Correlation between copy number variation genes and molecular subtypes

Lung Adenocarcinoma (Primary solid tumor)

23 May 2013 | analyses__2013_05_23

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variation genes and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1CF9N5G

Overview

Introduction

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

Summary

Testing the association between copy number variation of 79 peak regions and 12 molecular subtypes across 493 patients, 322 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', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 4(3q26.2) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_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', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
Amp Peak 11(7p11.2) cnvs correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 12(7q31.2) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 13(8p11.23) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 14(8p11.21) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 15(8q11.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 16(8q24.21) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 17(10p15.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 18(11q13.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 19(12p12.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 20(12q14.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 21(12q15) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 22(13q33.3) cnvs correlated to 'METHLYATION_CNMF'.
Amp Peak 23(14q13.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 24(16p11.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 25(17q12) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Amp Peak 26(17q23.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 27(18q11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 28(19q12) cnvs correlated to 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 29(20p11.21) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Amp Peak 30(20q13.33) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Amp Peak 31(22q11.22) cnvs correlated to 'CN_CNMF'.
Amp Peak 32(Xq28) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 1(1p36.13) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 2(1p13.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 4(2q37.3) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 5(3p21.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
Del Peak 7(3q29) cnvs correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 8(4p16.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 9(4q22.1) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 10(4q35.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 11(5q11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 12(5q31.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 14(6q22.31) cnvs correlated to 'METHLYATION_CNMF'.
Del Peak 15(6q26) cnvs correlated to 'METHLYATION_CNMF'.
Del Peak 16(8p23.2) cnvs correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
Del Peak 17(8p12) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
Del Peak 18(8p11.21) cnvs correlated to 'CN_CNMF'.
Del Peak 22(9q21.11) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 23(10p15.3) cnvs correlated to 'CN_CNMF'.
Del Peak 24(10q26.3) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 25(11p15.5) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 29(12q24.33) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 30(13q12.11) cnvs correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 31(13q12.13) cnvs correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 32(13q14.2) cnvs correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 33(13q34) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 35(15q11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
Del Peak 36(16q23.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 37(17p13.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 38(17p11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 39(18q21.32) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 40(18q23) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 41(19p13.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 42(19p13.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 43(19q13.33) cnvs correlated to 'CN_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 45(21q11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 46(22q13.32) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 47(Xp22.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 79 regions and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 322 significant findings detected.


