Correlation between copy number variation genes and molecular subtypes

Lung Adenocarcinoma (Primary solid tumor)

23 September 2013 | analyses__2013_09_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/C1765CPQ

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 79 peak regions and 12 molecular subtypes across 493 patients, 310 significant findings detected with Q value < 0.25.

Amp Peak 1(1p34.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 2(1p22.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 3(1q21.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 4(3q26.2) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 5(4q12) cnvs correlated to 'CN_CNMF'.
Amp Peak 6(5p15.33) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 7(5p13.1) cnvs correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 8(5q35.1) cnvs correlated to 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 9(6p21.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 10(7p21.1) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
Amp Peak 11(7p11.2) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 12(7q31.2) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 13(8p11.23) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 14(8p11.21) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 15(8q11.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 16(8q24.21) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 17(10p15.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 18(11q13.3) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 19(12p12.1) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 20(12q14.1) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 21(12q15) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 23(14q13.3) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 24(16p11.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 25(17q12) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 26(17q23.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 27(18q11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 28(19q12) cnvs correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 29(20p11.21) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 30(20q13.33) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 31(22q11.22) cnvs correlated to 'CN_CNMF'.
Amp Peak 32(Xq28) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 1(1p36.13) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 2(1p13.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 3(2q22.1) cnvs correlated to 'METHLYATION_CNMF'.
Del Peak 4(2q37.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 5(3p21.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
Del Peak 6(3q11.1) cnvs correlated to 'METHLYATION_CNMF'.
Del Peak 7(3q29) cnvs correlated to 'METHLYATION_CNMF'.
Del Peak 8(4p16.3) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 9(4q22.1) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 10(4q35.1) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 11(5q11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 12(5q31.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 14(6q22.31) cnvs correlated to 'METHLYATION_CNMF'.
Del Peak 15(6q26) cnvs correlated to 'METHLYATION_CNMF'.
Del Peak 16(8p23.2) cnvs correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 17(8p12) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
Del Peak 18(8p11.21) cnvs correlated to 'CN_CNMF'.
Del Peak 22(9q21.11) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 23(10p15.3) cnvs correlated to 'CN_CNMF'.
Del Peak 24(10q26.3) cnvs correlated to 'CN_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 25(11p15.5) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 28(12q12) cnvs correlated to 'MRNASEQ_CNMF'.
Del Peak 29(12q24.33) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 30(13q12.11) cnvs correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 31(13q12.13) cnvs correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 32(13q14.2) cnvs correlated to 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 33(13q34) cnvs correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 35(15q11.2) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
Del Peak 36(16q23.1) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 37(17p13.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 38(17p11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 39(18q21.32) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 40(18q23) cnvs correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 41(19p13.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 42(19p13.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 43(19q13.33) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 45(21q11.2) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 46(22q13.32) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 47(Xp22.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 79 regions and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 310 significant findings detected.


		Molecular subtypes	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 Peak 12(5q31 1)	0 (0%)	294	0.0936 (1.00)	0.199 (1.00)	1.03e-12 (9.45e-10)	8.84e-06 (0.00659)	0.00522 (1.00)	0.000339 (0.218)	9.04e-10 (8.06e-07)	7.1e-11 (6.39e-08)	1.22e-09 (1.08e-06)	1.81e-07 (0.00015)	2.65e-05 (0.0189)	2.15e-07 (0.000178)
Amp Peak 4(3q26 2)	0 (0%)	331	0.000264 (0.172)	0.00332 (1.00)	1.15e-05 (0.00851)	0.0433 (1.00)	0.00823 (1.00)	0.00678 (1.00)	2.81e-09 (2.47e-06)	3e-09 (2.64e-06)	1.43e-06 (0.00113)	2.31e-07 (0.000191)	0.000329 (0.212)	4.96e-05 (0.0344)
Amp Peak 15(8q11 1)	0 (0%)	269	0.00472 (1.00)	0.0134 (1.00)	1.23e-22 (1.16e-19)	1.47e-06 (0.00116)	0.0405 (1.00)	0.0538 (1.00)	2.22e-06 (0.00172)	1.32e-06 (0.00105)	1.31e-06 (0.00104)	1.47e-05 (0.0108)	8.04e-06 (0.00605)	6.49e-06 (0.00491)
Del Peak 11(5q11 2)	0 (0%)	320	0.26 (1.00)	0.254 (1.00)	2.13e-13 (1.97e-10)	0.000324 (0.209)	0.00164 (0.943)	0.000835 (0.507)	4.67e-09 (4.09e-06)	1.91e-11 (1.74e-08)	8.34e-10 (7.46e-07)	2.03e-06 (0.00159)	1.06e-06 (0.000848)	2.62e-09 (2.3e-06)
Del Peak 41(19p13 3)	0 (0%)	227	0.572 (1.00)	0.665 (1.00)	7.34e-06 (0.00554)	3.89e-11 (3.52e-08)	0.194 (1.00)	0.28 (1.00)	1.08e-13 (1e-10)	1.42e-11 (1.29e-08)	8.85e-06 (0.00659)	1.17e-08 (1.02e-05)	7.03e-05 (0.0483)	1.23e-07 (0.000103)
Del Peak 42(19p13 2)	0 (0%)	234	0.694 (1.00)	1 (1.00)	6.1e-07 (0.000493)	1.49e-12 (1.36e-09)	0.243 (1.00)	0.151 (1.00)	4.05e-14 (3.75e-11)	8.38e-12 (7.63e-09)	7.34e-06 (0.00554)	3.58e-08 (3.05e-05)	4.51e-05 (0.0314)	2.82e-07 (0.000233)
Del Peak 46(22q13 32)	0 (0%)	257	0.0692 (1.00)	0.0871 (1.00)	4.32e-13 (3.97e-10)	9e-06 (0.00669)	0.106 (1.00)	0.00262 (1.00)	9.24e-11 (8.31e-08)	2.79e-13 (2.57e-10)	1.2e-06 (0.000959)	3.5e-08 (2.99e-05)	8.37e-06 (0.00626)	1.07e-06 (0.000853)
Amp Peak 11(7p11 2)	0 (0%)	234	1 (1.00)	1 (1.00)	4.99e-22 (4.7e-19)	0.0122 (1.00)	0.000971 (0.581)	0.00179 (1.00)	1.49e-08 (1.29e-05)	6.91e-12 (6.29e-09)	2.59e-08 (2.23e-05)	0.000104 (0.0704)	2.93e-05 (0.0209)	3.26e-06 (0.0025)
Amp Peak 16(8q24 21)	0 (0%)	184	0.0343 (1.00)	0.0341 (1.00)	6.35e-19 (5.94e-16)	6.06e-08 (5.13e-05)	0.377 (1.00)	0.0647 (1.00)	1.68e-05 (0.0122)	9.15e-09 (7.96e-06)	9e-06 (0.00669)	0.00032 (0.207)	0.00171 (0.981)	0.000257 (0.168)
Amp Peak 18(11q13 3)	0 (0%)	330	0.00118 (0.7)	0.000736 (0.451)	5e-17 (4.67e-14)	0.00158 (0.917)	0.0425 (1.00)	0.0548 (1.00)	1.13e-07 (9.45e-05)	4.92e-11 (4.45e-08)	1.94e-09 (1.72e-06)	2.13e-06 (0.00166)	1.43e-06 (0.00113)	5.13e-05 (0.0356)
Amp Peak 19(12p12 1)	0 (0%)	323	0.198 (1.00)	0.033 (1.00)	6.39e-07 (0.000515)	0.145 (1.00)	0.0251 (1.00)	0.13 (1.00)	4.65e-07 (0.00038)	1.84e-08 (1.59e-05)	8.03e-06 (0.00604)	5.09e-06 (0.00386)	9.37e-07 (0.000752)	2.84e-06 (0.00218)
Amp Peak 20(12q14 1)	0 (0%)	336	0.406 (1.00)	0.302 (1.00)	5.25e-09 (4.59e-06)	0.00329 (1.00)	0.0115 (1.00)	0.0321 (1.00)	3.06e-11 (2.77e-08)	1.2e-12 (1.09e-09)	2.06e-08 (1.78e-05)	6.59e-09 (5.75e-06)	1.29e-07 (0.000108)	8.78e-10 (7.85e-07)
Amp Peak 21(12q15)	0 (0%)	335	0.221 (1.00)	0.103 (1.00)	2.89e-07 (0.000238)	0.00504 (1.00)	0.0157 (1.00)	0.038 (1.00)	2.14e-09 (1.9e-06)	8.58e-11 (7.72e-08)	1.46e-08 (1.27e-05)	4.39e-08 (3.73e-05)	6.72e-08 (5.68e-05)	7.88e-08 (6.65e-05)
Amp Peak 23(14q13 3)	0 (0%)	273	0.562 (1.00)	0.254 (1.00)	1.38e-14 (1.28e-11)	0.000402 (0.256)	0.0222 (1.00)	0.0492 (1.00)	2.72e-05 (0.0194)	9.59e-06 (0.0071)	1.98e-09 (1.76e-06)	2.98e-09 (2.62e-06)	4.18e-05 (0.0293)	1.78e-05 (0.0129)
Amp Peak 25(17q12)	0 (0%)	276	0.179 (1.00)	0.049 (1.00)	1.92e-13 (1.77e-10)	1.16e-05 (0.0086)	0.437 (1.00)	0.0065 (1.00)	1.77e-06 (0.00139)	2.48e-09 (2.19e-06)	1.7e-07 (0.000141)	3.3e-06 (0.00252)	0.00142 (0.833)	2.52e-05 (0.0181)
Amp Peak 27(18q11 2)	0 (0%)	396	0.195 (1.00)	0.0151 (1.00)	0.000102 (0.0689)	8.74e-06 (0.00652)	0.131 (1.00)	0.0291 (1.00)	9.11e-05 (0.0621)	2.62e-06 (0.00202)	0.000158 (0.105)	1.3e-07 (0.000109)	0.00463 (1.00)	1.69e-05 (0.0123)
Amp Peak 28(19q12)	0 (0%)	361	0.0514 (1.00)	0.0219 (1.00)	0.00128 (0.757)	3.75e-05 (0.0263)	0.179 (1.00)	0.389 (1.00)	2.4e-06 (0.00185)	4.81e-08 (4.08e-05)	5.95e-05 (0.0412)	9.91e-07 (0.000794)	8.73e-05 (0.0597)	4.13e-07 (0.000339)
Amp Peak 29(20p11 21)	0 (0%)	306	0.0611 (1.00)	0.0953 (1.00)	3.14e-05 (0.0222)	0.000329 (0.212)	0.193 (1.00)	0.124 (1.00)	0.00818 (1.00)	8.3e-06 (0.00622)	7.58e-05 (0.0519)	1.48e-05 (0.0108)	0.000152 (0.101)	3.5e-05 (0.0247)
Amp Peak 30(20q13 33)	0 (0%)	257	0.00559 (1.00)	0.0301 (1.00)	5.43e-09 (4.74e-06)	3.32e-05 (0.0235)	0.0121 (1.00)	0.00388 (1.00)	0.00202 (1.00)	0.000179 (0.118)	8.24e-06 (0.00618)	2.42e-08 (2.08e-05)	4.23e-05 (0.0295)	9.68e-05 (0.0658)
Del Peak 9(4q22 1)	0 (0%)	342	0.000214 (0.141)	9.89e-05 (0.0671)	1.2e-05 (0.00884)	0.0017 (0.976)	0.497 (1.00)	0.119 (1.00)	4.53e-08 (3.84e-05)	5.66e-11 (5.11e-08)	5.74e-07 (0.000466)	1.71e-06 (0.00134)	0.00422 (1.00)	0.00221 (1.00)
Del Peak 10(4q35 1)	0 (0%)	312	0.00204 (1.00)	0.00118 (0.699)	1.72e-08 (1.49e-05)	0.000508 (0.319)	0.0329 (1.00)	0.000534 (0.335)	8.81e-13 (8.08e-10)	2.67e-16 (2.49e-13)	2.23e-09 (1.97e-06)	8.26e-10 (7.4e-07)	1.96e-05 (0.0142)	4.69e-07 (0.000382)
Del Peak 22(9q21 11)	0 (0%)	250	0.0335 (1.00)	0.597 (1.00)	6.15e-07 (0.000497)	0.000348 (0.223)	0.375 (1.00)	0.0173 (1.00)	1.42e-05 (0.0104)	2.62e-08 (2.24e-05)	0.000103 (0.0693)	0.000101 (0.0682)	0.0101 (1.00)	2.48e-05 (0.0178)
Del Peak 32(13q14 2)	0 (0%)	223	0.00862 (1.00)	0.0218 (1.00)	1.48e-22 (1.39e-19)	0.0392 (1.00)	0.000253 (0.166)	4.43e-07 (0.000362)	2.27e-06 (0.00176)	3.18e-08 (2.72e-05)	0.000673 (0.416)	0.000297 (0.193)	0.000223 (0.146)	0.00211 (1.00)
Amp Peak 14(8p11 21)	0 (0%)	322	0.253 (1.00)	0.124 (1.00)	5.23e-24 (4.96e-21)	0.00149 (0.87)	0.0219 (1.00)	0.135 (1.00)	6.76e-07 (0.000545)	5.91e-07 (0.000479)	0.000535 (0.335)	6.43e-06 (0.00487)	0.000235 (0.154)	0.000293 (0.19)
Amp Peak 26(17q23 1)	0 (0%)	252	0.081 (1.00)	0.208 (1.00)	1.98e-14 (1.83e-11)	1.68e-07 (0.00014)	0.0611 (1.00)	0.00369 (1.00)	4.1e-08 (3.49e-05)	5.23e-13 (4.8e-10)	3.16e-07 (0.00026)	3.32e-05 (0.0235)	0.00753 (1.00)	0.000941 (0.566)
Del Peak 16(8p23 2)	0 (0%)	253	0.00526 (1.00)	0.00382 (1.00)	3.17e-23 (3e-20)	0.0813 (1.00)	0.00998 (1.00)	3.52e-05 (0.0248)	5.51e-07 (0.000448)	2.48e-08 (2.13e-05)	1.59e-05 (0.0116)	0.0143 (1.00)	0.000644 (0.4)	6.77e-05 (0.0467)
Del Peak 43(19q13 33)	0 (0%)	309	0.272 (1.00)	0.383 (1.00)	1.99e-07 (0.000165)	9.04e-07 (0.000727)	0.101 (1.00)	0.0998 (1.00)	6.03e-05 (0.0417)	0.000273 (0.178)	0.000258 (0.168)	6.24e-06 (0.00473)	0.0752 (1.00)	0.000834 (0.507)
Amp Peak 17(10p15 1)	0 (0%)	360	0.023 (1.00)	0.0262 (1.00)	4.31e-05 (0.03)	0.000123 (0.0823)	0.00493 (1.00)	0.00453 (1.00)	1.75e-09 (1.56e-06)	2.32e-09 (2.05e-06)	0.000527 (0.331)	4.57e-05 (0.0318)	0.0179 (1.00)	0.0043 (1.00)
Del Peak 5(3p21 31)	0 (0%)	257	0.132 (1.00)	0.478 (1.00)	5.06e-06 (0.00385)	1.67e-06 (0.00131)	0.0206 (1.00)	0.00244 (1.00)	3.45e-05 (0.0244)	2.64e-10 (2.37e-07)	1.17e-05 (0.00865)	0.00412 (1.00)	0.000722 (0.445)	0.000676 (0.417)
Del Peak 8(4p16 3)	0 (0%)	371	0.595 (1.00)	0.453 (1.00)	2.44e-05 (0.0175)	0.356 (1.00)	0.552 (1.00)	0.203 (1.00)	2.87e-05 (0.0204)	2.2e-07 (0.000182)	2.38e-06 (0.00184)	2.15e-06 (0.00167)	0.00465 (1.00)	0.00159 (0.917)
Del Peak 25(11p15 5)	0 (0%)	361	0.268 (1.00)	0.0576 (1.00)	2.53e-06 (0.00195)	0.0563 (1.00)	0.00991 (1.00)	0.0216 (1.00)	0.00309 (1.00)	1.95e-08 (1.68e-05)	0.000342 (0.219)	2.29e-05 (0.0165)	4.2e-05 (0.0294)	0.00241 (1.00)
Del Peak 45(21q11 2)	0 (0%)	330	0.0604 (1.00)	0.0501 (1.00)	4.85e-06 (0.00369)	0.0259 (1.00)	0.0727 (1.00)	0.00275 (1.00)	4.86e-13 (4.47e-10)	5.18e-10 (4.65e-07)	1.45e-05 (0.0107)	7.93e-08 (6.68e-05)	0.00222 (1.00)	0.000779 (0.476)
Amp Peak 10(7p21 1)	0 (0%)	225	0.743 (1.00)	1 (1.00)	1.04e-22 (9.8e-20)	0.00576 (1.00)	0.0083 (1.00)	0.00781 (1.00)	1.03e-07 (8.67e-05)	8.81e-10 (7.87e-07)	1.36e-05 (0.01)	0.00469 (1.00)	0.00246 (1.00)	0.000878 (0.53)
Del Peak 1(1p36 13)	0 (0%)	378	0.795 (1.00)	0.441 (1.00)	3.08e-05 (0.0219)	2.38e-05 (0.0171)	0.757 (1.00)	0.596 (1.00)	2.78e-08 (2.38e-05)	8.52e-07 (0.000686)	0.0437 (1.00)	0.00932 (1.00)	0.0887 (1.00)	0.153 (1.00)
Del Peak 17(8p12)	0 (0%)	278	0.106 (1.00)	0.12 (1.00)	3.23e-21 (3.04e-18)	0.0229 (1.00)	0.0368 (1.00)	0.00197 (1.00)	1.14e-06 (0.000912)	3.13e-08 (2.68e-05)	9.57e-05 (0.0651)	0.0207 (1.00)	0.000486 (0.307)	0.000594 (0.371)
Del Peak 30(13q12 11)	0 (0%)	213	0.00113 (0.673)	0.0134 (1.00)	1.98e-21 (1.86e-18)	0.00999 (1.00)	0.000778 (0.476)	2.04e-06 (0.00159)	3.33e-06 (0.00255)	5.38e-08 (4.56e-05)	0.000937 (0.564)	0.000731 (0.45)	0.00149 (0.869)	0.00697 (1.00)
Del Peak 31(13q12 13)	0 (0%)	212	0.00862 (1.00)	0.0218 (1.00)	1.29e-22 (1.22e-19)	0.0033 (1.00)	0.000455 (0.288)	3.7e-07 (0.000303)	1.2e-05 (0.00883)	1.81e-07 (0.00015)	0.00151 (0.876)	0.000477 (0.301)	0.00158 (0.917)	0.00712 (1.00)
Del Peak 33(13q34)	0 (0%)	263	0.0356 (1.00)	0.0445 (1.00)	7.07e-16 (6.58e-13)	0.038 (1.00)	0.000732 (0.45)	2.71e-05 (0.0194)	7.3e-05 (0.05)	1.99e-05 (0.0144)	0.0122 (1.00)	0.0172 (1.00)	0.0222 (1.00)	0.277 (1.00)
Del Peak 35(15q11 2)	0 (0%)	241	0.168 (1.00)	0.157 (1.00)	6.48e-11 (5.85e-08)	0.0184 (1.00)	0.0926 (1.00)	0.0351 (1.00)	3.52e-06 (0.00269)	4.48e-06 (0.00341)	2e-05 (0.0145)	0.00867 (1.00)	0.115 (1.00)	0.0277 (1.00)
Del Peak 37(17p13 3)	0 (0%)	226	0.386 (1.00)	0.609 (1.00)	5.27e-19 (4.94e-16)	8.9e-05 (0.0608)	0.0442 (1.00)	0.00121 (0.714)	1.51e-06 (0.00119)	8.24e-08 (6.94e-05)	0.00417 (1.00)	0.112 (1.00)	0.0768 (1.00)	0.00477 (1.00)
Del Peak 38(17p11 2)	0 (0%)	277	0.264 (1.00)	0.208 (1.00)	1.66e-16 (1.55e-13)	3.44e-07 (0.000284)	0.00382 (1.00)	0.000825 (0.502)	1.14e-06 (0.000912)	1.02e-07 (8.56e-05)	0.0292 (1.00)	0.0585 (1.00)	0.148 (1.00)	0.0157 (1.00)
Del Peak 40(18q23)	0 (0%)	255	0.029 (1.00)	0.0968 (1.00)	1.15e-14 (1.07e-11)	0.53 (1.00)	0.00424 (1.00)	0.000383 (0.245)	3.74e-05 (0.0263)	3.89e-06 (0.00297)	0.00291 (1.00)	0.33 (1.00)	0.106 (1.00)	0.0734 (1.00)
Amp Peak 3(1q21 3)	0 (0%)	138	0.362 (1.00)	0.465 (1.00)	5.98e-07 (0.000484)	3.89e-09 (3.41e-06)	0.238 (1.00)	0.305 (1.00)	0.0015 (0.874)	0.0521 (1.00)	0.0109 (1.00)	0.000106 (0.0715)	0.00723 (1.00)	0.00883 (1.00)
Amp Peak 7(5p13 1)	0 (0%)	202	0.263 (1.00)	0.897 (1.00)	2.29e-15 (2.13e-12)	0.127 (1.00)	0.424 (1.00)	0.114 (1.00)	0.0171 (1.00)	0.00131 (0.769)	0.000222 (0.146)	0.000458 (0.29)	0.0045 (1.00)	0.000127 (0.0844)
Amp Peak 12(7q31 2)	0 (0%)	287	0.482 (1.00)	0.429 (1.00)	4.48e-11 (4.06e-08)	0.0263 (1.00)	0.34 (1.00)	0.0924 (1.00)	2.52e-06 (0.00195)	1.18e-09 (1.05e-06)	0.000813 (0.496)	0.00782 (1.00)	0.0114 (1.00)	0.00606 (1.00)
Amp Peak 13(8p11 23)	0 (0%)	360	0.294 (1.00)	0.107 (1.00)	3.83e-21 (3.59e-18)	0.00108 (0.646)	0.0452 (1.00)	0.0707 (1.00)	1.34e-06 (0.00106)	2.14e-05 (0.0154)	0.0453 (1.00)	0.00158 (0.917)	0.142 (1.00)	0.0496 (1.00)
Amp Peak 32(Xq28)	0 (0%)	339	0.301 (1.00)	0.123 (1.00)	1.16e-12 (1.06e-09)	0.00783 (1.00)	0.106 (1.00)	0.0815 (1.00)	2.17e-06 (0.00169)	1.8e-06 (0.00141)	0.00967 (1.00)	0.135 (1.00)	0.00254 (1.00)	0.165 (1.00)
Del Peak 4(2q37 3)	0 (0%)	429	0.703 (1.00)	0.206 (1.00)	0.000183 (0.121)	0.000213 (0.14)	0.2 (1.00)	0.0856 (1.00)	0.0252 (1.00)	0.0386 (1.00)	0.00601 (1.00)	0.000108 (0.0725)	0.0213 (1.00)	0.000859 (0.52)
Del Peak 24(10q26 3)	0 (0%)	355	0.748 (1.00)	0.283 (1.00)	3.91e-07 (0.000321)	0.00551 (1.00)	0.000972 (0.581)	0.000956 (0.572)	0.026 (1.00)	0.0546 (1.00)	0.0122 (1.00)	0.00198 (1.00)	8.68e-06 (0.00648)	6.07e-05 (0.0419)
Del Peak 29(12q24 33)	0 (0%)	375	0.063 (1.00)	0.0396 (1.00)	8.07e-06 (0.00606)	0.294 (1.00)	0.0336 (1.00)	0.0306 (1.00)	1.27e-06 (0.00101)	0.00017 (0.113)	0.158 (1.00)	0.0044 (1.00)	0.173 (1.00)	0.0572 (1.00)
Del Peak 36(16q23 1)	0 (0%)	326	0.0587 (1.00)	0.312 (1.00)	1.62e-06 (0.00127)	0.00461 (1.00)	0.0159 (1.00)	0.0261 (1.00)	4.43e-07 (0.000362)	3.16e-09 (2.77e-06)	0.0376 (1.00)	0.0743 (1.00)	0.0391 (1.00)	0.00249 (1.00)
Del Peak 39(18q21 32)	0 (0%)	252	0.115 (1.00)	0.227 (1.00)	2.62e-13 (2.42e-10)	0.839 (1.00)	0.0154 (1.00)	0.000642 (0.4)	6.96e-05 (0.0479)	4.19e-05 (0.0293)	0.00691 (1.00)	0.375 (1.00)	0.264 (1.00)	0.101 (1.00)
Amp Peak 6(5p15 33)	0 (0%)	177	0.878 (1.00)	0.901 (1.00)	1.9e-18 (1.78e-15)	0.387 (1.00)	0.0749 (1.00)	0.0138 (1.00)	0.00232 (1.00)	0.00194 (1.00)	0.000591 (0.369)	0.000659 (0.408)	0.0127 (1.00)	0.000287 (0.187)
Amp Peak 9(6p21 1)	0 (0%)	311	0.675 (1.00)	0.206 (1.00)	4.66e-07 (0.00038)	2.24e-09 (1.98e-06)	0.128 (1.00)	0.939 (1.00)	0.0397 (1.00)	0.33 (1.00)	0.0447 (1.00)	0.0112 (1.00)	0.0638 (1.00)	0.0158 (1.00)
Del Peak 2(1p13 2)	0 (0%)	344	0.703 (1.00)	0.707 (1.00)	1.25e-07 (0.000104)	0.000878 (0.53)	0.748 (1.00)	0.133 (1.00)	2.01e-06 (0.00157)	0.00248 (1.00)	0.296 (1.00)	0.00721 (1.00)	0.215 (1.00)	0.0396 (1.00)
Del Peak 47(Xp22 2)	0 (0%)	351	0.691 (1.00)	0.896 (1.00)	1.52e-08 (1.31e-05)	0.032 (1.00)	0.0145 (1.00)	0.0321 (1.00)	0.00179 (1.00)	0.000113 (0.0756)	0.397 (1.00)	0.665 (1.00)	0.68 (1.00)	0.355 (1.00)
Amp Peak 1(1p34 3)	0 (0%)	365	0.553 (1.00)	0.384 (1.00)	1.81e-08 (1.56e-05)	0.845 (1.00)	0.317 (1.00)	0.104 (1.00)	0.137 (1.00)	0.439 (1.00)	0.147 (1.00)	0.149 (1.00)	0.313 (1.00)	0.578 (1.00)
Amp Peak 2(1p22 3)	0 (0%)	364	0.876 (1.00)	1 (1.00)	7.59e-09 (6.61e-06)	0.493 (1.00)	0.779 (1.00)	0.175 (1.00)	0.0132 (1.00)	0.00847 (1.00)	0.0941 (1.00)	0.0582 (1.00)	0.385 (1.00)	0.0532 (1.00)
Amp Peak 5(4q12)	0 (0%)	402	0.703 (1.00)	0.206 (1.00)	3.11e-12 (2.84e-09)	0.0172 (1.00)	0.218 (1.00)	0.0768 (1.00)	0.00641 (1.00)	0.000849 (0.514)	0.00908 (1.00)	0.0902 (1.00)	0.169 (1.00)	0.0151 (1.00)
Amp Peak 8(5q35 1)	0 (0%)	374	0.0862 (1.00)	0.453 (1.00)	0.0123 (1.00)	0.238 (1.00)	0.0276 (1.00)	0.0438 (1.00)	0.000413 (0.262)	2.38e-06 (0.00184)	0.00225 (1.00)	0.00133 (0.781)	0.00397 (1.00)	0.00384 (1.00)
Amp Peak 24(16p11 2)	0 (0%)	334	0.799 (1.00)	0.229 (1.00)	2.33e-06 (0.00181)	0.547 (1.00)	0.412 (1.00)	0.102 (1.00)	0.0609 (1.00)	0.204 (1.00)	0.0473 (1.00)	0.00743 (1.00)	0.287 (1.00)	0.264 (1.00)
Amp Peak 31(22q11 22)	0 (0%)	410	0.268 (1.00)	0.162 (1.00)	0.000124 (0.0828)	0.684 (1.00)	0.0265 (1.00)	0.0205 (1.00)	0.454 (1.00)	0.161 (1.00)	0.055 (1.00)	0.184 (1.00)	0.0374 (1.00)	0.207 (1.00)
Del Peak 3(2q22 1)	0 (0%)	446	0.869 (1.00)	0.78 (1.00)	0.00371 (1.00)	9.88e-05 (0.0671)	0.058 (1.00)	0.546 (1.00)	0.000946 (0.567)	0.00134 (0.787)	0.0698 (1.00)	0.00226 (1.00)	0.403 (1.00)	0.011 (1.00)
Del Peak 6(3q11 1)	0 (0%)	354	0.609 (1.00)	0.602 (1.00)	0.138 (1.00)	0.000315 (0.204)	0.773 (1.00)	0.537 (1.00)	0.0203 (1.00)	0.0101 (1.00)	0.833 (1.00)	0.989 (1.00)	0.98 (1.00)	0.81 (1.00)
Del Peak 7(3q29)	0 (0%)	359	0.71 (1.00)	0.602 (1.00)	0.0668 (1.00)	0.00011 (0.0737)	0.115 (1.00)	0.022 (1.00)	0.000392 (0.25)	0.00433 (1.00)	0.943 (1.00)	0.648 (1.00)	0.731 (1.00)	0.988 (1.00)
Del Peak 14(6q22 31)	0 (0%)	245	0.54 (1.00)	0.187 (1.00)	0.00575 (1.00)	3.5e-07 (0.000288)	0.692 (1.00)	0.123 (1.00)	0.14 (1.00)	0.431 (1.00)	0.667 (1.00)	0.167 (1.00)	0.458 (1.00)	0.332 (1.00)
Del Peak 15(6q26)	0 (0%)	243	0.368 (1.00)	0.276 (1.00)	0.000624 (0.389)	2.12e-05 (0.0153)	0.618 (1.00)	0.454 (1.00)	0.0339 (1.00)	0.138 (1.00)	0.683 (1.00)	0.236 (1.00)	0.181 (1.00)	0.563 (1.00)
Del Peak 18(8p11 21)	0 (0%)	381	0.795 (1.00)	0.504 (1.00)	2.61e-19 (2.45e-16)	0.195 (1.00)	0.291 (1.00)	0.293 (1.00)	0.0123 (1.00)	0.0321 (1.00)	0.232 (1.00)	0.571 (1.00)	0.21 (1.00)	0.43 (1.00)
Del Peak 23(10p15 3)	0 (0%)	373	1 (1.00)	1 (1.00)	1.86e-05 (0.0135)	0.06 (1.00)	0.52 (1.00)	0.133 (1.00)	0.501 (1.00)	0.584 (1.00)	0.0063 (1.00)	0.00896 (1.00)	0.000506 (0.319)	0.00388 (1.00)
Del Peak 28(12q12)	0 (0%)	400	0.597 (1.00)	0.644 (1.00)	0.00105 (0.628)	0.038 (1.00)	0.0252 (1.00)	0.0377 (1.00)	0.000148 (0.0986)	0.00945 (1.00)	0.0823 (1.00)	0.0231 (1.00)	0.709 (1.00)	0.424 (1.00)
Amp Peak 22(13q33 3)	0 (0%)	420	0.172 (1.00)	0.105 (1.00)	0.0772 (1.00)	0.000648 (0.402)	0.719 (1.00)	0.819 (1.00)	0.276 (1.00)	0.265 (1.00)	0.13 (1.00)	0.0921 (1.00)	0.22 (1.00)	0.0103 (1.00)
Del Peak 13(6q12)	0 (0%)	318	0.488 (1.00)	0.52 (1.00)	0.0201 (1.00)	0.057 (1.00)	0.325 (1.00)	0.827 (1.00)	0.506 (1.00)	0.675 (1.00)	0.0177 (1.00)	0.094 (1.00)	0.629 (1.00)	0.376 (1.00)
Del Peak 19(8q11 21)	0 (0%)	431	1 (1.00)	1 (1.00)	0.0031 (1.00)	0.624 (1.00)	0.309 (1.00)	1 (1.00)	0.281 (1.00)	0.215 (1.00)	0.244 (1.00)	0.673 (1.00)	0.893 (1.00)	0.803 (1.00)
Del Peak 20(9p23)	0 (0%)	224	0.521 (1.00)	0.901 (1.00)	0.00298 (1.00)	0.655 (1.00)	0.565 (1.00)	0.307 (1.00)	0.0643 (1.00)	0.00359 (1.00)	0.291 (1.00)	0.0958 (1.00)	0.476 (1.00)	0.237 (1.00)
Del Peak 21(9p21 3)	0 (0%)	219	0.521 (1.00)	0.901 (1.00)	0.00111 (0.661)	0.212 (1.00)	0.293 (1.00)	0.129 (1.00)	0.31 (1.00)	0.0135 (1.00)	0.245 (1.00)	0.191 (1.00)	0.633 (1.00)	0.419 (1.00)
Del Peak 26(11q25)	0 (0%)	384	0.108 (1.00)	0.0799 (1.00)	0.00392 (1.00)	0.000417 (0.265)	0.00412 (1.00)	0.22 (1.00)	0.00217 (1.00)	0.0166 (1.00)	0.2 (1.00)	0.0521 (1.00)	0.371 (1.00)	0.195 (1.00)
Del Peak 27(12p13 2)	0 (0%)	362	0.255 (1.00)	0.719 (1.00)	0.00588 (1.00)	0.00358 (1.00)	0.0102 (1.00)	0.0404 (1.00)	0.0248 (1.00)	0.081 (1.00)	0.794 (1.00)	0.988 (1.00)	0.533 (1.00)	0.714 (1.00)
Del Peak 34(14q32 33)	0 (0%)	349	0.703 (1.00)	0.302 (1.00)	0.0731 (1.00)	0.159 (1.00)	0.0799 (1.00)	0.037 (1.00)	0.0257 (1.00)	0.00327 (1.00)	0.102 (1.00)	0.0129 (1.00)	0.179 (1.00)	0.0677 (1.00)
Del Peak 44(20q13 12)	0 (0%)	410	0.17 (1.00)	0.874 (1.00)	0.444 (1.00)	0.117 (1.00)	0.104 (1.00)	0.412 (1.00)	0.157 (1.00)	0.548 (1.00)	0.19 (1.00)	0.129 (1.00)	0.012 (1.00)	0.314 (1.00)

