Correlation between copy number variation genes and molecular subtypes

Lung Adenocarcinoma (Primary solid tumor)

21 April 2013 | analyses__2013_04_21

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): Lung Adenocarcinoma (Primary solid tumor cohort) - 21 April 2013: Correlation between copy number variation genes and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1W66HRJ

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 82 peak regions and 10 molecular subtypes across 472 patients, 306 significant findings detected with Q value < 0.25.

Amp Peak 1(1p34.3) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Amp Peak 2(1p22.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 3(1q21.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 4(3q26.2) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 5(4q12) cnvs correlated to 'CN_CNMF'.
Amp Peak 6(5p15.33) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 7(5p13.1) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 8(5q35.1) cnvs correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and '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', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
Amp Peak 11(7p11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 12(7q31.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 13(8p11.23) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 14(8p11.21) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 15(8q11.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 16(8q24.21) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 17(10p15.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 18(11q13.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 19(12p12.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 20(12q14.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 21(12q15) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 23(14q13.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 24(17q12) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 25(17q23.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 26(18q11.2) cnvs correlated to 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 27(19q12) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 28(20p11.21) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 29(20q13.33) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 31(Xq28) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 1(1p36.13) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 2(1p13.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 3(1p13.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 5(2q37.3) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 6(3p21.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
Del Peak 8(3q29) cnvs correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 9(4p16.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 10(4q22.1) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 11(4q35.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 12(5q11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 13(5q22.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 15(6q22.31) cnvs correlated to 'METHLYATION_CNMF'.
Del Peak 16(6q26) cnvs correlated to 'METHLYATION_CNMF'.
Del Peak 17(8p23.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
Del Peak 18(8p12) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
Del Peak 19(8p11.21) cnvs correlated to 'CN_CNMF'.
Del Peak 21(9p23) cnvs correlated to 'CN_CNMF'.
Del Peak 22(9p21.3) cnvs correlated to 'CN_CNMF'.
Del Peak 23(9q21.11) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 25(10q26.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Del Peak 26(11p15.5) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 27(11q23.2) cnvs correlated to 'CN_CNMF'.
Del Peak 29(12p13.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 30(12q12) cnvs correlated to 'CN_CNMF'.
Del Peak 31(12q24.33) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 32(13q12.11) cnvs correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 33(13q12.13) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 34(13q14.2) cnvs correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 35(13q34) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 36(14q32.33) cnvs correlated to 'CN_CNMF'.
Del Peak 37(15q11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
Del Peak 38(16q23.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 39(16q24.3) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 40(17p13.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 41(18q21.32) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 42(18q23) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 43(19p13.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 44(19p13.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 45(19p12) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 46(19q13.33) cnvs correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 47(20p13) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 48(21q11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 49(21q21.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 50(22q13.32) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 51(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 82 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 306 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
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Chi-square test	Fisher's exact test	Fisher's exact test	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test
Del Peak 10(4q22 1)	0 (0%)	330	0.000214 (0.114)	9.89e-05 (0.0551)	3.67e-07 (0.00025)	9.89e-08 (7.07e-05)	0.151 (1.00)	0.0286 (1.00)	3.81e-06 (0.00242)	9.97e-14 (7.96e-11)	1.66e-08 (1.22e-05)	1.54e-06 (0.00101)
Amp Peak 4(3q26 2)	0 (0%)	315	0.000264 (0.139)	0.00332 (1.00)	5.01e-10 (3.85e-07)	5.52e-08 (3.98e-05)	0.000631 (0.32)	0.00307 (1.00)	1.62e-09 (1.23e-06)	5.62e-09 (4.22e-06)	1.46e-06 (0.000956)	2.21e-07 (0.000153)
Amp Peak 11(7p11 2)	0 (0%)	220	1 (1.00)	1 (1.00)	1.27e-18 (1.02e-15)	2e-05 (0.0118)	0.00114 (0.554)	0.000263 (0.139)	1.06e-08 (7.91e-06)	1.49e-10 (1.16e-07)	2.59e-07 (0.000179)	6.85e-05 (0.0388)
Amp Peak 24(17q12)	0 (0%)	264	0.179 (1.00)	0.049 (1.00)	6.08e-14 (4.87e-11)	8.27e-07 (0.000553)	0.0638 (1.00)	0.00016 (0.086)	9.56e-11 (7.47e-08)	2.02e-06 (0.0013)	7.33e-07 (0.000491)	1.1e-06 (0.000724)
Amp Peak 25(17q23 1)	0 (0%)	242	0.081 (1.00)	0.208 (1.00)	2.25e-14 (1.81e-11)	2.11e-08 (1.55e-05)	0.00156 (0.742)	4.12e-07 (0.000279)	2.7e-13 (2.15e-10)	5.99e-10 (4.58e-07)	1.54e-06 (0.00101)	5.68e-06 (0.00353)
Del Peak 11(4q35 1)	0 (0%)	300	0.00204 (0.938)	0.00118 (0.573)	7.48e-10 (5.71e-07)	1.36e-11 (1.07e-08)	0.0381 (1.00)	0.000196 (0.105)	2.47e-09 (1.87e-06)	7.36e-18 (5.94e-15)	1.57e-10 (1.22e-07)	1e-10 (7.83e-08)
Amp Peak 14(8p11 21)	0 (0%)	310	0.253 (1.00)	0.124 (1.00)	3.42e-21 (2.78e-18)	0.000128 (0.0697)	0.0149 (1.00)	0.00534 (1.00)	1.59e-05 (0.00949)	4.9e-07 (0.000331)	4.19e-05 (0.0242)	6.3e-06 (0.0039)
Amp Peak 15(8q11 1)	0 (0%)	258	0.00472 (1.00)	0.0134 (1.00)	3.04e-22 (2.49e-19)	1.14e-07 (8.08e-05)	0.0344 (1.00)	0.00467 (1.00)	5.35e-06 (0.00334)	2.26e-05 (0.0133)	1.94e-07 (0.000136)	8.84e-07 (0.000587)
Amp Peak 16(8q24 21)	0 (0%)	174	0.0343 (1.00)	0.0341 (1.00)	8.4e-20 (6.82e-17)	3.72e-08 (2.71e-05)	0.157 (1.00)	0.00162 (0.763)	6.65e-05 (0.0378)	3.27e-06 (0.00209)	8.41e-07 (0.00056)	1.26e-05 (0.00762)
Amp Peak 17(10p15 1)	0 (0%)	348	0.023 (1.00)	0.0262 (1.00)	4.17e-06 (0.00264)	2.59e-07 (0.000179)	0.00434 (1.00)	0.0346 (1.00)	6.78e-05 (0.0385)	2.08e-08 (1.54e-05)	0.000237 (0.125)	6.08e-05 (0.0346)
Amp Peak 18(11q13 3)	0 (0%)	315	0.00118 (0.573)	0.000736 (0.368)	5.94e-14 (4.76e-11)	1.94e-05 (0.0115)	0.0127 (1.00)	0.00689 (1.00)	3.07e-08 (2.25e-05)	9.49e-07 (0.000629)	2.08e-10 (1.61e-07)	2.03e-07 (0.000141)
Amp Peak 19(12p12 1)	0 (0%)	309	0.198 (1.00)	0.033 (1.00)	5.45e-22 (4.46e-19)	4.14e-06 (0.00262)	0.0345 (1.00)	0.0834 (1.00)	1.44e-05 (0.00863)	2.74e-07 (0.000188)	6.05e-06 (0.00376)	1.01e-05 (0.00621)
Amp Peak 20(12q14 1)	0 (0%)	324	0.406 (1.00)	0.302 (1.00)	2.65e-24 (2.17e-21)	1.45e-07 (0.000103)	0.0215 (1.00)	0.00722 (1.00)	2.93e-07 (0.000201)	3.88e-10 (2.98e-07)	6.24e-09 (4.68e-06)	4.09e-09 (3.09e-06)
Amp Peak 21(12q15)	0 (0%)	321	0.221 (1.00)	0.103 (1.00)	1.49e-21 (1.22e-18)	2.35e-08 (1.73e-05)	0.0146 (1.00)	0.00471 (1.00)	7.24e-08 (5.21e-05)	4.39e-09 (3.31e-06)	2.17e-09 (1.65e-06)	1.1e-07 (7.86e-05)
Amp Peak 23(14q13 3)	0 (0%)	261	0.562 (1.00)	0.254 (1.00)	2.03e-11 (1.6e-08)	4.73e-06 (0.00297)	0.00213 (0.972)	0.0122 (1.00)	1.28e-09 (9.76e-07)	3.84e-05 (0.0223)	8.7e-08 (6.23e-05)	2.61e-09 (1.98e-06)
Amp Peak 27(19q12)	0 (0%)	346	0.0514 (1.00)	0.0219 (1.00)	1.29e-08 (9.54e-06)	0.000304 (0.159)	0.0685 (1.00)	0.0791 (1.00)	0.000438 (0.226)	4.22e-08 (3.06e-05)	1.27e-06 (0.000834)	1.46e-06 (0.000956)
Del Peak 9(4p16 3)	0 (0%)	356	0.595 (1.00)	0.453 (1.00)	1.56e-05 (0.00931)	2.31e-05 (0.0136)	0.0232 (1.00)	0.0499 (1.00)	8.4e-07 (0.00056)	6.36e-11 (4.98e-08)	2.82e-07 (0.000194)	1.11e-07 (7.86e-05)
Del Peak 12(5q11 2)	0 (0%)	306	0.26 (1.00)	0.254 (1.00)	1.9e-12 (1.5e-09)	2.02e-07 (0.000141)	0.00426 (1.00)	0.0113 (1.00)	1.35e-06 (0.000888)	2.57e-09 (1.95e-06)	4.53e-08 (3.28e-05)	2.11e-06 (0.00136)
Del Peak 13(5q22 1)	0 (0%)	283	0.0447 (1.00)	0.0515 (1.00)	1.08e-12 (8.57e-10)	2.56e-08 (1.88e-05)	0.0017 (0.795)	0.00377 (1.00)	1.55e-08 (1.14e-05)	3.56e-10 (2.74e-07)	5.97e-10 (4.58e-07)	8.43e-09 (6.29e-06)
Del Peak 17(8p23 2)	0 (0%)	243	0.00526 (1.00)	0.00382 (1.00)	7.67e-17 (6.18e-14)	9.17e-05 (0.0514)	0.018 (1.00)	0.000354 (0.183)	8.22e-09 (6.14e-06)	2.29e-07 (0.000159)	3.58e-06 (0.00228)	0.00312 (1.00)
Del Peak 33(13q12 13)	0 (0%)	206	0.00862 (1.00)	0.0218 (1.00)	1.05e-19 (8.48e-17)	0.000107 (0.0596)	0.000524 (0.27)	6.68e-07 (0.00045)	1.2e-07 (8.53e-05)	8.17e-08 (5.86e-05)	0.00386 (1.00)	0.000138 (0.0749)
Del Peak 34(13q14 2)	0 (0%)	216	0.00862 (1.00)	0.0218 (1.00)	7.61e-22 (6.22e-19)	0.000783 (0.39)	0.000647 (0.327)	1.04e-05 (0.00636)	4.15e-09 (3.13e-06)	1.54e-07 (0.000109)	0.000206 (0.11)	4.69e-05 (0.027)
Del Peak 37(15q11 2)	0 (0%)	233	0.168 (1.00)	0.157 (1.00)	1.81e-10 (1.41e-07)	0.000193 (0.103)	0.0928 (1.00)	0.000161 (0.0866)	1.91e-13 (1.53e-10)	1.4e-05 (0.00841)	2.82e-05 (0.0165)	0.000803 (0.396)
Del Peak 43(19p13 3)	0 (0%)	220	0.572 (1.00)	0.665 (1.00)	2.6e-12 (2.05e-09)	2.35e-07 (0.000163)	0.564 (1.00)	0.306 (1.00)	3.43e-10 (2.64e-07)	3.14e-07 (0.000215)	3.65e-06 (0.00232)	1.63e-07 (0.000115)
Del Peak 44(19p13 2)	0 (0%)	226	0.694 (1.00)	1 (1.00)	1.25e-11 (9.88e-09)	2.22e-08 (1.63e-05)	0.378 (1.00)	0.187 (1.00)	3.34e-10 (2.58e-07)	4.01e-07 (0.000272)	2.46e-06 (0.00158)	2.87e-07 (0.000197)
Del Peak 48(21q11 2)	0 (0%)	315	0.0604 (1.00)	0.0501 (1.00)	3.1e-11 (2.44e-08)	0.000131 (0.0713)	0.00624 (1.00)	0.00469 (1.00)	3.59e-08 (2.61e-05)	3.78e-07 (0.000257)	2.25e-05 (0.0132)	3.55e-08 (2.59e-05)
Del Peak 49(21q21 3)	0 (0%)	319	0.0288 (1.00)	0.033 (1.00)	9.45e-11 (7.39e-08)	1.28e-05 (0.00773)	0.000525 (0.27)	0.00065 (0.328)	3.24e-10 (2.51e-07)	5.51e-10 (4.23e-07)	1.04e-05 (0.00633)	1.28e-07 (9.06e-05)
Del Peak 50(22q13 32)	0 (0%)	248	0.0692 (1.00)	0.0871 (1.00)	6.18e-13 (4.91e-10)	4.57e-08 (3.3e-05)	0.00863 (1.00)	0.0171 (1.00)	1.51e-10 (1.17e-07)	6.29e-11 (4.93e-08)	1.66e-07 (0.000117)	2.72e-08 (1.99e-05)
Amp Peak 10(7p21 1)	0 (0%)	211	0.743 (1.00)	1 (1.00)	6.95e-20 (5.65e-17)	4.93e-06 (0.00309)	0.00184 (0.858)	0.00104 (0.508)	7.66e-09 (5.73e-06)	7.98e-08 (5.73e-05)	8.38e-06 (0.00515)	0.00203 (0.938)
Del Peak 6(3p21 31)	0 (0%)	245	0.132 (1.00)	0.478 (1.00)	7.53e-06 (0.00465)	3.21e-06 (0.00206)	0.0411 (1.00)	0.00737 (1.00)	3.35e-05 (0.0195)	6.23e-09 (4.67e-06)	1.18e-05 (0.00715)	0.000743 (0.371)
Del Peak 18(8p12)	0 (0%)	267	0.106 (1.00)	0.12 (1.00)	1.83e-15 (1.47e-12)	1.95e-05 (0.0116)	0.0424 (1.00)	0.0222 (1.00)	4.61e-05 (0.0267)	5.37e-06 (0.00335)	5.26e-05 (0.0301)	0.00432 (1.00)
Del Peak 23(9q21 11)	0 (0%)	241	0.0335 (1.00)	0.597 (1.00)	1.49e-07 (0.000105)	5.08e-05 (0.0292)	0.0726 (1.00)	0.0112 (1.00)	0.000116 (0.0644)	1.67e-07 (0.000117)	0.00333 (1.00)	0.000126 (0.0689)
Del Peak 32(13q12 11)	0 (0%)	207	0.00113 (0.553)	0.0134 (1.00)	1.38e-19 (1.12e-16)	0.000608 (0.311)	0.00188 (0.873)	1.49e-06 (0.000971)	2.73e-07 (0.000188)	4.07e-08 (2.95e-05)	0.00248 (1.00)	8.51e-05 (0.0479)
Del Peak 45(19p12)	0 (0%)	273	0.519 (1.00)	0.658 (1.00)	9.72e-13 (7.71e-10)	1.71e-05 (0.0102)	0.603 (1.00)	0.266 (1.00)	0.00153 (0.726)	0.00012 (0.0662)	2.79e-05 (0.0164)	1.27e-05 (0.00765)
Amp Peak 3(1q21 3)	0 (0%)	136	0.362 (1.00)	0.465 (1.00)	5.64e-06 (0.00351)	8.32e-07 (0.000556)	0.458 (1.00)	0.357 (1.00)	4.43e-06 (0.00279)	0.473 (1.00)	0.000695 (0.35)	0.000211 (0.112)
Amp Peak 6(5p15 33)	0 (0%)	168	0.878 (1.00)	0.901 (1.00)	2.75e-21 (2.24e-18)	0.0397 (1.00)	0.0565 (1.00)	0.000798 (0.396)	1.77e-07 (0.000124)	0.00166 (0.777)	0.000225 (0.119)	0.000304 (0.159)
Amp Peak 7(5p13 1)	0 (0%)	192	0.263 (1.00)	0.897 (1.00)	5.67e-18 (4.58e-15)	0.0135 (1.00)	0.443 (1.00)	0.0187 (1.00)	0.000119 (0.0661)	0.00342 (1.00)	0.000122 (0.0671)	0.000274 (0.144)
Amp Peak 12(7q31 2)	0 (0%)	272	0.482 (1.00)	0.429 (1.00)	2.86e-09 (2.16e-06)	5.48e-05 (0.0313)	0.206 (1.00)	0.052 (1.00)	2.97e-06 (0.0019)	1.37e-08 (1.01e-05)	0.00637 (1.00)	0.00978 (1.00)
Amp Peak 13(8p11 23)	0 (0%)	346	0.294 (1.00)	0.107 (1.00)	2.17e-16 (1.75e-13)	8.25e-06 (0.00507)	0.0844 (1.00)	0.0267 (1.00)	0.00309 (1.00)	7.16e-06 (0.00443)	0.0131 (1.00)	0.000479 (0.247)
Amp Peak 26(18q11 2)	0 (0%)	378	0.195 (1.00)	0.0151 (1.00)	0.000918 (0.451)	1.07e-08 (7.93e-06)	0.0431 (1.00)	0.000816 (0.402)	0.000799 (0.396)	9.61e-05 (0.0538)	1.06e-05 (0.00643)	6.73e-07 (0.000452)
Amp Peak 28(20p11 21)	0 (0%)	293	0.0611 (1.00)	0.0953 (1.00)	1.1e-05 (0.00669)	0.00708 (1.00)	0.338 (1.00)	0.0379 (1.00)	0.000221 (0.117)	0.00159 (0.749)	0.000145 (0.0785)	7.51e-05 (0.0424)
Amp Peak 29(20q13 33)	0 (0%)	247	0.00559 (1.00)	0.0301 (1.00)	1.03e-07 (7.35e-05)	0.00296 (1.00)	0.00426 (1.00)	0.00335 (1.00)	1.37e-05 (0.00821)	0.0184 (1.00)	2.53e-06 (0.00163)	4.24e-07 (0.000287)
Del Peak 1(1p36 13)	0 (0%)	364	0.795 (1.00)	0.441 (1.00)	1.59e-06 (0.00104)	2.18e-05 (0.0129)	0.437 (1.00)	0.363 (1.00)	8.06e-06 (0.00497)	8.99e-06 (0.00551)	0.0253 (1.00)	0.00486 (1.00)
Del Peak 38(16q23 1)	0 (0%)	312	0.0587 (1.00)	0.312 (1.00)	2.59e-07 (0.000179)	0.00046 (0.237)	0.000698 (0.35)	0.0174 (1.00)	1.73e-06 (0.00112)	3.21e-07 (0.000219)	0.013 (1.00)	0.0559 (1.00)
Del Peak 40(17p13 3)	0 (0%)	220	0.386 (1.00)	0.609 (1.00)	2.78e-13 (2.21e-10)	7.56e-08 (5.44e-05)	0.0334 (1.00)	0.00158 (0.747)	5.6e-08 (4.04e-05)	9.79e-07 (0.000648)	0.0102 (1.00)	0.00603 (1.00)
Amp Peak 8(5q35 1)	0 (0%)	362	0.0862 (1.00)	0.453 (1.00)	0.00391 (1.00)	8.8e-07 (0.000585)	0.0909 (1.00)	0.2 (1.00)	4.73e-05 (0.0272)	0.000159 (0.0858)	0.0134 (1.00)	0.00294 (1.00)
Amp Peak 31(Xq28)	0 (0%)	321	0.301 (1.00)	0.123 (1.00)	3.01e-10 (2.33e-07)	5.94e-05 (0.0338)	0.0244 (1.00)	0.0308 (1.00)	0.00146 (0.696)	9.71e-05 (0.0543)	0.0059 (1.00)	0.033 (1.00)
Del Peak 25(10q26 3)	0 (0%)	342	0.748 (1.00)	0.283 (1.00)	4.78e-06 (0.003)	0.000256 (0.135)	0.00268 (1.00)	0.0237 (1.00)	5.65e-05 (0.0323)	0.00205 (0.938)	0.0532 (1.00)	0.00789 (1.00)
Del Peak 26(11p15 5)	0 (0%)	346	0.268 (1.00)	0.0576 (1.00)	4.04e-06 (0.00256)	0.012 (1.00)	0.00767 (1.00)	0.00204 (0.938)	0.00111 (0.54)	4.36e-06 (0.00275)	0.00453 (1.00)	0.000108 (0.0598)
Del Peak 35(13q34)	0 (0%)	255	0.0356 (1.00)	0.0445 (1.00)	2.2e-15 (1.77e-12)	0.0508 (1.00)	0.00359 (1.00)	0.00079 (0.392)	3.71e-06 (0.00236)	3.09e-05 (0.018)	0.0215 (1.00)	0.00462 (1.00)
Del Peak 39(16q24 3)	0 (0%)	294	0.16 (1.00)	0.631 (1.00)	1.66e-06 (0.00108)	0.00282 (1.00)	0.0186 (1.00)	0.08 (1.00)	2.9e-05 (0.0169)	4.88e-05 (0.028)	0.0216 (1.00)	0.0345 (1.00)
Del Peak 41(18q21 32)	0 (0%)	239	0.115 (1.00)	0.227 (1.00)	8.58e-10 (6.55e-07)	0.0508 (1.00)	0.00133 (0.638)	0.0023 (1.00)	9.08e-09 (6.76e-06)	0.00012 (0.0662)	0.00925 (1.00)	0.105 (1.00)
Del Peak 42(18q23)	0 (0%)	244	0.029 (1.00)	0.0968 (1.00)	9.31e-13 (7.39e-10)	0.0205 (1.00)	0.00395 (1.00)	0.00135 (0.65)	1.04e-08 (7.74e-06)	1.28e-05 (0.00773)	0.00388 (1.00)	0.0798 (1.00)
Del Peak 46(19q13 33)	0 (0%)	298	0.272 (1.00)	0.383 (1.00)	2.02e-07 (0.000141)	0.00292 (1.00)	0.0819 (1.00)	0.208 (1.00)	0.0184 (1.00)	0.00194 (0.9)	2.52e-05 (0.0147)	1.41e-05 (0.00844)
Amp Peak 1(1p34 3)	0 (0%)	347	0.553 (1.00)	0.384 (1.00)	5.41e-07 (0.000365)	0.00816 (1.00)	0.169 (1.00)	0.243 (1.00)	4.96e-06 (0.00311)	0.149 (1.00)	0.184 (1.00)	0.147 (1.00)
Amp Peak 9(6p21 1)	0 (0%)	299	0.675 (1.00)	0.206 (1.00)	0.000168 (0.0903)	1.05e-07 (7.46e-05)	0.081 (1.00)	0.609 (1.00)	0.00918 (1.00)	0.727 (1.00)	0.012 (1.00)	0.0168 (1.00)
Del Peak 2(1p13 3)	0 (0%)	333	0.844 (1.00)	0.896 (1.00)	9.97e-07 (0.000659)	9.81e-05 (0.0547)	0.626 (1.00)	0.717 (1.00)	0.00705 (1.00)	0.0574 (1.00)	0.0693 (1.00)	0.00638 (1.00)
Del Peak 3(1p13 1)	0 (0%)	335	0.703 (1.00)	0.707 (1.00)	1.93e-06 (0.00125)	2.2e-05 (0.013)	0.124 (1.00)	0.535 (1.00)	0.00221 (1.00)	0.0349 (1.00)	0.0702 (1.00)	0.0131 (1.00)
Del Peak 5(2q37 3)	0 (0%)	409	0.703 (1.00)	0.206 (1.00)	0.00033 (0.171)	0.0016 (0.756)	0.22 (1.00)	0.151 (1.00)	0.178 (1.00)	0.00905 (1.00)	0.00691 (1.00)	0.000153 (0.0827)
Del Peak 8(3q29)	0 (0%)	343	0.71 (1.00)	0.602 (1.00)	0.145 (1.00)	8.11e-05 (0.0457)	0.00515 (1.00)	0.0168 (1.00)	3.27e-08 (2.39e-05)	0.0171 (1.00)	0.666 (1.00)	0.684 (1.00)
Del Peak 29(12p13 2)	0 (0%)	346	0.255 (1.00)	0.719 (1.00)	0.000172 (0.0921)	7.21e-07 (0.000484)	0.0774 (1.00)	0.021 (1.00)	0.00802 (1.00)	0.111 (1.00)	0.824 (1.00)	1 (1.00)
Del Peak 31(12q24 33)	0 (0%)	357	0.063 (1.00)	0.0396 (1.00)	6.54e-06 (0.00405)	0.00195 (0.901)	0.0223 (1.00)	0.00328 (1.00)	0.000614 (0.313)	0.000306 (0.159)	0.0538 (1.00)	0.0151 (1.00)
Del Peak 47(20p13)	0 (0%)	351	0.105 (1.00)	0.268 (1.00)	2.4e-06 (0.00155)	0.000655 (0.33)	0.00552 (1.00)	0.00106 (0.52)	0.000127 (0.0693)	0.0117 (1.00)	0.742 (1.00)	0.772 (1.00)
Del Peak 51(Xp22 2)	0 (0%)	335	0.691 (1.00)	0.896 (1.00)	1.99e-07 (0.000139)	0.00131 (0.631)	0.0885 (1.00)	0.0284 (1.00)	0.0141 (1.00)	0.000322 (0.167)	0.499 (1.00)	0.244 (1.00)
Amp Peak 2(1p22 3)	0 (0%)	348	0.876 (1.00)	1 (1.00)	4.8e-07 (0.000324)	0.00253 (1.00)	0.183 (1.00)	0.399 (1.00)	0.00168 (0.788)	0.0091 (1.00)	0.136 (1.00)	0.131 (1.00)
Amp Peak 5(4q12)	0 (0%)	384	0.703 (1.00)	0.206 (1.00)	6.06e-09 (4.55e-06)	0.0314 (1.00)	0.0221 (1.00)	0.0265 (1.00)	0.155 (1.00)	0.0258 (1.00)	0.00241 (1.00)	0.00429 (1.00)
Del Peak 15(6q22 31)	0 (0%)	238	0.54 (1.00)	0.187 (1.00)	0.022 (1.00)	1.29e-06 (0.000849)	0.308 (1.00)	0.0544 (1.00)	0.0184 (1.00)	0.709 (1.00)	0.9 (1.00)	0.571 (1.00)
Del Peak 16(6q26)	0 (0%)	234	0.368 (1.00)	0.276 (1.00)	0.0119 (1.00)	8.64e-05 (0.0486)	0.168 (1.00)	0.00944 (1.00)	0.141 (1.00)	0.807 (1.00)	0.81 (1.00)	0.41 (1.00)
Del Peak 19(8p11 21)	0 (0%)	365	0.795 (1.00)	0.504 (1.00)	2.79e-11 (2.2e-08)	0.018 (1.00)	0.721 (1.00)	0.318 (1.00)	0.000627 (0.318)	0.185 (1.00)	0.0376 (1.00)	0.512 (1.00)
Del Peak 21(9p23)	0 (0%)	214	0.521 (1.00)	0.901 (1.00)	3.22e-07 (0.000219)	0.582 (1.00)	0.62 (1.00)	0.598 (1.00)	0.0154 (1.00)	0.0119 (1.00)	0.639 (1.00)	0.286 (1.00)
Del Peak 22(9p21 3)	0 (0%)	208	0.521 (1.00)	0.901 (1.00)	1.79e-06 (0.00116)	0.521 (1.00)	0.328 (1.00)	0.288 (1.00)	0.022 (1.00)	0.00284 (1.00)	0.934 (1.00)	0.464 (1.00)
Del Peak 27(11q23 2)	0 (0%)	363	0.433 (1.00)	0.453 (1.00)	0.000122 (0.0669)	0.0184 (1.00)	0.009 (1.00)	0.00266 (1.00)	0.00156 (0.742)	0.00172 (0.803)	0.00296 (1.00)	0.00545 (1.00)
Del Peak 30(12q12)	0 (0%)	382	0.597 (1.00)	0.644 (1.00)	1.19e-05 (0.00722)	0.021 (1.00)	0.107 (1.00)	0.0158 (1.00)	0.00415 (1.00)	0.0474 (1.00)	0.204 (1.00)	0.052 (1.00)
Del Peak 36(14q32 33)	0 (0%)	332	0.703 (1.00)	0.302 (1.00)	0.000135 (0.0734)	0.521 (1.00)	0.16 (1.00)	0.0627 (1.00)	0.131 (1.00)	0.0451 (1.00)	0.0909 (1.00)	0.0117 (1.00)
Amp Peak 22(13q33 3)	0 (0%)	400	0.172 (1.00)	0.105 (1.00)	0.433 (1.00)	0.00285 (1.00)	0.663 (1.00)	0.298 (1.00)	0.0293 (1.00)	0.229 (1.00)	0.129 (1.00)	0.0824 (1.00)
Amp Peak 30(22q11 22)	0 (0%)	391	0.268 (1.00)	0.162 (1.00)	0.0014 (0.671)	0.601 (1.00)	0.0232 (1.00)	0.119 (1.00)	0.44 (1.00)	0.0532 (1.00)	0.0402 (1.00)	0.125 (1.00)
Del Peak 4(2q22 1)	0 (0%)	425	0.869 (1.00)	0.78 (1.00)	0.00238 (1.00)	0.0379 (1.00)	0.0306 (1.00)	0.471 (1.00)	0.151 (1.00)	0.0213 (1.00)	0.0739 (1.00)	0.008 (1.00)
Del Peak 7(3q11 1)	0 (0%)	339	0.609 (1.00)	0.602 (1.00)	0.0414 (1.00)	0.0274 (1.00)	0.366 (1.00)	0.298 (1.00)	0.0472 (1.00)	0.0162 (1.00)	0.183 (1.00)	0.936 (1.00)
Del Peak 14(6q12)	0 (0%)	314	0.532 (1.00)	1 (1.00)	0.0598 (1.00)	0.0244 (1.00)	0.243 (1.00)	0.159 (1.00)	0.575 (1.00)	0.891 (1.00)	0.0536 (1.00)	0.476 (1.00)
Del Peak 20(8q11 21)	0 (0%)	413	1 (1.00)	1 (1.00)	0.796 (1.00)	0.0628 (1.00)	0.537 (1.00)	0.676 (1.00)	0.000831 (0.409)	0.604 (1.00)	0.151 (1.00)	0.464 (1.00)
Del Peak 24(10p15 3)	0 (0%)	359	1 (1.00)	1 (1.00)	0.000735 (0.368)	0.000614 (0.313)	0.504 (1.00)	0.56 (1.00)	0.000546 (0.28)	0.366 (1.00)	0.0266 (1.00)	0.0103 (1.00)
Del Peak 28(11q25)	0 (0%)	367	0.108 (1.00)	0.0799 (1.00)	0.00149 (0.711)	0.0454 (1.00)	0.0012 (0.581)	0.00644 (1.00)	0.0264 (1.00)	0.00517 (1.00)	0.141 (1.00)	0.0854 (1.00)