		Molecular subtypes	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
Del Peak 9(4q22 1)	0 (0%)	342	0.000214 (0.138)	9.89e-05 (0.0671)	1.2e-05 (0.0088)	6.24e-09 (5.5e-06)	0.151 (1.00)	0.0286 (1.00)	3.81e-06 (0.0029)	9.97e-14 (9.22e-11)	1.66e-08 (1.44e-05)	1.54e-06 (0.0012)	0.00379 (1.00)	0.000104 (0.0703)
Del Peak 10(4q35 1)	0 (0%)	312	0.00204 (1.00)	0.00118 (0.686)	1.72e-08 (1.49e-05)	1.23e-14 (1.14e-11)	0.0381 (1.00)	0.000196 (0.127)	2.47e-09 (2.21e-06)	7.36e-18 (6.88e-15)	1.57e-10 (1.42e-07)	1e-10 (9.13e-08)	3.01e-06 (0.0023)	1.42e-10 (1.29e-07)
Amp Peak 4(3q26 2)	0 (0%)	331	0.000264 (0.169)	0.00332 (1.00)	1.15e-05 (0.00845)	8.98e-09 (7.85e-06)	0.000631 (0.388)	0.00307 (1.00)	1.62e-09 (1.46e-06)	5.62e-09 (4.97e-06)	1.46e-06 (0.00114)	2.21e-07 (0.000182)	0.000781 (0.473)	0.000356 (0.224)
Amp Peak 11(7p11 2)	0 (0%)	234	1 (1.00)	1 (1.00)	4.99e-22 (4.7e-19)	0.00992 (1.00)	0.00114 (0.664)	0.000263 (0.168)	1.06e-08 (9.27e-06)	1.49e-10 (1.35e-07)	2.59e-07 (0.000214)	6.85e-05 (0.0471)	7.2e-05 (0.0493)	0.000361 (0.227)
Amp Peak 15(8q11 1)	0 (0%)	269	0.00472 (1.00)	0.0134 (1.00)	1.23e-22 (1.16e-19)	2.46e-08 (2.12e-05)	0.0344 (1.00)	0.00467 (1.00)	5.35e-06 (0.00402)	2.26e-05 (0.0162)	1.94e-07 (0.000161)	8.84e-07 (0.000699)	1.44e-06 (0.00113)	1.38e-05 (0.01)
Amp Peak 18(11q13 3)	0 (0%)	330	0.00118 (0.686)	0.000736 (0.448)	5e-17 (4.67e-14)	4.67e-06 (0.00354)	0.0127 (1.00)	0.00689 (1.00)	3.07e-08 (2.64e-05)	9.49e-07 (0.000749)	2.08e-10 (1.88e-07)	2.03e-07 (0.000168)	2.09e-07 (0.000173)	0.000122 (0.0814)
Amp Peak 19(12p12 1)	0 (0%)	323	0.198 (1.00)	0.033 (1.00)	6.39e-07 (0.00051)	3.23e-07 (0.000263)	0.0345 (1.00)	0.0834 (1.00)	1.44e-05 (0.0105)	2.74e-07 (0.000225)	6.05e-06 (0.00453)	1.01e-05 (0.00751)	2.46e-05 (0.0176)	0.000126 (0.0832)
Amp Peak 20(12q14 1)	0 (0%)	336	0.406 (1.00)	0.302 (1.00)	5.25e-09 (4.66e-06)	7.15e-08 (6.07e-05)	0.0215 (1.00)	0.00722 (1.00)	2.93e-07 (0.00024)	3.88e-10 (3.49e-07)	6.24e-09 (5.5e-06)	4.09e-09 (3.65e-06)	2.58e-06 (0.00199)	4.94e-09 (4.39e-06)
Amp Peak 21(12q15)	0 (0%)	335	0.221 (1.00)	0.103 (1.00)	2.89e-07 (0.000236)	9.85e-09 (8.6e-06)	0.0146 (1.00)	0.00471 (1.00)	7.24e-08 (6.13e-05)	4.39e-09 (3.91e-06)	2.17e-09 (1.95e-06)	1.1e-07 (9.3e-05)	4.96e-07 (0.000399)	7.07e-07 (0.000562)
Amp Peak 25(17q12)	0 (0%)	276	0.179 (1.00)	0.049 (1.00)	1.92e-13 (1.77e-10)	5.77e-09 (5.1e-06)	0.0638 (1.00)	0.00016 (0.104)	9.56e-11 (8.7e-08)	2.02e-06 (0.00156)	7.33e-07 (0.000582)	1.1e-06 (0.000863)	0.000227 (0.146)	0.000827 (0.495)
Del Peak 12(5q31 1)	0 (0%)	294	0.0936 (1.00)	0.199 (1.00)	1.03e-12 (9.47e-10)	3.03e-07 (0.000247)	0.00482 (1.00)	0.00447 (1.00)	1.24e-07 (0.000104)	8.32e-09 (7.29e-06)	1.44e-08 (1.25e-05)	7.1e-08 (6.03e-05)	5.47e-05 (0.038)	8.61e-05 (0.0587)
Del Peak 41(19p13 3)	0 (0%)	227	0.572 (1.00)	0.665 (1.00)	7.34e-06 (0.00547)	8.27e-07 (0.000656)	0.564 (1.00)	0.306 (1.00)	3.43e-10 (3.09e-07)	3.14e-07 (0.000257)	3.65e-06 (0.00278)	1.63e-07 (0.000136)	0.000119 (0.0798)	6.09e-06 (0.00456)
Del Peak 42(19p13 2)	0 (0%)	234	0.694 (1.00)	1 (1.00)	6.1e-07 (0.000489)	3.46e-08 (2.96e-05)	0.378 (1.00)	0.187 (1.00)	3.34e-10 (3.01e-07)	4.01e-07 (0.000325)	2.46e-06 (0.0019)	2.87e-07 (0.000235)	4.56e-05 (0.032)	1.11e-05 (0.00814)
Del Peak 46(22q13 32)	0 (0%)	257	0.0692 (1.00)	0.0871 (1.00)	4.32e-13 (3.97e-10)	2.97e-09 (2.65e-06)	0.00863 (1.00)	0.0171 (1.00)	1.51e-10 (1.36e-07)	6.29e-11 (5.74e-08)	1.66e-07 (0.000138)	2.72e-08 (2.34e-05)	0.000257 (0.165)	5.83e-07 (0.000468)
Amp Peak 14(8p11 21)	0 (0%)	322	0.253 (1.00)	0.124 (1.00)	5.23e-24 (4.96e-21)	0.00019 (0.123)	0.0149 (1.00)	0.00534 (1.00)	1.59e-05 (0.0115)	4.9e-07 (0.000394)	4.19e-05 (0.0294)	6.3e-06 (0.0047)	0.00152 (0.864)	6.14e-05 (0.0424)
Amp Peak 16(8q24 21)	0 (0%)	184	0.0343 (1.00)	0.0341 (1.00)	6.35e-19 (5.94e-16)	7.97e-09 (7e-06)	0.157 (1.00)	0.00162 (0.914)	6.65e-05 (0.0458)	3.27e-06 (0.0025)	8.41e-07 (0.000665)	1.26e-05 (0.00922)	0.00129 (0.741)	0.000109 (0.0735)
Amp Peak 23(14q13 3)	0 (0%)	273	0.562 (1.00)	0.254 (1.00)	1.38e-14 (1.28e-11)	5.81e-06 (0.00436)	0.00213 (1.00)	0.0122 (1.00)	1.28e-09 (1.15e-06)	3.84e-05 (0.027)	8.7e-08 (7.33e-05)	2.61e-09 (2.34e-06)	0.000489 (0.304)	0.000117 (0.0785)
Amp Peak 26(17q23 1)	0 (0%)	252	0.081 (1.00)	0.208 (1.00)	1.98e-14 (1.83e-11)	2.7e-11 (2.47e-08)	0.00156 (0.886)	4.12e-07 (0.000333)	2.7e-13 (2.49e-10)	5.99e-10 (5.39e-07)	1.54e-06 (0.0012)	5.68e-06 (0.00426)	0.00572 (1.00)	0.000743 (0.451)
Del Peak 8(4p16 3)	0 (0%)	371	0.595 (1.00)	0.453 (1.00)	2.44e-05 (0.0175)	1.58e-06 (0.00123)	0.0232 (1.00)	0.0499 (1.00)	8.4e-07 (0.000665)	6.36e-11 (5.8e-08)	2.82e-07 (0.000232)	1.11e-07 (9.3e-05)	0.00308 (1.00)	4.48e-05 (0.0314)
Del Peak 11(5q11 2)	0 (0%)	320	0.26 (1.00)	0.254 (1.00)	2.13e-13 (1.96e-10)	1.46e-07 (0.000122)	0.00426 (1.00)	0.0113 (1.00)	1.35e-06 (0.00106)	2.57e-09 (2.3e-06)	4.53e-08 (3.86e-05)	2.11e-06 (0.00163)	4.67e-06 (0.00354)	0.000517 (0.321)
Del Peak 32(13q14 2)	0 (0%)	223	0.00862 (1.00)	0.0218 (1.00)	1.48e-22 (1.39e-19)	0.0127 (1.00)	0.000647 (0.396)	1.04e-05 (0.00769)	4.15e-09 (3.69e-06)	1.54e-07 (0.000129)	0.000206 (0.133)	4.69e-05 (0.0327)	0.00132 (0.757)	0.000398 (0.249)
Del Peak 45(21q11 2)	0 (0%)	330	0.0604 (1.00)	0.0501 (1.00)	4.85e-06 (0.00366)	0.000254 (0.163)	0.00624 (1.00)	0.00469 (1.00)	3.59e-08 (3.07e-05)	3.78e-07 (0.000307)	2.25e-05 (0.0161)	3.55e-08 (3.04e-05)	0.0131 (1.00)	3.68e-05 (0.0259)
Amp Peak 17(10p15 1)	0 (0%)	360	0.023 (1.00)	0.0262 (1.00)	4.31e-05 (0.0302)	4.45e-07 (0.000359)	0.00434 (1.00)	0.0346 (1.00)	6.78e-05 (0.0467)	2.08e-08 (1.8e-05)	0.000237 (0.152)	6.08e-05 (0.042)	0.00504 (1.00)	0.00126 (0.729)
Amp Peak 27(18q11 2)	0 (0%)	396	0.195 (1.00)	0.0151 (1.00)	0.000102 (0.069)	3.44e-08 (2.95e-05)	0.0431 (1.00)	0.000816 (0.49)	0.000799 (0.481)	9.61e-05 (0.0653)	1.06e-05 (0.00778)	6.73e-07 (0.000537)	0.00981 (1.00)	2.66e-06 (0.00204)
Amp Peak 28(19q12)	0 (0%)	361	0.0514 (1.00)	0.0219 (1.00)	0.00128 (0.74)	1.34e-05 (0.0098)	0.0685 (1.00)	0.0791 (1.00)	0.000438 (0.273)	4.22e-08 (3.6e-05)	1.27e-06 (0.000994)	1.46e-06 (0.00114)	2.2e-05 (0.0158)	1.04e-05 (0.00766)
Amp Peak 29(20p11 21)	0 (0%)	306	0.0611 (1.00)	0.0953 (1.00)	3.14e-05 (0.0222)	3.59e-05 (0.0253)	0.338 (1.00)	0.0379 (1.00)	0.000221 (0.142)	0.00159 (0.897)	0.000145 (0.0954)	7.51e-05 (0.0514)	0.000108 (0.0725)	0.000423 (0.265)
Amp Peak 30(20q13 33)	0 (0%)	257	0.00559 (1.00)	0.0301 (1.00)	5.43e-09 (4.81e-06)	2.84e-05 (0.0203)	0.00426 (1.00)	0.00335 (1.00)	1.37e-05 (0.00996)	0.0184 (1.00)	2.53e-06 (0.00195)	4.24e-07 (0.000342)	1.45e-05 (0.0105)	0.000465 (0.29)
Del Peak 35(15q11 2)	0 (0%)	241	0.168 (1.00)	0.157 (1.00)	6.48e-11 (5.9e-08)	0.000186 (0.121)	0.0928 (1.00)	0.000161 (0.105)	1.91e-13 (1.77e-10)	1.4e-05 (0.0102)	2.82e-05 (0.0201)	0.000803 (0.482)	0.097 (1.00)	0.0119 (1.00)
Amp Peak 3(1q21 3)	0 (0%)	138	0.362 (1.00)	0.465 (1.00)	5.98e-07 (0.00048)	1.91e-08 (1.65e-05)	0.458 (1.00)	0.357 (1.00)	4.43e-06 (0.00336)	0.473 (1.00)	0.000695 (0.425)	0.000211 (0.136)	0.034 (1.00)	7e-05 (0.048)
Amp Peak 7(5p13 1)	0 (0%)	202	0.263 (1.00)	0.897 (1.00)	2.29e-15 (2.13e-12)	0.0018 (1.00)	0.443 (1.00)	0.0187 (1.00)	0.000119 (0.0798)	0.00342 (1.00)	0.000122 (0.0814)	0.000274 (0.175)	0.000276 (0.175)	0.00162 (0.914)
Del Peak 5(3p21 31)	0 (0%)	257	0.132 (1.00)	0.478 (1.00)	5.06e-06 (0.00381)	1.59e-07 (0.000133)	0.0411 (1.00)	0.00737 (1.00)	3.35e-05 (0.0237)	6.23e-09 (5.5e-06)	1.18e-05 (0.00865)	0.000743 (0.451)	0.000829 (0.495)	0.0285 (1.00)
Del Peak 16(8p23 2)	0 (0%)	253	0.00526 (1.00)	0.00382 (1.00)	3.17e-23 (3e-20)	0.000955 (0.566)	0.018 (1.00)	0.000354 (0.223)	8.22e-09 (7.2e-06)	2.29e-07 (0.000189)	3.58e-06 (0.00274)	0.00312 (1.00)	0.00107 (0.626)	0.00277 (1.00)
Del Peak 22(9q21 11)	0 (0%)	250	0.0335 (1.00)	0.597 (1.00)	6.15e-07 (0.000492)	1.97e-05 (0.0142)	0.0726 (1.00)	0.0112 (1.00)	0.000116 (0.078)	1.67e-07 (0.000139)	0.00333 (1.00)	0.000126 (0.0832)	0.0444 (1.00)	0.00136 (0.774)
Del Peak 30(13q12 11)	0 (0%)	213	0.00113 (0.663)	0.0134 (1.00)	1.98e-21 (1.86e-18)	0.00425 (1.00)	0.00188 (1.00)	1.49e-06 (0.00116)	2.73e-07 (0.000225)	4.07e-08 (3.48e-05)	0.00248 (1.00)	8.51e-05 (0.0581)	0.0134 (1.00)	0.00068 (0.416)
Del Peak 31(13q12 13)	0 (0%)	212	0.00862 (1.00)	0.0218 (1.00)	1.29e-22 (1.22e-19)	0.00169 (0.944)	0.000524 (0.325)	6.68e-07 (0.000533)	1.2e-07 (0.000101)	8.17e-08 (6.91e-05)	0.00386 (1.00)	0.000138 (0.0912)	0.0139 (1.00)	0.0007 (0.426)
Del Peak 38(17p11 2)	0 (0%)	277	0.264 (1.00)	0.208 (1.00)	1.66e-16 (1.55e-13)	8.4e-08 (7.09e-05)	0.00562 (1.00)	0.000294 (0.187)	7.3e-07 (0.00058)	1.52e-05 (0.011)	0.0378 (1.00)	0.00653 (1.00)	0.109 (1.00)	0.066 (1.00)
Amp Peak 6(5p15 33)	0 (0%)	177	0.878 (1.00)	0.901 (1.00)	1.9e-18 (1.78e-15)	0.0644 (1.00)	0.0565 (1.00)	0.000798 (0.481)	1.77e-07 (0.000147)	0.00166 (0.929)	0.000225 (0.145)	0.000304 (0.192)	0.0011 (0.647)	0.00118 (0.686)
Amp Peak 10(7p21 1)	0 (0%)	225	0.743 (1.00)	1 (1.00)	1.04e-22 (9.8e-20)	0.00662 (1.00)	0.00184 (1.00)	0.00104 (0.612)	7.66e-09 (6.73e-06)	7.98e-08 (6.75e-05)	8.38e-06 (0.00622)	0.00203 (1.00)	0.000835 (0.497)	0.0034 (1.00)
Del Peak 17(8p12)	0 (0%)	278	0.106 (1.00)	0.12 (1.00)	3.23e-21 (3.04e-18)	0.00161 (0.908)	0.0424 (1.00)	0.0222 (1.00)	4.61e-05 (0.0322)	5.37e-06 (0.00404)	5.26e-05 (0.0366)	0.00432 (1.00)	0.000827 (0.495)	0.00251 (1.00)
Del Peak 36(16q23 1)	0 (0%)	326	0.0587 (1.00)	0.312 (1.00)	1.62e-06 (0.00126)	0.000139 (0.0917)	0.000698 (0.426)	0.0174 (1.00)	1.73e-06 (0.00134)	3.21e-07 (0.000262)	0.013 (1.00)	0.0559 (1.00)	0.0186 (1.00)	0.088 (1.00)
Del Peak 37(17p13 3)	0 (0%)	226	0.386 (1.00)	0.609 (1.00)	5.27e-19 (4.94e-16)	6.05e-08 (5.14e-05)	0.0334 (1.00)	0.00158 (0.894)	5.6e-08 (4.77e-05)	9.79e-07 (0.000771)	0.0102 (1.00)	0.00603 (1.00)	0.0399 (1.00)	0.0602 (1.00)
Del Peak 43(19q13 33)	0 (0%)	309	0.272 (1.00)	0.383 (1.00)	1.99e-07 (0.000165)	0.0139 (1.00)	0.0819 (1.00)	0.208 (1.00)	0.0184 (1.00)	0.00194 (1.00)	2.52e-05 (0.018)	1.41e-05 (0.0102)	0.076 (1.00)	0.000155 (0.102)
Amp Peak 8(5q35 1)	0 (0%)	374	0.0862 (1.00)	0.453 (1.00)	0.0123 (1.00)	0.000104 (0.07)	0.0909 (1.00)	0.2 (1.00)	4.73e-05 (0.0329)	0.000159 (0.104)	0.0134 (1.00)	0.00294 (1.00)	0.0414 (1.00)	0.0907 (1.00)
Amp Peak 12(7q31 2)	0 (0%)	287	0.482 (1.00)	0.429 (1.00)	4.48e-11 (4.1e-08)	0.00491 (1.00)	0.206 (1.00)	0.052 (1.00)	2.97e-06 (0.00228)	1.37e-08 (1.19e-05)	0.00637 (1.00)	0.00978 (1.00)	0.0247 (1.00)	0.0429 (1.00)
Amp Peak 13(8p11 23)	0 (0%)	360	0.294 (1.00)	0.107 (1.00)	3.83e-21 (3.59e-18)	9.54e-05 (0.065)	0.0844 (1.00)	0.0267 (1.00)	0.00309 (1.00)	7.16e-06 (0.00534)	0.0131 (1.00)	0.000479 (0.298)	0.167 (1.00)	0.0131 (1.00)
Amp Peak 32(Xq28)	0 (0%)	339	0.301 (1.00)	0.123 (1.00)	1.16e-12 (1.07e-09)	0.000356 (0.224)	0.0244 (1.00)	0.0308 (1.00)	0.00146 (0.829)	9.71e-05 (0.066)	0.0059 (1.00)	0.033 (1.00)	0.0151 (1.00)	0.136 (1.00)
Del Peak 1(1p36 13)	0 (0%)	378	0.795 (1.00)	0.441 (1.00)	3.08e-05 (0.0219)	0.000534 (0.331)	0.437 (1.00)	0.363 (1.00)	8.06e-06 (0.006)	8.99e-06 (0.00666)	0.0253 (1.00)	0.00486 (1.00)	0.183 (1.00)	0.0233 (1.00)
Del Peak 25(11p15 5)	0 (0%)	361	0.268 (1.00)	0.0576 (1.00)	2.53e-06 (0.00195)	0.0196 (1.00)	0.00767 (1.00)	0.00204 (1.00)	0.00111 (0.648)	4.36e-06 (0.00332)	0.00453 (1.00)	0.000108 (0.0725)	0.0195 (1.00)	0.00478 (1.00)
Del Peak 33(13q34)	0 (0%)	263	0.0356 (1.00)	0.0445 (1.00)	7.07e-16 (6.58e-13)	0.141 (1.00)	0.00359 (1.00)	0.00079 (0.477)	3.71e-06 (0.00282)	3.09e-05 (0.022)	0.0215 (1.00)	0.00462 (1.00)	0.0674 (1.00)	0.0465 (1.00)
Del Peak 39(18q21 32)	0 (0%)	252	0.115 (1.00)	0.227 (1.00)	2.62e-13 (2.41e-10)	0.336 (1.00)	0.00133 (0.759)	0.0023 (1.00)	9.08e-09 (7.94e-06)	0.00012 (0.08)	0.00925 (1.00)	0.105 (1.00)	0.141 (1.00)	0.239 (1.00)
Del Peak 40(18q23)	0 (0%)	255	0.029 (1.00)	0.0968 (1.00)	1.15e-14 (1.07e-11)	0.245 (1.00)	0.00395 (1.00)	0.00135 (0.773)	1.04e-08 (9.08e-06)	1.28e-05 (0.00938)	0.00388 (1.00)	0.0798 (1.00)	0.0418 (1.00)	0.372 (1.00)
Amp Peak 1(1p34 3)	0 (0%)	365	0.553 (1.00)	0.384 (1.00)	1.81e-08 (1.57e-05)	0.217 (1.00)	0.169 (1.00)	0.243 (1.00)	4.96e-06 (0.00375)	0.149 (1.00)	0.184 (1.00)	0.147 (1.00)	0.188 (1.00)	0.852 (1.00)
Amp Peak 9(6p21 1)	0 (0%)	311	0.675 (1.00)	0.206 (1.00)	4.66e-07 (0.000376)	5.14e-09 (4.57e-06)	0.081 (1.00)	0.609 (1.00)	0.00918 (1.00)	0.727 (1.00)	0.012 (1.00)	0.0168 (1.00)	0.06 (1.00)	0.038 (1.00)
Del Peak 2(1p13 2)	0 (0%)	344	0.703 (1.00)	0.707 (1.00)	1.25e-07 (0.000104)	0.00019 (0.123)	0.173 (1.00)	0.665 (1.00)	0.00132 (0.757)	0.0235 (1.00)	0.0879 (1.00)	0.0101 (1.00)	0.216 (1.00)	0.123 (1.00)
Del Peak 4(2q37 3)	0 (0%)	429	0.703 (1.00)	0.206 (1.00)	0.000183 (0.119)	0.00742 (1.00)	0.22 (1.00)	0.151 (1.00)	0.178 (1.00)	0.00905 (1.00)	0.00691 (1.00)	0.000153 (0.101)	0.0214 (1.00)	0.00117 (0.681)
Del Peak 7(3q29)	0 (0%)	359	0.71 (1.00)	0.602 (1.00)	0.0668 (1.00)	3.43e-05 (0.0243)	0.00515 (1.00)	0.0168 (1.00)	3.27e-08 (2.81e-05)	0.0171 (1.00)	0.666 (1.00)	0.684 (1.00)	0.786 (1.00)	0.764 (1.00)
Del Peak 24(10q26 3)	0 (0%)	355	0.748 (1.00)	0.283 (1.00)	3.91e-07 (0.000318)	0.000847 (0.503)	0.00268 (1.00)	0.0237 (1.00)	5.65e-05 (0.0392)	0.00205 (1.00)	0.0532 (1.00)	0.00789 (1.00)	0.00988 (1.00)	0.00485 (1.00)
Del Peak 29(12q24 33)	0 (0%)	375	0.063 (1.00)	0.0396 (1.00)	8.07e-06 (0.006)	0.133 (1.00)	0.0223 (1.00)	0.00328 (1.00)	0.000614 (0.379)	0.000306 (0.194)	0.0538 (1.00)	0.0151 (1.00)	0.137 (1.00)	0.0842 (1.00)
Del Peak 47(Xp22 2)	0 (0%)	351	0.691 (1.00)	0.896 (1.00)	1.52e-08 (1.32e-05)	0.0084 (1.00)	0.0885 (1.00)	0.0284 (1.00)	0.0141 (1.00)	0.000322 (0.203)	0.499 (1.00)	0.244 (1.00)	0.683 (1.00)	0.569 (1.00)
Amp Peak 2(1p22 3)	0 (0%)	364	0.876 (1.00)	1 (1.00)	7.59e-09 (6.68e-06)	0.352 (1.00)	0.183 (1.00)	0.399 (1.00)	0.00168 (0.943)	0.0091 (1.00)	0.136 (1.00)	0.131 (1.00)	1 (1.00)	0.0987 (1.00)
Amp Peak 5(4q12)	0 (0%)	402	0.703 (1.00)	0.206 (1.00)	3.11e-12 (2.85e-09)	0.0477 (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)	0.161 (1.00)	0.0793 (1.00)
Amp Peak 22(13q33 3)	0 (0%)	420	0.172 (1.00)	0.105 (1.00)	0.0772 (1.00)	5.61e-05 (0.039)	0.663 (1.00)	0.298 (1.00)	0.0293 (1.00)	0.229 (1.00)	0.129 (1.00)	0.0824 (1.00)	0.137 (1.00)	0.224 (1.00)
Amp Peak 24(16p11 2)	0 (0%)	334	0.799 (1.00)	0.229 (1.00)	2.33e-06 (0.0018)	0.0316 (1.00)	0.232 (1.00)	0.125 (1.00)	0.00568 (1.00)	0.273 (1.00)	0.111 (1.00)	0.0311 (1.00)	0.158 (1.00)	0.334 (1.00)
Amp Peak 31(22q11 22)	0 (0%)	410	0.268 (1.00)	0.162 (1.00)	0.000124 (0.0823)	0.378 (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)	0.00804 (1.00)	0.704 (1.00)
Del Peak 14(6q22 31)	0 (0%)	245	0.54 (1.00)	0.187 (1.00)	0.00575 (1.00)	4.04e-07 (0.000327)	0.308 (1.00)	0.0544 (1.00)	0.0184 (1.00)	0.709 (1.00)	0.9 (1.00)	0.571 (1.00)	0.637 (1.00)	0.0184 (1.00)
Del Peak 15(6q26)	0 (0%)	243	0.368 (1.00)	0.276 (1.00)	0.000624 (0.385)	6.31e-05 (0.0436)	0.168 (1.00)	0.00944 (1.00)	0.141 (1.00)	0.807 (1.00)	0.81 (1.00)	0.41 (1.00)	0.673 (1.00)	0.0232 (1.00)
Del Peak 18(8p11 21)	0 (0%)	381	0.795 (1.00)	0.504 (1.00)	2.61e-19 (2.45e-16)	0.411 (1.00)	0.721 (1.00)	0.318 (1.00)	0.000627 (0.385)	0.185 (1.00)	0.0376 (1.00)	0.512 (1.00)	0.108 (1.00)	0.0321 (1.00)
Del Peak 23(10p15 3)	0 (0%)	373	1 (1.00)	1 (1.00)	1.86e-05 (0.0134)	0.00187 (1.00)	0.504 (1.00)	0.56 (1.00)	0.000546 (0.337)	0.366 (1.00)	0.0266 (1.00)	0.0103 (1.00)	0.00103 (0.61)	0.000853 (0.506)
Del Peak 3(2q22 1)	0 (0%)	446	0.869 (1.00)	0.78 (1.00)	0.00371 (1.00)	0.0135 (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)	0.0419 (1.00)	0.0266 (1.00)
Del Peak 6(3q11 1)	0 (0%)	354	0.609 (1.00)	0.602 (1.00)	0.138 (1.00)	0.005 (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)	0.928 (1.00)	0.975 (1.00)
Del Peak 13(6q12)	0 (0%)	318	0.488 (1.00)	0.52 (1.00)	0.0201 (1.00)	0.0349 (1.00)	0.233 (1.00)	0.25 (1.00)	0.471 (1.00)	0.836 (1.00)	0.125 (1.00)	0.702 (1.00)	0.701 (1.00)	0.042 (1.00)
Del Peak 19(8q11 21)	0 (0%)	431	1 (1.00)	1 (1.00)	0.0031 (1.00)	0.879 (1.00)	0.537 (1.00)	0.676 (1.00)	0.000831 (0.495)	0.604 (1.00)	0.151 (1.00)	0.464 (1.00)	0.538 (1.00)	0.19 (1.00)
Del Peak 20(9p23)	0 (0%)	224	0.521 (1.00)	0.901 (1.00)	0.00298 (1.00)	0.46 (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)	0.79 (1.00)	0.344 (1.00)
Del Peak 21(9p21 3)	0 (0%)	219	0.521 (1.00)	0.901 (1.00)	0.00111 (0.651)	0.292 (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)	0.819 (1.00)	0.632 (1.00)
Del Peak 26(11q25)	0 (0%)	384	0.108 (1.00)	0.0799 (1.00)	0.00392 (1.00)	0.0775 (1.00)	0.0012 (0.695)	0.00644 (1.00)	0.0264 (1.00)	0.00517 (1.00)	0.141 (1.00)	0.0854 (1.00)	0.418 (1.00)	0.539 (1.00)
Del Peak 27(12p13 2)	0 (0%)	362	0.255 (1.00)	0.719 (1.00)	0.00588 (1.00)	0.00169 (0.944)	0.0774 (1.00)	0.021 (1.00)	0.00802 (1.00)	0.111 (1.00)	0.824 (1.00)	1 (1.00)	0.943 (1.00)	0.933 (1.00)
Del Peak 28(12q12)	0 (0%)	400	0.597 (1.00)	0.644 (1.00)	0.00105 (0.62)	0.0659 (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)	0.287 (1.00)	0.187 (1.00)
Del Peak 34(14q32 33)	0 (0%)	349	0.703 (1.00)	0.302 (1.00)	0.0731 (1.00)	0.519 (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)	0.632 (1.00)	0.548 (1.00)
Del Peak 44(20q13 12)	0 (0%)	410	0.17 (1.00)	0.874 (1.00)	0.444 (1.00)	0.389 (1.00)	0.034 (1.00)	0.137 (1.00)	0.0146 (1.00)	0.0892 (1.00)	0.113 (1.00)	0.0946 (1.00)	0.351 (1.00)	0.758 (1.00)