'Amp Peak 1(1p34.3)' versus 'CN_CNMF'

P value = 1.81e-08 (Fisher's exact test), Q value = 1.6e-05

Table S1. Gene #1: 'Amp Peak 1(1p34.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
AMP PEAK 1(1P34.3) CNV	77	34	17
AMP PEAK 1(1P34.3) WILD-TYPE	110	180	75

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1p34.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 2(1p22.3)' versus 'CN_CNMF'

P value = 7.59e-09 (Fisher's exact test), Q value = 6.6e-06

Table S2. Gene #2: 'Amp Peak 2(1p22.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
AMP PEAK 2(1P22.3) CNV	77	31	21
AMP PEAK 2(1P22.3) WILD-TYPE	110	183	71

Figure S2. Get High-res Image Gene #2: 'Amp Peak 2(1p22.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 3(1q21.3)' versus 'CN_CNMF'

P value = 5.98e-07 (Fisher's exact test), Q value = 0.00048

Table S3. Gene #3: 'Amp Peak 3(1q21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
AMP PEAK 3(1Q21.3) CNV	146	129	80
AMP PEAK 3(1Q21.3) WILD-TYPE	41	85	12

Figure S3. Get High-res Image Gene #3: 'Amp Peak 3(1q21.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 3(1q21.3)' versus 'METHLYATION_CNMF'

P value = 3.89e-09 (Fisher's exact test), Q value = 3.4e-06

Table S4. Gene #3: 'Amp Peak 3(1q21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
AMP PEAK 3(1Q21.3) CNV	123	107	83
AMP PEAK 3(1Q21.3) WILD-TYPE	18	33	67

Figure S4. Get High-res Image Gene #3: 'Amp Peak 3(1q21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 3(1q21.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000106 (Fisher's exact test), Q value = 0.072

Table S5. Gene #3: 'Amp Peak 3(1q21.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
AMP PEAK 3(1Q21.3) CNV	31	200	120
AMP PEAK 3(1Q21.3) WILD-TYPE	20	49	68

Figure S5. Get High-res Image Gene #3: 'Amp Peak 3(1q21.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 4(3q26.2)' versus 'MRNA_CNMF'

P value = 0.000264 (Fisher's exact test), Q value = 0.17

Table S6. Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	5	9	12	6
AMP PEAK 4(3Q26.2) CNV	0	6	0	4
AMP PEAK 4(3Q26.2) WILD-TYPE	5	3	12	2

Figure S6. Get High-res Image Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 4(3q26.2)' versus 'CN_CNMF'

P value = 1.15e-05 (Fisher's exact test), Q value = 0.0085

Table S7. Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
AMP PEAK 4(3Q26.2) CNV	69	48	45
AMP PEAK 4(3Q26.2) WILD-TYPE	118	166	47

Figure S7. Get High-res Image Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 4(3q26.2)' versus 'MRNASEQ_CNMF'

P value = 2.81e-09 (Fisher's exact test), Q value = 2.5e-06

Table S8. Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
AMP PEAK 4(3Q26.2) CNV	23	67	66
AMP PEAK 4(3Q26.2) WILD-TYPE	132	94	84

Figure S8. Get High-res Image Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 4(3q26.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-09 (Fisher's exact test), Q value = 2.6e-06

Table S9. Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
AMP PEAK 4(3Q26.2) CNV	49	39	68
AMP PEAK 4(3Q26.2) WILD-TYPE	69	169	72

Figure S9. Get High-res Image Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 4(3q26.2)' versus 'MIRSEQ_CNMF'

