 1.94e-05 (Fisher's exact test), Q value = 0.013

Table S51. Gene #35: 'Del Peak 11(4p15.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	106	101
DEL PEAK 11(4P15.2) CNV	42	62	27
DEL PEAK 11(4P15.2) WILD-TYPE	57	44	74

Figure S51. Get High-res Image Gene #35: 'Del Peak 11(4p15.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 11(4p15.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.24

Table S52. Gene #35: 'Del Peak 11(4p15.2)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	117	96
DEL PEAK 11(4P15.2) CNV	29	64	38
DEL PEAK 11(4P15.2) WILD-TYPE	73	53	58

Figure S52. Get High-res Image Gene #35: 'Del Peak 11(4p15.2)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'Del Peak 12(4q22.1)' versus 'CN_CNMF'

P value = 1.21e-13 (Chi-square test), Q value = 8.4e-11

Table S53. Gene #36: 'Del Peak 12(4q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
DEL PEAK 12(4Q22.1) CNV	31	39	7	1	24	7	2	10
DEL PEAK 12(4Q22.1) WILD-TYPE	55	17	70	30	52	11	7	5

Figure S53. Get High-res Image Gene #36: 'Del Peak 12(4q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 13(4q35.2)' versus 'CN_CNMF'

P value = 2.03e-10 (Chi-square test), Q value = 1.4e-07

Table S54. Gene #37: 'Del Peak 13(4q35.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
DEL PEAK 13(4Q35.2) CNV	34	35	11	3	40	10	5	11
DEL PEAK 13(4Q35.2) WILD-TYPE	52	21	66	28	36	8	4	4

Figure S54. Get High-res Image Gene #37: 'Del Peak 13(4q35.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 14(5q11.2)' versus 'CN_CNMF'

P value = 7.05e-17 (Chi-square test), Q value = 4.9e-14

Table S55. Gene #38: 'Del Peak 14(5q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
DEL PEAK 14(5Q11.2) CNV	43	36	5	1	37	11	2	13
DEL PEAK 14(5Q11.2) WILD-TYPE	43	20	72	30	39	7	7	2

Figure S55. Get High-res Image Gene #38: 'Del Peak 14(5q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 15(5q15)' versus 'CN_CNMF'

P value = 5.86e-16 (Chi-square test), Q value = 4.1e-13

Table S56. Gene #39: 'Del Peak 15(5q15)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
DEL PEAK 15(5Q15) CNV	44	36	8	1	36	11	2	14
DEL PEAK 15(5Q15) WILD-TYPE	42	20	69	30	40	7	7	1

Figure S56. Get High-res Image Gene #39: 'Del Peak 15(5q15)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 15(5q15)' versus 'METHLYATION_CNMF'

P value = 4.73e-05 (Fisher's exact test), Q value = 0.03

Table S57. Gene #39: 'Del Peak 15(5q15)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	106	101
DEL PEAK 15(5Q15) CNV	55	50	26
DEL PEAK 15(5Q15) WILD-TYPE	44	56	75

Figure S57. Get High-res Image Gene #39: 'Del Peak 15(5q15)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 15(5q15)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000402 (Fisher's exact test), Q value = 0.24

Table S58. Gene #39: 'Del Peak 15(5q15)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	84	120
DEL PEAK 15(5Q15) CNV	44	22	64
DEL PEAK 15(5Q15) WILD-TYPE	51	62	56

Figure S58. Get High-res Image Gene #39: 'Del Peak 15(5q15)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 15(5q15)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000403 (Fisher's exact test), Q value = 0.24

Table S59. Gene #39: 'Del Peak 15(5q15)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	117	96
DEL PEAK 15(5Q15) CNV	29	64	39
DEL PEAK 15(5Q15) WILD-TYPE	73	53	57

Figure S59. Get High-res Image Gene #39: 'Del Peak 15(5q15)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'Del Peak 16(5q35.3)' versus 'CN_CNMF'

P value = 2.14e-14 (Chi-square test), Q value = 1.5e-11

Table S60. Gene #40: 'Del Peak 16(5q35.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
DEL PEAK 16(5Q35.3) CNV	34	40	8	1	34	10	3	11
DEL PEAK 16(5Q35.3) WILD-TYPE	52	16	69	30	42	8	6	4