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

P value = 5.41e-07 (Fisher's exact test), Q value = 0.00036

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
AMP PEAK 1(1P34.3) CNV	64	33	21	7
AMP PEAK 1(1P34.3) WILD-TYPE	84	155	66	42

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

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

P value = 4.96e-06 (Chi-square test), Q value = 0.0031

Table S2. Gene #1: 'Amp Peak 1(1p34.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
AMP PEAK 1(1P34.3) CNV	22	33	15	6	5	13	8	3	4
AMP PEAK 1(1P34.3) WILD-TYPE	53	22	41	36	24	35	31	21	19

Figure S2. Get High-res Image Gene #1: 'Amp Peak 1(1p34.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 4.8e-07 (Fisher's exact test), Q value = 0.00032

Table S3. Gene #2: 'Amp Peak 2(1p22.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
AMP PEAK 2(1P22.3) CNV	64	31	20	9
AMP PEAK 2(1P22.3) WILD-TYPE	84	157	67	40

Figure S3. 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 = 5.64e-06 (Fisher's exact test), Q value = 0.0035

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
AMP PEAK 3(1Q21.3) CNV	118	110	65	43
AMP PEAK 3(1Q21.3) WILD-TYPE	30	78	22	6

Figure S4. 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 = 8.32e-07 (Chi-square test), Q value = 0.00056

Table S5. Gene #3: 'Amp Peak 3(1q21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
AMP PEAK 3(1Q21.3) CNV	63	82	70	52	22
AMP PEAK 3(1Q21.3) WILD-TYPE	27	12	25	48	3

Figure S5. Get High-res Image Gene #3: 'Amp Peak 3(1q21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 4.43e-06 (Chi-square test), Q value = 0.0028

Table S6. Gene #3: 'Amp Peak 3(1q21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
AMP PEAK 3(1Q21.3) CNV	58	39	35	40	18	42	18	15	12
AMP PEAK 3(1Q21.3) WILD-TYPE	17	16	21	2	11	6	21	9	11

Figure S6. Get High-res Image Gene #3: 'Amp Peak 3(1q21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 0.000211 (Fisher's exact test), Q value = 0.11

Table S7. Gene #3: 'Amp Peak 3(1q21.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
AMP PEAK 3(1Q21.3) CNV	105	193	34
AMP PEAK 3(1Q21.3) WILD-TYPE	59	51	25

Figure S7. 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 = 0.14

Table S8. 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 S8. 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 = 5.01e-10 (Fisher's exact test), Q value = 3.8e-07

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
AMP PEAK 4(3Q26.2) CNV	52	35	52	18
AMP PEAK 4(3Q26.2) WILD-TYPE	96	153	35	31

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

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

P value = 5.52e-08 (Chi-square test), Q value = 4e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
AMP PEAK 4(3Q26.2) CNV	7	43	31	36	14
AMP PEAK 4(3Q26.2) WILD-TYPE	83	51	64	64	11

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

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

P value = 1.62e-09 (Chi-square test), Q value = 1.2e-06

Table S11. Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
AMP PEAK 4(3Q26.2) CNV	28	10	39	4	13	19	14	10	2
AMP PEAK 4(3Q26.2) WILD-TYPE	47	45	17	38	16	29	25	14	21

Figure S11. 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 = 5.62e-09 (Fisher's exact test), Q value = 4.2e-06

Table S12. Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
AMP PEAK 4(3Q26.2) CNV	29	44	66
AMP PEAK 4(3Q26.2) WILD-TYPE	129	61	62

Figure S12. 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 = 1.46e-06 (Fisher's exact test), Q value = 0.00096

Table S13. Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
AMP PEAK 4(3Q26.2) CNV	36	91	28
AMP PEAK 4(3Q26.2) WILD-TYPE	135	107	70

Figure S13. 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 = 2.21e-07 (Fisher's exact test), Q value = 0.00015

Table S14. Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
AMP PEAK 4(3Q26.2) CNV	34	109	12
AMP PEAK 4(3Q26.2) WILD-TYPE	130	135	47

Figure S14. Get High-res Image Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 6.06e-09 (Fisher's exact test), Q value = 4.6e-06

Table S15. Gene #5: 'Amp Peak 5(4q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
AMP PEAK 5(4Q12) CNV	45	13	25	5
AMP PEAK 5(4Q12) WILD-TYPE	103	175	62	44

Figure S15. 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 = 2.75e-21 (Fisher's exact test), Q value = 2.2e-18

Table S16. Gene #6: 'Amp Peak 6(5p15.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
AMP PEAK 6(5P15.33) CNV	136	83	48	37
AMP PEAK 6(5P15.33) WILD-TYPE	12	105	39	12