P value = 1.43e-06 (Fisher's exact test), Q value = 0.0011

Table S10. Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 4(3Q26.2) CNV	37	102	21
AMP PEAK 4(3Q26.2) WILD-TYPE	142	129	57

Figure S10. Get High-res Image Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 4(3q26.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.31e-07 (Fisher's exact test), Q value = 0.00019

Table S11. Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
AMP PEAK 4(3Q26.2) CNV	9	110	41
AMP PEAK 4(3Q26.2) WILD-TYPE	42	139	147

Figure S11. Get High-res Image Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 4(3q26.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000329 (Fisher's exact test), Q value = 0.21

Table S12. Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
AMP PEAK 4(3Q26.2) CNV	34	80	22
AMP PEAK 4(3Q26.2) WILD-TYPE	121	112	56

Figure S12. Get High-res Image Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 4(3q26.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.96e-05 (Fisher's exact test), Q value = 0.034

Table S13. Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
AMP PEAK 4(3Q26.2) CNV	14	81	41
AMP PEAK 4(3Q26.2) WILD-TYPE	35	107	147

Figure S13. Get High-res Image Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 5(4q12)' versus 'CN_CNMF'

P value = 3.11e-12 (Fisher's exact test), Q value = 2.8e-09

Table S14. Gene #5: 'Amp Peak 5(4q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
AMP PEAK 5(4Q12) CNV	64	14	13
AMP PEAK 5(4Q12) WILD-TYPE	123	200	79

Figure S14. Get High-res Image Gene #5: 'Amp Peak 5(4q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 6(5p15.33)' versus 'CN_CNMF'

P value = 1.9e-18 (Fisher's exact test), Q value = 1.8e-15

Table S15. Gene #6: 'Amp Peak 6(5p15.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
AMP PEAK 6(5P15.33) CNV	161	94	61
AMP PEAK 6(5P15.33) WILD-TYPE	26	120	31

Figure S15. Get High-res Image Gene #6: 'Amp Peak 6(5p15.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 6(5p15.33)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000287 (Fisher's exact test), Q value = 0.19

Table S16. Gene #6: 'Amp Peak 6(5p15.33)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
AMP PEAK 6(5P15.33) CNV	31	141	104
AMP PEAK 6(5P15.33) WILD-TYPE	18	47	84

Figure S16. Get High-res Image Gene #6: 'Amp Peak 6(5p15.33)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 7(5p13.1)' versus 'CN_CNMF'

P value = 2.29e-15 (Fisher's exact test), Q value = 2.1e-12

Table S17. Gene #7: 'Amp Peak 7(5p13.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
AMP PEAK 7(5P13.1) CNV	147	84	60
AMP PEAK 7(5P13.1) WILD-TYPE	40	130	32

Figure S17. Get High-res Image Gene #7: 'Amp Peak 7(5p13.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 7(5p13.1)' versus 'MIRSEQ_CNMF'

P value = 0.000222 (Fisher's exact test), Q value = 0.15

Table S18. Gene #7: 'Amp Peak 7(5p13.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 7(5P13.1) CNV	85	155	50
AMP PEAK 7(5P13.1) WILD-TYPE	94	76	28

Figure S18. Get High-res Image Gene #7: 'Amp Peak 7(5p13.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 7(5p13.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000127 (Fisher's exact test), Q value = 0.084

Table S19. Gene #7: 'Amp Peak 7(5p13.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
AMP PEAK 7(5P13.1) CNV	30	133	93
AMP PEAK 7(5P13.1) WILD-TYPE	19	55	95

Figure S19. Get High-res Image Gene #7: 'Amp Peak 7(5p13.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 8(5q35.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.38e-06 (Fisher's exact test), Q value = 0.0018

Table S20. Gene #8: 'Amp Peak 8(5q35.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
AMP PEAK 8(5Q35.1) CNV	28	66	13
AMP PEAK 8(5Q35.1) WILD-TYPE	90	142	127

Figure S20. Get High-res Image Gene #8: 'Amp Peak 8(5q35.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 9(6p21.1)' versus 'CN_CNMF'

P value = 4.66e-07 (Fisher's exact test), Q value = 0.00038

Table S21. Gene #9: 'Amp Peak 9(6p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
AMP PEAK 9(6P21.1) CNV	78	53	51
AMP PEAK 9(6P21.1) WILD-TYPE	109	161	41

Figure S21. Get High-res Image Gene #9: 'Amp Peak 9(6p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 9(6p21.1)' versus 'METHLYATION_CNMF'

P value = 2.24e-09 (Fisher's exact test), Q value = 2e-06

Table S22. Gene #9: 'Amp Peak 9(6p21.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
AMP PEAK 9(6P21.1) CNV	75	57	28
AMP PEAK 9(6P21.1) WILD-TYPE	66	83	122

Figure S22. Get High-res Image Gene #9: 'Amp Peak 9(6p21.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 10(7p21.1)' versus 'CN_CNMF'

P value = 1.04e-22 (Fisher's exact test), Q value = 9.8e-20

Table S23. Gene #10: 'Amp Peak 10(7p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
AMP PEAK 10(7P21.1) CNV	154	78	36
AMP PEAK 10(7P21.1) WILD-TYPE	33	136	56

Figure S23. Get High-res Image Gene #10: 'Amp Peak 10(7p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 10(7p21.1)' versus 'MRNASEQ_CNMF'

P value = 1.03e-07 (Fisher's exact test), Q value = 8.7e-05

Table S24. Gene #10: 'Amp Peak 10(7p21.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
AMP PEAK 10(7P21.1) CNV	72	117	67
AMP PEAK 10(7P21.1) WILD-TYPE	83	44	83

Figure S24. Get High-res Image Gene #10: 'Amp Peak 10(7p21.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 10(7p21.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.81e-10 (Fisher's exact test), Q value = 7.9e-07

Table S25. Gene #10: 'Amp Peak 10(7p21.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
AMP PEAK 10(7P21.1) CNV	93	89	74
AMP PEAK 10(7P21.1) WILD-TYPE	25	119	66

Figure S25. Get High-res Image Gene #10: 'Amp Peak 10(7p21.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 10(7p21.1)' versus 'MIRSEQ_CNMF'

P value = 1.36e-05 (Fisher's exact test), Q value = 0.01

Table S26. Gene #10: 'Amp Peak 10(7p21.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 10(7P21.1) CNV	74	136	55
AMP PEAK 10(7P21.1) WILD-TYPE	105	95	23

Figure S26. Get High-res Image Gene #10: 'Amp Peak 10(7p21.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 11(7p11.2)' versus 'CN_CNMF'

P value = 4.99e-22 (Fisher's exact test), Q value = 4.7e-19

Table S27. Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
AMP PEAK 11(7P11.2) CNV	150	73	36
AMP PEAK 11(7P11.2) WILD-TYPE	37	141	56

Figure S27. Get High-res Image Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 11(7p11.2)' versus 'MRNASEQ_CNMF'

P value = 1.49e-08 (Fisher's exact test), Q value = 1.3e-05

Table S28. Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
AMP PEAK 11(7P11.2) CNV	65	116	67
AMP PEAK 11(7P11.2) WILD-TYPE	90	45	83

Figure S28. Get High-res Image Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 11(7p11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.91e-12 (Fisher's exact test), Q value = 6.3e-09

Table S29. Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
AMP PEAK 11(7P11.2) CNV	93	80	75
AMP PEAK 11(7P11.2) WILD-TYPE	25	128	65

Figure S29. Get High-res Image Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 11(7p11.2)' versus 'MIRSEQ_CNMF'

P value = 2.59e-08 (Fisher's exact test), Q value = 2.2e-05

Table S30. Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 11(7P11.2) CNV	64	137	55
AMP PEAK 11(7P11.2) WILD-TYPE	115	94	23

Figure S30. Get High-res Image Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 11(7p11.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000104 (Fisher's exact test), Q value = 0.07

Table S31. Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
AMP PEAK 11(7P11.2) CNV	33	147	76
AMP PEAK 11(7P11.2) WILD-TYPE	18	102	112

Figure S31. Get High-res Image Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 11(7p11.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.93e-05 (Fisher's exact test), Q value = 0.021

Table S32. Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
AMP PEAK 11(7P11.2) CNV	59	114	50
AMP PEAK 11(7P11.2) WILD-TYPE	96	78	28

Figure S32. Get High-res Image Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 11(7p11.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.26e-06 (Fisher's exact test), Q value = 0.0025

Table S33. Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
AMP PEAK 11(7P11.2) CNV	35	114	74
AMP PEAK 11(7P11.2) WILD-TYPE	14	74	114

Figure S33. Get High-res Image Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 12(7q31.2)' versus 'CN_CNMF'

P value = 4.48e-11 (Fisher's exact test), Q value = 4.1e-08

Table S34. Gene #12: 'Amp Peak 12(7q31.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
AMP PEAK 12(7Q31.2) CNV	114	59	33
AMP PEAK 12(7Q31.2) WILD-TYPE	73	155	59

Figure S34. Get High-res Image Gene #12: 'Amp Peak 12(7q31.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 12(7q31.2)' versus 'MRNASEQ_CNMF'

P value = 2.52e-06 (Fisher's exact test), Q value = 0.0019

Table S35. Gene #12: 'Amp Peak 12(7q31.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
AMP PEAK 12(7Q31.2) CNV	48	93	55
AMP PEAK 12(7Q31.2) WILD-TYPE	107	68	95

Figure S35. Get High-res Image Gene #12: 'Amp Peak 12(7q31.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 12(7q31.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.18e-09 (Fisher's exact test), Q value = 1.1e-06

Table S36. Gene #12: 'Amp Peak 12(7q31.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
AMP PEAK 12(7Q31.2) CNV	78	62	56
AMP PEAK 12(7Q31.2) WILD-TYPE	40	146	84

Figure S36. Get High-res Image Gene #12: 'Amp Peak 12(7q31.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 13(8p11.23)' versus 'CN_CNMF'

P value = 3.83e-21 (Fisher's exact test), Q value = 3.6e-18

Table S37. Gene #13: 'Amp Peak 13(8p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
AMP PEAK 13(8P11.23) CNV	30	39	64
AMP PEAK 13(8P11.23) WILD-TYPE	157	175	28

Figure S37. Get High-res Image Gene #13: 'Amp Peak 13(8p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 13(8p11.23)' versus 'MRNASEQ_CNMF'

P value = 1.34e-06 (Fisher's exact test), Q value = 0.0011

Table S38. Gene #13: 'Amp Peak 13(8p11.23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
AMP PEAK 13(8P11.23) CNV	27	33	63
AMP PEAK 13(8P11.23) WILD-TYPE	128	128	87

Figure S38. Get High-res Image Gene #13: 'Amp Peak 13(8p11.23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 13(8p11.23)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.14e-05 (Fisher's exact test), Q value = 0.015

Table S39. Gene #13: 'Amp Peak 13(8p11.23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
AMP PEAK 13(8P11.23) CNV	28	38	57
AMP PEAK 13(8P11.23) WILD-TYPE	90	170	83

Figure S39. Get High-res Image Gene #13: 'Amp Peak 13(8p11.23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 14(8p11.21)' versus 'CN_CNMF'

P value = 5.23e-24 (Fisher's exact test), Q value = 5e-21

Table S40. Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
AMP PEAK 14(8P11.21) CNV	48	48	75
AMP PEAK 14(8P11.21) WILD-TYPE	139	166	17

Figure S40. Get High-res Image Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 14(8p11.21)' versus 'MRNASEQ_CNMF'

P value = 6.76e-07 (Fisher's exact test), Q value = 0.00055

Table S41. Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
AMP PEAK 14(8P11.21) CNV	32	52	74
AMP PEAK 14(8P11.21) WILD-TYPE	123	109	76

Figure S41. Get High-res Image Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 14(8p11.21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.91e-07 (Fisher's exact test), Q value = 0.00048

Table S42. Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
AMP PEAK 14(8P11.21) CNV	45	45	68
AMP PEAK 14(8P11.21) WILD-TYPE	73	163	72

Figure S42. Get High-res Image Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 14(8p11.21)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.43e-06 (Fisher's exact test), Q value = 0.0049

Table S43. Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
AMP PEAK 14(8P11.21) CNV	17	111	42
AMP PEAK 14(8P11.21) WILD-TYPE	34	138	146

Figure S43. Get High-res Image Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 14(8p11.21)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000235 (Fisher's exact test), Q value = 0.15

Table S44. Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
AMP PEAK 14(8P11.21) CNV	37	86	27
AMP PEAK 14(8P11.21) WILD-TYPE	118	106	51

Figure S44. Get High-res Image Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 14(8p11.21)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000293 (Fisher's exact test), Q value = 0.19

Table S45. Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
AMP PEAK 14(8P11.21) CNV	20	83	47
AMP PEAK 14(8P11.21) WILD-TYPE	29	105	141

Figure S45. Get High-res Image Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 15(8q11.1)' versus 'CN_CNMF'

P value = 1.23e-22 (Fisher's exact test), Q value = 1.2e-19

Table S46. Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
AMP PEAK 15(8Q11.1) CNV	90	55	79
AMP PEAK 15(8Q11.1) WILD-TYPE	97	159	13

Figure S46. Get High-res Image Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 15(8q11.1)' versus 'METHLYATION_CNMF'

P value = 1.47e-06 (Fisher's exact test), Q value = 0.0012

Table S47. Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
AMP PEAK 15(8Q11.1) CNV	78	75	43
AMP PEAK 15(8Q11.1) WILD-TYPE	63	65	107

Figure S47. Get High-res Image Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 15(8q11.1)' versus 'MRNASEQ_CNMF'

P value = 2.22e-06 (Fisher's exact test), Q value = 0.0017

Table S48. Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
AMP PEAK 15(8Q11.1) CNV	46	78	87
AMP PEAK 15(8Q11.1) WILD-TYPE	109	83	63

Figure S48. Get High-res Image Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 15(8q11.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.32e-06 (Fisher's exact test), Q value = 0.001

Table S49. Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
AMP PEAK 15(8Q11.1) CNV	62	67	82
AMP PEAK 15(8Q11.1) WILD-TYPE	56	141	58

Figure S49. Get High-res Image Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 15(8q11.1)' versus 'MIRSEQ_CNMF'

P value = 1.31e-06 (Fisher's exact test), Q value = 0.001

Table S50. Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 15(8Q11.1) CNV	55	130	37
AMP PEAK 15(8Q11.1) WILD-TYPE	124	101	41

Figure S50. Get High-res Image Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 15(8q11.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.47e-05 (Fisher's exact test), Q value = 0.011

Table S51. Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
AMP PEAK 15(8Q11.1) CNV	24	137	61
AMP PEAK 15(8Q11.1) WILD-TYPE	27	112	127

Figure S51. Get High-res Image Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 15(8q11.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.04e-06 (Fisher's exact test), Q value = 0.006

Table S52. Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
AMP PEAK 15(8Q11.1) CNV	48	109	37
AMP PEAK 15(8Q11.1) WILD-TYPE	107	83	41

Figure S52. Get High-res Image Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 15(8q11.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.49e-06 (Fisher's exact test), Q value = 0.0049

Table S53. Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
AMP PEAK 15(8Q11.1) CNV	27	106	61
AMP PEAK 15(8Q11.1) WILD-TYPE	22	82	127

Figure S53. Get High-res Image Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 16(8q24.21)' versus 'CN_CNMF'

P value = 6.35e-19 (Fisher's exact test), Q value = 5.9e-16

Table S54. Gene #16: 'Amp Peak 16(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
AMP PEAK 16(8Q24.21) CNV	135	90	84
AMP PEAK 16(8Q24.21) WILD-TYPE	52	124	8

Figure S54. Get High-res Image Gene #16: 'Amp Peak 16(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 16(8q24.21)' versus 'METHLYATION_CNMF'

P value = 6.06e-08 (Fisher's exact test), Q value = 5.1e-05

Table S55. Gene #16: 'Amp Peak 16(8q24.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
AMP PEAK 16(8Q24.21) CNV	97	105	66
AMP PEAK 16(8Q24.21) WILD-TYPE	44	35	84

Figure S55. Get High-res Image Gene #16: 'Amp Peak 16(8q24.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 16(8q24.21)' versus 'MRNASEQ_CNMF'

P value = 1.68e-05 (Fisher's exact test), Q value = 0.012

Table S56. Gene #16: 'Amp Peak 16(8q24.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
AMP PEAK 16(8Q24.21) CNV	74	115	103
AMP PEAK 16(8Q24.21) WILD-TYPE	81	46	47

Figure S56. Get High-res Image Gene #16: 'Amp Peak 16(8q24.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 16(8q24.21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.15e-09 (Fisher's exact test), Q value = 8e-06

Table S57. Gene #16: 'Amp Peak 16(8q24.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
AMP PEAK 16(8Q24.21) CNV	91	99	102
AMP PEAK 16(8Q24.21) WILD-TYPE	27	109	38

Figure S57. Get High-res Image Gene #16: 'Amp Peak 16(8q24.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 16(8q24.21)' versus 'MIRSEQ_CNMF'

P value = 9e-06 (Fisher's exact test), Q value = 0.0067

Table S58. Gene #16: 'Amp Peak 16(8q24.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 16(8Q24.21) CNV	88	167	51
AMP PEAK 16(8Q24.21) WILD-TYPE	91	64	27

Figure S58. Get High-res Image Gene #16: 'Amp Peak 16(8q24.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 16(8q24.21)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.21

Table S59. Gene #16: 'Amp Peak 16(8q24.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
AMP PEAK 16(8Q24.21) CNV	30	177	99
AMP PEAK 16(8Q24.21) WILD-TYPE	21	72	89

Figure S59. Get High-res Image Gene #16: 'Amp Peak 16(8q24.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 16(8q24.21)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000257 (Fisher's exact test), Q value = 0.17

Table S60. Gene #16: 'Amp Peak 16(8q24.21)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
AMP PEAK 16(8Q24.21) CNV	32	135	97
AMP PEAK 16(8Q24.21) WILD-TYPE	17	53	91

Figure S60. Get High-res Image Gene #16: 'Amp Peak 16(8q24.21)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 17(10p15.1)' versus 'CN_CNMF'

P value = 4.31e-05 (Fisher's exact test), Q value = 0.03

Table S61. Gene #17: 'Amp Peak 17(10p15.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
AMP PEAK 17(10P15.1) CNV	57	38	38
AMP PEAK 17(10P15.1) WILD-TYPE	130	176	54

Figure S61. Get High-res Image Gene #17: 'Amp Peak 17(10p15.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 17(10p15.1)' versus 'METHLYATION_CNMF'

P value = 0.000123 (Fisher's exact test), Q value = 0.082

Table S62. Gene #17: 'Amp Peak 17(10p15.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
AMP PEAK 17(10P15.1) CNV	47	46	22
AMP PEAK 17(10P15.1) WILD-TYPE	94	94	128

Figure S62. Get High-res Image Gene #17: 'Amp Peak 17(10p15.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 17(10p15.1)' versus 'MRNASEQ_CNMF'

P value = 1.75e-09 (Fisher's exact test), Q value = 1.6e-06

Table S63. Gene #17: 'Amp Peak 17(10p15.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
AMP PEAK 17(10P15.1) CNV	16	44	62
AMP PEAK 17(10P15.1) WILD-TYPE	139	117	88

