Correlation between copy number variation genes and molecular subtypes

Stomach Adenocarcinoma (Primary solid tumor)

23 May 2013 | analyses__2013_05_23

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variation genes and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1HT2MDK

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 8 molecular subtypes across 306 patients, 276 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', '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', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 4(3q27.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 5(5p13.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 6(6p21.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 7(6q12) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 8(6q21) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 9(7p22.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', 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 12(8p23.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 13(8q24.21) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', 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 'MIRSEQ_CNMF' 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 'METHLYATION_CNMF'.
Amp Peak 22(13q12.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 23(13q22.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 24(15q26.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
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', 'MIRSEQ_MATURE_CNMF', 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', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 2(1p13.2) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
Del Peak 5(2q37.2) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 6(3p26.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 7(3p14.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 8(3q26.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
Del Peak 9(4p16.3) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 10(4q22.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 11(4q34.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', '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', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 15(6q26) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 16(7q31.1) cnvs correlated to 'CN_CNMF'.
Del Peak 17(7q36.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 18(8p23.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 19(9p23) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 20(9p21.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 21(9q21.11) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 22(10p15.1) cnvs correlated to 'CN_CNMF'.
Del Peak 23(10q22.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 24(10q23.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 25(11p15.4) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 26(11q23.2) cnvs correlated to 'CN_CNMF'.
Del Peak 27(12p13.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 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_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 30(14q32.33) cnvs correlated to 'CN_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'.
Del Peak 34(17p12) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', 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', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 38(19q13.11) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 39(20p12.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 40(20p12.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 41(21q11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 42(21q22.13) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 43(22q13.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 44(Xp22.2) cnvs correlated to 'CN_CNMF'.
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 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 276 significant findings detected.


		Molecular subtypes	CN CNMF	METHLYATION CNMF	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	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 27(19q12)	0 (0%)	216	1.67e-15 (9.79e-13)	1.01e-10 (5.54e-08)	1.2e-09 (6.43e-07)	2.98e-06 (0.00141)	8.13e-12 (4.53e-09)	1.65e-13 (9.45e-11)	0.000583 (0.195)	7.16e-13 (4.07e-10)
Del Peak 12(5q11 2)	0 (0%)	203	6.54e-28 (3.93e-25)	2.49e-14 (1.44e-11)	8.02e-10 (4.33e-07)	6.02e-08 (3.08e-05)	8.45e-12 (4.7e-09)	4.02e-10 (2.18e-07)	3.7e-08 (1.9e-05)	3.53e-15 (2.06e-12)
Del Peak 13(5q23 2)	0 (0%)	213	2.48e-23 (1.48e-20)	2.29e-12 (1.29e-09)	1.03e-09 (5.56e-07)	1.87e-07 (9.44e-05)	1.02e-12 (5.74e-10)	1.93e-09 (1.03e-06)	4.84e-09 (2.54e-06)	4.75e-14 (2.73e-11)
Del Peak 31(15q15 1)	0 (0%)	227	6.44e-13 (3.66e-10)	2.11e-07 (0.000106)	6.08e-05 (0.0252)	6.26e-07 (0.000307)	1.98e-09 (1.06e-06)	2.82e-08 (1.45e-05)	0.000552 (0.186)	1.06e-05 (0.00478)
Del Peak 32(16p13 3)	0 (0%)	248	7.42e-11 (4.1e-08)	4.14e-05 (0.0174)	1.46e-05 (0.00644)	0.000222 (0.0827)	1.39e-05 (0.00616)	0.000685 (0.228)	2.91e-06 (0.00138)	1.53e-06 (0.000738)
Del Peak 34(17p12)	0 (0%)	191	1.81e-23 (1.08e-20)	3.28e-11 (1.82e-08)	3.94e-06 (0.00185)	1.68e-06 (0.000808)	6.21e-08 (3.16e-05)	1.15e-07 (5.83e-05)	9.05e-06 (0.0041)	4.08e-09 (2.15e-06)
Del Peak 37(19p13 3)	0 (0%)	207	2.35e-27 (1.41e-24)	2.33e-16 (1.37e-13)	9.11e-13 (5.17e-10)	2.02e-15 (1.19e-12)	2.39e-22 (1.42e-19)	9.69e-24 (5.79e-21)	3.97e-05 (0.0168)	6.13e-17 (3.62e-14)
Amp Peak 2(1q21 3)	0 (0%)	198	4.55e-20 (2.7e-17)	4.32e-11 (2.39e-08)	4.8e-08 (2.46e-05)	0.00222 (0.638)	1.81e-08 (9.39e-06)	2.28e-09 (1.22e-06)	6.85e-07 (0.000334)	1.48e-08 (7.68e-06)
Amp Peak 3(1q42 3)	0 (0%)	201	5.52e-14 (3.18e-11)	1.15e-07 (5.83e-05)	1.1e-05 (0.00494)	0.017 (1.00)	2.41e-09 (1.28e-06)	1.95e-09 (1.04e-06)	2.38e-05 (0.0103)	1.02e-06 (0.000496)
Amp Peak 5(5p13 1)	0 (0%)	219	1.64e-14 (9.54e-12)	2.09e-07 (0.000105)	5.95e-05 (0.0247)	0.0318 (1.00)	0.000514 (0.174)	2.46e-06 (0.00117)	0.000427 (0.147)	2.43e-06 (0.00116)
Amp Peak 6(6p21 1)	0 (0%)	226	3.1e-17 (1.83e-14)	2.19e-10 (1.2e-07)	0.000687 (0.228)	0.114 (1.00)	1.77e-05 (0.0077)	5.57e-07 (0.000274)	2.43e-05 (0.0105)	3.9e-07 (0.000193)
Amp Peak 7(6q12)	0 (0%)	246	2.98e-09 (1.57e-06)	2.31e-08 (1.19e-05)	0.00016 (0.0611)	0.0029 (0.819)	8.12e-05 (0.0331)	2.71e-05 (0.0116)	0.00034 (0.12)	2.11e-05 (0.00917)
Amp Peak 28(20q13 2)	0 (0%)	105	5.63e-21 (3.34e-18)	4.24e-12 (2.37e-09)	5.18e-07 (0.000255)	9.04e-06 (0.0041)	5.53e-10 (3e-07)	2.15e-12 (1.21e-09)	0.00364 (0.974)	6.91e-09 (3.62e-06)
Del Peak 9(4p16 3)	0 (0%)	194	2.89e-10 (1.57e-07)	0.000991 (0.311)	9.87e-05 (0.0394)	0.000624 (0.208)	1.59e-05 (0.00697)	0.000212 (0.079)	2.57e-05 (0.011)	1.25e-05 (0.00555)
Del Peak 20(9p21 3)	0 (0%)	188	6.29e-16 (3.7e-13)	1.92e-10 (1.05e-07)	2.58e-07 (0.000129)	0.000195 (0.0731)	0.000188 (0.071)	6.23e-06 (0.00285)	0.00704 (1.00)	8.99e-05 (0.0362)
Amp Peak 25(17q12)	0 (0%)	214	9.54e-13 (5.39e-10)	2.68e-06 (0.00127)	5.76e-05 (0.024)	0.000717 (0.235)	6.09e-06 (0.00279)	5.92e-06 (0.00272)	0.0862 (1.00)	0.00616 (1.00)
Del Peak 7(3p14 2)	0 (0%)	204	9.33e-13 (5.28e-10)	1.24e-06 (6e-04)	0.000502 (0.171)	0.00177 (0.524)	7.45e-06 (0.0034)	1.75e-06 (0.000841)	0.0328 (1.00)	4.17e-06 (0.00196)
Del Peak 11(4q34 3)	0 (0%)	179	1.07e-14 (6.22e-12)	1.87e-06 (0.000897)	0.000109 (0.0433)	0.00915 (1.00)	1.69e-06 (0.000815)	1.84e-05 (0.008)	0.00126 (0.391)	4.71e-06 (0.00219)
Del Peak 18(8p23 2)	0 (0%)	229	4.3e-14 (2.48e-11)	8.11e-06 (0.00368)	0.00314 (0.869)	0.000232 (0.0859)	5.92e-05 (0.0246)	1.58e-05 (0.00695)	0.0407 (1.00)	9.23e-06 (0.00415)
Del Peak 24(10q23 31)	0 (0%)	233	2.72e-12 (1.53e-09)	5.23e-06 (0.00242)	0.0136 (1.00)	0.0179 (1.00)	3.07e-05 (0.013)	1.16e-05 (0.00521)	0.000315 (0.112)	0.00031 (0.111)
Del Peak 27(12p13 31)	0 (0%)	256	1.49e-10 (8.16e-08)	5.7e-06 (0.00263)	4.64e-06 (0.00216)	0.000297 (0.107)	0.000389 (0.135)	0.00222 (0.638)	0.0192 (1.00)	0.000154 (0.0591)
Amp Peak 22(13q12 3)	0 (0%)	190	7.07e-10 (3.82e-07)	4.55e-06 (0.00212)	0.0432 (1.00)	0.796 (1.00)	0.00037 (0.129)	0.000119 (0.047)	0.00358 (0.964)	0.000161 (0.0614)
Amp Peak 23(13q22 1)	0 (0%)	185	1.54e-08 (8.01e-06)	4.13e-05 (0.0174)	0.00168 (0.5)	0.0403 (1.00)	2.98e-07 (0.000148)	6.01e-07 (0.000295)	0.00193 (0.559)	1.48e-06 (0.000716)
Del Peak 6(3p26 1)	0 (0%)	222	2.64e-10 (1.44e-07)	0.000307 (0.11)	0.00199 (0.576)	0.16 (1.00)	0.000143 (0.0552)	6.32e-05 (0.0261)	0.19 (1.00)	0.000719 (0.235)
Del Peak 17(7q36 3)	0 (0%)	248	1.82e-14 (1.05e-11)	1.31e-05 (0.00579)	0.000677 (0.225)	0.00463 (1.00)	0.000781 (0.253)	3.06e-05 (0.013)	0.0109 (1.00)	9.56e-05 (0.0383)
Del Peak 29(14q21 1)	0 (0%)	235	7.69e-07 (0.000374)	0.0159 (1.00)	0.000837 (0.27)	0.000175 (0.0663)	0.000142 (0.0547)	0.000162 (0.0616)	0.0363 (1.00)	0.000236 (0.087)
Del Peak 38(19q13 11)	0 (0%)	263	2.69e-09 (1.42e-06)	8.49e-05 (0.0345)	0.00179 (0.528)	0.00294 (0.823)	2.44e-05 (0.0105)	6.42e-07 (0.000314)	0.014 (1.00)	4.89e-06 (0.00227)
Del Peak 41(21q11 2)	0 (0%)	198	1.39e-10 (7.61e-08)	2.71e-05 (0.0116)	0.000496 (0.169)	8.98e-05 (0.0362)	0.00189 (0.551)	0.000125 (0.049)	0.0032 (0.879)	0.0108 (1.00)
Del Peak 42(21q22 13)	0 (0%)	191	1.56e-09 (8.37e-07)	0.000362 (0.127)	0.00589 (1.00)	0.000197 (0.0738)	0.000693 (0.229)	8.02e-05 (0.0328)	0.107 (1.00)	0.00632 (1.00)
Del Peak 43(22q13 31)	0 (0%)	205	9.68e-15 (5.63e-12)	0.000135 (0.0524)	0.000993 (0.311)	0.00317 (0.875)	4.36e-05 (0.0183)	6.47e-06 (0.00296)	0.0787 (1.00)	0.000122 (0.0483)
Amp Peak 9(7p22 3)	0 (0%)	149	8.25e-14 (4.74e-11)	1.74e-05 (0.0076)	0.0116 (1.00)	0.625 (1.00)	0.02 (1.00)	0.000332 (0.118)	0.0773 (1.00)	0.000245 (0.0902)
Amp Peak 13(8q24 21)	0 (0%)	101	2.63e-06 (0.00125)	4.46e-05 (0.0187)	0.0576 (1.00)	0.0318 (1.00)	0.0029 (0.819)	0.000388 (0.135)	0.00576 (1.00)	6.79e-05 (0.028)
Del Peak 1(1p36 11)	0 (0%)	223	4.2e-15 (2.45e-12)	0.000396 (0.137)	0.000883 (0.281)	0.00887 (1.00)	0.000129 (0.0499)	0.000119 (0.0472)	0.0128 (1.00)	0.00191 (0.557)
Del Peak 8(3q26 31)	0 (0%)	272	4.23e-06 (0.00198)	0.000107 (0.0427)	0.000267 (0.0972)	0.00931 (1.00)	0.000521 (0.176)	0.0211 (1.00)	0.0328 (1.00)	0.00687 (1.00)
Del Peak 10(4q22 1)	0 (0%)	171	6.72e-19 (3.98e-16)	3.85e-07 (0.000191)	0.0419 (1.00)	0.0342 (1.00)	9.2e-06 (0.00415)	0.000369 (0.129)	0.00578 (1.00)	0.000962 (0.304)
Del Peak 14(6p25 3)	0 (0%)	237	5.01e-07 (0.000247)	0.000576 (0.194)	0.00466 (1.00)	0.0268 (1.00)	9.72e-05 (0.0389)	0.000337 (0.119)	0.0561 (1.00)	0.0263 (1.00)
Del Peak 19(9p23)	0 (0%)	186	2.66e-15 (1.56e-12)	8.76e-05 (0.0355)	0.000127 (0.0495)	0.00127 (0.392)	0.00145 (0.443)	5.55e-05 (0.0232)	0.0758 (1.00)	0.00222 (0.638)
Del Peak 21(9q21 11)	0 (0%)	233	2.97e-08 (1.53e-05)	0.000223 (0.0829)	0.0112 (1.00)	0.0185 (1.00)	0.0258 (1.00)	0.000363 (0.127)	0.00101 (0.314)	2.25e-05 (0.00976)
Del Peak 23(10q22 3)	0 (0%)	257	2.43e-09 (1.29e-06)	0.000718 (0.235)	0.0266 (1.00)	0.0789 (1.00)	0.00329 (0.901)	0.000168 (0.0638)	0.0203 (1.00)	0.000285 (0.103)
Amp Peak 24(15q26 1)	0 (0%)	237	1.03e-13 (5.91e-11)	0.000441 (0.151)	7.59e-05 (0.0311)	0.000883 (0.281)	0.0452 (1.00)	0.00878 (1.00)	0.0293 (1.00)	0.0209 (1.00)
Del Peak 15(6q26)	0 (0%)	244	0.000128 (0.0496)	0.0711 (1.00)	0.000124 (0.0487)	7.5e-05 (0.0308)	0.149 (1.00)	0.0356 (1.00)	0.329 (1.00)	0.339 (1.00)
Amp Peak 8(6q21)	0 (0%)	250	4.38e-09 (2.3e-06)	1.68e-05 (0.00736)	0.00432 (1.00)	0.0136 (1.00)	0.00798 (1.00)	0.0059 (1.00)	0.00142 (0.435)	0.000858 (0.275)
Amp Peak 18(11p13)	0 (0%)	252	0.00658 (1.00)	0.186 (1.00)	0.0166 (1.00)	0.00529 (1.00)	0.000266 (0.0972)	0.000387 (0.135)	0.147 (1.00)	0.00862 (1.00)
Amp Peak 26(18q11 2)	0 (0%)	216	3.31e-06 (0.00156)	0.000306 (0.11)	0.0214 (1.00)	0.0942 (1.00)	0.0063 (1.00)	0.0171 (1.00)	0.196 (1.00)	0.0731 (1.00)
Del Peak 2(1p13 2)	0 (0%)	247	5.4e-12 (3.01e-09)	0.00669 (1.00)	0.00344 (0.929)	0.0131 (1.00)	0.00028 (0.102)	0.00134 (0.412)	0.241 (1.00)	0.0151 (1.00)
Del Peak 5(2q37 2)	0 (0%)	259	0.000191 (0.0717)	0.00736 (1.00)	0.0642 (1.00)	0.45 (1.00)	0.00168 (0.5)	8.76e-05 (0.0355)	0.0706 (1.00)	0.00402 (1.00)
Del Peak 25(11p15 4)	0 (0%)	247	2.96e-08 (1.53e-05)	8.05e-06 (0.00366)	0.102 (1.00)	0.0374 (1.00)	0.00167 (0.5)	0.00156 (0.474)	0.222 (1.00)	0.00329 (0.901)
Del Peak 30(14q32 33)	0 (0%)	217	9.24e-09 (4.83e-06)	0.0422 (1.00)	0.0111 (1.00)	8.24e-05 (0.0335)	0.0347 (1.00)	0.0183 (1.00)	0.0274 (1.00)	0.00623 (1.00)
Del Peak 35(17q24 3)	0 (0%)	251	1.32e-10 (7.24e-08)	0.000251 (0.0922)	0.00184 (0.539)	0.0204 (1.00)	0.0049 (1.00)	0.00648 (1.00)	0.0205 (1.00)	0.0212 (1.00)
Del Peak 39(20p12 1)	0 (0%)	254	1.21e-08 (6.3e-06)	0.000701 (0.23)	0.0033 (0.901)	0.0407 (1.00)	0.00166 (0.5)	0.00435 (1.00)	0.0504 (1.00)	0.00531 (1.00)
Del Peak 40(20p12 1)	0 (0%)	254	1.21e-08 (6.3e-06)	0.000701 (0.23)	0.0033 (0.901)	0.0407 (1.00)	0.00166 (0.5)	0.00435 (1.00)	0.0504 (1.00)	0.00531 (1.00)
Amp Peak 1(1p36 22)	0 (0%)	270	1.19e-07 (6.02e-05)	0.00304 (0.845)	0.0138 (1.00)	0.249 (1.00)	0.208 (1.00)	0.105 (1.00)	0.741 (1.00)	0.0706 (1.00)
Amp Peak 4(3q27 1)	0 (0%)	203	1.21e-05 (0.00537)	0.00363 (0.974)	0.289 (1.00)	0.129 (1.00)	0.0537 (1.00)	0.00427 (1.00)	0.687 (1.00)	0.00503 (1.00)
Amp Peak 10(7p11 2)	0 (0%)	163	4.23e-12 (2.37e-09)	0.00995 (1.00)	0.0635 (1.00)	0.816 (1.00)	0.12 (1.00)	0.0102 (1.00)	0.0866 (1.00)	0.00394 (1.00)
Amp Peak 11(7q21 2)	0 (0%)	169	2.36e-11 (1.31e-08)	0.0196 (1.00)	0.276 (1.00)	0.828 (1.00)	0.301 (1.00)	0.042 (1.00)	0.387 (1.00)	0.129 (1.00)
Amp Peak 12(8p23 1)	0 (0%)	185	3.39e-13 (1.94e-10)	0.00298 (0.832)	0.454 (1.00)	0.00826 (1.00)	0.0466 (1.00)	0.326 (1.00)	0.248 (1.00)	0.0503 (1.00)
Amp Peak 15(9q34 3)	0 (0%)	232	2.86e-07 (0.000143)	0.00517 (1.00)	0.022 (1.00)	0.55 (1.00)	0.0505 (1.00)	0.191 (1.00)	0.0686 (1.00)	0.0301 (1.00)
Amp Peak 16(10q22 2)	0 (0%)	250	9.41e-08 (4.78e-05)	0.0746 (1.00)	0.0055 (1.00)	0.0095 (1.00)	0.073 (1.00)	0.0567 (1.00)	0.00683 (1.00)	0.0379 (1.00)
Amp Peak 17(10q26 13)	0 (0%)	245	1.18e-05 (0.00527)	0.00128 (0.395)	0.00869 (1.00)	0.0177 (1.00)	0.123 (1.00)	0.00493 (1.00)	0.231 (1.00)	0.00874 (1.00)
Amp Peak 19(11q13 3)	0 (0%)	238	3.27e-05 (0.0139)	0.194 (1.00)	0.483 (1.00)	0.297 (1.00)	0.00182 (0.535)	0.0132 (1.00)	0.00271 (0.769)	0.163 (1.00)
Amp Peak 20(12p12 1)	0 (0%)	220	0.000304 (0.109)	0.0114 (1.00)	0.388 (1.00)	0.798 (1.00)	0.13 (1.00)	0.0606 (1.00)	0.00522 (1.00)	0.115 (1.00)
Amp Peak 21(12q15)	0 (0%)	229	0.00803 (1.00)	0.000489 (0.167)	0.479 (1.00)	0.412 (1.00)	0.0301 (1.00)	0.0191 (1.00)	0.0757 (1.00)	0.221 (1.00)
Amp Peak 29(Xq27 3)	0 (0%)	246	0.000155 (0.0594)	0.191 (1.00)	0.0667 (1.00)	0.736 (1.00)	0.111 (1.00)	0.615 (1.00)	0.00463 (1.00)	0.00858 (1.00)
Del Peak 16(7q31 1)	0 (0%)	262	3.11e-07 (0.000154)	0.00116 (0.362)	0.144 (1.00)	0.337 (1.00)	0.022 (1.00)	0.247 (1.00)	0.000863 (0.276)	0.0591 (1.00)
Del Peak 22(10p15 1)	0 (0%)	268	0.000124 (0.0487)	0.277 (1.00)	0.291 (1.00)	0.627 (1.00)	0.238 (1.00)	0.346 (1.00)	0.0794 (1.00)	0.156 (1.00)
Del Peak 26(11q23 2)	0 (0%)	244	0.000264 (0.0967)	0.00167 (0.5)	0.00078 (0.253)	0.103 (1.00)	0.287 (1.00)	0.431 (1.00)	0.935 (1.00)	0.202 (1.00)
Del Peak 28(13q12 11)	0 (0%)	262	2.32e-06 (0.00111)	0.126 (1.00)	0.176 (1.00)	0.0124 (1.00)	0.541 (1.00)	0.24 (1.00)	0.0619 (1.00)	0.113 (1.00)
Del Peak 33(16q23 1)	0 (0%)	188	2.22e-07 (0.000111)	0.00289 (0.819)	0.0379 (1.00)	0.0588 (1.00)	0.0121 (1.00)	0.0129 (1.00)	0.0108 (1.00)	0.000881 (0.281)
Del Peak 36(18q21 2)	0 (0%)	173	4.49e-13 (2.56e-10)	0.00256 (0.731)	0.0185 (1.00)	0.0294 (1.00)	0.00716 (1.00)	0.00415 (1.00)	0.0717 (1.00)	0.0159 (1.00)
Del Peak 44(Xp22 2)	0 (0%)	245	1.44e-09 (7.74e-07)	0.00162 (0.492)	0.0517 (1.00)	0.146 (1.00)	0.0228 (1.00)	0.000984 (0.31)	0.232 (1.00)	0.0142 (1.00)
Del Peak 45(Xp21 1)	0 (0%)	254	6.22e-08 (3.17e-05)	0.00407 (1.00)	0.172 (1.00)	0.139 (1.00)	0.222 (1.00)	0.366 (1.00)	0.72 (1.00)	0.259 (1.00)
Del Peak 46(Xq21 33)	0 (0%)	264	5.77e-06 (0.00266)	0.0352 (1.00)	0.0746 (1.00)	0.014 (1.00)	0.0702 (1.00)	0.212 (1.00)	0.079 (1.00)	0.0618 (1.00)
Amp Peak 14(9p24 1)	0 (0%)	257	0.364 (1.00)	0.0878 (1.00)	0.633 (1.00)	0.306 (1.00)	0.277 (1.00)	0.303 (1.00)	0.297 (1.00)	0.0448 (1.00)
Del Peak 3(1q44)	0 (0%)	283	0.0185 (1.00)	0.00748 (1.00)	0.573 (1.00)	0.651 (1.00)	0.13 (1.00)	0.0791 (1.00)	0.123 (1.00)	0.0826 (1.00)
Del Peak 4(2q32 1)	0 (0%)	264	0.00895 (1.00)	0.108 (1.00)	0.46 (1.00)	0.9 (1.00)	0.0333 (1.00)	0.133 (1.00)	0.571 (1.00)	0.742 (1.00)

