Correlation between copy number variation genes and molecular subtypes

Stomach Adenocarcinoma (Primary solid tumor)

23 September 2013 | analyses__2013_09_23

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variation genes and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1154FDC

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 75 peak regions and 10 molecular subtypes across 305 patients, 267 significant findings detected with Q value < 0.25.

Amp Peak 1(1p36.22) cnvs correlated to 'CN_CNMF'.
Amp Peak 2(1q21.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 3(1q42.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 4(3q26.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 5(5p13.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 6(6p21.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 7(6q12) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 8(6q21) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 9(7p22.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 10(7p11.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 11(7q21.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 13(8q24.21) cnvs correlated to 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 15(9q34.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 16(10q22.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 17(10q26.13) cnvs correlated to 'CN_CNMF'.
Amp Peak 18(11p13) cnvs correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 19(11q13.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 20(12p12.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 21(12q15) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 22(13q12.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 23(13q22.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 24(15q26.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 25(17q12) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 26(18q11.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 27(19q12) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 28(20q13.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 29(Xq27.3) cnvs correlated to 'CN_CNMF'.
Del Peak 1(1p36.11) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 2(1p13.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 4(2q32.1) cnvs correlated to 'CN_CNMF'.
Del Peak 5(2q37.2) cnvs correlated to 'CN_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 6(3p26.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 7(3p14.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 8(3q26.31) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 9(4p16.3) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 10(4q22.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 11(4q34.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 12(5q11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 13(5q23.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 14(6p25.3) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 15(6q26) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 16(7q31.1) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
Del Peak 17(7q36.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 18(8p23.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 19(9p23) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Del Peak 20(9p21.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 21(9q21.11) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 22(10p15.1) cnvs correlated to 'CN_CNMF'.
Del Peak 23(10q22.3) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 24(10q23.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 25(11p15.4) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 27(12p13.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 28(13q12.11) cnvs correlated to 'CN_CNMF'.
Del Peak 29(14q21.1) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 30(14q32.33) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 31(15q15.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 32(16p13.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 33(16q23.1) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 34(17p12) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 35(17q24.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 36(18q21.2) cnvs correlated to 'CN_CNMF'.
Del Peak 37(19p13.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 38(19q13.11) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 39(20p12.1) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
Del Peak 40(20p12.1) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
Del Peak 41(21q11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
Del Peak 42(21q22.13) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 43(22q13.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 44(Xp22.2) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 45(Xp21.1) cnvs correlated to 'CN_CNMF'.
Del Peak 46(Xq21.33) cnvs correlated to 'CN_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 75 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 267 significant findings detected.


		Molecular subtypes	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	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
Amp Peak 2(1q21 3)	0 (0%)	197	1.99e-18 (1.47e-15)	4.32e-11 (3.01e-08)	0.0481 (1.00)	0.00923 (1.00)	3.14e-12 (2.22e-09)	4.74e-07 (0.000303)	9.54e-09 (6.39e-06)	3.09e-08 (2.04e-05)	0.000347 (0.174)	6.39e-10 (4.37e-07)
Del Peak 12(5q11 2)	0 (0%)	202	5.94e-27 (4.45e-24)	2.49e-14 (1.8e-11)	0.308 (1.00)	0.438 (1.00)	2.81e-11 (1.96e-08)	1.5e-10 (1.03e-07)	2.77e-09 (1.87e-06)	6.55e-12 (4.6e-09)	2.99e-06 (0.00186)	1.03e-12 (7.37e-10)
Del Peak 13(5q23 2)	0 (0%)	212	1.44e-22 (1.07e-19)	2.29e-12 (1.63e-09)	0.175 (1.00)	0.238 (1.00)	1.69e-12 (1.2e-09)	5.1e-09 (3.44e-06)	2.4e-10 (1.65e-07)	5.29e-11 (3.69e-08)	8.17e-07 (0.00052)	1.45e-12 (1.04e-09)
Del Peak 31(15q15 1)	0 (0%)	226	1.74e-13 (1.25e-10)	2.11e-07 (0.000136)	0.00548 (1.00)	0.00669 (1.00)	7.15e-08 (4.68e-05)	2.66e-08 (1.76e-05)	6.44e-06 (0.0039)	1.84e-08 (1.22e-05)	0.000455 (0.222)	4.09e-05 (0.0236)
Del Peak 32(16p13 3)	0 (0%)	247	6e-11 (4.17e-08)	4.14e-05 (0.0238)	0.59 (1.00)	0.838 (1.00)	3.44e-08 (2.27e-05)	1.11e-09 (7.56e-07)	0.000144 (0.0772)	4.97e-06 (0.00305)	0.000157 (0.084)	5.41e-07 (0.000345)
Amp Peak 3(1q42 3)	0 (0%)	200	3.53e-14 (2.55e-11)	1.15e-07 (7.49e-05)	0.316 (1.00)	0.31 (1.00)	4.21e-09 (2.85e-06)	0.000172 (0.0905)	1.93e-08 (1.29e-05)	6.61e-09 (4.45e-06)	0.0178 (1.00)	7.28e-08 (4.75e-05)
Amp Peak 5(5p13 1)	0 (0%)	218	7.48e-14 (5.39e-11)	2.09e-07 (0.000135)	0.776 (1.00)	1 (1.00)	2.52e-08 (1.67e-05)	0.000161 (0.0856)	0.000347 (0.174)	1.99e-06 (0.00124)	0.0334 (1.00)	5.84e-06 (0.00357)
Amp Peak 27(19q12)	0 (0%)	215	1.06e-15 (7.79e-13)	1.01e-10 (6.96e-08)	0.0032 (1.00)	0.0157 (1.00)	1.01e-13 (7.29e-11)	5.62e-09 (3.79e-06)	4.4e-06 (0.00272)	2.1e-14 (1.52e-11)	0.173 (1.00)	7.05e-13 (5.05e-10)
Amp Peak 28(20q13 2)	0 (0%)	104	2.4e-24 (1.8e-21)	4.24e-12 (2.99e-09)	0.00499 (1.00)	0.739 (1.00)	4.25e-08 (2.79e-05)	1.77e-05 (0.0104)	1.28e-06 (0.000809)	4.4e-12 (3.1e-09)	0.064 (1.00)	1.79e-09 (1.21e-06)
Del Peak 7(3p14 2)	0 (0%)	203	6.14e-11 (4.26e-08)	1.24e-06 (0.000783)	0.442 (1.00)	0.953 (1.00)	0.000242 (0.124)	0.00023 (0.119)	0.000363 (0.181)	4.35e-05 (0.0249)	0.0613 (1.00)	6.08e-06 (0.00371)
Del Peak 11(4q34 3)	0 (0%)	178	1.07e-14 (7.79e-12)	1.87e-06 (0.00117)	0.0748 (1.00)	0.881 (1.00)	4.25e-05 (0.0243)	4.38e-05 (0.025)	5.29e-05 (0.03)	8.16e-07 (0.00052)	0.141 (1.00)	9.19e-05 (0.0507)
Del Peak 34(17p12)	0 (0%)	190	3.09e-29 (2.32e-26)	3.28e-11 (2.29e-08)	0.387 (1.00)	0.428 (1.00)	3.29e-08 (2.17e-05)	4.33e-07 (0.000278)	5.57e-05 (0.0314)	1.66e-07 (0.000107)	0.00102 (0.467)	1.38e-08 (9.21e-06)
Del Peak 37(19p13 3)	0 (0%)	206	5.42e-29 (4.06e-26)	2.33e-16 (1.72e-13)	0.00224 (0.976)	0.238 (1.00)	1.23e-16 (9.05e-14)	3.38e-16 (2.48e-13)	4.71e-07 (0.000302)	2.85e-21 (2.12e-18)	0.00143 (0.639)	2.21e-19 (1.64e-16)
Amp Peak 6(6p21 1)	0 (0%)	225	2.84e-16 (2.09e-13)	2.19e-10 (1.51e-07)	0.147 (1.00)	0.45 (1.00)	0.000233 (0.12)	0.00871 (1.00)	6.05e-05 (0.0341)	1.3e-06 (0.000823)	0.0535 (1.00)	4.96e-06 (0.00305)
Amp Peak 7(6q12)	0 (0%)	245	1.37e-09 (9.29e-07)	2.31e-08 (1.53e-05)	0.0241 (1.00)	0.145 (1.00)	4.18e-06 (0.00259)	0.000118 (0.0642)	0.000864 (0.404)	5.15e-05 (0.0292)	0.0581 (1.00)	4.63e-06 (0.00285)
Amp Peak 25(17q12)	0 (0%)	213	1.12e-14 (8.13e-12)	2.68e-06 (0.00166)	0.734 (1.00)	0.535 (1.00)	0.000158 (0.0844)	0.00022 (0.114)	0.000353 (0.176)	0.000163 (0.0861)	0.171 (1.00)	0.00227 (0.983)
Del Peak 1(1p36 11)	0 (0%)	222	9.62e-15 (7.02e-12)	0.000396 (0.194)	0.191 (1.00)	0.0436 (1.00)	0.000113 (0.0619)	0.000962 (0.447)	7.87e-05 (0.0439)	7.84e-05 (0.0437)	0.0067 (1.00)	0.00034 (0.171)
Del Peak 9(4p16 3)	0 (0%)	193	6.3e-12 (4.44e-09)	0.000991 (0.458)	0.465 (1.00)	0.227 (1.00)	0.000126 (0.0683)	0.000207 (0.108)	0.000183 (0.0959)	1.1e-06 (0.000699)	0.00224 (0.976)	6.09e-06 (0.00371)
Del Peak 17(7q36 3)	0 (0%)	247	1.05e-14 (7.65e-12)	1.31e-05 (0.00775)	0.392 (1.00)	0.802 (1.00)	2.44e-06 (0.00152)	1.36e-05 (0.00807)	0.0124 (1.00)	7.11e-05 (0.0398)	0.0383 (1.00)	0.000105 (0.0576)
Del Peak 18(8p23 2)	0 (0%)	228	5.17e-15 (3.77e-12)	8.11e-06 (0.00487)	0.105 (1.00)	0.146 (1.00)	8.14e-06 (0.00489)	9.92e-06 (0.00591)	0.00504 (1.00)	7.96e-08 (5.19e-05)	0.0244 (1.00)	0.000214 (0.111)
Del Peak 20(9p21 3)	0 (0%)	187	9.23e-19 (6.85e-16)	1.92e-10 (1.33e-07)	0.000123 (0.0666)	0.153 (1.00)	1.7e-08 (1.14e-05)	0.000117 (0.0635)	0.0273 (1.00)	0.00139 (0.624)	0.864 (1.00)	0.000159 (0.085)
Del Peak 24(10q23 31)	0 (0%)	232	3.01e-12 (2.13e-09)	5.23e-06 (0.0032)	0.069 (1.00)	0.159 (1.00)	3.27e-06 (0.00203)	0.00297 (1.00)	0.000374 (0.185)	1.07e-05 (0.00639)	0.25 (1.00)	0.000501 (0.242)
Del Peak 43(22q13 31)	0 (0%)	204	1.65e-17 (1.22e-14)	0.000135 (0.0732)	0.083 (1.00)	0.4 (1.00)	0.000245 (0.125)	0.00372 (1.00)	9.98e-05 (0.0548)	1.38e-06 (0.000866)	0.0754 (1.00)	3.52e-05 (0.0204)
Amp Peak 8(6q21)	0 (0%)	249	3.9e-08 (2.56e-05)	1.68e-05 (0.00988)	0.236 (1.00)	0.425 (1.00)	2.74e-05 (0.0159)	1.11e-05 (0.00659)	0.00357 (1.00)	0.001 (0.463)	0.0371 (1.00)	1.56e-05 (0.00922)
Amp Peak 23(13q22 1)	0 (0%)	184	1.06e-07 (6.87e-05)	4.13e-05 (0.0238)	0.0948 (1.00)	0.288 (1.00)	0.000291 (0.147)	0.00171 (0.753)	0.00363 (1.00)	4.6e-05 (0.0262)	0.00474 (1.00)	3.79e-05 (0.0219)
Del Peak 27(12p13 31)	0 (0%)	255	9.87e-12 (6.92e-09)	5.7e-06 (0.00349)	0.609 (1.00)	0.932 (1.00)	1.49e-07 (9.69e-05)	1.36e-06 (0.000854)	0.0324 (1.00)	0.0112 (1.00)	0.239 (1.00)	5.52e-05 (0.0312)
Del Peak 38(19q13 11)	0 (0%)	262	3.88e-10 (2.66e-07)	8.49e-05 (0.0471)	0.134 (1.00)	0.763 (1.00)	0.000257 (0.131)	0.00683 (1.00)	0.00134 (0.605)	1.47e-06 (0.000926)	0.0059 (1.00)	8.5e-05 (0.0471)
Del Peak 41(21q11 2)	0 (0%)	198	5.88e-11 (4.1e-08)	2.71e-05 (0.0158)	0.282 (1.00)	0.172 (1.00)	0.000283 (0.143)	8.18e-07 (0.00052)	0.000211 (0.11)	0.0213 (1.00)	0.0767 (1.00)	0.00191 (0.84)
Amp Peak 13(8q24 21)	0 (0%)	101	0.000626 (0.299)	4.46e-05 (0.0254)	0.377 (1.00)	0.624 (1.00)	0.00931 (1.00)	0.116 (1.00)	0.00128 (0.58)	0.000181 (0.0952)	0.00014 (0.0753)	0.000254 (0.129)
Amp Peak 24(15q26 1)	0 (0%)	236	1.24e-12 (8.86e-10)	0.000441 (0.216)	0.354 (1.00)	0.764 (1.00)	6.61e-05 (0.0371)	2.41e-05 (0.0141)	0.0633 (1.00)	0.0202 (1.00)	0.00855 (1.00)	0.0938 (1.00)
Del Peak 6(3p26 2)	0 (0%)	222	7.13e-12 (5.01e-09)	5.74e-05 (0.0324)	0.201 (1.00)	0.982 (1.00)	0.00151 (0.672)	0.0112 (1.00)	0.000453 (0.221)	0.000238 (0.122)	0.0833 (1.00)	0.00257 (1.00)
Del Peak 25(11p15 4)	0 (0%)	246	2.15e-08 (1.43e-05)	8.05e-06 (0.00485)	1.57e-05 (0.00926)	0.00118 (0.541)	0.00456 (1.00)	0.000842 (0.396)	0.492 (1.00)	8.29e-05 (0.0461)	0.256 (1.00)	0.00599 (1.00)
Del Peak 29(14q21 1)	0 (0%)	234	9.49e-09 (6.37e-06)	0.0159 (1.00)	0.181 (1.00)	0.479 (1.00)	0.000157 (0.084)	0.000189 (0.0987)	0.0049 (1.00)	0.000533 (0.257)	0.582 (1.00)	0.00039 (0.192)
Amp Peak 9(7p22 3)	0 (0%)	148	1.41e-18 (1.04e-15)	1.74e-05 (0.0102)	0.37 (1.00)	0.908 (1.00)	0.00152 (0.676)	0.0306 (1.00)	0.0126 (1.00)	0.00123 (0.558)	0.00408 (1.00)	0.000233 (0.12)
Del Peak 5(2q37 2)	0 (0%)	258	0.000202 (0.105)	0.00736 (1.00)	0.259 (1.00)	0.284 (1.00)	0.00685 (1.00)	0.389 (1.00)	0.0109 (1.00)	1.56e-06 (0.000979)	0.158 (1.00)	0.00039 (0.192)
Del Peak 10(4q22 1)	0 (0%)	170	6.41e-19 (4.76e-16)	3.85e-07 (0.000247)	0.144 (1.00)	0.767 (1.00)	0.00258 (1.00)	0.000907 (0.422)	0.0113 (1.00)	4.14e-05 (0.0238)	0.103 (1.00)	0.00452 (1.00)
Del Peak 19(9p23)	0 (0%)	185	3.41e-18 (2.52e-15)	8.76e-05 (0.0484)	0.0477 (1.00)	0.512 (1.00)	9.85e-06 (0.00589)	0.00231 (0.994)	0.0325 (1.00)	0.00453 (1.00)	0.852 (1.00)	0.00204 (0.894)
Del Peak 30(14q32 33)	0 (0%)	216	1.24e-09 (8.43e-07)	0.0422 (1.00)	0.876 (1.00)	0.589 (1.00)	0.000377 (0.186)	1.38e-05 (0.00818)	0.0344 (1.00)	0.1 (1.00)	0.108 (1.00)	0.0116 (1.00)
Del Peak 42(21q22 13)	0 (0%)	191	9.31e-11 (6.45e-08)	0.000362 (0.18)	0.0754 (1.00)	0.352 (1.00)	0.00234 (1.00)	8.78e-06 (0.00526)	0.00756 (1.00)	0.0086 (1.00)	0.0993 (1.00)	0.005 (1.00)
Amp Peak 18(11p13)	0 (0%)	251	0.0023 (0.992)	0.186 (1.00)	0.674 (1.00)	0.451 (1.00)	0.000988 (0.457)	0.000456 (0.222)	0.0493 (1.00)	2.48e-05 (0.0145)	0.275 (1.00)	0.0054 (1.00)
Amp Peak 21(12q15)	0 (0%)	228	0.000162 (0.0858)	0.000489 (0.237)	0.133 (1.00)	0.628 (1.00)	0.107 (1.00)	0.0177 (1.00)	0.145 (1.00)	0.0673 (1.00)	0.11 (1.00)	0.0551 (1.00)
Amp Peak 22(13q12 3)	0 (0%)	189	2.43e-10 (1.67e-07)	4.55e-06 (0.0028)	0.262 (1.00)	0.428 (1.00)	0.00782 (1.00)	0.375 (1.00)	0.00969 (1.00)	0.00683 (1.00)	0.0596 (1.00)	0.00918 (1.00)
Amp Peak 26(18q11 2)	0 (0%)	215	1.75e-07 (0.000113)	0.000306 (0.154)	0.306 (1.00)	0.0364 (1.00)	0.00666 (1.00)	0.0147 (1.00)	0.0386 (1.00)	0.0135 (1.00)	0.0322 (1.00)	0.0423 (1.00)
Del Peak 2(1p13 2)	0 (0%)	246	4.74e-13 (3.4e-10)	0.00669 (1.00)	0.128 (1.00)	0.169 (1.00)	0.000147 (0.0787)	0.000575 (0.276)	0.00347 (1.00)	0.0114 (1.00)	0.404 (1.00)	0.0272 (1.00)
Del Peak 8(3q26 31)	0 (0%)	271	9.89e-06 (0.0059)	0.000107 (0.0586)	0.193 (1.00)	0.711 (1.00)	0.00136 (0.611)	0.0068 (1.00)	0.000788 (0.372)	0.00632 (1.00)	0.166 (1.00)	0.0154 (1.00)
Del Peak 14(6p25 3)	0 (0%)	237	2.4e-07 (0.000155)	0.000576 (0.277)	0.466 (1.00)	0.205 (1.00)	0.00163 (0.724)	0.00124 (0.561)	0.0104 (1.00)	6.11e-06 (0.00372)	0.104 (1.00)	0.0105 (1.00)
Del Peak 15(6q26)	0 (0%)	243	7.24e-06 (0.00437)	0.0711 (1.00)	0.591 (1.00)	0.0901 (1.00)	0.00122 (0.554)	0.000394 (0.194)	0.279 (1.00)	0.0169 (1.00)	0.187 (1.00)	0.0908 (1.00)
Del Peak 16(7q31 1)	0 (0%)	261	2.75e-07 (0.000177)	0.00116 (0.533)	0.483 (1.00)	0.78 (1.00)	0.0266 (1.00)	0.0869 (1.00)	0.0168 (1.00)	0.0677 (1.00)	9.87e-05 (0.0543)	0.045 (1.00)
Del Peak 21(9q21 11)	0 (0%)	232	2.52e-12 (1.79e-09)	0.000223 (0.115)	0.163 (1.00)	0.528 (1.00)	0.0143 (1.00)	0.148 (1.00)	0.0225 (1.00)	0.0124 (1.00)	0.465 (1.00)	0.00116 (0.531)
Del Peak 23(10q22 3)	0 (0%)	256	4.61e-10 (3.16e-07)	0.000718 (0.34)	0.749 (1.00)	0.453 (1.00)	0.000185 (0.0971)	0.00948 (1.00)	0.0115 (1.00)	0.000677 (0.323)	0.117 (1.00)	0.0111 (1.00)
Del Peak 33(16q23 1)	0 (0%)	187	4.29e-08 (2.82e-05)	0.00289 (1.00)	0.683 (1.00)	0.243 (1.00)	0.00137 (0.614)	2.9e-05 (0.0168)	0.0106 (1.00)	0.0021 (0.917)	0.00224 (0.976)	0.00539 (1.00)
Del Peak 35(17q24 3)	0 (0%)	250	1.44e-10 (9.92e-08)	0.000251 (0.128)	0.399 (1.00)	0.357 (1.00)	0.000864 (0.404)	0.00806 (1.00)	0.00235 (1.00)	0.000809 (0.381)	0.0769 (1.00)	0.0987 (1.00)
Del Peak 39(20p12 1)	0 (0%)	253	2.86e-12 (2.03e-09)	0.000701 (0.333)	0.736 (1.00)	0.66 (1.00)	0.013 (1.00)	0.0158 (1.00)	0.000162 (0.0858)	0.00916 (1.00)	0.233 (1.00)	0.0143 (1.00)
Del Peak 40(20p12 1)	0 (0%)	253	2.86e-12 (2.03e-09)	0.000701 (0.333)	0.736 (1.00)	0.66 (1.00)	0.013 (1.00)	0.0158 (1.00)	0.000162 (0.0858)	0.00916 (1.00)	0.233 (1.00)	0.0143 (1.00)
Del Peak 44(Xp22 2)	0 (0%)	244	1.04e-09 (7.12e-07)	0.00162 (0.72)	0.391 (1.00)	0.617 (1.00)	0.00326 (1.00)	0.0288 (1.00)	0.143 (1.00)	0.000375 (0.186)	0.676 (1.00)	0.00728 (1.00)
Amp Peak 1(1p36 22)	0 (0%)	269	5.23e-08 (3.43e-05)	0.00304 (1.00)	0.637 (1.00)	0.0881 (1.00)	0.000854 (0.4)	0.00887 (1.00)	0.975 (1.00)	0.0249 (1.00)	0.758 (1.00)	0.0247 (1.00)
Amp Peak 4(3q26 2)	0 (0%)	204	6.78e-05 (0.038)	0.00743 (1.00)	0.972 (1.00)	0.0986 (1.00)	0.369 (1.00)	0.325 (1.00)	0.425 (1.00)	0.146 (1.00)	0.319 (1.00)	0.00418 (1.00)
Amp Peak 10(7p11 2)	0 (0%)	162	5.33e-16 (3.91e-13)	0.00995 (1.00)	0.828 (1.00)	0.921 (1.00)	0.111 (1.00)	0.448 (1.00)	0.0221 (1.00)	0.0315 (1.00)	0.0178 (1.00)	0.0437 (1.00)
Amp Peak 11(7q21 2)	0 (0%)	168	3.07e-15 (2.25e-12)	0.0196 (1.00)	0.211 (1.00)	0.625 (1.00)	0.366 (1.00)	0.41 (1.00)	0.299 (1.00)	0.174 (1.00)	0.287 (1.00)	0.0839 (1.00)
Amp Peak 15(9q34 3)	0 (0%)	231	2.12e-06 (0.00132)	0.00517 (1.00)	0.671 (1.00)	0.175 (1.00)	0.0214 (1.00)	0.0103 (1.00)	0.215 (1.00)	0.081 (1.00)	0.0321 (1.00)	0.0143 (1.00)
Amp Peak 16(10q22 2)	0 (0%)	249	6.25e-06 (0.0038)	0.0746 (1.00)	0.0366 (1.00)	0.204 (1.00)	0.0116 (1.00)	0.00825 (1.00)	0.105 (1.00)	0.0487 (1.00)	0.173 (1.00)	0.0438 (1.00)
Amp Peak 17(10q26 13)	0 (0%)	244	0.000361 (0.18)	0.00128 (0.58)	0.0511 (1.00)	0.256 (1.00)	0.00289 (1.00)	0.0036 (1.00)	0.444 (1.00)	0.00919 (1.00)	0.895 (1.00)	0.0158 (1.00)
Amp Peak 19(11q13 3)	0 (0%)	237	7.17e-06 (0.00434)	0.194 (1.00)	0.194 (1.00)	0.718 (1.00)	0.105 (1.00)	0.0129 (1.00)	0.00059 (0.283)	0.0437 (1.00)	0.0129 (1.00)	0.0539 (1.00)
Amp Peak 20(12p12 1)	0 (0%)	219	6.12e-05 (0.0344)	0.0114 (1.00)	0.341 (1.00)	0.0872 (1.00)	0.298 (1.00)	0.439 (1.00)	0.0167 (1.00)	0.101 (1.00)	0.0131 (1.00)	0.0877 (1.00)
Amp Peak 29(Xq27 3)	0 (0%)	245	2.18e-05 (0.0128)	0.191 (1.00)	0.98 (1.00)	0.633 (1.00)	0.055 (1.00)	0.646 (1.00)	0.0553 (1.00)	0.932 (1.00)	0.0715 (1.00)	0.228 (1.00)
Del Peak 4(2q32 1)	0 (0%)	263	0.000291 (0.147)	0.108 (1.00)	0.49 (1.00)	0.221 (1.00)	0.086 (1.00)	0.83 (1.00)	0.403 (1.00)	0.033 (1.00)	0.617 (1.00)	0.515 (1.00)
Del Peak 22(10p15 1)	0 (0%)	267	0.000115 (0.0627)	0.277 (1.00)	0.412 (1.00)	0.616 (1.00)	0.244 (1.00)	0.234 (1.00)	0.132 (1.00)	0.0423 (1.00)	0.154 (1.00)	0.406 (1.00)
Del Peak 28(13q12 11)	0 (0%)	261	9.84e-05 (0.0542)	0.126 (1.00)	0.435 (1.00)	0.082 (1.00)	0.259 (1.00)	0.0295 (1.00)	0.509 (1.00)	0.0729 (1.00)	0.868 (1.00)	0.0495 (1.00)
Del Peak 36(18q21 2)	0 (0%)	172	3.44e-14 (2.48e-11)	0.00256 (1.00)	0.736 (1.00)	0.933 (1.00)	0.000569 (0.274)	0.00196 (0.862)	0.0136 (1.00)	0.00304 (1.00)	0.148 (1.00)	0.0146 (1.00)
Del Peak 45(Xp21 1)	0 (0%)	253	6.99e-09 (4.69e-06)	0.00407 (1.00)	0.0483 (1.00)	0.913 (1.00)	0.0904 (1.00)	0.013 (1.00)	0.683 (1.00)	0.0952 (1.00)	0.976 (1.00)	0.113 (1.00)
Del Peak 46(Xq21 33)	0 (0%)	263	7.29e-06 (0.00439)	0.0352 (1.00)	0.731 (1.00)	0.329 (1.00)	0.0293 (1.00)	0.00284 (1.00)	0.106 (1.00)	0.0253 (1.00)	0.482 (1.00)	0.0232 (1.00)
Amp Peak 12(8p23 1)	0 (0%)	184	0.000862 (0.404)	0.00298 (1.00)	0.611 (1.00)	0.716 (1.00)	0.0283 (1.00)	0.00238 (1.00)	0.304 (1.00)	0.0225 (1.00)	0.161 (1.00)	0.0393 (1.00)
Amp Peak 14(9p24 1)	0 (0%)	256	0.582 (1.00)	0.0878 (1.00)	0.615 (1.00)	0.0148 (1.00)	0.0893 (1.00)	0.0473 (1.00)	0.188 (1.00)	0.0139 (1.00)	0.0299 (1.00)	0.13 (1.00)
Del Peak 3(1q44)	0 (0%)	282	0.0145 (1.00)	0.00748 (1.00)	0.618 (1.00)	0.207 (1.00)	0.17 (1.00)	0.0129 (1.00)	0.166 (1.00)	0.133 (1.00)	0.0502 (1.00)	0.0853 (1.00)
Del Peak 26(11q23 2)	0 (0%)	243	0.00069 (0.328)	0.00167 (0.736)	0.791 (1.00)	0.513 (1.00)	0.00707 (1.00)	0.233 (1.00)	0.326 (1.00)	0.538 (1.00)	0.421 (1.00)	0.622 (1.00)