Figure S60. Get High-res Image Gene #40: 'Del Peak 16(5q35.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 16(5q35.3)' versus 'METHLYATION_CNMF'

P value = 2.58e-06 (Fisher's exact test), Q value = 0.0017

Table S61. Gene #40: 'Del Peak 16(5q35.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	106	101
DEL PEAK 16(5Q35.3) CNV	54	46	21
DEL PEAK 16(5Q35.3) WILD-TYPE	45	60	80

Figure S61. Get High-res Image Gene #40: 'Del Peak 16(5q35.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 21(8p23.2)' versus 'CN_CNMF'

P value = 3.72e-16 (Chi-square test), Q value = 2.6e-13

Table S62. Gene #45: 'Del Peak 21(8p23.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
DEL PEAK 21(8P23.2) CNV	68	21	17	12	53	15	7	14
DEL PEAK 21(8P23.2) WILD-TYPE	18	35	60	19	23	3	2	1

Figure S62. Get High-res Image Gene #45: 'Del Peak 21(8p23.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 21(8p23.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000335 (Fisher's exact test), Q value = 0.21

Table S63. Gene #45: 'Del Peak 21(8p23.2)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	5	93	92	125
DEL PEAK 21(8P23.2) CNV	2	37	61	80
DEL PEAK 21(8P23.2) WILD-TYPE	3	56	31	45

Figure S63. Get High-res Image Gene #45: 'Del Peak 21(8p23.2)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 22(9p23)' versus 'CN_CNMF'

P value = 9.87e-14 (Chi-square test), Q value = 6.9e-11

Table S64. Gene #46: 'Del Peak 22(9p23)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
DEL PEAK 22(9P23) CNV	51	33	7	10	48	9	0	11
DEL PEAK 22(9P23) WILD-TYPE	35	23	70	21	28	9	9	4

Figure S64. Get High-res Image Gene #46: 'Del Peak 22(9p23)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 23(9p21.3)' versus 'CN_CNMF'

P value = 3.41e-10 (Chi-square test), Q value = 2.3e-07

Table S65. Gene #47: 'Del Peak 23(9p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
DEL PEAK 23(9P21.3) CNV	66	37	21	14	55	8	2	9
DEL PEAK 23(9P21.3) WILD-TYPE	20	19	56	17	21	10	7	6

Figure S65. Get High-res Image Gene #47: 'Del Peak 23(9p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 24(9q21.11)' versus 'CN_CNMF'

P value = 1.33e-05 (Chi-square test), Q value = 0.0087

Table S66. Gene #48: 'Del Peak 24(9q21.11)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
DEL PEAK 24(9Q21.11) CNV	30	7	4	3	13	4	0	6
DEL PEAK 24(9Q21.11) WILD-TYPE	56	49	73	28	63	14	9	9

Figure S66. Get High-res Image Gene #48: 'Del Peak 24(9q21.11)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 28(10q23.31)' versus 'METHLYATION_CNMF'

P value = 0.000159 (Fisher's exact test), Q value = 0.099

Table S67. Gene #52: 'Del Peak 28(10q23.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	106	101
DEL PEAK 28(10Q23.31) CNV	28	40	13
DEL PEAK 28(10Q23.31) WILD-TYPE	71	66	88

Figure S67. Get High-res Image Gene #52: 'Del Peak 28(10q23.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 29(11p15.4)' versus 'CN_CNMF'

P value = 4.83e-11 (Chi-square test), Q value = 3.3e-08

Table S68. Gene #53: 'Del Peak 29(11p15.4)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
DEL PEAK 29(11P15.4) CNV	45	30	12	3	11	7	0	7
DEL PEAK 29(11P15.4) WILD-TYPE	41	26	65	28	65	11	9	8

Figure S68. Get High-res Image Gene #53: 'Del Peak 29(11p15.4)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 29(11p15.4)' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.05e-09 (Fisher's exact test), Q value = 2.1e-06