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

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

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

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

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

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

P value = 4.96e-06 (Chi-square test), Q value = 0.0037

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 = 7.59e-09 (Fisher's exact test), Q value = 6.7e-06

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

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

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

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

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

Figure 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 = 1.91e-08 (Fisher's exact test), Q value = 1.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
AMP PEAK 3(1Q21.3) CNV	59	96	83	51
AMP PEAK 3(1Q21.3) WILD-TYPE	27	12	27	49

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 = 0.0034

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 = 0.14

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 3(1q21.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.048

Table S8. Gene #3: 'Amp Peak 3(1q21.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	46	205
AMP PEAK 3(1Q21.3) CNV	105	22	163
AMP PEAK 3(1Q21.3) WILD-TYPE	48	24	42

Figure S8. Get High-res Image Gene #3: 'Amp Peak 3(1q21.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

Table S9. 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 S9. Get High-res Image Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

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

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

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

Figure S10. 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 = 8.98e-09 (Fisher's exact test), Q value = 7.9e-06

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
AMP PEAK 4(3Q26.2) CNV	7	52	37	35
AMP PEAK 4(3Q26.2) WILD-TYPE	79	56	73	65

Figure S11. 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 = 1.5e-06

Table S12. 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 S12. 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 = 5e-06

Table S13. 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 S13. 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 = 0.0011

Table S14. 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 S14. 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 = 0.00018

Table S15. 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 S15. Get High-res Image Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 0.000356 (Fisher's exact test), Q value = 0.22

Table S16. Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	46	205
AMP PEAK 4(3Q26.2) CNV	37	9	85
AMP PEAK 4(3Q26.2) WILD-TYPE	116	37	120

Figure S16. Get High-res Image Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 3.11e-12 (Fisher's exact test), Q value = 2.9e-09

Table S17. Gene #5: 'Amp Peak 5(4q12)' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S17. Get High-res Image Gene #5: 'Amp Peak 5(4q12)' versus Molecular Subtype #3: 'CN_CNMF'

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

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

Table S18. Gene #6: 'Amp Peak 6(5p15.33)' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S18. 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 = 0.00015

Table S19. 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 S19. 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 = 0.14

Table S20. 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 S20. 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 = 0.19

Table S21. 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 S21. 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 = 2.29e-15 (Fisher's exact test), Q value = 2.1e-12

Table S22. Gene #7: 'Amp Peak 7(5p13.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S22. 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 = 0.08

Table S23. 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 S23. 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 = 0.081

Table S24. 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 S24. 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 = 0.17

Table S25. 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 S25. Get High-res Image Gene #7: 'Amp Peak 7(5p13.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 0.000276 (Fisher's exact test), Q value = 0.18

Table S26. Gene #7: 'Amp Peak 7(5p13.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	174	73
AMP PEAK 7(5P13.1) CNV	78	124	43
AMP PEAK 7(5P13.1) WILD-TYPE	79	50	30

Figure S26. Get High-res Image Gene #7: 'Amp Peak 7(5p13.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

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

Table S27. Gene #8: 'Amp Peak 8(5q35.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
AMP PEAK 8(5Q35.1) CNV	37	18	23	18
AMP PEAK 8(5Q35.1) WILD-TYPE	49	90	87	82

Figure S27. 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 = 0.033

Table S28. 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 S28. 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 = 0.1

Table S29. 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 S29. Get High-res Image Gene #8: 'Amp Peak 8(5q35.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

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

Table S30. Gene #9: 'Amp Peak 9(6p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S30. 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 = 5.14e-09 (Fisher's exact test), Q value = 4.6e-06

Table S31. Gene #9: 'Amp Peak 9(6p21.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
AMP PEAK 9(6P21.1) CNV	30	63	41	16
AMP PEAK 9(6P21.1) WILD-TYPE	56	45	69	84

Figure S31. Get High-res Image Gene #9: 'Amp Peak 9(6p21.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

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

Table S32. Gene #10: 'Amp Peak 10(7p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S32. Get High-res Image Gene #10: 'Amp Peak 10(7p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 7.66e-09 (Chi-square test), Q value = 6.7e-06

Table S33. 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 S33. 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 = 6.8e-05

Table S34. 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 S34. 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 = 0.0062

Table S35. 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 S35. Get High-res Image Gene #10: 'Amp Peak 10(7p21.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

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

Table S36. Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S36. Get High-res Image Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 0.000263 (Fisher's exact test), Q value = 0.17

Table S37. 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 S37. 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 = 9.3e-06

Table S38. 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 S38. 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 = 1.3e-07

Table S39. 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 S39. 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 = 0.00021

Table S40. 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 S40. 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 = 0.047

Table S41. 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 S41. Get High-res Image Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 7.2e-05 (Fisher's exact test), Q value = 0.049

Table S42. Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	174	73
AMP PEAK 11(7P11.2) CNV	63	105	48
AMP PEAK 11(7P11.2) WILD-TYPE	94	69	25

Figure S42. Get High-res Image Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 0.000361 (Fisher's exact test), Q value = 0.23

Table S43. Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	46	205
AMP PEAK 11(7P11.2) CNV	63	31	122
AMP PEAK 11(7P11.2) WILD-TYPE	90	15	83

Figure S43. Get High-res Image Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

Table S44. Gene #12: 'Amp Peak 12(7q31.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S44. Get High-res Image Gene #12: 'Amp Peak 12(7q31.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 2.97e-06 (Chi-square test), Q value = 0.0023

Table S45. 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 S45. 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 = 1.2e-05

Table S46. 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 S46. Get High-res Image Gene #12: 'Amp Peak 12(7q31.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

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

Table S47. Gene #13: 'Amp Peak 13(8p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S47. 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 = 9.54e-05 (Fisher's exact test), Q value = 0.065

Table S48. Gene #13: 'Amp Peak 13(8p11.23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
AMP PEAK 13(8P11.23) CNV	16	47	25	19
AMP PEAK 13(8P11.23) WILD-TYPE	70	61	85	81

Figure S48. 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 = 0.0053

Table S49. 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 S49. Get High-res Image Gene #13: 'Amp Peak 13(8p11.23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

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

Table S50. Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S50. 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 = 0.00019 (Fisher's exact test), Q value = 0.12

Table S51. Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
AMP PEAK 14(8P11.21) CNV	19	55	37	29
AMP PEAK 14(8P11.21) WILD-TYPE	67	53	73	71

Figure S51. 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 = 0.011

Table S52. 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 S52. 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 = 0.00039

Table S53. 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 S53. 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 = 0.029

Table S54. 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 S54. 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 = 0.0047

Table S55. 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 S55. Get High-res Image Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 6.14e-05 (Fisher's exact test), Q value = 0.042

Table S56. Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	46	205
AMP PEAK 14(8P11.21) CNV	35	14	92
AMP PEAK 14(8P11.21) WILD-TYPE	118	32	113

Figure S56. Get High-res Image Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

Table S57. Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S57. 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 = 2.46e-08 (Fisher's exact test), Q value = 2.1e-05

Table S58. Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
AMP PEAK 15(8Q11.1) CNV	24	70	58	31
AMP PEAK 15(8Q11.1) WILD-TYPE	62	38	52	69

Figure S58. 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 = 0.004

Table S59. 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 S59. 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 = 0.016

Table S60. 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 S60. 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 = 0.00016

Table S61. 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 S61. 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 = 7e-04

Table S62. 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 S62. Get High-res Image Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 1.44e-06 (Fisher's exact test), Q value = 0.0011

Table S63. Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	174	73
AMP PEAK 15(8Q11.1) CNV	50	104	30
AMP PEAK 15(8Q11.1) WILD-TYPE	107	70	43

Figure S63. Get High-res Image Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 1.38e-05 (Fisher's exact test), Q value = 0.01

Table S64. Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	46	205
AMP PEAK 15(8Q11.1) CNV	47	24	113
AMP PEAK 15(8Q11.1) WILD-TYPE	106	22	92

Figure S64. Get High-res Image Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

Table S65. Gene #16: 'Amp Peak 16(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S65. 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 = 7.97e-09 (Fisher's exact test), Q value = 7e-06

Table S66. Gene #16: 'Amp Peak 16(8q24.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
AMP PEAK 16(8Q24.21) CNV	37	86	80	49
AMP PEAK 16(8Q24.21) WILD-TYPE	49	22	30	51

Figure S66. 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 = 0.046

Table S67. 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 S67. 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 = 0.0025

Table S68. 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 S68. 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 = 0.00067

Table S69. 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 S69. 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 = 0.0092

Table S70. 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 S70. Get High-res Image Gene #16: 'Amp Peak 16(8q24.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 0.000109 (Fisher's exact test), Q value = 0.073

Table S71. Gene #16: 'Amp Peak 16(8q24.21)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	46	205
AMP PEAK 16(8Q24.21) CNV	76	30	147
AMP PEAK 16(8Q24.21) WILD-TYPE	77	16	58

Figure S71. Get High-res Image Gene #16: 'Amp Peak 16(8q24.21)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

Table S72. Gene #17: 'Amp Peak 17(10p15.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S72. 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 = 4.45e-07 (Fisher's exact test), Q value = 0.00036

Table S73. Gene #17: 'Amp Peak 17(10p15.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
AMP PEAK 17(10P15.1) CNV	7	43	36	19
AMP PEAK 17(10P15.1) WILD-TYPE	79	65	74	81

Figure S73. 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 = 0.047

Table S74. 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 S74. 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 = 1.8e-05

Table S75. 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 S75. 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 = 0.15

Table S76. 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 S76. 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 = 0.042

Table S77. 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 S77. Get High-res Image Gene #17: 'Amp Peak 17(10p15.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

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

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

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

Figure S78. 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 = 4.67e-06 (Fisher's exact test), Q value = 0.0035

Table S79. Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
AMP PEAK 18(11Q13.3) CNV	14	49	47	24
AMP PEAK 18(11Q13.3) WILD-TYPE	72	59	63	76

Figure S79. 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 = 2.6e-05

Table S80. 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 S80. 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 = 0.00075

Table S81. 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 S81. 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 = 1.9e-07

Table S82. 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 S82. 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 = 0.00017

Table S83. 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 S83. Get High-res Image Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 2.09e-07 (Fisher's exact test), Q value = 0.00017

Table S84. Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	174	73
AMP PEAK 18(11Q13.3) CNV	28	80	25
AMP PEAK 18(11Q13.3) WILD-TYPE	129	94	48

Figure S84. Get High-res Image Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 0.000122 (Fisher's exact test), Q value = 0.081

Table S85. Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	46	205
AMP PEAK 18(11Q13.3) CNV	32	15	86
AMP PEAK 18(11Q13.3) WILD-TYPE	121	31	119

Figure S85. Get High-res Image Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 6.39e-07 (Fisher's exact test), Q value = 0.00051

Table S86. Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S86. 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 = 3.23e-07 (Fisher's exact test), Q value = 0.00026

Table S87. Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
AMP PEAK 19(12P12.1) CNV	9	50	39	38
AMP PEAK 19(12P12.1) WILD-TYPE	77	58	71	62

Figure S87. 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 = 0.01

Table S88. 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 S88. 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 = 0.00023

Table S89. 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 S89. 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 = 0.0045

Table S90. 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 S90. 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 = 0.0075

Table S91. 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 S91. Get High-res Image Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 2.46e-05 (Fisher's exact test), Q value = 0.018

Table S92. Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	174	73
AMP PEAK 19(12P12.1) CNV	34	79	23
AMP PEAK 19(12P12.1) WILD-TYPE	123	95	50

Figure S92. Get High-res Image Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 0.000126 (Fisher's exact test), Q value = 0.083

Table S93. Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	46	205
AMP PEAK 19(12P12.1) CNV	35	12	89
AMP PEAK 19(12P12.1) WILD-TYPE	118	34	116

Figure S93. Get High-res Image Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 5.25e-09 (Fisher's exact test), Q value = 4.7e-06

Table S94. Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S94. 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 = 7.15e-08 (Fisher's exact test), Q value = 6.1e-05

Table S95. Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
AMP PEAK 20(12Q14.1) CNV	10	54	28	32
AMP PEAK 20(12Q14.1) WILD-TYPE	76	54	82	68

Figure S95. 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 = 0.00024

Table S96. 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 S96. 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 = 3.5e-07

Table S97. 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 S97. 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 = 5.5e-06

Table S98. 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 S98. 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 = 3.6e-06

Table S99. 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 S99. Get High-res Image Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 2.58e-06 (Fisher's exact test), Q value = 0.002

Table S100. Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	174	73
AMP PEAK 20(12Q14.1) CNV	27	74	23
AMP PEAK 20(12Q14.1) WILD-TYPE	130	100	50

Figure S100. Get High-res Image Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 4.94e-09 (Fisher's exact test), Q value = 4.4e-06

Table S101. Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	46	205
AMP PEAK 20(12Q14.1) CNV	22	12	90
AMP PEAK 20(12Q14.1) WILD-TYPE	131	34	115

Figure S101. Get High-res Image Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

Table S102. Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S102. 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 = 9.85e-09 (Fisher's exact test), Q value = 8.6e-06

Table S103. Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
AMP PEAK 21(12Q15) CNV	10	57	30	31
AMP PEAK 21(12Q15) WILD-TYPE	76	51	80	69

Figure S103. 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 = 6.1e-05

Table S104. 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 S104. 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 = 3.9e-06

Table S105. 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 S105. 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 = 1.9e-06

Table S106. 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 S106. 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 = 9.3e-05

Table S107. 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 S107. Get High-res Image Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 4.96e-07 (Fisher's exact test), Q value = 4e-04

Table S108. Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	174	73
AMP PEAK 21(12Q15) CNV	27	77	24
AMP PEAK 21(12Q15) WILD-TYPE	130	97	49

Figure S108. Get High-res Image Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 7.07e-07 (Fisher's exact test), Q value = 0.00056

Table S109. Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	46	205
AMP PEAK 21(12Q15) CNV	26	14	88
AMP PEAK 21(12Q15) WILD-TYPE	127	32	117

Figure S109. Get High-res Image Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 22(13q33.3)' versus 'METHLYATION_CNMF'

P value = 5.61e-05 (Fisher's exact test), Q value = 0.039

Table S110. Gene #22: 'Amp Peak 22(13q33.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
AMP PEAK 22(13Q33.3) CNV	13	31	12	6
AMP PEAK 22(13Q33.3) WILD-TYPE	73	77	98	94