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

P value = 1.19e-07 (Fisher's exact test), Q value = 6e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 1(1P36.22) CNV	2	4	3	27
AMP PEAK 1(1P36.22) WILD-TYPE	135	24	25	86

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 = 4.55e-20 (Fisher's exact test), Q value = 2.7e-17

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 2(1Q21.3) CNV	12	12	12	72
AMP PEAK 2(1Q21.3) WILD-TYPE	125	16	16	41

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 = 2.4e-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 = 4.8e-08 (Chi-square test), Q value = 2.5e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	41	35	37	50
AMP PEAK 2(1Q21.3) CNV	9	6	10	12	35
AMP PEAK 2(1Q21.3) WILD-TYPE	36	35	25	25	15

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

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

P value = 1.81e-08 (Fisher's exact test), Q value = 9.4e-06

Table S5. Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	69	97	57
AMP PEAK 2(1Q21.3) CNV	14	13	33	39
AMP PEAK 2(1Q21.3) WILD-TYPE	47	56	64	18

Figure S5. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

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

P value = 2.28e-09 (Fisher's exact test), Q value = 1.2e-06

Table S6. Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
AMP PEAK 2(1Q21.3) CNV	47	20	32
AMP PEAK 2(1Q21.3) WILD-TYPE	24	69	92

Figure S6. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

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

P value = 6.85e-07 (Fisher's exact test), Q value = 0.00033

Table S7. Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	67	103
AMP PEAK 2(1Q21.3) CNV	13	14	55
AMP PEAK 2(1Q21.3) WILD-TYPE	54	53	48

Figure S7. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

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

P value = 1.48e-08 (Fisher's exact test), Q value = 7.7e-06

Table S8. Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	83	96
AMP PEAK 2(1Q21.3) CNV	38	14	30
AMP PEAK 2(1Q21.3) WILD-TYPE	20	69	66

Figure S8. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 5.52e-14 (Fisher's exact test), Q value = 3.2e-11