Figure S63. Get High-res Image Gene #17: 'Amp Peak 17(10p15.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 17(10p15.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.32e-09 (Fisher's exact test), Q value = 2.1e-06

Table S64. Gene #17: 'Amp Peak 17(10p15.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
AMP PEAK 17(10P15.1) CNV	33	28	61
AMP PEAK 17(10P15.1) WILD-TYPE	85	180	79

Figure S64. Get High-res Image Gene #17: 'Amp Peak 17(10p15.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 17(10p15.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.57e-05 (Fisher's exact test), Q value = 0.032

Table S65. Gene #17: 'Amp Peak 17(10p15.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
AMP PEAK 17(10P15.1) CNV	8	88	34
AMP PEAK 17(10P15.1) WILD-TYPE	43	161	154

Figure S65. Get High-res Image Gene #17: 'Amp Peak 17(10p15.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 18(11q13.3)' versus 'CN_CNMF'

P value = 5e-17 (Fisher's exact test), Q value = 4.7e-14

Table S66. Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
AMP PEAK 18(11Q13.3) CNV	85	28	50
AMP PEAK 18(11Q13.3) WILD-TYPE	102	186	42

Figure S66. Get High-res Image Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 18(11q13.3)' versus 'MRNASEQ_CNMF'

P value = 1.13e-07 (Fisher's exact test), Q value = 9.5e-05

Table S67. Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
AMP PEAK 18(11Q13.3) CNV	26	63	67
AMP PEAK 18(11Q13.3) WILD-TYPE	129	98	83

Figure S67. Get High-res Image Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 18(11q13.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.92e-11 (Fisher's exact test), Q value = 4.4e-08

Table S68. Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
AMP PEAK 18(11Q13.3) CNV	50	36	70
AMP PEAK 18(11Q13.3) WILD-TYPE	68	172	70

Figure S68. Get High-res Image Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 18(11q13.3)' versus 'MIRSEQ_CNMF'

P value = 1.94e-09 (Fisher's exact test), Q value = 1.7e-06

Table S69. Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 18(11Q13.3) CNV	29	104	27
AMP PEAK 18(11Q13.3) WILD-TYPE	150	127	51

Figure S69. Get High-res Image Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 18(11q13.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.13e-06 (Fisher's exact test), Q value = 0.0017

Table S70. Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
AMP PEAK 18(11Q13.3) CNV	15	107	38
AMP PEAK 18(11Q13.3) WILD-TYPE	36	142	150

Figure S70. Get High-res Image Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 18(11q13.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.43e-06 (Fisher's exact test), Q value = 0.0011

Table S71. Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
AMP PEAK 18(11Q13.3) CNV	28	84	27
AMP PEAK 18(11Q13.3) WILD-TYPE	127	108	51

Figure S71. Get High-res Image Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 18(11q13.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.13e-05 (Fisher's exact test), Q value = 0.036

Table S72. Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
AMP PEAK 18(11Q13.3) CNV	17	81	41
AMP PEAK 18(11Q13.3) WILD-TYPE	32	107	147

Figure S72. Get High-res Image Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 19(12p12.1)' versus 'CN_CNMF'

P value = 6.39e-07 (Fisher's exact test), Q value = 0.00052

Table S73. Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
AMP PEAK 19(12P12.1) CNV	68	51	51
AMP PEAK 19(12P12.1) WILD-TYPE	119	163	41

Figure S73. Get High-res Image Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 19(12p12.1)' versus 'MRNASEQ_CNMF'

P value = 4.65e-07 (Fisher's exact test), Q value = 0.00038

Table S74. Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
AMP PEAK 19(12P12.1) CNV	29	64	69
AMP PEAK 19(12P12.1) WILD-TYPE	126	97	81

Figure S74. Get High-res Image Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 19(12p12.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.84e-08 (Fisher's exact test), Q value = 1.6e-05

Table S75. Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
AMP PEAK 19(12P12.1) CNV	46	44	72
AMP PEAK 19(12P12.1) WILD-TYPE	72	164	68

Figure S75. Get High-res Image Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 19(12p12.1)' versus 'MIRSEQ_CNMF'

P value = 8.03e-06 (Fisher's exact test), Q value = 0.006

Table S76. Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 19(12P12.1) CNV	41	104	22
AMP PEAK 19(12P12.1) WILD-TYPE	138	127	56

Figure S76. Get High-res Image Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 19(12p12.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.09e-06 (Fisher's exact test), Q value = 0.0039

Table S77. Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
AMP PEAK 19(12P12.1) CNV	11	111	45
AMP PEAK 19(12P12.1) WILD-TYPE	40	138	143

Figure S77. Get High-res Image Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 19(12p12.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.37e-07 (Fisher's exact test), Q value = 0.00075

Table S78. Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
AMP PEAK 19(12P12.1) CNV	30	88	25
AMP PEAK 19(12P12.1) WILD-TYPE	125	104	53

Figure S78. Get High-res Image Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 19(12p12.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.84e-06 (Fisher's exact test), Q value = 0.0022

Table S79. Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
AMP PEAK 19(12P12.1) CNV	15	87	41
AMP PEAK 19(12P12.1) WILD-TYPE	34	101	147

Figure S79. Get High-res Image Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 20(12q14.1)' versus 'CN_CNMF'

P value = 5.25e-09 (Fisher's exact test), Q value = 4.6e-06

Table S80. Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
AMP PEAK 20(12Q14.1) CNV	59	45	53
AMP PEAK 20(12Q14.1) WILD-TYPE	128	169	39

Figure S80. Get High-res Image Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 20(12q14.1)' versus 'MRNASEQ_CNMF'

P value = 3.06e-11 (Fisher's exact test), Q value = 2.8e-08

Table S81. Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
AMP PEAK 20(12Q14.1) CNV	22	49	76
AMP PEAK 20(12Q14.1) WILD-TYPE	133	112	74

Figure S81. Get High-res Image Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 20(12q14.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.2e-12 (Fisher's exact test), Q value = 1.1e-09

Table S82. Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
AMP PEAK 20(12Q14.1) CNV	34	36	77
AMP PEAK 20(12Q14.1) WILD-TYPE	84	172	63

Figure S82. Get High-res Image Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 20(12q14.1)' versus 'MIRSEQ_CNMF'

P value = 2.06e-08 (Fisher's exact test), Q value = 1.8e-05

Table S83. Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 20(12Q14.1) CNV	32	103	20
AMP PEAK 20(12Q14.1) WILD-TYPE	147	128	58

Figure S83. Get High-res Image Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 20(12q14.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.59e-09 (Fisher's exact test), Q value = 5.7e-06

Table S84. Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
AMP PEAK 20(12Q14.1) CNV	12	110	33
AMP PEAK 20(12Q14.1) WILD-TYPE	39	139	155

Figure S84. Get High-res Image Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 20(12q14.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.29e-07 (Fisher's exact test), Q value = 0.00011

Table S85. Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
AMP PEAK 20(12Q14.1) CNV	24	82	27
AMP PEAK 20(12Q14.1) WILD-TYPE	131	110	51

Figure S85. Get High-res Image Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 20(12q14.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.78e-10 (Fisher's exact test), Q value = 7.9e-07

Table S86. Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
AMP PEAK 20(12Q14.1) CNV	16	87	30
AMP PEAK 20(12Q14.1) WILD-TYPE	33	101	158

Figure S86. Get High-res Image Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 21(12q15)' versus 'CN_CNMF'

P value = 2.89e-07 (Fisher's exact test), Q value = 0.00024

Table S87. Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
AMP PEAK 21(12Q15) CNV	58	49	51
AMP PEAK 21(12Q15) WILD-TYPE	129	165	41

Figure S87. Get High-res Image Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 21(12q15)' versus 'MRNASEQ_CNMF'

P value = 2.14e-09 (Fisher's exact test), Q value = 1.9e-06

Table S88. Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
AMP PEAK 21(12Q15) CNV	27	46	76
AMP PEAK 21(12Q15) WILD-TYPE	128	115	74

Figure S88. Get High-res Image Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 21(12q15)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.58e-11 (Fisher's exact test), Q value = 7.7e-08

Table S89. Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
AMP PEAK 21(12Q15) CNV	32	41	76
AMP PEAK 21(12Q15) WILD-TYPE	86	167	64

Figure S89. Get High-res Image Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 21(12q15)' versus 'MIRSEQ_CNMF'

P value = 1.46e-08 (Fisher's exact test), Q value = 1.3e-05

Table S90. Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 21(12Q15) CNV	32	104	21
AMP PEAK 21(12Q15) WILD-TYPE	147	127	57

Figure S90. Get High-res Image Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 21(12q15)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.39e-08 (Fisher's exact test), Q value = 3.7e-05

Table S91. Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
AMP PEAK 21(12Q15) CNV	14	109	34
AMP PEAK 21(12Q15) WILD-TYPE	37	140	154

Figure S91. Get High-res Image Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 21(12q15)' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.72e-08 (Fisher's exact test), Q value = 5.7e-05

Table S92. Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
AMP PEAK 21(12Q15) CNV	24	83	28
AMP PEAK 21(12Q15) WILD-TYPE	131	109	50

Figure S92. Get High-res Image Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 21(12q15)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.88e-08 (Fisher's exact test), Q value = 6.7e-05

Table S93. Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
AMP PEAK 21(12Q15) CNV	16	85	34
AMP PEAK 21(12Q15) WILD-TYPE	33	103	154

Figure S93. Get High-res Image Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 23(14q13.3)' versus 'CN_CNMF'

P value = 1.38e-14 (Fisher's exact test), Q value = 1.3e-11

Table S94. Gene #23: 'Amp Peak 23(14q13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
AMP PEAK 23(14Q13.3) CNV	100	55	65
AMP PEAK 23(14Q13.3) WILD-TYPE	87	159	27

Figure S94. Get High-res Image Gene #23: 'Amp Peak 23(14q13.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 23(14q13.3)' versus 'MRNASEQ_CNMF'

P value = 2.72e-05 (Fisher's exact test), Q value = 0.019

Table S95. Gene #23: 'Amp Peak 23(14q13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
AMP PEAK 23(14Q13.3) CNV	47	88	74
AMP PEAK 23(14Q13.3) WILD-TYPE	108	73	76

Figure S95. Get High-res Image Gene #23: 'Amp Peak 23(14q13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 23(14q13.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.59e-06 (Fisher's exact test), Q value = 0.0071

Table S96. Gene #23: 'Amp Peak 23(14q13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
AMP PEAK 23(14Q13.3) CNV	67	68	74
AMP PEAK 23(14Q13.3) WILD-TYPE	51	140	66

Figure S96. Get High-res Image Gene #23: 'Amp Peak 23(14q13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 23(14q13.3)' versus 'MIRSEQ_CNMF'

P value = 1.98e-09 (Fisher's exact test), Q value = 1.8e-06

Table S97. Gene #23: 'Amp Peak 23(14q13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 23(14Q13.3) CNV	47	131	39
AMP PEAK 23(14Q13.3) WILD-TYPE	132	100	39

Figure S97. Get High-res Image Gene #23: 'Amp Peak 23(14q13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 23(14q13.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.98e-09 (Fisher's exact test), Q value = 2.6e-06

Table S98. Gene #23: 'Amp Peak 23(14q13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
AMP PEAK 23(14Q13.3) CNV	25	141	51
AMP PEAK 23(14Q13.3) WILD-TYPE	26	108	137

Figure S98. Get High-res Image Gene #23: 'Amp Peak 23(14q13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 23(14q13.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.18e-05 (Fisher's exact test), Q value = 0.029

Table S99. Gene #23: 'Amp Peak 23(14q13.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
AMP PEAK 23(14Q13.3) CNV	47	100	42
AMP PEAK 23(14Q13.3) WILD-TYPE	108	92	36

Figure S99. Get High-res Image Gene #23: 'Amp Peak 23(14q13.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 23(14q13.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.78e-05 (Fisher's exact test), Q value = 0.013

Table S100. Gene #23: 'Amp Peak 23(14q13.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
AMP PEAK 23(14Q13.3) CNV	28	101	60
AMP PEAK 23(14Q13.3) WILD-TYPE	21	87	128

Figure S100. Get High-res Image Gene #23: 'Amp Peak 23(14q13.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 24(16p11.2)' versus 'CN_CNMF'

P value = 2.33e-06 (Fisher's exact test), Q value = 0.0018

Table S101. Gene #24: 'Amp Peak 24(16p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
AMP PEAK 24(16P11.2) CNV	82	44	33
AMP PEAK 24(16P11.2) WILD-TYPE	105	170	59

Figure S101. Get High-res Image Gene #24: 'Amp Peak 24(16p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 25(17q12)' versus 'CN_CNMF'

P value = 1.92e-13 (Fisher's exact test), Q value = 1.8e-10

Table S102. Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
AMP PEAK 25(17Q12) CNV	111	53	53
AMP PEAK 25(17Q12) WILD-TYPE	76	161	39

Figure S102. Get High-res Image Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 25(17q12)' versus 'METHLYATION_CNMF'

P value = 1.16e-05 (Fisher's exact test), Q value = 0.0086

Table S103. Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
AMP PEAK 25(17Q12) CNV	64	77	42
AMP PEAK 25(17Q12) WILD-TYPE	77	63	108

Figure S103. Get High-res Image Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 25(17q12)' versus 'MRNASEQ_CNMF'

P value = 1.77e-06 (Fisher's exact test), Q value = 0.0014

Table S104. Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
AMP PEAK 25(17Q12) CNV	44	91	70
AMP PEAK 25(17Q12) WILD-TYPE	111	70	80

Figure S104. Get High-res Image Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 25(17q12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.48e-09 (Fisher's exact test), Q value = 2.2e-06

Table S105. Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
AMP PEAK 25(17Q12) CNV	72	59	74
AMP PEAK 25(17Q12) WILD-TYPE	46	149	66

Figure S105. Get High-res Image Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 25(17q12)' versus 'MIRSEQ_CNMF'

P value = 1.7e-07 (Fisher's exact test), Q value = 0.00014

Table S106. Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 25(17Q12) CNV	53	131	31
AMP PEAK 25(17Q12) WILD-TYPE	126	100	47

Figure S106. Get High-res Image Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 25(17q12)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.3e-06 (Fisher's exact test), Q value = 0.0025

Table S107. Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
AMP PEAK 25(17Q12) CNV	18	137	60
AMP PEAK 25(17Q12) WILD-TYPE	33	112	128

Figure S107. Get High-res Image Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 25(17q12)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.52e-05 (Fisher's exact test), Q value = 0.018

Table S108. Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
AMP PEAK 25(17Q12) CNV	20	103	59
AMP PEAK 25(17Q12) WILD-TYPE	29	85	129

Figure S108. Get High-res Image Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 26(17q23.1)' versus 'CN_CNMF'

P value = 1.98e-14 (Fisher's exact test), Q value = 1.8e-11

Table S109. Gene #26: 'Amp Peak 26(17q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
AMP PEAK 26(17Q23.1) CNV	125	62	54
AMP PEAK 26(17Q23.1) WILD-TYPE	62	152	38

Figure S109. Get High-res Image Gene #26: 'Amp Peak 26(17q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 26(17q23.1)' versus 'METHLYATION_CNMF'

P value = 1.68e-07 (Fisher's exact test), Q value = 0.00014

Table S110. Gene #26: 'Amp Peak 26(17q23.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
AMP PEAK 26(17Q23.1) CNV	64	92	50
AMP PEAK 26(17Q23.1) WILD-TYPE	77	48	100

Figure S110. Get High-res Image Gene #26: 'Amp Peak 26(17q23.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 26(17q23.1)' versus 'MRNASEQ_CNMF'

P value = 4.1e-08 (Fisher's exact test), Q value = 3.5e-05

Table S111. Gene #26: 'Amp Peak 26(17q23.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
AMP PEAK 26(17Q23.1) CNV	52	106	69
AMP PEAK 26(17Q23.1) WILD-TYPE	103	55	81

Figure S111. Get High-res Image Gene #26: 'Amp Peak 26(17q23.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 26(17q23.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.23e-13 (Fisher's exact test), Q value = 4.8e-10

Table S112. Gene #26: 'Amp Peak 26(17q23.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
AMP PEAK 26(17Q23.1) CNV	85	64	78
AMP PEAK 26(17Q23.1) WILD-TYPE	33	144	62

Figure S112. Get High-res Image Gene #26: 'Amp Peak 26(17q23.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 26(17q23.1)' versus 'MIRSEQ_CNMF'

P value = 3.16e-07 (Fisher's exact test), Q value = 0.00026

Table S113. Gene #26: 'Amp Peak 26(17q23.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 26(17Q23.1) CNV	62	142	35
AMP PEAK 26(17Q23.1) WILD-TYPE	117	89	43

Figure S113. Get High-res Image Gene #26: 'Amp Peak 26(17q23.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 26(17q23.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.32e-05 (Fisher's exact test), Q value = 0.024

Table S114. Gene #26: 'Amp Peak 26(17q23.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
AMP PEAK 26(17Q23.1) CNV	20	147	72
AMP PEAK 26(17Q23.1) WILD-TYPE	31	102	116

Figure S114. Get High-res Image Gene #26: 'Amp Peak 26(17q23.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 27(18q11.2)' versus 'CN_CNMF'

P value = 0.000102 (Fisher's exact test), Q value = 0.069

Table S115. Gene #27: 'Amp Peak 27(18q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
AMP PEAK 27(18Q11.2) CNV	43	25	29
AMP PEAK 27(18Q11.2) WILD-TYPE	144	189	63

Figure S115. Get High-res Image Gene #27: 'Amp Peak 27(18q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 27(18q11.2)' versus 'METHLYATION_CNMF'

P value = 8.74e-06 (Fisher's exact test), Q value = 0.0065

Table S116. Gene #27: 'Amp Peak 27(18q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
AMP PEAK 27(18Q11.2) CNV	46	26	15
AMP PEAK 27(18Q11.2) WILD-TYPE	95	114	135

Figure S116. Get High-res Image Gene #27: 'Amp Peak 27(18q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 27(18q11.2)' versus 'MRNASEQ_CNMF'

P value = 9.11e-05 (Fisher's exact test), Q value = 0.062

Table S117. Gene #27: 'Amp Peak 27(18q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
AMP PEAK 27(18Q11.2) CNV	17	30	46
AMP PEAK 27(18Q11.2) WILD-TYPE	138	131	104

Figure S117. Get High-res Image Gene #27: 'Amp Peak 27(18q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 27(18q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.62e-06 (Fisher's exact test), Q value = 0.002

Table S118. Gene #27: 'Amp Peak 27(18q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
AMP PEAK 27(18Q11.2) CNV	20	25	48
AMP PEAK 27(18Q11.2) WILD-TYPE	98	183	92

Figure S118. Get High-res Image Gene #27: 'Amp Peak 27(18q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 27(18q11.2)' versus 'MIRSEQ_CNMF'

P value = 0.000158 (Fisher's exact test), Q value = 0.11

Table S119. Gene #27: 'Amp Peak 27(18q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 27(18Q11.2) CNV	19	62	15
AMP PEAK 27(18Q11.2) WILD-TYPE	160	169	63

Figure S119. Get High-res Image Gene #27: 'Amp Peak 27(18q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 27(18q11.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.3e-07 (Fisher's exact test), Q value = 0.00011