Figure S110. Get High-res Image Gene #22: 'Amp Peak 22(13q33.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

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

Table S111. Gene #23: 'Amp Peak 23(14q13.3)' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S111. 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 = 5.81e-06 (Fisher's exact test), Q value = 0.0044

Table S112. Gene #23: 'Amp Peak 23(14q13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
AMP PEAK 23(14Q13.3) CNV	29	68	53	31
AMP PEAK 23(14Q13.3) WILD-TYPE	57	40	57	69

Figure S112. 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 = 1.2e-06

Table S113. 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 S113. 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 = 0.027

Table S114. 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 S114. 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 = 7.3e-05

Table S115. 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 S115. 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 = 2.3e-06

Table S116. 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 S116. Get High-res Image Gene #23: 'Amp Peak 23(14q13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 0.000117 (Fisher's exact test), Q value = 0.078

Table S117. Gene #23: 'Amp Peak 23(14q13.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	46	205
AMP PEAK 23(14Q13.3) CNV	48	22	110
AMP PEAK 23(14Q13.3) WILD-TYPE	105	24	95

Figure S117. Get High-res Image Gene #23: 'Amp Peak 23(14q13.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

Table S118. Gene #24: 'Amp Peak 24(16p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S118. Get High-res Image Gene #24: 'Amp Peak 24(16p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

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

Table S119. Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S119. Get High-res Image Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 5.77e-09 (Fisher's exact test), Q value = 5.1e-06

Table S120. Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
AMP PEAK 25(17Q12) CNV	18	62	62	31
AMP PEAK 25(17Q12) WILD-TYPE	68	46	48	69

Figure S120. Get High-res Image Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

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

Table S121. Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	89	65	58
AMP PEAK 25(17Q12) CNV	3	52	33	20
AMP PEAK 25(17Q12) WILD-TYPE	20	37	32	38

Figure S121. Get High-res Image Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

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

P value = 9.56e-11 (Chi-square test), Q value = 8.7e-08

Table S122. Gene #25: 'Amp Peak 25(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 25(17Q12) CNV	53	30	30	6	9	23	10	11	1
AMP PEAK 25(17Q12) WILD-TYPE	22	25	26	36	20	25	29	13	22

Figure S122. Get High-res Image Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 2.02e-06 (Fisher's exact test), Q value = 0.0016

Table S123. Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
AMP PEAK 25(17Q12) CNV	48	65	60
AMP PEAK 25(17Q12) WILD-TYPE	110	40	68

Figure S123. Get High-res Image Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 7.33e-07 (Fisher's exact test), Q value = 0.00058

Table S124. Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
AMP PEAK 25(17Q12) CNV	50	112	44
AMP PEAK 25(17Q12) WILD-TYPE	121	86	54

Figure S124. Get High-res Image Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

P value = 1.1e-06 (Fisher's exact test), Q value = 0.00086

Table S125. Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
AMP PEAK 25(17Q12) CNV	49	135	22
AMP PEAK 25(17Q12) WILD-TYPE	115	109	37

Figure S125. Get High-res Image Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 0.000227 (Fisher's exact test), Q value = 0.15

Table S126. Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	174	73
AMP PEAK 25(17Q12) CNV	49	93	31
AMP PEAK 25(17Q12) WILD-TYPE	108	81	42

Figure S126. Get High-res Image Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

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

Table S127. Gene #26: 'Amp Peak 26(17q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S127. Get High-res Image Gene #26: 'Amp Peak 26(17q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 2.7e-11 (Fisher's exact test), Q value = 2.5e-08

Table S128. Gene #26: 'Amp Peak 26(17q23.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
AMP PEAK 26(17Q23.1) CNV	19	62	75	36
AMP PEAK 26(17Q23.1) WILD-TYPE	67	46	35	64

Figure S128. Get High-res Image Gene #26: 'Amp Peak 26(17q23.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 4.12e-07 (Fisher's exact test), Q value = 0.00033

Table S129. Gene #26: 'Amp Peak 26(17q23.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	89	65	58
AMP PEAK 26(17Q23.1) CNV	3	57	38	17
AMP PEAK 26(17Q23.1) WILD-TYPE	20	32	27	41

Figure S129. Get High-res Image Gene #26: 'Amp Peak 26(17q23.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

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

P value = 2.7e-13 (Chi-square test), Q value = 2.5e-10

Table S130. Gene #26: 'Amp Peak 26(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 26(17Q23.1) CNV	61	32	32	8	6	23	15	10	2
AMP PEAK 26(17Q23.1) WILD-TYPE	14	23	24	34	23	25	24	14	21

Figure S130. Get High-res Image Gene #26: 'Amp Peak 26(17q23.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 5.99e-10 (Fisher's exact test), Q value = 5.4e-07

Table S131. Gene #26: 'Amp Peak 26(17q23.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
AMP PEAK 26(17Q23.1) CNV	49	75	65
AMP PEAK 26(17Q23.1) WILD-TYPE	109	30	63

Figure S131. Get High-res Image Gene #26: 'Amp Peak 26(17q23.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 1.54e-06 (Fisher's exact test), Q value = 0.0012

Table S132. Gene #26: 'Amp Peak 26(17q23.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
AMP PEAK 26(17Q23.1) CNV	58	120	50
AMP PEAK 26(17Q23.1) WILD-TYPE	113	78	48

Figure S132. Get High-res Image Gene #26: 'Amp Peak 26(17q23.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

P value = 5.68e-06 (Fisher's exact test), Q value = 0.0043

Table S133. Gene #26: 'Amp Peak 26(17q23.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
AMP PEAK 26(17Q23.1) CNV	58	145	25
AMP PEAK 26(17Q23.1) WILD-TYPE	106	99	34

Figure S133. Get High-res Image Gene #26: 'Amp Peak 26(17q23.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

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

Table S134. Gene #27: 'Amp Peak 27(18q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S134. Get High-res Image Gene #27: 'Amp Peak 27(18q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 3.44e-08 (Fisher's exact test), Q value = 3e-05

Table S135. Gene #27: 'Amp Peak 27(18q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
AMP PEAK 27(18Q11.2) CNV	6	43	23	12
AMP PEAK 27(18Q11.2) WILD-TYPE	80	65	87	88

Figure S135. Get High-res Image Gene #27: 'Amp Peak 27(18q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 9.61e-05 (Fisher's exact test), Q value = 0.065

Table S136. Gene #27: 'Amp Peak 27(18q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
AMP PEAK 27(18Q11.2) CNV	19	21	42
AMP PEAK 27(18Q11.2) WILD-TYPE	139	84	86

Figure S136. Get High-res Image Gene #27: 'Amp Peak 27(18q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 1.06e-05 (Fisher's exact test), Q value = 0.0078

Table S137. Gene #27: 'Amp Peak 27(18q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
AMP PEAK 27(18Q11.2) CNV	16	57	20
AMP PEAK 27(18Q11.2) WILD-TYPE	155	141	78

Figure S137. Get High-res Image Gene #27: 'Amp Peak 27(18q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

P value = 6.73e-07 (Fisher's exact test), Q value = 0.00054

Table S138. Gene #27: 'Amp Peak 27(18q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
AMP PEAK 27(18Q11.2) CNV	18	71	4
AMP PEAK 27(18Q11.2) WILD-TYPE	146	173	55

Figure S138. Get High-res Image Gene #27: 'Amp Peak 27(18q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 2.66e-06 (Fisher's exact test), Q value = 0.002

Table S139. Gene #27: 'Amp Peak 27(18q11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	46	205
AMP PEAK 27(18Q11.2) CNV	17	4	63
AMP PEAK 27(18Q11.2) WILD-TYPE	136	42	142

Figure S139. Get High-res Image Gene #27: 'Amp Peak 27(18q11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 1.34e-05 (Fisher's exact test), Q value = 0.0098

Table S140. Gene #28: 'Amp Peak 28(19q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
AMP PEAK 28(19Q12) CNV	16	50	21	25
AMP PEAK 28(19Q12) WILD-TYPE	70	58	89	75

Figure S140. Get High-res Image Gene #28: 'Amp Peak 28(19q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 4.22e-08 (Fisher's exact test), Q value = 3.6e-05

Table S141. Gene #28: 'Amp Peak 28(19q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
AMP PEAK 28(19Q12) CNV	19	32	53
AMP PEAK 28(19Q12) WILD-TYPE	139	73	75

Figure S141. Get High-res Image Gene #28: 'Amp Peak 28(19q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 1.27e-06 (Fisher's exact test), Q value = 0.00099

Table S142. Gene #28: 'Amp Peak 28(19q12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
AMP PEAK 28(19Q12) CNV	25	76	25
AMP PEAK 28(19Q12) WILD-TYPE	146	122	73

Figure S142. Get High-res Image Gene #28: 'Amp Peak 28(19q12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

P value = 1.46e-06 (Fisher's exact test), Q value = 0.0011

Table S143. Gene #28: 'Amp Peak 28(19q12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
AMP PEAK 28(19Q12) CNV	29	90	7
AMP PEAK 28(19Q12) WILD-TYPE	135	154	52

Figure S143. Get High-res Image Gene #28: 'Amp Peak 28(19q12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 2.2e-05 (Fisher's exact test), Q value = 0.016

Table S144. Gene #28: 'Amp Peak 28(19q12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	174	73
AMP PEAK 28(19Q12) CNV	25	67	20
AMP PEAK 28(19Q12) WILD-TYPE	132	107	53

Figure S144. Get High-res Image Gene #28: 'Amp Peak 28(19q12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 1.04e-05 (Fisher's exact test), Q value = 0.0077

Table S145. Gene #28: 'Amp Peak 28(19q12)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	46	205
AMP PEAK 28(19Q12) CNV	28	6	78
AMP PEAK 28(19Q12) WILD-TYPE	125	40	127

Figure S145. Get High-res Image Gene #28: 'Amp Peak 28(19q12)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

Table S146. Gene #29: 'Amp Peak 29(20p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S146. Get High-res Image Gene #29: 'Amp Peak 29(20p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 3.59e-05 (Fisher's exact test), Q value = 0.025

Table S147. Gene #29: 'Amp Peak 29(20p11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
AMP PEAK 29(20P11.21) CNV	22	61	36	33
AMP PEAK 29(20P11.21) WILD-TYPE	64	47	74	67

Figure S147. Get High-res Image Gene #29: 'Amp Peak 29(20p11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 0.000221 (Chi-square test), Q value = 0.14

Table S148. Gene #29: 'Amp Peak 29(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 29(20P11.21) CNV	23	24	33	15	9	26	8	9	3
AMP PEAK 29(20P11.21) WILD-TYPE	52	31	23	27	20	22	31	15	20

Figure S148. Get High-res Image Gene #29: 'Amp Peak 29(20p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 0.000145 (Fisher's exact test), Q value = 0.095

Table S149. Gene #29: 'Amp Peak 29(20p11.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
AMP PEAK 29(20P11.21) CNV	44	91	42
AMP PEAK 29(20P11.21) WILD-TYPE	127	107	56

Figure S149. Get High-res Image Gene #29: 'Amp Peak 29(20p11.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

P value = 7.51e-05 (Fisher's exact test), Q value = 0.051

Table S150. Gene #29: 'Amp Peak 29(20p11.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
AMP PEAK 29(20P11.21) CNV	42	114	21
AMP PEAK 29(20P11.21) WILD-TYPE	122	130	38

Figure S150. Get High-res Image Gene #29: 'Amp Peak 29(20p11.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 0.000108 (Fisher's exact test), Q value = 0.073

Table S151. Gene #29: 'Amp Peak 29(20p11.21)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	174	73
AMP PEAK 29(20P11.21) CNV	41	85	27
AMP PEAK 29(20P11.21) WILD-TYPE	116	89	46

Figure S151. Get High-res Image Gene #29: 'Amp Peak 29(20p11.21)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 5.43e-09 (Fisher's exact test), Q value = 4.8e-06

Table S152. Gene #30: 'Amp Peak 30(20q13.33)' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S152. Get High-res Image Gene #30: 'Amp Peak 30(20q13.33)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 2.84e-05 (Fisher's exact test), Q value = 0.02

Table S153. Gene #30: 'Amp Peak 30(20q13.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
AMP PEAK 30(20Q13.33) CNV	33	71	51	35
AMP PEAK 30(20Q13.33) WILD-TYPE	53	37	59	65

Figure S153. Get High-res Image Gene #30: 'Amp Peak 30(20q13.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 1.37e-05 (Chi-square test), Q value = 0.01

Table S154. Gene #30: 'Amp Peak 30(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 30(20Q13.33) CNV	37	31	37	15	9	33	14	11	3
AMP PEAK 30(20Q13.33) WILD-TYPE	38	24	19	27	20	15	25	13	20

Figure S154. Get High-res Image Gene #30: 'Amp Peak 30(20q13.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 2.53e-06 (Fisher's exact test), Q value = 0.002

Table S155. Gene #30: 'Amp Peak 30(20q13.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
AMP PEAK 30(20Q13.33) CNV	58	119	44
AMP PEAK 30(20Q13.33) WILD-TYPE	113	79	54

Figure S155. Get High-res Image Gene #30: 'Amp Peak 30(20q13.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

P value = 4.24e-07 (Fisher's exact test), Q value = 0.00034

Table S156. Gene #30: 'Amp Peak 30(20q13.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
AMP PEAK 30(20Q13.33) CNV	51	142	28
AMP PEAK 30(20Q13.33) WILD-TYPE	113	102	31

Figure S156. Get High-res Image Gene #30: 'Amp Peak 30(20q13.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 1.45e-05 (Fisher's exact test), Q value = 0.011

Table S157. Gene #30: 'Amp Peak 30(20q13.33)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	174	73
AMP PEAK 30(20Q13.33) CNV	55	105	31
AMP PEAK 30(20Q13.33) WILD-TYPE	102	69	42

Figure S157. Get High-res Image Gene #30: 'Amp Peak 30(20q13.33)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 0.000124 (Fisher's exact test), Q value = 0.082

Table S158. Gene #31: 'Amp Peak 31(22q11.22)' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S158. Get High-res Image Gene #31: 'Amp Peak 31(22q11.22)' versus Molecular Subtype #3: 'CN_CNMF'

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

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

Table S159. Gene #32: 'Amp Peak 32(Xq28)' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S159. Get High-res Image Gene #32: 'Amp Peak 32(Xq28)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 0.000356 (Fisher's exact test), Q value = 0.22

Table S160. Gene #32: 'Amp Peak 32(Xq28)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
AMP PEAK 32(XQ28) CNV	16	42	45	22
AMP PEAK 32(XQ28) WILD-TYPE	70	66	65	78

Figure S160. Get High-res Image Gene #32: 'Amp Peak 32(Xq28)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 9.71e-05 (Fisher's exact test), Q value = 0.066

Table S161. Gene #32: 'Amp Peak 32(Xq28)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
AMP PEAK 32(XQ28) CNV	35	50	42
AMP PEAK 32(XQ28) WILD-TYPE	123	55	86

Figure S161. Get High-res Image Gene #32: 'Amp Peak 32(Xq28)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

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

Table S162. Gene #33: 'Del Peak 1(1p36.13)' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S162. Get High-res Image Gene #33: 'Del Peak 1(1p36.13)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 8.06e-06 (Chi-square test), Q value = 0.006

Table S163. Gene #33: '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 S163. Get High-res Image Gene #33: 'Del Peak 1(1p36.13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 8.99e-06 (Fisher's exact test), Q value = 0.0067

Table S164. Gene #33: '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 S164. Get High-res Image Gene #33: 'Del Peak 1(1p36.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

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

Table S165. Gene #34: 'Del Peak 2(1p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S165. Get High-res Image Gene #34: 'Del Peak 2(1p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 0.00019 (Fisher's exact test), Q value = 0.12