'Amp Peak 1(1p36.22)' versus 'CN_CNMF'

P value = 5.23e-08 (Fisher's exact test), Q value = 3.4e-05

Table S1. Gene #1: 'Amp Peak 1(1p36.22)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
AMP PEAK 1(1P36.22) CNV	3	7	26
AMP PEAK 1(1P36.22) WILD-TYPE	147	39	83

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1p36.22)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 2(1q21.3)' versus 'CN_CNMF'

P value = 1.99e-18 (Fisher's exact test), Q value = 1.5e-15

Table S2. Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
AMP PEAK 2(1Q21.3) CNV	17	24	67
AMP PEAK 2(1Q21.3) WILD-TYPE	133	22	42

Figure S2. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 2(1q21.3)' versus 'METHLYATION_CNMF'

P value = 4.32e-11 (Fisher's exact test), Q value = 3e-08

Table S3. Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
AMP PEAK 2(1Q21.3) CNV	4	26	11	50
AMP PEAK 2(1Q21.3) WILD-TYPE	33	54	54	26

Figure S3. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 2(1q21.3)' versus 'MRNASEQ_CNMF'

P value = 3.14e-12 (Chi-square test), Q value = 2.2e-09

Table S4. Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	63	43	42	62
AMP PEAK 2(1Q21.3) CNV	11	10	14	14	46
AMP PEAK 2(1Q21.3) WILD-TYPE	50	53	29	28	16

Figure S4. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Amp Peak 2(1q21.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.74e-07 (Fisher's exact test), Q value = 3e-04

Table S5. Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	141	64
AMP PEAK 2(1Q21.3) CNV	11	45	39
AMP PEAK 2(1Q21.3) WILD-TYPE	55	96	25

Figure S5. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 2(1q21.3)' versus 'MIRSEQ_CNMF'

P value = 9.54e-09 (Fisher's exact test), Q value = 6.4e-06

Table S6. Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	91	114
AMP PEAK 2(1Q21.3) CNV	24	19	65
AMP PEAK 2(1Q21.3) WILD-TYPE	76	72	49

Figure S6. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Amp Peak 2(1q21.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.09e-08 (Fisher's exact test), Q value = 2e-05

Table S7. Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	133	77	95
AMP PEAK 2(1Q21.3) CNV	35	49	24
AMP PEAK 2(1Q21.3) WILD-TYPE	98	28	71

Figure S7. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 2(1q21.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000347 (Fisher's exact test), Q value = 0.17

Table S8. Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	78	127
AMP PEAK 2(1Q21.3) CNV	13	18	60
AMP PEAK 2(1Q21.3) WILD-TYPE	41	60	67

Figure S8. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 2(1q21.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.39e-10 (Fisher's exact test), Q value = 4.4e-07

Table S9. Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	72	130
AMP PEAK 2(1Q21.3) CNV	40	12	39
AMP PEAK 2(1Q21.3) WILD-TYPE	17	60	91

Figure S9. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 3(1q42.3)' versus 'CN_CNMF'

P value = 3.53e-14 (Fisher's exact test), Q value = 2.6e-11

Table S10. Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
AMP PEAK 3(1Q42.3) CNV	20	24	61
AMP PEAK 3(1Q42.3) WILD-TYPE	130	22	48