Table S9. Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 3(1Q42.3) CNV	16	14	11	64
AMP PEAK 3(1Q42.3) WILD-TYPE	121	14	17	49

Figure S9. 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 = 5.8e-05

Table S10. 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 S10. 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 = 1.1e-05 (Chi-square test), Q value = 0.0049

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	41	35	37	50
AMP PEAK 3(1Q42.3) CNV	9	8	10	12	32
AMP PEAK 3(1Q42.3) WILD-TYPE	36	33	25	25	18

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

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

P value = 2.41e-09 (Fisher's exact test), Q value = 1.3e-06

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	69	97	57
AMP PEAK 3(1Q42.3) CNV	9	16	35	39
AMP PEAK 3(1Q42.3) WILD-TYPE	52	53	62	18

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

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

P value = 1.95e-09 (Fisher's exact test), Q value = 1e-06

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
AMP PEAK 3(1Q42.3) CNV	47	24	28
AMP PEAK 3(1Q42.3) WILD-TYPE	24	65	96

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

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

P value = 2.38e-05 (Fisher's exact test), Q value = 0.01

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	67	103
AMP PEAK 3(1Q42.3) CNV	13	18	53
AMP PEAK 3(1Q42.3) WILD-TYPE	54	49	50

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

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

P value = 1.02e-06 (Fisher's exact test), Q value = 5e-04

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	83	96
AMP PEAK 3(1Q42.3) CNV	37	18	29
AMP PEAK 3(1Q42.3) WILD-TYPE	21	65	67

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

'Amp Peak 4(3q27.1)' versus 'CN_CNMF'

P value = 1.21e-05 (Fisher's exact test), Q value = 0.0054

Table S16. Gene #4: 'Amp Peak 4(3q27.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 4(3Q27.1) CNV	26	12	14	51
AMP PEAK 4(3Q27.1) WILD-TYPE	111	16	14	62

Figure S16. Get High-res Image Gene #4: 'Amp Peak 4(3q27.1)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 1.64e-14 (Fisher's exact test), Q value = 9.5e-12

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 5(5P13.1) CNV	12	9	5	61
AMP PEAK 5(5P13.1) WILD-TYPE	125	19	23	52

Figure S17. 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 = 0.00011

Table S18. 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 S18. 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 = 5.95e-05 (Chi-square test), Q value = 0.025

Table S19. Gene #5: 'Amp Peak 5(5p13.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	41	35	37	50
AMP PEAK 5(5P13.1) CNV	9	8	7	10	29
AMP PEAK 5(5P13.1) WILD-TYPE	36	33	28	27	21

Figure S19. Get High-res Image Gene #5: 'Amp Peak 5(5p13.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

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

P value = 0.000514 (Fisher's exact test), Q value = 0.17

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	69	97	57
AMP PEAK 5(5P13.1) CNV	13	13	26	29
AMP PEAK 5(5P13.1) WILD-TYPE	48	56	71	28

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

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

P value = 2.46e-06 (Fisher's exact test), Q value = 0.0012

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
AMP PEAK 5(5P13.1) CNV	37	22	22
AMP PEAK 5(5P13.1) WILD-TYPE	34	67	102

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

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

P value = 0.000427 (Fisher's exact test), Q value = 0.15

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	67	103
AMP PEAK 5(5P13.1) CNV	14	10	42
AMP PEAK 5(5P13.1) WILD-TYPE	53	57	61

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

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

P value = 2.43e-06 (Fisher's exact test), Q value = 0.0012

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	83	96
AMP PEAK 5(5P13.1) CNV	31	12	23
AMP PEAK 5(5P13.1) WILD-TYPE	27	71	73

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

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

P value = 3.1e-17 (Fisher's exact test), Q value = 1.8e-14

Table S24. Gene #6: 'Amp Peak 6(6p21.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 6(6P21.1) CNV	6	7	9	58
AMP PEAK 6(6P21.1) WILD-TYPE	131	21	19	55

Figure S24. 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 = 1.2e-07

Table S25. 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 S25. 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 = 0.000687 (Chi-square test), Q value = 0.23

Table S26. Gene #6: 'Amp Peak 6(6p21.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	41	35	37	50
AMP PEAK 6(6P21.1) CNV	6	6	8	11	24
AMP PEAK 6(6P21.1) WILD-TYPE	39	35	27	26	26

Figure S26. Get High-res Image Gene #6: 'Amp Peak 6(6p21.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

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

P value = 1.77e-05 (Fisher's exact test), Q value = 0.0077

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	69	97	57
AMP PEAK 6(6P21.1) CNV	12	10	24	30
AMP PEAK 6(6P21.1) WILD-TYPE	49	59	73	27

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

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

P value = 5.57e-07 (Fisher's exact test), Q value = 0.00027

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
AMP PEAK 6(6P21.1) CNV	37	17	22
AMP PEAK 6(6P21.1) WILD-TYPE	34	72	102

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

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

P value = 2.43e-05 (Fisher's exact test), Q value = 0.01

Table S29. Gene #6: 'Amp Peak 6(6p21.1)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	67	103
AMP PEAK 6(6P21.1) CNV	10	9	42
AMP PEAK 6(6P21.1) WILD-TYPE	57	58	61

Figure S29. Get High-res Image Gene #6: 'Amp Peak 6(6p21.1)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

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

P value = 3.9e-07 (Fisher's exact test), Q value = 0.00019

Table S30. Gene #6: 'Amp Peak 6(6p21.1)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	83	96
AMP PEAK 6(6P21.1) CNV	31	11	19
AMP PEAK 6(6P21.1) WILD-TYPE	27	72	77

Figure S30. Get High-res Image Gene #6: 'Amp Peak 6(6p21.1)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 2.98e-09 (Fisher's exact test), Q value = 1.6e-06

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 7(6Q12) CNV	7	5	7	41
AMP PEAK 7(6Q12) WILD-TYPE	130	23	21	72

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 = 1.2e-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 = 0.00016 (Chi-square test), Q value = 0.061

Table S33. Gene #7: 'Amp Peak 7(6q12)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	41	35	37	50
AMP PEAK 7(6Q12) CNV	4	4	7	5	21
AMP PEAK 7(6Q12) WILD-TYPE	41	37	28	32	29

Figure S33. Get High-res Image Gene #7: 'Amp Peak 7(6q12)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

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

P value = 8.12e-05 (Fisher's exact test), Q value = 0.033

Table S34. Gene #7: 'Amp Peak 7(6q12)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	69	97	57
AMP PEAK 7(6Q12) CNV	8	7	17	24
AMP PEAK 7(6Q12) WILD-TYPE	53	62	80	33

Figure S34. Get High-res Image Gene #7: 'Amp Peak 7(6q12)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

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

P value = 2.71e-05 (Fisher's exact test), Q value = 0.012

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
AMP PEAK 7(6Q12) CNV	28	12	16
AMP PEAK 7(6Q12) WILD-TYPE	43	77	108

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

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

P value = 0.00034 (Fisher's exact test), Q value = 0.12

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	67	103
AMP PEAK 7(6Q12) CNV	5	7	30
AMP PEAK 7(6Q12) WILD-TYPE	62	60	73

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

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

P value = 2.11e-05 (Fisher's exact test), Q value = 0.0092

Table S37. Gene #7: 'Amp Peak 7(6q12)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	83	96
AMP PEAK 7(6Q12) CNV	22	6	14
AMP PEAK 7(6Q12) WILD-TYPE	36	77	82

Figure S37. Get High-res Image Gene #7: 'Amp Peak 7(6q12)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 4.38e-09 (Fisher's exact test), Q value = 2.3e-06

Table S38. Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 8(6Q21) CNV	6	4	9	37
AMP PEAK 8(6Q21) WILD-TYPE	131	24	19	76

Figure S38. 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 = 0.0074

Table S39. 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 S39. Get High-res Image Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 8.25e-14 (Fisher's exact test), Q value = 4.7e-11

Table S40. Gene #9: 'Amp Peak 9(7p22.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 9(7P22.3) CNV	40	26	14	77
AMP PEAK 9(7P22.3) WILD-TYPE	97	2	14	36

Figure S40. 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 = 0.0076

Table S41. 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 S41. Get High-res Image Gene #9: 'Amp Peak 9(7p22.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 0.000332 (Fisher's exact test), Q value = 0.12

Table S42. Gene #9: 'Amp Peak 9(7p22.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
AMP PEAK 9(7P22.3) CNV	51	39	56
AMP PEAK 9(7P22.3) WILD-TYPE	20	50	68

Figure S42. Get High-res Image Gene #9: 'Amp Peak 9(7p22.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

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

P value = 0.000245 (Fisher's exact test), Q value = 0.09

Table S43. Gene #9: 'Amp Peak 9(7p22.3)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	83	96
AMP PEAK 9(7P22.3) CNV	41	30	51
AMP PEAK 9(7P22.3) WILD-TYPE	17	53	45

Figure S43. Get High-res Image Gene #9: 'Amp Peak 9(7p22.3)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 4.23e-12 (Fisher's exact test), Q value = 2.4e-09

Table S44. Gene #10: 'Amp Peak 10(7p11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 10(7P11.2) CNV	39	27	14	63
AMP PEAK 10(7P11.2) WILD-TYPE	98	1	14	50

Figure S44. 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 = 2.36e-11 (Fisher's exact test), Q value = 1.3e-08

Table S45. Gene #11: 'Amp Peak 11(7q21.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 11(7Q21.2) CNV	39	27	13	58
AMP PEAK 11(7Q21.2) WILD-TYPE	98	1	15	55

Figure S45. Get High-res Image Gene #11: 'Amp Peak 11(7q21.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 12(8p23.1)' versus 'CN_CNMF'

P value = 3.39e-13 (Fisher's exact test), Q value = 1.9e-10

Table S46. Gene #12: 'Amp Peak 12(8p23.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 12(8P23.1) CNV	52	13	28	28
AMP PEAK 12(8P23.1) WILD-TYPE	85	15	0	85

Figure S46. Get High-res Image Gene #12: 'Amp Peak 12(8p23.1)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 2.63e-06 (Fisher's exact test), Q value = 0.0013

Table S47. Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 13(8Q24.21) CNV	71	19	24	91
AMP PEAK 13(8Q24.21) WILD-TYPE	66	9	4	22

Figure S47. Get High-res Image Gene #13: 'Amp Peak 13(8q24.21)' 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 = 0.019

Table S48. 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 S48. 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 = 0.000388 (Fisher's exact test), Q value = 0.13

Table S49. Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
AMP PEAK 13(8Q24.21) CNV	60	51	77
AMP PEAK 13(8Q24.21) WILD-TYPE	11	38	47

Figure S49. Get High-res Image Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

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

P value = 6.79e-05 (Fisher's exact test), Q value = 0.028

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	83	96
AMP PEAK 13(8Q24.21) CNV	49	41	62
AMP PEAK 13(8Q24.21) WILD-TYPE	9	42	34

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

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

P value = 2.86e-07 (Fisher's exact test), Q value = 0.00014

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 15(9Q34.3) CNV	15	7	5	47
AMP PEAK 15(9Q34.3) WILD-TYPE	122	21	23	66

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 = 9.41e-08 (Fisher's exact test), Q value = 4.8e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 16(10Q22.2) CNV	8	3	10	35
AMP PEAK 16(10Q22.2) WILD-TYPE	129	25	18	78

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 = 1.18e-05 (Fisher's exact test), Q value = 0.0053

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 17(10Q26.13) CNV	12	4	8	37
AMP PEAK 17(10Q26.13) WILD-TYPE	125	24	20	76

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

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

P value = 0.000266 (Fisher's exact test), Q value = 0.097

Table S54. Gene #18: 'Amp Peak 18(11p13)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	69	97	57
AMP PEAK 18(11P13) CNV	7	12	9	21
AMP PEAK 18(11P13) WILD-TYPE	54	57	88	36

Figure S54. Get High-res Image Gene #18: 'Amp Peak 18(11p13)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

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

P value = 0.000387 (Fisher's exact test), Q value = 0.13

Table S55. Gene #18: 'Amp Peak 18(11p13)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
AMP PEAK 18(11P13) CNV	23	14	12
AMP PEAK 18(11P13) WILD-TYPE	48	75	112

Figure S55. Get High-res Image Gene #18: 'Amp Peak 18(11p13)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

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

P value = 3.27e-05 (Fisher's exact test), Q value = 0.014

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 19(11Q13.3) CNV	15	5	8	40
AMP PEAK 19(11Q13.3) WILD-TYPE	122	23	20	73

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 = 0.000304 (Fisher's exact test), Q value = 0.11

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 20(12P12.1) CNV	24	6	9	47
AMP PEAK 20(12P12.1) WILD-TYPE	113	22	19	66

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

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

P value = 0.000489 (Fisher's exact test), Q value = 0.17

Table S58. 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 S58. 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 = 7.07e-10 (Fisher's exact test), Q value = 3.8e-07

Table S59. Gene #22: 'Amp Peak 22(13q12.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 22(13Q12.3) CNV	31	21	5	59
AMP PEAK 22(13Q12.3) WILD-TYPE	106	7	23	54