Table S69. Gene #53: 'Del Peak 29(11p15.4)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	117	96
DEL PEAK 29(11P15.4) CNV	14	60	23
DEL PEAK 29(11P15.4) WILD-TYPE	88	57	73

Figure S69. Get High-res Image Gene #53: 'Del Peak 29(11p15.4)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'Del Peak 29(11p15.4)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000321 (Fisher's exact test), Q value = 0.2

Table S70. Gene #53: 'Del Peak 29(11p15.4)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	5	93	92	125
DEL PEAK 29(11P15.4) CNV	2	44	19	32
DEL PEAK 29(11P15.4) WILD-TYPE	3	49	73	93

Figure S70. Get High-res Image Gene #53: 'Del Peak 29(11p15.4)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 30(11q14.2)' versus 'CN_CNMF'

P value = 2.56e-20 (Chi-square test), Q value = 1.8e-17

Table S71. Gene #54: 'Del Peak 30(11q14.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
DEL PEAK 30(11Q14.2) CNV	70	22	16	9	8	5	3	3
DEL PEAK 30(11Q14.2) WILD-TYPE	16	34	61	22	68	13	6	12

Figure S71. Get High-res Image Gene #54: 'Del Peak 30(11q14.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 31(11q23.1)' versus 'CN_CNMF'

P value = 1.28e-20 (Chi-square test), Q value = 9e-18

Table S72. Gene #55: 'Del Peak 31(11q23.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
DEL PEAK 31(11Q23.1) CNV	78	30	22	16	14	9	4	2
DEL PEAK 31(11Q23.1) WILD-TYPE	8	26	55	15	62	9	5	13

Figure S72. Get High-res Image Gene #55: 'Del Peak 31(11q23.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 31(11q23.1)' versus 'METHLYATION_CNMF'

P value = 3.94e-06 (Fisher's exact test), Q value = 0.0026

Table S73. Gene #55: 'Del Peak 31(11q23.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	106	101
DEL PEAK 31(11Q23.1) CNV	41	72	36
DEL PEAK 31(11Q23.1) WILD-TYPE	58	34	65

Figure S73. Get High-res Image Gene #55: 'Del Peak 31(11q23.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 31(11q23.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.14

Table S74. Gene #55: 'Del Peak 31(11q23.1)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	84	120
DEL PEAK 31(11Q23.1) CNV	37	33	76
DEL PEAK 31(11Q23.1) WILD-TYPE	58	51	44

Figure S74. Get High-res Image Gene #55: 'Del Peak 31(11q23.1)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 33(13q12.11)' versus 'CN_CNMF'

P value = 7.7e-11 (Chi-square test), Q value = 5.3e-08

Table S75. Gene #57: 'Del Peak 33(13q12.11)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
DEL PEAK 33(13Q12.11) CNV	45	41	11	7	43	11	4	6
DEL PEAK 33(13Q12.11) WILD-TYPE	41	15	66	24	33	7	5	9

Figure S75. Get High-res Image Gene #57: 'Del Peak 33(13q12.11)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 34(13q14.2)' versus 'CN_CNMF'

P value = 8.8e-07 (Chi-square test), Q value = 0.00059

Table S76. Gene #58: 'Del Peak 34(13q14.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
DEL PEAK 34(13Q14.2) CNV	42	38	18	8	38	10	2	2
DEL PEAK 34(13Q14.2) WILD-TYPE	44	18	59	23	38	8	7	13

Figure S76. Get High-res Image Gene #58: 'Del Peak 34(13q14.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 34(13q14.2)' versus 'METHLYATION_CNMF'

P value = 0.000281 (Fisher's exact test), Q value = 0.17

Table S77. Gene #58: 'Del Peak 34(13q14.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	106	101
DEL PEAK 34(13Q14.2) CNV	47	56	27
DEL PEAK 34(13Q14.2) WILD-TYPE	52	50	74

Figure S77. Get High-res Image Gene #58: 'Del Peak 34(13q14.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 34(13q14.2)' versus 'MRNASEQ_CNMF'

P value = 5.7e-05 (Fisher's exact test), Q value = 0.036

Table S78. Gene #58: 'Del Peak 34(13q14.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	91	90
DEL PEAK 34(13Q14.2) CNV	66	39	23
DEL PEAK 34(13Q14.2) WILD-TYPE	52	52	67