Figure S10. Get High-res Image Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 3(1q42.3)' versus 'METHLYATION_CNMF'

P value = 1.15e-07 (Fisher's exact test), Q value = 7.5e-05

Table S11. Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
AMP PEAK 3(1Q42.3) CNV	5	24	14	46
AMP PEAK 3(1Q42.3) WILD-TYPE	32	56	51	30

Figure S11. Get High-res Image Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 3(1q42.3)' versus 'MRNASEQ_CNMF'

P value = 4.21e-09 (Chi-square test), Q value = 2.8e-06

Table S12. Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	63	43	42	62
AMP PEAK 3(1Q42.3) CNV	12	13	10	13	42
AMP PEAK 3(1Q42.3) WILD-TYPE	49	50	33	29	20

Figure S12. Get High-res Image Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Amp Peak 3(1q42.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000172 (Fisher's exact test), Q value = 0.09

Table S13. Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	141	64
AMP PEAK 3(1Q42.3) CNV	15	40	35
AMP PEAK 3(1Q42.3) WILD-TYPE	51	101	29

Figure S13. Get High-res Image Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 3(1q42.3)' versus 'MIRSEQ_CNMF'

P value = 1.93e-08 (Fisher's exact test), Q value = 1.3e-05

Table S14. Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	91	114
AMP PEAK 3(1Q42.3) CNV	19	23	63
AMP PEAK 3(1Q42.3) WILD-TYPE	81	68	51

Figure S14. Get High-res Image Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Amp Peak 3(1q42.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.61e-09 (Fisher's exact test), Q value = 4.4e-06

Table S15. Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	133	77	95
AMP PEAK 3(1Q42.3) CNV	31	49	25
AMP PEAK 3(1Q42.3) WILD-TYPE	102	28	70

Figure S15. Get High-res Image Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 3(1q42.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.28e-08 (Fisher's exact test), Q value = 4.8e-05

Table S16. Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	72	130
AMP PEAK 3(1Q42.3) CNV	38	15	37
AMP PEAK 3(1Q42.3) WILD-TYPE	19	57	93

Figure S16. Get High-res Image Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 6.78e-05 (Fisher's exact test), Q value = 0.038

Table S17. Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
AMP PEAK 4(3Q26.2) CNV	32	19	50
AMP PEAK 4(3Q26.2) WILD-TYPE	118	27	59

Figure S17. Get High-res Image Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 7.48e-14 (Fisher's exact test), Q value = 5.4e-11

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
AMP PEAK 5(5P13.1) CNV	14	17	56
AMP PEAK 5(5P13.1) WILD-TYPE	136	29	53

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

'Amp Peak 5(5p13.1)' versus 'METHLYATION_CNMF'

P value = 2.09e-07 (Fisher's exact test), Q value = 0.00014

Table S19. Gene #5: 'Amp Peak 5(5p13.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
AMP PEAK 5(5P13.1) CNV	7	20	6	39
AMP PEAK 5(5P13.1) WILD-TYPE	30	60	59	37

Figure S19. Get High-res Image Gene #5: 'Amp Peak 5(5p13.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 2.52e-08 (Chi-square test), Q value = 1.7e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	63	43	42	62
AMP PEAK 5(5P13.1) CNV	11	9	9	10	37
AMP PEAK 5(5P13.1) WILD-TYPE	50	54	34	32	25

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

'Amp Peak 5(5p13.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000161 (Fisher's exact test), Q value = 0.086

Table S21. Gene #5: 'Amp Peak 5(5p13.1)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	141	64
AMP PEAK 5(5P13.1) CNV	11	34	31
AMP PEAK 5(5P13.1) WILD-TYPE	55	107	33

Figure S21. Get High-res Image Gene #5: 'Amp Peak 5(5p13.1)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

P value = 0.000347 (Fisher's exact test), Q value = 0.17

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	91	114
AMP PEAK 5(5P13.1) CNV	21	18	48
AMP PEAK 5(5P13.1) WILD-TYPE	79	73	66

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

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

P value = 1.99e-06 (Fisher's exact test), Q value = 0.0012

Table S23. Gene #5: 'Amp Peak 5(5p13.1)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	133	77	95
AMP PEAK 5(5P13.1) CNV	26	40	21
AMP PEAK 5(5P13.1) WILD-TYPE	107	37	74

Figure S23. Get High-res Image Gene #5: 'Amp Peak 5(5p13.1)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

P value = 5.84e-06 (Fisher's exact test), Q value = 0.0036

Table S24. Gene #5: 'Amp Peak 5(5p13.1)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	72	130
AMP PEAK 5(5P13.1) CNV	30	10	32
AMP PEAK 5(5P13.1) WILD-TYPE	27	62	98

Figure S24. Get High-res Image Gene #5: 'Amp Peak 5(5p13.1)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 2.84e-16 (Fisher's exact test), Q value = 2.1e-13

Table S25. Gene #6: 'Amp Peak 6(6p21.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
AMP PEAK 6(6P21.1) CNV	9	17	54
AMP PEAK 6(6P21.1) WILD-TYPE	141	29	55

Figure S25. Get High-res Image Gene #6: 'Amp Peak 6(6p21.1)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 2.19e-10 (Fisher's exact test), Q value = 1.5e-07

Table S26. Gene #6: 'Amp Peak 6(6p21.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
AMP PEAK 6(6P21.1) CNV	1	20	5	38
AMP PEAK 6(6P21.1) WILD-TYPE	36	60	60	38

Figure S26. Get High-res Image Gene #6: 'Amp Peak 6(6p21.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 6(6p21.1)' versus 'MRNASEQ_CNMF'

P value = 0.000233 (Chi-square test), Q value = 0.12

Table S27. Gene #6: 'Amp Peak 6(6p21.1)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	63	43	42	62
AMP PEAK 6(6P21.1) CNV	9	10	10	12	29
AMP PEAK 6(6P21.1) WILD-TYPE	52	53	33	30	33

Figure S27. Get High-res Image Gene #6: 'Amp Peak 6(6p21.1)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Amp Peak 6(6p21.1)' versus 'MIRSEQ_CNMF'

P value = 6.05e-05 (Fisher's exact test), Q value = 0.034

Table S28. Gene #6: 'Amp Peak 6(6p21.1)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	91	114
AMP PEAK 6(6P21.1) CNV	21	13	46
AMP PEAK 6(6P21.1) WILD-TYPE	79	78	68

Figure S28. Get High-res Image Gene #6: 'Amp Peak 6(6p21.1)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Amp Peak 6(6p21.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.3e-06 (Fisher's exact test), Q value = 0.00082

Table S29. Gene #6: 'Amp Peak 6(6p21.1)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	133	77	95
AMP PEAK 6(6P21.1) CNV	27	38	15
AMP PEAK 6(6P21.1) WILD-TYPE	106	39	80

Figure S29. Get High-res Image Gene #6: 'Amp Peak 6(6p21.1)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 6(6p21.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.96e-06 (Fisher's exact test), Q value = 0.0031

Table S30. Gene #6: 'Amp Peak 6(6p21.1)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	72	130
AMP PEAK 6(6P21.1) CNV	28	8	29
AMP PEAK 6(6P21.1) WILD-TYPE	29	64	101

Figure S30. Get High-res Image Gene #6: 'Amp Peak 6(6p21.1)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 1.37e-09 (Fisher's exact test), Q value = 9.3e-07

Table S31. Gene #7: 'Amp Peak 7(6q12)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
AMP PEAK 7(6Q12) CNV	9	11	40
AMP PEAK 7(6Q12) WILD-TYPE	141	35	69

Figure S31. Get High-res Image Gene #7: 'Amp Peak 7(6q12)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 2.31e-08 (Fisher's exact test), Q value = 1.5e-05

Table S32. Gene #7: 'Amp Peak 7(6q12)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
AMP PEAK 7(6Q12) CNV	1	14	2	29
AMP PEAK 7(6Q12) WILD-TYPE	36	66	63	47

Figure S32. Get High-res Image Gene #7: 'Amp Peak 7(6q12)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 4.18e-06 (Chi-square test), Q value = 0.0026

Table S33. Gene #7: 'Amp Peak 7(6q12)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	63	43	42	62
AMP PEAK 7(6Q12) CNV	5	7	8	7	27
AMP PEAK 7(6Q12) WILD-TYPE	56	56	35	35	35

Figure S33. Get High-res Image Gene #7: 'Amp Peak 7(6q12)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

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

P value = 0.000118 (Fisher's exact test), Q value = 0.064

Table S34. Gene #7: 'Amp Peak 7(6q12)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	141	64
AMP PEAK 7(6Q12) CNV	7	22	25
AMP PEAK 7(6Q12) WILD-TYPE	59	119	39

Figure S34. Get High-res Image Gene #7: 'Amp Peak 7(6q12)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

P value = 5.15e-05 (Fisher's exact test), Q value = 0.029

Table S35. Gene #7: 'Amp Peak 7(6q12)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	133	77	95
AMP PEAK 7(6Q12) CNV	20	29	11
AMP PEAK 7(6Q12) WILD-TYPE	113	48	84

Figure S35. Get High-res Image Gene #7: 'Amp Peak 7(6q12)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

P value = 4.63e-06 (Fisher's exact test), Q value = 0.0029

Table S36. Gene #7: 'Amp Peak 7(6q12)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	72	130
AMP PEAK 7(6Q12) CNV	23	5	18
AMP PEAK 7(6Q12) WILD-TYPE	34	67	112

Figure S36. Get High-res Image Gene #7: 'Amp Peak 7(6q12)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 8(6q21)' versus 'CN_CNMF'

P value = 3.9e-08 (Fisher's exact test), Q value = 2.6e-05

Table S37. Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
AMP PEAK 8(6Q21) CNV	9	11	36
AMP PEAK 8(6Q21) WILD-TYPE	141	35	73

Figure S37. Get High-res Image Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 8(6q21)' versus 'METHLYATION_CNMF'

P value = 1.68e-05 (Fisher's exact test), Q value = 0.0099

Table S38. Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
AMP PEAK 8(6Q21) CNV	1	13	4	25
AMP PEAK 8(6Q21) WILD-TYPE	36	67	61	51

Figure S38. Get High-res Image Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 8(6q21)' versus 'MRNASEQ_CNMF'

P value = 2.74e-05 (Chi-square test), Q value = 0.016

Table S39. Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	63	43	42	62
AMP PEAK 8(6Q21) CNV	6	7	7	5	25
AMP PEAK 8(6Q21) WILD-TYPE	55	56	36	37	37

Figure S39. Get High-res Image Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Amp Peak 8(6q21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.11e-05 (Fisher's exact test), Q value = 0.0066

Table S40. Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	141	64
AMP PEAK 8(6Q21) CNV	5	20	25
AMP PEAK 8(6Q21) WILD-TYPE	61	121	39

Figure S40. Get High-res Image Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 8(6q21)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.56e-05 (Fisher's exact test), Q value = 0.0092

Table S41. Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	72	130
AMP PEAK 8(6Q21) CNV	21	4	18
AMP PEAK 8(6Q21) WILD-TYPE	36	68	112

Figure S41. Get High-res Image Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 9(7p22.3)' versus 'CN_CNMF'

P value = 1.41e-18 (Fisher's exact test), Q value = 1e-15

Table S42. Gene #9: 'Amp Peak 9(7p22.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
AMP PEAK 9(7P22.3) CNV	42	43	72
AMP PEAK 9(7P22.3) WILD-TYPE	108	3	37

Figure S42. Get High-res Image Gene #9: 'Amp Peak 9(7p22.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 9(7p22.3)' versus 'METHLYATION_CNMF'

P value = 1.74e-05 (Fisher's exact test), Q value = 0.01

Table S43. Gene #9: 'Amp Peak 9(7p22.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
AMP PEAK 9(7P22.3) CNV	17	47	18	51
AMP PEAK 9(7P22.3) WILD-TYPE	20	33	47	25

Figure S43. Get High-res Image Gene #9: 'Amp Peak 9(7p22.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 9(7p22.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000233 (Fisher's exact test), Q value = 0.12

Table S44. Gene #9: 'Amp Peak 9(7p22.3)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	72	130
AMP PEAK 9(7P22.3) CNV	42	28	63
AMP PEAK 9(7P22.3) WILD-TYPE	15	44	67

Figure S44. Get High-res Image Gene #9: 'Amp Peak 9(7p22.3)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 10(7p11.2)' versus 'CN_CNMF'

P value = 5.33e-16 (Fisher's exact test), Q value = 3.9e-13

Table S45. Gene #10: 'Amp Peak 10(7p11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
AMP PEAK 10(7P11.2) CNV	40	42	61
AMP PEAK 10(7P11.2) WILD-TYPE	110	4	48

Figure S45. Get High-res Image Gene #10: 'Amp Peak 10(7p11.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 11(7q21.2)' versus 'CN_CNMF'

P value = 3.07e-15 (Fisher's exact test), Q value = 2.2e-12

Table S46. Gene #11: 'Amp Peak 11(7q21.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
AMP PEAK 11(7Q21.2) CNV	40	42	55
AMP PEAK 11(7Q21.2) WILD-TYPE	110	4	54

Figure S46. Get High-res Image Gene #11: 'Amp Peak 11(7q21.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 13(8q24.21)' versus 'METHLYATION_CNMF'

P value = 4.46e-05 (Fisher's exact test), Q value = 0.025

Table S47. Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
AMP PEAK 13(8Q24.21) CNV	18	58	31	61
AMP PEAK 13(8Q24.21) WILD-TYPE	19	22	34	15

Figure S47. Get High-res Image Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 13(8q24.21)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000181 (Fisher's exact test), Q value = 0.095

Table S48. Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	133	77	95
AMP PEAK 13(8Q24.21) CNV	86	65	53
AMP PEAK 13(8Q24.21) WILD-TYPE	47	12	42

Figure S48. Get High-res Image Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 13(8q24.21)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.075

Table S49. Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	78	127
AMP PEAK 13(8Q24.21) CNV	35	37	97
AMP PEAK 13(8Q24.21) WILD-TYPE	19	41	30

Figure S49. Get High-res Image Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 13(8q24.21)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000254 (Fisher's exact test), Q value = 0.13

Table S50. Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	72	130
AMP PEAK 13(8Q24.21) CNV	47	35	87
AMP PEAK 13(8Q24.21) WILD-TYPE	10	37	43

Figure S50. Get High-res Image Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 15(9q34.3)' versus 'CN_CNMF'

P value = 2.12e-06 (Fisher's exact test), Q value = 0.0013

Table S51. Gene #15: 'Amp Peak 15(9q34.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
AMP PEAK 15(9Q34.3) CNV	18	14	42
AMP PEAK 15(9Q34.3) WILD-TYPE	132	32	67

Figure S51. Get High-res Image Gene #15: 'Amp Peak 15(9q34.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 16(10q22.2)' versus 'CN_CNMF'

P value = 6.25e-06 (Fisher's exact test), Q value = 0.0038

Table S52. Gene #16: 'Amp Peak 16(10q22.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
AMP PEAK 16(10Q22.2) CNV	14	6	36
AMP PEAK 16(10Q22.2) WILD-TYPE	136	40	73

Figure S52. Get High-res Image Gene #16: 'Amp Peak 16(10q22.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 17(10q26.13)' versus 'CN_CNMF'

P value = 0.000361 (Fisher's exact test), Q value = 0.18

Table S53. Gene #17: 'Amp Peak 17(10q26.13)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
AMP PEAK 17(10Q26.13) CNV	17	10	34
AMP PEAK 17(10Q26.13) WILD-TYPE	133	36	75

Figure S53. Get High-res Image Gene #17: 'Amp Peak 17(10q26.13)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 18(11p13)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000456 (Fisher's exact test), Q value = 0.22

Table S54. Gene #18: 'Amp Peak 18(11p13)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	141	64
AMP PEAK 18(11P13) CNV	12	14	21
AMP PEAK 18(11P13) WILD-TYPE	54	127	43