Figure S59. 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 = 0.0021

Table S60. 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 S60. Get High-res Image Gene #22: 'Amp Peak 22(13q12.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 0.00037 (Fisher's exact test), Q value = 0.13

Table S61. Gene #22: 'Amp Peak 22(13q12.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	69	97	57
AMP PEAK 22(13Q12.3) CNV	19	18	35	35
AMP PEAK 22(13Q12.3) WILD-TYPE	42	51	62	22

Figure S61. Get High-res Image Gene #22: 'Amp Peak 22(13q12.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

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

P value = 0.000119 (Fisher's exact test), Q value = 0.047

Table S62. Gene #22: 'Amp Peak 22(13q12.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
AMP PEAK 22(13Q12.3) CNV	42	28	37
AMP PEAK 22(13Q12.3) WILD-TYPE	29	61	87

Figure S62. Get High-res Image Gene #22: 'Amp Peak 22(13q12.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

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

P value = 0.000161 (Fisher's exact test), Q value = 0.061

Table S63. Gene #22: 'Amp Peak 22(13q12.3)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	83	96
AMP PEAK 22(13Q12.3) CNV	34	20	34
AMP PEAK 22(13Q12.3) WILD-TYPE	24	63	62

Figure S63. Get High-res Image Gene #22: 'Amp Peak 22(13q12.3)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 1.54e-08 (Fisher's exact test), Q value = 8e-06

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 23(13Q22.1) CNV	35	20	5	61
AMP PEAK 23(13Q22.1) WILD-TYPE	102	8	23	52

Figure S64. 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 = 0.017

Table S65. 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 S65. Get High-res Image Gene #23: 'Amp Peak 23(13q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 2.98e-07 (Fisher's exact test), Q value = 0.00015

Table S66. Gene #23: 'Amp Peak 23(13q22.1)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	69	97	57
AMP PEAK 23(13Q22.1) CNV	22	18	30	41
AMP PEAK 23(13Q22.1) WILD-TYPE	39	51	67	16

Figure S66. Get High-res Image Gene #23: 'Amp Peak 23(13q22.1)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

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

P value = 6.01e-07 (Fisher's exact test), Q value = 3e-04

Table S67. Gene #23: 'Amp Peak 23(13q22.1)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
AMP PEAK 23(13Q22.1) CNV	47	26	38
AMP PEAK 23(13Q22.1) WILD-TYPE	24	63	86

Figure S67. Get High-res Image Gene #23: 'Amp Peak 23(13q22.1)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

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

P value = 1.48e-06 (Fisher's exact test), Q value = 0.00072

Table S68. Gene #23: 'Amp Peak 23(13q22.1)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	83	96
AMP PEAK 23(13Q22.1) CNV	38	20	30
AMP PEAK 23(13Q22.1) WILD-TYPE	20	63	66

Figure S68. Get High-res Image Gene #23: 'Amp Peak 23(13q22.1)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 1.03e-13 (Fisher's exact test), Q value = 5.9e-11

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 24(15Q26.1) CNV	10	5	1	53
AMP PEAK 24(15Q26.1) WILD-TYPE	127	23	27	60

Figure S69. 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 = 0.15

Table S70. 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 S70. 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 = 7.59e-05 (Chi-square test), Q value = 0.031

Table S71. Gene #24: 'Amp Peak 24(15q26.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	41	35	37	50
AMP PEAK 24(15Q26.1) CNV	6	2	12	8	22
AMP PEAK 24(15Q26.1) WILD-TYPE	39	39	23	29	28

Figure S71. Get High-res Image Gene #24: 'Amp Peak 24(15q26.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

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

P value = 9.54e-13 (Fisher's exact test), Q value = 5.4e-10

Table S72. Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 25(17Q12) CNV	16	9	5	62
AMP PEAK 25(17Q12) WILD-TYPE	121	19	23	51

Figure S72. 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 = 0.0013

Table S73. 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 S73. 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 = 5.76e-05 (Chi-square test), Q value = 0.024

Table S74. Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	41	35	37	50
AMP PEAK 25(17Q12) CNV	6	6	13	8	26
AMP PEAK 25(17Q12) WILD-TYPE	39	35	22	29	24

Figure S74. Get High-res Image Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

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

P value = 0.000717 (Fisher's exact test), Q value = 0.23

Table S75. Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	42	55	69
AMP PEAK 25(17Q12) CNV	5	15	25	14
AMP PEAK 25(17Q12) WILD-TYPE	37	27	30	55

Figure S75. Get High-res Image Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

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

P value = 6.09e-06 (Fisher's exact test), Q value = 0.0028

Table S76. Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	69	97	57
AMP PEAK 25(17Q12) CNV	13	13	24	33
AMP PEAK 25(17Q12) WILD-TYPE	48	56	73	24

Figure S76. Get High-res Image Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

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

P value = 5.92e-06 (Fisher's exact test), Q value = 0.0027

Table S77. Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
AMP PEAK 25(17Q12) CNV	37	23	23
AMP PEAK 25(17Q12) WILD-TYPE	34	66	101

Figure S77. Get High-res Image Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

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

P value = 3.31e-06 (Fisher's exact test), Q value = 0.0016

Table S78. Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 26(18Q11.2) CNV	23	8	6	53
AMP PEAK 26(18Q11.2) WILD-TYPE	114	20	22	60

Figure S78. 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 = 0.11

Table S79. 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 S79. 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 = 1.67e-15 (Fisher's exact test), Q value = 9.8e-13

Table S80. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 27(19Q12) CNV	14	9	3	64
AMP PEAK 27(19Q12) WILD-TYPE	123	19	25	49

Figure S80. 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 = 5.5e-08

Table S81. 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 S81. 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 = 1.2e-09 (Chi-square test), Q value = 6.4e-07

Table S82. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	41	35	37	50
AMP PEAK 27(19Q12) CNV	7	4	7	8	33
AMP PEAK 27(19Q12) WILD-TYPE	38	37	28	29	17

Figure S82. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

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

P value = 2.98e-06 (Fisher's exact test), Q value = 0.0014

Table S83. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	42	55	69
AMP PEAK 27(19Q12) CNV	4	12	30	13
AMP PEAK 27(19Q12) WILD-TYPE	38	30	25	56

Figure S83. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

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

P value = 8.13e-12 (Fisher's exact test), Q value = 4.5e-09

Table S84. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	69	97	57
AMP PEAK 27(19Q12) CNV	10	11	22	40
AMP PEAK 27(19Q12) WILD-TYPE	51	58	75	17

Figure S84. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

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

P value = 1.65e-13 (Fisher's exact test), Q value = 9.5e-11

Table S85. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
AMP PEAK 27(19Q12) CNV	47	16	20
AMP PEAK 27(19Q12) WILD-TYPE	24	73	104

Figure S85. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

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

P value = 0.000583 (Fisher's exact test), Q value = 0.2

Table S86. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	67	103
AMP PEAK 27(19Q12) CNV	13	14	45
AMP PEAK 27(19Q12) WILD-TYPE	54	53	58

Figure S86. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

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

P value = 7.16e-13 (Fisher's exact test), Q value = 4.1e-10

Table S87. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	83	96
AMP PEAK 27(19Q12) CNV	41	13	18
AMP PEAK 27(19Q12) WILD-TYPE	17	70	78

Figure S87. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 5.63e-21 (Fisher's exact test), Q value = 3.3e-18

Table S88. Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 28(20Q13.2) CNV	52	27	20	102
AMP PEAK 28(20Q13.2) WILD-TYPE	85	1	8	11

Figure S88. 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 = 2.4e-09

Table S89. 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 S89. 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 = 5.18e-07 (Chi-square test), Q value = 0.00026

Table S90. Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	41	35	37	50
AMP PEAK 28(20Q13.2) CNV	19	21	23	24	48
AMP PEAK 28(20Q13.2) WILD-TYPE	26	20	12	13	2

Figure S90. Get High-res Image Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

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

P value = 9.04e-06 (Fisher's exact test), Q value = 0.0041

Table S91. Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	42	55	69
AMP PEAK 28(20Q13.2) CNV	20	33	47	35
AMP PEAK 28(20Q13.2) WILD-TYPE	22	9	8	34

Figure S91. Get High-res Image Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

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

P value = 5.53e-10 (Fisher's exact test), Q value = 3e-07

Table S92. Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	69	97	57
AMP PEAK 28(20Q13.2) CNV	36	35	59	56
AMP PEAK 28(20Q13.2) WILD-TYPE	25	34	38	1

Figure S92. Get High-res Image Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

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

P value = 2.15e-12 (Fisher's exact test), Q value = 1.2e-09

Table S93. Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
AMP PEAK 28(20Q13.2) CNV	69	46	71
AMP PEAK 28(20Q13.2) WILD-TYPE	2	43	53

Figure S93. Get High-res Image Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

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

P value = 6.91e-09 (Fisher's exact test), Q value = 3.6e-06

Table S94. Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	83	96
AMP PEAK 28(20Q13.2) CNV	55	41	60
AMP PEAK 28(20Q13.2) WILD-TYPE	3	42	36

Figure S94. Get High-res Image Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 0.000155 (Fisher's exact test), Q value = 0.059

Table S95. Gene #29: 'Amp Peak 29(Xq27.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 29(XQ27.3) CNV	13	10	5	32
AMP PEAK 29(XQ27.3) WILD-TYPE	124	18	23	81

Figure S95. 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 = 4.2e-15 (Fisher's exact test), Q value = 2.4e-12

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 1(1P36.11) CNV	10	7	6	60
DEL PEAK 1(1P36.11) WILD-TYPE	127	21	22	53

Figure S96. 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 = 0.14

Table S97. 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 S97. Get High-res Image Gene #30: 'Del Peak 1(1p36.11)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 0.000129 (Fisher's exact test), Q value = 0.05

Table S98. Gene #30: 'Del Peak 1(1p36.11)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	69	97	57
DEL PEAK 1(1P36.11) CNV	19	8	21	26
DEL PEAK 1(1P36.11) WILD-TYPE	42	61	76	31

Figure S98. Get High-res Image Gene #30: 'Del Peak 1(1p36.11)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

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

P value = 0.000119 (Fisher's exact test), Q value = 0.047

Table S99. Gene #30: 'Del Peak 1(1p36.11)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
DEL PEAK 1(1P36.11) CNV	32	14	28
DEL PEAK 1(1P36.11) WILD-TYPE	39	75	96

Figure S99. Get High-res Image Gene #30: 'Del Peak 1(1p36.11)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

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

P value = 5.4e-12 (Fisher's exact test), Q value = 3e-09

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 2(1P13.2) CNV	6	6	2	45
DEL PEAK 2(1P13.2) WILD-TYPE	131	22	26	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 'MIRSEQ_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	69	97	57
DEL PEAK 2(1P13.2) CNV	12	7	12	22
DEL PEAK 2(1P13.2) WILD-TYPE	49	62	85	35

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

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

P value = 0.000191 (Fisher's exact test), Q value = 0.072

Table S102. Gene #34: 'Del Peak 5(2q37.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 5(2Q37.2) CNV	9	3	6	29
DEL PEAK 5(2Q37.2) WILD-TYPE	128	25	22	84

Figure S102. 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 = 8.76e-05 (Fisher's exact test), Q value = 0.035

Table S103. Gene #34: 'Del Peak 5(2q37.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
DEL PEAK 5(2Q37.2) CNV	23	10	11
DEL PEAK 5(2Q37.2) WILD-TYPE	48	79	113

Figure S103. Get High-res Image Gene #34: 'Del Peak 5(2q37.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 6(3p26.1)' versus 'CN_CNMF'

P value = 2.64e-10 (Fisher's exact test), Q value = 1.4e-07

Table S104. Gene #35: 'Del Peak 6(3p26.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 6(3P26.1) CNV	13	11	8	52
DEL PEAK 6(3P26.1) WILD-TYPE	124	17	20	61

Figure S104. Get High-res Image Gene #35: 'Del Peak 6(3p26.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 6(3p26.1)' versus 'METHLYATION_CNMF'

P value = 0.000307 (Fisher's exact test), Q value = 0.11

Table S105. Gene #35: 'Del Peak 6(3p26.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
DEL PEAK 6(3P26.1) CNV	7	22	8	33
DEL PEAK 6(3P26.1) WILD-TYPE	30	58	57	43

Figure S105. Get High-res Image Gene #35: 'Del Peak 6(3p26.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 6(3p26.1)' versus 'MIRSEQ_CNMF'

P value = 0.000143 (Fisher's exact test), Q value = 0.055

Table S106. Gene #35: 'Del Peak 6(3p26.1)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	69	97	57
DEL PEAK 6(3P26.1) CNV	15	11	22	29
DEL PEAK 6(3P26.1) WILD-TYPE	46	58	75	28

Figure S106. Get High-res Image Gene #35: 'Del Peak 6(3p26.1)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'Del Peak 6(3p26.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.32e-05 (Fisher's exact test), Q value = 0.026

Table S107. Gene #35: 'Del Peak 6(3p26.1)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
DEL PEAK 6(3P26.1) CNV	34	18	25
DEL PEAK 6(3P26.1) WILD-TYPE	37	71	99