Figure S78. Get High-res Image Gene #58: 'Del Peak 34(13q14.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 34(13q14.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.46e-05 (Fisher's exact test), Q value = 0.041

Table S79. Gene #58: 'Del Peak 34(13q14.2)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	84	120
DEL PEAK 34(13Q14.2) CNV	38	22	68
DEL PEAK 34(13Q14.2) WILD-TYPE	57	62	52

Figure S79. Get High-res Image Gene #58: 'Del Peak 34(13q14.2)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 34(13q14.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.29e-05 (Fisher's exact test), Q value = 0.034

Table S80. Gene #58: 'Del Peak 34(13q14.2)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	117	96
DEL PEAK 34(13Q14.2) CNV	29	67	36
DEL PEAK 34(13Q14.2) WILD-TYPE	73	50	60

Figure S80. Get High-res Image Gene #58: 'Del Peak 34(13q14.2)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'Del Peak 36(14q32.32)' versus 'METHLYATION_CNMF'

P value = 6.74e-08 (Fisher's exact test), Q value = 4.6e-05

Table S81. Gene #60: 'Del Peak 36(14q32.32)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	106	101
DEL PEAK 36(14Q32.32) CNV	7	34	6
DEL PEAK 36(14Q32.32) WILD-TYPE	92	72	95

Figure S81. Get High-res Image Gene #60: 'Del Peak 36(14q32.32)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 36(14q32.32)' versus 'MRNASEQ_CNMF'

P value = 0.000242 (Fisher's exact test), Q value = 0.15

Table S82. Gene #60: 'Del Peak 36(14q32.32)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	91	90
DEL PEAK 36(14Q32.32) CNV	30	11	5
DEL PEAK 36(14Q32.32) WILD-TYPE	88	80	85

Figure S82. Get High-res Image Gene #60: 'Del Peak 36(14q32.32)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 36(14q32.32)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.8e-05 (Fisher's exact test), Q value = 0.062

Table S83. Gene #60: 'Del Peak 36(14q32.32)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	84	120
DEL PEAK 36(14Q32.32) CNV	11	4	31
DEL PEAK 36(14Q32.32) WILD-TYPE	84	80	89

Figure S83. Get High-res Image Gene #60: 'Del Peak 36(14q32.32)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 36(14q32.32)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.32e-06 (Fisher's exact test), Q value = 0.0015

Table S84. Gene #60: 'Del Peak 36(14q32.32)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	5	93	92	125
DEL PEAK 36(14Q32.32) CNV	0	28	3	15
DEL PEAK 36(14Q32.32) WILD-TYPE	5	65	89	110

Figure S84. Get High-res Image Gene #60: 'Del Peak 36(14q32.32)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 37(15q15.1)' versus 'CN_CNMF'

P value = 1.19e-06 (Chi-square test), Q value = 0.00079

Table S85. Gene #61: 'Del Peak 37(15q15.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
DEL PEAK 37(15Q15.1) CNV	18	9	6	11	16	8	7	7
DEL PEAK 37(15Q15.1) WILD-TYPE	68	47	71	20	60	10	2	8

Figure S85. Get High-res Image Gene #61: 'Del Peak 37(15q15.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 38(16q12.1)' versus 'METHLYATION_CNMF'

P value = 4.05e-09 (Fisher's exact test), Q value = 2.8e-06

Table S86. Gene #62: 'Del Peak 38(16q12.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	106	101
DEL PEAK 38(16Q12.1) CNV	7	38	7
DEL PEAK 38(16Q12.1) WILD-TYPE	92	68	94

Figure S86. Get High-res Image Gene #62: 'Del Peak 38(16q12.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 38(16q12.1)' versus 'MRNASEQ_CNMF'

P value = 7.1e-08 (Fisher's exact test), Q value = 4.8e-05

Table S87. Gene #62: 'Del Peak 38(16q12.1)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	91	90
DEL PEAK 38(16Q12.1) CNV	38	9	4
DEL PEAK 38(16Q12.1) WILD-TYPE	80	82	86