Figure S16. Get High-res Image Gene #6: 'Amp Peak 6(5p15.33)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 1.77e-07 (Chi-square test), Q value = 0.00012

Table S17. Gene #6: 'Amp Peak 6(5p15.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
AMP PEAK 6(5P15.33) CNV	59	44	44	21	8	31	18	15	11
AMP PEAK 6(5P15.33) WILD-TYPE	16	11	12	21	21	17	21	9	12

Figure S17. Get High-res Image Gene #6: 'Amp Peak 6(5p15.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 0.000225 (Fisher's exact test), Q value = 0.12

Table S18. Gene #6: 'Amp Peak 6(5p15.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
AMP PEAK 6(5P15.33) CNV	92	147	64
AMP PEAK 6(5P15.33) WILD-TYPE	79	51	34

Figure S18. Get High-res Image Gene #6: 'Amp Peak 6(5p15.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

P value = 0.000304 (Fisher's exact test), Q value = 0.16

Table S19. Gene #6: 'Amp Peak 6(5p15.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
AMP PEAK 6(5P15.33) CNV	87	177	39
AMP PEAK 6(5P15.33) WILD-TYPE	77	67	20

Figure S19. Get High-res Image Gene #6: 'Amp Peak 6(5p15.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 5.67e-18 (Fisher's exact test), Q value = 4.6e-15

Table S20. Gene #7: 'Amp Peak 7(5p13.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
AMP PEAK 7(5P13.1) CNV	124	75	42	39
AMP PEAK 7(5P13.1) WILD-TYPE	24	113	45	10

Figure S20. Get High-res Image Gene #7: 'Amp Peak 7(5p13.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 0.000119 (Chi-square test), Q value = 0.066

Table S21. Gene #7: 'Amp Peak 7(5p13.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
AMP PEAK 7(5P13.1) CNV	48	38	41	19	7	32	18	14	10
AMP PEAK 7(5P13.1) WILD-TYPE	27	17	15	23	22	16	21	10	13

Figure S21. Get High-res Image Gene #7: 'Amp Peak 7(5p13.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 0.000122 (Fisher's exact test), Q value = 0.067

Table S22. Gene #7: 'Amp Peak 7(5p13.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
AMP PEAK 7(5P13.1) CNV	82	138	59
AMP PEAK 7(5P13.1) WILD-TYPE	89	60	39

Figure S22. Get High-res Image Gene #7: 'Amp Peak 7(5p13.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

P value = 0.000274 (Fisher's exact test), Q value = 0.14

Table S23. Gene #7: 'Amp Peak 7(5p13.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
AMP PEAK 7(5P13.1) CNV	78	165	36
AMP PEAK 7(5P13.1) WILD-TYPE	86	79	23

Figure S23. Get High-res Image Gene #7: 'Amp Peak 7(5p13.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 8.8e-07 (Chi-square test), Q value = 0.00058

Table S24. Gene #8: 'Amp Peak 8(5q35.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
AMP PEAK 8(5Q35.1) CNV	41	14	16	17	8
AMP PEAK 8(5Q35.1) WILD-TYPE	49	80	79	83	17

Figure S24. Get High-res Image Gene #8: 'Amp Peak 8(5q35.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 4.73e-05 (Chi-square test), Q value = 0.027

Table S25. Gene #8: 'Amp Peak 8(5q35.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
AMP PEAK 8(5Q35.1) CNV	17	27	5	9	2	10	9	6	3
AMP PEAK 8(5Q35.1) WILD-TYPE	58	28	51	33	27	38	30	18	20

Figure S25. Get High-res Image Gene #8: 'Amp Peak 8(5q35.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 0.000159 (Fisher's exact test), Q value = 0.086

Table S26. Gene #8: 'Amp Peak 8(5q35.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
AMP PEAK 8(5Q35.1) CNV	49	25	14
AMP PEAK 8(5Q35.1) WILD-TYPE	109	80	114

Figure S26. 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 = 0.000168 (Fisher's exact test), Q value = 0.09

Table S27. Gene #9: 'Amp Peak 9(6p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
AMP PEAK 9(6P21.1) CNV	62	49	34	28
AMP PEAK 9(6P21.1) WILD-TYPE	86	139	53	21

Figure S27. 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 = 1.05e-07 (Chi-square test), Q value = 7.5e-05

Table S28. Gene #9: 'Amp Peak 9(6p21.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
AMP PEAK 9(6P21.1) CNV	31	54	34	17	14
AMP PEAK 9(6P21.1) WILD-TYPE	59	40	61	83	11

Figure S28. 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 = 6.95e-20 (Fisher's exact test), Q value = 5.6e-17

Table S29. Gene #10: 'Amp Peak 10(7p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
AMP PEAK 10(7P21.1) CNV	125	70	50	16
AMP PEAK 10(7P21.1) WILD-TYPE	23	118	37	33

Figure S29. Get High-res Image Gene #10: 'Amp Peak 10(7p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 4.93e-06 (Chi-square test), Q value = 0.0031

Table S30. Gene #10: 'Amp Peak 10(7p21.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
AMP PEAK 10(7P21.1) CNV	37	45	62	55	24
AMP PEAK 10(7P21.1) WILD-TYPE	53	49	33	45	1

Figure S30. Get High-res Image Gene #10: 'Amp Peak 10(7p21.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 7.66e-09 (Chi-square test), Q value = 5.7e-06

Table S31. Gene #10: 'Amp Peak 10(7p21.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
AMP PEAK 10(7P21.1) CNV	59	40	28	12	11	21	25	13	5
AMP PEAK 10(7P21.1) WILD-TYPE	16	15	28	30	18	27	14	11	18

Figure S31. 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 = 7.98e-08 (Fisher's exact test), Q value = 5.7e-05

Table S32. Gene #10: 'Amp Peak 10(7p21.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
AMP PEAK 10(7P21.1) CNV	67	81	66
AMP PEAK 10(7P21.1) WILD-TYPE	91	24	62

Figure S32. 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 = 8.38e-06 (Fisher's exact test), Q value = 0.0051

Table S33. Gene #10: 'Amp Peak 10(7p21.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
AMP PEAK 10(7P21.1) CNV	72	116	70
AMP PEAK 10(7P21.1) WILD-TYPE	99	82	28

Figure S33. 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 = 1.27e-18 (Fisher's exact test), Q value = 1e-15

Table S34. Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
AMP PEAK 11(7P11.2) CNV	120	66	51	15
AMP PEAK 11(7P11.2) WILD-TYPE	28	122	36	34

Figure S34. Get High-res Image Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 2e-05 (Chi-square test), Q value = 0.012

Table S35. Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
AMP PEAK 11(7P11.2) CNV	35	44	58	57	23
AMP PEAK 11(7P11.2) WILD-TYPE	55	50	37	43	2

Figure S35. Get High-res Image Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 0.000263 (Fisher's exact test), Q value = 0.14

Table S36. Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	89	65	58
AMP PEAK 11(7P11.2) CNV	7	62	37	23
AMP PEAK 11(7P11.2) WILD-TYPE	16	27	28	35

Figure S36. Get High-res Image Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

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

P value = 1.06e-08 (Chi-square test), Q value = 7.9e-06

Table S37. Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
AMP PEAK 11(7P11.2) CNV	58	37	28	11	10	19	25	12	5
AMP PEAK 11(7P11.2) WILD-TYPE	17	18	28	31	19	29	14	12	18

Figure S37. 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 = 1.49e-10 (Fisher's exact test), Q value = 1.2e-07

Table S38. Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
AMP PEAK 11(7P11.2) CNV	58	82	65
AMP PEAK 11(7P11.2) WILD-TYPE	100	23	63

Figure S38. 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-07 (Fisher's exact test), Q value = 0.00018

Table S39. Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
AMP PEAK 11(7P11.2) CNV	64	117	68
AMP PEAK 11(7P11.2) WILD-TYPE	107	81	30

Figure S39. 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 = 6.85e-05 (Fisher's exact test), Q value = 0.039

Table S40. Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
AMP PEAK 11(7P11.2) CNV	65	147	37
AMP PEAK 11(7P11.2) WILD-TYPE	99	97	22

Figure S40. Get High-res Image Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 2.86e-09 (Fisher's exact test), Q value = 2.2e-06

Table S41. Gene #12: 'Amp Peak 12(7q31.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
AMP PEAK 12(7Q31.2) CNV	94	54	34	18
AMP PEAK 12(7Q31.2) WILD-TYPE	54	134	53	31

Figure S41. Get High-res Image Gene #12: 'Amp Peak 12(7q31.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 5.48e-05 (Chi-square test), Q value = 0.031

Table S42. Gene #12: 'Amp Peak 12(7q31.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
AMP PEAK 12(7Q31.2) CNV	26	29	51	48	17
AMP PEAK 12(7Q31.2) WILD-TYPE	64	65	44	52	8

Figure S42. Get High-res Image Gene #12: 'Amp Peak 12(7q31.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 2.97e-06 (Chi-square test), Q value = 0.0019

Table S43. Gene #12: 'Amp Peak 12(7q31.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
AMP PEAK 12(7Q31.2) CNV	48	29	24	9	7	13	20	11	4
AMP PEAK 12(7Q31.2) WILD-TYPE	27	26	32	33	22	35	19	13	19

Figure S43. 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 = 1.37e-08 (Fisher's exact test), Q value = 1e-05

Table S44. Gene #12: 'Amp Peak 12(7q31.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
AMP PEAK 12(7Q31.2) CNV	48	70	47
AMP PEAK 12(7Q31.2) WILD-TYPE	110	35	81

Figure S44. 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 = 2.17e-16 (Fisher's exact test), Q value = 1.7e-13

Table S45. Gene #13: 'Amp Peak 13(8p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
AMP PEAK 13(8P11.23) CNV	34	26	28	38
AMP PEAK 13(8P11.23) WILD-TYPE	114	162	59	11

Figure S45. Get High-res Image Gene #13: 'Amp Peak 13(8p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 8.25e-06 (Chi-square test), Q value = 0.0051

Table S46. Gene #13: 'Amp Peak 13(8p11.23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
AMP PEAK 13(8P11.23) CNV	18	45	20	19	5
AMP PEAK 13(8P11.23) WILD-TYPE	72	49	75	81	20

Figure S46. Get High-res Image Gene #13: 'Amp Peak 13(8p11.23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 7.16e-06 (Fisher's exact test), Q value = 0.0044

Table S47. Gene #13: 'Amp Peak 13(8p11.23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
AMP PEAK 13(8P11.23) CNV	28	27	56
AMP PEAK 13(8P11.23) WILD-TYPE	130	78	72

Figure S47. Get High-res Image Gene #13: 'Amp Peak 13(8p11.23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 0.000479 (Fisher's exact test), Q value = 0.25

Table S48. Gene #13: 'Amp Peak 13(8p11.23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
AMP PEAK 13(8P11.23) CNV	27	82	15
AMP PEAK 13(8P11.23) WILD-TYPE	137	162	44

Figure S48. Get High-res Image Gene #13: 'Amp Peak 13(8p11.23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 3.42e-21 (Fisher's exact test), Q value = 2.8e-18

Table S49. Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
AMP PEAK 14(8P11.21) CNV	47	32	39	44
AMP PEAK 14(8P11.21) WILD-TYPE	101	156	48	5

Figure S49. Get High-res Image Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 0.000128 (Chi-square test), Q value = 0.07

Table S50. Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
AMP PEAK 14(8P11.21) CNV	21	51	32	29	7
AMP PEAK 14(8P11.21) WILD-TYPE	69	43	63	71	18

Figure S50. Get High-res Image Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 1.59e-05 (Chi-square test), Q value = 0.0095

Table S51. Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
AMP PEAK 14(8P11.21) CNV	27	13	32	16	8	27	7	6	3
AMP PEAK 14(8P11.21) WILD-TYPE	48	42	24	26	21	21	32	18	20

Figure S51. 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 = 4.9e-07 (Fisher's exact test), Q value = 0.00033

Table S52. Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
AMP PEAK 14(8P11.21) CNV	33	41	65
AMP PEAK 14(8P11.21) WILD-TYPE	125	64	63

Figure S52. Get High-res Image Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 4.19e-05 (Fisher's exact test), Q value = 0.024

Table S53. Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
AMP PEAK 14(8P11.21) CNV	39	89	33
AMP PEAK 14(8P11.21) WILD-TYPE	132	109	65

Figure S53. Get High-res Image Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

P value = 6.3e-06 (Fisher's exact test), Q value = 0.0039

Table S54. Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
AMP PEAK 14(8P11.21) CNV	34	107	20
AMP PEAK 14(8P11.21) WILD-TYPE	130	137	39

Figure S54. Get High-res Image Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 3.04e-22 (Fisher's exact test), Q value = 2.5e-19

Table S55. Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
AMP PEAK 15(8Q11.1) CNV	85	39	46	44
AMP PEAK 15(8Q11.1) WILD-TYPE	63	149	41	5

Figure S55. 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 = 1.14e-07 (Chi-square test), Q value = 8.1e-05

Table S56. Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
AMP PEAK 15(8Q11.1) CNV	25	62	52	32	12
AMP PEAK 15(8Q11.1) WILD-TYPE	65	32	43	68	13

Figure S56. 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 = 5.35e-06 (Chi-square test), Q value = 0.0033

Table S57. Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
AMP PEAK 15(8Q11.1) CNV	38	22	33	18	10	34	7	11	4
AMP PEAK 15(8Q11.1) WILD-TYPE	37	33	23	24	19	14	32	13	19

Figure S57. 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 = 2.26e-05 (Fisher's exact test), Q value = 0.013

Table S58. Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
AMP PEAK 15(8Q11.1) CNV	50	53	74
AMP PEAK 15(8Q11.1) WILD-TYPE	108	52	54

Figure S58. 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 = 1.94e-07 (Fisher's exact test), Q value = 0.00014

Table S59. Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
AMP PEAK 15(8Q11.1) CNV	50	114	48
AMP PEAK 15(8Q11.1) WILD-TYPE	121	84	50

Figure S59. 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 = 8.84e-07 (Fisher's exact test), Q value = 0.00059

Table S60. Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
AMP PEAK 15(8Q11.1) CNV	49	137	26
AMP PEAK 15(8Q11.1) WILD-TYPE	115	107	33

Figure S60. Get High-res Image Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 8.4e-20 (Fisher's exact test), Q value = 6.8e-17

Table S61. Gene #16: 'Amp Peak 16(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
AMP PEAK 16(8Q24.21) CNV	113	73	65	47
AMP PEAK 16(8Q24.21) WILD-TYPE	35	115	22	2

Figure S61. 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 = 3.72e-08 (Chi-square test), Q value = 2.7e-05

Table S62. Gene #16: 'Amp Peak 16(8q24.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
AMP PEAK 16(8Q24.21) CNV	39	76	71	50	16
AMP PEAK 16(8Q24.21) WILD-TYPE	51	18	24	50	9

Figure S62. 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 = 6.65e-05 (Chi-square test), Q value = 0.038

Table S63. Gene #16: 'Amp Peak 16(8q24.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
AMP PEAK 16(8Q24.21) CNV	55	34	37	27	11	41	20	13	8
AMP PEAK 16(8Q24.21) WILD-TYPE	20	21	19	15	18	7	19	11	15

Figure S63. 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 = 3.27e-06 (Fisher's exact test), Q value = 0.0021

Table S64. Gene #16: 'Amp Peak 16(8q24.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
AMP PEAK 16(8Q24.21) CNV	76	79	91
AMP PEAK 16(8Q24.21) WILD-TYPE	82	26	37

Figure S64. 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 = 8.41e-07 (Fisher's exact test), Q value = 0.00056

Table S65. Gene #16: 'Amp Peak 16(8q24.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
AMP PEAK 16(8Q24.21) CNV	82	147	66
AMP PEAK 16(8Q24.21) WILD-TYPE	89	51	32

Figure S65. 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 = 1.26e-05 (Fisher's exact test), Q value = 0.0076

Table S66. Gene #16: 'Amp Peak 16(8q24.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
AMP PEAK 16(8Q24.21) CNV	81	177	37
AMP PEAK 16(8Q24.21) WILD-TYPE	83	67	22

Figure S66. Get High-res Image Gene #16: 'Amp Peak 16(8q24.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 4.17e-06 (Fisher's exact test), Q value = 0.0026

Table S67. Gene #17: 'Amp Peak 17(10p15.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
AMP PEAK 17(10P15.1) CNV	39	29	34	22
AMP PEAK 17(10P15.1) WILD-TYPE	109	159	53	27

Figure S67. 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 = 2.59e-07 (Chi-square test), Q value = 0.00018

Table S68. Gene #17: 'Amp Peak 17(10p15.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
AMP PEAK 17(10P15.1) CNV	7	39	35	20	4
AMP PEAK 17(10P15.1) WILD-TYPE	83	55	60	80	21

Figure S68. 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 = 6.78e-05 (Chi-square test), Q value = 0.038

Table S69. Gene #17: 'Amp Peak 17(10p15.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
AMP PEAK 17(10P15.1) CNV	24	2	25	14	10	15	9	4	2
AMP PEAK 17(10P15.1) WILD-TYPE	51	53	31	28	19	33	30	20	21

Figure S69. 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 = 2.08e-08 (Fisher's exact test), Q value = 1.5e-05

Table S70. Gene #17: 'Amp Peak 17(10p15.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
AMP PEAK 17(10P15.1) CNV	21	27	57
AMP PEAK 17(10P15.1) WILD-TYPE	137	78	71

Figure S70. Get High-res Image Gene #17: 'Amp Peak 17(10p15.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 0.000237 (Fisher's exact test), Q value = 0.13

Table S71. Gene #17: 'Amp Peak 17(10p15.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
AMP PEAK 17(10P15.1) CNV	28	69	24
AMP PEAK 17(10P15.1) WILD-TYPE	143	129	74

Figure S71. Get High-res Image Gene #17: 'Amp Peak 17(10p15.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

P value = 6.08e-05 (Fisher's exact test), Q value = 0.035

Table S72. Gene #17: 'Amp Peak 17(10p15.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
AMP PEAK 17(10P15.1) CNV	27	84	10
AMP PEAK 17(10P15.1) WILD-TYPE	137	160	49