Figure S54. Get High-res Image Gene #18: 'Amp Peak 18(11p13)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 18(11p13)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.48e-05 (Fisher's exact test), Q value = 0.014

Table S55. Gene #18: 'Amp Peak 18(11p13)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	133	77	95
AMP PEAK 18(11P13) CNV	11	26	17
AMP PEAK 18(11P13) WILD-TYPE	122	51	78

Figure S55. Get High-res Image Gene #18: 'Amp Peak 18(11p13)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 19(11q13.3)' versus 'CN_CNMF'

P value = 7.17e-06 (Fisher's exact test), Q value = 0.0043

Table S56. Gene #19: 'Amp Peak 19(11q13.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
AMP PEAK 19(11Q13.3) CNV	18	9	41
AMP PEAK 19(11Q13.3) WILD-TYPE	132	37	68

Figure S56. Get High-res Image Gene #19: 'Amp Peak 19(11q13.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 20(12p12.1)' versus 'CN_CNMF'

P value = 6.12e-05 (Fisher's exact test), Q value = 0.034

Table S57. Gene #20: 'Amp Peak 20(12p12.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
AMP PEAK 20(12P12.1) CNV	27	12	47
AMP PEAK 20(12P12.1) WILD-TYPE	123	34	62

Figure S57. Get High-res Image Gene #20: 'Amp Peak 20(12p12.1)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 0.000162 (Fisher's exact test), Q value = 0.086

Table S58. Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
AMP PEAK 21(12Q15) CNV	26	8	43
AMP PEAK 21(12Q15) WILD-TYPE	124	38	66

Figure S58. Get High-res Image Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 0.000489 (Fisher's exact test), Q value = 0.24

Table S59. Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
AMP PEAK 21(12Q15) CNV	15	12	10	28
AMP PEAK 21(12Q15) WILD-TYPE	22	68	55	48

Figure S59. Get High-res Image Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 22(13q12.3)' versus 'CN_CNMF'

P value = 2.43e-10 (Fisher's exact test), Q value = 1.7e-07

Table S60. Gene #22: 'Amp Peak 22(13q12.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
AMP PEAK 22(13Q12.3) CNV	30	30	56
AMP PEAK 22(13Q12.3) WILD-TYPE	120	16	53

Figure S60. Get High-res Image Gene #22: 'Amp Peak 22(13q12.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 22(13q12.3)' versus 'METHLYATION_CNMF'

P value = 4.55e-06 (Fisher's exact test), Q value = 0.0028

Table S61. Gene #22: 'Amp Peak 22(13q12.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
AMP PEAK 22(13Q12.3) CNV	8	25	17	47
AMP PEAK 22(13Q12.3) WILD-TYPE	29	55	48	29

Figure S61. Get High-res Image Gene #22: 'Amp Peak 22(13q12.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 23(13q22.1)' versus 'CN_CNMF'

P value = 1.06e-07 (Fisher's exact test), Q value = 6.9e-05

Table S62. Gene #23: 'Amp Peak 23(13q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
AMP PEAK 23(13Q22.1) CNV	36	28	57
AMP PEAK 23(13Q22.1) WILD-TYPE	114	18	52

Figure S62. Get High-res Image Gene #23: 'Amp Peak 23(13q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 23(13q22.1)' versus 'METHLYATION_CNMF'

P value = 4.13e-05 (Fisher's exact test), Q value = 0.024

Table S63. Gene #23: 'Amp Peak 23(13q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
AMP PEAK 23(13Q22.1) CNV	11	24	17	46
AMP PEAK 23(13Q22.1) WILD-TYPE	26	56	48	30

Figure S63. Get High-res Image Gene #23: 'Amp Peak 23(13q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 23(13q22.1)' versus 'MRNASEQ_CNMF'

P value = 0.000291 (Chi-square test), Q value = 0.15

Table S64. Gene #23: 'Amp Peak 23(13q22.1)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	63	43	42	62
AMP PEAK 23(13Q22.1) CNV	21	16	11	20	37
AMP PEAK 23(13Q22.1) WILD-TYPE	40	47	32	22	25

Figure S64. Get High-res Image Gene #23: 'Amp Peak 23(13q22.1)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Amp Peak 23(13q22.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.6e-05 (Fisher's exact test), Q value = 0.026

Table S65. Gene #23: 'Amp Peak 23(13q22.1)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	133	77	95
AMP PEAK 23(13Q22.1) CNV	46	47	28
AMP PEAK 23(13Q22.1) WILD-TYPE	87	30	67

Figure S65. Get High-res Image Gene #23: 'Amp Peak 23(13q22.1)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 23(13q22.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.79e-05 (Fisher's exact test), Q value = 0.022

Table S66. Gene #23: 'Amp Peak 23(13q22.1)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	72	130
AMP PEAK 23(13Q22.1) CNV	36	19	43
AMP PEAK 23(13Q22.1) WILD-TYPE	21	53	87

Figure S66. Get High-res Image Gene #23: 'Amp Peak 23(13q22.1)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 24(15q26.1)' versus 'CN_CNMF'

P value = 1.24e-12 (Fisher's exact test), Q value = 8.9e-10

Table S67. Gene #24: 'Amp Peak 24(15q26.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
AMP PEAK 24(15Q26.1) CNV	11	8	50
AMP PEAK 24(15Q26.1) WILD-TYPE	139	38	59

Figure S67. Get High-res Image Gene #24: 'Amp Peak 24(15q26.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 24(15q26.1)' versus 'METHLYATION_CNMF'

P value = 0.000441 (Fisher's exact test), Q value = 0.22

Table S68. Gene #24: 'Amp Peak 24(15q26.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
AMP PEAK 24(15Q26.1) CNV	1	21	11	26
AMP PEAK 24(15Q26.1) WILD-TYPE	36	59	54	50

Figure S68. Get High-res Image Gene #24: 'Amp Peak 24(15q26.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 24(15q26.1)' versus 'MRNASEQ_CNMF'

P value = 6.61e-05 (Chi-square test), Q value = 0.037

Table S69. Gene #24: 'Amp Peak 24(15q26.1)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	63	43	42	62
AMP PEAK 24(15Q26.1) CNV	10	4	11	11	26
AMP PEAK 24(15Q26.1) WILD-TYPE	51	59	32	31	36

Figure S69. Get High-res Image Gene #24: 'Amp Peak 24(15q26.1)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Amp Peak 24(15q26.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.41e-05 (Fisher's exact test), Q value = 0.014

Table S70. Gene #24: 'Amp Peak 24(15q26.1)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	141	64
AMP PEAK 24(15Q26.1) CNV	7	27	28
AMP PEAK 24(15Q26.1) WILD-TYPE	59	114	36

Figure S70. Get High-res Image Gene #24: 'Amp Peak 24(15q26.1)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

P value = 1.12e-14 (Fisher's exact test), Q value = 8.1e-12

Table S71. Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
AMP PEAK 25(17Q12) CNV	16	15	61
AMP PEAK 25(17Q12) WILD-TYPE	134	31	48

Figure S71. Get High-res Image Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 2.68e-06 (Fisher's exact test), Q value = 0.0017

Table S72. Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
AMP PEAK 25(17Q12) CNV	11	16	11	41
AMP PEAK 25(17Q12) WILD-TYPE	26	64	54	35

Figure S72. Get High-res Image Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 0.000158 (Chi-square test), Q value = 0.084

Table S73. Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	63	43	42	62
AMP PEAK 25(17Q12) CNV	13	11	13	9	32
AMP PEAK 25(17Q12) WILD-TYPE	48	52	30	33	30

Figure S73. Get High-res Image Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

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

P value = 0.00022 (Fisher's exact test), Q value = 0.11

Table S74. Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	141	64
AMP PEAK 25(17Q12) CNV	11	36	31
AMP PEAK 25(17Q12) WILD-TYPE	55	105	33

Figure S74. Get High-res Image Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

P value = 0.000353 (Fisher's exact test), Q value = 0.18

Table S75. Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	91	114
AMP PEAK 25(17Q12) CNV	23	19	50
AMP PEAK 25(17Q12) WILD-TYPE	77	72	64

Figure S75. Get High-res Image Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

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

P value = 0.000163 (Fisher's exact test), Q value = 0.086

Table S76. Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	133	77	95
AMP PEAK 25(17Q12) CNV	30	38	24
AMP PEAK 25(17Q12) WILD-TYPE	103	39	71

Figure S76. Get High-res Image Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

P value = 1.75e-07 (Fisher's exact test), Q value = 0.00011

Table S77. Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
AMP PEAK 26(18Q11.2) CNV	25	12	53
AMP PEAK 26(18Q11.2) WILD-TYPE	125	34	56

Figure S77. Get High-res Image Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 0.000306 (Fisher's exact test), Q value = 0.15

Table S78. Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
AMP PEAK 26(18Q11.2) CNV	4	18	16	35
AMP PEAK 26(18Q11.2) WILD-TYPE	33	62	49	41

Figure S78. Get High-res Image Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 1.06e-15 (Fisher's exact test), Q value = 7.8e-13

Table S79. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
AMP PEAK 27(19Q12) CNV	15	13	62
AMP PEAK 27(19Q12) WILD-TYPE	135	33	47

Figure S79. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 1.01e-10 (Fisher's exact test), Q value = 7e-08

Table S80. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
AMP PEAK 27(19Q12) CNV	8	13	10	47
AMP PEAK 27(19Q12) WILD-TYPE	29	67	55	29

Figure S80. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 1.01e-13 (Chi-square test), Q value = 7.3e-11

Table S81. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	63	43	42	62
AMP PEAK 27(19Q12) CNV	10	8	8	8	43
AMP PEAK 27(19Q12) WILD-TYPE	51	55	35	34	19

Figure S81. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

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

P value = 5.62e-09 (Fisher's exact test), Q value = 3.8e-06

Table S82. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	141	64
AMP PEAK 27(19Q12) CNV	7	33	37
AMP PEAK 27(19Q12) WILD-TYPE	59	108	27

Figure S82. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

P value = 4.4e-06 (Fisher's exact test), Q value = 0.0027

Table S83. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	91	114
AMP PEAK 27(19Q12) CNV	20	17	53
AMP PEAK 27(19Q12) WILD-TYPE	80	74	61

Figure S83. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

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

P value = 2.1e-14 (Fisher's exact test), Q value = 1.5e-11

Table S84. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	133	77	95
AMP PEAK 27(19Q12) CNV	21	51	18
AMP PEAK 27(19Q12) WILD-TYPE	112	26	77

Figure S84. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

P value = 7.05e-13 (Fisher's exact test), Q value = 5.1e-10

Table S85. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	72	130
AMP PEAK 27(19Q12) CNV	41	12	26
AMP PEAK 27(19Q12) WILD-TYPE	16	60	104

Figure S85. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 28(20q13.2)' versus 'CN_CNMF'

P value = 2.4e-24 (Fisher's exact test), Q value = 1.8e-21

Table S86. Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
AMP PEAK 28(20Q13.2) CNV	58	45	98
AMP PEAK 28(20Q13.2) WILD-TYPE	92	1	11

Figure S86. Get High-res Image Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 28(20q13.2)' versus 'METHLYATION_CNMF'

P value = 4.24e-12 (Fisher's exact test), Q value = 3e-09

Table S87. Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
AMP PEAK 28(20Q13.2) CNV	27	42	29	72
AMP PEAK 28(20Q13.2) WILD-TYPE	10	38	36	4

Figure S87. Get High-res Image Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 28(20q13.2)' versus 'MRNASEQ_CNMF'

P value = 4.25e-08 (Chi-square test), Q value = 2.8e-05

Table S88. Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	63	43	42	62
AMP PEAK 28(20Q13.2) CNV	28	32	29	27	59
AMP PEAK 28(20Q13.2) WILD-TYPE	33	31	14	15	3

Figure S88. Get High-res Image Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Amp Peak 28(20q13.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.77e-05 (Fisher's exact test), Q value = 0.01

Table S89. Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	141	64
AMP PEAK 28(20Q13.2) CNV	32	88	55
AMP PEAK 28(20Q13.2) WILD-TYPE	34	53	9

Figure S89. Get High-res Image Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 28(20q13.2)' versus 'MIRSEQ_CNMF'

P value = 1.28e-06 (Fisher's exact test), Q value = 0.00081

Table S90. Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	91	114
AMP PEAK 28(20Q13.2) CNV	59	47	95
AMP PEAK 28(20Q13.2) WILD-TYPE	41	44	19

Figure S90. Get High-res Image Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Amp Peak 28(20q13.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.4e-12 (Fisher's exact test), Q value = 3.1e-09

Table S91. Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	133	77	95
AMP PEAK 28(20Q13.2) CNV	77	74	50
AMP PEAK 28(20Q13.2) WILD-TYPE	56	3	45

Figure S91. Get High-res Image Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 28(20q13.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.79e-09 (Fisher's exact test), Q value = 1.2e-06

Table S92. Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	72	130
AMP PEAK 28(20Q13.2) CNV	55	36	80
AMP PEAK 28(20Q13.2) WILD-TYPE	2	36	50

Figure S92. Get High-res Image Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 29(Xq27.3)' versus 'CN_CNMF'

P value = 2.18e-05 (Fisher's exact test), Q value = 0.013

Table S93. Gene #29: 'Amp Peak 29(Xq27.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
AMP PEAK 29(XQ27.3) CNV	14	15	31
AMP PEAK 29(XQ27.3) WILD-TYPE	136	31	78

Figure S93. Get High-res Image Gene #29: 'Amp Peak 29(Xq27.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 1(1p36.11)' versus 'CN_CNMF'

P value = 9.62e-15 (Fisher's exact test), Q value = 7e-12

Table S94. Gene #30: 'Del Peak 1(1p36.11)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 1(1P36.11) CNV	12	15	56
DEL PEAK 1(1P36.11) WILD-TYPE	138	31	53

Figure S94. Get High-res Image Gene #30: 'Del Peak 1(1p36.11)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 1(1p36.11)' versus 'METHLYATION_CNMF'

P value = 0.000396 (Fisher's exact test), Q value = 0.19

Table S95. Gene #30: 'Del Peak 1(1p36.11)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
DEL PEAK 1(1P36.11) CNV	4	21	9	31
DEL PEAK 1(1P36.11) WILD-TYPE	33	59	56	45

Figure S95. Get High-res Image Gene #30: 'Del Peak 1(1p36.11)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 1(1p36.11)' versus 'MRNASEQ_CNMF'

P value = 0.000113 (Chi-square test), Q value = 0.062

Table S96. Gene #30: 'Del Peak 1(1p36.11)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	63	43	42	62
DEL PEAK 1(1P36.11) CNV	12	6	15	12	28
DEL PEAK 1(1P36.11) WILD-TYPE	49	57	28	30	34

Figure S96. Get High-res Image Gene #30: 'Del Peak 1(1p36.11)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 1(1p36.11)' versus 'MIRSEQ_CNMF'

P value = 7.87e-05 (Fisher's exact test), Q value = 0.044

Table S97. Gene #30: 'Del Peak 1(1p36.11)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	91	114
DEL PEAK 1(1P36.11) CNV	28	11	44
DEL PEAK 1(1P36.11) WILD-TYPE	72	80	70

Figure S97. Get High-res Image Gene #30: 'Del Peak 1(1p36.11)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 1(1p36.11)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.84e-05 (Fisher's exact test), Q value = 0.044

Table S98. Gene #30: 'Del Peak 1(1p36.11)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	133	77	95
DEL PEAK 1(1P36.11) CNV	33	35	15
DEL PEAK 1(1P36.11) WILD-TYPE	100	42	80

Figure S98. Get High-res Image Gene #30: 'Del Peak 1(1p36.11)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 1(1p36.11)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.17

Table S99. Gene #30: 'Del Peak 1(1p36.11)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	72	130
DEL PEAK 1(1P36.11) CNV	26	11	29
DEL PEAK 1(1P36.11) WILD-TYPE	31	61	101