Figure S107. Get High-res Image Gene #35: 'Del Peak 6(3p26.1)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 6(3p26.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000719 (Fisher's exact test), Q value = 0.23

Table S108. Gene #35: 'Del Peak 6(3p26.1)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	83	96
DEL PEAK 6(3P26.1) CNV	26	13	24
DEL PEAK 6(3P26.1) WILD-TYPE	32	70	72

Figure S108. Get High-res Image Gene #35: 'Del Peak 6(3p26.1)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 9.33e-13 (Fisher's exact test), Q value = 5.3e-10

Table S109. Gene #36: 'Del Peak 7(3p14.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 7(3P14.2) CNV	17	11	10	64
DEL PEAK 7(3P14.2) WILD-TYPE	120	17	18	49

Figure S109. 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 = 6e-04

Table S110. 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 S110. 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 = 0.000502 (Chi-square test), Q value = 0.17

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	41	35	37	50
DEL PEAK 7(3P14.2) CNV	9	6	11	12	27
DEL PEAK 7(3P14.2) WILD-TYPE	36	35	24	25	23

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

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

P value = 7.45e-06 (Fisher's exact test), Q value = 0.0034

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	69	97	57
DEL PEAK 7(3P14.2) CNV	21	12	27	34
DEL PEAK 7(3P14.2) WILD-TYPE	40	57	70	23

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

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

P value = 1.75e-06 (Fisher's exact test), Q value = 0.00084

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
DEL PEAK 7(3P14.2) CNV	41	18	35
DEL PEAK 7(3P14.2) WILD-TYPE	30	71	89

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

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

P value = 4.17e-06 (Fisher's exact test), Q value = 0.002

Table S114. Gene #36: 'Del Peak 7(3p14.2)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	83	96
DEL PEAK 7(3P14.2) CNV	34	15	32
DEL PEAK 7(3P14.2) WILD-TYPE	24	68	64

Figure S114. Get High-res Image Gene #36: 'Del Peak 7(3p14.2)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 4.23e-06 (Fisher's exact test), Q value = 0.002

Table S115. Gene #37: 'Del Peak 8(3q26.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 8(3Q26.31) CNV	4	3	1	26
DEL PEAK 8(3Q26.31) WILD-TYPE	133	25	27	87

Figure S115. 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 = 0.043

Table S116. 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 S116. Get High-res Image Gene #37: 'Del Peak 8(3q26.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 0.000267 (Chi-square test), Q value = 0.097

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	41	35	37	50
DEL PEAK 8(3Q26.31) CNV	1	0	1	8	10
DEL PEAK 8(3Q26.31) WILD-TYPE	44	41	34	29	40

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

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

P value = 0.000521 (Fisher's exact test), Q value = 0.18

Table S118. Gene #37: 'Del Peak 8(3q26.31)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	69	97	57
DEL PEAK 8(3Q26.31) CNV	2	3	14	14
DEL PEAK 8(3Q26.31) WILD-TYPE	59	66	83	43

Figure S118. Get High-res Image Gene #37: 'Del Peak 8(3q26.31)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

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

P value = 2.89e-10 (Fisher's exact test), Q value = 1.6e-07

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 9(4P16.3) CNV	24	12	10	66
DEL PEAK 9(4P16.3) WILD-TYPE	113	16	18	47

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 = 9.87e-05 (Chi-square test), Q value = 0.039

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	41	35	37	50
DEL PEAK 9(4P16.3) CNV	8	14	10	10	31
DEL PEAK 9(4P16.3) WILD-TYPE	37	27	25	27	19

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

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

P value = 0.000624 (Fisher's exact test), Q value = 0.21

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	42	55	69
DEL PEAK 9(4P16.3) CNV	13	11	32	17
DEL PEAK 9(4P16.3) WILD-TYPE	29	31	23	52

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

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

P value = 1.59e-05 (Fisher's exact test), Q value = 0.007

Table S122. Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	69	97	57
DEL PEAK 9(4P16.3) CNV	9	25	38	33
DEL PEAK 9(4P16.3) WILD-TYPE	52	44	59	24

Figure S122. Get High-res Image Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

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

P value = 0.000212 (Fisher's exact test), Q value = 0.079

Table S123. Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
DEL PEAK 9(4P16.3) CNV	40	32	33
DEL PEAK 9(4P16.3) WILD-TYPE	31	57	91

Figure S123. Get High-res Image Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

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

P value = 2.57e-05 (Fisher's exact test), Q value = 0.011

Table S124. Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	67	103
DEL PEAK 9(4P16.3) CNV	10	28	49
DEL PEAK 9(4P16.3) WILD-TYPE	57	39	54

Figure S124. Get High-res Image Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

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

P value = 1.25e-05 (Fisher's exact test), Q value = 0.0056

Table S125. Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	83	96
DEL PEAK 9(4P16.3) CNV	36	28	23
DEL PEAK 9(4P16.3) WILD-TYPE	22	55	73

Figure S125. Get High-res Image Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 6.72e-19 (Fisher's exact test), Q value = 4e-16

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 10(4Q22.1) CNV	24	18	11	82
DEL PEAK 10(4Q22.1) WILD-TYPE	113	10	17	31

Figure S126. 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 = 0.00019

Table S127. 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 S127. Get High-res Image Gene #39: 'Del Peak 10(4q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 9.2e-06 (Fisher's exact test), Q value = 0.0041

Table S128. Gene #39: 'Del Peak 10(4q22.1)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	69	97	57
DEL PEAK 10(4Q22.1) CNV	17	23	46	40
DEL PEAK 10(4Q22.1) WILD-TYPE	44	46	51	17

Figure S128. Get High-res Image Gene #39: 'Del Peak 10(4q22.1)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

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

P value = 0.000369 (Fisher's exact test), Q value = 0.13

Table S129. Gene #39: 'Del Peak 10(4q22.1)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
DEL PEAK 10(4Q22.1) CNV	46	33	47
DEL PEAK 10(4Q22.1) WILD-TYPE	25	56	77

Figure S129. Get High-res Image Gene #39: 'Del Peak 10(4q22.1)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

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

P value = 1.07e-14 (Fisher's exact test), Q value = 6.2e-12

Table S130. Gene #40: 'Del Peak 11(4q34.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 11(4Q34.3) CNV	26	15	9	77
DEL PEAK 11(4Q34.3) WILD-TYPE	111	13	19	36

Figure S130. 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 = 9e-04

Table S131. 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 S131. 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 = 0.000109 (Chi-square test), Q value = 0.043

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	41	35	37	50
DEL PEAK 11(4Q34.3) CNV	8	15	16	16	33
DEL PEAK 11(4Q34.3) WILD-TYPE	37	26	19	21	17

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

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

P value = 1.69e-06 (Fisher's exact test), Q value = 0.00082

Table S133. Gene #40: 'Del Peak 11(4q34.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	69	97	57
DEL PEAK 11(4Q34.3) CNV	16	24	36	41
DEL PEAK 11(4Q34.3) WILD-TYPE	45	45	61	16

Figure S133. Get High-res Image Gene #40: 'Del Peak 11(4q34.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

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

P value = 1.84e-05 (Fisher's exact test), Q value = 0.008

Table S134. Gene #40: 'Del Peak 11(4q34.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
DEL PEAK 11(4Q34.3) CNV	46	32	39
DEL PEAK 11(4Q34.3) WILD-TYPE	25	57	85

Figure S134. Get High-res Image Gene #40: 'Del Peak 11(4q34.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

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

P value = 4.71e-06 (Fisher's exact test), Q value = 0.0022

Table S135. Gene #40: 'Del Peak 11(4q34.3)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	83	96
DEL PEAK 11(4Q34.3) CNV	40	31	28
DEL PEAK 11(4Q34.3) WILD-TYPE	18	52	68

Figure S135. Get High-res Image Gene #40: 'Del Peak 11(4q34.3)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 6.54e-28 (Fisher's exact test), Q value = 3.9e-25

Table S136. Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 12(5Q11.2) CNV	6	11	9	77
DEL PEAK 12(5Q11.2) WILD-TYPE	131	17	19	36

Figure S136. 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 = 1.4e-11

Table S137. 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 S137. 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 = 8.02e-10 (Chi-square test), Q value = 4.3e-07

Table S138. Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	41	35	37	50
DEL PEAK 12(5Q11.2) CNV	10	2	7	14	34
DEL PEAK 12(5Q11.2) WILD-TYPE	35	39	28	23	16

Figure S138. Get High-res Image Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

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

P value = 6.02e-08 (Fisher's exact test), Q value = 3.1e-05

Table S139. Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	42	55	69
DEL PEAK 12(5Q11.2) CNV	3	12	34	18
DEL PEAK 12(5Q11.2) WILD-TYPE	39	30	21	51

Figure S139. Get High-res Image Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

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

P value = 8.45e-12 (Fisher's exact test), Q value = 4.7e-09

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	69	97	57
DEL PEAK 12(5Q11.2) CNV	15	6	35	39
DEL PEAK 12(5Q11.2) WILD-TYPE	46	63	62	18

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

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

P value = 4.02e-10 (Fisher's exact test), Q value = 2.2e-07

Table S141. Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
DEL PEAK 12(5Q11.2) CNV	46	15	34
DEL PEAK 12(5Q11.2) WILD-TYPE	25	74	90

Figure S141. Get High-res Image Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

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

P value = 3.7e-08 (Fisher's exact test), Q value = 1.9e-05

Table S142. Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	67	103
DEL PEAK 12(5Q11.2) CNV	17	9	56
DEL PEAK 12(5Q11.2) WILD-TYPE	50	58	47

Figure S142. Get High-res Image Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

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

P value = 3.53e-15 (Fisher's exact test), Q value = 2.1e-12

Table S143. Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	83	96
DEL PEAK 12(5Q11.2) CNV	44	9	29
DEL PEAK 12(5Q11.2) WILD-TYPE	14	74	67

Figure S143. Get High-res Image Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 2.48e-23 (Fisher's exact test), Q value = 1.5e-20

Table S144. Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 13(5Q23.2) CNV	5	12	9	67
DEL PEAK 13(5Q23.2) WILD-TYPE	132	16	19	46

Figure S144. 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 = 1.3e-09

Table S145. 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 S145. 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 = 1.03e-09 (Chi-square test), Q value = 5.6e-07

Table S146. Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	41	35	37	50
DEL PEAK 13(5Q23.2) CNV	11	1	5	12	32
DEL PEAK 13(5Q23.2) WILD-TYPE	34	40	30	25	18

Figure S146. Get High-res Image Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

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

P value = 1.87e-07 (Fisher's exact test), Q value = 9.4e-05

Table S147. Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	42	55	69
DEL PEAK 13(5Q23.2) CNV	2	10	31	18
DEL PEAK 13(5Q23.2) WILD-TYPE	40	32	24	51

Figure S147. Get High-res Image Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

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

P value = 1.02e-12 (Fisher's exact test), Q value = 5.7e-10

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	69	97	57
DEL PEAK 13(5Q23.2) CNV	9	5	32	37
DEL PEAK 13(5Q23.2) WILD-TYPE	52	64	65	20

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

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

P value = 1.93e-09 (Fisher's exact test), Q value = 1e-06

Table S149. Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
DEL PEAK 13(5Q23.2) CNV	41	11	31
DEL PEAK 13(5Q23.2) WILD-TYPE	30	78	93

Figure S149. Get High-res Image Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

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

P value = 4.84e-09 (Fisher's exact test), Q value = 2.5e-06

Table S150. Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	67	103
DEL PEAK 13(5Q23.2) CNV	12	7	52
DEL PEAK 13(5Q23.2) WILD-TYPE	55	60	51

Figure S150. Get High-res Image Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

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

P value = 4.75e-14 (Fisher's exact test), Q value = 2.7e-11

Table S151. Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	83	96
DEL PEAK 13(5Q23.2) CNV	40	7	24
DEL PEAK 13(5Q23.2) WILD-TYPE	18	76	72

Figure S151. Get High-res Image Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 5.01e-07 (Fisher's exact test), Q value = 0.00025

Table S152. Gene #43: 'Del Peak 14(6p25.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 14(6P25.3) CNV	15	6	3	45
DEL PEAK 14(6P25.3) WILD-TYPE	122	22	25	68

Figure S152. Get High-res Image Gene #43: 'Del Peak 14(6p25.3)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 0.000576 (Fisher's exact test), Q value = 0.19

Table S153. Gene #43: 'Del Peak 14(6p25.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
DEL PEAK 14(6P25.3) CNV	3	20	9	29
DEL PEAK 14(6P25.3) WILD-TYPE	34	60	56	47

Figure S153. Get High-res Image Gene #43: 'Del Peak 14(6p25.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 9.72e-05 (Fisher's exact test), Q value = 0.039

Table S154. Gene #43: 'Del Peak 14(6p25.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	69	97	57
DEL PEAK 14(6P25.3) CNV	12	9	16	26
DEL PEAK 14(6P25.3) WILD-TYPE	49	60	81	31

Figure S154. Get High-res Image Gene #43: 'Del Peak 14(6p25.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