Figure S72. 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 = 5.94e-14 (Fisher's exact test), Q value = 4.8e-11

Table S73. Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
AMP PEAK 18(11Q13.3) CNV	69	24	42	22
AMP PEAK 18(11Q13.3) WILD-TYPE	79	164	45	27

Figure S73. Get High-res Image Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 1.94e-05 (Chi-square test), Q value = 0.011

Table S74. Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
AMP PEAK 18(11Q13.3) CNV	15	43	43	25	8
AMP PEAK 18(11Q13.3) WILD-TYPE	75	51	52	75	17

Figure S74. Get High-res Image Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 3.07e-08 (Chi-square test), Q value = 2.2e-05

Table S75. Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
AMP PEAK 18(11Q13.3) CNV	34	21	23	4	9	30	7	3	2
AMP PEAK 18(11Q13.3) WILD-TYPE	41	34	33	38	20	18	32	21	21

Figure S75. 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 = 9.49e-07 (Fisher's exact test), Q value = 0.00063

Table S76. Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
AMP PEAK 18(11Q13.3) CNV	30	47	56
AMP PEAK 18(11Q13.3) WILD-TYPE	128	58	72

Figure S76. 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 = 2.08e-10 (Fisher's exact test), Q value = 1.6e-07

Table S77. Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
AMP PEAK 18(11Q13.3) CNV	26	93	35
AMP PEAK 18(11Q13.3) WILD-TYPE	145	105	63

Figure S77. 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 = 2.03e-07 (Fisher's exact test), Q value = 0.00014

Table S78. Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
AMP PEAK 18(11Q13.3) CNV	29	106	19
AMP PEAK 18(11Q13.3) WILD-TYPE	135	138	40

Figure S78. Get High-res Image Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 5.45e-22 (Fisher's exact test), Q value = 4.5e-19

Table S79. Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
AMP PEAK 19(12P12.1) CNV	42	36	70	15
AMP PEAK 19(12P12.1) WILD-TYPE	106	152	17	34

Figure S79. Get High-res Image Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 4.14e-06 (Chi-square test), Q value = 0.0026

Table S80. Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
AMP PEAK 19(12P12.1) CNV	10	44	35	40	7
AMP PEAK 19(12P12.1) WILD-TYPE	80	50	60	60	18

Figure S80. Get High-res Image Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 1.44e-05 (Chi-square test), Q value = 0.0086

Table S81. Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
AMP PEAK 19(12P12.1) CNV	29	12	24	7	16	26	16	6	1
AMP PEAK 19(12P12.1) WILD-TYPE	46	43	32	35	13	22	23	18	22

Figure S81. 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 = 2.74e-07 (Fisher's exact test), Q value = 0.00019

Table S82. Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
AMP PEAK 19(12P12.1) CNV	32	40	65
AMP PEAK 19(12P12.1) WILD-TYPE	126	65	63

Figure S82. 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 = 6.05e-06 (Fisher's exact test), Q value = 0.0038

Table S83. Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
AMP PEAK 19(12P12.1) CNV	39	92	29
AMP PEAK 19(12P12.1) WILD-TYPE	132	106	69

Figure S83. 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 = 1.01e-05 (Fisher's exact test), Q value = 0.0062

Table S84. Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
AMP PEAK 19(12P12.1) CNV	40	108	12
AMP PEAK 19(12P12.1) WILD-TYPE	124	136	47

Figure S84. Get High-res Image Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 2.65e-24 (Fisher's exact test), Q value = 2.2e-21

Table S85. Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
AMP PEAK 20(12Q14.1) CNV	29	32	68	19
AMP PEAK 20(12Q14.1) WILD-TYPE	119	156	19	30

Figure S85. Get High-res Image Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 1.45e-07 (Chi-square test), Q value = 1e-04

Table S86. Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
AMP PEAK 20(12Q14.1) CNV	11	49	25	34	5
AMP PEAK 20(12Q14.1) WILD-TYPE	79	45	70	66	20

Figure S86. Get High-res Image Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 2.93e-07 (Chi-square test), Q value = 2e-04

Table S87. Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
AMP PEAK 20(12Q14.1) CNV	18	12	23	7	13	30	13	4	1
AMP PEAK 20(12Q14.1) WILD-TYPE	57	43	33	35	16	18	26	20	22

Figure S87. 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 = 3.88e-10 (Fisher's exact test), Q value = 3e-07

Table S88. Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
AMP PEAK 20(12Q14.1) CNV	26	28	67
AMP PEAK 20(12Q14.1) WILD-TYPE	132	77	61

Figure S88. 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 = 6.24e-09 (Fisher's exact test), Q value = 4.7e-06

Table S89. Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
AMP PEAK 20(12Q14.1) CNV	29	91	26
AMP PEAK 20(12Q14.1) WILD-TYPE	142	107	72

Figure S89. 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 = 4.09e-09 (Fisher's exact test), Q value = 3.1e-06

Table S90. Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
AMP PEAK 20(12Q14.1) CNV	28	107	11
AMP PEAK 20(12Q14.1) WILD-TYPE	136	137	48

Figure S90. Get High-res Image Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 1.49e-21 (Fisher's exact test), Q value = 1.2e-18

Table S91. Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
AMP PEAK 21(12Q15) CNV	31	34	66	20
AMP PEAK 21(12Q15) WILD-TYPE	117	154	21	29

Figure S91. Get High-res Image Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 2.35e-08 (Chi-square test), Q value = 1.7e-05

Table S92. Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
AMP PEAK 21(12Q15) CNV	11	52	25	32	8
AMP PEAK 21(12Q15) WILD-TYPE	79	42	70	68	17

Figure S92. Get High-res Image Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 7.24e-08 (Chi-square test), Q value = 5.2e-05

Table S93. Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
AMP PEAK 21(12Q15) CNV	17	13	23	7	15	31	12	6	1
AMP PEAK 21(12Q15) WILD-TYPE	58	42	33	35	14	17	27	18	22

Figure S93. 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 = 4.39e-09 (Fisher's exact test), Q value = 3.3e-06

Table S94. Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
AMP PEAK 21(12Q15) CNV	32	25	68
AMP PEAK 21(12Q15) WILD-TYPE	126	80	60

Figure S94. 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 = 2.17e-09 (Fisher's exact test), Q value = 1.6e-06

Table S95. Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
AMP PEAK 21(12Q15) CNV	30	94	26
AMP PEAK 21(12Q15) WILD-TYPE	141	104	72

Figure S95. 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 = 1.1e-07 (Fisher's exact test), Q value = 7.9e-05

Table S96. Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
AMP PEAK 21(12Q15) CNV	29	106	15
AMP PEAK 21(12Q15) WILD-TYPE	135	138	44

Figure S96. Get High-res Image Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 2.03e-11 (Fisher's exact test), Q value = 1.6e-08

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
AMP PEAK 23(14Q13.3) CNV	80	48	48	35
AMP PEAK 23(14Q13.3) WILD-TYPE	68	140	39	14

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

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

P value = 4.73e-06 (Chi-square test), Q value = 0.003

Table S98. Gene #23: 'Amp Peak 23(14q13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
AMP PEAK 23(14Q13.3) CNV	29	56	47	31	18
AMP PEAK 23(14Q13.3) WILD-TYPE	61	38	48	69	7

Figure S98. Get High-res Image Gene #23: 'Amp Peak 23(14q13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 1.28e-09 (Chi-square test), Q value = 9.8e-07

Table S99. Gene #23: 'Amp Peak 23(14q13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
AMP PEAK 23(14Q13.3) CNV	40	22	31	9	6	40	11	8	7
AMP PEAK 23(14Q13.3) WILD-TYPE	35	33	25	33	23	8	28	16	16

Figure S99. 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 = 3.84e-05 (Fisher's exact test), Q value = 0.022

Table S100. Gene #23: 'Amp Peak 23(14q13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
AMP PEAK 23(14Q13.3) CNV	49	59	66
AMP PEAK 23(14Q13.3) WILD-TYPE	109	46	62

Figure S100. 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 = 8.7e-08 (Fisher's exact test), Q value = 6.2e-05

Table S101. Gene #23: 'Amp Peak 23(14q13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
AMP PEAK 23(14Q13.3) CNV	47	108	53
AMP PEAK 23(14Q13.3) WILD-TYPE	124	90	45

Figure S101. 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 = 2.61e-09 (Fisher's exact test), Q value = 2e-06

Table S102. Gene #23: 'Amp Peak 23(14q13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
AMP PEAK 23(14Q13.3) CNV	42	138	28
AMP PEAK 23(14Q13.3) WILD-TYPE	122	106	31

Figure S102. Get High-res Image Gene #23: 'Amp Peak 23(14q13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 24(17q12)' versus 'CN_CNMF'

P value = 6.08e-14 (Fisher's exact test), Q value = 4.9e-11

Table S103. Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
AMP PEAK 24(17Q12) CNV	90	42	52	24
AMP PEAK 24(17Q12) WILD-TYPE	58	146	35	25

Figure S103. Get High-res Image Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 24(17q12)' versus 'METHLYATION_CNMF'

P value = 8.27e-07 (Chi-square test), Q value = 0.00055

Table S104. Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
AMP PEAK 24(17Q12) CNV	22	51	54	31	15
AMP PEAK 24(17Q12) WILD-TYPE	68	43	41	69	10

Figure S104. Get High-res Image Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 24(17q12)' versus 'RPPA_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.086

Table S105. Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	89	65	58
AMP PEAK 24(17Q12) CNV	3	52	33	20
AMP PEAK 24(17Q12) WILD-TYPE	20	37	32	38

Figure S105. Get High-res Image Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 24(17q12)' versus 'MRNASEQ_CNMF'

P value = 9.56e-11 (Chi-square test), Q value = 7.5e-08

Table S106. Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
AMP PEAK 24(17Q12) CNV	53	30	30	6	9	23	10	11	1
AMP PEAK 24(17Q12) WILD-TYPE	22	25	26	36	20	25	29	13	22

Figure S106. Get High-res Image Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 24(17q12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.02e-06 (Fisher's exact test), Q value = 0.0013

Table S107. Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
AMP PEAK 24(17Q12) CNV	48	65	60
AMP PEAK 24(17Q12) WILD-TYPE	110	40	68

Figure S107. Get High-res Image Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 24(17q12)' versus 'MIRSEQ_CNMF'

P value = 7.33e-07 (Fisher's exact test), Q value = 0.00049

Table S108. Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
AMP PEAK 24(17Q12) CNV	50	112	44
AMP PEAK 24(17Q12) WILD-TYPE	121	86	54

Figure S108. Get High-res Image Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 24(17q12)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.1e-06 (Fisher's exact test), Q value = 0.00072

Table S109. Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
AMP PEAK 24(17Q12) CNV	49	135	22
AMP PEAK 24(17Q12) WILD-TYPE	115	109	37

Figure S109. Get High-res Image Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 25(17q23.1)' versus 'CN_CNMF'

P value = 2.25e-14 (Fisher's exact test), Q value = 1.8e-11

Table S110. Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
AMP PEAK 25(17Q23.1) CNV	100	51	56	23
AMP PEAK 25(17Q23.1) WILD-TYPE	48	137	31	26

Figure S110. Get High-res Image Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 25(17q23.1)' versus 'METHLYATION_CNMF'

P value = 2.11e-08 (Chi-square test), Q value = 1.6e-05

Table S111. Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
AMP PEAK 25(17Q23.1) CNV	24	52	65	36	15
AMP PEAK 25(17Q23.1) WILD-TYPE	66	42	30	64	10

Figure S111. Get High-res Image Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 25(17q23.1)' versus 'RPPA_CHIERARCHICAL'

P value = 4.12e-07 (Fisher's exact test), Q value = 0.00028

Table S112. Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	89	65	58
AMP PEAK 25(17Q23.1) CNV	3	57	38	17
AMP PEAK 25(17Q23.1) WILD-TYPE	20	32	27	41

Figure S112. Get High-res Image Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 25(17q23.1)' versus 'MRNASEQ_CNMF'

P value = 2.7e-13 (Chi-square test), Q value = 2.2e-10

Table S113. Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
AMP PEAK 25(17Q23.1) CNV	61	32	32	8	6	23	15	10	2
AMP PEAK 25(17Q23.1) WILD-TYPE	14	23	24	34	23	25	24	14	21

Figure S113. Get High-res Image Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 25(17q23.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.99e-10 (Fisher's exact test), Q value = 4.6e-07

Table S114. Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
AMP PEAK 25(17Q23.1) CNV	49	75	65
AMP PEAK 25(17Q23.1) WILD-TYPE	109	30	63

Figure S114. Get High-res Image Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 25(17q23.1)' versus 'MIRSEQ_CNMF'

P value = 1.54e-06 (Fisher's exact test), Q value = 0.001

Table S115. Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
AMP PEAK 25(17Q23.1) CNV	58	120	50
AMP PEAK 25(17Q23.1) WILD-TYPE	113	78	48

Figure S115. Get High-res Image Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 25(17q23.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.68e-06 (Fisher's exact test), Q value = 0.0035

Table S116. Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
AMP PEAK 25(17Q23.1) CNV	58	145	25
AMP PEAK 25(17Q23.1) WILD-TYPE	106	99	34

Figure S116. Get High-res Image Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 26(18q11.2)' versus 'METHLYATION_CNMF'

P value = 1.07e-08 (Chi-square test), Q value = 7.9e-06

Table S117. Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
AMP PEAK 26(18Q11.2) CNV	7	40	19	11	7
AMP PEAK 26(18Q11.2) WILD-TYPE	83	54	76	89	18

Figure S117. Get High-res Image Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 26(18q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.61e-05 (Fisher's exact test), Q value = 0.054

Table S118. Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
AMP PEAK 26(18Q11.2) CNV	19	21	42
AMP PEAK 26(18Q11.2) WILD-TYPE	139	84	86

Figure S118. Get High-res Image Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 26(18q11.2)' versus 'MIRSEQ_CNMF'

P value = 1.06e-05 (Fisher's exact test), Q value = 0.0064

Table S119. Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
AMP PEAK 26(18Q11.2) CNV	16	57	20
AMP PEAK 26(18Q11.2) WILD-TYPE	155	141	78

Figure S119. Get High-res Image Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 26(18q11.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.73e-07 (Fisher's exact test), Q value = 0.00045

Table S120. Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
AMP PEAK 26(18Q11.2) CNV	18	71	4
AMP PEAK 26(18Q11.2) WILD-TYPE	146	173	55

Figure S120. Get High-res Image Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 27(19q12)' versus 'CN_CNMF'

P value = 1.29e-08 (Fisher's exact test), Q value = 9.5e-06

Table S121. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
AMP PEAK 27(19Q12) CNV	36	28	43	19
AMP PEAK 27(19Q12) WILD-TYPE	112	160	44	30

Figure S121. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 27(19q12)' versus 'METHLYATION_CNMF'

P value = 0.000304 (Chi-square test), Q value = 0.16

Table S122. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
AMP PEAK 27(19Q12) CNV	15	41	21	25	10
AMP PEAK 27(19Q12) WILD-TYPE	75	53	74	75	15

Figure S122. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 27(19q12)' versus 'MRNASEQ_CNMF'

P value = 0.000438 (Chi-square test), Q value = 0.23

Table S123. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
AMP PEAK 27(19Q12) CNV	21	7	24	14	6	19	8	5	0
AMP PEAK 27(19Q12) WILD-TYPE	54	48	32	28	23	29	31	19	23

Figure S123. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 27(19q12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.22e-08 (Fisher's exact test), Q value = 3.1e-05

Table S124. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
AMP PEAK 27(19Q12) CNV	19	32	53
AMP PEAK 27(19Q12) WILD-TYPE	139	73	75

Figure S124. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 27(19q12)' versus 'MIRSEQ_CNMF'

P value = 1.27e-06 (Fisher's exact test), Q value = 0.00083

Table S125. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
AMP PEAK 27(19Q12) CNV	25	76	25
AMP PEAK 27(19Q12) WILD-TYPE	146	122	73

Figure S125. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 27(19q12)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.46e-06 (Fisher's exact test), Q value = 0.00096

Table S126. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
AMP PEAK 27(19Q12) CNV	29	90	7
AMP PEAK 27(19Q12) WILD-TYPE	135	154	52

Figure S126. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 28(20p11.21)' versus 'CN_CNMF'

P value = 1.1e-05 (Fisher's exact test), Q value = 0.0067

Table S127. Gene #28: 'Amp Peak 28(20p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
AMP PEAK 28(20P11.21) CNV	53	52	44	30
AMP PEAK 28(20P11.21) WILD-TYPE	95	136	43	19

Figure S127. Get High-res Image Gene #28: 'Amp Peak 28(20p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 28(20p11.21)' versus 'MRNASEQ_CNMF'

P value = 0.000221 (Chi-square test), Q value = 0.12

Table S128. Gene #28: 'Amp Peak 28(20p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
AMP PEAK 28(20P11.21) CNV	23	24	33	15	9	26	8	9	3
AMP PEAK 28(20P11.21) WILD-TYPE	52	31	23	27	20	22	31	15	20

Figure S128. Get High-res Image Gene #28: 'Amp Peak 28(20p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 28(20p11.21)' versus 'MIRSEQ_CNMF'

P value = 0.000145 (Fisher's exact test), Q value = 0.078

Table S129. Gene #28: 'Amp Peak 28(20p11.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
AMP PEAK 28(20P11.21) CNV	44	91	42
AMP PEAK 28(20P11.21) WILD-TYPE	127	107	56

Figure S129. Get High-res Image Gene #28: 'Amp Peak 28(20p11.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 28(20p11.21)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.51e-05 (Fisher's exact test), Q value = 0.042

Table S130. Gene #28: 'Amp Peak 28(20p11.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
AMP PEAK 28(20P11.21) CNV	42	114	21
AMP PEAK 28(20P11.21) WILD-TYPE	122	130	38

Figure S130. Get High-res Image Gene #28: 'Amp Peak 28(20p11.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 29(20q13.33)' versus 'CN_CNMF'

P value = 1.03e-07 (Fisher's exact test), Q value = 7.4e-05

Table S131. Gene #29: 'Amp Peak 29(20q13.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
AMP PEAK 29(20Q13.33) CNV	77	61	52	35
AMP PEAK 29(20Q13.33) WILD-TYPE	71	127	35	14