Figure S87. Get High-res Image Gene #62: 'Del Peak 38(16q12.1)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 38(16q12.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.91e-07 (Fisher's exact test), Q value = 0.00026

Table S88. Gene #62: 'Del Peak 38(16q12.1)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	84	120
DEL PEAK 38(16Q12.1) CNV	7	6	38
DEL PEAK 38(16Q12.1) WILD-TYPE	88	78	82

Figure S88. Get High-res Image Gene #62: 'Del Peak 38(16q12.1)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 38(16q12.1)' versus 'MIRSEQ_CNMF'

P value = 0.000157 (Fisher's exact test), Q value = 0.098

Table S89. Gene #62: 'Del Peak 38(16q12.1)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	134	104
DEL PEAK 38(16Q12.1) CNV	15	38	9
DEL PEAK 38(16Q12.1) WILD-TYPE	98	96	95

Figure S89. Get High-res Image Gene #62: 'Del Peak 38(16q12.1)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 38(16q12.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.88e-06 (Fisher's exact test), Q value = 0.0058

Table S90. Gene #62: 'Del Peak 38(16q12.1)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	117	96
DEL PEAK 38(16Q12.1) CNV	8	35	9
DEL PEAK 38(16Q12.1) WILD-TYPE	94	82	87

Figure S90. Get High-res Image Gene #62: 'Del Peak 38(16q12.1)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'Del Peak 38(16q12.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.44e-05 (Fisher's exact test), Q value = 0.022

Table S91. Gene #62: 'Del Peak 38(16q12.1)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	5	93	92	125
DEL PEAK 38(16Q12.1) CNV	1	30	8	13
DEL PEAK 38(16Q12.1) WILD-TYPE	4	63	84	112

Figure S91. Get High-res Image Gene #62: 'Del Peak 38(16q12.1)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 39(16q23.3)' versus 'METHLYATION_CNMF'

P value = 1.86e-05 (Fisher's exact test), Q value = 0.012

Table S92. Gene #63: 'Del Peak 39(16q23.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	106	101
DEL PEAK 39(16Q23.3) CNV	11	37	13
DEL PEAK 39(16Q23.3) WILD-TYPE	88	69	88

Figure S92. Get High-res Image Gene #63: 'Del Peak 39(16q23.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 39(16q23.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.88e-05 (Fisher's exact test), Q value = 0.056

Table S93. Gene #63: 'Del Peak 39(16q23.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	84	120
DEL PEAK 39(16Q23.3) CNV	11	9	38
DEL PEAK 39(16Q23.3) WILD-TYPE	84	75	82

Figure S93. Get High-res Image Gene #63: 'Del Peak 39(16q23.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 41(18q21.2)' versus 'CN_CNMF'

P value = 3.89e-20 (Chi-square test), Q value = 2.7e-17

Table S94. Gene #65: 'Del Peak 41(18q21.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
DEL PEAK 41(18Q21.2) CNV	57	24	7	11	62	13	9	8
DEL PEAK 41(18Q21.2) WILD-TYPE	29	32	70	20	14	5	0	7

Figure S94. Get High-res Image Gene #65: 'Del Peak 41(18q21.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 41(18q21.2)' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.1

Table S95. Gene #65: 'Del Peak 41(18q21.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	106	101
DEL PEAK 41(18Q21.2) CNV	66	40	55
DEL PEAK 41(18Q21.2) WILD-TYPE	33	66	46

Figure S95. Get High-res Image Gene #65: 'Del Peak 41(18q21.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 42(18q23)' versus 'CN_CNMF'

P value = 1.08e-22 (Chi-square test), Q value = 7.6e-20

Table S96. Gene #66: 'Del Peak 42(18q23)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
DEL PEAK 42(18Q23) CNV	62	30	7	11	66	13	8	10
DEL PEAK 42(18Q23) WILD-TYPE	24	26	70	20	10	5	1	5

Figure S96. Get High-res Image Gene #66: 'Del Peak 42(18q23)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 43(19p13.3)' versus 'CN_CNMF'