Figure S99. Get High-res Image Gene #30: 'Del Peak 1(1p36.11)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 4.74e-13 (Fisher's exact test), Q value = 3.4e-10

Table S100. Gene #31: 'Del Peak 2(1p13.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 2(1P13.2) CNV	5	13	41
DEL PEAK 2(1P13.2) WILD-TYPE	145	33	68

Figure S100. Get High-res Image Gene #31: 'Del Peak 2(1p13.2)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 0.000147 (Chi-square test), Q value = 0.079

Table S101. Gene #31: 'Del Peak 2(1p13.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	63	43	42	62
DEL PEAK 2(1P13.2) CNV	9	4	5	8	23
DEL PEAK 2(1P13.2) WILD-TYPE	52	59	38	34	39

Figure S101. Get High-res Image Gene #31: 'Del Peak 2(1p13.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 4(2q32.1)' versus 'CN_CNMF'

P value = 0.000291 (Fisher's exact test), Q value = 0.15

Table S102. Gene #33: 'Del Peak 4(2q32.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 4(2Q32.1) CNV	12	3	27
DEL PEAK 4(2Q32.1) WILD-TYPE	138	43	82

Figure S102. Get High-res Image Gene #33: 'Del Peak 4(2q32.1)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 0.000202 (Fisher's exact test), Q value = 0.11

Table S103. Gene #34: 'Del Peak 5(2q37.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 5(2Q37.2) CNV	11	8	28
DEL PEAK 5(2Q37.2) WILD-TYPE	139	38	81

Figure S103. Get High-res Image Gene #34: 'Del Peak 5(2q37.2)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 1.56e-06 (Fisher's exact test), Q value = 0.00098

Table S104. Gene #34: 'Del Peak 5(2q37.2)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	133	77	95
DEL PEAK 5(2Q37.2) CNV	12	27	8
DEL PEAK 5(2Q37.2) WILD-TYPE	121	50	87

Figure S104. Get High-res Image Gene #34: 'Del Peak 5(2q37.2)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 5(2q37.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.19

Table S105. Gene #34: 'Del Peak 5(2q37.2)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	72	130
DEL PEAK 5(2Q37.2) CNV	19	5	19
DEL PEAK 5(2Q37.2) WILD-TYPE	38	67	111

Figure S105. Get High-res Image Gene #34: 'Del Peak 5(2q37.2)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 6(3p26.2)' versus 'CN_CNMF'

P value = 7.13e-12 (Fisher's exact test), Q value = 5e-09

Table S106. Gene #35: 'Del Peak 6(3p26.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 6(3P26.2) CNV	14	20	49
DEL PEAK 6(3P26.2) WILD-TYPE	136	26	60

Figure S106. Get High-res Image Gene #35: 'Del Peak 6(3p26.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 6(3p26.2)' versus 'METHLYATION_CNMF'

P value = 5.74e-05 (Fisher's exact test), Q value = 0.032

Table S107. Gene #35: 'Del Peak 6(3p26.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
DEL PEAK 6(3P26.2) CNV	7	22	7	34
DEL PEAK 6(3P26.2) WILD-TYPE	30	58	58	42

Figure S107. Get High-res Image Gene #35: 'Del Peak 6(3p26.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 6(3p26.2)' versus 'MIRSEQ_CNMF'

P value = 0.000453 (Fisher's exact test), Q value = 0.22

Table S108. Gene #35: 'Del Peak 6(3p26.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	91	114
DEL PEAK 6(3P26.2) CNV	19	18	46
DEL PEAK 6(3P26.2) WILD-TYPE	81	73	68

Figure S108. Get High-res Image Gene #35: 'Del Peak 6(3p26.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 6(3p26.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000238 (Fisher's exact test), Q value = 0.12

Table S109. Gene #35: 'Del Peak 6(3p26.2)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	133	77	95
DEL PEAK 6(3P26.2) CNV	30	35	18
DEL PEAK 6(3P26.2) WILD-TYPE	103	42	77

Figure S109. Get High-res Image Gene #35: 'Del Peak 6(3p26.2)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 7(3p14.2)' versus 'CN_CNMF'

P value = 6.14e-11 (Fisher's exact test), Q value = 4.3e-08

Table S110. Gene #36: 'Del Peak 7(3p14.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 7(3P14.2) CNV	23	20	59
DEL PEAK 7(3P14.2) WILD-TYPE	127	26	50

Figure S110. Get High-res Image Gene #36: 'Del Peak 7(3p14.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 7(3p14.2)' versus 'METHLYATION_CNMF'

P value = 1.24e-06 (Fisher's exact test), Q value = 0.00078

Table S111. Gene #36: 'Del Peak 7(3p14.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
DEL PEAK 7(3P14.2) CNV	13	26	8	42
DEL PEAK 7(3P14.2) WILD-TYPE	24	54	57	34

Figure S111. Get High-res Image Gene #36: 'Del Peak 7(3p14.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 7(3p14.2)' versus 'MRNASEQ_CNMF'

P value = 0.000242 (Chi-square test), Q value = 0.12

Table S112. Gene #36: 'Del Peak 7(3p14.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	63	43	42	62
DEL PEAK 7(3P14.2) CNV	16	10	13	15	33
DEL PEAK 7(3P14.2) WILD-TYPE	45	53	30	27	29

Figure S112. Get High-res Image Gene #36: 'Del Peak 7(3p14.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 7(3p14.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.12

Table S113. Gene #36: 'Del Peak 7(3p14.2)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	141	64
DEL PEAK 7(3P14.2) CNV	11	44	32
DEL PEAK 7(3P14.2) WILD-TYPE	55	97	32

Figure S113. Get High-res Image Gene #36: 'Del Peak 7(3p14.2)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 7(3p14.2)' versus 'MIRSEQ_CNMF'

P value = 0.000363 (Fisher's exact test), Q value = 0.18

Table S114. Gene #36: 'Del Peak 7(3p14.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	91	114
DEL PEAK 7(3P14.2) CNV	27	21	54
DEL PEAK 7(3P14.2) WILD-TYPE	73	70	60

Figure S114. Get High-res Image Gene #36: 'Del Peak 7(3p14.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 7(3p14.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.35e-05 (Fisher's exact test), Q value = 0.025

Table S115. Gene #36: 'Del Peak 7(3p14.2)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	133	77	95
DEL PEAK 7(3P14.2) CNV	41	41	20
DEL PEAK 7(3P14.2) WILD-TYPE	92	36	75

Figure S115. Get High-res Image Gene #36: 'Del Peak 7(3p14.2)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 7(3p14.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.08e-06 (Fisher's exact test), Q value = 0.0037

Table S116. Gene #36: 'Del Peak 7(3p14.2)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	72	130
DEL PEAK 7(3P14.2) CNV	33	12	44
DEL PEAK 7(3P14.2) WILD-TYPE	24	60	86

Figure S116. Get High-res Image Gene #36: 'Del Peak 7(3p14.2)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 8(3q26.31)' versus 'CN_CNMF'

P value = 9.89e-06 (Fisher's exact test), Q value = 0.0059

Table S117. Gene #37: 'Del Peak 8(3q26.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 8(3Q26.31) CNV	5	5	24
DEL PEAK 8(3Q26.31) WILD-TYPE	145	41	85

Figure S117. Get High-res Image Gene #37: 'Del Peak 8(3q26.31)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 8(3q26.31)' versus 'METHLYATION_CNMF'

P value = 0.000107 (Fisher's exact test), Q value = 0.059

Table S118. Gene #37: 'Del Peak 8(3q26.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
DEL PEAK 8(3Q26.31) CNV	2	11	0	16
DEL PEAK 8(3Q26.31) WILD-TYPE	35	69	65	60

Figure S118. Get High-res Image Gene #37: 'Del Peak 8(3q26.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 6.3e-12 (Fisher's exact test), Q value = 4.4e-09

Table S119. Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 9(4P16.3) CNV	26	22	64
DEL PEAK 9(4P16.3) WILD-TYPE	124	24	45

Figure S119. Get High-res Image Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 0.000126 (Chi-square test), Q value = 0.068

Table S120. Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	63	43	42	62
DEL PEAK 9(4P16.3) CNV	11	23	14	12	36
DEL PEAK 9(4P16.3) WILD-TYPE	50	40	29	30	26

Figure S120. Get High-res Image Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

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

P value = 0.000207 (Fisher's exact test), Q value = 0.11

Table S121. Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	141	64
DEL PEAK 9(4P16.3) CNV	23	37	36
DEL PEAK 9(4P16.3) WILD-TYPE	43	104	28

Figure S121. Get High-res Image Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

P value = 0.000183 (Fisher's exact test), Q value = 0.096

Table S122. Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	91	114
DEL PEAK 9(4P16.3) CNV	22	34	56
DEL PEAK 9(4P16.3) WILD-TYPE	78	57	58

Figure S122. Get High-res Image Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

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

P value = 1.1e-06 (Fisher's exact test), Q value = 7e-04

Table S123. Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	133	77	95
DEL PEAK 9(4P16.3) CNV	33	47	32
DEL PEAK 9(4P16.3) WILD-TYPE	100	30	63

Figure S123. Get High-res Image Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

P value = 6.09e-06 (Fisher's exact test), Q value = 0.0037

Table S124. Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	72	130
DEL PEAK 9(4P16.3) CNV	36	25	33
DEL PEAK 9(4P16.3) WILD-TYPE	21	47	97

Figure S124. Get High-res Image Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 6.41e-19 (Fisher's exact test), Q value = 4.8e-16

Table S125. Gene #39: 'Del Peak 10(4q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 10(4Q22.1) CNV	28	29	78
DEL PEAK 10(4Q22.1) WILD-TYPE	122	17	31

Figure S125. Get High-res Image Gene #39: 'Del Peak 10(4q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 3.85e-07 (Fisher's exact test), Q value = 0.00025

Table S126. Gene #39: 'Del Peak 10(4q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
DEL PEAK 10(4Q22.1) CNV	6	36	21	51
DEL PEAK 10(4Q22.1) WILD-TYPE	31	44	44	25

Figure S126. Get High-res Image Gene #39: 'Del Peak 10(4q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 4.14e-05 (Fisher's exact test), Q value = 0.024

Table S127. Gene #39: 'Del Peak 10(4q22.1)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	133	77	95
DEL PEAK 10(4Q22.1) CNV	50	51	34
DEL PEAK 10(4Q22.1) WILD-TYPE	83	26	61

Figure S127. Get High-res Image Gene #39: 'Del Peak 10(4q22.1)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 11(4q34.3)' versus 'CN_CNMF'

P value = 1.07e-14 (Fisher's exact test), Q value = 7.8e-12

Table S128. Gene #40: 'Del Peak 11(4q34.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 11(4Q34.3) CNV	29	26	72
DEL PEAK 11(4Q34.3) WILD-TYPE	121	20	37

Figure S128. Get High-res Image Gene #40: 'Del Peak 11(4q34.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 11(4q34.3)' versus 'METHLYATION_CNMF'

P value = 1.87e-06 (Fisher's exact test), Q value = 0.0012

Table S129. Gene #40: 'Del Peak 11(4q34.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
DEL PEAK 11(4Q34.3) CNV	4	32	25	47
DEL PEAK 11(4Q34.3) WILD-TYPE	33	48	40	29

Figure S129. Get High-res Image Gene #40: 'Del Peak 11(4q34.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 11(4q34.3)' versus 'MRNASEQ_CNMF'

P value = 4.25e-05 (Chi-square test), Q value = 0.024

Table S130. Gene #40: 'Del Peak 11(4q34.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	63	43	42	62
DEL PEAK 11(4Q34.3) CNV	14	22	19	17	41
DEL PEAK 11(4Q34.3) WILD-TYPE	47	41	24	25	21

Figure S130. Get High-res Image Gene #40: 'Del Peak 11(4q34.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 11(4q34.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.38e-05 (Fisher's exact test), Q value = 0.025

Table S131. Gene #40: 'Del Peak 11(4q34.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	141	64
DEL PEAK 11(4Q34.3) CNV	25	46	42
DEL PEAK 11(4Q34.3) WILD-TYPE	41	95	22

Figure S131. Get High-res Image Gene #40: 'Del Peak 11(4q34.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 11(4q34.3)' versus 'MIRSEQ_CNMF'

P value = 5.29e-05 (Fisher's exact test), Q value = 0.03

Table S132. Gene #40: 'Del Peak 11(4q34.3)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	91	114
DEL PEAK 11(4Q34.3) CNV	31	30	66
DEL PEAK 11(4Q34.3) WILD-TYPE	69	61	48

Figure S132. Get High-res Image Gene #40: 'Del Peak 11(4q34.3)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 11(4q34.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.16e-07 (Fisher's exact test), Q value = 0.00052

Table S133. Gene #40: 'Del Peak 11(4q34.3)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	133	77	95
DEL PEAK 11(4Q34.3) CNV	44	52	31
DEL PEAK 11(4Q34.3) WILD-TYPE	89	25	64

Figure S133. Get High-res Image Gene #40: 'Del Peak 11(4q34.3)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 11(4q34.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.19e-05 (Fisher's exact test), Q value = 0.051

Table S134. Gene #40: 'Del Peak 11(4q34.3)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	72	130
DEL PEAK 11(4Q34.3) CNV	38	28	43
DEL PEAK 11(4Q34.3) WILD-TYPE	19	44	87

Figure S134. Get High-res Image Gene #40: 'Del Peak 11(4q34.3)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 5.94e-27 (Fisher's exact test), Q value = 4.4e-24

Table S135. Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 12(5Q11.2) CNV	9	21	73
DEL PEAK 12(5Q11.2) WILD-TYPE	141	25	36

Figure S135. Get High-res Image Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 2.49e-14 (Fisher's exact test), Q value = 1.8e-11

Table S136. Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
DEL PEAK 12(5Q11.2) CNV	3	28	7	51
DEL PEAK 12(5Q11.2) WILD-TYPE	34	52	58	25

Figure S136. Get High-res Image Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 2.81e-11 (Chi-square test), Q value = 2e-08

Table S137. Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	63	43	42	62
DEL PEAK 12(5Q11.2) CNV	16	4	10	16	41
DEL PEAK 12(5Q11.2) WILD-TYPE	45	59	33	26	21

Figure S137. Get High-res Image Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

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

P value = 1.5e-10 (Fisher's exact test), Q value = 1e-07

Table S138. Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	141	64
DEL PEAK 12(5Q11.2) CNV	7	39	41
DEL PEAK 12(5Q11.2) WILD-TYPE	59	102	23

Figure S138. Get High-res Image Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

P value = 2.77e-09 (Fisher's exact test), Q value = 1.9e-06

Table S139. Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	91	114
DEL PEAK 12(5Q11.2) CNV	28	13	62
DEL PEAK 12(5Q11.2) WILD-TYPE	72	78	52

Figure S139. Get High-res Image Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

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

P value = 6.55e-12 (Fisher's exact test), Q value = 4.6e-09

Table S140. Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	133	77	95
DEL PEAK 12(5Q11.2) CNV	40	50	13
DEL PEAK 12(5Q11.2) WILD-TYPE	93	27	82

Figure S140. Get High-res Image Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

P value = 2.99e-06 (Fisher's exact test), Q value = 0.0019

Table S141. Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	78	127
DEL PEAK 12(5Q11.2) CNV	16	12	62
DEL PEAK 12(5Q11.2) WILD-TYPE	38	66	65

Figure S141. Get High-res Image Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

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

P value = 1.03e-12 (Fisher's exact test), Q value = 7.4e-10

Table S142. Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	72	130
DEL PEAK 12(5Q11.2) CNV	42	9	39
DEL PEAK 12(5Q11.2) WILD-TYPE	15	63	91

Figure S142. Get High-res Image Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 13(5q23.2)' versus 'CN_CNMF'