Table S166. Gene #34: 'Del Peak 2(1p13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
DEL PEAK 2(1P13.2) CNV	25	43	30	13
DEL PEAK 2(1P13.2) WILD-TYPE	61	65	80	87

Figure S166. Get High-res Image Gene #34: 'Del Peak 2(1p13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

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

Table S167. Gene #36: 'Del Peak 4(2q37.3)' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S167. Get High-res Image Gene #36: 'Del Peak 4(2q37.3)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 0.000153 (Fisher's exact test), Q value = 0.1

Table S168. Gene #36: 'Del Peak 4(2q37.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
DEL PEAK 4(2Q37.3) CNV	10	48	5
DEL PEAK 4(2Q37.3) WILD-TYPE	154	196	54

Figure S168. Get High-res Image Gene #36: 'Del Peak 4(2q37.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

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

Table S169. Gene #37: 'Del Peak 5(3p21.31)' versus Molecular Subtype #3: 'CN_CNMF'

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

Figure S169. Get High-res Image Gene #37: 'Del Peak 5(3p21.31)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 1.59e-07 (Fisher's exact test), Q value = 0.00013

Table S170. Gene #37: 'Del Peak 5(3p21.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
DEL PEAK 5(3P21.31) CNV	32	78	47	39
DEL PEAK 5(3P21.31) WILD-TYPE	54	30	63	61

Figure S170. Get High-res Image Gene #37: 'Del Peak 5(3p21.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 3.35e-05 (Chi-square test), Q value = 0.024

Table S171. Gene #37: 'Del Peak 5(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 5(3P21.31) CNV	32	26	42	15	12	29	19	12	3
DEL PEAK 5(3P21.31) WILD-TYPE	43	29	14	27	17	19	20	12	20

Figure S171. Get High-res Image Gene #37: 'Del Peak 5(3p21.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 6.23e-09 (Fisher's exact test), Q value = 5.5e-06

Table S172. Gene #37: 'Del Peak 5(3p21.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 5(3P21.31) CNV	53	48	89
DEL PEAK 5(3P21.31) WILD-TYPE	105	57	39

Figure S172. Get High-res Image Gene #37: 'Del Peak 5(3p21.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 1.18e-05 (Fisher's exact test), Q value = 0.0086

Table S173. Gene #37: 'Del Peak 5(3p21.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
DEL PEAK 5(3P21.31) CNV	57	110	56
DEL PEAK 5(3P21.31) WILD-TYPE	114	88	42

Figure S173. Get High-res Image Gene #37: 'Del Peak 5(3p21.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 7(3q29)' versus 'METHLYATION_CNMF'

P value = 3.43e-05 (Fisher's exact test), Q value = 0.024

Table S174. Gene #39: 'Del Peak 7(3q29)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
DEL PEAK 7(3Q29) CNV	34	39	33	12
DEL PEAK 7(3Q29) WILD-TYPE	52	69	77	88

Figure S174. Get High-res Image Gene #39: 'Del Peak 7(3q29)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 7(3q29)' versus 'MRNASEQ_CNMF'

P value = 3.27e-08 (Chi-square test), Q value = 2.8e-05

Table S175. Gene #39: 'Del Peak 7(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 7(3Q29) CNV	18	17	9	18	8	30	2	4	4
DEL PEAK 7(3Q29) WILD-TYPE	57	38	47	24	21	18	37	20	19

Figure S175. Get High-res Image Gene #39: 'Del Peak 7(3q29)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 8(4p16.3)' versus 'CN_CNMF'

P value = 2.44e-05 (Fisher's exact test), Q value = 0.017

Table S176. Gene #40: 'Del Peak 8(4p16.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 8(4P16.3) CNV	49	35	38
DEL PEAK 8(4P16.3) WILD-TYPE	138	179	54

Figure S176. Get High-res Image Gene #40: 'Del Peak 8(4p16.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 8(4p16.3)' versus 'METHLYATION_CNMF'

P value = 1.58e-06 (Fisher's exact test), Q value = 0.0012

Table S177. Gene #40: 'Del Peak 8(4p16.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
DEL PEAK 8(4P16.3) CNV	7	44	23	26
DEL PEAK 8(4P16.3) WILD-TYPE	79	64	87	74

Figure S177. Get High-res Image Gene #40: 'Del Peak 8(4p16.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 8(4p16.3)' versus 'MRNASEQ_CNMF'

P value = 8.4e-07 (Chi-square test), Q value = 0.00067

Table S178. Gene #40: 'Del Peak 8(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 8(4P16.3) CNV	11	12	26	3	8	23	7	7	2
DEL PEAK 8(4P16.3) WILD-TYPE	64	43	30	39	21	25	32	17	21

Figure S178. Get High-res Image Gene #40: 'Del Peak 8(4p16.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 8(4p16.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.36e-11 (Fisher's exact test), Q value = 5.8e-08

Table S179. Gene #40: 'Del Peak 8(4p16.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 8(4P16.3) CNV	16	25	58
DEL PEAK 8(4P16.3) WILD-TYPE	142	80	70

Figure S179. Get High-res Image Gene #40: 'Del Peak 8(4p16.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 8(4p16.3)' versus 'MIRSEQ_CNMF'

P value = 2.82e-07 (Fisher's exact test), Q value = 0.00023

Table S180. Gene #40: 'Del Peak 8(4p16.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
DEL PEAK 8(4P16.3) CNV	20	71	24
DEL PEAK 8(4P16.3) WILD-TYPE	151	127	74

Figure S180. Get High-res Image Gene #40: 'Del Peak 8(4p16.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 8(4p16.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.11e-07 (Fisher's exact test), Q value = 9.3e-05

Table S181. Gene #40: 'Del Peak 8(4p16.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
DEL PEAK 8(4P16.3) CNV	20	86	9
DEL PEAK 8(4P16.3) WILD-TYPE	144	158	50

Figure S181. Get High-res Image Gene #40: 'Del Peak 8(4p16.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 8(4p16.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.48e-05 (Fisher's exact test), Q value = 0.031

Table S182. Gene #40: 'Del Peak 8(4p16.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	46	205
DEL PEAK 8(4P16.3) CNV	24	6	70
DEL PEAK 8(4P16.3) WILD-TYPE	129	40	135

Figure S182. Get High-res Image Gene #40: 'Del Peak 8(4p16.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 9(4q22.1)' versus 'MRNA_CNMF'

P value = 0.000214 (Fisher's exact test), Q value = 0.14

Table S183. Gene #41: 'Del Peak 9(4q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S183. Get High-res Image Gene #41: 'Del Peak 9(4q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 9(4q22.1)' versus 'MRNA_CHIERARCHICAL'

P value = 9.89e-05 (Fisher's exact test), Q value = 0.067

Table S184. Gene #41: 'Del Peak 9(4q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S184. Get High-res Image Gene #41: 'Del Peak 9(4q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 9(4q22.1)' versus 'CN_CNMF'

P value = 1.2e-05 (Fisher's exact test), Q value = 0.0088

Table S185. Gene #41: 'Del Peak 9(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 9(4Q22.1) CNV	64	44	43
DEL PEAK 9(4Q22.1) WILD-TYPE	123	170	49

Figure S185. Get High-res Image Gene #41: 'Del Peak 9(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 9(4q22.1)' versus 'METHLYATION_CNMF'

P value = 6.24e-09 (Fisher's exact test), Q value = 5.5e-06

Table S186. Gene #41: 'Del Peak 9(4q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
DEL PEAK 9(4Q22.1) CNV	8	54	28	29
DEL PEAK 9(4Q22.1) WILD-TYPE	78	54	82	71

Figure S186. Get High-res Image Gene #41: 'Del Peak 9(4q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 9(4q22.1)' versus 'MRNASEQ_CNMF'

P value = 3.81e-06 (Chi-square test), Q value = 0.0029

Table S187. Gene #41: 'Del Peak 9(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 9(4Q22.1) CNV	12	17	27	6	9	25	11	8	1
DEL PEAK 9(4Q22.1) WILD-TYPE	63	38	29	36	20	23	28	16	22

Figure S187. Get High-res Image Gene #41: 'Del Peak 9(4q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 9(4q22.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.97e-14 (Fisher's exact test), Q value = 9.2e-11

Table S188. Gene #41: 'Del Peak 9(4q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 9(4Q22.1) CNV	21	25	70
DEL PEAK 9(4Q22.1) WILD-TYPE	137	80	58

Figure S188. Get High-res Image Gene #41: 'Del Peak 9(4q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 9(4q22.1)' versus 'MIRSEQ_CNMF'

P value = 1.66e-08 (Fisher's exact test), Q value = 1.4e-05

Table S189. Gene #41: 'Del Peak 9(4q22.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
DEL PEAK 9(4Q22.1) CNV	25	84	32
DEL PEAK 9(4Q22.1) WILD-TYPE	146	114	66

Figure S189. Get High-res Image Gene #41: 'Del Peak 9(4q22.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 9(4q22.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.54e-06 (Fisher's exact test), Q value = 0.0012

Table S190. Gene #41: 'Del Peak 9(4q22.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
DEL PEAK 9(4Q22.1) CNV	30	99	12
DEL PEAK 9(4Q22.1) WILD-TYPE	134	145	47

Figure S190. Get High-res Image Gene #41: 'Del Peak 9(4q22.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 9(4q22.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S191. Gene #41: 'Del Peak 9(4q22.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	46	205
DEL PEAK 9(4Q22.1) CNV	30	9	80
DEL PEAK 9(4Q22.1) WILD-TYPE	123	37	125

Figure S191. Get High-res Image Gene #41: 'Del Peak 9(4q22.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 10(4q35.1)' versus 'CN_CNMF'

P value = 1.72e-08 (Fisher's exact test), Q value = 1.5e-05

Table S192. Gene #42: 'Del Peak 10(4q35.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 10(4Q35.1) CNV	76	51	54
DEL PEAK 10(4Q35.1) WILD-TYPE	111	163	38

Figure S192. Get High-res Image Gene #42: 'Del Peak 10(4q35.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 10(4q35.1)' versus 'METHLYATION_CNMF'

P value = 1.23e-14 (Fisher's exact test), Q value = 1.1e-11

Table S193. Gene #42: 'Del Peak 10(4q35.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
DEL PEAK 10(4Q35.1) CNV	7	68	38	35
DEL PEAK 10(4Q35.1) WILD-TYPE	79	40	72	65

Figure S193. Get High-res Image Gene #42: 'Del Peak 10(4q35.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 10(4q35.1)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000196 (Fisher's exact test), Q value = 0.13

Table S194. Gene #42: 'Del Peak 10(4q35.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	89	65	58
DEL PEAK 10(4Q35.1) CNV	11	32	39	13
DEL PEAK 10(4Q35.1) WILD-TYPE	12	57	26	45

Figure S194. Get High-res Image Gene #42: 'Del Peak 10(4q35.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 10(4q35.1)' versus 'MRNASEQ_CNMF'

P value = 2.47e-09 (Chi-square test), Q value = 2.2e-06

Table S195. Gene #42: 'Del Peak 10(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 10(4Q35.1) CNV	18	14	35	7	10	31	13	10	2
DEL PEAK 10(4Q35.1) WILD-TYPE	57	41	21	35	19	17	26	14	21

Figure S195. Get High-res Image Gene #42: 'Del Peak 10(4q35.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 10(4q35.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.36e-18 (Fisher's exact test), Q value = 6.9e-15

Table S196. Gene #42: 'Del Peak 10(4q35.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 10(4Q35.1) CNV	28	27	85
DEL PEAK 10(4Q35.1) WILD-TYPE	130	78	43

Figure S196. Get High-res Image Gene #42: 'Del Peak 10(4q35.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 10(4q35.1)' versus 'MIRSEQ_CNMF'

P value = 1.57e-10 (Fisher's exact test), Q value = 1.4e-07

Table S197. Gene #42: 'Del Peak 10(4q35.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
DEL PEAK 10(4Q35.1) CNV	34	105	32
DEL PEAK 10(4Q35.1) WILD-TYPE	137	93	66

Figure S197. Get High-res Image Gene #42: 'Del Peak 10(4q35.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 10(4q35.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-10 (Fisher's exact test), Q value = 9.1e-08

Table S198. Gene #42: 'Del Peak 10(4q35.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

Figure S198. Get High-res Image Gene #42: 'Del Peak 10(4q35.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 10(4q35.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.01e-06 (Fisher's exact test), Q value = 0.0023

Table S199. Gene #42: 'Del Peak 10(4q35.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	174	73
DEL PEAK 10(4Q35.1) CNV	40	88	20
DEL PEAK 10(4Q35.1) WILD-TYPE	117	86	53

Figure S199. Get High-res Image Gene #42: 'Del Peak 10(4q35.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 10(4q35.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.42e-10 (Fisher's exact test), Q value = 1.3e-07

Table S200. Gene #42: 'Del Peak 10(4q35.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	46	205
DEL PEAK 10(4Q35.1) CNV	34	7	107
DEL PEAK 10(4Q35.1) WILD-TYPE	119	39	98

Figure S200. Get High-res Image Gene #42: 'Del Peak 10(4q35.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 11(5q11.2)' versus 'CN_CNMF'

P value = 2.13e-13 (Fisher's exact test), Q value = 2e-10

Table S201. Gene #43: 'Del Peak 11(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 11(5Q11.2) CNV	93	36	44
DEL PEAK 11(5Q11.2) WILD-TYPE	94	178	48

Figure S201. Get High-res Image Gene #43: 'Del Peak 11(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 11(5q11.2)' versus 'METHLYATION_CNMF'

P value = 1.46e-07 (Fisher's exact test), Q value = 0.00012

Table S202. Gene #43: 'Del Peak 11(5q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
DEL PEAK 11(5Q11.2) CNV	13	58	39	28
DEL PEAK 11(5Q11.2) WILD-TYPE	73	50	71	72

Figure S202. Get High-res Image Gene #43: 'Del Peak 11(5q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 11(5q11.2)' versus 'MRNASEQ_CNMF'

P value = 1.35e-06 (Chi-square test), Q value = 0.0011

Table S203. Gene #43: 'Del Peak 11(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 11(5Q11.2) CNV	32	18	36	6	11	20	8	8	2
DEL PEAK 11(5Q11.2) WILD-TYPE	43	37	20	36	18	28	31	16	21

Figure S203. Get High-res Image Gene #43: 'Del Peak 11(5q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 11(5q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.57e-09 (Fisher's exact test), Q value = 2.3e-06

Table S204. Gene #43: 'Del Peak 11(5q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 11(5Q11.2) CNV	30	42	69
DEL PEAK 11(5Q11.2) WILD-TYPE	128	63	59

Figure S204. Get High-res Image Gene #43: 'Del Peak 11(5q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 11(5q11.2)' versus 'MIRSEQ_CNMF'

P value = 4.53e-08 (Fisher's exact test), Q value = 3.9e-05

Table S205. Gene #43: 'Del Peak 11(5q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
DEL PEAK 11(5Q11.2) CNV	34	96	33
DEL PEAK 11(5Q11.2) WILD-TYPE	137	102	65

Figure S205. Get High-res Image Gene #43: 'Del Peak 11(5q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 11(5q11.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.11e-06 (Fisher's exact test), Q value = 0.0016

Table S206. Gene #43: 'Del Peak 11(5q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
DEL PEAK 11(5Q11.2) CNV	36	111	16
DEL PEAK 11(5Q11.2) WILD-TYPE	128	133	43

Figure S206. Get High-res Image Gene #43: 'Del Peak 11(5q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 11(5q11.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.67e-06 (Fisher's exact test), Q value = 0.0035