Figure S131. Get High-res Image Gene #29: 'Amp Peak 29(20q13.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 29(20q13.33)' versus 'MRNASEQ_CNMF'

P value = 1.37e-05 (Chi-square test), Q value = 0.0082

Table S132. Gene #29: 'Amp Peak 29(20q13.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
AMP PEAK 29(20Q13.33) CNV	37	31	37	15	9	33	14	11	3
AMP PEAK 29(20Q13.33) WILD-TYPE	38	24	19	27	20	15	25	13	20

Figure S132. Get High-res Image Gene #29: 'Amp Peak 29(20q13.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 29(20q13.33)' versus 'MIRSEQ_CNMF'

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

Table S133. Gene #29: 'Amp Peak 29(20q13.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
AMP PEAK 29(20Q13.33) CNV	58	119	44
AMP PEAK 29(20Q13.33) WILD-TYPE	113	79	54

Figure S133. Get High-res Image Gene #29: 'Amp Peak 29(20q13.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 29(20q13.33)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.24e-07 (Fisher's exact test), Q value = 0.00029

Table S134. Gene #29: 'Amp Peak 29(20q13.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
AMP PEAK 29(20Q13.33) CNV	51	142	28
AMP PEAK 29(20Q13.33) WILD-TYPE	113	102	31

Figure S134. Get High-res Image Gene #29: 'Amp Peak 29(20q13.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 31(Xq28)' versus 'CN_CNMF'

P value = 3.01e-10 (Fisher's exact test), Q value = 2.3e-07

Table S135. Gene #31: 'Amp Peak 31(Xq28)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
AMP PEAK 31(XQ28) CNV	73	29	31	18
AMP PEAK 31(XQ28) WILD-TYPE	75	159	56	31

Figure S135. Get High-res Image Gene #31: 'Amp Peak 31(Xq28)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 31(Xq28)' versus 'METHLYATION_CNMF'

P value = 5.94e-05 (Chi-square test), Q value = 0.034

Table S136. Gene #31: 'Amp Peak 31(Xq28)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
AMP PEAK 31(XQ28) CNV	15	34	43	22	11
AMP PEAK 31(XQ28) WILD-TYPE	75	60	52	78	14

Figure S136. Get High-res Image Gene #31: 'Amp Peak 31(Xq28)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 31(Xq28)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.71e-05 (Fisher's exact test), Q value = 0.054

Table S137. Gene #31: 'Amp Peak 31(Xq28)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
AMP PEAK 31(XQ28) CNV	35	50	42
AMP PEAK 31(XQ28) WILD-TYPE	123	55	86

Figure S137. Get High-res Image Gene #31: 'Amp Peak 31(Xq28)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 1.59e-06 (Fisher's exact test), Q value = 0.001

Table S138. Gene #32: 'Del Peak 1(1p36.13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 1(1P36.13) CNV	19	38	27	24
DEL PEAK 1(1P36.13) WILD-TYPE	129	150	60	25

Figure S138. Get High-res Image Gene #32: 'Del Peak 1(1p36.13)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 2.18e-05 (Chi-square test), Q value = 0.013

Table S139. Gene #32: 'Del Peak 1(1p36.13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
DEL PEAK 1(1P36.13) CNV	11	38	22	15	4
DEL PEAK 1(1P36.13) WILD-TYPE	79	56	73	85	21

Figure S139. Get High-res Image Gene #32: 'Del Peak 1(1p36.13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 8.06e-06 (Chi-square test), Q value = 0.005

Table S140. Gene #32: 'Del Peak 1(1p36.13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
DEL PEAK 1(1P36.13) CNV	17	4	13	8	8	25	10	1	3
DEL PEAK 1(1P36.13) WILD-TYPE	58	51	43	34	21	23	29	23	20

Figure S140. Get High-res Image Gene #32: 'Del Peak 1(1p36.13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 8.99e-06 (Fisher's exact test), Q value = 0.0055

Table S141. Gene #32: 'Del Peak 1(1p36.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 1(1P36.13) CNV	19	24	46
DEL PEAK 1(1P36.13) WILD-TYPE	139	81	82

Figure S141. Get High-res Image Gene #32: 'Del Peak 1(1p36.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 2(1p13.3)' versus 'CN_CNMF'

P value = 9.97e-07 (Fisher's exact test), Q value = 0.00066

Table S142. Gene #33: 'Del Peak 2(1p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 2(1P13.3) CNV	29	46	37	27
DEL PEAK 2(1P13.3) WILD-TYPE	119	142	50	22

Figure S142. Get High-res Image Gene #33: 'Del Peak 2(1p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 2(1p13.3)' versus 'METHLYATION_CNMF'

P value = 9.81e-05 (Chi-square test), Q value = 0.055

Table S143. Gene #33: 'Del Peak 2(1p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
DEL PEAK 2(1P13.3) CNV	25	41	27	13	5
DEL PEAK 2(1P13.3) WILD-TYPE	65	53	68	87	20

Figure S143. Get High-res Image Gene #33: 'Del Peak 2(1p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 3(1p13.1)' versus 'CN_CNMF'

P value = 1.93e-06 (Fisher's exact test), Q value = 0.0013

Table S144. Gene #34: 'Del Peak 3(1p13.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 3(1P13.1) CNV	31	42	40	24
DEL PEAK 3(1P13.1) WILD-TYPE	117	146	47	25

Figure S144. Get High-res Image Gene #34: 'Del Peak 3(1p13.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 3(1p13.1)' versus 'METHLYATION_CNMF'

P value = 2.2e-05 (Chi-square test), Q value = 0.013

Table S145. Gene #34: 'Del Peak 3(1p13.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
DEL PEAK 3(1P13.1) CNV	22	40	32	12	4
DEL PEAK 3(1P13.1) WILD-TYPE	68	54	63	88	21

Figure S145. Get High-res Image Gene #34: 'Del Peak 3(1p13.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 5(2q37.3)' versus 'CN_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.17

Table S146. Gene #36: 'Del Peak 5(2q37.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 5(2Q37.3) CNV	30	12	10	11
DEL PEAK 5(2Q37.3) WILD-TYPE	118	176	77	38

Figure S146. Get High-res Image Gene #36: 'Del Peak 5(2q37.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 5(2q37.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000153 (Fisher's exact test), Q value = 0.083

Table S147. Gene #36: 'Del Peak 5(2q37.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
DEL PEAK 5(2Q37.3) CNV	10	48	5
DEL PEAK 5(2Q37.3) WILD-TYPE	154	196	54

Figure S147. Get High-res Image Gene #36: 'Del Peak 5(2q37.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 6(3p21.31)' versus 'CN_CNMF'

P value = 7.53e-06 (Fisher's exact test), Q value = 0.0046

Table S148. Gene #37: 'Del Peak 6(3p21.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 6(3P21.31) CNV	77	65	53	32
DEL PEAK 6(3P21.31) WILD-TYPE	71	123	34	17

Figure S148. Get High-res Image Gene #37: 'Del Peak 6(3p21.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 6(3p21.31)' versus 'METHLYATION_CNMF'

P value = 3.21e-06 (Chi-square test), Q value = 0.0021

Table S149. Gene #37: 'Del Peak 6(3p21.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
DEL PEAK 6(3P21.31) CNV	32	67	43	39	15
DEL PEAK 6(3P21.31) WILD-TYPE	58	27	52	61	10

Figure S149. Get High-res Image Gene #37: 'Del Peak 6(3p21.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 6(3p21.31)' versus 'MRNASEQ_CNMF'

P value = 3.35e-05 (Chi-square test), Q value = 0.019

Table S150. Gene #37: 'Del Peak 6(3p21.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
DEL PEAK 6(3P21.31) CNV	32	26	42	15	12	29	19	12	3
DEL PEAK 6(3P21.31) WILD-TYPE	43	29	14	27	17	19	20	12	20

Figure S150. Get High-res Image Gene #37: 'Del Peak 6(3p21.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 6(3p21.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.23e-09 (Fisher's exact test), Q value = 4.7e-06

Table S151. Gene #37: 'Del Peak 6(3p21.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 6(3P21.31) CNV	53	48	89
DEL PEAK 6(3P21.31) WILD-TYPE	105	57	39

Figure S151. Get High-res Image Gene #37: 'Del Peak 6(3p21.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 6(3p21.31)' versus 'MIRSEQ_CNMF'

P value = 1.18e-05 (Fisher's exact test), Q value = 0.0071

Table S152. Gene #37: 'Del Peak 6(3p21.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
DEL PEAK 6(3P21.31) CNV	57	110	56
DEL PEAK 6(3P21.31) WILD-TYPE	114	88	42

Figure S152. Get High-res Image Gene #37: 'Del Peak 6(3p21.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 8(3q29)' versus 'METHLYATION_CNMF'

P value = 8.11e-05 (Chi-square test), Q value = 0.046

Table S153. Gene #39: 'Del Peak 8(3q29)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
DEL PEAK 8(3Q29) CNV	35	36	29	11	7
DEL PEAK 8(3Q29) WILD-TYPE	55	58	66	89	18

Figure S153. Get High-res Image Gene #39: 'Del Peak 8(3q29)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 8(3q29)' versus 'MRNASEQ_CNMF'

P value = 3.27e-08 (Chi-square test), Q value = 2.4e-05

Table S154. Gene #39: 'Del Peak 8(3q29)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
DEL PEAK 8(3Q29) CNV	18	17	9	18	8	30	2	4	4
DEL PEAK 8(3Q29) WILD-TYPE	57	38	47	24	21	18	37	20	19

Figure S154. Get High-res Image Gene #39: 'Del Peak 8(3q29)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 9(4p16.3)' versus 'CN_CNMF'

P value = 1.56e-05 (Fisher's exact test), Q value = 0.0093

Table S155. Gene #40: 'Del Peak 9(4p16.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 9(4P16.3) CNV	37	28	28	23
DEL PEAK 9(4P16.3) WILD-TYPE	111	160	59	26

Figure S155. Get High-res Image Gene #40: 'Del Peak 9(4p16.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 9(4p16.3)' versus 'METHLYATION_CNMF'

P value = 2.31e-05 (Chi-square test), Q value = 0.014

Table S156. Gene #40: 'Del Peak 9(4p16.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
DEL PEAK 9(4P16.3) CNV	7	38	22	26	7
DEL PEAK 9(4P16.3) WILD-TYPE	83	56	73	74	18

Figure S156. Get High-res Image Gene #40: 'Del Peak 9(4p16.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 9(4p16.3)' versus 'MRNASEQ_CNMF'

P value = 8.4e-07 (Chi-square test), Q value = 0.00056

Table S157. Gene #40: 'Del Peak 9(4p16.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
DEL PEAK 9(4P16.3) CNV	11	12	26	3	8	23	7	7	2
DEL PEAK 9(4P16.3) WILD-TYPE	64	43	30	39	21	25	32	17	21

Figure S157. Get High-res Image Gene #40: 'Del Peak 9(4p16.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 9(4p16.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.36e-11 (Fisher's exact test), Q value = 5e-08

Table S158. Gene #40: 'Del Peak 9(4p16.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 9(4P16.3) CNV	16	25	58
DEL PEAK 9(4P16.3) WILD-TYPE	142	80	70

Figure S158. Get High-res Image Gene #40: 'Del Peak 9(4p16.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 9(4p16.3)' versus 'MIRSEQ_CNMF'

P value = 2.82e-07 (Fisher's exact test), Q value = 0.00019

Table S159. Gene #40: 'Del Peak 9(4p16.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
DEL PEAK 9(4P16.3) CNV	20	71	24
DEL PEAK 9(4P16.3) WILD-TYPE	151	127	74

Figure S159. Get High-res Image Gene #40: 'Del Peak 9(4p16.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 9(4p16.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.11e-07 (Fisher's exact test), Q value = 7.9e-05

Table S160. Gene #40: 'Del Peak 9(4p16.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
DEL PEAK 9(4P16.3) CNV	20	86	9
DEL PEAK 9(4P16.3) WILD-TYPE	144	158	50

Figure S160. Get High-res Image Gene #40: 'Del Peak 9(4p16.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 10(4q22.1)' versus 'MRNA_CNMF'

P value = 0.000214 (Fisher's exact test), Q value = 0.11

Table S161. Gene #41: 'Del Peak 10(4q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	5	9	12	6
DEL PEAK 10(4Q22.1) CNV	3	1	0	5
DEL PEAK 10(4Q22.1) WILD-TYPE	2	8	12	1

Figure S161. Get High-res Image Gene #41: 'Del Peak 10(4q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 10(4q22.1)' versus 'MRNA_CHIERARCHICAL'

P value = 9.89e-05 (Fisher's exact test), Q value = 0.055

Table S162. Gene #41: 'Del Peak 10(4q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	13	12
DEL PEAK 10(4Q22.1) CNV	6	0	3
DEL PEAK 10(4Q22.1) WILD-TYPE	1	13	9

Figure S162. Get High-res Image Gene #41: 'Del Peak 10(4q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 10(4q22.1)' versus 'CN_CNMF'

P value = 3.67e-07 (Fisher's exact test), Q value = 0.00025

Table S163. Gene #41: 'Del Peak 10(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 10(4Q22.1) CNV	48	32	42	20
DEL PEAK 10(4Q22.1) WILD-TYPE	100	156	45	29

Figure S163. Get High-res Image Gene #41: 'Del Peak 10(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 10(4q22.1)' versus 'METHLYATION_CNMF'

P value = 9.89e-08 (Chi-square test), Q value = 7.1e-05

Table S164. Gene #41: 'Del Peak 10(4q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
DEL PEAK 10(4Q22.1) CNV	8	45	25	29	12
DEL PEAK 10(4Q22.1) WILD-TYPE	82	49	70	71	13

Figure S164. Get High-res Image Gene #41: 'Del Peak 10(4q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 10(4q22.1)' versus 'MRNASEQ_CNMF'

P value = 3.81e-06 (Chi-square test), Q value = 0.0024

Table S165. Gene #41: 'Del Peak 10(4q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
DEL PEAK 10(4Q22.1) CNV	12	17	27	6	9	25	11	8	1
DEL PEAK 10(4Q22.1) WILD-TYPE	63	38	29	36	20	23	28	16	22

Figure S165. Get High-res Image Gene #41: 'Del Peak 10(4q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 10(4q22.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.97e-14 (Fisher's exact test), Q value = 8e-11

Table S166. Gene #41: 'Del Peak 10(4q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 10(4Q22.1) CNV	21	25	70
DEL PEAK 10(4Q22.1) WILD-TYPE	137	80	58

Figure S166. Get High-res Image Gene #41: 'Del Peak 10(4q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 10(4q22.1)' versus 'MIRSEQ_CNMF'

P value = 1.66e-08 (Fisher's exact test), Q value = 1.2e-05

Table S167. Gene #41: 'Del Peak 10(4q22.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
DEL PEAK 10(4Q22.1) CNV	25	84	32
DEL PEAK 10(4Q22.1) WILD-TYPE	146	114	66

Figure S167. Get High-res Image Gene #41: 'Del Peak 10(4q22.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 10(4q22.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.54e-06 (Fisher's exact test), Q value = 0.001

Table S168. Gene #41: 'Del Peak 10(4q22.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
DEL PEAK 10(4Q22.1) CNV	30	99	12
DEL PEAK 10(4Q22.1) WILD-TYPE	134	145	47

Figure S168. Get High-res Image Gene #41: 'Del Peak 10(4q22.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 11(4q35.1)' versus 'CN_CNMF'

P value = 7.48e-10 (Fisher's exact test), Q value = 5.7e-07

Table S169. Gene #42: 'Del Peak 11(4q35.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 11(4Q35.1) CNV	58	38	50	26
DEL PEAK 11(4Q35.1) WILD-TYPE	90	150	37	23

Figure S169. Get High-res Image Gene #42: 'Del Peak 11(4q35.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 11(4q35.1)' versus 'METHLYATION_CNMF'

P value = 1.36e-11 (Chi-square test), Q value = 1.1e-08

Table S170. Gene #42: 'Del Peak 11(4q35.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
DEL PEAK 11(4Q35.1) CNV	8	58	35	35	12
DEL PEAK 11(4Q35.1) WILD-TYPE	82	36	60	65	13

Figure S170. Get High-res Image Gene #42: 'Del Peak 11(4q35.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 11(4q35.1)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000196 (Fisher's exact test), Q value = 0.1

Table S171. Gene #42: 'Del Peak 11(4q35.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	89	65	58
DEL PEAK 11(4Q35.1) CNV	11	32	39	13
DEL PEAK 11(4Q35.1) WILD-TYPE	12	57	26	45

Figure S171. Get High-res Image Gene #42: 'Del Peak 11(4q35.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 11(4q35.1)' versus 'MRNASEQ_CNMF'

P value = 2.47e-09 (Chi-square test), Q value = 1.9e-06

Table S172. Gene #42: 'Del Peak 11(4q35.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
DEL PEAK 11(4Q35.1) CNV	18	14	35	7	10	31	13	10	2
DEL PEAK 11(4Q35.1) WILD-TYPE	57	41	21	35	19	17	26	14	21

Figure S172. Get High-res Image Gene #42: 'Del Peak 11(4q35.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 11(4q35.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.36e-18 (Fisher's exact test), Q value = 5.9e-15

Table S173. Gene #42: 'Del Peak 11(4q35.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 11(4Q35.1) CNV	28	27	85
DEL PEAK 11(4Q35.1) WILD-TYPE	130	78	43

Figure S173. Get High-res Image Gene #42: 'Del Peak 11(4q35.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 11(4q35.1)' versus 'MIRSEQ_CNMF'

P value = 1.57e-10 (Fisher's exact test), Q value = 1.2e-07

Table S174. Gene #42: 'Del Peak 11(4q35.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
DEL PEAK 11(4Q35.1) CNV	34	105	32
DEL PEAK 11(4Q35.1) WILD-TYPE	137	93	66