P value = 1.44e-22 (Fisher's exact test), Q value = 1.1e-19

Table S143. Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 13(5Q23.2) CNV	8	22	63
DEL PEAK 13(5Q23.2) WILD-TYPE	142	24	46

Figure S143. Get High-res Image Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 13(5q23.2)' versus 'METHLYATION_CNMF'

P value = 2.29e-12 (Fisher's exact test), Q value = 1.6e-09

Table S144. Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
DEL PEAK 13(5Q23.2) CNV	5	23	5	47
DEL PEAK 13(5Q23.2) WILD-TYPE	32	57	60	29

Figure S144. Get High-res Image Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 13(5q23.2)' versus 'MRNASEQ_CNMF'

P value = 1.69e-12 (Chi-square test), Q value = 1.2e-09

Table S145. Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	63	43	42	62
DEL PEAK 13(5Q23.2) CNV	14	3	9	15	41
DEL PEAK 13(5Q23.2) WILD-TYPE	47	60	34	27	21

Figure S145. Get High-res Image Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 13(5q23.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.1e-09 (Fisher's exact test), Q value = 3.4e-06

Table S146. Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	141	64
DEL PEAK 13(5Q23.2) CNV	6	39	37
DEL PEAK 13(5Q23.2) WILD-TYPE	60	102	27

Figure S146. Get High-res Image Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 13(5q23.2)' versus 'MIRSEQ_CNMF'

P value = 2.4e-10 (Fisher's exact test), Q value = 1.6e-07

Table S147. Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	91	114
DEL PEAK 13(5Q23.2) CNV	22	11	60
DEL PEAK 13(5Q23.2) WILD-TYPE	78	80	54

Figure S147. Get High-res Image Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 13(5q23.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.29e-11 (Fisher's exact test), Q value = 3.7e-08

Table S148. Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	133	77	95
DEL PEAK 13(5Q23.2) CNV	40	44	9
DEL PEAK 13(5Q23.2) WILD-TYPE	93	33	86

Figure S148. Get High-res Image Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 13(5q23.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.17e-07 (Fisher's exact test), Q value = 0.00052

Table S149. Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	78	127
DEL PEAK 13(5Q23.2) CNV	11	11	59
DEL PEAK 13(5Q23.2) WILD-TYPE	43	67	68

Figure S149. Get High-res Image Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'Del Peak 13(5q23.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.45e-12 (Fisher's exact test), Q value = 1e-09

Table S150. Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	72	130
DEL PEAK 13(5Q23.2) CNV	40	8	33
DEL PEAK 13(5Q23.2) WILD-TYPE	17	64	97

Figure S150. Get High-res Image Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 14(6p25.3)' versus 'CN_CNMF'

P value = 2.4e-07 (Fisher's exact test), Q value = 0.00015

Table S151. Gene #43: 'Del Peak 14(6p25.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 14(6P25.3) CNV	15	11	42
DEL PEAK 14(6P25.3) WILD-TYPE	135	35	67

Figure S151. Get High-res Image Gene #43: 'Del Peak 14(6p25.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 14(6p25.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.11e-06 (Fisher's exact test), Q value = 0.0037

Table S152. Gene #43: 'Del Peak 14(6p25.3)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	133	77	95
DEL PEAK 14(6P25.3) CNV	23	33	12
DEL PEAK 14(6P25.3) WILD-TYPE	110	44	83

Figure S152. Get High-res Image Gene #43: 'Del Peak 14(6p25.3)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

P value = 7.24e-06 (Fisher's exact test), Q value = 0.0044

Table S153. Gene #44: 'Del Peak 15(6q26)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 15(6Q26) CNV	14	13	35
DEL PEAK 15(6Q26) WILD-TYPE	136	33	74

Figure S153. Get High-res Image Gene #44: 'Del Peak 15(6q26)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 0.000394 (Fisher's exact test), Q value = 0.19

Table S154. Gene #44: 'Del Peak 15(6q26)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	141	64
DEL PEAK 15(6Q26) CNV	6	28	24
DEL PEAK 15(6Q26) WILD-TYPE	60	113	40

Figure S154. Get High-res Image Gene #44: 'Del Peak 15(6q26)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 16(7q31.1)' versus 'CN_CNMF'

P value = 2.75e-07 (Fisher's exact test), Q value = 0.00018

Table S155. Gene #45: 'Del Peak 16(7q31.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 16(7Q31.1) CNV	8	4	32
DEL PEAK 16(7Q31.1) WILD-TYPE	142	42	77

Figure S155. Get High-res Image Gene #45: 'Del Peak 16(7q31.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 16(7q31.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.87e-05 (Fisher's exact test), Q value = 0.054

Table S156. Gene #45: 'Del Peak 16(7q31.1)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	78	127
DEL PEAK 16(7Q31.1) CNV	2	5	30
DEL PEAK 16(7Q31.1) WILD-TYPE	52	73	97

Figure S156. Get High-res Image Gene #45: 'Del Peak 16(7q31.1)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'Del Peak 17(7q36.3)' versus 'CN_CNMF'

P value = 1.05e-14 (Fisher's exact test), Q value = 7.7e-12

Table S157. Gene #46: 'Del Peak 17(7q36.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 17(7Q36.3) CNV	7	4	47
DEL PEAK 17(7Q36.3) WILD-TYPE	143	42	62

Figure S157. Get High-res Image Gene #46: 'Del Peak 17(7q36.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 17(7q36.3)' versus 'METHLYATION_CNMF'

P value = 1.31e-05 (Fisher's exact test), Q value = 0.0078

Table S158. Gene #46: 'Del Peak 17(7q36.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
DEL PEAK 17(7Q36.3) CNV	0	19	6	24
DEL PEAK 17(7Q36.3) WILD-TYPE	37	61	59	52

Figure S158. Get High-res Image Gene #46: 'Del Peak 17(7q36.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 17(7q36.3)' versus 'MRNASEQ_CNMF'

P value = 2.44e-06 (Chi-square test), Q value = 0.0015

Table S159. Gene #46: 'Del Peak 17(7q36.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	63	43	42	62
DEL PEAK 17(7Q36.3) CNV	7	7	7	4	27
DEL PEAK 17(7Q36.3) WILD-TYPE	54	56	36	38	35

Figure S159. Get High-res Image Gene #46: 'Del Peak 17(7q36.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 17(7q36.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.36e-05 (Fisher's exact test), Q value = 0.0081

Table S160. Gene #46: 'Del Peak 17(7q36.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	141	64
DEL PEAK 17(7Q36.3) CNV	7	19	26
DEL PEAK 17(7Q36.3) WILD-TYPE	59	122	38

Figure S160. Get High-res Image Gene #46: 'Del Peak 17(7q36.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 17(7q36.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.11e-05 (Fisher's exact test), Q value = 0.04

Table S161. Gene #46: 'Del Peak 17(7q36.3)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	133	77	95
DEL PEAK 17(7Q36.3) CNV	20	28	10
DEL PEAK 17(7Q36.3) WILD-TYPE	113	49	85

Figure S161. Get High-res Image Gene #46: 'Del Peak 17(7q36.3)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 17(7q36.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000105 (Fisher's exact test), Q value = 0.058

Table S162. Gene #46: 'Del Peak 17(7q36.3)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	72	130
DEL PEAK 17(7Q36.3) CNV	22	6	22
DEL PEAK 17(7Q36.3) WILD-TYPE	35	66	108

Figure S162. Get High-res Image Gene #46: 'Del Peak 17(7q36.3)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 18(8p23.2)' versus 'CN_CNMF'

P value = 5.17e-15 (Fisher's exact test), Q value = 3.8e-12

Table S163. Gene #47: 'Del Peak 18(8p23.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 18(8P23.2) CNV	10	13	54
DEL PEAK 18(8P23.2) WILD-TYPE	140	33	55

Figure S163. Get High-res Image Gene #47: 'Del Peak 18(8p23.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 18(8p23.2)' versus 'METHLYATION_CNMF'

P value = 8.11e-06 (Fisher's exact test), Q value = 0.0049

Table S164. Gene #47: 'Del Peak 18(8p23.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
DEL PEAK 18(8P23.2) CNV	3	17	10	35
DEL PEAK 18(8P23.2) WILD-TYPE	34	63	55	41

Figure S164. Get High-res Image Gene #47: 'Del Peak 18(8p23.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 18(8p23.2)' versus 'MRNASEQ_CNMF'

P value = 8.14e-06 (Chi-square test), Q value = 0.0049

Table S165. Gene #47: 'Del Peak 18(8p23.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	63	43	42	62
DEL PEAK 18(8P23.2) CNV	10	9	7	10	31
DEL PEAK 18(8P23.2) WILD-TYPE	51	54	36	32	31

Figure S165. Get High-res Image Gene #47: 'Del Peak 18(8p23.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 18(8p23.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.92e-06 (Fisher's exact test), Q value = 0.0059

Table S166. Gene #47: 'Del Peak 18(8p23.2)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	141	64
DEL PEAK 18(8P23.2) CNV	12	24	31
DEL PEAK 18(8P23.2) WILD-TYPE	54	117	33

Figure S166. Get High-res Image Gene #47: 'Del Peak 18(8p23.2)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 18(8p23.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.96e-08 (Fisher's exact test), Q value = 5.2e-05

Table S167. Gene #47: 'Del Peak 18(8p23.2)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	133	77	95
DEL PEAK 18(8P23.2) CNV	21	39	17
DEL PEAK 18(8P23.2) WILD-TYPE	112	38	78

Figure S167. Get High-res Image Gene #47: 'Del Peak 18(8p23.2)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 18(8p23.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S168. Gene #47: 'Del Peak 18(8p23.2)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	72	130
DEL PEAK 18(8P23.2) CNV	27	14	25
DEL PEAK 18(8P23.2) WILD-TYPE	30	58	105

Figure S168. Get High-res Image Gene #47: 'Del Peak 18(8p23.2)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 19(9p23)' versus 'CN_CNMF'

P value = 3.41e-18 (Fisher's exact test), Q value = 2.5e-15

Table S169. Gene #48: 'Del Peak 19(9p23)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 19(9P23) CNV	25	18	77
DEL PEAK 19(9P23) WILD-TYPE	125	28	32

Figure S169. Get High-res Image Gene #48: 'Del Peak 19(9p23)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 19(9p23)' versus 'METHLYATION_CNMF'

P value = 8.76e-05 (Fisher's exact test), Q value = 0.048

Table S170. Gene #48: 'Del Peak 19(9p23)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
DEL PEAK 19(9P23) CNV	7	29	20	45
DEL PEAK 19(9P23) WILD-TYPE	30	51	45	31

Figure S170. Get High-res Image Gene #48: 'Del Peak 19(9p23)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 19(9p23)' versus 'MRNASEQ_CNMF'

P value = 9.85e-06 (Chi-square test), Q value = 0.0059

Table S171. Gene #48: 'Del Peak 19(9p23)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	63	43	42	62
DEL PEAK 19(9P23) CNV	13	18	22	15	39
DEL PEAK 19(9P23) WILD-TYPE	48	45	21	27	23

Figure S171. Get High-res Image Gene #48: 'Del Peak 19(9p23)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 20(9p21.3)' versus 'CN_CNMF'

P value = 9.23e-19 (Fisher's exact test), Q value = 6.9e-16

Table S172. Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 20(9P21.3) CNV	24	17	77
DEL PEAK 20(9P21.3) WILD-TYPE	126	29	32

Figure S172. Get High-res Image Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 20(9p21.3)' versus 'METHLYATION_CNMF'

P value = 1.92e-10 (Fisher's exact test), Q value = 1.3e-07

Table S173. Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
DEL PEAK 20(9P21.3) CNV	1	29	21	49
DEL PEAK 20(9P21.3) WILD-TYPE	36	51	44	27

Figure S173. Get High-res Image Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 20(9p21.3)' versus 'RPPA_CNMF'

P value = 0.000123 (Fisher's exact test), Q value = 0.067

Table S174. Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	90	91
DEL PEAK 20(9P21.3) CNV	17	40	46
DEL PEAK 20(9P21.3) WILD-TYPE	64	50	45

Figure S174. Get High-res Image Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #3: 'RPPA_CNMF'

'Del Peak 20(9p21.3)' versus 'MRNASEQ_CNMF'

P value = 1.7e-08 (Chi-square test), Q value = 1.1e-05

Table S175. Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	63	43	42	62
DEL PEAK 20(9P21.3) CNV	9	18	22	16	42
DEL PEAK 20(9P21.3) WILD-TYPE	52	45	21	26	20

Figure S175. Get High-res Image Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 20(9p21.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000117 (Fisher's exact test), Q value = 0.063

Table S176. Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	141	64
DEL PEAK 20(9P21.3) CNV	21	46	40
DEL PEAK 20(9P21.3) WILD-TYPE	45	95	24

Figure S176. Get High-res Image Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 20(9p21.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000159 (Fisher's exact test), Q value = 0.085

Table S177. Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	72	130
DEL PEAK 20(9P21.3) CNV	36	24	41
DEL PEAK 20(9P21.3) WILD-TYPE	21	48	89

Figure S177. Get High-res Image Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 21(9q21.11)' versus 'CN_CNMF'

P value = 2.52e-12 (Fisher's exact test), Q value = 1.8e-09

Table S178. Gene #50: 'Del Peak 21(9q21.11)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 21(9Q21.11) CNV	12	10	51
DEL PEAK 21(9Q21.11) WILD-TYPE	138	36	58

Figure S178. Get High-res Image Gene #50: 'Del Peak 21(9q21.11)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 21(9q21.11)' versus 'METHLYATION_CNMF'

P value = 0.000223 (Fisher's exact test), Q value = 0.12

Table S179. Gene #50: 'Del Peak 21(9q21.11)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
DEL PEAK 21(9Q21.11) CNV	2	18	13	31
DEL PEAK 21(9Q21.11) WILD-TYPE	35	62	52	45

Figure S179. Get High-res Image Gene #50: 'Del Peak 21(9q21.11)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 22(10p15.1)' versus 'CN_CNMF'

P value = 0.000115 (Fisher's exact test), Q value = 0.063

Table S180. Gene #51: 'Del Peak 22(10p15.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 22(10P15.1) CNV	7	9	22
DEL PEAK 22(10P15.1) WILD-TYPE	143	37	87

Figure S180. Get High-res Image Gene #51: 'Del Peak 22(10p15.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 23(10q22.3)' versus 'CN_CNMF'

P value = 4.61e-10 (Fisher's exact test), Q value = 3.2e-07

Table S181. Gene #52: 'Del Peak 23(10q22.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 23(10Q22.3) CNV	5	17	27
DEL PEAK 23(10Q22.3) WILD-TYPE	145	29	82

Figure S181. Get High-res Image Gene #52: 'Del Peak 23(10q22.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 23(10q22.3)' versus 'MRNASEQ_CNMF'

P value = 0.000185 (Chi-square test), Q value = 0.097

Table S182. Gene #52: 'Del Peak 23(10q22.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	63	43	42	62
DEL PEAK 23(10Q22.3) CNV	6	3	3	9	19
DEL PEAK 23(10Q22.3) WILD-TYPE	55	60	40	33	43

Figure S182. Get High-res Image Gene #52: 'Del Peak 23(10q22.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 24(10q23.31)' versus 'CN_CNMF'

P value = 3.01e-12 (Fisher's exact test), Q value = 2.1e-09

Table S183. Gene #53: 'Del Peak 24(10q23.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 24(10Q23.31) CNV	10	19	44
DEL PEAK 24(10Q23.31) WILD-TYPE	140	27	65

Figure S183. Get High-res Image Gene #53: 'Del Peak 24(10q23.31)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 24(10q23.31)' versus 'METHLYATION_CNMF'

P value = 5.23e-06 (Fisher's exact test), Q value = 0.0032

Table S184. Gene #53: 'Del Peak 24(10q23.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
DEL PEAK 24(10Q23.31) CNV	4	12	9	34
DEL PEAK 24(10Q23.31) WILD-TYPE	33	68	56	42