Table S207. Gene #43: 'Del Peak 11(5q11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	174	73
DEL PEAK 11(5Q11.2) CNV	33	81	23
DEL PEAK 11(5Q11.2) WILD-TYPE	124	93	50

Figure S207. Get High-res Image Gene #43: 'Del Peak 11(5q11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 12(5q31.1)' versus 'CN_CNMF'

P value = 1.03e-12 (Fisher's exact test), Q value = 9.5e-10

Table S208. Gene #44: 'Del Peak 12(5q31.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 12(5Q31.1) CNV	100	47	52
DEL PEAK 12(5Q31.1) WILD-TYPE	87	167	40

Figure S208. Get High-res Image Gene #44: 'Del Peak 12(5q31.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 12(5q31.1)' versus 'METHLYATION_CNMF'

P value = 3.03e-07 (Fisher's exact test), Q value = 0.00025

Table S209. Gene #44: 'Del Peak 12(5q31.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
DEL PEAK 12(5Q31.1) CNV	16	62	50	36
DEL PEAK 12(5Q31.1) WILD-TYPE	70	46	60	64

Figure S209. Get High-res Image Gene #44: 'Del Peak 12(5q31.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 12(5q31.1)' versus 'MRNASEQ_CNMF'

P value = 1.24e-07 (Chi-square test), Q value = 1e-04

Table S210. Gene #44: 'Del Peak 12(5q31.1)' 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 12(5Q31.1) CNV	41	15	40	9	11	24	11	9	4
DEL PEAK 12(5Q31.1) WILD-TYPE	34	40	16	33	18	24	28	15	19

Figure S210. Get High-res Image Gene #44: 'Del Peak 12(5q31.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 12(5q31.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.32e-09 (Fisher's exact test), Q value = 7.3e-06

Table S211. Gene #44: 'Del Peak 12(5q31.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 12(5Q31.1) CNV	39	49	76
DEL PEAK 12(5Q31.1) WILD-TYPE	119	56	52

Figure S211. Get High-res Image Gene #44: 'Del Peak 12(5q31.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 12(5q31.1)' versus 'MIRSEQ_CNMF'

P value = 1.44e-08 (Fisher's exact test), Q value = 1.3e-05

Table S212. Gene #44: 'Del Peak 12(5q31.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
DEL PEAK 12(5Q31.1) CNV	42	109	38
DEL PEAK 12(5Q31.1) WILD-TYPE	129	89	60

Figure S212. Get High-res Image Gene #44: 'Del Peak 12(5q31.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 12(5q31.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.1e-08 (Fisher's exact test), Q value = 6e-05

Table S213. Gene #44: 'Del Peak 12(5q31.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
DEL PEAK 12(5Q31.1) CNV	44	129	16
DEL PEAK 12(5Q31.1) WILD-TYPE	120	115	43

Figure S213. Get High-res Image Gene #44: 'Del Peak 12(5q31.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 12(5q31.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.47e-05 (Fisher's exact test), Q value = 0.038

Table S214. Gene #44: 'Del Peak 12(5q31.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	174	73
DEL PEAK 12(5Q31.1) CNV	45	91	27
DEL PEAK 12(5Q31.1) WILD-TYPE	112	83	46

Figure S214. Get High-res Image Gene #44: 'Del Peak 12(5q31.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 12(5q31.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.61e-05 (Fisher's exact test), Q value = 0.059

Table S215. Gene #44: 'Del Peak 12(5q31.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	46	205
DEL PEAK 12(5Q31.1) CNV	46	13	104
DEL PEAK 12(5Q31.1) WILD-TYPE	107	33	101

Figure S215. Get High-res Image Gene #44: 'Del Peak 12(5q31.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 14(6q22.31)' versus 'METHLYATION_CNMF'

P value = 4.04e-07 (Fisher's exact test), Q value = 0.00033

Table S216. Gene #46: 'Del Peak 14(6q22.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
DEL PEAK 14(6Q22.31) CNV	48	56	71	27
DEL PEAK 14(6Q22.31) WILD-TYPE	38	52	39	73

Figure S216. Get High-res Image Gene #46: 'Del Peak 14(6q22.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 15(6q26)' versus 'METHLYATION_CNMF'

P value = 6.31e-05 (Fisher's exact test), Q value = 0.044

Table S217. Gene #47: 'Del Peak 15(6q26)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
DEL PEAK 15(6Q26) CNV	46	59	66	30
DEL PEAK 15(6Q26) WILD-TYPE	40	49	44	70

Figure S217. Get High-res Image Gene #47: 'Del Peak 15(6q26)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 16(8p23.2)' versus 'CN_CNMF'

P value = 3.17e-23 (Fisher's exact test), Q value = 3e-20

Table S218. Gene #48: 'Del Peak 16(8p23.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 16(8P23.2) CNV	142	56	42
DEL PEAK 16(8P23.2) WILD-TYPE	45	158	50

Figure S218. Get High-res Image Gene #48: 'Del Peak 16(8p23.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 16(8p23.2)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000354 (Fisher's exact test), Q value = 0.22

Table S219. Gene #48: 'Del Peak 16(8p23.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	89	65	58
DEL PEAK 16(8P23.2) CNV	10	56	34	16
DEL PEAK 16(8P23.2) WILD-TYPE	13	33	31	42

Figure S219. Get High-res Image Gene #48: 'Del Peak 16(8p23.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 16(8p23.2)' versus 'MRNASEQ_CNMF'

P value = 8.22e-09 (Chi-square test), Q value = 7.2e-06

Table S220. Gene #48: 'Del Peak 16(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 16(8P23.2) CNV	55	33	35	8	7	20	17	10	6
DEL PEAK 16(8P23.2) WILD-TYPE	20	22	21	34	22	28	22	14	17

Figure S220. Get High-res Image Gene #48: 'Del Peak 16(8p23.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 16(8p23.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.29e-07 (Fisher's exact test), Q value = 0.00019

Table S221. Gene #48: 'Del Peak 16(8p23.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 16(8P23.2) CNV	57	74	60
DEL PEAK 16(8P23.2) WILD-TYPE	101	31	68

Figure S221. Get High-res Image Gene #48: 'Del Peak 16(8p23.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 16(8p23.2)' versus 'MIRSEQ_CNMF'

P value = 3.58e-06 (Fisher's exact test), Q value = 0.0027

Table S222. Gene #48: 'Del Peak 16(8p23.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
DEL PEAK 16(8P23.2) CNV	57	111	58
DEL PEAK 16(8P23.2) WILD-TYPE	114	87	40

Figure S222. Get High-res Image Gene #48: 'Del Peak 16(8p23.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 17(8p12)' versus 'CN_CNMF'

P value = 3.23e-21 (Fisher's exact test), Q value = 3e-18

Table S223. Gene #49: 'Del Peak 17(8p12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 17(8P12) CNV	131	49	35
DEL PEAK 17(8P12) WILD-TYPE	56	165	57

Figure S223. Get High-res Image Gene #49: 'Del Peak 17(8p12)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 17(8p12)' versus 'MRNASEQ_CNMF'

P value = 4.61e-05 (Chi-square test), Q value = 0.032

Table S224. Gene #49: 'Del Peak 17(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 17(8P12) CNV	48	29	28	9	7	20	15	9	5
DEL PEAK 17(8P12) WILD-TYPE	27	26	28	33	22	28	24	15	18

Figure S224. Get High-res Image Gene #49: 'Del Peak 17(8p12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 17(8p12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.37e-06 (Fisher's exact test), Q value = 0.004

Table S225. Gene #49: 'Del Peak 17(8p12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 17(8P12) CNV	51	66	53
DEL PEAK 17(8P12) WILD-TYPE	107	39	75

Figure S225. Get High-res Image Gene #49: 'Del Peak 17(8p12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 17(8p12)' versus 'MIRSEQ_CNMF'

P value = 5.26e-05 (Fisher's exact test), Q value = 0.037

Table S226. Gene #49: 'Del Peak 17(8p12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
DEL PEAK 17(8P12) CNV	52	105	45
DEL PEAK 17(8P12) WILD-TYPE	119	93	53

Figure S226. Get High-res Image Gene #49: 'Del Peak 17(8p12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 18(8p11.21)' versus 'CN_CNMF'

P value = 2.61e-19 (Fisher's exact test), Q value = 2.5e-16

Table S227. Gene #50: 'Del Peak 18(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 18(8P11.21) CNV	83	26	3
DEL PEAK 18(8P11.21) WILD-TYPE	104	188	89

Figure S227. Get High-res Image Gene #50: 'Del Peak 18(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 22(9q21.11)' versus 'CN_CNMF'

P value = 6.15e-07 (Fisher's exact test), Q value = 0.00049

Table S228. Gene #54: 'Del Peak 22(9q21.11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 22(9Q21.11) CNV	99	80	64
DEL PEAK 22(9Q21.11) WILD-TYPE	88	134	28

Figure S228. Get High-res Image Gene #54: 'Del Peak 22(9q21.11)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 22(9q21.11)' versus 'METHLYATION_CNMF'

P value = 1.97e-05 (Fisher's exact test), Q value = 0.014

Table S229. Gene #54: 'Del Peak 22(9q21.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
DEL PEAK 22(9Q21.11) CNV	34	74	43	46
DEL PEAK 22(9Q21.11) WILD-TYPE	52	34	67	54

Figure S229. Get High-res Image Gene #54: 'Del Peak 22(9q21.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 22(9q21.11)' versus 'MRNASEQ_CNMF'

P value = 0.000116 (Chi-square test), Q value = 0.078

Table S230. Gene #54: 'Del Peak 22(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 22(9Q21.11) CNV	36	34	40	14	13	29	15	9	5
DEL PEAK 22(9Q21.11) WILD-TYPE	39	21	16	28	16	19	24	15	18

Figure S230. Get High-res Image Gene #54: 'Del Peak 22(9q21.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 22(9q21.11)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.67e-07 (Fisher's exact test), Q value = 0.00014

Table S231. Gene #54: 'Del Peak 22(9q21.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 22(9Q21.11) CNV	59	47	89
DEL PEAK 22(9Q21.11) WILD-TYPE	99	58	39

Figure S231. Get High-res Image Gene #54: 'Del Peak 22(9q21.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 22(9q21.11)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000126 (Fisher's exact test), Q value = 0.083

Table S232. Gene #54: 'Del Peak 22(9q21.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
DEL PEAK 22(9Q21.11) CNV	63	142	23
DEL PEAK 22(9Q21.11) WILD-TYPE	101	102	36

Figure S232. Get High-res Image Gene #54: 'Del Peak 22(9q21.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 23(10p15.3)' versus 'CN_CNMF'

P value = 1.86e-05 (Fisher's exact test), Q value = 0.013

Table S233. Gene #55: 'Del Peak 23(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 23(10P15.3) CNV	63	31	26
DEL PEAK 23(10P15.3) WILD-TYPE	124	183	66

Figure S233. Get High-res Image Gene #55: 'Del Peak 23(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 24(10q26.3)' versus 'CN_CNMF'

P value = 3.91e-07 (Fisher's exact test), Q value = 0.00032

Table S234. Gene #56: 'Del Peak 24(10q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 24(10Q26.3) CNV	73	34	31
DEL PEAK 24(10Q26.3) WILD-TYPE	114	180	61

Figure S234. Get High-res Image Gene #56: 'Del Peak 24(10q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 24(10q26.3)' versus 'MRNASEQ_CNMF'

P value = 5.65e-05 (Chi-square test), Q value = 0.039

Table S235. Gene #56: 'Del Peak 24(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 24(10Q26.3) CNV	27	24	20	0	11	9	11	4	4
DEL PEAK 24(10Q26.3) WILD-TYPE	48	31	36	42	18	39	28	20	19

Figure S235. Get High-res Image Gene #56: 'Del Peak 24(10q26.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 25(11p15.5)' versus 'CN_CNMF'

P value = 2.53e-06 (Fisher's exact test), Q value = 0.0019

Table S236. Gene #57: 'Del Peak 25(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 25(11P15.5) CNV	71	34	27
DEL PEAK 25(11P15.5) WILD-TYPE	116	180	65

Figure S236. Get High-res Image Gene #57: 'Del Peak 25(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 25(11p15.5)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.36e-06 (Fisher's exact test), Q value = 0.0033

Table S237. Gene #57: 'Del Peak 25(11p15.5)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 25(11P15.5) CNV	21	30	49
DEL PEAK 25(11P15.5) WILD-TYPE	137	75	79

Figure S237. Get High-res Image Gene #57: 'Del Peak 25(11p15.5)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 25(11p15.5)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000108 (Fisher's exact test), Q value = 0.073

Table S238. Gene #57: 'Del Peak 25(11p15.5)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
DEL PEAK 25(11P15.5) CNV	35	83	6
DEL PEAK 25(11P15.5) WILD-TYPE	129	161	53

Figure S238. Get High-res Image Gene #57: 'Del Peak 25(11p15.5)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 29(12q24.33)' versus 'CN_CNMF'

P value = 8.07e-06 (Fisher's exact test), Q value = 0.006

Table S239. Gene #61: 'Del Peak 29(12q24.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 29(12Q24.33) CNV	63	47	8
DEL PEAK 29(12Q24.33) WILD-TYPE	124	167	84

Figure S239. Get High-res Image Gene #61: 'Del Peak 29(12q24.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 29(12q24.33)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000306 (Fisher's exact test), Q value = 0.19

Table S240. Gene #61: 'Del Peak 29(12q24.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 29(12Q24.33) CNV	48	29	15
DEL PEAK 29(12Q24.33) WILD-TYPE	110	76	113

Figure S240. Get High-res Image Gene #61: 'Del Peak 29(12q24.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 30(13q12.11)' versus 'CN_CNMF'

P value = 1.98e-21 (Fisher's exact test), Q value = 1.9e-18

Table S241. Gene #62: 'Del Peak 30(13q12.11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 30(13Q12.11) CNV	143	69	68
DEL PEAK 30(13Q12.11) WILD-TYPE	44	145	24

Figure S241. Get High-res Image Gene #62: 'Del Peak 30(13q12.11)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 30(13q12.11)' versus 'RPPA_CHIERARCHICAL'

P value = 1.49e-06 (Fisher's exact test), Q value = 0.0012

Table S242. Gene #62: 'Del Peak 30(13q12.11)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	89	65	58
DEL PEAK 30(13Q12.11) CNV	8	66	39	19
DEL PEAK 30(13Q12.11) WILD-TYPE	15	23	26	39

Figure S242. Get High-res Image Gene #62: 'Del Peak 30(13q12.11)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 30(13q12.11)' versus 'MRNASEQ_CNMF'

P value = 2.73e-07 (Chi-square test), Q value = 0.00022

Table S243. Gene #62: 'Del Peak 30(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 30(13Q12.11) CNV	53	30	41	14	9	34	21	11	5
DEL PEAK 30(13Q12.11) WILD-TYPE	22	25	15	28	20	14	18	13	18

Figure S243. Get High-res Image Gene #62: 'Del Peak 30(13q12.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 30(13q12.11)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.07e-08 (Fisher's exact test), Q value = 3.5e-05

Table S244. Gene #62: 'Del Peak 30(13q12.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 30(13Q12.11) CNV	60	71	87
DEL PEAK 30(13Q12.11) WILD-TYPE	98	34	41

Figure S244. Get High-res Image Gene #62: 'Del Peak 30(13q12.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 30(13q12.11)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.51e-05 (Fisher's exact test), Q value = 0.058

Table S245. Gene #62: 'Del Peak 30(13q12.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
DEL PEAK 30(13Q12.11) CNV	76	161	27
DEL PEAK 30(13Q12.11) WILD-TYPE	88	83	32

Figure S245. Get High-res Image Gene #62: 'Del Peak 30(13q12.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 31(13q12.13)' versus 'CN_CNMF'