Figure S174. Get High-res Image Gene #42: 'Del Peak 11(4q35.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 11(4q35.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-10 (Fisher's exact test), Q value = 7.8e-08

Table S175. Gene #42: 'Del Peak 11(4q35.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
DEL PEAK 11(4Q35.1) CNV	37	124	10
DEL PEAK 11(4Q35.1) WILD-TYPE	127	120	49

Figure S175. Get High-res Image Gene #42: 'Del Peak 11(4q35.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 12(5q11.2)' versus 'CN_CNMF'

P value = 1.9e-12 (Fisher's exact test), Q value = 1.5e-09

Table S176. Gene #43: 'Del Peak 12(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 12(5Q11.2) CNV	70	29	44	23
DEL PEAK 12(5Q11.2) WILD-TYPE	78	159	43	26

Figure S176. Get High-res Image Gene #43: 'Del Peak 12(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 12(5q11.2)' versus 'METHLYATION_CNMF'

P value = 2.02e-07 (Chi-square test), Q value = 0.00014

Table S177. Gene #43: 'Del Peak 12(5q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
DEL PEAK 12(5Q11.2) CNV	12	47	35	29	15
DEL PEAK 12(5Q11.2) WILD-TYPE	78	47	60	71	10

Figure S177. Get High-res Image Gene #43: 'Del Peak 12(5q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 12(5q11.2)' versus 'MRNASEQ_CNMF'

P value = 1.35e-06 (Chi-square test), Q value = 0.00089

Table S178. Gene #43: 'Del Peak 12(5q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
DEL PEAK 12(5Q11.2) CNV	32	18	36	6	11	20	8	8	2
DEL PEAK 12(5Q11.2) WILD-TYPE	43	37	20	36	18	28	31	16	21

Figure S178. Get High-res Image Gene #43: 'Del Peak 12(5q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 12(5q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.57e-09 (Fisher's exact test), Q value = 1.9e-06

Table S179. Gene #43: 'Del Peak 12(5q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 12(5Q11.2) CNV	30	42	69
DEL PEAK 12(5Q11.2) WILD-TYPE	128	63	59

Figure S179. Get High-res Image Gene #43: 'Del Peak 12(5q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 12(5q11.2)' versus 'MIRSEQ_CNMF'

P value = 4.53e-08 (Fisher's exact test), Q value = 3.3e-05

Table S180. Gene #43: 'Del Peak 12(5q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
DEL PEAK 12(5Q11.2) CNV	34	96	33
DEL PEAK 12(5Q11.2) WILD-TYPE	137	102	65

Figure S180. Get High-res Image Gene #43: 'Del Peak 12(5q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 12(5q11.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.11e-06 (Fisher's exact test), Q value = 0.0014

Table S181. Gene #43: 'Del Peak 12(5q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
DEL PEAK 12(5Q11.2) CNV	36	111	16
DEL PEAK 12(5Q11.2) WILD-TYPE	128	133	43

Figure S181. Get High-res Image Gene #43: 'Del Peak 12(5q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 13(5q22.1)' versus 'CN_CNMF'

P value = 1.08e-12 (Fisher's exact test), Q value = 8.6e-10

Table S182. Gene #44: 'Del Peak 13(5q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 13(5Q22.1) CNV	75	37	52	25
DEL PEAK 13(5Q22.1) WILD-TYPE	73	151	35	24

Figure S182. Get High-res Image Gene #44: 'Del Peak 13(5q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 13(5q22.1)' versus 'METHLYATION_CNMF'

P value = 2.56e-08 (Chi-square test), Q value = 1.9e-05

Table S183. Gene #44: 'Del Peak 13(5q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
DEL PEAK 13(5Q22.1) CNV	14	52	43	37	17
DEL PEAK 13(5Q22.1) WILD-TYPE	76	42	52	63	8

Figure S183. Get High-res Image Gene #44: 'Del Peak 13(5q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 13(5q22.1)' versus 'MRNASEQ_CNMF'

P value = 1.55e-08 (Chi-square test), Q value = 1.1e-05

Table S184. Gene #44: 'Del Peak 13(5q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
DEL PEAK 13(5Q22.1) CNV	40	14	41	8	11	24	11	9	4
DEL PEAK 13(5Q22.1) WILD-TYPE	35	41	15	34	18	24	28	15	19

Figure S184. Get High-res Image Gene #44: 'Del Peak 13(5q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 13(5q22.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.56e-10 (Fisher's exact test), Q value = 2.7e-07

Table S185. Gene #44: 'Del Peak 13(5q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 13(5Q22.1) CNV	36	49	77
DEL PEAK 13(5Q22.1) WILD-TYPE	122	56	51

Figure S185. Get High-res Image Gene #44: 'Del Peak 13(5q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 13(5q22.1)' versus 'MIRSEQ_CNMF'

P value = 5.97e-10 (Fisher's exact test), Q value = 4.6e-07

Table S186. Gene #44: 'Del Peak 13(5q22.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
DEL PEAK 13(5Q22.1) CNV	38	109	39
DEL PEAK 13(5Q22.1) WILD-TYPE	133	89	59

Figure S186. Get High-res Image Gene #44: 'Del Peak 13(5q22.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 13(5q22.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.43e-09 (Fisher's exact test), Q value = 6.3e-06

Table S187. Gene #44: 'Del Peak 13(5q22.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
DEL PEAK 13(5Q22.1) CNV	40	129	17
DEL PEAK 13(5Q22.1) WILD-TYPE	124	115	42

Figure S187. Get High-res Image Gene #44: 'Del Peak 13(5q22.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 15(6q22.31)' versus 'METHLYATION_CNMF'

P value = 1.29e-06 (Chi-square test), Q value = 0.00085

Table S188. Gene #46: 'Del Peak 15(6q22.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
DEL PEAK 15(6Q22.31) CNV	51	52	62	28	9
DEL PEAK 15(6Q22.31) WILD-TYPE	39	42	33	72	16

Figure S188. Get High-res Image Gene #46: 'Del Peak 15(6q22.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 16(6q26)' versus 'METHLYATION_CNMF'

P value = 8.64e-05 (Chi-square test), Q value = 0.049

Table S189. Gene #47: 'Del Peak 16(6q26)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
DEL PEAK 16(6Q26) CNV	49	54	58	31	9
DEL PEAK 16(6Q26) WILD-TYPE	41	40	37	69	16

Figure S189. Get High-res Image Gene #47: 'Del Peak 16(6q26)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 17(8p23.2)' versus 'CN_CNMF'

P value = 7.67e-17 (Fisher's exact test), Q value = 6.2e-14

Table S190. Gene #48: 'Del Peak 17(8p23.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 17(8P23.2) CNV	107	49	51	22
DEL PEAK 17(8P23.2) WILD-TYPE	41	139	36	27

Figure S190. Get High-res Image Gene #48: 'Del Peak 17(8p23.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 17(8p23.2)' versus 'METHLYATION_CNMF'

P value = 9.17e-05 (Chi-square test), Q value = 0.051

Table S191. Gene #48: 'Del Peak 17(8p23.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
DEL PEAK 17(8P23.2) CNV	26	45	58	47	17
DEL PEAK 17(8P23.2) WILD-TYPE	64	49	37	53	8

Figure S191. Get High-res Image Gene #48: 'Del Peak 17(8p23.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 17(8p23.2)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000354 (Fisher's exact test), Q value = 0.18

Table S192. Gene #48: 'Del Peak 17(8p23.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	89	65	58
DEL PEAK 17(8P23.2) CNV	10	56	34	16
DEL PEAK 17(8P23.2) WILD-TYPE	13	33	31	42

Figure S192. Get High-res Image Gene #48: 'Del Peak 17(8p23.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 17(8p23.2)' versus 'MRNASEQ_CNMF'

P value = 8.22e-09 (Chi-square test), Q value = 6.1e-06

Table S193. Gene #48: 'Del Peak 17(8p23.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
DEL PEAK 17(8P23.2) CNV	55	33	35	8	7	20	17	10	6
DEL PEAK 17(8P23.2) WILD-TYPE	20	22	21	34	22	28	22	14	17

Figure S193. Get High-res Image Gene #48: 'Del Peak 17(8p23.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 17(8p23.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.29e-07 (Fisher's exact test), Q value = 0.00016

Table S194. Gene #48: 'Del Peak 17(8p23.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 17(8P23.2) CNV	57	74	60
DEL PEAK 17(8P23.2) WILD-TYPE	101	31	68

Figure S194. Get High-res Image Gene #48: 'Del Peak 17(8p23.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 17(8p23.2)' versus 'MIRSEQ_CNMF'

P value = 3.58e-06 (Fisher's exact test), Q value = 0.0023

Table S195. Gene #48: 'Del Peak 17(8p23.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
DEL PEAK 17(8P23.2) CNV	57	111	58
DEL PEAK 17(8P23.2) WILD-TYPE	114	87	40

Figure S195. Get High-res Image Gene #48: 'Del Peak 17(8p23.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 18(8p12)' versus 'CN_CNMF'

P value = 1.83e-15 (Fisher's exact test), Q value = 1.5e-12

Table S196. Gene #49: 'Del Peak 18(8p12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 18(8P12) CNV	101	45	43	16
DEL PEAK 18(8P12) WILD-TYPE	47	143	44	33

Figure S196. Get High-res Image Gene #49: 'Del Peak 18(8p12)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 18(8p12)' versus 'METHLYATION_CNMF'

P value = 1.95e-05 (Chi-square test), Q value = 0.012

Table S197. Gene #49: 'Del Peak 18(8p12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
DEL PEAK 18(8P12) CNV	23	39	54	43	18
DEL PEAK 18(8P12) WILD-TYPE	67	55	41	57	7

Figure S197. Get High-res Image Gene #49: 'Del Peak 18(8p12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 18(8p12)' versus 'MRNASEQ_CNMF'

P value = 4.61e-05 (Chi-square test), Q value = 0.027

Table S198. Gene #49: 'Del Peak 18(8p12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
DEL PEAK 18(8P12) CNV	48	29	28	9	7	20	15	9	5
DEL PEAK 18(8P12) WILD-TYPE	27	26	28	33	22	28	24	15	18

Figure S198. Get High-res Image Gene #49: 'Del Peak 18(8p12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 18(8p12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.37e-06 (Fisher's exact test), Q value = 0.0033

Table S199. Gene #49: 'Del Peak 18(8p12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 18(8P12) CNV	51	66	53
DEL PEAK 18(8P12) WILD-TYPE	107	39	75

Figure S199. Get High-res Image Gene #49: 'Del Peak 18(8p12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 18(8p12)' versus 'MIRSEQ_CNMF'

P value = 5.26e-05 (Fisher's exact test), Q value = 0.03

Table S200. Gene #49: 'Del Peak 18(8p12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
DEL PEAK 18(8P12) CNV	52	105	45
DEL PEAK 18(8P12) WILD-TYPE	119	93	53

Figure S200. Get High-res Image Gene #49: 'Del Peak 18(8p12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 19(8p11.21)' versus 'CN_CNMF'

P value = 2.79e-11 (Fisher's exact test), Q value = 2.2e-08

Table S201. Gene #50: 'Del Peak 19(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 19(8P11.21) CNV	59	27	21	0
DEL PEAK 19(8P11.21) WILD-TYPE	89	161	66	49

Figure S201. Get High-res Image Gene #50: 'Del Peak 19(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 21(9p23)' versus 'CN_CNMF'

P value = 3.22e-07 (Fisher's exact test), Q value = 0.00022

Table S202. Gene #52: 'Del Peak 21(9p23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 21(9P23) CNV	88	85	67	18
DEL PEAK 21(9P23) WILD-TYPE	60	103	20	31

Figure S202. Get High-res Image Gene #52: 'Del Peak 21(9p23)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 22(9p21.3)' versus 'CN_CNMF'

P value = 1.79e-06 (Fisher's exact test), Q value = 0.0012

Table S203. Gene #53: 'Del Peak 22(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 22(9P21.3) CNV	91	89	66	18
DEL PEAK 22(9P21.3) WILD-TYPE	57	99	21	31

Figure S203. Get High-res Image Gene #53: 'Del Peak 22(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 23(9q21.11)' versus 'CN_CNMF'

P value = 1.49e-07 (Fisher's exact test), Q value = 0.00011

Table S204. Gene #54: 'Del Peak 23(9q21.11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 23(9Q21.11) CNV	73	66	61	31
DEL PEAK 23(9Q21.11) WILD-TYPE	75	122	26	18

Figure S204. Get High-res Image Gene #54: 'Del Peak 23(9q21.11)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 23(9q21.11)' versus 'METHLYATION_CNMF'

P value = 5.08e-05 (Chi-square test), Q value = 0.029

Table S205. Gene #54: 'Del Peak 23(9q21.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
DEL PEAK 23(9Q21.11) CNV	36	66	36	46	13
DEL PEAK 23(9Q21.11) WILD-TYPE	54	28	59	54	12

Figure S205. Get High-res Image Gene #54: 'Del Peak 23(9q21.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 23(9q21.11)' versus 'MRNASEQ_CNMF'

P value = 0.000116 (Chi-square test), Q value = 0.064

Table S206. Gene #54: 'Del Peak 23(9q21.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
DEL PEAK 23(9Q21.11) CNV	36	34	40	14	13	29	15	9	5
DEL PEAK 23(9Q21.11) WILD-TYPE	39	21	16	28	16	19	24	15	18

Figure S206. Get High-res Image Gene #54: 'Del Peak 23(9q21.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 23(9q21.11)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.67e-07 (Fisher's exact test), Q value = 0.00012

Table S207. Gene #54: 'Del Peak 23(9q21.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 23(9Q21.11) CNV	59	47	89
DEL PEAK 23(9Q21.11) WILD-TYPE	99	58	39

Figure S207. Get High-res Image Gene #54: 'Del Peak 23(9q21.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 23(9q21.11)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000126 (Fisher's exact test), Q value = 0.069

Table S208. Gene #54: 'Del Peak 23(9q21.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
DEL PEAK 23(9Q21.11) CNV	63	142	23
DEL PEAK 23(9Q21.11) WILD-TYPE	101	102	36

Figure S208. Get High-res Image Gene #54: 'Del Peak 23(9q21.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 25(10q26.3)' versus 'CN_CNMF'

P value = 4.78e-06 (Fisher's exact test), Q value = 0.003

Table S209. Gene #56: 'Del Peak 25(10q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 25(10Q26.3) CNV	63	32	21	14
DEL PEAK 25(10Q26.3) WILD-TYPE	85	156	66	35

Figure S209. Get High-res Image Gene #56: 'Del Peak 25(10q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 25(10q26.3)' versus 'METHLYATION_CNMF'

P value = 0.000256 (Chi-square test), Q value = 0.13

Table S210. Gene #56: 'Del Peak 25(10q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
DEL PEAK 25(10Q26.3) CNV	18	31	29	16	14
DEL PEAK 25(10Q26.3) WILD-TYPE	72	63	66	84	11

Figure S210. Get High-res Image Gene #56: 'Del Peak 25(10q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 25(10q26.3)' versus 'MRNASEQ_CNMF'

P value = 5.65e-05 (Chi-square test), Q value = 0.032

Table S211. Gene #56: 'Del Peak 25(10q26.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
DEL PEAK 25(10Q26.3) CNV	27	24	20	0	11	9	11	4	4
DEL PEAK 25(10Q26.3) WILD-TYPE	48	31	36	42	18	39	28	20	19

Figure S211. Get High-res Image Gene #56: 'Del Peak 25(10q26.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 26(11p15.5)' versus 'CN_CNMF'

P value = 4.04e-06 (Fisher's exact test), Q value = 0.0026

Table S212. Gene #57: 'Del Peak 26(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 26(11P15.5) CNV	54	27	32	13
DEL PEAK 26(11P15.5) WILD-TYPE	94	161	55	36

Figure S212. Get High-res Image Gene #57: 'Del Peak 26(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 26(11p15.5)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.36e-06 (Fisher's exact test), Q value = 0.0028

Table S213. Gene #57: 'Del Peak 26(11p15.5)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 26(11P15.5) CNV	21	30	49
DEL PEAK 26(11P15.5) WILD-TYPE	137	75	79

Figure S213. Get High-res Image Gene #57: 'Del Peak 26(11p15.5)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 26(11p15.5)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000108 (Fisher's exact test), Q value = 0.06

Table S214. Gene #57: 'Del Peak 26(11p15.5)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
DEL PEAK 26(11P15.5) CNV	35	83	6
DEL PEAK 26(11P15.5) WILD-TYPE	129	161	53

Figure S214. Get High-res Image Gene #57: 'Del Peak 26(11p15.5)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 27(11q23.2)' versus 'CN_CNMF'

P value = 0.000122 (Fisher's exact test), Q value = 0.067

Table S215. Gene #58: 'Del Peak 27(11q23.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 27(11Q23.2) CNV	30	29	32	18
DEL PEAK 27(11Q23.2) WILD-TYPE	118	159	55	31

Figure S215. Get High-res Image Gene #58: 'Del Peak 27(11q23.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 29(12p13.2)' versus 'CN_CNMF'

P value = 0.000172 (Fisher's exact test), Q value = 0.092

Table S216. Gene #60: 'Del Peak 29(12p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 29(12P13.2) CNV	59	41	14	12
DEL PEAK 29(12P13.2) WILD-TYPE	89	147	73	37

Figure S216. Get High-res Image Gene #60: 'Del Peak 29(12p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 29(12p13.2)' versus 'METHLYATION_CNMF'

P value = 7.21e-07 (Chi-square test), Q value = 0.00048

Table S217. Gene #60: 'Del Peak 29(12p13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
DEL PEAK 29(12P13.2) CNV	24	17	34	14	16
DEL PEAK 29(12P13.2) WILD-TYPE	66	77	61	86	9

Figure S217. Get High-res Image Gene #60: 'Del Peak 29(12p13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 30(12q12)' versus 'CN_CNMF'

P value = 1.19e-05 (Fisher's exact test), Q value = 0.0072

Table S218. Gene #61: 'Del Peak 30(12q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 30(12Q12) CNV	47	29	6	8
DEL PEAK 30(12Q12) WILD-TYPE	101	159	81	41