Table S120. Gene #27: 'Amp Peak 27(18q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
AMP PEAK 27(18Q11.2) CNV	3	73	20
AMP PEAK 27(18Q11.2) WILD-TYPE	48	176	168

Figure S120. Get High-res Image Gene #27: 'Amp Peak 27(18q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 27(18q11.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.69e-05 (Fisher's exact test), Q value = 0.012

Table S121. Gene #27: 'Amp Peak 27(18q11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
AMP PEAK 27(18Q11.2) CNV	6	58	23
AMP PEAK 27(18Q11.2) WILD-TYPE	43	130	165

Figure S121. Get High-res Image Gene #27: 'Amp Peak 27(18q11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 28(19q12)' versus 'METHLYATION_CNMF'

P value = 3.75e-05 (Fisher's exact test), Q value = 0.026

Table S122. Gene #28: 'Amp Peak 28(19q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
AMP PEAK 28(19Q12) CNV	59	28	32
AMP PEAK 28(19Q12) WILD-TYPE	82	112	118

Figure S122. Get High-res Image Gene #28: 'Amp Peak 28(19q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 28(19q12)' versus 'MRNASEQ_CNMF'

P value = 2.4e-06 (Fisher's exact test), Q value = 0.0019

Table S123. Gene #28: 'Amp Peak 28(19q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
AMP PEAK 28(19Q12) CNV	21	45	58
AMP PEAK 28(19Q12) WILD-TYPE	134	116	92

Figure S123. Get High-res Image Gene #28: 'Amp Peak 28(19q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 28(19q12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.81e-08 (Fisher's exact test), Q value = 4.1e-05

Table S124. Gene #28: 'Amp Peak 28(19q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
AMP PEAK 28(19Q12) CNV	33	31	60
AMP PEAK 28(19Q12) WILD-TYPE	85	177	80

Figure S124. Get High-res Image Gene #28: 'Amp Peak 28(19q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 28(19q12)' versus 'MIRSEQ_CNMF'

P value = 5.95e-05 (Fisher's exact test), Q value = 0.041

Table S125. Gene #28: 'Amp Peak 28(19q12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 28(19Q12) CNV	30	83	19
AMP PEAK 28(19Q12) WILD-TYPE	149	148	59

Figure S125. Get High-res Image Gene #28: 'Amp Peak 28(19q12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 28(19q12)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.91e-07 (Fisher's exact test), Q value = 0.00079

Table S126. Gene #28: 'Amp Peak 28(19q12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
AMP PEAK 28(19Q12) CNV	5	92	35
AMP PEAK 28(19Q12) WILD-TYPE	46	157	153

Figure S126. Get High-res Image Gene #28: 'Amp Peak 28(19q12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 28(19q12)' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.73e-05 (Fisher's exact test), Q value = 0.06

Table S127. Gene #28: 'Amp Peak 28(19q12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
AMP PEAK 28(19Q12) CNV	28	73	17
AMP PEAK 28(19Q12) WILD-TYPE	127	119	61

Figure S127. Get High-res Image Gene #28: 'Amp Peak 28(19q12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 28(19q12)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.13e-07 (Fisher's exact test), Q value = 0.00034

Table S128. Gene #28: 'Amp Peak 28(19q12)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
AMP PEAK 28(19Q12) CNV	7	77	34
AMP PEAK 28(19Q12) WILD-TYPE	42	111	154

Figure S128. Get High-res Image Gene #28: 'Amp Peak 28(19q12)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 29(20p11.21)' versus 'CN_CNMF'

P value = 3.14e-05 (Fisher's exact test), Q value = 0.022

Table S129. Gene #29: 'Amp Peak 29(20p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
AMP PEAK 29(20P11.21) CNV	73	62	52
AMP PEAK 29(20P11.21) WILD-TYPE	114	152	40

Figure S129. Get High-res Image Gene #29: 'Amp Peak 29(20p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 29(20p11.21)' versus 'METHLYATION_CNMF'

P value = 0.000329 (Fisher's exact test), Q value = 0.21

Table S130. Gene #29: 'Amp Peak 29(20p11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
AMP PEAK 29(20P11.21) CNV	71	46	43
AMP PEAK 29(20P11.21) WILD-TYPE	70	94	107

Figure S130. Get High-res Image Gene #29: 'Amp Peak 29(20p11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 29(20p11.21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.3e-06 (Fisher's exact test), Q value = 0.0062

Table S131. Gene #29: 'Amp Peak 29(20p11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
AMP PEAK 29(20P11.21) CNV	43	58	75
AMP PEAK 29(20P11.21) WILD-TYPE	75	150	65

Figure S131. Get High-res Image Gene #29: 'Amp Peak 29(20p11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 29(20p11.21)' versus 'MIRSEQ_CNMF'

P value = 7.58e-05 (Fisher's exact test), Q value = 0.052

Table S132. Gene #29: 'Amp Peak 29(20p11.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 29(20P11.21) CNV	46	107	32
AMP PEAK 29(20P11.21) WILD-TYPE	133	124	46

Figure S132. Get High-res Image Gene #29: 'Amp Peak 29(20p11.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 29(20p11.21)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.48e-05 (Fisher's exact test), Q value = 0.011

Table S133. Gene #29: 'Amp Peak 29(20p11.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
AMP PEAK 29(20P11.21) CNV	23	115	47
AMP PEAK 29(20P11.21) WILD-TYPE	28	134	141

Figure S133. Get High-res Image Gene #29: 'Amp Peak 29(20p11.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 29(20p11.21)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000152 (Fisher's exact test), Q value = 0.1

Table S134. Gene #29: 'Amp Peak 29(20p11.21)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
AMP PEAK 29(20P11.21) CNV	39	89	33
AMP PEAK 29(20P11.21) WILD-TYPE	116	103	45

Figure S134. Get High-res Image Gene #29: 'Amp Peak 29(20p11.21)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 29(20p11.21)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.5e-05 (Fisher's exact test), Q value = 0.025

Table S135. Gene #29: 'Amp Peak 29(20p11.21)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
AMP PEAK 29(20P11.21) CNV	22	90	49
AMP PEAK 29(20P11.21) WILD-TYPE	27	98	139

Figure S135. Get High-res Image Gene #29: 'Amp Peak 29(20p11.21)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 30(20q13.33)' versus 'CN_CNMF'

P value = 5.43e-09 (Fisher's exact test), Q value = 4.7e-06

Table S136. Gene #30: 'Amp Peak 30(20q13.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
AMP PEAK 30(20Q13.33) CNV	102	71	63
AMP PEAK 30(20Q13.33) WILD-TYPE	85	143	29

Figure S136. Get High-res Image Gene #30: 'Amp Peak 30(20q13.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 30(20q13.33)' versus 'METHLYATION_CNMF'

P value = 3.32e-05 (Fisher's exact test), Q value = 0.024

Table S137. Gene #30: 'Amp Peak 30(20q13.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
AMP PEAK 30(20Q13.33) CNV	84	69	50
AMP PEAK 30(20Q13.33) WILD-TYPE	57	71	100

Figure S137. Get High-res Image Gene #30: 'Amp Peak 30(20q13.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 30(20q13.33)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000179 (Fisher's exact test), Q value = 0.12

Table S138. Gene #30: 'Amp Peak 30(20q13.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
AMP PEAK 30(20Q13.33) CNV	62	77	82
AMP PEAK 30(20Q13.33) WILD-TYPE	56	131	58

Figure S138. Get High-res Image Gene #30: 'Amp Peak 30(20q13.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 30(20q13.33)' versus 'MIRSEQ_CNMF'

P value = 8.24e-06 (Fisher's exact test), Q value = 0.0062

Table S139. Gene #30: 'Amp Peak 30(20q13.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
AMP PEAK 30(20Q13.33) CNV	62	135	35
AMP PEAK 30(20Q13.33) WILD-TYPE	117	96	43

Figure S139. Get High-res Image Gene #30: 'Amp Peak 30(20q13.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 30(20q13.33)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.42e-08 (Fisher's exact test), Q value = 2.1e-05

Table S140. Gene #30: 'Amp Peak 30(20q13.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
AMP PEAK 30(20Q13.33) CNV	28	146	58
AMP PEAK 30(20Q13.33) WILD-TYPE	23	103	130

Figure S140. Get High-res Image Gene #30: 'Amp Peak 30(20q13.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 30(20q13.33)' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.23e-05 (Fisher's exact test), Q value = 0.03

Table S141. Gene #30: 'Amp Peak 30(20q13.33)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
AMP PEAK 30(20Q13.33) CNV	53	112	37
AMP PEAK 30(20Q13.33) WILD-TYPE	102	80	41

Figure S141. Get High-res Image Gene #30: 'Amp Peak 30(20q13.33)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 30(20q13.33)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.68e-05 (Fisher's exact test), Q value = 0.066

Table S142. Gene #30: 'Amp Peak 30(20q13.33)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
AMP PEAK 30(20Q13.33) CNV	25	109	68
AMP PEAK 30(20Q13.33) WILD-TYPE	24	79	120

Figure S142. Get High-res Image Gene #30: 'Amp Peak 30(20q13.33)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 31(22q11.22)' versus 'CN_CNMF'

P value = 0.000124 (Fisher's exact test), Q value = 0.083

Table S143. Gene #31: 'Amp Peak 31(22q11.22)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
AMP PEAK 31(22Q11.22) CNV	47	20	16
AMP PEAK 31(22Q11.22) WILD-TYPE	140	194	76

Figure S143. Get High-res Image Gene #31: 'Amp Peak 31(22q11.22)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 32(Xq28)' versus 'CN_CNMF'

P value = 1.16e-12 (Fisher's exact test), Q value = 1.1e-09

Table S144. Gene #32: 'Amp Peak 32(Xq28)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
AMP PEAK 32(XQ28) CNV	91	32	31
AMP PEAK 32(XQ28) WILD-TYPE	96	182	61

Figure S144. Get High-res Image Gene #32: 'Amp Peak 32(Xq28)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 32(Xq28)' versus 'MRNASEQ_CNMF'

P value = 2.17e-06 (Fisher's exact test), Q value = 0.0017

Table S145. Gene #32: 'Amp Peak 32(Xq28)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
AMP PEAK 32(XQ28) CNV	31	75	45
AMP PEAK 32(XQ28) WILD-TYPE	124	86	105

Figure S145. Get High-res Image Gene #32: 'Amp Peak 32(Xq28)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 32(Xq28)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.8e-06 (Fisher's exact test), Q value = 0.0014

Table S146. Gene #32: 'Amp Peak 32(Xq28)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
AMP PEAK 32(XQ28) CNV	59	46	46
AMP PEAK 32(XQ28) WILD-TYPE	59	162	94

Figure S146. Get High-res Image Gene #32: 'Amp Peak 32(Xq28)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 3.08e-05 (Fisher's exact test), Q value = 0.022

Table S147. Gene #33: 'Del Peak 1(1p36.13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 1(1P36.13) CNV	30	47	38
DEL PEAK 1(1P36.13) WILD-TYPE	157	167	54

Figure S147. Get High-res Image Gene #33: 'Del Peak 1(1p36.13)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 2.38e-05 (Fisher's exact test), Q value = 0.017

Table S148. Gene #33: 'Del Peak 1(1p36.13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
DEL PEAK 1(1P36.13) CNV	47	35	17
DEL PEAK 1(1P36.13) WILD-TYPE	94	105	133

Figure S148. Get High-res Image Gene #33: 'Del Peak 1(1p36.13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 2.78e-08 (Fisher's exact test), Q value = 2.4e-05

Table S149. Gene #33: 'Del Peak 1(1p36.13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
DEL PEAK 1(1P36.13) CNV	14	35	55
DEL PEAK 1(1P36.13) WILD-TYPE	141	126	95

Figure S149. Get High-res Image Gene #33: 'Del Peak 1(1p36.13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 8.52e-07 (Fisher's exact test), Q value = 0.00069

Table S150. Gene #33: 'Del Peak 1(1p36.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
DEL PEAK 1(1P36.13) CNV	29	25	50
DEL PEAK 1(1P36.13) WILD-TYPE	89	183	90

Figure S150. Get High-res Image Gene #33: 'Del Peak 1(1p36.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 1.25e-07 (Fisher's exact test), Q value = 1e-04

Table S151. Gene #34: 'Del Peak 2(1p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 2(1P13.2) CNV	45	53	51
DEL PEAK 2(1P13.2) WILD-TYPE	142	161	41

Figure S151. Get High-res Image Gene #34: 'Del Peak 2(1p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 2.01e-06 (Fisher's exact test), Q value = 0.0016

Table S152. Gene #34: 'Del Peak 2(1p13.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
DEL PEAK 2(1P13.2) CNV	30	38	67
DEL PEAK 2(1P13.2) WILD-TYPE	125	123	83

Figure S152. Get High-res Image Gene #34: 'Del Peak 2(1p13.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 3(2q22.1)' versus 'METHLYATION_CNMF'

P value = 9.88e-05 (Fisher's exact test), Q value = 0.067

Table S153. Gene #35: 'Del Peak 3(2q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
DEL PEAK 3(2Q22.1) CNV	24	13	4
DEL PEAK 3(2Q22.1) WILD-TYPE	117	127	146

Figure S153. Get High-res Image Gene #35: 'Del Peak 3(2q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 4(2q37.3)' versus 'CN_CNMF'

P value = 0.000183 (Fisher's exact test), Q value = 0.12

Table S154. Gene #36: 'Del Peak 4(2q37.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 4(2Q37.3) CNV	34	13	17
DEL PEAK 4(2Q37.3) WILD-TYPE	153	201	75

Figure S154. Get High-res Image Gene #36: 'Del Peak 4(2q37.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 4(2q37.3)' versus 'METHLYATION_CNMF'

P value = 0.000213 (Fisher's exact test), Q value = 0.14

Table S155. Gene #36: 'Del Peak 4(2q37.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
DEL PEAK 4(2Q37.3) CNV	25	22	6
DEL PEAK 4(2Q37.3) WILD-TYPE	116	118	144

Figure S155. Get High-res Image Gene #36: 'Del Peak 4(2q37.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 4(2q37.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000108 (Fisher's exact test), Q value = 0.072

Table S156. Gene #36: 'Del Peak 4(2q37.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
DEL PEAK 4(2Q37.3) CNV	5	48	11
DEL PEAK 4(2Q37.3) WILD-TYPE	46	201	177

Figure S156. Get High-res Image Gene #36: 'Del Peak 4(2q37.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 5(3p21.31)' versus 'CN_CNMF'

P value = 5.06e-06 (Fisher's exact test), Q value = 0.0038

Table S157. Gene #37: 'Del Peak 5(3p21.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 5(3P21.31) CNV	100	77	59
DEL PEAK 5(3P21.31) WILD-TYPE	87	137	33

Figure S157. Get High-res Image Gene #37: 'Del Peak 5(3p21.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 5(3p21.31)' versus 'METHLYATION_CNMF'

P value = 1.67e-06 (Fisher's exact test), Q value = 0.0013

Table S158. Gene #37: 'Del Peak 5(3p21.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
DEL PEAK 5(3P21.31) CNV	93	57	58
DEL PEAK 5(3P21.31) WILD-TYPE	48	83	92

Figure S158. Get High-res Image Gene #37: 'Del Peak 5(3p21.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 5(3p21.31)' versus 'MRNASEQ_CNMF'

P value = 3.45e-05 (Fisher's exact test), Q value = 0.024

Table S159. Gene #37: 'Del Peak 5(3p21.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
DEL PEAK 5(3P21.31) CNV	55	76	92
DEL PEAK 5(3P21.31) WILD-TYPE	100	85	58

Figure S159. Get High-res Image Gene #37: 'Del Peak 5(3p21.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 5(3p21.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.64e-10 (Fisher's exact test), Q value = 2.4e-07

Table S160. Gene #37: 'Del Peak 5(3p21.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
DEL PEAK 5(3P21.31) CNV	54	71	98
DEL PEAK 5(3P21.31) WILD-TYPE	64	137	42

Figure S160. Get High-res Image Gene #37: 'Del Peak 5(3p21.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 5(3p21.31)' versus 'MIRSEQ_CNMF'

P value = 1.17e-05 (Fisher's exact test), Q value = 0.0087

Table S161. Gene #37: 'Del Peak 5(3p21.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 5(3P21.31) CNV	60	127	45
DEL PEAK 5(3P21.31) WILD-TYPE	119	104	33

Figure S161. Get High-res Image Gene #37: 'Del Peak 5(3p21.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 6(3q11.1)' versus 'METHLYATION_CNMF'

P value = 0.000315 (Fisher's exact test), Q value = 0.2

Table S162. Gene #38: 'Del Peak 6(3q11.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
DEL PEAK 6(3Q11.1) CNV	60	38	32
DEL PEAK 6(3Q11.1) WILD-TYPE	81	102	118

Figure S162. Get High-res Image Gene #38: 'Del Peak 6(3q11.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 7(3q29)' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.074

Table S163. Gene #39: 'Del Peak 7(3q29)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
DEL PEAK 7(3Q29) CNV	56	42	26
DEL PEAK 7(3Q29) WILD-TYPE	85	98	124

Figure S163. Get High-res Image Gene #39: 'Del Peak 7(3q29)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 8(4p16.3)' versus 'CN_CNMF'

P value = 2.44e-05 (Fisher's exact test), Q value = 0.018

Table S164. Gene #40: 'Del Peak 8(4p16.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 8(4P16.3) CNV	49	35	38
DEL PEAK 8(4P16.3) WILD-TYPE	138	179	54

Figure S164. Get High-res Image Gene #40: 'Del Peak 8(4p16.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 8(4p16.3)' versus 'MRNASEQ_CNMF'

P value = 2.87e-05 (Fisher's exact test), Q value = 0.02

Table S165. Gene #40: 'Del Peak 8(4p16.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
DEL PEAK 8(4P16.3) CNV	22	38	55
DEL PEAK 8(4P16.3) WILD-TYPE	133	123	95

Figure S165. Get High-res Image Gene #40: 'Del Peak 8(4p16.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 8(4p16.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.2e-07 (Fisher's exact test), Q value = 0.00018

Table S166. Gene #40: 'Del Peak 8(4p16.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
DEL PEAK 8(4P16.3) CNV	28	30	57
DEL PEAK 8(4P16.3) WILD-TYPE	90	178	83

Figure S166. Get High-res Image Gene #40: 'Del Peak 8(4p16.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 8(4p16.3)' versus 'MIRSEQ_CNMF'

P value = 2.38e-06 (Fisher's exact test), Q value = 0.0018

Table S167. Gene #40: 'Del Peak 8(4p16.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 8(4P16.3) CNV	23	79	19
DEL PEAK 8(4P16.3) WILD-TYPE	156	152	59

Figure S167. Get High-res Image Gene #40: 'Del Peak 8(4p16.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 8(4p16.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.15e-06 (Fisher's exact test), Q value = 0.0017

Table S168. Gene #40: 'Del Peak 8(4p16.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
DEL PEAK 8(4P16.3) CNV	7	86	28
DEL PEAK 8(4P16.3) WILD-TYPE	44	163	160