P value = 1.29e-22 (Fisher's exact test), Q value = 1.2e-19

Table S246. Gene #63: 'Del Peak 31(13q12.13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 31(13Q12.13) CNV	144	68	69
DEL PEAK 31(13Q12.13) WILD-TYPE	43	146	23

Figure S246. Get High-res Image Gene #63: 'Del Peak 31(13q12.13)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 31(13q12.13)' versus 'RPPA_CHIERARCHICAL'

P value = 6.68e-07 (Fisher's exact test), Q value = 0.00053

Table S247. Gene #63: 'Del Peak 31(13q12.13)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	89	65	58
DEL PEAK 31(13Q12.13) CNV	8	67	39	19
DEL PEAK 31(13Q12.13) WILD-TYPE	15	22	26	39

Figure S247. Get High-res Image Gene #63: 'Del Peak 31(13q12.13)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 31(13q12.13)' versus 'MRNASEQ_CNMF'

P value = 1.2e-07 (Chi-square test), Q value = 1e-04

Table S248. Gene #63: 'Del Peak 31(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 31(13Q12.13) CNV	55	30	38	14	9	36	21	11	5
DEL PEAK 31(13Q12.13) WILD-TYPE	20	25	18	28	20	12	18	13	18

Figure S248. Get High-res Image Gene #63: 'Del Peak 31(13q12.13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 31(13q12.13)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.17e-08 (Fisher's exact test), Q value = 6.9e-05

Table S249. Gene #63: 'Del Peak 31(13q12.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 31(13Q12.13) CNV	61	72	86
DEL PEAK 31(13Q12.13) WILD-TYPE	97	33	42

Figure S249. Get High-res Image Gene #63: 'Del Peak 31(13q12.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 31(13q12.13)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000138 (Fisher's exact test), Q value = 0.091

Table S250. Gene #63: 'Del Peak 31(13q12.13)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
DEL PEAK 31(13Q12.13) CNV	77	161	27
DEL PEAK 31(13Q12.13) WILD-TYPE	87	83	32

Figure S250. Get High-res Image Gene #63: 'Del Peak 31(13q12.13)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 32(13q14.2)' versus 'CN_CNMF'

P value = 1.48e-22 (Fisher's exact test), Q value = 1.4e-19

Table S251. Gene #64: 'Del Peak 32(13q14.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 32(13Q14.2) CNV	139	63	68
DEL PEAK 32(13Q14.2) WILD-TYPE	48	151	24

Figure S251. Get High-res Image Gene #64: 'Del Peak 32(13q14.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 32(13q14.2)' versus 'RPPA_CHIERARCHICAL'

P value = 1.04e-05 (Fisher's exact test), Q value = 0.0077

Table S252. Gene #64: 'Del Peak 32(13q14.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	89	65	58
DEL PEAK 32(13Q14.2) CNV	8	60	40	17
DEL PEAK 32(13Q14.2) WILD-TYPE	15	29	25	41

Figure S252. Get High-res Image Gene #64: 'Del Peak 32(13q14.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 32(13q14.2)' versus 'MRNASEQ_CNMF'

P value = 4.15e-09 (Chi-square test), Q value = 3.7e-06

Table S253. Gene #64: 'Del Peak 32(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 32(13Q14.2) CNV	53	32	33	12	7	36	20	11	3
DEL PEAK 32(13Q14.2) WILD-TYPE	22	23	23	30	22	12	19	13	20

Figure S253. Get High-res Image Gene #64: 'Del Peak 32(13q14.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 32(13q14.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.54e-07 (Fisher's exact test), Q value = 0.00013

Table S254. Gene #64: 'Del Peak 32(13q14.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 32(13Q14.2) CNV	57	71	79
DEL PEAK 32(13Q14.2) WILD-TYPE	101	34	49

Figure S254. Get High-res Image Gene #64: 'Del Peak 32(13q14.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 32(13q14.2)' versus 'MIRSEQ_CNMF'

P value = 0.000206 (Fisher's exact test), Q value = 0.13

Table S255. Gene #64: 'Del Peak 32(13q14.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
DEL PEAK 32(13Q14.2) CNV	73	127	53
DEL PEAK 32(13Q14.2) WILD-TYPE	98	71	45

Figure S255. Get High-res Image Gene #64: 'Del Peak 32(13q14.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 32(13q14.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.69e-05 (Fisher's exact test), Q value = 0.033

Table S256. Gene #64: 'Del Peak 32(13q14.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
DEL PEAK 32(13Q14.2) CNV	73	156	24
DEL PEAK 32(13Q14.2) WILD-TYPE	91	88	35

Figure S256. Get High-res Image Gene #64: 'Del Peak 32(13q14.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 32(13q14.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000398 (Fisher's exact test), Q value = 0.25

Table S257. Gene #64: 'Del Peak 32(13q14.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	46	205
DEL PEAK 32(13Q14.2) CNV	65	24	130
DEL PEAK 32(13Q14.2) WILD-TYPE	88	22	75

Figure S257. Get High-res Image Gene #64: 'Del Peak 32(13q14.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 33(13q34)' versus 'CN_CNMF'

P value = 7.07e-16 (Fisher's exact test), Q value = 6.6e-13

Table S258. Gene #65: 'Del Peak 33(13q34)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 33(13Q34) CNV	113	55	62
DEL PEAK 33(13Q34) WILD-TYPE	74	159	30

Figure S258. Get High-res Image Gene #65: 'Del Peak 33(13q34)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 33(13q34)' versus 'MRNASEQ_CNMF'

P value = 3.71e-06 (Chi-square test), Q value = 0.0028

Table S259. Gene #65: 'Del Peak 33(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 33(13Q34) CNV	45	24	29	13	6	32	16	11	2
DEL PEAK 33(13Q34) WILD-TYPE	30	31	27	29	23	16	23	13	21

Figure S259. Get High-res Image Gene #65: 'Del Peak 33(13q34)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 33(13q34)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.09e-05 (Fisher's exact test), Q value = 0.022

Table S260. Gene #65: 'Del Peak 33(13q34)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 33(13Q34) CNV	50	58	70
DEL PEAK 33(13Q34) WILD-TYPE	108	47	58

Figure S260. Get High-res Image Gene #65: 'Del Peak 33(13q34)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 35(15q11.2)' versus 'CN_CNMF'

P value = 6.48e-11 (Fisher's exact test), Q value = 5.9e-08

Table S261. Gene #67: 'Del Peak 35(15q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 35(15Q11.2) CNV	122	72	58
DEL PEAK 35(15Q11.2) WILD-TYPE	65	142	34

Figure S261. Get High-res Image Gene #67: 'Del Peak 35(15q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 35(15q11.2)' versus 'METHLYATION_CNMF'

P value = 0.000186 (Fisher's exact test), Q value = 0.12

Table S262. Gene #67: 'Del Peak 35(15q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
DEL PEAK 35(15Q11.2) CNV	29	59	70	44
DEL PEAK 35(15Q11.2) WILD-TYPE	57	49	40	56

Figure S262. Get High-res Image Gene #67: 'Del Peak 35(15q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 35(15q11.2)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000161 (Fisher's exact test), Q value = 0.11

Table S263. Gene #67: 'Del Peak 35(15q11.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	89	65	58
DEL PEAK 35(15Q11.2) CNV	10	59	33	17
DEL PEAK 35(15Q11.2) WILD-TYPE	13	30	32	41

Figure S263. Get High-res Image Gene #67: 'Del Peak 35(15q11.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 35(15q11.2)' versus 'MRNASEQ_CNMF'

P value = 1.91e-13 (Chi-square test), Q value = 1.8e-10

Table S264. Gene #67: 'Del Peak 35(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 35(15Q11.2) CNV	58	34	30	6	7	34	13	7	6
DEL PEAK 35(15Q11.2) WILD-TYPE	17	21	26	36	22	14	26	17	17

Figure S264. Get High-res Image Gene #67: 'Del Peak 35(15q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 35(15q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.4e-05 (Fisher's exact test), Q value = 0.01

Table S265. Gene #67: 'Del Peak 35(15q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 35(15Q11.2) CNV	60	71	64
DEL PEAK 35(15Q11.2) WILD-TYPE	98	34	64

Figure S265. Get High-res Image Gene #67: 'Del Peak 35(15q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 35(15q11.2)' versus 'MIRSEQ_CNMF'

P value = 2.82e-05 (Fisher's exact test), Q value = 0.02

Table S266. Gene #67: 'Del Peak 35(15q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
DEL PEAK 35(15Q11.2) CNV	63	117	57
DEL PEAK 35(15Q11.2) WILD-TYPE	108	81	41

Figure S266. Get High-res Image Gene #67: 'Del Peak 35(15q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 36(16q23.1)' versus 'CN_CNMF'

P value = 1.62e-06 (Fisher's exact test), Q value = 0.0013

Table S267. Gene #68: 'Del Peak 36(16q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 36(16Q23.1) CNV	82	46	39
DEL PEAK 36(16Q23.1) WILD-TYPE	105	168	53

Figure S267. Get High-res Image Gene #68: 'Del Peak 36(16q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 36(16q23.1)' versus 'METHLYATION_CNMF'

P value = 0.000139 (Fisher's exact test), Q value = 0.092

Table S268. Gene #68: 'Del Peak 36(16q23.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
DEL PEAK 36(16Q23.1) CNV	14	45	47	30
DEL PEAK 36(16Q23.1) WILD-TYPE	72	63	63	70

Figure S268. Get High-res Image Gene #68: 'Del Peak 36(16q23.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 36(16q23.1)' versus 'MRNASEQ_CNMF'

P value = 1.73e-06 (Chi-square test), Q value = 0.0013

Table S269. Gene #68: 'Del Peak 36(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 36(16Q23.1) CNV	38	15	28	5	5	20	16	4	2
DEL PEAK 36(16Q23.1) WILD-TYPE	37	40	28	37	24	28	23	20	21

Figure S269. Get High-res Image Gene #68: 'Del Peak 36(16q23.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 36(16q23.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.21e-07 (Fisher's exact test), Q value = 0.00026

Table S270. Gene #68: 'Del Peak 36(16q23.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 36(16Q23.1) CNV	30	52	51
DEL PEAK 36(16Q23.1) WILD-TYPE	128	53	77

Figure S270. Get High-res Image Gene #68: 'Del Peak 36(16q23.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 37(17p13.3)' versus 'CN_CNMF'

P value = 5.27e-19 (Fisher's exact test), Q value = 4.9e-16

Table S271. Gene #69: 'Del Peak 37(17p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 37(17P13.3) CNV	145	70	52
DEL PEAK 37(17P13.3) WILD-TYPE	42	144	40

Figure S271. Get High-res Image Gene #69: 'Del Peak 37(17p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 37(17p13.3)' versus 'METHLYATION_CNMF'

P value = 6.05e-08 (Fisher's exact test), Q value = 5.1e-05

Table S272. Gene #69: 'Del Peak 37(17p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
DEL PEAK 37(17P13.3) CNV	27	62	79	44
DEL PEAK 37(17P13.3) WILD-TYPE	59	46	31	56

Figure S272. Get High-res Image Gene #69: 'Del Peak 37(17p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 37(17p13.3)' versus 'MRNASEQ_CNMF'

P value = 5.6e-08 (Chi-square test), Q value = 4.8e-05

Table S273. Gene #69: 'Del Peak 37(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 37(17P13.3) CNV	57	38	32	7	14	29	21	9	9
DEL PEAK 37(17P13.3) WILD-TYPE	18	17	24	35	15	19	18	15	14

Figure S273. Get High-res Image Gene #69: 'Del Peak 37(17p13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 37(17p13.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.79e-07 (Fisher's exact test), Q value = 0.00077

Table S274. Gene #69: 'Del Peak 37(17p13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 37(17P13.3) CNV	66	78	72
DEL PEAK 37(17P13.3) WILD-TYPE	92	27	56

Figure S274. Get High-res Image Gene #69: 'Del Peak 37(17p13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 38(17p11.2)' versus 'CN_CNMF'

P value = 1.66e-16 (Fisher's exact test), Q value = 1.5e-13

Table S275. Gene #70: 'Del Peak 38(17p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 38(17P11.2) CNV	121	50	45
DEL PEAK 38(17P11.2) WILD-TYPE	66	164	47

Figure S275. Get High-res Image Gene #70: 'Del Peak 38(17p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 38(17p11.2)' versus 'METHLYATION_CNMF'

P value = 8.4e-08 (Fisher's exact test), Q value = 7.1e-05

Table S276. Gene #70: 'Del Peak 38(17p11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
DEL PEAK 38(17P11.2) CNV	23	43	72	34
DEL PEAK 38(17P11.2) WILD-TYPE	63	65	38	66

Figure S276. Get High-res Image Gene #70: 'Del Peak 38(17p11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 38(17p11.2)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000294 (Fisher's exact test), Q value = 0.19

Table S277. Gene #70: 'Del Peak 38(17p11.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	89	65	58
DEL PEAK 38(17P11.2) CNV	8	57	37	18
DEL PEAK 38(17P11.2) WILD-TYPE	15	32	28	40

Figure S277. Get High-res Image Gene #70: 'Del Peak 38(17p11.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 38(17p11.2)' versus 'MRNASEQ_CNMF'

P value = 7.3e-07 (Chi-square test), Q value = 0.00058

Table S278. Gene #70: 'Del Peak 38(17p11.2)' 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 38(17P11.2) CNV	51	32	30	7	13	18	17	7	5
DEL PEAK 38(17P11.2) WILD-TYPE	24	23	26	35	16	30	22	17	18

Figure S278. Get High-res Image Gene #70: 'Del Peak 38(17p11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 38(17p11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.52e-05 (Fisher's exact test), Q value = 0.011

Table S279. Gene #70: 'Del Peak 38(17p11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 38(17P11.2) CNV	56	68	56
DEL PEAK 38(17P11.2) WILD-TYPE	102	37	72

Figure S279. Get High-res Image Gene #70: 'Del Peak 38(17p11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 39(18q21.32)' versus 'CN_CNMF'

P value = 2.62e-13 (Fisher's exact test), Q value = 2.4e-10

Table S280. Gene #71: 'Del Peak 39(18q21.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 39(18Q21.32) CNV	132	75	34
DEL PEAK 39(18Q21.32) WILD-TYPE	55	139	58

Figure S280. Get High-res Image Gene #71: 'Del Peak 39(18q21.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 39(18q21.32)' versus 'MRNASEQ_CNMF'

P value = 9.08e-09 (Chi-square test), Q value = 7.9e-06

Table S281. Gene #71: 'Del Peak 39(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 39(18Q21.32) CNV	48	39	31	8	15	15	25	9	4
DEL PEAK 39(18Q21.32) WILD-TYPE	27	16	25	34	14	33	14	15	19

Figure S281. Get High-res Image Gene #71: 'Del Peak 39(18q21.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 39(18q21.32)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.08

Table S282. Gene #71: 'Del Peak 39(18q21.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 39(18Q21.32) CNV	64	70	60
DEL PEAK 39(18Q21.32) WILD-TYPE	94	35	68

Figure S282. Get High-res Image Gene #71: 'Del Peak 39(18q21.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 40(18q23)' versus 'CN_CNMF'

P value = 1.15e-14 (Fisher's exact test), Q value = 1.1e-11

Table S283. Gene #72: 'Del Peak 40(18q23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 40(18Q23) CNV	133	73	32
DEL PEAK 40(18Q23) WILD-TYPE	54	141	60

Figure S283. Get High-res Image Gene #72: 'Del Peak 40(18q23)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 40(18q23)' versus 'MRNASEQ_CNMF'

P value = 1.04e-08 (Chi-square test), Q value = 9.1e-06

Table S284. Gene #72: 'Del Peak 40(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 40(18Q23) CNV	49	37	28	7	15	15	25	9	4
DEL PEAK 40(18Q23) WILD-TYPE	26	18	28	35	14	33	14	15	19