Figure S218. Get High-res Image Gene #61: 'Del Peak 30(12q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 31(12q24.33)' versus 'CN_CNMF'

P value = 6.54e-06 (Fisher's exact test), Q value = 0.004

Table S219. Gene #62: 'Del Peak 31(12q24.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 31(12Q24.33) CNV	55	45	10	5
DEL PEAK 31(12Q24.33) WILD-TYPE	93	143	77	44

Figure S219. Get High-res Image Gene #62: 'Del Peak 31(12q24.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 31(12q24.33)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000306 (Fisher's exact test), Q value = 0.16

Table S220. Gene #62: 'Del Peak 31(12q24.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 31(12Q24.33) CNV	48	29	15
DEL PEAK 31(12Q24.33) WILD-TYPE	110	76	113

Figure S220. Get High-res Image Gene #62: 'Del Peak 31(12q24.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 32(13q12.11)' versus 'CN_CNMF'

P value = 1.38e-19 (Fisher's exact test), Q value = 1.1e-16

Table S221. Gene #63: 'Del Peak 32(13q12.11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 32(13Q12.11) CNV	118	58	59	30
DEL PEAK 32(13Q12.11) WILD-TYPE	30	130	28	19

Figure S221. Get High-res Image Gene #63: 'Del Peak 32(13q12.11)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 32(13q12.11)' versus 'RPPA_CHIERARCHICAL'

P value = 1.49e-06 (Fisher's exact test), Q value = 0.00097

Table S222. Gene #63: 'Del Peak 32(13q12.11)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	89	65	58
DEL PEAK 32(13Q12.11) CNV	8	66	39	19
DEL PEAK 32(13Q12.11) WILD-TYPE	15	23	26	39

Figure S222. Get High-res Image Gene #63: 'Del Peak 32(13q12.11)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 32(13q12.11)' versus 'MRNASEQ_CNMF'

P value = 2.73e-07 (Chi-square test), Q value = 0.00019

Table S223. Gene #63: 'Del Peak 32(13q12.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
DEL PEAK 32(13Q12.11) CNV	53	30	41	14	9	34	21	11	5
DEL PEAK 32(13Q12.11) WILD-TYPE	22	25	15	28	20	14	18	13	18

Figure S223. Get High-res Image Gene #63: 'Del Peak 32(13q12.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 32(13q12.11)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.07e-08 (Fisher's exact test), Q value = 3e-05

Table S224. Gene #63: 'Del Peak 32(13q12.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 32(13Q12.11) CNV	60	71	87
DEL PEAK 32(13Q12.11) WILD-TYPE	98	34	41

Figure S224. Get High-res Image Gene #63: 'Del Peak 32(13q12.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 32(13q12.11)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.51e-05 (Fisher's exact test), Q value = 0.048

Table S225. Gene #63: 'Del Peak 32(13q12.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
DEL PEAK 32(13Q12.11) CNV	76	161	27
DEL PEAK 32(13Q12.11) WILD-TYPE	88	83	32

Figure S225. Get High-res Image Gene #63: 'Del Peak 32(13q12.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 1.05e-19 (Fisher's exact test), Q value = 8.5e-17

Table S226. Gene #64: 'Del Peak 33(13q12.13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 33(13Q12.13) CNV	120	59	56	31
DEL PEAK 33(13Q12.13) WILD-TYPE	28	129	31	18

Figure S226. Get High-res Image Gene #64: 'Del Peak 33(13q12.13)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 33(13q12.13)' versus 'METHLYATION_CNMF'

P value = 0.000107 (Chi-square test), Q value = 0.06

Table S227. Gene #64: 'Del Peak 33(13q12.13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
DEL PEAK 33(13Q12.13) CNV	38	59	66	49	20
DEL PEAK 33(13Q12.13) WILD-TYPE	52	35	29	51	5

Figure S227. Get High-res Image Gene #64: 'Del Peak 33(13q12.13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 33(13q12.13)' versus 'RPPA_CHIERARCHICAL'

P value = 6.68e-07 (Fisher's exact test), Q value = 0.00045

Table S228. Gene #64: 'Del Peak 33(13q12.13)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	89	65	58
DEL PEAK 33(13Q12.13) CNV	8	67	39	19
DEL PEAK 33(13Q12.13) WILD-TYPE	15	22	26	39

Figure S228. Get High-res Image Gene #64: 'Del Peak 33(13q12.13)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 33(13q12.13)' versus 'MRNASEQ_CNMF'

P value = 1.2e-07 (Chi-square test), Q value = 8.5e-05

Table S229. Gene #64: 'Del Peak 33(13q12.13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
DEL PEAK 33(13Q12.13) CNV	55	30	38	14	9	36	21	11	5
DEL PEAK 33(13Q12.13) WILD-TYPE	20	25	18	28	20	12	18	13	18

Figure S229. Get High-res Image Gene #64: 'Del Peak 33(13q12.13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 33(13q12.13)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.17e-08 (Fisher's exact test), Q value = 5.9e-05

Table S230. Gene #64: 'Del Peak 33(13q12.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 33(13Q12.13) CNV	61	72	86
DEL PEAK 33(13Q12.13) WILD-TYPE	97	33	42

Figure S230. Get High-res Image Gene #64: 'Del Peak 33(13q12.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 33(13q12.13)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000138 (Fisher's exact test), Q value = 0.075

Table S231. Gene #64: 'Del Peak 33(13q12.13)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
DEL PEAK 33(13Q12.13) CNV	77	161	27
DEL PEAK 33(13Q12.13) WILD-TYPE	87	83	32

Figure S231. Get High-res Image Gene #64: 'Del Peak 33(13q12.13)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 7.61e-22 (Fisher's exact test), Q value = 6.2e-19

Table S232. Gene #65: 'Del Peak 34(13q14.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 34(13Q14.2) CNV	117	52	52	35
DEL PEAK 34(13Q14.2) WILD-TYPE	31	136	35	14

Figure S232. Get High-res Image Gene #65: 'Del Peak 34(13q14.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 1.04e-05 (Fisher's exact test), Q value = 0.0064

Table S233. Gene #65: 'Del Peak 34(13q14.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	89	65	58
DEL PEAK 34(13Q14.2) CNV	8	60	40	17
DEL PEAK 34(13Q14.2) WILD-TYPE	15	29	25	41

Figure S233. Get High-res Image Gene #65: 'Del Peak 34(13q14.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

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

P value = 4.15e-09 (Chi-square test), Q value = 3.1e-06

Table S234. Gene #65: 'Del Peak 34(13q14.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
DEL PEAK 34(13Q14.2) CNV	53	32	33	12	7	36	20	11	3
DEL PEAK 34(13Q14.2) WILD-TYPE	22	23	23	30	22	12	19	13	20

Figure S234. Get High-res Image Gene #65: 'Del Peak 34(13q14.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 1.54e-07 (Fisher's exact test), Q value = 0.00011

Table S235. Gene #65: 'Del Peak 34(13q14.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 34(13Q14.2) CNV	57	71	79
DEL PEAK 34(13Q14.2) WILD-TYPE	101	34	49

Figure S235. Get High-res Image Gene #65: 'Del Peak 34(13q14.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 0.000206 (Fisher's exact test), Q value = 0.11

Table S236. Gene #65: 'Del Peak 34(13q14.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
DEL PEAK 34(13Q14.2) CNV	73	127	53
DEL PEAK 34(13Q14.2) WILD-TYPE	98	71	45

Figure S236. Get High-res Image Gene #65: 'Del Peak 34(13q14.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

P value = 4.69e-05 (Fisher's exact test), Q value = 0.027

Table S237. Gene #65: 'Del Peak 34(13q14.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
DEL PEAK 34(13Q14.2) CNV	73	156	24
DEL PEAK 34(13Q14.2) WILD-TYPE	91	88	35

Figure S237. Get High-res Image Gene #65: 'Del Peak 34(13q14.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 35(13q34)' versus 'CN_CNMF'

P value = 2.2e-15 (Fisher's exact test), Q value = 1.8e-12

Table S238. Gene #66: 'Del Peak 35(13q34)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 35(13Q34) CNV	95	43	49	30
DEL PEAK 35(13Q34) WILD-TYPE	53	145	38	19

Figure S238. Get High-res Image Gene #66: 'Del Peak 35(13q34)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 35(13q34)' versus 'MRNASEQ_CNMF'

P value = 3.71e-06 (Chi-square test), Q value = 0.0024

Table S239. Gene #66: 'Del Peak 35(13q34)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
DEL PEAK 35(13Q34) CNV	45	24	29	13	6	32	16	11	2
DEL PEAK 35(13Q34) WILD-TYPE	30	31	27	29	23	16	23	13	21

Figure S239. Get High-res Image Gene #66: 'Del Peak 35(13q34)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 35(13q34)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.09e-05 (Fisher's exact test), Q value = 0.018

Table S240. Gene #66: 'Del Peak 35(13q34)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 35(13Q34) CNV	50	58	70
DEL PEAK 35(13Q34) WILD-TYPE	108	47	58

Figure S240. Get High-res Image Gene #66: 'Del Peak 35(13q34)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 36(14q32.33)' versus 'CN_CNMF'

P value = 0.000135 (Fisher's exact test), Q value = 0.073

Table S241. Gene #67: 'Del Peak 36(14q32.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 36(14Q32.33) CNV	46	46	41	7
DEL PEAK 36(14Q32.33) WILD-TYPE	102	142	46	42

Figure S241. Get High-res Image Gene #67: 'Del Peak 36(14q32.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 37(15q11.2)' versus 'CN_CNMF'

P value = 1.81e-10 (Fisher's exact test), Q value = 1.4e-07

Table S242. Gene #68: 'Del Peak 37(15q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 37(15Q11.2) CNV	104	63	42	30
DEL PEAK 37(15Q11.2) WILD-TYPE	44	125	45	19

Figure S242. Get High-res Image Gene #68: 'Del Peak 37(15q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 37(15q11.2)' versus 'METHLYATION_CNMF'

P value = 0.000193 (Chi-square test), Q value = 0.1

Table S243. Gene #68: 'Del Peak 37(15q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
DEL PEAK 37(15Q11.2) CNV	31	48	59	45	19
DEL PEAK 37(15Q11.2) WILD-TYPE	59	46	36	55	6

Figure S243. Get High-res Image Gene #68: 'Del Peak 37(15q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 37(15q11.2)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000161 (Fisher's exact test), Q value = 0.087

Table S244. Gene #68: 'Del Peak 37(15q11.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	89	65	58
DEL PEAK 37(15Q11.2) CNV	10	59	33	17
DEL PEAK 37(15Q11.2) WILD-TYPE	13	30	32	41

Figure S244. Get High-res Image Gene #68: 'Del Peak 37(15q11.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 37(15q11.2)' versus 'MRNASEQ_CNMF'

P value = 1.91e-13 (Chi-square test), Q value = 1.5e-10

Table S245. Gene #68: 'Del Peak 37(15q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
DEL PEAK 37(15Q11.2) CNV	58	34	30	6	7	34	13	7	6
DEL PEAK 37(15Q11.2) WILD-TYPE	17	21	26	36	22	14	26	17	17

Figure S245. Get High-res Image Gene #68: 'Del Peak 37(15q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 37(15q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.4e-05 (Fisher's exact test), Q value = 0.0084

Table S246. Gene #68: 'Del Peak 37(15q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 37(15Q11.2) CNV	60	71	64
DEL PEAK 37(15Q11.2) WILD-TYPE	98	34	64

Figure S246. Get High-res Image Gene #68: 'Del Peak 37(15q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 37(15q11.2)' versus 'MIRSEQ_CNMF'

P value = 2.82e-05 (Fisher's exact test), Q value = 0.016

Table S247. Gene #68: 'Del Peak 37(15q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
DEL PEAK 37(15Q11.2) CNV	63	117	57
DEL PEAK 37(15Q11.2) WILD-TYPE	108	81	41

Figure S247. Get High-res Image Gene #68: 'Del Peak 37(15q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 38(16q23.1)' versus 'CN_CNMF'

P value = 2.59e-07 (Fisher's exact test), Q value = 0.00018

Table S248. Gene #69: 'Del Peak 38(16q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 38(16Q23.1) CNV	68	37	40	15
DEL PEAK 38(16Q23.1) WILD-TYPE	80	151	47	34

Figure S248. Get High-res Image Gene #69: 'Del Peak 38(16q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 38(16q23.1)' versus 'METHLYATION_CNMF'

P value = 0.00046 (Chi-square test), Q value = 0.24

Table S249. Gene #69: 'Del Peak 38(16q23.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
DEL PEAK 38(16Q23.1) CNV	16	40	43	30	7
DEL PEAK 38(16Q23.1) WILD-TYPE	74	54	52	70	18

Figure S249. Get High-res Image Gene #69: 'Del Peak 38(16q23.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 38(16q23.1)' versus 'MRNASEQ_CNMF'

P value = 1.73e-06 (Chi-square test), Q value = 0.0011

Table S250. Gene #69: 'Del Peak 38(16q23.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
DEL PEAK 38(16Q23.1) CNV	38	15	28	5	5	20	16	4	2
DEL PEAK 38(16Q23.1) WILD-TYPE	37	40	28	37	24	28	23	20	21

Figure S250. Get High-res Image Gene #69: 'Del Peak 38(16q23.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 38(16q23.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.21e-07 (Fisher's exact test), Q value = 0.00022

Table S251. Gene #69: 'Del Peak 38(16q23.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 38(16Q23.1) CNV	30	52	51
DEL PEAK 38(16Q23.1) WILD-TYPE	128	53	77

Figure S251. Get High-res Image Gene #69: 'Del Peak 38(16q23.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 39(16q24.3)' versus 'CN_CNMF'

P value = 1.66e-06 (Fisher's exact test), Q value = 0.0011

Table S252. Gene #70: 'Del Peak 39(16q24.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 39(16Q24.3) CNV	73	45	43	17
DEL PEAK 39(16Q24.3) WILD-TYPE	75	143	44	32

Figure S252. Get High-res Image Gene #70: 'Del Peak 39(16q24.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 39(16q24.3)' versus 'MRNASEQ_CNMF'

P value = 2.9e-05 (Chi-square test), Q value = 0.017

Table S253. Gene #70: 'Del Peak 39(16q24.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
DEL PEAK 39(16Q24.3) CNV	43	16	27	8	6	24	15	5	5
DEL PEAK 39(16Q24.3) WILD-TYPE	32	39	29	34	23	24	24	19	18

Figure S253. Get High-res Image Gene #70: 'Del Peak 39(16q24.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 39(16q24.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.88e-05 (Fisher's exact test), Q value = 0.028

Table S254. Gene #70: 'Del Peak 39(16q24.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 39(16Q24.3) CNV	40	53	56
DEL PEAK 39(16Q24.3) WILD-TYPE	118	52	72

Figure S254. Get High-res Image Gene #70: 'Del Peak 39(16q24.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 40(17p13.3)' versus 'CN_CNMF'

P value = 2.78e-13 (Fisher's exact test), Q value = 2.2e-10

Table S255. Gene #71: 'Del Peak 40(17p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 40(17P13.3) CNV	111	63	53	25
DEL PEAK 40(17P13.3) WILD-TYPE	37	125	34	24

Figure S255. Get High-res Image Gene #71: 'Del Peak 40(17p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 40(17p13.3)' versus 'METHLYATION_CNMF'

P value = 7.56e-08 (Chi-square test), Q value = 5.4e-05

Table S256. Gene #71: 'Del Peak 40(17p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
DEL PEAK 40(17P13.3) CNV	29	51	69	44	19
DEL PEAK 40(17P13.3) WILD-TYPE	61	43	26	56	6

Figure S256. Get High-res Image Gene #71: 'Del Peak 40(17p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 40(17p13.3)' versus 'MRNASEQ_CNMF'

P value = 5.6e-08 (Chi-square test), Q value = 4e-05

Table S257. Gene #71: 'Del Peak 40(17p13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
DEL PEAK 40(17P13.3) CNV	57	38	32	7	14	29	21	9	9
DEL PEAK 40(17P13.3) WILD-TYPE	18	17	24	35	15	19	18	15	14

Figure S257. Get High-res Image Gene #71: 'Del Peak 40(17p13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 40(17p13.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.79e-07 (Fisher's exact test), Q value = 0.00065

Table S258. Gene #71: 'Del Peak 40(17p13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 40(17P13.3) CNV	66	78	72
DEL PEAK 40(17P13.3) WILD-TYPE	92	27	56

Figure S258. Get High-res Image Gene #71: 'Del Peak 40(17p13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 41(18q21.32)' versus 'CN_CNMF'

P value = 8.58e-10 (Fisher's exact test), Q value = 6.5e-07

Table S259. Gene #72: 'Del Peak 41(18q21.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 41(18Q21.32) CNV	102	69	48	14
DEL PEAK 41(18Q21.32) WILD-TYPE	46	119	39	35

Figure S259. Get High-res Image Gene #72: 'Del Peak 41(18q21.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 41(18q21.32)' versus 'MRNASEQ_CNMF'

P value = 9.08e-09 (Chi-square test), Q value = 6.8e-06

Table S260. Gene #72: 'Del Peak 41(18q21.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
DEL PEAK 41(18Q21.32) CNV	48	39	31	8	15	15	25	9	4
DEL PEAK 41(18Q21.32) WILD-TYPE	27	16	25	34	14	33	14	15	19

Figure S260. Get High-res Image Gene #72: 'Del Peak 41(18q21.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 41(18q21.32)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.066

Table S261. Gene #72: 'Del Peak 41(18q21.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 41(18Q21.32) CNV	64	70	60
DEL PEAK 41(18Q21.32) WILD-TYPE	94	35	68

Figure S261. Get High-res Image Gene #72: 'Del Peak 41(18q21.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 9.31e-13 (Fisher's exact test), Q value = 7.4e-10

Table S262. Gene #73: 'Del Peak 42(18q23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 42(18Q23) CNV	104	65	48	11
DEL PEAK 42(18Q23) WILD-TYPE	44	123	39	38