P value = 0.000105 (Chi-square test), Q value = 0.066

Table S97. Gene #67: 'Del Peak 43(19p13.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
DEL PEAK 43(19P13.3) CNV	39	19	6	11	27	7	4	6
DEL PEAK 43(19P13.3) WILD-TYPE	47	37	71	20	49	11	5	9

Figure S97. Get High-res Image Gene #67: 'Del Peak 43(19p13.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 44(19q13.43)' versus 'CN_CNMF'

P value = 8.73e-06 (Chi-square test), Q value = 0.0057

Table S98. Gene #68: 'Del Peak 44(19q13.43)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
DEL PEAK 44(19Q13.43) CNV	20	19	3	2	15	2	2	8
DEL PEAK 44(19Q13.43) WILD-TYPE	66	37	74	29	61	16	7	7

Figure S98. Get High-res Image Gene #68: 'Del Peak 44(19q13.43)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 45(Xp21.3)' versus 'CN_CNMF'

P value = 2.14e-07 (Chi-square test), Q value = 0.00014

Table S99. Gene #69: 'Del Peak 45(Xp21.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
DEL PEAK 45(XP21.3) CNV	36	25	9	3	24	9	4	11
DEL PEAK 45(XP21.3) WILD-TYPE	50	31	68	28	52	9	5	4

Figure S99. Get High-res Image Gene #69: 'Del Peak 45(Xp21.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 46(Xp11.3)' versus 'CN_CNMF'

P value = 1.29e-08 (Chi-square test), Q value = 8.7e-06

Table S100. Gene #70: 'Del Peak 46(Xp11.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
DEL PEAK 46(XP11.3) CNV	37	26	8	2	23	7	5	11
DEL PEAK 46(XP11.3) WILD-TYPE	49	30	69	29	53	11	4	4

Figure S100. Get High-res Image Gene #70: 'Del Peak 46(Xp11.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 47(Xq21.33)' versus 'CN_CNMF'

P value = 7.56e-07 (Chi-square test), Q value = 0.00051

Table S101. Gene #71: 'Del Peak 47(Xq21.33)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	86	56	77	31	76	18	9	15
DEL PEAK 47(XQ21.33) CNV	23	20	4	0	8	1	0	3
DEL PEAK 47(XQ21.33) WILD-TYPE	63	36	73	31	68	17	9	12

Figure S101. Get High-res Image Gene #71: 'Del Peak 47(Xq21.33)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 47(Xq21.33)' versus 'METHLYATION_CNMF'

P value = 0.000338 (Fisher's exact test), Q value = 0.21

Table S102. Gene #71: 'Del Peak 47(Xq21.33)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	106	101
DEL PEAK 47(XQ21.33) CNV	21	26	6
DEL PEAK 47(XQ21.33) WILD-TYPE	78	80	95

Figure S102. Get High-res Image Gene #71: 'Del Peak 47(Xq21.33)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 47(Xq21.33)' versus 'MIRSEQ_CNMF'

P value = 2.36e-05 (Fisher's exact test), Q value = 0.015

Table S103. Gene #71: 'Del Peak 47(Xq21.33)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	134	104
DEL PEAK 47(XQ21.33) CNV	11	37	8
DEL PEAK 47(XQ21.33) WILD-TYPE	102	97	96

Figure S103. Get High-res Image Gene #71: 'Del Peak 47(Xq21.33)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 47(Xq21.33)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000164 (Fisher's exact test), Q value = 0.1

Table S104. Gene #71: 'Del Peak 47(Xq21.33)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	102	117	96
DEL PEAK 47(XQ21.33) CNV	8	31	9
DEL PEAK 47(XQ21.33) WILD-TYPE	94	86	87

Figure S104. Get High-res Image Gene #71: 'Del Peak 47(Xq21.33)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

Methods & Data

Input

Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
Molecular subtype file = HNSC-TP.transferedmergedcluster.txt
Number of patients = 368
Number of copy number variation regions = 71
Number of molecular subtypes = 10
Exclude regions that fewer than K tumors have alterations, K = 3

Chi-square test

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

Fisher's exact test

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

Q value calculation

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

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References

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

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

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

[4] GISTIC_version2

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