Figure S168. Get High-res Image Gene #40: 'Del Peak 8(4p16.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 9(4q22.1)' versus 'MRNA_CNMF'

P value = 0.000214 (Fisher's exact test), Q value = 0.14

Table S169. Gene #41: 'Del Peak 9(4q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	5	9	12	6
DEL PEAK 9(4Q22.1) CNV	3	1	0	5
DEL PEAK 9(4Q22.1) WILD-TYPE	2	8	12	1

Figure S169. Get High-res Image Gene #41: 'Del Peak 9(4q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 9(4q22.1)' versus 'MRNA_CHIERARCHICAL'

P value = 9.89e-05 (Fisher's exact test), Q value = 0.067

Table S170. Gene #41: 'Del Peak 9(4q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	13	12
DEL PEAK 9(4Q22.1) CNV	6	0	3
DEL PEAK 9(4Q22.1) WILD-TYPE	1	13	9

Figure S170. Get High-res Image Gene #41: 'Del Peak 9(4q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 9(4q22.1)' versus 'CN_CNMF'

P value = 1.2e-05 (Fisher's exact test), Q value = 0.0088

Table S171. Gene #41: 'Del Peak 9(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 9(4Q22.1) CNV	64	44	43
DEL PEAK 9(4Q22.1) WILD-TYPE	123	170	49

Figure S171. Get High-res Image Gene #41: 'Del Peak 9(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 9(4q22.1)' versus 'MRNASEQ_CNMF'

P value = 4.53e-08 (Fisher's exact test), Q value = 3.8e-05

Table S172. Gene #41: 'Del Peak 9(4q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
DEL PEAK 9(4Q22.1) CNV	27	42	71
DEL PEAK 9(4Q22.1) WILD-TYPE	128	119	79

Figure S172. Get High-res Image Gene #41: 'Del Peak 9(4q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 9(4q22.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.66e-11 (Fisher's exact test), Q value = 5.1e-08

Table S173. Gene #41: 'Del Peak 9(4q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
DEL PEAK 9(4Q22.1) CNV	30	37	73
DEL PEAK 9(4Q22.1) WILD-TYPE	88	171	67

Figure S173. Get High-res Image Gene #41: 'Del Peak 9(4q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 9(4q22.1)' versus 'MIRSEQ_CNMF'

P value = 5.74e-07 (Fisher's exact test), Q value = 0.00047

Table S174. Gene #41: 'Del Peak 9(4q22.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 9(4Q22.1) CNV	30	94	26
DEL PEAK 9(4Q22.1) WILD-TYPE	149	137	52

Figure S174. Get High-res Image Gene #41: 'Del Peak 9(4q22.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 9(4q22.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.71e-06 (Fisher's exact test), Q value = 0.0013

Table S175. Gene #41: 'Del Peak 9(4q22.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
DEL PEAK 9(4Q22.1) CNV	13	102	35
DEL PEAK 9(4Q22.1) WILD-TYPE	38	147	153

Figure S175. Get High-res Image Gene #41: 'Del Peak 9(4q22.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 10(4q35.1)' versus 'CN_CNMF'

P value = 1.72e-08 (Fisher's exact test), Q value = 1.5e-05

Table S176. Gene #42: 'Del Peak 10(4q35.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 10(4Q35.1) CNV	76	51	54
DEL PEAK 10(4Q35.1) WILD-TYPE	111	163	38

Figure S176. Get High-res Image Gene #42: 'Del Peak 10(4q35.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 10(4q35.1)' versus 'MRNASEQ_CNMF'

P value = 8.81e-13 (Fisher's exact test), Q value = 8.1e-10

Table S177. Gene #42: 'Del Peak 10(4q35.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
DEL PEAK 10(4Q35.1) CNV	30	50	89
DEL PEAK 10(4Q35.1) WILD-TYPE	125	111	61

Figure S177. Get High-res Image Gene #42: 'Del Peak 10(4q35.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 10(4q35.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.67e-16 (Fisher's exact test), Q value = 2.5e-13

Table S178. Gene #42: 'Del Peak 10(4q35.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
DEL PEAK 10(4Q35.1) CNV	33	45	91
DEL PEAK 10(4Q35.1) WILD-TYPE	85	163	49

Figure S178. Get High-res Image Gene #42: 'Del Peak 10(4q35.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 10(4q35.1)' versus 'MIRSEQ_CNMF'

P value = 2.23e-09 (Fisher's exact test), Q value = 2e-06

Table S179. Gene #42: 'Del Peak 10(4q35.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 10(4Q35.1) CNV	39	118	23
DEL PEAK 10(4Q35.1) WILD-TYPE	140	113	55

Figure S179. Get High-res Image Gene #42: 'Del Peak 10(4q35.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 10(4q35.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.26e-10 (Fisher's exact test), Q value = 7.4e-07

Table S180. Gene #42: 'Del Peak 10(4q35.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
DEL PEAK 10(4Q35.1) CNV	12	126	42
DEL PEAK 10(4Q35.1) WILD-TYPE	39	123	146

Figure S180. Get High-res Image Gene #42: 'Del Peak 10(4q35.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 10(4q35.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.96e-05 (Fisher's exact test), Q value = 0.014

Table S181. Gene #42: 'Del Peak 10(4q35.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
DEL PEAK 10(4Q35.1) CNV	41	94	22
DEL PEAK 10(4Q35.1) WILD-TYPE	114	98	56

Figure S181. Get High-res Image Gene #42: 'Del Peak 10(4q35.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 10(4q35.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.69e-07 (Fisher's exact test), Q value = 0.00038

Table S182. Gene #42: 'Del Peak 10(4q35.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
DEL PEAK 10(4Q35.1) CNV	14	96	47
DEL PEAK 10(4Q35.1) WILD-TYPE	35	92	141

Figure S182. Get High-res Image Gene #42: 'Del Peak 10(4q35.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 11(5q11.2)' versus 'CN_CNMF'

P value = 2.13e-13 (Fisher's exact test), Q value = 2e-10

Table S183. Gene #43: 'Del Peak 11(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 11(5Q11.2) CNV	93	36	44
DEL PEAK 11(5Q11.2) WILD-TYPE	94	178	48

Figure S183. Get High-res Image Gene #43: 'Del Peak 11(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 11(5q11.2)' versus 'METHLYATION_CNMF'

P value = 0.000324 (Fisher's exact test), Q value = 0.21

Table S184. Gene #43: 'Del Peak 11(5q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
DEL PEAK 11(5Q11.2) CNV	63	49	34
DEL PEAK 11(5Q11.2) WILD-TYPE	78	91	116

Figure S184. Get High-res Image Gene #43: 'Del Peak 11(5q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 11(5q11.2)' versus 'MRNASEQ_CNMF'

P value = 4.67e-09 (Fisher's exact test), Q value = 4.1e-06

Table S185. Gene #43: 'Del Peak 11(5q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
DEL PEAK 11(5Q11.2) CNV	26	66	72
DEL PEAK 11(5Q11.2) WILD-TYPE	129	95	78

Figure S185. Get High-res Image Gene #43: 'Del Peak 11(5q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 11(5q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.91e-11 (Fisher's exact test), Q value = 1.7e-08

Table S186. Gene #43: 'Del Peak 11(5q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
DEL PEAK 11(5Q11.2) CNV	47	40	77
DEL PEAK 11(5Q11.2) WILD-TYPE	71	168	63

Figure S186. Get High-res Image Gene #43: 'Del Peak 11(5q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 11(5q11.2)' versus 'MIRSEQ_CNMF'

P value = 8.34e-10 (Fisher's exact test), Q value = 7.5e-07

Table S187. Gene #43: 'Del Peak 11(5q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 11(5Q11.2) CNV	33	112	25
DEL PEAK 11(5Q11.2) WILD-TYPE	146	119	53

Figure S187. Get High-res Image Gene #43: 'Del Peak 11(5q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 11(5q11.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.03e-06 (Fisher's exact test), Q value = 0.0016

Table S188. Gene #43: 'Del Peak 11(5q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
DEL PEAK 11(5Q11.2) CNV	15	113	42
DEL PEAK 11(5Q11.2) WILD-TYPE	36	136	146

Figure S188. Get High-res Image Gene #43: 'Del Peak 11(5q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 11(5q11.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.06e-06 (Fisher's exact test), Q value = 0.00085

Table S189. Gene #43: 'Del Peak 11(5q11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
DEL PEAK 11(5Q11.2) CNV	31	89	24
DEL PEAK 11(5Q11.2) WILD-TYPE	124	103	54

Figure S189. Get High-res Image Gene #43: 'Del Peak 11(5q11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 11(5q11.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.62e-09 (Fisher's exact test), Q value = 2.3e-06

Table S190. Gene #43: 'Del Peak 11(5q11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
DEL PEAK 11(5Q11.2) CNV	12	94	38
DEL PEAK 11(5Q11.2) WILD-TYPE	37	94	150

Figure S190. Get High-res Image Gene #43: 'Del Peak 11(5q11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 12(5q31.1)' versus 'CN_CNMF'

P value = 1.03e-12 (Fisher's exact test), Q value = 9.5e-10

Table S191. Gene #44: 'Del Peak 12(5q31.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 12(5Q31.1) CNV	100	47	52
DEL PEAK 12(5Q31.1) WILD-TYPE	87	167	40

Figure S191. Get High-res Image Gene #44: 'Del Peak 12(5q31.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 12(5q31.1)' versus 'METHLYATION_CNMF'

P value = 8.84e-06 (Fisher's exact test), Q value = 0.0066

Table S192. Gene #44: 'Del Peak 12(5q31.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
DEL PEAK 12(5Q31.1) CNV	70	65	37
DEL PEAK 12(5Q31.1) WILD-TYPE	71	75	113

Figure S192. Get High-res Image Gene #44: 'Del Peak 12(5q31.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 12(5q31.1)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000339 (Fisher's exact test), Q value = 0.22

Table S193. Gene #44: 'Del Peak 12(5q31.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	106	70	59
DEL PEAK 12(5Q31.1) CNV	49	17	34
DEL PEAK 12(5Q31.1) WILD-TYPE	57	53	25

Figure S193. Get High-res Image Gene #44: 'Del Peak 12(5q31.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 12(5q31.1)' versus 'MRNASEQ_CNMF'

P value = 9.04e-10 (Fisher's exact test), Q value = 8.1e-07

Table S194. Gene #44: 'Del Peak 12(5q31.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
DEL PEAK 12(5Q31.1) CNV	32	78	80
DEL PEAK 12(5Q31.1) WILD-TYPE	123	83	70

Figure S194. Get High-res Image Gene #44: 'Del Peak 12(5q31.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 12(5q31.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.1e-11 (Fisher's exact test), Q value = 6.4e-08

Table S195. Gene #44: 'Del Peak 12(5q31.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
DEL PEAK 12(5Q31.1) CNV	55	51	84
DEL PEAK 12(5Q31.1) WILD-TYPE	63	157	56

Figure S195. Get High-res Image Gene #44: 'Del Peak 12(5q31.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 12(5q31.1)' versus 'MIRSEQ_CNMF'

P value = 1.22e-09 (Fisher's exact test), Q value = 1.1e-06

Table S196. Gene #44: 'Del Peak 12(5q31.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 12(5Q31.1) CNV	43	126	27
DEL PEAK 12(5Q31.1) WILD-TYPE	136	105	51

Figure S196. Get High-res Image Gene #44: 'Del Peak 12(5q31.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 12(5q31.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.81e-07 (Fisher's exact test), Q value = 0.00015

Table S197. Gene #44: 'Del Peak 12(5q31.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
DEL PEAK 12(5Q31.1) CNV	15	130	51
DEL PEAK 12(5Q31.1) WILD-TYPE	36	119	137

Figure S197. Get High-res Image Gene #44: 'Del Peak 12(5q31.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 12(5q31.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.65e-05 (Fisher's exact test), Q value = 0.019

Table S198. Gene #44: 'Del Peak 12(5q31.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
DEL PEAK 12(5Q31.1) CNV	43	99	28
DEL PEAK 12(5Q31.1) WILD-TYPE	112	93	50

Figure S198. Get High-res Image Gene #44: 'Del Peak 12(5q31.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 12(5q31.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.15e-07 (Fisher's exact test), Q value = 0.00018

Table S199. Gene #44: 'Del Peak 12(5q31.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
DEL PEAK 12(5Q31.1) CNV	14	103	53
DEL PEAK 12(5Q31.1) WILD-TYPE	35	85	135

Figure S199. Get High-res Image Gene #44: 'Del Peak 12(5q31.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 14(6q22.31)' versus 'METHLYATION_CNMF'

P value = 3.5e-07 (Fisher's exact test), Q value = 0.00029

Table S200. Gene #46: 'Del Peak 14(6q22.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
DEL PEAK 14(6Q22.31) CNV	74	94	53
DEL PEAK 14(6Q22.31) WILD-TYPE	67	46	97

Figure S200. Get High-res Image Gene #46: 'Del Peak 14(6q22.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 15(6q26)' versus 'METHLYATION_CNMF'

P value = 2.12e-05 (Fisher's exact test), Q value = 0.015

Table S201. Gene #47: 'Del Peak 15(6q26)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
DEL PEAK 15(6Q26) CNV	79	85	53
DEL PEAK 15(6Q26) WILD-TYPE	62	55	97

Figure S201. Get High-res Image Gene #47: 'Del Peak 15(6q26)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 16(8p23.2)' versus 'CN_CNMF'

P value = 3.17e-23 (Fisher's exact test), Q value = 3e-20

Table S202. Gene #48: 'Del Peak 16(8p23.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 16(8P23.2) CNV	142	56	42
DEL PEAK 16(8P23.2) WILD-TYPE	45	158	50

Figure S202. Get High-res Image Gene #48: 'Del Peak 16(8p23.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 16(8p23.2)' versus 'RPPA_CHIERARCHICAL'

P value = 3.52e-05 (Fisher's exact test), Q value = 0.025

Table S203. Gene #48: 'Del Peak 16(8p23.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	106	70	59
DEL PEAK 16(8P23.2) CNV	67	20	29
DEL PEAK 16(8P23.2) WILD-TYPE	39	50	30

Figure S203. Get High-res Image Gene #48: 'Del Peak 16(8p23.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 16(8p23.2)' versus 'MRNASEQ_CNMF'

P value = 5.51e-07 (Fisher's exact test), Q value = 0.00045

Table S204. Gene #48: 'Del Peak 16(8p23.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
DEL PEAK 16(8P23.2) CNV	57	105	64
DEL PEAK 16(8P23.2) WILD-TYPE	98	56	86

Figure S204. Get High-res Image Gene #48: 'Del Peak 16(8p23.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 16(8p23.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.48e-08 (Fisher's exact test), Q value = 2.1e-05

Table S205. Gene #48: 'Del Peak 16(8p23.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
DEL PEAK 16(8P23.2) CNV	83	76	67
DEL PEAK 16(8P23.2) WILD-TYPE	35	132	73

Figure S205. Get High-res Image Gene #48: 'Del Peak 16(8p23.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 16(8p23.2)' versus 'MIRSEQ_CNMF'

P value = 1.59e-05 (Fisher's exact test), Q value = 0.012

Table S206. Gene #48: 'Del Peak 16(8p23.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 16(8P23.2) CNV	62	130	45
DEL PEAK 16(8P23.2) WILD-TYPE	117	101	33

Figure S206. Get High-res Image Gene #48: 'Del Peak 16(8p23.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 16(8p23.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.77e-05 (Fisher's exact test), Q value = 0.047

Table S207. Gene #48: 'Del Peak 16(8p23.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
DEL PEAK 16(8P23.2) CNV	20	112	71
DEL PEAK 16(8P23.2) WILD-TYPE	29	76	117

Figure S207. Get High-res Image Gene #48: 'Del Peak 16(8p23.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 17(8p12)' versus 'CN_CNMF'

P value = 3.23e-21 (Fisher's exact test), Q value = 3e-18

Table S208. Gene #49: 'Del Peak 17(8p12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 17(8P12) CNV	131	49	35
DEL PEAK 17(8P12) WILD-TYPE	56	165	57

Figure S208. Get High-res Image Gene #49: 'Del Peak 17(8p12)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 17(8p12)' versus 'MRNASEQ_CNMF'

P value = 1.14e-06 (Fisher's exact test), Q value = 0.00091

Table S209. Gene #49: 'Del Peak 17(8p12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
DEL PEAK 17(8P12) CNV	49	96	58
DEL PEAK 17(8P12) WILD-TYPE	106	65	92

Figure S209. Get High-res Image Gene #49: 'Del Peak 17(8p12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 17(8p12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.13e-08 (Fisher's exact test), Q value = 2.7e-05

Table S210. Gene #49: 'Del Peak 17(8p12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
DEL PEAK 17(8P12) CNV	77	66	60
DEL PEAK 17(8P12) WILD-TYPE	41	142	80

Figure S210. Get High-res Image Gene #49: 'Del Peak 17(8p12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 17(8p12)' versus 'MIRSEQ_CNMF'

P value = 9.57e-05 (Fisher's exact test), Q value = 0.065

Table S211. Gene #49: 'Del Peak 17(8p12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 17(8P12) CNV	56	121	35
DEL PEAK 17(8P12) WILD-TYPE	123	110	43

Figure S211. Get High-res Image Gene #49: 'Del Peak 17(8p12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 18(8p11.21)' versus 'CN_CNMF'

P value = 2.61e-19 (Fisher's exact test), Q value = 2.5e-16

Table S212. Gene #50: 'Del Peak 18(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 18(8P11.21) CNV	83	26	3
DEL PEAK 18(8P11.21) WILD-TYPE	104	188	89

Figure S212. Get High-res Image Gene #50: 'Del Peak 18(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 22(9q21.11)' versus 'CN_CNMF'

P value = 6.15e-07 (Fisher's exact test), Q value = 5e-04

Table S213. Gene #54: 'Del Peak 22(9q21.11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 22(9Q21.11) CNV	99	80	64
DEL PEAK 22(9Q21.11) WILD-TYPE	88	134	28

Figure S213. Get High-res Image Gene #54: 'Del Peak 22(9q21.11)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 22(9q21.11)' versus 'METHLYATION_CNMF'

P value = 0.000348 (Fisher's exact test), Q value = 0.22

Table S214. Gene #54: 'Del Peak 22(9q21.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
DEL PEAK 22(9Q21.11) CNV	88	57	65
DEL PEAK 22(9Q21.11) WILD-TYPE	53	83	85

Figure S214. Get High-res Image Gene #54: 'Del Peak 22(9q21.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 22(9q21.11)' versus 'MRNASEQ_CNMF'

P value = 1.42e-05 (Fisher's exact test), Q value = 0.01

Table S215. Gene #54: 'Del Peak 22(9q21.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
DEL PEAK 22(9Q21.11) CNV	60	73	97
DEL PEAK 22(9Q21.11) WILD-TYPE	95	88	53

Figure S215. Get High-res Image Gene #54: 'Del Peak 22(9q21.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 22(9q21.11)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.62e-08 (Fisher's exact test), Q value = 2.2e-05