Figure S262. Get High-res Image Gene #73: 'Del Peak 42(18q23)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 1.04e-08 (Chi-square test), Q value = 7.7e-06

Table S263. Gene #73: 'Del Peak 42(18q23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
DEL PEAK 42(18Q23) CNV	49	37	28	7	15	15	25	9	4
DEL PEAK 42(18Q23) WILD-TYPE	26	18	28	35	14	33	14	15	19

Figure S263. Get High-res Image Gene #73: 'Del Peak 42(18q23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 1.28e-05 (Fisher's exact test), Q value = 0.0077

Table S264. Gene #73: 'Del Peak 42(18q23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 42(18Q23) CNV	61	71	57
DEL PEAK 42(18Q23) WILD-TYPE	97	34	71

Figure S264. Get High-res Image Gene #73: 'Del Peak 42(18q23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 2.6e-12 (Fisher's exact test), Q value = 2.1e-09

Table S265. Gene #74: 'Del Peak 43(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 43(19P13.3) CNV	77	69	70	36
DEL PEAK 43(19P13.3) WILD-TYPE	71	119	17	13

Figure S265. Get High-res Image Gene #74: 'Del Peak 43(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 2.35e-07 (Chi-square test), Q value = 0.00016

Table S266. Gene #74: 'Del Peak 43(19p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
DEL PEAK 43(19P13.3) CNV	38	73	41	46	18
DEL PEAK 43(19P13.3) WILD-TYPE	52	21	54	54	7

Figure S266. Get High-res Image Gene #74: 'Del Peak 43(19p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 3.43e-10 (Chi-square test), Q value = 2.6e-07

Table S267. Gene #74: 'Del Peak 43(19p13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
DEL PEAK 43(19P13.3) CNV	35	28	42	35	16	32	14	5	3
DEL PEAK 43(19P13.3) WILD-TYPE	40	27	14	7	13	16	25	19	20

Figure S267. Get High-res Image Gene #74: 'Del Peak 43(19p13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 3.14e-07 (Fisher's exact test), Q value = 0.00022

Table S268. Gene #74: 'Del Peak 43(19p13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 43(19P13.3) CNV	65	52	93
DEL PEAK 43(19P13.3) WILD-TYPE	93	53	35

Figure S268. Get High-res Image Gene #74: 'Del Peak 43(19p13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 3.65e-06 (Fisher's exact test), Q value = 0.0023

Table S269. Gene #74: 'Del Peak 43(19p13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
DEL PEAK 43(19P13.3) CNV	71	131	45
DEL PEAK 43(19P13.3) WILD-TYPE	100	67	53

Figure S269. Get High-res Image Gene #74: 'Del Peak 43(19p13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

P value = 1.63e-07 (Fisher's exact test), Q value = 0.00011

Table S270. Gene #74: 'Del Peak 43(19p13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
DEL PEAK 43(19P13.3) CNV	66	159	22
DEL PEAK 43(19P13.3) WILD-TYPE	98	85	37

Figure S270. Get High-res Image Gene #74: 'Del Peak 43(19p13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 44(19p13.2)' versus 'CN_CNMF'

P value = 1.25e-11 (Fisher's exact test), Q value = 9.9e-09

Table S271. Gene #75: 'Del Peak 44(19p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 44(19P13.2) CNV	77	66	66	37
DEL PEAK 44(19P13.2) WILD-TYPE	71	122	21	12

Figure S271. Get High-res Image Gene #75: 'Del Peak 44(19p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 44(19p13.2)' versus 'METHLYATION_CNMF'

P value = 2.22e-08 (Chi-square test), Q value = 1.6e-05

Table S272. Gene #75: 'Del Peak 44(19p13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
DEL PEAK 44(19P13.2) CNV	35	74	43	42	17
DEL PEAK 44(19P13.2) WILD-TYPE	55	20	52	58	8

Figure S272. Get High-res Image Gene #75: 'Del Peak 44(19p13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 44(19p13.2)' versus 'MRNASEQ_CNMF'

P value = 3.34e-10 (Chi-square test), Q value = 2.6e-07

Table S273. Gene #75: 'Del Peak 44(19p13.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
DEL PEAK 44(19P13.2) CNV	37	26	34	34	15	37	11	5	3
DEL PEAK 44(19P13.2) WILD-TYPE	38	29	22	8	14	11	28	19	20

Figure S273. Get High-res Image Gene #75: 'Del Peak 44(19p13.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 44(19p13.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.01e-07 (Fisher's exact test), Q value = 0.00027

Table S274. Gene #75: 'Del Peak 44(19p13.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 44(19P13.2) CNV	61	51	90
DEL PEAK 44(19P13.2) WILD-TYPE	97	54	38

Figure S274. Get High-res Image Gene #75: 'Del Peak 44(19p13.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 44(19p13.2)' versus 'MIRSEQ_CNMF'

P value = 2.46e-06 (Fisher's exact test), Q value = 0.0016

Table S275. Gene #75: 'Del Peak 44(19p13.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
DEL PEAK 44(19P13.2) CNV	69	129	43
DEL PEAK 44(19P13.2) WILD-TYPE	102	69	55

Figure S275. Get High-res Image Gene #75: 'Del Peak 44(19p13.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 44(19p13.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.87e-07 (Fisher's exact test), Q value = 2e-04

Table S276. Gene #75: 'Del Peak 44(19p13.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
DEL PEAK 44(19P13.2) CNV	66	155	20
DEL PEAK 44(19P13.2) WILD-TYPE	98	89	39

Figure S276. Get High-res Image Gene #75: 'Del Peak 44(19p13.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 45(19p12)' versus 'CN_CNMF'

P value = 9.72e-13 (Fisher's exact test), Q value = 7.7e-10

Table S277. Gene #76: 'Del Peak 45(19p12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 45(19P12) CNV	75	41	55	28
DEL PEAK 45(19P12) WILD-TYPE	73	147	32	21

Figure S277. Get High-res Image Gene #76: 'Del Peak 45(19p12)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 45(19p12)' versus 'METHLYATION_CNMF'

P value = 1.71e-05 (Chi-square test), Q value = 0.01

Table S278. Gene #76: 'Del Peak 45(19p12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
DEL PEAK 45(19P12) CNV	26	56	40	32	16
DEL PEAK 45(19P12) WILD-TYPE	64	38	55	68	9

Figure S278. Get High-res Image Gene #76: 'Del Peak 45(19p12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 45(19p12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.066

Table S279. Gene #76: 'Del Peak 45(19p12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 45(19P12) CNV	45	51	65
DEL PEAK 45(19P12) WILD-TYPE	113	54	63

Figure S279. Get High-res Image Gene #76: 'Del Peak 45(19p12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 45(19p12)' versus 'MIRSEQ_CNMF'

P value = 2.79e-05 (Fisher's exact test), Q value = 0.016

Table S280. Gene #76: 'Del Peak 45(19p12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
DEL PEAK 45(19P12) CNV	52	106	37
DEL PEAK 45(19P12) WILD-TYPE	119	92	61

Figure S280. Get High-res Image Gene #76: 'Del Peak 45(19p12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 45(19p12)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.27e-05 (Fisher's exact test), Q value = 0.0077

Table S281. Gene #76: 'Del Peak 45(19p12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
DEL PEAK 45(19P12) CNV	49	127	19
DEL PEAK 45(19P12) WILD-TYPE	115	117	40

Figure S281. Get High-res Image Gene #76: 'Del Peak 45(19p12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 46(19q13.33)' versus 'CN_CNMF'

P value = 2.02e-07 (Fisher's exact test), Q value = 0.00014

Table S282. Gene #77: 'Del Peak 46(19q13.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 46(19Q13.33) CNV	75	41	39	19
DEL PEAK 46(19Q13.33) WILD-TYPE	73	147	48	30

Figure S282. Get High-res Image Gene #77: 'Del Peak 46(19q13.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 46(19q13.33)' versus 'MIRSEQ_CNMF'

P value = 2.52e-05 (Fisher's exact test), Q value = 0.015

Table S283. Gene #77: 'Del Peak 46(19q13.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
DEL PEAK 46(19Q13.33) CNV	42	94	34
DEL PEAK 46(19Q13.33) WILD-TYPE	129	104	64

Figure S283. Get High-res Image Gene #77: 'Del Peak 46(19q13.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 46(19q13.33)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.41e-05 (Fisher's exact test), Q value = 0.0084

Table S284. Gene #77: 'Del Peak 46(19q13.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
DEL PEAK 46(19Q13.33) CNV	40	113	17
DEL PEAK 46(19Q13.33) WILD-TYPE	124	131	42

Figure S284. Get High-res Image Gene #77: 'Del Peak 46(19q13.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 47(20p13)' versus 'CN_CNMF'

P value = 2.4e-06 (Fisher's exact test), Q value = 0.0015

Table S285. Gene #78: 'Del Peak 47(20p13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 47(20P13) CNV	59	31	25	6
DEL PEAK 47(20P13) WILD-TYPE	89	157	62	43

Figure S285. Get High-res Image Gene #78: 'Del Peak 47(20p13)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 47(20p13)' versus 'MRNASEQ_CNMF'

P value = 0.000127 (Chi-square test), Q value = 0.069

Table S286. Gene #78: 'Del Peak 47(20p13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
DEL PEAK 47(20P13) CNV	31	15	9	3	4	9	16	3	5
DEL PEAK 47(20P13) WILD-TYPE	44	40	47	39	25	39	23	21	18

Figure S286. Get High-res Image Gene #78: 'Del Peak 47(20p13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 48(21q11.2)' versus 'CN_CNMF'

P value = 3.1e-11 (Fisher's exact test), Q value = 2.4e-08

Table S287. Gene #79: 'Del Peak 48(21q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 48(21Q11.2) CNV	32	46	51	28
DEL PEAK 48(21Q11.2) WILD-TYPE	116	142	36	21

Figure S287. Get High-res Image Gene #79: 'Del Peak 48(21q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 48(21q11.2)' versus 'METHLYATION_CNMF'

P value = 0.000131 (Chi-square test), Q value = 0.071

Table S288. Gene #79: 'Del Peak 48(21q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
DEL PEAK 48(21Q11.2) CNV	14	44	34	34	5
DEL PEAK 48(21Q11.2) WILD-TYPE	76	50	61	66	20

Figure S288. Get High-res Image Gene #79: 'Del Peak 48(21q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 48(21q11.2)' versus 'MRNASEQ_CNMF'

P value = 3.59e-08 (Chi-square test), Q value = 2.6e-05

Table S289. Gene #79: 'Del Peak 48(21q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
DEL PEAK 48(21Q11.2) CNV	27	10	23	8	11	32	19	4	1
DEL PEAK 48(21Q11.2) WILD-TYPE	48	45	33	34	18	16	20	20	22

Figure S289. Get High-res Image Gene #79: 'Del Peak 48(21q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 48(21q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.78e-07 (Fisher's exact test), Q value = 0.00026

Table S290. Gene #79: 'Del Peak 48(21q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 48(21Q11.2) CNV	33	36	66
DEL PEAK 48(21Q11.2) WILD-TYPE	125	69	62

Figure S290. Get High-res Image Gene #79: 'Del Peak 48(21q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 48(21q11.2)' versus 'MIRSEQ_CNMF'

P value = 2.25e-05 (Fisher's exact test), Q value = 0.013

Table S291. Gene #79: 'Del Peak 48(21q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
DEL PEAK 48(21Q11.2) CNV	38	88	28
DEL PEAK 48(21Q11.2) WILD-TYPE	133	110	70

Figure S291. Get High-res Image Gene #79: 'Del Peak 48(21q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 48(21q11.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.55e-08 (Fisher's exact test), Q value = 2.6e-05

Table S292. Gene #79: 'Del Peak 48(21q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
DEL PEAK 48(21Q11.2) CNV	33	110	11
DEL PEAK 48(21Q11.2) WILD-TYPE	131	134	48

Figure S292. Get High-res Image Gene #79: 'Del Peak 48(21q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 49(21q21.3)' versus 'CN_CNMF'

P value = 9.45e-11 (Fisher's exact test), Q value = 7.4e-08

Table S293. Gene #80: 'Del Peak 49(21q21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 49(21Q21.3) CNV	32	44	49	28
DEL PEAK 49(21Q21.3) WILD-TYPE	116	144	38	21

Figure S293. Get High-res Image Gene #80: 'Del Peak 49(21q21.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 49(21q21.3)' versus 'METHLYATION_CNMF'

P value = 1.28e-05 (Chi-square test), Q value = 0.0077

Table S294. Gene #80: 'Del Peak 49(21q21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
DEL PEAK 49(21Q21.3) CNV	12	45	28	35	5
DEL PEAK 49(21Q21.3) WILD-TYPE	78	49	67	65	20

Figure S294. Get High-res Image Gene #80: 'Del Peak 49(21q21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 49(21q21.3)' versus 'MRNASEQ_CNMF'

P value = 3.24e-10 (Chi-square test), Q value = 2.5e-07

Table S295. Gene #80: 'Del Peak 49(21q21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
DEL PEAK 49(21Q21.3) CNV	23	10	25	8	9	35	18	4	1
DEL PEAK 49(21Q21.3) WILD-TYPE	52	45	31	34	20	13	21	20	22

Figure S295. Get High-res Image Gene #80: 'Del Peak 49(21q21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 49(21q21.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.51e-10 (Fisher's exact test), Q value = 4.2e-07

Table S296. Gene #80: 'Del Peak 49(21q21.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 49(21Q21.3) CNV	30	32	71
DEL PEAK 49(21Q21.3) WILD-TYPE	128	73	57

Figure S296. Get High-res Image Gene #80: 'Del Peak 49(21q21.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 49(21q21.3)' versus 'MIRSEQ_CNMF'

P value = 1.04e-05 (Fisher's exact test), Q value = 0.0063

Table S297. Gene #80: 'Del Peak 49(21q21.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
DEL PEAK 49(21Q21.3) CNV	34	85	30
DEL PEAK 49(21Q21.3) WILD-TYPE	137	113	68

Figure S297. Get High-res Image Gene #80: 'Del Peak 49(21q21.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 49(21q21.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.28e-07 (Fisher's exact test), Q value = 9.1e-05

Table S298. Gene #80: 'Del Peak 49(21q21.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
DEL PEAK 49(21Q21.3) CNV	32	106	11
DEL PEAK 49(21Q21.3) WILD-TYPE	132	138	48

Figure S298. Get High-res Image Gene #80: 'Del Peak 49(21q21.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 50(22q13.32)' versus 'CN_CNMF'

P value = 6.18e-13 (Fisher's exact test), Q value = 4.9e-10

Table S299. Gene #81: 'Del Peak 50(22q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 50(22Q13.32) CNV	90	49	52	33
DEL PEAK 50(22Q13.32) WILD-TYPE	58	139	35	16

Figure S299. Get High-res Image Gene #81: 'Del Peak 50(22q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 50(22q13.32)' versus 'METHLYATION_CNMF'

P value = 4.57e-08 (Chi-square test), Q value = 3.3e-05

Table S300. Gene #81: 'Del Peak 50(22q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	90	94	95	100	25
DEL PEAK 50(22Q13.32) CNV	20	58	57	41	15
DEL PEAK 50(22Q13.32) WILD-TYPE	70	36	38	59	10

Figure S300. Get High-res Image Gene #81: 'Del Peak 50(22q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 50(22q13.32)' versus 'MRNASEQ_CNMF'

P value = 1.51e-10 (Chi-square test), Q value = 1.2e-07

Table S301. Gene #81: 'Del Peak 50(22q13.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	75	55	56	42	29	48	39	24	23
DEL PEAK 50(22Q13.32) CNV	51	16	33	10	14	36	17	5	4
DEL PEAK 50(22Q13.32) WILD-TYPE	24	39	23	32	15	12	22	19	19

Figure S301. Get High-res Image Gene #81: 'Del Peak 50(22q13.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 50(22q13.32)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.29e-11 (Fisher's exact test), Q value = 4.9e-08

Table S302. Gene #81: 'Del Peak 50(22q13.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 50(22Q13.32) CNV	44	56	86
DEL PEAK 50(22Q13.32) WILD-TYPE	114	49	42

Figure S302. Get High-res Image Gene #81: 'Del Peak 50(22q13.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 50(22q13.32)' versus 'MIRSEQ_CNMF'

P value = 1.66e-07 (Fisher's exact test), Q value = 0.00012

Table S303. Gene #81: 'Del Peak 50(22q13.32)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
DEL PEAK 50(22Q13.32) CNV	55	121	45
DEL PEAK 50(22Q13.32) WILD-TYPE	116	77	53

Figure S303. Get High-res Image Gene #81: 'Del Peak 50(22q13.32)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 50(22q13.32)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.72e-08 (Fisher's exact test), Q value = 2e-05

Table S304. Gene #81: 'Del Peak 50(22q13.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
DEL PEAK 50(22Q13.32) CNV	53	147	21
DEL PEAK 50(22Q13.32) WILD-TYPE	111	97	38

Figure S304. Get High-res Image Gene #81: 'Del Peak 50(22q13.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 51(Xp22.2)' versus 'CN_CNMF'

P value = 1.99e-07 (Fisher's exact test), Q value = 0.00014

Table S305. Gene #82: 'Del Peak 51(Xp22.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	188	87	49
DEL PEAK 51(XP22.2) CNV	68	32	25	12
DEL PEAK 51(XP22.2) WILD-TYPE	80	156	62	37

Figure S305. Get High-res Image Gene #82: 'Del Peak 51(Xp22.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 51(Xp22.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000322 (Fisher's exact test), Q value = 0.17

Table S306. Gene #82: 'Del Peak 51(Xp22.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 51(XP22.2) CNV	33	46	34
DEL PEAK 51(XP22.2) WILD-TYPE	125	59	94

Figure S306. Get High-res Image Gene #82: 'Del Peak 51(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 = 472
Number of copy number variation regions = 82
Number of molecular subtypes = 10
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

Chi-square test

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

Q value calculation

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

Download Results

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

References

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

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

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

[4] GISTIC_version2

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