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

P value = 0.000337 (Fisher's exact test), Q value = 0.12

Table S155. Gene #43: 'Del Peak 14(6p25.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
DEL PEAK 14(6P25.3) CNV	28	12	23
DEL PEAK 14(6P25.3) WILD-TYPE	43	77	101

Figure S155. Get High-res Image Gene #43: 'Del Peak 14(6p25.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

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

P value = 0.000128 (Fisher's exact test), Q value = 0.05

Table S156. Gene #44: 'Del Peak 15(6q26)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 15(6Q26) CNV	14	9	4	35
DEL PEAK 15(6Q26) WILD-TYPE	123	19	24	78

Figure S156. Get High-res Image Gene #44: 'Del Peak 15(6q26)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 0.000124 (Chi-square test), Q value = 0.049

Table S157. Gene #44: 'Del Peak 15(6q26)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	41	35	37	50
DEL PEAK 15(6Q26) CNV	8	3	16	4	17
DEL PEAK 15(6Q26) WILD-TYPE	37	38	19	33	33

Figure S157. Get High-res Image Gene #44: 'Del Peak 15(6q26)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

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

P value = 7.5e-05 (Fisher's exact test), Q value = 0.031

Table S158. Gene #44: 'Del Peak 15(6q26)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	42	55	69
DEL PEAK 15(6Q26) CNV	3	14	22	9
DEL PEAK 15(6Q26) WILD-TYPE	39	28	33	60

Figure S158. Get High-res Image Gene #44: 'Del Peak 15(6q26)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

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

P value = 3.11e-07 (Fisher's exact test), Q value = 0.00015

Table S159. Gene #45: 'Del Peak 16(7q31.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 16(7Q31.1) CNV	6	1	5	32
DEL PEAK 16(7Q31.1) WILD-TYPE	131	27	23	81

Figure S159. Get High-res Image Gene #45: 'Del Peak 16(7q31.1)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 1.82e-14 (Fisher's exact test), Q value = 1.1e-11

Table S160. Gene #46: 'Del Peak 17(7q36.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 17(7Q36.3) CNV	4	2	5	47
DEL PEAK 17(7Q36.3) WILD-TYPE	133	26	23	66

Figure S160. 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 = 0.0058

Table S161. 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 S161. 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 = 0.000677 (Chi-square test), Q value = 0.23

Table S162. Gene #46: 'Del Peak 17(7q36.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	41	35	37	50
DEL PEAK 17(7Q36.3) CNV	4	6	6	4	20
DEL PEAK 17(7Q36.3) WILD-TYPE	41	35	29	33	30

Figure S162. Get High-res Image Gene #46: 'Del Peak 17(7q36.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

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

P value = 3.06e-05 (Fisher's exact test), Q value = 0.013

Table S163. Gene #46: 'Del Peak 17(7q36.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
DEL PEAK 17(7Q36.3) CNV	27	9	18
DEL PEAK 17(7Q36.3) WILD-TYPE	44	80	106

Figure S163. Get High-res Image Gene #46: 'Del Peak 17(7q36.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

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

P value = 9.56e-05 (Fisher's exact test), Q value = 0.038

Table S164. Gene #46: 'Del Peak 17(7q36.3)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	83	96
DEL PEAK 17(7Q36.3) CNV	22	7	17
DEL PEAK 17(7Q36.3) WILD-TYPE	36	76	79

Figure S164. Get High-res Image Gene #46: 'Del Peak 17(7q36.3)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 18(8p23.2)' versus 'CN_CNMF'

P value = 4.3e-14 (Fisher's exact test), Q value = 2.5e-11

Table S165. Gene #47: 'Del Peak 18(8p23.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 18(8P23.2) CNV	13	9	0	55
DEL PEAK 18(8P23.2) WILD-TYPE	124	19	28	58

Figure S165. 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 = 0.0037

Table S166. 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 S166. Get High-res Image Gene #47: 'Del Peak 18(8p23.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 18(8p23.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000232 (Fisher's exact test), Q value = 0.086

Table S167. Gene #47: 'Del Peak 18(8p23.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	42	55	69
DEL PEAK 18(8P23.2) CNV	8	11	26	9
DEL PEAK 18(8P23.2) WILD-TYPE	34	31	29	60

Figure S167. Get High-res Image Gene #47: 'Del Peak 18(8p23.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 18(8p23.2)' versus 'MIRSEQ_CNMF'

P value = 5.92e-05 (Fisher's exact test), Q value = 0.025

Table S168. Gene #47: 'Del Peak 18(8p23.2)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	69	97	57
DEL PEAK 18(8P23.2) CNV	10	12	23	29
DEL PEAK 18(8P23.2) WILD-TYPE	51	57	74	28

Figure S168. Get High-res Image Gene #47: 'Del Peak 18(8p23.2)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'Del Peak 18(8p23.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.58e-05 (Fisher's exact test), Q value = 0.007

Table S169. Gene #47: 'Del Peak 18(8p23.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
DEL PEAK 18(8P23.2) CNV	34	15	25
DEL PEAK 18(8P23.2) WILD-TYPE	37	74	99

Figure S169. Get High-res Image Gene #47: 'Del Peak 18(8p23.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 18(8p23.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.23e-06 (Fisher's exact test), Q value = 0.0042

Table S170. Gene #47: 'Del Peak 18(8p23.2)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	83	96
DEL PEAK 18(8P23.2) CNV	30	14	19
DEL PEAK 18(8P23.2) WILD-TYPE	28	69	77

Figure S170. Get High-res Image Gene #47: 'Del Peak 18(8p23.2)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 19(9p23)' versus 'CN_CNMF'

P value = 2.66e-15 (Fisher's exact test), Q value = 1.6e-12

Table S171. Gene #48: 'Del Peak 19(9p23)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 19(9P23) CNV	22	10	13	75
DEL PEAK 19(9P23) WILD-TYPE	115	18	15	38

Figure S171. 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 = 0.035

Table S172. 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 S172. 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 = 0.000127 (Chi-square test), Q value = 0.049

Table S173. Gene #48: 'Del Peak 19(9p23)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	41	35	37	50
DEL PEAK 19(9P23) CNV	11	13	20	13	33
DEL PEAK 19(9P23) WILD-TYPE	34	28	15	24	17

Figure S173. Get High-res Image Gene #48: 'Del Peak 19(9p23)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 19(9p23)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.55e-05 (Fisher's exact test), Q value = 0.023

Table S174. Gene #48: 'Del Peak 19(9p23)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
DEL PEAK 19(9P23) CNV	44	33	37
DEL PEAK 19(9P23) WILD-TYPE	27	56	87

Figure S174. Get High-res Image Gene #48: 'Del Peak 19(9p23)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 20(9p21.3)' versus 'CN_CNMF'

P value = 6.29e-16 (Fisher's exact test), Q value = 3.7e-13

Table S175. Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 20(9P21.3) CNV	22	8	12	76
DEL PEAK 20(9P21.3) WILD-TYPE	115	20	16	37

Figure S175. 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 = 1.1e-07

Table S176. 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 S176. Get High-res Image Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 20(9p21.3)' versus 'MRNASEQ_CNMF'

P value = 2.58e-07 (Chi-square test), Q value = 0.00013

Table S177. Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	41	35	37	50
DEL PEAK 20(9P21.3) CNV	6	12	19	15	35
DEL PEAK 20(9P21.3) WILD-TYPE	39	29	16	22	15

Figure S177. Get High-res Image Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 20(9p21.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000195 (Fisher's exact test), Q value = 0.073

Table S178. Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	42	55	69
DEL PEAK 20(9P21.3) CNV	14	20	35	18
DEL PEAK 20(9P21.3) WILD-TYPE	28	22	20	51

Figure S178. Get High-res Image Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 20(9p21.3)' versus 'MIRSEQ_CNMF'

P value = 0.000188 (Fisher's exact test), Q value = 0.071

Table S179. Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	69	97	57
DEL PEAK 20(9P21.3) CNV	18	23	33	37
DEL PEAK 20(9P21.3) WILD-TYPE	43	46	64	20

Figure S179. Get High-res Image Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'Del Peak 20(9p21.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.23e-06 (Fisher's exact test), Q value = 0.0029

Table S180. Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
DEL PEAK 20(9P21.3) CNV	45	31	35
DEL PEAK 20(9P21.3) WILD-TYPE	26	58	89

Figure S180. Get High-res Image Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 20(9p21.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.99e-05 (Fisher's exact test), Q value = 0.036

Table S181. Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	83	96
DEL PEAK 20(9P21.3) CNV	37	28	29
DEL PEAK 20(9P21.3) WILD-TYPE	21	55	67

Figure S181. Get High-res Image Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 21(9q21.11)' versus 'CN_CNMF'

P value = 2.97e-08 (Fisher's exact test), Q value = 1.5e-05

Table S182. Gene #50: 'Del Peak 21(9q21.11)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 21(9Q21.11) CNV	12	7	8	46
DEL PEAK 21(9Q21.11) WILD-TYPE	125	21	20	67

Figure S182. 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 = 0.083

Table S183. 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 S183. Get High-res Image Gene #50: 'Del Peak 21(9q21.11)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 21(9q21.11)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000363 (Fisher's exact test), Q value = 0.13

Table S184. Gene #50: 'Del Peak 21(9q21.11)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
DEL PEAK 21(9Q21.11) CNV	30	18	21
DEL PEAK 21(9Q21.11) WILD-TYPE	41	71	103

Figure S184. Get High-res Image Gene #50: 'Del Peak 21(9q21.11)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 21(9q21.11)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.25e-05 (Fisher's exact test), Q value = 0.0098

Table S185. Gene #50: 'Del Peak 21(9q21.11)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	83	96
DEL PEAK 21(9Q21.11) CNV	28	18	14
DEL PEAK 21(9Q21.11) WILD-TYPE	30	65	82

Figure S185. Get High-res Image Gene #50: 'Del Peak 21(9q21.11)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 22(10p15.1)' versus 'CN_CNMF'

P value = 0.000124 (Fisher's exact test), Q value = 0.049

Table S186. Gene #51: 'Del Peak 22(10p15.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 22(10P15.1) CNV	6	3	3	26
DEL PEAK 22(10P15.1) WILD-TYPE	131	25	25	87

Figure S186. 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 = 2.43e-09 (Fisher's exact test), Q value = 1.3e-06

Table S187. Gene #52: 'Del Peak 23(10q22.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 23(10Q22.3) CNV	4	9	3	33
DEL PEAK 23(10Q22.3) WILD-TYPE	133	19	25	80

Figure S187. Get High-res Image Gene #52: 'Del Peak 23(10q22.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 23(10q22.3)' versus 'METHLYATION_CNMF'

P value = 0.000718 (Fisher's exact test), Q value = 0.23

Table S188. Gene #52: 'Del Peak 23(10q22.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
DEL PEAK 23(10Q22.3) CNV	2	9	6	23
DEL PEAK 23(10Q22.3) WILD-TYPE	35	71	59	53

Figure S188. Get High-res Image Gene #52: 'Del Peak 23(10q22.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 23(10q22.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000168 (Fisher's exact test), Q value = 0.064

Table S189. Gene #52: 'Del Peak 23(10q22.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
DEL PEAK 23(10Q22.3) CNV	22	6	17
DEL PEAK 23(10Q22.3) WILD-TYPE	49	83	107

Figure S189. Get High-res Image Gene #52: 'Del Peak 23(10q22.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 23(10q22.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000285 (Fisher's exact test), Q value = 0.1

Table S190. Gene #52: 'Del Peak 23(10q22.3)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	83	96
DEL PEAK 23(10Q22.3) CNV	17	4	15
DEL PEAK 23(10Q22.3) WILD-TYPE	41	79	81

Figure S190. Get High-res Image Gene #52: 'Del Peak 23(10q22.3)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 24(10q23.31)' versus 'CN_CNMF'

P value = 2.72e-12 (Fisher's exact test), Q value = 1.5e-09

Table S191. Gene #53: 'Del Peak 24(10q23.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 24(10Q23.31) CNV	7	10	9	47
DEL PEAK 24(10Q23.31) WILD-TYPE	130	18	19	66

Figure S191. 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 = 0.0024

Table S192. 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 S192. Get High-res Image Gene #53: 'Del Peak 24(10q23.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 24(10q23.31)' versus 'MIRSEQ_CNMF'

P value = 3.07e-05 (Fisher's exact test), Q value = 0.013

Table S193. Gene #53: 'Del Peak 24(10q23.31)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	69	97	57
DEL PEAK 24(10Q23.31) CNV	13	6	23	26
DEL PEAK 24(10Q23.31) WILD-TYPE	48	63	74	31

Figure S193. Get High-res Image Gene #53: 'Del Peak 24(10q23.31)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'Del Peak 24(10q23.31)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.16e-05 (Fisher's exact test), Q value = 0.0052

Table S194. Gene #53: 'Del Peak 24(10q23.31)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
DEL PEAK 24(10Q23.31) CNV	31	10	27
DEL PEAK 24(10Q23.31) WILD-TYPE	40	79	97

Figure S194. Get High-res Image Gene #53: 'Del Peak 24(10q23.31)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 24(10q23.31)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000315 (Fisher's exact test), Q value = 0.11