Figure S284. Get High-res Image Gene #72: 'Del Peak 40(18q23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 40(18q23)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.28e-05 (Fisher's exact test), Q value = 0.0094

Table S285. Gene #72: 'Del Peak 40(18q23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 40(18Q23) CNV	61	71	57
DEL PEAK 40(18Q23) WILD-TYPE	97	34	71

Figure S285. Get High-res Image Gene #72: 'Del Peak 40(18q23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 41(19p13.3)' versus 'CN_CNMF'

P value = 7.34e-06 (Fisher's exact test), Q value = 0.0055

Table S286. Gene #73: 'Del Peak 41(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 41(19P13.3) CNV	106	93	67
DEL PEAK 41(19P13.3) WILD-TYPE	81	121	25

Figure S286. Get High-res Image Gene #73: 'Del Peak 41(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 41(19p13.3)' versus 'METHLYATION_CNMF'

P value = 8.27e-07 (Fisher's exact test), Q value = 0.00066

Table S287. Gene #73: 'Del Peak 41(19p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
DEL PEAK 41(19P13.3) CNV	39	82	49	46
DEL PEAK 41(19P13.3) WILD-TYPE	47	26	61	54

Figure S287. Get High-res Image Gene #73: 'Del Peak 41(19p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 41(19p13.3)' versus 'MRNASEQ_CNMF'

P value = 3.43e-10 (Chi-square test), Q value = 3.1e-07

Table S288. Gene #73: 'Del Peak 41(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 41(19P13.3) CNV	35	28	42	35	16	32	14	5	3
DEL PEAK 41(19P13.3) WILD-TYPE	40	27	14	7	13	16	25	19	20

Figure S288. Get High-res Image Gene #73: 'Del Peak 41(19p13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 41(19p13.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.14e-07 (Fisher's exact test), Q value = 0.00026

Table S289. Gene #73: 'Del Peak 41(19p13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 41(19P13.3) CNV	65	52	93
DEL PEAK 41(19P13.3) WILD-TYPE	93	53	35

Figure S289. Get High-res Image Gene #73: 'Del Peak 41(19p13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 41(19p13.3)' versus 'MIRSEQ_CNMF'

P value = 3.65e-06 (Fisher's exact test), Q value = 0.0028

Table S290. Gene #73: 'Del Peak 41(19p13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
DEL PEAK 41(19P13.3) CNV	71	131	45
DEL PEAK 41(19P13.3) WILD-TYPE	100	67	53

Figure S290. Get High-res Image Gene #73: 'Del Peak 41(19p13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 41(19p13.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.63e-07 (Fisher's exact test), Q value = 0.00014

Table S291. Gene #73: 'Del Peak 41(19p13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
DEL PEAK 41(19P13.3) CNV	66	159	22
DEL PEAK 41(19P13.3) WILD-TYPE	98	85	37

Figure S291. Get High-res Image Gene #73: 'Del Peak 41(19p13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 41(19p13.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000119 (Fisher's exact test), Q value = 0.08

Table S292. Gene #73: 'Del Peak 41(19p13.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	174	73
DEL PEAK 41(19P13.3) CNV	69	114	33
DEL PEAK 41(19P13.3) WILD-TYPE	88	60	40

Figure S292. Get High-res Image Gene #73: 'Del Peak 41(19p13.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 41(19p13.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.09e-06 (Fisher's exact test), Q value = 0.0046

Table S293. Gene #73: 'Del Peak 41(19p13.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	46	205
DEL PEAK 41(19P13.3) CNV	62	20	134
DEL PEAK 41(19P13.3) WILD-TYPE	91	26	71

Figure S293. Get High-res Image Gene #73: 'Del Peak 41(19p13.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 42(19p13.2)' versus 'CN_CNMF'

P value = 6.1e-07 (Fisher's exact test), Q value = 0.00049

Table S294. Gene #74: 'Del Peak 42(19p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 42(19P13.2) CNV	107	86	66
DEL PEAK 42(19P13.2) WILD-TYPE	80	128	26

Figure S294. Get High-res Image Gene #74: 'Del Peak 42(19p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 42(19p13.2)' versus 'METHLYATION_CNMF'

P value = 3.46e-08 (Fisher's exact test), Q value = 3e-05

Table S295. Gene #74: 'Del Peak 42(19p13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
DEL PEAK 42(19P13.2) CNV	36	83	50	42
DEL PEAK 42(19P13.2) WILD-TYPE	50	25	60	58

Figure S295. Get High-res Image Gene #74: 'Del Peak 42(19p13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 42(19p13.2)' versus 'MRNASEQ_CNMF'

P value = 3.34e-10 (Chi-square test), Q value = 3e-07

Table S296. Gene #74: 'Del Peak 42(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 42(19P13.2) CNV	37	26	34	34	15	37	11	5	3
DEL PEAK 42(19P13.2) WILD-TYPE	38	29	22	8	14	11	28	19	20

Figure S296. Get High-res Image Gene #74: 'Del Peak 42(19p13.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 42(19p13.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.01e-07 (Fisher's exact test), Q value = 0.00033

Table S297. Gene #74: 'Del Peak 42(19p13.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 42(19P13.2) CNV	61	51	90
DEL PEAK 42(19P13.2) WILD-TYPE	97	54	38

Figure S297. Get High-res Image Gene #74: 'Del Peak 42(19p13.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 42(19p13.2)' versus 'MIRSEQ_CNMF'

P value = 2.46e-06 (Fisher's exact test), Q value = 0.0019

Table S298. Gene #74: 'Del Peak 42(19p13.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
DEL PEAK 42(19P13.2) CNV	69	129	43
DEL PEAK 42(19P13.2) WILD-TYPE	102	69	55

Figure S298. Get High-res Image Gene #74: 'Del Peak 42(19p13.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 42(19p13.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.87e-07 (Fisher's exact test), Q value = 0.00024

Table S299. Gene #74: 'Del Peak 42(19p13.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
DEL PEAK 42(19P13.2) CNV	66	155	20
DEL PEAK 42(19P13.2) WILD-TYPE	98	89	39

Figure S299. Get High-res Image Gene #74: 'Del Peak 42(19p13.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 42(19p13.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.56e-05 (Fisher's exact test), Q value = 0.032

Table S300. Gene #74: 'Del Peak 42(19p13.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	174	73
DEL PEAK 42(19P13.2) CNV	66	113	32
DEL PEAK 42(19P13.2) WILD-TYPE	91	61	41

Figure S300. Get High-res Image Gene #74: 'Del Peak 42(19p13.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 42(19p13.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.11e-05 (Fisher's exact test), Q value = 0.0081

Table S301. Gene #74: 'Del Peak 42(19p13.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	46	205
DEL PEAK 42(19P13.2) CNV	61	19	131
DEL PEAK 42(19P13.2) WILD-TYPE	92	27	74

Figure S301. Get High-res Image Gene #74: 'Del Peak 42(19p13.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 43(19q13.33)' versus 'CN_CNMF'

P value = 1.99e-07 (Fisher's exact test), Q value = 0.00016

Table S302. Gene #75: 'Del Peak 43(19q13.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 43(19Q13.33) CNV	95	52	37
DEL PEAK 43(19Q13.33) WILD-TYPE	92	162	55

Figure S302. Get High-res Image Gene #75: 'Del Peak 43(19q13.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 43(19q13.33)' versus 'MIRSEQ_CNMF'

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

Table S303. Gene #75: 'Del Peak 43(19q13.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
DEL PEAK 43(19Q13.33) CNV	42	94	34
DEL PEAK 43(19Q13.33) WILD-TYPE	129	104	64

Figure S303. Get High-res Image Gene #75: 'Del Peak 43(19q13.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 43(19q13.33)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.41e-05 (Fisher's exact test), Q value = 0.01

Table S304. Gene #75: 'Del Peak 43(19q13.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
DEL PEAK 43(19Q13.33) CNV	40	113	17
DEL PEAK 43(19Q13.33) WILD-TYPE	124	131	42

Figure S304. Get High-res Image Gene #75: 'Del Peak 43(19q13.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 43(19q13.33)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000155 (Fisher's exact test), Q value = 0.1

Table S305. Gene #75: 'Del Peak 43(19q13.33)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	46	205
DEL PEAK 43(19Q13.33) CNV	34	18	88
DEL PEAK 43(19Q13.33) WILD-TYPE	119	28	117

Figure S305. Get High-res Image Gene #75: 'Del Peak 43(19q13.33)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 45(21q11.2)' versus 'CN_CNMF'

P value = 4.85e-06 (Fisher's exact test), Q value = 0.0037

Table S306. Gene #77: 'Del Peak 45(21q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 45(21Q11.2) CNV	54	58	51
DEL PEAK 45(21Q11.2) WILD-TYPE	133	156	41

Figure S306. Get High-res Image Gene #77: 'Del Peak 45(21q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 45(21q11.2)' versus 'METHLYATION_CNMF'

P value = 0.000254 (Fisher's exact test), Q value = 0.16

Table S307. Gene #77: 'Del Peak 45(21q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
DEL PEAK 45(21Q11.2) CNV	13	47	37	34
DEL PEAK 45(21Q11.2) WILD-TYPE	73	61	73	66

Figure S307. Get High-res Image Gene #77: 'Del Peak 45(21q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 45(21q11.2)' versus 'MRNASEQ_CNMF'

P value = 3.59e-08 (Chi-square test), Q value = 3.1e-05

Table S308. Gene #77: 'Del Peak 45(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 45(21Q11.2) CNV	27	10	23	8	11	32	19	4	1
DEL PEAK 45(21Q11.2) WILD-TYPE	48	45	33	34	18	16	20	20	22

Figure S308. Get High-res Image Gene #77: 'Del Peak 45(21q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 45(21q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.78e-07 (Fisher's exact test), Q value = 0.00031

Table S309. Gene #77: 'Del Peak 45(21q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 45(21Q11.2) CNV	33	36	66
DEL PEAK 45(21Q11.2) WILD-TYPE	125	69	62

Figure S309. Get High-res Image Gene #77: 'Del Peak 45(21q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 45(21q11.2)' versus 'MIRSEQ_CNMF'

P value = 2.25e-05 (Fisher's exact test), Q value = 0.016

Table S310. Gene #77: 'Del Peak 45(21q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
DEL PEAK 45(21Q11.2) CNV	38	88	28
DEL PEAK 45(21Q11.2) WILD-TYPE	133	110	70

Figure S310. Get High-res Image Gene #77: 'Del Peak 45(21q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 45(21q11.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.55e-08 (Fisher's exact test), Q value = 3e-05

Table S311. Gene #77: 'Del Peak 45(21q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
DEL PEAK 45(21Q11.2) CNV	33	110	11
DEL PEAK 45(21Q11.2) WILD-TYPE	131	134	48

Figure S311. Get High-res Image Gene #77: 'Del Peak 45(21q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 45(21q11.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.68e-05 (Fisher's exact test), Q value = 0.026

Table S312. Gene #77: 'Del Peak 45(21q11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	46	205
DEL PEAK 45(21Q11.2) CNV	31	13	87
DEL PEAK 45(21Q11.2) WILD-TYPE	122	33	118

Figure S312. Get High-res Image Gene #77: 'Del Peak 45(21q11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 46(22q13.32)' versus 'CN_CNMF'

P value = 4.32e-13 (Fisher's exact test), Q value = 4e-10

Table S313. Gene #78: 'Del Peak 46(22q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 46(22Q13.32) CNV	108	63	65
DEL PEAK 46(22Q13.32) WILD-TYPE	79	151	27

Figure S313. Get High-res Image Gene #78: 'Del Peak 46(22q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 46(22q13.32)' versus 'METHLYATION_CNMF'

P value = 2.97e-09 (Fisher's exact test), Q value = 2.7e-06

Table S314. Gene #78: 'Del Peak 46(22q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	86	108	110	100
DEL PEAK 46(22Q13.32) CNV	18	64	68	41
DEL PEAK 46(22Q13.32) WILD-TYPE	68	44	42	59

Figure S314. Get High-res Image Gene #78: 'Del Peak 46(22q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 46(22q13.32)' versus 'MRNASEQ_CNMF'

P value = 1.51e-10 (Chi-square test), Q value = 1.4e-07

Table S315. Gene #78: 'Del Peak 46(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 46(22Q13.32) CNV	51	16	33	10	14	36	17	5	4
DEL PEAK 46(22Q13.32) WILD-TYPE	24	39	23	32	15	12	22	19	19

Figure S315. Get High-res Image Gene #78: 'Del Peak 46(22q13.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 46(22q13.32)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.29e-11 (Fisher's exact test), Q value = 5.7e-08

Table S316. Gene #78: 'Del Peak 46(22q13.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 46(22Q13.32) CNV	44	56	86
DEL PEAK 46(22Q13.32) WILD-TYPE	114	49	42

Figure S316. Get High-res Image Gene #78: 'Del Peak 46(22q13.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 46(22q13.32)' versus 'MIRSEQ_CNMF'

P value = 1.66e-07 (Fisher's exact test), Q value = 0.00014

Table S317. Gene #78: 'Del Peak 46(22q13.32)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	198	98
DEL PEAK 46(22Q13.32) CNV	55	121	45
DEL PEAK 46(22Q13.32) WILD-TYPE	116	77	53

Figure S317. Get High-res Image Gene #78: 'Del Peak 46(22q13.32)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 46(22q13.32)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.72e-08 (Fisher's exact test), Q value = 2.3e-05

Table S318. Gene #78: 'Del Peak 46(22q13.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	244	59
DEL PEAK 46(22Q13.32) CNV	53	147	21
DEL PEAK 46(22Q13.32) WILD-TYPE	111	97	38

Figure S318. Get High-res Image Gene #78: 'Del Peak 46(22q13.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 46(22q13.32)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000257 (Fisher's exact test), Q value = 0.16

Table S319. Gene #78: 'Del Peak 46(22q13.32)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	157	174	73
DEL PEAK 46(22Q13.32) CNV	59	102	29
DEL PEAK 46(22Q13.32) WILD-TYPE	98	72	44

Figure S319. Get High-res Image Gene #78: 'Del Peak 46(22q13.32)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 46(22q13.32)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.83e-07 (Fisher's exact test), Q value = 0.00047

Table S320. Gene #78: 'Del Peak 46(22q13.32)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	46	205
DEL PEAK 46(22Q13.32) CNV	50	17	123
DEL PEAK 46(22Q13.32) WILD-TYPE	103	29	82

Figure S320. Get High-res Image Gene #78: 'Del Peak 46(22q13.32)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 47(Xp22.2)' versus 'CN_CNMF'

P value = 1.52e-08 (Fisher's exact test), Q value = 1.3e-05

Table S321. Gene #79: 'Del Peak 47(Xp22.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	187	214	92
DEL PEAK 47(XP22.2) CNV	82	36	24
DEL PEAK 47(XP22.2) WILD-TYPE	105	178	68

Figure S321. Get High-res Image Gene #79: 'Del Peak 47(Xp22.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 47(Xp22.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000322 (Fisher's exact test), Q value = 0.2

Table S322. Gene #79: 'Del Peak 47(Xp22.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	105	128
DEL PEAK 47(XP22.2) CNV	33	46	34
DEL PEAK 47(XP22.2) WILD-TYPE	125	59	94

Figure S322. Get High-res Image Gene #79: 'Del Peak 47(Xp22.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
Molecular subtype file = LUAD-TP.transferedmergedcluster.txt
Number of patients = 493
Number of copy number variation regions = 79
Number of molecular subtypes = 12
Exclude regions that fewer than K tumors have alterations, K = 3

Fisher's exact test

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

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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