Table S216. Gene #54: 'Del Peak 22(9q21.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
DEL PEAK 22(9Q21.11) CNV	50	82	98
DEL PEAK 22(9Q21.11) WILD-TYPE	68	126	42

Figure S216. Get High-res Image Gene #54: 'Del Peak 22(9q21.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 22(9q21.11)' versus 'MIRSEQ_CNMF'

P value = 0.000103 (Fisher's exact test), Q value = 0.069

Table S217. Gene #54: 'Del Peak 22(9q21.11)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 22(9Q21.11) CNV	66	126	48
DEL PEAK 22(9Q21.11) WILD-TYPE	113	105	30

Figure S217. Get High-res Image Gene #54: 'Del Peak 22(9q21.11)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 22(9q21.11)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000101 (Fisher's exact test), Q value = 0.068

Table S218. Gene #54: 'Del Peak 22(9q21.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
DEL PEAK 22(9Q21.11) CNV	21	146	73
DEL PEAK 22(9Q21.11) WILD-TYPE	30	103	115

Figure S218. Get High-res Image Gene #54: 'Del Peak 22(9q21.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 22(9q21.11)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.48e-05 (Fisher's exact test), Q value = 0.018

Table S219. Gene #54: 'Del Peak 22(9q21.11)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
DEL PEAK 22(9Q21.11) CNV	26	113	69
DEL PEAK 22(9Q21.11) WILD-TYPE	23	75	119

Figure S219. Get High-res Image Gene #54: 'Del Peak 22(9q21.11)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 23(10p15.3)' versus 'CN_CNMF'

P value = 1.86e-05 (Fisher's exact test), Q value = 0.013

Table S220. Gene #55: 'Del Peak 23(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 23(10P15.3) CNV	63	31	26
DEL PEAK 23(10P15.3) WILD-TYPE	124	183	66

Figure S220. Get High-res Image Gene #55: 'Del Peak 23(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 24(10q26.3)' versus 'CN_CNMF'

P value = 3.91e-07 (Fisher's exact test), Q value = 0.00032

Table S221. Gene #56: 'Del Peak 24(10q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 24(10Q26.3) CNV	73	34	31
DEL PEAK 24(10Q26.3) WILD-TYPE	114	180	61

Figure S221. Get High-res Image Gene #56: 'Del Peak 24(10q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 24(10q26.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.68e-06 (Fisher's exact test), Q value = 0.0065

Table S222. Gene #56: 'Del Peak 24(10q26.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
DEL PEAK 24(10Q26.3) CNV	23	60	33
DEL PEAK 24(10Q26.3) WILD-TYPE	132	132	45

Figure S222. Get High-res Image Gene #56: 'Del Peak 24(10q26.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 24(10q26.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.07e-05 (Fisher's exact test), Q value = 0.042

Table S223. Gene #56: 'Del Peak 24(10q26.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
DEL PEAK 24(10Q26.3) CNV	20	64	32
DEL PEAK 24(10Q26.3) WILD-TYPE	29	124	156

Figure S223. Get High-res Image Gene #56: 'Del Peak 24(10q26.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 25(11p15.5)' versus 'CN_CNMF'

P value = 2.53e-06 (Fisher's exact test), Q value = 0.0019

Table S224. Gene #57: 'Del Peak 25(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 25(11P15.5) CNV	71	34	27
DEL PEAK 25(11P15.5) WILD-TYPE	116	180	65

Figure S224. Get High-res Image Gene #57: 'Del Peak 25(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 25(11p15.5)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.95e-08 (Fisher's exact test), Q value = 1.7e-05

Table S225. Gene #57: 'Del Peak 25(11p15.5)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
DEL PEAK 25(11P15.5) CNV	34	29	59
DEL PEAK 25(11P15.5) WILD-TYPE	84	179	81

Figure S225. Get High-res Image Gene #57: 'Del Peak 25(11p15.5)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 25(11p15.5)' versus 'MIRSEQ_CNMF'

P value = 0.000342 (Fisher's exact test), Q value = 0.22

Table S226. Gene #57: 'Del Peak 25(11p15.5)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 25(11P15.5) CNV	33	81	16
DEL PEAK 25(11P15.5) WILD-TYPE	146	150	62

Figure S226. Get High-res Image Gene #57: 'Del Peak 25(11p15.5)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 25(11p15.5)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.29e-05 (Fisher's exact test), Q value = 0.016

Table S227. Gene #57: 'Del Peak 25(11p15.5)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
DEL PEAK 25(11P15.5) CNV	4	86	40
DEL PEAK 25(11P15.5) WILD-TYPE	47	163	148

Figure S227. Get High-res Image Gene #57: 'Del Peak 25(11p15.5)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 25(11p15.5)' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.2e-05 (Fisher's exact test), Q value = 0.029

Table S228. Gene #57: 'Del Peak 25(11p15.5)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
DEL PEAK 25(11P15.5) CNV	28	72	14
DEL PEAK 25(11P15.5) WILD-TYPE	127	120	64

Figure S228. Get High-res Image Gene #57: 'Del Peak 25(11p15.5)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 28(12q12)' versus 'MRNASEQ_CNMF'

P value = 0.000148 (Fisher's exact test), Q value = 0.099

Table S229. Gene #60: 'Del Peak 28(12q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
DEL PEAK 28(12Q12) CNV	33	42	13
DEL PEAK 28(12Q12) WILD-TYPE	122	119	137

Figure S229. Get High-res Image Gene #60: 'Del Peak 28(12q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 29(12q24.33)' versus 'CN_CNMF'

P value = 8.07e-06 (Fisher's exact test), Q value = 0.0061

Table S230. Gene #61: 'Del Peak 29(12q24.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 29(12Q24.33) CNV	63	47	8
DEL PEAK 29(12Q24.33) WILD-TYPE	124	167	84

Figure S230. Get High-res Image Gene #61: 'Del Peak 29(12q24.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 29(12q24.33)' versus 'MRNASEQ_CNMF'

P value = 1.27e-06 (Fisher's exact test), Q value = 0.001

Table S231. Gene #61: 'Del Peak 29(12q24.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
DEL PEAK 29(12Q24.33) CNV	49	49	15
DEL PEAK 29(12Q24.33) WILD-TYPE	106	112	135

Figure S231. Get High-res Image Gene #61: 'Del Peak 29(12q24.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 29(12q24.33)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.11

Table S232. Gene #61: 'Del Peak 29(12q24.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
DEL PEAK 29(12Q24.33) CNV	34	62	17
DEL PEAK 29(12Q24.33) WILD-TYPE	84	146	123

Figure S232. Get High-res Image Gene #61: 'Del Peak 29(12q24.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 30(13q12.11)' versus 'CN_CNMF'

P value = 1.98e-21 (Fisher's exact test), Q value = 1.9e-18

Table S233. Gene #62: 'Del Peak 30(13q12.11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 30(13Q12.11) CNV	143	69	68
DEL PEAK 30(13Q12.11) WILD-TYPE	44	145	24

Figure S233. Get High-res Image Gene #62: 'Del Peak 30(13q12.11)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 30(13q12.11)' versus 'RPPA_CHIERARCHICAL'

P value = 2.04e-06 (Fisher's exact test), Q value = 0.0016

Table S234. Gene #62: 'Del Peak 30(13q12.11)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	106	70	59
DEL PEAK 30(13Q12.11) CNV	76	23	33
DEL PEAK 30(13Q12.11) WILD-TYPE	30	47	26

Figure S234. Get High-res Image Gene #62: 'Del Peak 30(13q12.11)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 30(13q12.11)' versus 'MRNASEQ_CNMF'

P value = 3.33e-06 (Fisher's exact test), Q value = 0.0026

Table S235. Gene #62: 'Del Peak 30(13q12.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
DEL PEAK 30(13Q12.11) CNV	63	110	88
DEL PEAK 30(13Q12.11) WILD-TYPE	92	51	62

Figure S235. Get High-res Image Gene #62: 'Del Peak 30(13q12.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 30(13q12.11)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.38e-08 (Fisher's exact test), Q value = 4.6e-05

Table S236. Gene #62: 'Del Peak 30(13q12.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
DEL PEAK 30(13Q12.11) CNV	83	86	92
DEL PEAK 30(13Q12.11) WILD-TYPE	35	122	48

Figure S236. Get High-res Image Gene #62: 'Del Peak 30(13q12.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 31(13q12.13)' versus 'CN_CNMF'

P value = 1.29e-22 (Fisher's exact test), Q value = 1.2e-19

Table S237. Gene #63: 'Del Peak 31(13q12.13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 31(13Q12.13) CNV	144	68	69
DEL PEAK 31(13Q12.13) WILD-TYPE	43	146	23

Figure S237. Get High-res Image Gene #63: 'Del Peak 31(13q12.13)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 31(13q12.13)' versus 'RPPA_CHIERARCHICAL'

P value = 3.7e-07 (Fisher's exact test), Q value = 3e-04

Table S238. Gene #63: 'Del Peak 31(13q12.13)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	106	70	59
DEL PEAK 31(13Q12.13) CNV	77	22	34
DEL PEAK 31(13Q12.13) WILD-TYPE	29	48	25

Figure S238. Get High-res Image Gene #63: 'Del Peak 31(13q12.13)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 31(13q12.13)' versus 'MRNASEQ_CNMF'

P value = 1.2e-05 (Fisher's exact test), Q value = 0.0088

Table S239. Gene #63: 'Del Peak 31(13q12.13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
DEL PEAK 31(13Q12.13) CNV	65	110	87
DEL PEAK 31(13Q12.13) WILD-TYPE	90	51	63

Figure S239. Get High-res Image Gene #63: 'Del Peak 31(13q12.13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 31(13q12.13)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.81e-07 (Fisher's exact test), Q value = 0.00015

Table S240. Gene #63: 'Del Peak 31(13q12.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
DEL PEAK 31(13Q12.13) CNV	84	88	90
DEL PEAK 31(13Q12.13) WILD-TYPE	34	120	50

Figure S240. Get High-res Image Gene #63: 'Del Peak 31(13q12.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 32(13q14.2)' versus 'CN_CNMF'

P value = 1.48e-22 (Fisher's exact test), Q value = 1.4e-19

Table S241. Gene #64: 'Del Peak 32(13q14.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 32(13Q14.2) CNV	139	63	68
DEL PEAK 32(13Q14.2) WILD-TYPE	48	151	24

Figure S241. Get High-res Image Gene #64: 'Del Peak 32(13q14.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 32(13q14.2)' versus 'RPPA_CNMF'

P value = 0.000253 (Fisher's exact test), Q value = 0.17

Table S242. Gene #64: 'Del Peak 32(13q14.2)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	68	73
DEL PEAK 32(13Q14.2) CNV	62	23	40
DEL PEAK 32(13Q14.2) WILD-TYPE	32	45	33

Figure S242. Get High-res Image Gene #64: 'Del Peak 32(13q14.2)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 32(13q14.2)' versus 'RPPA_CHIERARCHICAL'

P value = 4.43e-07 (Fisher's exact test), Q value = 0.00036

Table S243. Gene #64: 'Del Peak 32(13q14.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	106	70	59
DEL PEAK 32(13Q14.2) CNV	72	19	34
DEL PEAK 32(13Q14.2) WILD-TYPE	34	51	25

Figure S243. Get High-res Image Gene #64: 'Del Peak 32(13q14.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 32(13q14.2)' versus 'MRNASEQ_CNMF'

P value = 2.27e-06 (Fisher's exact test), Q value = 0.0018

Table S244. Gene #64: 'Del Peak 32(13q14.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
DEL PEAK 32(13Q14.2) CNV	59	106	87
DEL PEAK 32(13Q14.2) WILD-TYPE	96	55	63

Figure S244. Get High-res Image Gene #64: 'Del Peak 32(13q14.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 32(13q14.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.18e-08 (Fisher's exact test), Q value = 2.7e-05

Table S245. Gene #64: 'Del Peak 32(13q14.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
DEL PEAK 32(13Q14.2) CNV	83	82	87
DEL PEAK 32(13Q14.2) WILD-TYPE	35	126	53

Figure S245. Get High-res Image Gene #64: 'Del Peak 32(13q14.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 32(13q14.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000297 (Fisher's exact test), Q value = 0.19

Table S246. Gene #64: 'Del Peak 32(13q14.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
DEL PEAK 32(13Q14.2) CNV	21	158	88
DEL PEAK 32(13Q14.2) WILD-TYPE	30	91	100

Figure S246. Get High-res Image Gene #64: 'Del Peak 32(13q14.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 32(13q14.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000223 (Fisher's exact test), Q value = 0.15

Table S247. Gene #64: 'Del Peak 32(13q14.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
DEL PEAK 32(13Q14.2) CNV	66	124	43
DEL PEAK 32(13Q14.2) WILD-TYPE	89	68	35

Figure S247. Get High-res Image Gene #64: 'Del Peak 32(13q14.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 33(13q34)' versus 'CN_CNMF'

P value = 7.07e-16 (Fisher's exact test), Q value = 6.6e-13

Table S248. Gene #65: 'Del Peak 33(13q34)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 33(13Q34) CNV	113	55	62
DEL PEAK 33(13Q34) WILD-TYPE	74	159	30

Figure S248. Get High-res Image Gene #65: 'Del Peak 33(13q34)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 33(13q34)' versus 'RPPA_CHIERARCHICAL'

P value = 2.71e-05 (Fisher's exact test), Q value = 0.019

Table S249. Gene #65: 'Del Peak 33(13q34)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	106	70	59
DEL PEAK 33(13Q34) CNV	57	15	31
DEL PEAK 33(13Q34) WILD-TYPE	49	55	28

Figure S249. Get High-res Image Gene #65: 'Del Peak 33(13q34)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 33(13q34)' versus 'MRNASEQ_CNMF'

P value = 7.3e-05 (Fisher's exact test), Q value = 0.05

Table S250. Gene #65: 'Del Peak 33(13q34)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
DEL PEAK 33(13Q34) CNV	50	90	74
DEL PEAK 33(13Q34) WILD-TYPE	105	71	76

Figure S250. Get High-res Image Gene #65: 'Del Peak 33(13q34)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 33(13q34)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.99e-05 (Fisher's exact test), Q value = 0.014

Table S251. Gene #65: 'Del Peak 33(13q34)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
DEL PEAK 33(13Q34) CNV	68	71	75
DEL PEAK 33(13Q34) WILD-TYPE	50	137	65

Figure S251. Get High-res Image Gene #65: 'Del Peak 33(13q34)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 35(15q11.2)' versus 'CN_CNMF'

P value = 6.48e-11 (Fisher's exact test), Q value = 5.8e-08

Table S252. Gene #67: 'Del Peak 35(15q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 35(15Q11.2) CNV	122	72	58
DEL PEAK 35(15Q11.2) WILD-TYPE	65	142	34

Figure S252. Get High-res Image Gene #67: 'Del Peak 35(15q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 35(15q11.2)' versus 'MRNASEQ_CNMF'

P value = 3.52e-06 (Fisher's exact test), Q value = 0.0027

Table S253. Gene #67: 'Del Peak 35(15q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
DEL PEAK 35(15Q11.2) CNV	61	106	67
DEL PEAK 35(15Q11.2) WILD-TYPE	94	55	83

Figure S253. Get High-res Image Gene #67: 'Del Peak 35(15q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 35(15q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.48e-06 (Fisher's exact test), Q value = 0.0034

Table S254. Gene #67: 'Del Peak 35(15q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
DEL PEAK 35(15Q11.2) CNV	80	82	72
DEL PEAK 35(15Q11.2) WILD-TYPE	38	126	68

Figure S254. Get High-res Image Gene #67: 'Del Peak 35(15q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 35(15q11.2)' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S255. Gene #67: 'Del Peak 35(15q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 35(15Q11.2) CNV	67	136	47
DEL PEAK 35(15Q11.2) WILD-TYPE	112	95	31

Figure S255. Get High-res Image Gene #67: 'Del Peak 35(15q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 36(16q23.1)' versus 'CN_CNMF'

P value = 1.62e-06 (Fisher's exact test), Q value = 0.0013

Table S256. Gene #68: 'Del Peak 36(16q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 36(16Q23.1) CNV	82	46	39
DEL PEAK 36(16Q23.1) WILD-TYPE	105	168	53

Figure S256. Get High-res Image Gene #68: 'Del Peak 36(16q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 36(16q23.1)' versus 'MRNASEQ_CNMF'

P value = 4.43e-07 (Fisher's exact test), Q value = 0.00036

Table S257. Gene #68: 'Del Peak 36(16q23.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
DEL PEAK 36(16Q23.1) CNV	30	77	52
DEL PEAK 36(16Q23.1) WILD-TYPE	125	84	98

Figure S257. Get High-res Image Gene #68: 'Del Peak 36(16q23.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 36(16q23.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.16e-09 (Fisher's exact test), Q value = 2.8e-06

Table S258. Gene #68: 'Del Peak 36(16q23.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
DEL PEAK 36(16Q23.1) CNV	63	42	54
DEL PEAK 36(16Q23.1) WILD-TYPE	55	166	86

Figure S258. Get High-res Image Gene #68: 'Del Peak 36(16q23.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 37(17p13.3)' versus 'CN_CNMF'

P value = 5.27e-19 (Fisher's exact test), Q value = 4.9e-16

Table S259. Gene #69: 'Del Peak 37(17p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 37(17P13.3) CNV	145	70	52
DEL PEAK 37(17P13.3) WILD-TYPE	42	144	40

Figure S259. Get High-res Image Gene #69: 'Del Peak 37(17p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 37(17p13.3)' versus 'METHLYATION_CNMF'

P value = 8.9e-05 (Fisher's exact test), Q value = 0.061

Table S260. Gene #69: 'Del Peak 37(17p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
DEL PEAK 37(17P13.3) CNV	74	94	63
DEL PEAK 37(17P13.3) WILD-TYPE	67	46	87

Figure S260. Get High-res Image Gene #69: 'Del Peak 37(17p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 37(17p13.3)' versus 'MRNASEQ_CNMF'

P value = 1.51e-06 (Fisher's exact test), Q value = 0.0012

Table S261. Gene #69: 'Del Peak 37(17p13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
DEL PEAK 37(17P13.3) CNV	63	111	75
DEL PEAK 37(17P13.3) WILD-TYPE	92	50	75

Figure S261. Get High-res Image Gene #69: 'Del Peak 37(17p13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 37(17p13.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.24e-08 (Fisher's exact test), Q value = 6.9e-05

Table S262. Gene #69: 'Del Peak 37(17p13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
DEL PEAK 37(17P13.3) CNV	87	86	76
DEL PEAK 37(17P13.3) WILD-TYPE	31	122	64

Figure S262. Get High-res Image Gene #69: 'Del Peak 37(17p13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 38(17p11.2)' versus 'CN_CNMF'

P value = 1.66e-16 (Fisher's exact test), Q value = 1.5e-13

Table S263. Gene #70: 'Del Peak 38(17p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 38(17P11.2) CNV	121	50	45
DEL PEAK 38(17P11.2) WILD-TYPE	66	164	47