Table S195. Gene #53: 'Del Peak 24(10q23.31)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	67	103
DEL PEAK 24(10Q23.31) CNV	11	7	36
DEL PEAK 24(10Q23.31) WILD-TYPE	56	60	67

Figure S195. Get High-res Image Gene #53: 'Del Peak 24(10q23.31)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'Del Peak 24(10q23.31)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.11

Table S196. Gene #53: 'Del Peak 24(10q23.31)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	83	96
DEL PEAK 24(10Q23.31) CNV	24	10	20
DEL PEAK 24(10Q23.31) WILD-TYPE	34	73	76

Figure S196. Get High-res Image Gene #53: 'Del Peak 24(10q23.31)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 25(11p15.4)' versus 'CN_CNMF'

P value = 2.96e-08 (Fisher's exact test), Q value = 1.5e-05

Table S197. Gene #54: 'Del Peak 25(11p15.4)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 25(11P15.4) CNV	9	3	6	41
DEL PEAK 25(11P15.4) WILD-TYPE	128	25	22	72

Figure S197. 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 = 0.0037

Table S198. 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 S198. Get High-res Image Gene #54: 'Del Peak 25(11p15.4)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 26(11q23.2)' versus 'CN_CNMF'

P value = 0.000264 (Fisher's exact test), Q value = 0.097

Table S199. Gene #55: 'Del Peak 26(11q23.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 26(11Q23.2) CNV	15	6	4	37
DEL PEAK 26(11Q23.2) WILD-TYPE	122	22	24	76

Figure S199. Get High-res Image Gene #55: 'Del Peak 26(11q23.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 27(12p13.31)' versus 'CN_CNMF'

P value = 1.49e-10 (Fisher's exact test), Q value = 8.2e-08

Table S200. Gene #56: 'Del Peak 27(12p13.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 27(12P13.31) CNV	3	5	5	37
DEL PEAK 27(12P13.31) WILD-TYPE	134	23	23	76

Figure S200. 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 = 0.0026

Table S201. 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 S201. 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 = 4.64e-06 (Chi-square test), Q value = 0.0022

Table S202. Gene #56: 'Del Peak 27(12p13.31)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	41	35	37	50
DEL PEAK 27(12P13.31) CNV	3	2	5	3	20
DEL PEAK 27(12P13.31) WILD-TYPE	42	39	30	34	30

Figure S202. Get High-res Image Gene #56: 'Del Peak 27(12p13.31)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 27(12p13.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000297 (Fisher's exact test), Q value = 0.11

Table S203. Gene #56: 'Del Peak 27(12p13.31)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	42	55	69
DEL PEAK 27(12P13.31) CNV	2	5	19	7
DEL PEAK 27(12P13.31) WILD-TYPE	40	37	36	62

Figure S203. Get High-res Image Gene #56: 'Del Peak 27(12p13.31)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 27(12p13.31)' versus 'MIRSEQ_CNMF'

P value = 0.000389 (Fisher's exact test), Q value = 0.13

Table S204. Gene #56: 'Del Peak 27(12p13.31)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	69	97	57
DEL PEAK 27(12P13.31) CNV	9	6	10	20
DEL PEAK 27(12P13.31) WILD-TYPE	52	63	87	37

Figure S204. Get High-res Image Gene #56: 'Del Peak 27(12p13.31)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'Del Peak 27(12p13.31)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000154 (Fisher's exact test), Q value = 0.059

Table S205. Gene #56: 'Del Peak 27(12p13.31)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	83	96
DEL PEAK 27(12P13.31) CNV	20	7	11
DEL PEAK 27(12P13.31) WILD-TYPE	38	76	85

Figure S205. Get High-res Image Gene #56: 'Del Peak 27(12p13.31)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 28(13q12.11)' versus 'CN_CNMF'

P value = 2.32e-06 (Fisher's exact test), Q value = 0.0011

Table S206. Gene #57: 'Del Peak 28(13q12.11)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 28(13Q12.11) CNV	6	2	6	30
DEL PEAK 28(13Q12.11) WILD-TYPE	131	26	22	83

Figure S206. 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 = 7.69e-07 (Fisher's exact test), Q value = 0.00037

Table S207. Gene #58: 'Del Peak 29(14q21.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 29(14Q21.1) CNV	13	8	7	43
DEL PEAK 29(14Q21.1) WILD-TYPE	124	20	21	70

Figure S207. Get High-res Image Gene #58: 'Del Peak 29(14q21.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 29(14q21.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000175 (Fisher's exact test), Q value = 0.066

Table S208. Gene #58: 'Del Peak 29(14q21.1)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	42	55	69
DEL PEAK 29(14Q21.1) CNV	8	8	25	8
DEL PEAK 29(14Q21.1) WILD-TYPE	34	34	30	61

Figure S208. Get High-res Image Gene #58: 'Del Peak 29(14q21.1)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 29(14q21.1)' versus 'MIRSEQ_CNMF'

P value = 0.000142 (Fisher's exact test), Q value = 0.055

Table S209. Gene #58: 'Del Peak 29(14q21.1)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	69	97	57
DEL PEAK 29(14Q21.1) CNV	9	15	17	27
DEL PEAK 29(14Q21.1) WILD-TYPE	52	54	80	30

Figure S209. Get High-res Image Gene #58: 'Del Peak 29(14q21.1)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'Del Peak 29(14q21.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000162 (Fisher's exact test), Q value = 0.062

Table S210. Gene #58: 'Del Peak 29(14q21.1)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
DEL PEAK 29(14Q21.1) CNV	30	19	19
DEL PEAK 29(14Q21.1) WILD-TYPE	41	70	105

Figure S210. Get High-res Image Gene #58: 'Del Peak 29(14q21.1)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 29(14q21.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000236 (Fisher's exact test), Q value = 0.087

Table S211. Gene #58: 'Del Peak 29(14q21.1)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	83	96
DEL PEAK 29(14Q21.1) CNV	26	17	15
DEL PEAK 29(14Q21.1) WILD-TYPE	32	66	81

Figure S211. Get High-res Image Gene #58: 'Del Peak 29(14q21.1)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 30(14q32.33)' versus 'CN_CNMF'

P value = 9.24e-09 (Fisher's exact test), Q value = 4.8e-06

Table S212. Gene #59: 'Del Peak 30(14q32.33)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 30(14Q32.33) CNV	17	9	9	54
DEL PEAK 30(14Q32.33) WILD-TYPE	120	19	19	59

Figure S212. Get High-res Image Gene #59: 'Del Peak 30(14q32.33)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 30(14q32.33)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.24e-05 (Fisher's exact test), Q value = 0.034

Table S213. Gene #59: 'Del Peak 30(14q32.33)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	42	55	69
DEL PEAK 30(14Q32.33) CNV	8	12	28	10
DEL PEAK 30(14Q32.33) WILD-TYPE	34	30	27	59

Figure S213. Get High-res Image Gene #59: 'Del Peak 30(14q32.33)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 31(15q15.1)' versus 'CN_CNMF'

P value = 6.44e-13 (Fisher's exact test), Q value = 3.7e-10

Table S214. Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 31(15Q15.1) CNV	9	10	7	53
DEL PEAK 31(15Q15.1) WILD-TYPE	128	18	21	60

Figure S214. 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 = 0.00011

Table S215. 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 S215. 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 = 6.08e-05 (Chi-square test), Q value = 0.025

Table S216. Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	41	35	37	50
DEL PEAK 31(15Q15.1) CNV	7	2	12	8	23
DEL PEAK 31(15Q15.1) WILD-TYPE	38	39	23	29	27

Figure S216. Get High-res Image Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 31(15q15.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.26e-07 (Fisher's exact test), Q value = 0.00031

Table S217. Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	42	55	69
DEL PEAK 31(15Q15.1) CNV	1	13	26	12
DEL PEAK 31(15Q15.1) WILD-TYPE	41	29	29	57

Figure S217. Get High-res Image Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 31(15q15.1)' versus 'MIRSEQ_CNMF'

P value = 1.98e-09 (Fisher's exact test), Q value = 1.1e-06

Table S218. Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	69	97	57
DEL PEAK 31(15Q15.1) CNV	12	4	24	32
DEL PEAK 31(15Q15.1) WILD-TYPE	49	65	73	25

Figure S218. Get High-res Image Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'Del Peak 31(15q15.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.82e-08 (Fisher's exact test), Q value = 1.5e-05

Table S219. Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
DEL PEAK 31(15Q15.1) CNV	36	9	27
DEL PEAK 31(15Q15.1) WILD-TYPE	35	80	97

Figure S219. Get High-res Image Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 31(15q15.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000552 (Fisher's exact test), Q value = 0.19

Table S220. Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	67	103
DEL PEAK 31(15Q15.1) CNV	15	7	37
DEL PEAK 31(15Q15.1) WILD-TYPE	52	60	66

Figure S220. Get High-res Image Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'Del Peak 31(15q15.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.06e-05 (Fisher's exact test), Q value = 0.0048

Table S221. Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	83	96
DEL PEAK 31(15Q15.1) CNV	27	9	23
DEL PEAK 31(15Q15.1) WILD-TYPE	31	74	73

Figure S221. Get High-res Image Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 32(16p13.3)' versus 'CN_CNMF'

P value = 7.42e-11 (Fisher's exact test), Q value = 4.1e-08

Table S222. Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 32(16P13.3) CNV	7	2	5	44
DEL PEAK 32(16P13.3) WILD-TYPE	130	26	23	69

Figure S222. 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 = 0.017

Table S223. 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 S223. 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 = 1.46e-05 (Chi-square test), Q value = 0.0064

Table S224. Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	41	35	37	50
DEL PEAK 32(16P13.3) CNV	5	3	4	2	20
DEL PEAK 32(16P13.3) WILD-TYPE	40	38	31	35	30

Figure S224. Get High-res Image Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 32(16p13.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000222 (Fisher's exact test), Q value = 0.083

Table S225. Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	42	55	69
DEL PEAK 32(16P13.3) CNV	4	4	20	6
DEL PEAK 32(16P13.3) WILD-TYPE	38	38	35	63

Figure S225. Get High-res Image Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 32(16p13.3)' versus 'MIRSEQ_CNMF'

P value = 1.39e-05 (Fisher's exact test), Q value = 0.0062

Table S226. Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	69	97	57
DEL PEAK 32(16P13.3) CNV	4	6	21	22
DEL PEAK 32(16P13.3) WILD-TYPE	57	63	76	35

Figure S226. Get High-res Image Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'Del Peak 32(16p13.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000685 (Fisher's exact test), Q value = 0.23

Table S227. Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
DEL PEAK 32(16P13.3) CNV	24	9	20
DEL PEAK 32(16P13.3) WILD-TYPE	47	80	104

Figure S227. Get High-res Image Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 32(16p13.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.91e-06 (Fisher's exact test), Q value = 0.0014

Table S228. Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	67	103
DEL PEAK 32(16P13.3) CNV	3	8	34
DEL PEAK 32(16P13.3) WILD-TYPE	64	59	69

Figure S228. Get High-res Image Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'Del Peak 32(16p13.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.53e-06 (Fisher's exact test), Q value = 0.00074

Table S229. Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	83	96
DEL PEAK 32(16P13.3) CNV	25	7	13
DEL PEAK 32(16P13.3) WILD-TYPE	33	76	83

Figure S229. Get High-res Image Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 33(16q23.1)' versus 'CN_CNMF'

P value = 2.22e-07 (Fisher's exact test), Q value = 0.00011

Table S230. Gene #62: 'Del Peak 33(16q23.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 33(16Q23.1) CNV	33	12	7	66
DEL PEAK 33(16Q23.1) WILD-TYPE	104	16	21	47

Figure S230. Get High-res Image Gene #62: 'Del Peak 33(16q23.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 34(17p12)' versus 'CN_CNMF'

P value = 1.81e-23 (Fisher's exact test), Q value = 1.1e-20

Table S231. Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 34(17P12) CNV	13	14	9	79
DEL PEAK 34(17P12) WILD-TYPE	124	14	19	34

Figure S231. 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 = 1.8e-08

Table S232. 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 S232. 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 = 3.94e-06 (Chi-square test), Q value = 0.0018

Table S233. Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	41	35	37	50
DEL PEAK 34(17P12) CNV	11	5	16	14	32
DEL PEAK 34(17P12) WILD-TYPE	34	36	19	23	18

Figure S233. Get High-res Image Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 34(17p12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.68e-06 (Fisher's exact test), Q value = 0.00081

Table S234. Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	42	55	69
DEL PEAK 34(17P12) CNV	6	18	35	19
DEL PEAK 34(17P12) WILD-TYPE	36	24	20	50

Figure S234. Get High-res Image Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 34(17p12)' versus 'MIRSEQ_CNMF'

P value = 6.21e-08 (Fisher's exact test), Q value = 3.2e-05

Table S235. Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	69	97	57
DEL PEAK 34(17P12) CNV	18	14	33	40
DEL PEAK 34(17P12) WILD-TYPE	43	55	64	17

Figure S235. Get High-res Image Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'Del Peak 34(17p12)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.15e-07 (Fisher's exact test), Q value = 5.8e-05