Figure S184. Get High-res Image Gene #53: 'Del Peak 24(10q23.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 24(10q23.31)' versus 'MRNASEQ_CNMF'

P value = 3.27e-06 (Chi-square test), Q value = 0.002

Table S185. Gene #53: 'Del Peak 24(10q23.31)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	63	43	42	62
DEL PEAK 24(10Q23.31) CNV	7	5	8	14	27
DEL PEAK 24(10Q23.31) WILD-TYPE	54	58	35	28	35

Figure S185. Get High-res Image Gene #53: 'Del Peak 24(10q23.31)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 24(10q23.31)' versus 'MIRSEQ_CNMF'

P value = 0.000374 (Fisher's exact test), Q value = 0.19

Table S186. Gene #53: 'Del Peak 24(10q23.31)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	91	114
DEL PEAK 24(10Q23.31) CNV	24	10	39
DEL PEAK 24(10Q23.31) WILD-TYPE	76	81	75

Figure S186. Get High-res Image Gene #53: 'Del Peak 24(10q23.31)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 24(10q23.31)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.07e-05 (Fisher's exact test), Q value = 0.0064

Table S187. Gene #53: 'Del Peak 24(10q23.31)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	133	77	95
DEL PEAK 24(10Q23.31) CNV	29	33	11
DEL PEAK 24(10Q23.31) WILD-TYPE	104	44	84

Figure S187. Get High-res Image Gene #53: 'Del Peak 24(10q23.31)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 24(10q23.31)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000501 (Fisher's exact test), Q value = 0.24

Table S188. Gene #53: 'Del Peak 24(10q23.31)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	72	130
DEL PEAK 24(10Q23.31) CNV	23	8	28
DEL PEAK 24(10Q23.31) WILD-TYPE	34	64	102

Figure S188. Get High-res Image Gene #53: 'Del Peak 24(10q23.31)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 25(11p15.4)' versus 'CN_CNMF'

P value = 2.15e-08 (Fisher's exact test), Q value = 1.4e-05

Table S189. Gene #54: 'Del Peak 25(11p15.4)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 25(11P15.4) CNV	11	8	40
DEL PEAK 25(11P15.4) WILD-TYPE	139	38	69

Figure S189. Get High-res Image Gene #54: 'Del Peak 25(11p15.4)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 25(11p15.4)' versus 'METHLYATION_CNMF'

P value = 8.05e-06 (Fisher's exact test), Q value = 0.0048

Table S190. Gene #54: 'Del Peak 25(11p15.4)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
DEL PEAK 25(11P15.4) CNV	2	9	6	28
DEL PEAK 25(11P15.4) WILD-TYPE	35	71	59	48

Figure S190. Get High-res Image Gene #54: 'Del Peak 25(11p15.4)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 25(11p15.4)' versus 'RPPA_CNMF'

P value = 1.57e-05 (Fisher's exact test), Q value = 0.0093

Table S191. Gene #54: 'Del Peak 25(11p15.4)' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	90	91
DEL PEAK 25(11P15.4) CNV	6	14	32
DEL PEAK 25(11P15.4) WILD-TYPE	75	76	59

Figure S191. Get High-res Image Gene #54: 'Del Peak 25(11p15.4)' versus Molecular Subtype #3: 'RPPA_CNMF'

'Del Peak 25(11p15.4)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.29e-05 (Fisher's exact test), Q value = 0.046

Table S192. Gene #54: 'Del Peak 25(11p15.4)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	133	77	95
DEL PEAK 25(11P15.4) CNV	21	28	10
DEL PEAK 25(11P15.4) WILD-TYPE	112	49	85

Figure S192. Get High-res Image Gene #54: 'Del Peak 25(11p15.4)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 27(12p13.31)' versus 'CN_CNMF'

P value = 9.87e-12 (Fisher's exact test), Q value = 6.9e-09

Table S193. Gene #56: 'Del Peak 27(12p13.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 27(12P13.31) CNV	4	9	37
DEL PEAK 27(12P13.31) WILD-TYPE	146	37	72

Figure S193. Get High-res Image Gene #56: 'Del Peak 27(12p13.31)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 27(12p13.31)' versus 'METHLYATION_CNMF'

P value = 5.7e-06 (Fisher's exact test), Q value = 0.0035

Table S194. Gene #56: 'Del Peak 27(12p13.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
DEL PEAK 27(12P13.31) CNV	2	10	4	27
DEL PEAK 27(12P13.31) WILD-TYPE	35	70	61	49

Figure S194. Get High-res Image Gene #56: 'Del Peak 27(12p13.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 27(12p13.31)' versus 'MRNASEQ_CNMF'

P value = 1.49e-07 (Chi-square test), Q value = 9.7e-05

Table S195. Gene #56: 'Del Peak 27(12p13.31)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	63	43	42	62
DEL PEAK 27(12P13.31) CNV	4	4	6	4	25
DEL PEAK 27(12P13.31) WILD-TYPE	57	59	37	38	37

Figure S195. Get High-res Image Gene #56: 'Del Peak 27(12p13.31)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 27(12p13.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.36e-06 (Fisher's exact test), Q value = 0.00085

Table S196. Gene #56: 'Del Peak 27(12p13.31)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	141	64
DEL PEAK 27(12P13.31) CNV	4	15	24
DEL PEAK 27(12P13.31) WILD-TYPE	62	126	40

Figure S196. Get High-res Image Gene #56: 'Del Peak 27(12p13.31)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 27(12p13.31)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.52e-05 (Fisher's exact test), Q value = 0.031

Table S197. Gene #56: 'Del Peak 27(12p13.31)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	72	130
DEL PEAK 27(12P13.31) CNV	21	6	16
DEL PEAK 27(12P13.31) WILD-TYPE	36	66	114

Figure S197. Get High-res Image Gene #56: 'Del Peak 27(12p13.31)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 28(13q12.11)' versus 'CN_CNMF'

P value = 9.84e-05 (Fisher's exact test), Q value = 0.054

Table S198. Gene #57: 'Del Peak 28(13q12.11)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 28(13Q12.11) CNV	10	6	28
DEL PEAK 28(13Q12.11) WILD-TYPE	140	40	81

Figure S198. Get High-res Image Gene #57: 'Del Peak 28(13q12.11)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 29(14q21.1)' versus 'CN_CNMF'

P value = 9.49e-09 (Fisher's exact test), Q value = 6.4e-06

Table S199. Gene #58: 'Del Peak 29(14q21.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 29(14Q21.1) CNV	15	10	46
DEL PEAK 29(14Q21.1) WILD-TYPE	135	36	63

Figure S199. Get High-res Image Gene #58: 'Del Peak 29(14q21.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 29(14q21.1)' versus 'MRNASEQ_CNMF'

P value = 0.000157 (Chi-square test), Q value = 0.084

Table S200. Gene #58: 'Del Peak 29(14q21.1)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	63	43	42	62
DEL PEAK 29(14Q21.1) CNV	9	12	10	5	28
DEL PEAK 29(14Q21.1) WILD-TYPE	52	51	33	37	34

Figure S200. Get High-res Image Gene #58: 'Del Peak 29(14q21.1)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 29(14q21.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000189 (Fisher's exact test), Q value = 0.099

Table S201. Gene #58: 'Del Peak 29(14q21.1)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	141	64
DEL PEAK 29(14Q21.1) CNV	12	24	28
DEL PEAK 29(14Q21.1) WILD-TYPE	54	117	36

Figure S201. Get High-res Image Gene #58: 'Del Peak 29(14q21.1)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 29(14q21.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.19

Table S202. Gene #58: 'Del Peak 29(14q21.1)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	72	130
DEL PEAK 29(14Q21.1) CNV	25	14	22
DEL PEAK 29(14Q21.1) WILD-TYPE	32	58	108

Figure S202. Get High-res Image Gene #58: 'Del Peak 29(14q21.1)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 30(14q32.33)' versus 'CN_CNMF'

P value = 1.24e-09 (Fisher's exact test), Q value = 8.4e-07

Table S203. Gene #59: 'Del Peak 30(14q32.33)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 30(14Q32.33) CNV	21	13	55
DEL PEAK 30(14Q32.33) WILD-TYPE	129	33	54

Figure S203. Get High-res Image Gene #59: 'Del Peak 30(14q32.33)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 30(14q32.33)' versus 'MRNASEQ_CNMF'

P value = 0.000377 (Chi-square test), Q value = 0.19

Table S204. Gene #59: 'Del Peak 30(14q32.33)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	63	43	42	62
DEL PEAK 30(14Q32.33) CNV	15	15	11	8	33
DEL PEAK 30(14Q32.33) WILD-TYPE	46	48	32	34	29

Figure S204. Get High-res Image Gene #59: 'Del Peak 30(14q32.33)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 30(14q32.33)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.38e-05 (Fisher's exact test), Q value = 0.0082

Table S205. Gene #59: 'Del Peak 30(14q32.33)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	141	64
DEL PEAK 30(14Q32.33) CNV	14	33	35
DEL PEAK 30(14Q32.33) WILD-TYPE	52	108	29

Figure S205. Get High-res Image Gene #59: 'Del Peak 30(14q32.33)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 31(15q15.1)' versus 'CN_CNMF'

P value = 1.74e-13 (Fisher's exact test), Q value = 1.3e-10

Table S206. Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 31(15Q15.1) CNV	11	18	50
DEL PEAK 31(15Q15.1) WILD-TYPE	139	28	59

Figure S206. Get High-res Image Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 31(15q15.1)' versus 'METHLYATION_CNMF'

P value = 2.11e-07 (Fisher's exact test), Q value = 0.00014

Table S207. Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
DEL PEAK 31(15Q15.1) CNV	5	16	7	38
DEL PEAK 31(15Q15.1) WILD-TYPE	32	64	58	38

Figure S207. Get High-res Image Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 31(15q15.1)' versus 'MRNASEQ_CNMF'

P value = 7.15e-08 (Chi-square test), Q value = 4.7e-05

Table S208. Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	63	43	42	62
DEL PEAK 31(15Q15.1) CNV	11	3	15	8	31
DEL PEAK 31(15Q15.1) WILD-TYPE	50	60	28	34	31

Figure S208. Get High-res Image Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 31(15q15.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.66e-08 (Fisher's exact test), Q value = 1.8e-05

Table S209. Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	141	64
DEL PEAK 31(15Q15.1) CNV	4	32	32
DEL PEAK 31(15Q15.1) WILD-TYPE	62	109	32

Figure S209. Get High-res Image Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 31(15q15.1)' versus 'MIRSEQ_CNMF'

P value = 6.44e-06 (Fisher's exact test), Q value = 0.0039

Table S210. Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	91	114
DEL PEAK 31(15Q15.1) CNV	23	10	46
DEL PEAK 31(15Q15.1) WILD-TYPE	77	81	68

Figure S210. Get High-res Image Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 31(15q15.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.84e-08 (Fisher's exact test), Q value = 1.2e-05

Table S211. Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	133	77	95
DEL PEAK 31(15Q15.1) CNV	32	38	9
DEL PEAK 31(15Q15.1) WILD-TYPE	101	39	86

Figure S211. Get High-res Image Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 31(15q15.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000455 (Fisher's exact test), Q value = 0.22

Table S212. Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	78	127
DEL PEAK 31(15Q15.1) CNV	16	8	42
DEL PEAK 31(15Q15.1) WILD-TYPE	38	70	85

Figure S212. Get High-res Image Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'Del Peak 31(15q15.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.09e-05 (Fisher's exact test), Q value = 0.024

Table S213. Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	72	130
DEL PEAK 31(15Q15.1) CNV	25	7	34
DEL PEAK 31(15Q15.1) WILD-TYPE	32	65	96

Figure S213. Get High-res Image Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 32(16p13.3)' versus 'CN_CNMF'

P value = 6e-11 (Fisher's exact test), Q value = 4.2e-08

Table S214. Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 32(16P13.3) CNV	9	6	43
DEL PEAK 32(16P13.3) WILD-TYPE	141	40	66

Figure S214. Get High-res Image Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 32(16p13.3)' versus 'METHLYATION_CNMF'

P value = 4.14e-05 (Fisher's exact test), Q value = 0.024

Table S215. Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
DEL PEAK 32(16P13.3) CNV	1	14	7	27
DEL PEAK 32(16P13.3) WILD-TYPE	36	66	58	49

Figure S215. Get High-res Image Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 32(16p13.3)' versus 'MRNASEQ_CNMF'

P value = 3.44e-08 (Chi-square test), Q value = 2.3e-05

Table S216. Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	63	43	42	62
DEL PEAK 32(16P13.3) CNV	8	6	3	4	28
DEL PEAK 32(16P13.3) WILD-TYPE	53	57	40	38	34

Figure S216. Get High-res Image Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 32(16p13.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.11e-09 (Fisher's exact test), Q value = 7.6e-07

Table S217. Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	141	64
DEL PEAK 32(16P13.3) CNV	6	13	30
DEL PEAK 32(16P13.3) WILD-TYPE	60	128	34

Figure S217. Get High-res Image Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 32(16p13.3)' versus 'MIRSEQ_CNMF'

P value = 0.000144 (Fisher's exact test), Q value = 0.077

Table S218. Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	91	114
DEL PEAK 32(16P13.3) CNV	12	10	36
DEL PEAK 32(16P13.3) WILD-TYPE	88	81	78

Figure S218. Get High-res Image Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 32(16p13.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.97e-06 (Fisher's exact test), Q value = 0.0031

Table S219. Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	133	77	95
DEL PEAK 32(16P13.3) CNV	18	30	10
DEL PEAK 32(16P13.3) WILD-TYPE	115	47	85

Figure S219. Get High-res Image Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 32(16p13.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000157 (Fisher's exact test), Q value = 0.084

Table S220. Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	78	127
DEL PEAK 32(16P13.3) CNV	2	12	36
DEL PEAK 32(16P13.3) WILD-TYPE	52	66	91

Figure S220. Get High-res Image Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'Del Peak 32(16p13.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.41e-07 (Fisher's exact test), Q value = 0.00035

Table S221. Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	72	130
DEL PEAK 32(16P13.3) CNV	26	7	17
DEL PEAK 32(16P13.3) WILD-TYPE	31	65	113

Figure S221. Get High-res Image Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 33(16q23.1)' versus 'CN_CNMF'

P value = 4.29e-08 (Fisher's exact test), Q value = 2.8e-05

Table S222. Gene #62: 'Del Peak 33(16q23.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 33(16Q23.1) CNV	35	19	64
DEL PEAK 33(16Q23.1) WILD-TYPE	115	27	45

Figure S222. Get High-res Image Gene #62: 'Del Peak 33(16q23.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 33(16q23.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.9e-05 (Fisher's exact test), Q value = 0.017

Table S223. Gene #62: 'Del Peak 33(16q23.1)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	141	64
DEL PEAK 33(16Q23.1) CNV	17	48	40
DEL PEAK 33(16Q23.1) WILD-TYPE	49	93	24

Figure S223. Get High-res Image Gene #62: 'Del Peak 33(16q23.1)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 34(17p12)' versus 'CN_CNMF'

P value = 3.09e-29 (Fisher's exact test), Q value = 2.3e-26

Table S224. Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 34(17P12) CNV	12	23	80
DEL PEAK 34(17P12) WILD-TYPE	138	23	29

Figure S224. Get High-res Image Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 34(17p12)' versus 'METHLYATION_CNMF'

P value = 3.28e-11 (Fisher's exact test), Q value = 2.3e-08

Table S225. Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
DEL PEAK 34(17P12) CNV	4	30	13	52
DEL PEAK 34(17P12) WILD-TYPE	33	50	52	24

Figure S225. Get High-res Image Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 34(17p12)' versus 'MRNASEQ_CNMF'

P value = 3.29e-08 (Chi-square test), Q value = 2.2e-05

Table S226. Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	63	43	42	62
DEL PEAK 34(17P12) CNV	15	11	17	13	42
DEL PEAK 34(17P12) WILD-TYPE	46	52	26	29	20