Figure S263. Get High-res Image Gene #70: 'Del Peak 38(17p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 38(17p11.2)' versus 'METHLYATION_CNMF'

P value = 3.44e-07 (Fisher's exact test), Q value = 0.00028

Table S264. Gene #70: 'Del Peak 38(17p11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
DEL PEAK 38(17P11.2) CNV	52	86	47
DEL PEAK 38(17P11.2) WILD-TYPE	89	54	103

Figure S264. Get High-res Image Gene #70: 'Del Peak 38(17p11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 38(17p11.2)' versus 'MRNASEQ_CNMF'

P value = 1.14e-06 (Fisher's exact test), Q value = 0.00091

Table S265. Gene #70: 'Del Peak 38(17p11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
DEL PEAK 38(17P11.2) CNV	49	96	58
DEL PEAK 38(17P11.2) WILD-TYPE	106	65	92

Figure S265. Get High-res Image Gene #70: 'Del Peak 38(17p11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 38(17p11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.02e-07 (Fisher's exact test), Q value = 8.6e-05

Table S266. Gene #70: 'Del Peak 38(17p11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
DEL PEAK 38(17P11.2) CNV	77	69	57
DEL PEAK 38(17P11.2) WILD-TYPE	41	139	83

Figure S266. Get High-res Image Gene #70: 'Del Peak 38(17p11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 39(18q21.32)' versus 'CN_CNMF'

P value = 2.62e-13 (Fisher's exact test), Q value = 2.4e-10

Table S267. Gene #71: 'Del Peak 39(18q21.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 39(18Q21.32) CNV	132	75	34
DEL PEAK 39(18Q21.32) WILD-TYPE	55	139	58

Figure S267. Get High-res Image Gene #71: 'Del Peak 39(18q21.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 39(18q21.32)' versus 'MRNASEQ_CNMF'

P value = 6.96e-05 (Fisher's exact test), Q value = 0.048

Table S268. Gene #71: 'Del Peak 39(18q21.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
DEL PEAK 39(18Q21.32) CNV	61	101	67
DEL PEAK 39(18Q21.32) WILD-TYPE	94	60	83

Figure S268. Get High-res Image Gene #71: 'Del Peak 39(18q21.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 39(18q21.32)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.19e-05 (Fisher's exact test), Q value = 0.029

Table S269. Gene #71: 'Del Peak 39(18q21.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
DEL PEAK 39(18Q21.32) CNV	78	84	67
DEL PEAK 39(18Q21.32) WILD-TYPE	40	124	73

Figure S269. Get High-res Image Gene #71: 'Del Peak 39(18q21.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 40(18q23)' versus 'CN_CNMF'

P value = 1.15e-14 (Fisher's exact test), Q value = 1.1e-11

Table S270. Gene #72: 'Del Peak 40(18q23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 40(18Q23) CNV	133	73	32
DEL PEAK 40(18Q23) WILD-TYPE	54	141	60

Figure S270. Get High-res Image Gene #72: 'Del Peak 40(18q23)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 40(18q23)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000383 (Fisher's exact test), Q value = 0.24

Table S271. Gene #72: 'Del Peak 40(18q23)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	106	70	59
DEL PEAK 40(18Q23) CNV	67	23	29
DEL PEAK 40(18Q23) WILD-TYPE	39	47	30

Figure S271. Get High-res Image Gene #72: 'Del Peak 40(18q23)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 40(18q23)' versus 'MRNASEQ_CNMF'

P value = 3.74e-05 (Fisher's exact test), Q value = 0.026

Table S272. Gene #72: 'Del Peak 40(18q23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
DEL PEAK 40(18Q23) CNV	59	100	65
DEL PEAK 40(18Q23) WILD-TYPE	96	61	85

Figure S272. Get High-res Image Gene #72: 'Del Peak 40(18q23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 40(18q23)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.89e-06 (Fisher's exact test), Q value = 0.003

Table S273. Gene #72: 'Del Peak 40(18q23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
DEL PEAK 40(18Q23) CNV	79	80	65
DEL PEAK 40(18Q23) WILD-TYPE	39	128	75

Figure S273. Get High-res Image Gene #72: 'Del Peak 40(18q23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 41(19p13.3)' versus 'CN_CNMF'

P value = 7.34e-06 (Fisher's exact test), Q value = 0.0055

Table S274. Gene #73: 'Del Peak 41(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 41(19P13.3) CNV	106	93	67
DEL PEAK 41(19P13.3) WILD-TYPE	81	121	25

Figure S274. Get High-res Image Gene #73: 'Del Peak 41(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 41(19p13.3)' versus 'METHLYATION_CNMF'

P value = 3.89e-11 (Fisher's exact test), Q value = 3.5e-08

Table S275. Gene #73: 'Del Peak 41(19p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
DEL PEAK 41(19P13.3) CNV	108	65	58
DEL PEAK 41(19P13.3) WILD-TYPE	33	75	92

Figure S275. Get High-res Image Gene #73: 'Del Peak 41(19p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 41(19p13.3)' versus 'MRNASEQ_CNMF'

P value = 1.08e-13 (Fisher's exact test), Q value = 1e-10

Table S276. Gene #73: 'Del Peak 41(19p13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
DEL PEAK 41(19P13.3) CNV	54	78	116
DEL PEAK 41(19P13.3) WILD-TYPE	101	83	34

Figure S276. Get High-res Image Gene #73: 'Del Peak 41(19p13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 41(19p13.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.42e-11 (Fisher's exact test), Q value = 1.3e-08

Table S277. Gene #73: 'Del Peak 41(19p13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
DEL PEAK 41(19P13.3) CNV	57	83	108
DEL PEAK 41(19P13.3) WILD-TYPE	61	125	32

Figure S277. Get High-res Image Gene #73: 'Del Peak 41(19p13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 41(19p13.3)' versus 'MIRSEQ_CNMF'

P value = 8.85e-06 (Fisher's exact test), Q value = 0.0066

Table S278. Gene #73: 'Del Peak 41(19p13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 41(19P13.3) CNV	78	150	33
DEL PEAK 41(19P13.3) WILD-TYPE	101	81	45

Figure S278. Get High-res Image Gene #73: 'Del Peak 41(19p13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 41(19p13.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.17e-08 (Fisher's exact test), Q value = 1e-05

Table S279. Gene #73: 'Del Peak 41(19p13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
DEL PEAK 41(19P13.3) CNV	18	166	77
DEL PEAK 41(19P13.3) WILD-TYPE	33	83	111

Figure S279. Get High-res Image Gene #73: 'Del Peak 41(19p13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 41(19p13.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.03e-05 (Fisher's exact test), Q value = 0.048

Table S280. Gene #73: 'Del Peak 41(19p13.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
DEL PEAK 41(19P13.3) CNV	71	126	33
DEL PEAK 41(19P13.3) WILD-TYPE	84	66	45

Figure S280. Get High-res Image Gene #73: 'Del Peak 41(19p13.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 41(19p13.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.23e-07 (Fisher's exact test), Q value = 1e-04

Table S281. Gene #73: 'Del Peak 41(19p13.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
DEL PEAK 41(19P13.3) CNV	18	130	82
DEL PEAK 41(19P13.3) WILD-TYPE	31	58	106

Figure S281. Get High-res Image Gene #73: 'Del Peak 41(19p13.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 42(19p13.2)' versus 'CN_CNMF'

P value = 6.1e-07 (Fisher's exact test), Q value = 0.00049

Table S282. Gene #74: 'Del Peak 42(19p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 42(19P13.2) CNV	107	86	66
DEL PEAK 42(19P13.2) WILD-TYPE	80	128	26

Figure S282. Get High-res Image Gene #74: 'Del Peak 42(19p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 42(19p13.2)' versus 'METHLYATION_CNMF'

P value = 1.49e-12 (Fisher's exact test), Q value = 1.4e-09

Table S283. Gene #74: 'Del Peak 42(19p13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
DEL PEAK 42(19P13.2) CNV	107	67	51
DEL PEAK 42(19P13.2) WILD-TYPE	34	73	99

Figure S283. Get High-res Image Gene #74: 'Del Peak 42(19p13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 42(19p13.2)' versus 'MRNASEQ_CNMF'

P value = 4.05e-14 (Fisher's exact test), Q value = 3.7e-11

Table S284. Gene #74: 'Del Peak 42(19p13.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
DEL PEAK 42(19P13.2) CNV	50	78	114
DEL PEAK 42(19P13.2) WILD-TYPE	105	83	36

Figure S284. Get High-res Image Gene #74: 'Del Peak 42(19p13.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 42(19p13.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.38e-12 (Fisher's exact test), Q value = 7.6e-09

Table S285. Gene #74: 'Del Peak 42(19p13.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
DEL PEAK 42(19P13.2) CNV	58	78	106
DEL PEAK 42(19P13.2) WILD-TYPE	60	130	34

Figure S285. Get High-res Image Gene #74: 'Del Peak 42(19p13.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 42(19p13.2)' versus 'MIRSEQ_CNMF'

P value = 7.34e-06 (Fisher's exact test), Q value = 0.0055

Table S286. Gene #74: 'Del Peak 42(19p13.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 42(19P13.2) CNV	75	147	32
DEL PEAK 42(19P13.2) WILD-TYPE	104	84	46

Figure S286. Get High-res Image Gene #74: 'Del Peak 42(19p13.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 42(19p13.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.58e-08 (Fisher's exact test), Q value = 3e-05

Table S287. Gene #74: 'Del Peak 42(19p13.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
DEL PEAK 42(19P13.2) CNV	16	161	77
DEL PEAK 42(19P13.2) WILD-TYPE	35	88	111

Figure S287. Get High-res Image Gene #74: 'Del Peak 42(19p13.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 42(19p13.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.51e-05 (Fisher's exact test), Q value = 0.031

Table S288. Gene #74: 'Del Peak 42(19p13.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
DEL PEAK 42(19P13.2) CNV	67	124	33
DEL PEAK 42(19P13.2) WILD-TYPE	88	68	45

Figure S288. Get High-res Image Gene #74: 'Del Peak 42(19p13.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 42(19p13.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.82e-07 (Fisher's exact test), Q value = 0.00023

Table S289. Gene #74: 'Del Peak 42(19p13.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
DEL PEAK 42(19P13.2) CNV	19	127	78
DEL PEAK 42(19P13.2) WILD-TYPE	30	61	110

Figure S289. Get High-res Image Gene #74: 'Del Peak 42(19p13.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 43(19q13.33)' versus 'CN_CNMF'

P value = 1.99e-07 (Fisher's exact test), Q value = 0.00017

Table S290. Gene #75: 'Del Peak 43(19q13.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 43(19Q13.33) CNV	95	52	37
DEL PEAK 43(19Q13.33) WILD-TYPE	92	162	55

Figure S290. Get High-res Image Gene #75: 'Del Peak 43(19q13.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 43(19q13.33)' versus 'METHLYATION_CNMF'

P value = 9.04e-07 (Fisher's exact test), Q value = 0.00073

Table S291. Gene #75: 'Del Peak 43(19q13.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
DEL PEAK 43(19Q13.33) CNV	68	56	30
DEL PEAK 43(19Q13.33) WILD-TYPE	73	84	120

Figure S291. Get High-res Image Gene #75: 'Del Peak 43(19q13.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 43(19q13.33)' versus 'MRNASEQ_CNMF'

P value = 6.03e-05 (Fisher's exact test), Q value = 0.042

Table S292. Gene #75: 'Del Peak 43(19q13.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
DEL PEAK 43(19Q13.33) CNV	36	69	67
DEL PEAK 43(19Q13.33) WILD-TYPE	119	92	83

Figure S292. Get High-res Image Gene #75: 'Del Peak 43(19q13.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 43(19q13.33)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000273 (Fisher's exact test), Q value = 0.18

Table S293. Gene #75: 'Del Peak 43(19q13.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
DEL PEAK 43(19Q13.33) CNV	54	56	62
DEL PEAK 43(19Q13.33) WILD-TYPE	64	152	78

Figure S293. Get High-res Image Gene #75: 'Del Peak 43(19q13.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 43(19q13.33)' versus 'MIRSEQ_CNMF'

P value = 0.000258 (Fisher's exact test), Q value = 0.17

Table S294. Gene #75: 'Del Peak 43(19q13.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 43(19Q13.33) CNV	46	104	30
DEL PEAK 43(19Q13.33) WILD-TYPE	133	127	48

Figure S294. Get High-res Image Gene #75: 'Del Peak 43(19q13.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 43(19q13.33)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.24e-06 (Fisher's exact test), Q value = 0.0047

Table S295. Gene #75: 'Del Peak 43(19q13.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
DEL PEAK 43(19Q13.33) CNV	17	117	46
DEL PEAK 43(19Q13.33) WILD-TYPE	34	132	142

Figure S295. Get High-res Image Gene #75: 'Del Peak 43(19q13.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 45(21q11.2)' versus 'CN_CNMF'

P value = 4.85e-06 (Fisher's exact test), Q value = 0.0037

Table S296. Gene #77: 'Del Peak 45(21q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 45(21Q11.2) CNV	54	58	51
DEL PEAK 45(21Q11.2) WILD-TYPE	133	156	41

Figure S296. Get High-res Image Gene #77: 'Del Peak 45(21q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 45(21q11.2)' versus 'MRNASEQ_CNMF'

P value = 4.86e-13 (Fisher's exact test), Q value = 4.5e-10

Table S297. Gene #77: 'Del Peak 45(21q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
DEL PEAK 45(21Q11.2) CNV	18	61	74
DEL PEAK 45(21Q11.2) WILD-TYPE	137	100	76

Figure S297. Get High-res Image Gene #77: 'Del Peak 45(21q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 45(21q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.18e-10 (Fisher's exact test), Q value = 4.6e-07

Table S298. Gene #77: 'Del Peak 45(21q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
DEL PEAK 45(21Q11.2) CNV	39	40	74
DEL PEAK 45(21Q11.2) WILD-TYPE	79	168	66

Figure S298. Get High-res Image Gene #77: 'Del Peak 45(21q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 45(21q11.2)' versus 'MIRSEQ_CNMF'

P value = 1.45e-05 (Fisher's exact test), Q value = 0.011

Table S299. Gene #77: 'Del Peak 45(21q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 45(21Q11.2) CNV	40	100	20
DEL PEAK 45(21Q11.2) WILD-TYPE	139	131	58

Figure S299. Get High-res Image Gene #77: 'Del Peak 45(21q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 45(21q11.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.93e-08 (Fisher's exact test), Q value = 6.7e-05

Table S300. Gene #77: 'Del Peak 45(21q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
DEL PEAK 45(21Q11.2) CNV	9	111	40
DEL PEAK 45(21Q11.2) WILD-TYPE	42	138	148

Figure S300. Get High-res Image Gene #77: 'Del Peak 45(21q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 46(22q13.32)' versus 'CN_CNMF'

P value = 4.32e-13 (Fisher's exact test), Q value = 4e-10

Table S301. Gene #78: 'Del Peak 46(22q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 46(22Q13.32) CNV	108	63	65
DEL PEAK 46(22Q13.32) WILD-TYPE	79	151	27

Figure S301. Get High-res Image Gene #78: 'Del Peak 46(22q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 46(22q13.32)' versus 'METHLYATION_CNMF'

P value = 9e-06 (Fisher's exact test), Q value = 0.0067

Table S302. Gene #78: 'Del Peak 46(22q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	140	150
DEL PEAK 46(22Q13.32) CNV	73	84	49
DEL PEAK 46(22Q13.32) WILD-TYPE	68	56	101

Figure S302. Get High-res Image Gene #78: 'Del Peak 46(22q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 46(22q13.32)' versus 'MRNASEQ_CNMF'

P value = 9.24e-11 (Fisher's exact test), Q value = 8.3e-08

Table S303. Gene #78: 'Del Peak 46(22q13.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	161	150
DEL PEAK 46(22Q13.32) CNV	40	85	94
DEL PEAK 46(22Q13.32) WILD-TYPE	115	76	56

Figure S303. Get High-res Image Gene #78: 'Del Peak 46(22q13.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 46(22q13.32)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.79e-13 (Fisher's exact test), Q value = 2.6e-10

Table S304. Gene #78: 'Del Peak 46(22q13.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
DEL PEAK 46(22Q13.32) CNV	65	59	95
DEL PEAK 46(22Q13.32) WILD-TYPE	53	149	45

Figure S304. Get High-res Image Gene #78: 'Del Peak 46(22q13.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 46(22q13.32)' versus 'MIRSEQ_CNMF'

P value = 1.2e-06 (Fisher's exact test), Q value = 0.00096

Table S305. Gene #78: 'Del Peak 46(22q13.32)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	231	78
DEL PEAK 46(22Q13.32) CNV	60	137	36
DEL PEAK 46(22Q13.32) WILD-TYPE	119	94	42

Figure S305. Get High-res Image Gene #78: 'Del Peak 46(22q13.32)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 46(22q13.32)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.5e-08 (Fisher's exact test), Q value = 3e-05

Table S306. Gene #78: 'Del Peak 46(22q13.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	51	249	188
DEL PEAK 46(22Q13.32) CNV	17	151	65
DEL PEAK 46(22Q13.32) WILD-TYPE	34	98	123

Figure S306. Get High-res Image Gene #78: 'Del Peak 46(22q13.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 46(22q13.32)' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.37e-06 (Fisher's exact test), Q value = 0.0063

Table S307. Gene #78: 'Del Peak 46(22q13.32)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	155	192	78
DEL PEAK 46(22Q13.32) CNV	57	116	29
DEL PEAK 46(22Q13.32) WILD-TYPE	98	76	49

Figure S307. Get High-res Image Gene #78: 'Del Peak 46(22q13.32)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 46(22q13.32)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.07e-06 (Fisher's exact test), Q value = 0.00085

Table S308. Gene #78: 'Del Peak 46(22q13.32)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	188	188
DEL PEAK 46(22Q13.32) CNV	19	116	67
DEL PEAK 46(22Q13.32) WILD-TYPE	30	72	121

Figure S308. Get High-res Image Gene #78: 'Del Peak 46(22q13.32)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 47(Xp22.2)' versus 'CN_CNMF'

P value = 1.52e-08 (Fisher's exact test), Q value = 1.3e-05

Table S309. Gene #79: 'Del Peak 47(Xp22.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 47(XP22.2) CNV	82	36	24
DEL PEAK 47(XP22.2) WILD-TYPE	105	178	68

Figure S309. Get High-res Image Gene #79: 'Del Peak 47(Xp22.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 47(Xp22.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000113 (Fisher's exact test), Q value = 0.076

Table S310. Gene #79: 'Del Peak 47(Xp22.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	208	140
DEL PEAK 47(XP22.2) CNV	53	48	35
DEL PEAK 47(XP22.2) WILD-TYPE	65	160	105

Figure S310. Get High-res Image Gene #79: 'Del Peak 47(Xp22.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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 = LUAD-TP.transferedmergedcluster.txt
Number of patients = 493
Number of copy number variation regions = 79
Number of molecular subtypes = 12
Exclude regions 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)

[3] GISTIC_version2

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