Table S236. Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
DEL PEAK 34(17P12) CNV	46	21	38
DEL PEAK 34(17P12) WILD-TYPE	25	68	86

Figure S236. Get High-res Image Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 34(17p12)' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.05e-06 (Fisher's exact test), Q value = 0.0041

Table S237. Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	67	103
DEL PEAK 34(17P12) CNV	17	16	57
DEL PEAK 34(17P12) WILD-TYPE	50	51	46

Figure S237. Get High-res Image Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'Del Peak 34(17p12)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.08e-09 (Fisher's exact test), Q value = 2.1e-06

Table S238. Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	83	96
DEL PEAK 34(17P12) CNV	42	20	28
DEL PEAK 34(17P12) WILD-TYPE	16	63	68

Figure S238. Get High-res Image Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 35(17q24.3)' versus 'CN_CNMF'

P value = 1.32e-10 (Fisher's exact test), Q value = 7.2e-08

Table S239. Gene #64: 'Del Peak 35(17q24.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 35(17Q24.3) CNV	4	6	6	39
DEL PEAK 35(17Q24.3) WILD-TYPE	133	22	22	74

Figure S239. 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 = 0.092

Table S240. 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 S240. 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 = 4.49e-13 (Fisher's exact test), Q value = 2.6e-10

Table S241. Gene #65: 'Del Peak 36(18q21.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 36(18Q21.2) CNV	31	20	8	74
DEL PEAK 36(18Q21.2) WILD-TYPE	106	8	20	39

Figure S241. 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 = 2.35e-27 (Fisher's exact test), Q value = 1.4e-24

Table S242. Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 37(19P13.3) CNV	6	10	7	76
DEL PEAK 37(19P13.3) WILD-TYPE	131	18	21	37

Figure S242. 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 = 1.4e-13

Table S243. 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 S243. 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 = 9.11e-13 (Chi-square test), Q value = 5.2e-10

Table S244. Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	41	35	37	50
DEL PEAK 37(19P13.3) CNV	8	2	10	10	38
DEL PEAK 37(19P13.3) WILD-TYPE	37	39	25	27	12

Figure S244. Get High-res Image Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 37(19p13.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.02e-15 (Fisher's exact test), Q value = 1.2e-12

Table S245. Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	42	55	69
DEL PEAK 37(19P13.3) CNV	0	13	40	15
DEL PEAK 37(19P13.3) WILD-TYPE	42	29	15	54

Figure S245. Get High-res Image Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 37(19p13.3)' versus 'MIRSEQ_CNMF'

P value = 2.39e-22 (Fisher's exact test), Q value = 1.4e-19

Table S246. Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	69	97	57
DEL PEAK 37(19P13.3) CNV	11	7	24	50
DEL PEAK 37(19P13.3) WILD-TYPE	50	62	73	7

Figure S246. Get High-res Image Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'Del Peak 37(19p13.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.69e-24 (Fisher's exact test), Q value = 5.8e-21

Table S247. Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
DEL PEAK 37(19P13.3) CNV	58	10	24
DEL PEAK 37(19P13.3) WILD-TYPE	13	79	100

Figure S247. Get High-res Image Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 37(19p13.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.97e-05 (Fisher's exact test), Q value = 0.017

Table S248. Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	67	103
DEL PEAK 37(19P13.3) CNV	15	12	49
DEL PEAK 37(19P13.3) WILD-TYPE	52	55	54

Figure S248. Get High-res Image Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'Del Peak 37(19p13.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.13e-17 (Fisher's exact test), Q value = 3.6e-14

Table S249. Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	83	96
DEL PEAK 37(19P13.3) CNV	44	7	25
DEL PEAK 37(19P13.3) WILD-TYPE	14	76	71

Figure S249. Get High-res Image Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 38(19q13.11)' versus 'CN_CNMF'

P value = 2.69e-09 (Fisher's exact test), Q value = 1.4e-06

Table S250. Gene #67: 'Del Peak 38(19q13.11)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 38(19Q13.11) CNV	2	5	5	31
DEL PEAK 38(19Q13.11) WILD-TYPE	135	23	23	82

Figure S250. 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 = 0.034

Table S251. 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 S251. Get High-res Image Gene #67: 'Del Peak 38(19q13.11)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 38(19q13.11)' versus 'MIRSEQ_CNMF'

P value = 2.44e-05 (Fisher's exact test), Q value = 0.01

Table S252. Gene #67: 'Del Peak 38(19q13.11)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	69	97	57
DEL PEAK 38(19Q13.11) CNV	8	4	8	20
DEL PEAK 38(19Q13.11) WILD-TYPE	53	65	89	37

Figure S252. Get High-res Image Gene #67: 'Del Peak 38(19q13.11)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'Del Peak 38(19q13.11)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.42e-07 (Fisher's exact test), Q value = 0.00031

Table S253. Gene #67: 'Del Peak 38(19q13.11)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
DEL PEAK 38(19Q13.11) CNV	24	4	12
DEL PEAK 38(19Q13.11) WILD-TYPE	47	85	112

Figure S253. Get High-res Image Gene #67: 'Del Peak 38(19q13.11)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 38(19q13.11)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.89e-06 (Fisher's exact test), Q value = 0.0023

Table S254. Gene #67: 'Del Peak 38(19q13.11)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	83	96
DEL PEAK 38(19Q13.11) CNV	19	3	10
DEL PEAK 38(19Q13.11) WILD-TYPE	39	80	86

Figure S254. Get High-res Image Gene #67: 'Del Peak 38(19q13.11)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 39(20p12.1)' versus 'CN_CNMF'

P value = 1.21e-08 (Fisher's exact test), Q value = 6.3e-06

Table S255. Gene #68: 'Del Peak 39(20p12.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 39(20P12.1) CNV	11	0	2	39
DEL PEAK 39(20P12.1) WILD-TYPE	126	28	26	74

Figure S255. Get High-res Image Gene #68: 'Del Peak 39(20p12.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 39(20p12.1)' versus 'METHLYATION_CNMF'

P value = 0.000701 (Fisher's exact test), Q value = 0.23

Table S256. Gene #68: 'Del Peak 39(20p12.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
DEL PEAK 39(20P12.1) CNV	4	14	4	24
DEL PEAK 39(20P12.1) WILD-TYPE	33	66	61	52

Figure S256. Get High-res Image Gene #68: 'Del Peak 39(20p12.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 40(20p12.1)' versus 'CN_CNMF'

P value = 1.21e-08 (Fisher's exact test), Q value = 6.3e-06

Table S257. Gene #69: 'Del Peak 40(20p12.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 40(20P12.1) CNV	11	0	2	39
DEL PEAK 40(20P12.1) WILD-TYPE	126	28	26	74

Figure S257. Get High-res Image Gene #69: 'Del Peak 40(20p12.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 40(20p12.1)' versus 'METHLYATION_CNMF'

P value = 0.000701 (Fisher's exact test), Q value = 0.23

Table S258. Gene #69: 'Del Peak 40(20p12.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	80	65	76
DEL PEAK 40(20P12.1) CNV	4	14	4	24
DEL PEAK 40(20P12.1) WILD-TYPE	33	66	61	52

Figure S258. Get High-res Image Gene #69: 'Del Peak 40(20p12.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 41(21q11.2)' versus 'CN_CNMF'

P value = 1.39e-10 (Fisher's exact test), Q value = 7.6e-08

Table S259. Gene #70: 'Del Peak 41(21q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 41(21Q11.2) CNV	22	9	13	64
DEL PEAK 41(21Q11.2) WILD-TYPE	115	19	15	49

Figure S259. 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 = 0.012

Table S260. 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 S260. 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 = 0.000496 (Chi-square test), Q value = 0.17

Table S261. Gene #70: 'Del Peak 41(21q11.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	41	35	37	50
DEL PEAK 41(21Q11.2) CNV	12	9	10	10	30
DEL PEAK 41(21Q11.2) WILD-TYPE	33	32	25	27	20

Figure S261. Get High-res Image Gene #70: 'Del Peak 41(21q11.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 41(21q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.98e-05 (Fisher's exact test), Q value = 0.036

Table S262. Gene #70: 'Del Peak 41(21q11.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	42	55	69
DEL PEAK 41(21Q11.2) CNV	10	11	33	17
DEL PEAK 41(21Q11.2) WILD-TYPE	32	31	22	52

Figure S262. Get High-res Image Gene #70: 'Del Peak 41(21q11.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 41(21q11.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000125 (Fisher's exact test), Q value = 0.049

Table S263. Gene #70: 'Del Peak 41(21q11.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
DEL PEAK 41(21Q11.2) CNV	38	31	29
DEL PEAK 41(21Q11.2) WILD-TYPE	33	58	95

Figure S263. Get High-res Image Gene #70: 'Del Peak 41(21q11.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 42(21q22.13)' versus 'CN_CNMF'

P value = 1.56e-09 (Fisher's exact test), Q value = 8.4e-07

Table S264. Gene #71: 'Del Peak 42(21q22.13)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 42(21Q22.13) CNV	25	12	14	64
DEL PEAK 42(21Q22.13) WILD-TYPE	112	16	14	49

Figure S264. 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 = 0.13

Table S265. 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 S265. 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 = 0.000197 (Fisher's exact test), Q value = 0.074

Table S266. Gene #71: 'Del Peak 42(21q22.13)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	42	55	69
DEL PEAK 42(21Q22.13) CNV	13	9	33	19
DEL PEAK 42(21Q22.13) WILD-TYPE	29	33	22	50

Figure S266. Get High-res Image Gene #71: 'Del Peak 42(21q22.13)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 42(21q22.13)' versus 'MIRSEQ_CNMF'

P value = 0.000693 (Fisher's exact test), Q value = 0.23

Table S267. Gene #71: 'Del Peak 42(21q22.13)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	69	97	57
DEL PEAK 42(21Q22.13) CNV	18	25	27	34
DEL PEAK 42(21Q22.13) WILD-TYPE	43	44	70	23

Figure S267. Get High-res Image Gene #71: 'Del Peak 42(21q22.13)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'Del Peak 42(21q22.13)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.02e-05 (Fisher's exact test), Q value = 0.033

Table S268. Gene #71: 'Del Peak 42(21q22.13)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
DEL PEAK 42(21Q22.13) CNV	41	30	33
DEL PEAK 42(21Q22.13) WILD-TYPE	30	59	91

Figure S268. Get High-res Image Gene #71: 'Del Peak 42(21q22.13)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 43(22q13.31)' versus 'CN_CNMF'

P value = 9.68e-15 (Fisher's exact test), Q value = 5.6e-12

Table S269. Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 43(22Q13.31) CNV	15	9	11	66
DEL PEAK 43(22Q13.31) WILD-TYPE	122	19	17	47

Figure S269. 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 = 0.052

Table S270. 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 S270. Get High-res Image Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 43(22q13.31)' versus 'MIRSEQ_CNMF'

P value = 4.36e-05 (Fisher's exact test), Q value = 0.018

Table S271. Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	69	97	57
DEL PEAK 43(22Q13.31) CNV	15	17	26	34
DEL PEAK 43(22Q13.31) WILD-TYPE	46	52	71	23

Figure S271. Get High-res Image Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'Del Peak 43(22q13.31)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.47e-06 (Fisher's exact test), Q value = 0.003

Table S272. Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	89	124
DEL PEAK 43(22Q13.31) CNV	40	20	32
DEL PEAK 43(22Q13.31) WILD-TYPE	31	69	92

Figure S272. Get High-res Image Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 43(22q13.31)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000122 (Fisher's exact test), Q value = 0.048

Table S273. Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	83	96
DEL PEAK 43(22Q13.31) CNV	32	19	25
DEL PEAK 43(22Q13.31) WILD-TYPE	26	64	71

Figure S273. Get High-res Image Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 44(Xp22.2)' versus 'CN_CNMF'

P value = 1.44e-09 (Fisher's exact test), Q value = 7.7e-07

Table S274. Gene #73: 'Del Peak 44(Xp22.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 44(XP22.2) CNV	10	3	3	45
DEL PEAK 44(XP22.2) WILD-TYPE	127	25	25	68

Figure S274. Get High-res Image Gene #73: 'Del Peak 44(Xp22.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 45(Xp21.1)' versus 'CN_CNMF'

P value = 6.22e-08 (Fisher's exact test), Q value = 3.2e-05

Table S275. Gene #74: 'Del Peak 45(Xp21.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 45(XP21.1) CNV	8	4	2	38
DEL PEAK 45(XP21.1) WILD-TYPE	129	24	26	75

Figure S275. 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 = 5.77e-06 (Fisher's exact test), Q value = 0.0027

Table S276. Gene #75: 'Del Peak 46(Xq21.33)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 46(XQ21.33) CNV	7	4	1	30
DEL PEAK 46(XQ21.33) WILD-TYPE	130	24	27	83

Figure S276. 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 = 306
Number of copy number variation regions = 75
Number of molecular subtypes = 8
Exclude regions that fewer than K tumors have alterations, K = 3

Fisher's exact test

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

Chi-square test

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

Q value calculation

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

Download Results

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

References

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

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

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

[4] GISTIC_version2

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