Figure S226. Get High-res Image Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 34(17p12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.33e-07 (Fisher's exact test), Q value = 0.00028

Table S227. Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	141	64
DEL PEAK 34(17P12) CNV	14	43	41
DEL PEAK 34(17P12) WILD-TYPE	52	98	23

Figure S227. Get High-res Image Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 34(17p12)' versus 'MIRSEQ_CNMF'

P value = 5.57e-05 (Fisher's exact test), Q value = 0.031

Table S228. Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	91	114
DEL PEAK 34(17P12) CNV	36	20	59
DEL PEAK 34(17P12) WILD-TYPE	64	71	55

Figure S228. Get High-res Image Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 34(17p12)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.66e-07 (Fisher's exact test), Q value = 0.00011

Table S229. Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	133	77	95
DEL PEAK 34(17P12) CNV	44	49	22
DEL PEAK 34(17P12) WILD-TYPE	89	28	73

Figure S229. Get High-res Image Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 34(17p12)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.38e-08 (Fisher's exact test), Q value = 9.2e-06

Table S230. Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	72	130
DEL PEAK 34(17P12) CNV	41	16	43
DEL PEAK 34(17P12) WILD-TYPE	16	56	87

Figure S230. Get High-res Image Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 35(17q24.3)' versus 'CN_CNMF'

P value = 1.44e-10 (Fisher's exact test), Q value = 9.9e-08

Table S231. Gene #64: 'Del Peak 35(17q24.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 35(17Q24.3) CNV	6	12	37
DEL PEAK 35(17Q24.3) WILD-TYPE	144	34	72

Figure S231. Get High-res Image Gene #64: 'Del Peak 35(17q24.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 35(17q24.3)' versus 'METHLYATION_CNMF'

P value = 0.000251 (Fisher's exact test), Q value = 0.13

Table S232. Gene #64: 'Del Peak 35(17q24.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
DEL PEAK 35(17Q24.3) CNV	0	17	6	20
DEL PEAK 35(17Q24.3) WILD-TYPE	37	63	59	56

Figure S232. Get High-res Image Gene #64: 'Del Peak 35(17q24.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 36(18q21.2)' versus 'CN_CNMF'

P value = 3.44e-14 (Fisher's exact test), Q value = 2.5e-11

Table S233. Gene #65: 'Del Peak 36(18q21.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 36(18Q21.2) CNV	32	31	70
DEL PEAK 36(18Q21.2) WILD-TYPE	118	15	39

Figure S233. Get High-res Image Gene #65: 'Del Peak 36(18q21.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 37(19p13.3)' versus 'CN_CNMF'

P value = 5.42e-29 (Fisher's exact test), Q value = 4.1e-26

Table S234. Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 37(19P13.3) CNV	7	18	74
DEL PEAK 37(19P13.3) WILD-TYPE	143	28	35

Figure S234. Get High-res Image Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 37(19p13.3)' versus 'METHLYATION_CNMF'

P value = 2.33e-16 (Fisher's exact test), Q value = 1.7e-13

Table S235. Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
DEL PEAK 37(19P13.3) CNV	4	19	6	53
DEL PEAK 37(19P13.3) WILD-TYPE	33	61	59	23

Figure S235. Get High-res Image Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 37(19p13.3)' versus 'MRNASEQ_CNMF'

P value = 1.23e-16 (Chi-square test), Q value = 9.1e-14

Table S236. Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	63	43	42	62
DEL PEAK 37(19P13.3) CNV	13	5	11	10	48
DEL PEAK 37(19P13.3) WILD-TYPE	48	58	32	32	14

Figure S236. Get High-res Image Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 37(19p13.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.38e-16 (Fisher's exact test), Q value = 2.5e-13

Table S237. Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	141	64
DEL PEAK 37(19P13.3) CNV	4	37	46
DEL PEAK 37(19P13.3) WILD-TYPE	62	104	18

Figure S237. Get High-res Image Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 37(19p13.3)' versus 'MIRSEQ_CNMF'

P value = 4.71e-07 (Fisher's exact test), Q value = 3e-04

Table S238. Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	91	114
DEL PEAK 37(19P13.3) CNV	25	16	58
DEL PEAK 37(19P13.3) WILD-TYPE	75	75	56

Figure S238. Get High-res Image Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 37(19p13.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.85e-21 (Fisher's exact test), Q value = 2.1e-18

Table S239. Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	133	77	95
DEL PEAK 37(19P13.3) CNV	30	59	10
DEL PEAK 37(19P13.3) WILD-TYPE	103	18	85

Figure S239. Get High-res Image Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 37(19p13.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.21e-19 (Fisher's exact test), Q value = 1.6e-16

Table S240. Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	72	130
DEL PEAK 37(19P13.3) CNV	45	4	34
DEL PEAK 37(19P13.3) WILD-TYPE	12	68	96

Figure S240. Get High-res Image Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 38(19q13.11)' versus 'CN_CNMF'

P value = 3.88e-10 (Fisher's exact test), Q value = 2.7e-07

Table S241. Gene #67: 'Del Peak 38(19q13.11)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 38(19Q13.11) CNV	3	9	31
DEL PEAK 38(19Q13.11) WILD-TYPE	147	37	78

Figure S241. Get High-res Image Gene #67: 'Del Peak 38(19q13.11)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 38(19q13.11)' versus 'METHLYATION_CNMF'

P value = 8.49e-05 (Fisher's exact test), Q value = 0.047

Table S242. Gene #67: 'Del Peak 38(19q13.11)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
DEL PEAK 38(19Q13.11) CNV	1	12	2	20
DEL PEAK 38(19Q13.11) WILD-TYPE	36	68	63	56

Figure S242. Get High-res Image Gene #67: 'Del Peak 38(19q13.11)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 38(19q13.11)' versus 'MRNASEQ_CNMF'

P value = 0.000257 (Chi-square test), Q value = 0.13

Table S243. Gene #67: 'Del Peak 38(19q13.11)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	63	43	42	62
DEL PEAK 38(19Q13.11) CNV	6	2	5	6	19
DEL PEAK 38(19Q13.11) WILD-TYPE	55	61	38	36	43

Figure S243. Get High-res Image Gene #67: 'Del Peak 38(19q13.11)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 38(19q13.11)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.47e-06 (Fisher's exact test), Q value = 0.00093

Table S244. Gene #67: 'Del Peak 38(19q13.11)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	133	77	95
DEL PEAK 38(19Q13.11) CNV	13	25	5
DEL PEAK 38(19Q13.11) WILD-TYPE	120	52	90

Figure S244. Get High-res Image Gene #67: 'Del Peak 38(19q13.11)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 38(19q13.11)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.5e-05 (Fisher's exact test), Q value = 0.047

Table S245. Gene #67: 'Del Peak 38(19q13.11)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	72	130
DEL PEAK 38(19Q13.11) CNV	18	4	13
DEL PEAK 38(19Q13.11) WILD-TYPE	39	68	117

Figure S245. Get High-res Image Gene #67: 'Del Peak 38(19q13.11)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 39(20p12.1)' versus 'CN_CNMF'

P value = 2.86e-12 (Fisher's exact test), Q value = 2e-09

Table S246. Gene #68: 'Del Peak 39(20p12.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 39(20P12.1) CNV	11	0	41
DEL PEAK 39(20P12.1) WILD-TYPE	139	46	68

Figure S246. Get High-res Image Gene #68: 'Del Peak 39(20p12.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 39(20p12.1)' versus 'MIRSEQ_CNMF'

P value = 0.000162 (Fisher's exact test), Q value = 0.086

Table S247. Gene #68: 'Del Peak 39(20p12.1)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	91	114
DEL PEAK 39(20P12.1) CNV	9	10	33
DEL PEAK 39(20P12.1) WILD-TYPE	91	81	81

Figure S247. Get High-res Image Gene #68: 'Del Peak 39(20p12.1)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 40(20p12.1)' versus 'CN_CNMF'

P value = 2.86e-12 (Fisher's exact test), Q value = 2e-09

Table S248. Gene #69: 'Del Peak 40(20p12.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 40(20P12.1) CNV	11	0	41
DEL PEAK 40(20P12.1) WILD-TYPE	139	46	68

Figure S248. Get High-res Image Gene #69: 'Del Peak 40(20p12.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 40(20p12.1)' versus 'MIRSEQ_CNMF'

P value = 0.000162 (Fisher's exact test), Q value = 0.086

Table S249. Gene #69: 'Del Peak 40(20p12.1)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	91	114
DEL PEAK 40(20P12.1) CNV	9	10	33
DEL PEAK 40(20P12.1) WILD-TYPE	91	81	81

Figure S249. Get High-res Image Gene #69: 'Del Peak 40(20p12.1)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 41(21q11.2)' versus 'CN_CNMF'

P value = 5.88e-11 (Fisher's exact test), Q value = 4.1e-08

Table S250. Gene #70: 'Del Peak 41(21q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 41(21Q11.2) CNV	25	21	61
DEL PEAK 41(21Q11.2) WILD-TYPE	125	25	48

Figure S250. Get High-res Image Gene #70: 'Del Peak 41(21q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 41(21q11.2)' versus 'METHLYATION_CNMF'

P value = 2.71e-05 (Fisher's exact test), Q value = 0.016

Table S251. Gene #70: 'Del Peak 41(21q11.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
DEL PEAK 41(21Q11.2) CNV	4	30	18	41
DEL PEAK 41(21Q11.2) WILD-TYPE	33	50	47	35

Figure S251. Get High-res Image Gene #70: 'Del Peak 41(21q11.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 41(21q11.2)' versus 'MRNASEQ_CNMF'

P value = 0.000283 (Chi-square test), Q value = 0.14

Table S252. Gene #70: 'Del Peak 41(21q11.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	63	43	42	62
DEL PEAK 41(21Q11.2) CNV	16	18	10	12	36
DEL PEAK 41(21Q11.2) WILD-TYPE	45	45	33	30	26

Figure S252. Get High-res Image Gene #70: 'Del Peak 41(21q11.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 41(21q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.18e-07 (Fisher's exact test), Q value = 0.00052

Table S253. Gene #70: 'Del Peak 41(21q11.2)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	141	64
DEL PEAK 41(21Q11.2) CNV	21	32	39
DEL PEAK 41(21Q11.2) WILD-TYPE	45	109	25

Figure S253. Get High-res Image Gene #70: 'Del Peak 41(21q11.2)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 41(21q11.2)' versus 'MIRSEQ_CNMF'

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

Table S254. Gene #70: 'Del Peak 41(21q11.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	91	114
DEL PEAK 41(21Q11.2) CNV	23	28	56
DEL PEAK 41(21Q11.2) WILD-TYPE	77	63	58

Figure S254. Get High-res Image Gene #70: 'Del Peak 41(21q11.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 42(21q22.13)' versus 'CN_CNMF'

P value = 9.31e-11 (Fisher's exact test), Q value = 6.4e-08

Table S255. Gene #71: 'Del Peak 42(21q22.13)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 42(21Q22.13) CNV	28	24	62
DEL PEAK 42(21Q22.13) WILD-TYPE	122	22	47

Figure S255. Get High-res Image Gene #71: 'Del Peak 42(21q22.13)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 42(21q22.13)' versus 'METHLYATION_CNMF'

P value = 0.000362 (Fisher's exact test), Q value = 0.18

Table S256. Gene #71: 'Del Peak 42(21q22.13)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
DEL PEAK 42(21Q22.13) CNV	4	34	21	37
DEL PEAK 42(21Q22.13) WILD-TYPE	33	46	44	39

Figure S256. Get High-res Image Gene #71: 'Del Peak 42(21q22.13)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 42(21q22.13)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.78e-06 (Fisher's exact test), Q value = 0.0053

Table S257. Gene #71: 'Del Peak 42(21q22.13)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	141	64
DEL PEAK 42(21Q22.13) CNV	24	36	39
DEL PEAK 42(21Q22.13) WILD-TYPE	42	105	25

Figure S257. Get High-res Image Gene #71: 'Del Peak 42(21q22.13)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 43(22q13.31)' versus 'CN_CNMF'

P value = 1.65e-17 (Fisher's exact test), Q value = 1.2e-14

Table S258. Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 43(22Q13.31) CNV	16	19	66
DEL PEAK 43(22Q13.31) WILD-TYPE	134	27	43

Figure S258. Get High-res Image Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 43(22q13.31)' versus 'METHLYATION_CNMF'

P value = 0.000135 (Fisher's exact test), Q value = 0.073

Table S259. Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
DEL PEAK 43(22Q13.31) CNV	4	28	15	37
DEL PEAK 43(22Q13.31) WILD-TYPE	33	52	50	39

Figure S259. Get High-res Image Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 43(22q13.31)' versus 'MRNASEQ_CNMF'

P value = 0.000245 (Chi-square test), Q value = 0.13

Table S260. Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	61	63	43	42	62
DEL PEAK 43(22Q13.31) CNV	14	14	16	10	34
DEL PEAK 43(22Q13.31) WILD-TYPE	47	49	27	32	28

Figure S260. Get High-res Image Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 43(22q13.31)' versus 'MIRSEQ_CNMF'

P value = 9.98e-05 (Fisher's exact test), Q value = 0.055

Table S261. Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	91	114
DEL PEAK 43(22Q13.31) CNV	23	23	55
DEL PEAK 43(22Q13.31) WILD-TYPE	77	68	59

Figure S261. Get High-res Image Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 43(22q13.31)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.38e-06 (Fisher's exact test), Q value = 0.00087

Table S262. Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	133	77	95
DEL PEAK 43(22Q13.31) CNV	37	44	20
DEL PEAK 43(22Q13.31) WILD-TYPE	96	33	75

Figure S262. Get High-res Image Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 43(22q13.31)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.52e-05 (Fisher's exact test), Q value = 0.02

Table S263. Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	72	130
DEL PEAK 43(22Q13.31) CNV	33	16	36
DEL PEAK 43(22Q13.31) WILD-TYPE	24	56	94

Figure S263. Get High-res Image Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 44(Xp22.2)' versus 'CN_CNMF'

P value = 1.04e-09 (Fisher's exact test), Q value = 7.1e-07

Table S264. Gene #73: 'Del Peak 44(Xp22.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 44(XP22.2) CNV	11	7	43
DEL PEAK 44(XP22.2) WILD-TYPE	139	39	66

Figure S264. Get High-res Image Gene #73: 'Del Peak 44(Xp22.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 44(Xp22.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000375 (Fisher's exact test), Q value = 0.19

Table S265. Gene #73: 'Del Peak 44(Xp22.2)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	133	77	95
DEL PEAK 44(XP22.2) CNV	19	28	14
DEL PEAK 44(XP22.2) WILD-TYPE	114	49	81

Figure S265. Get High-res Image Gene #73: 'Del Peak 44(Xp22.2)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 45(Xp21.1)' versus 'CN_CNMF'

P value = 6.99e-09 (Fisher's exact test), Q value = 4.7e-06

Table S266. Gene #74: 'Del Peak 45(Xp21.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 45(XP21.1) CNV	8	7	37
DEL PEAK 45(XP21.1) WILD-TYPE	142	39	72

Figure S266. Get High-res Image Gene #74: 'Del Peak 45(Xp21.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 46(Xq21.33)' versus 'CN_CNMF'

P value = 7.29e-06 (Fisher's exact test), Q value = 0.0044

Table S267. Gene #75: 'Del Peak 46(Xq21.33)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	46	109
DEL PEAK 46(XQ21.33) CNV	7	8	27
DEL PEAK 46(XQ21.33) WILD-TYPE	143	38	82

Figure S267. Get High-res Image Gene #75: 'Del Peak 46(Xq21.33)' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data

Input

Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
Molecular subtype file = STAD-TP.transferedmergedcluster.txt
Number of patients = 305
Number of copy number variation regions = 75
Number of molecular subtypes = 10
Exclude regions that fewer than K tumors have alterations, K = 3

Fisher's exact test

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

Chi-square test

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

Q value calculation

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

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

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

[2] 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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