Correlation between copy number variation genes and molecular subtypes

Overview

Introduction

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

Summary

Testing the association between copy number variation of 75 peak regions and 10 molecular subtypes across 575 patients, 166 significant findings detected with Q value < 0.25.

Amp Peak 1(1q31.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 2(2q33.1) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 3(5p12) cnvs correlated to 'CN_CNMF'.
Amp Peak 5(6p21.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 6(7p21.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 7(8p11.23) cnvs correlated to 'CN_CNMF'.
Amp Peak 8(8p11.21) cnvs correlated to 'CN_CNMF'.
Amp Peak 9(8q12.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 10(8q24.21) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Amp Peak 12(11p15.5) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 14(13q12.13) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 15(13q12.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 16(13q22.1) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 18(16p11.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Amp Peak 19(17q12) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Amp Peak 20(17q24.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Amp Peak 21(19p13.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 22(19q12) cnvs correlated to 'CN_CNMF'.
Amp Peak 23(20p11.23) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 24(20p11.21) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 25(20q11.21) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 26(20q12) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 27(20q13.32) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 28(Xq28) cnvs correlated to 'CN_CNMF'.
Del Peak 1(1p36.11) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 2(1p33) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 3(1p13.2) cnvs correlated to 'CN_CNMF'.
Del Peak 10(4p16.1) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 11(4q22.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 12(4q35.1) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 13(5q11.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 14(5q22.2) cnvs correlated to 'CN_CNMF'.
Del Peak 18(8p23.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Del Peak 19(8p22) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 20(8p11.21) cnvs correlated to 'CN_CNMF'.
Del Peak 23(10p15.3) cnvs correlated to 'CN_CNMF'.
Del Peak 24(10q21.1) cnvs correlated to 'CN_CNMF'.
Del Peak 25(10q23.31) cnvs correlated to 'CN_CNMF'.
Del Peak 26(10q25.2) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 28(12p13.1) cnvs correlated to 'CN_CNMF'.
Del Peak 29(12q21.2) cnvs correlated to 'CN_CNMF'.
Del Peak 30(14q22.1) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 31(15q11.2) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 32(15q21.1) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 33(15q22.33) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 36(17p12) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 38(18p11.31) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 39(18q12.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 40(18q21.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 41(18q22.1) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 42(19p13.3) cnvs correlated to 'CN_CNMF'.
Del Peak 43(19q13.43) cnvs correlated to 'CN_CNMF'.
Del Peak 44(20p12.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 45(20p12.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 46(21q11.2) cnvs correlated to 'CN_CNMF'.
Del Peak 47(22q13.32) cnvs correlated to 'CN_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 75 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 166 significant findings detected.


		Molecular subtypes	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
Del Peak 30(14q22 1)	0 (0%)	390	0.000117 (0.0708)	0.00012 (0.0723)	1.95e-28 (1.43e-25)	8.14e-06 (0.0051)	0.000318 (0.188)	0.121 (1.00)	4.09e-08 (2.71e-05)	3.08e-05 (0.0189)	0.127 (1.00)	0.439 (1.00)
Amp Peak 14(13q12 13)	0 (0%)	204	3.25e-08 (2.16e-05)	1.57e-06 (0.001)	6.42e-44 (4.79e-41)	8.91e-11 (6.11e-08)	0.0131 (1.00)	0.064 (1.00)	8e-11 (5.5e-08)	4.97e-07 (0.000324)	0.0136 (1.00)	0.237 (1.00)
Amp Peak 15(13q12 2)	0 (0%)	209	9.96e-07 (0.000646)	1.97e-05 (0.0122)	2.2e-45 (1.65e-42)	2.31e-11 (1.59e-08)	0.0319 (1.00)	0.169 (1.00)	2.13e-10 (1.46e-07)	1.08e-06 (0.000701)	0.026 (1.00)	0.285 (1.00)
Amp Peak 16(13q22 1)	0 (0%)	204	7.58e-06 (0.00477)	7.24e-05 (0.0439)	7.69e-42 (5.7e-39)	2.99e-09 (2.02e-06)	0.0808 (1.00)	0.174 (1.00)	9.82e-10 (6.68e-07)	5.36e-07 (0.000349)	0.0301 (1.00)	0.0471 (1.00)
Amp Peak 24(20p11 21)	0 (0%)	236	0.000239 (0.142)	1.54e-06 (0.000988)	8.57e-23 (6.25e-20)	6.98e-06 (0.00441)	0.00713 (1.00)	0.158 (1.00)	4.83e-09 (3.24e-06)	3.8e-09 (2.55e-06)	0.107 (1.00)	0.188 (1.00)
Amp Peak 25(20q11 21)	0 (0%)	136	4.15e-15 (2.93e-12)	7.48e-14 (5.22e-11)	1.54e-42 (1.14e-39)	2.13e-16 (1.52e-13)	0.0129 (1.00)	0.0103 (1.00)	1.59e-19 (1.16e-16)	5.25e-18 (3.78e-15)	0.124 (1.00)	0.0189 (1.00)
Amp Peak 26(20q12)	0 (0%)	134	3.23e-16 (2.31e-13)	3.27e-15 (2.32e-12)	5.84e-43 (4.34e-40)	3.56e-15 (2.52e-12)	0.00687 (1.00)	0.00555 (1.00)	5.42e-19 (3.92e-16)	1.81e-17 (1.3e-14)	0.065 (1.00)	0.00779 (1.00)
Amp Peak 27(20q13 32)	0 (0%)	131	2.88e-15 (2.04e-12)	1.25e-13 (8.71e-11)	5.66e-43 (4.22e-40)	3.21e-14 (2.25e-11)	0.013 (1.00)	0.0044 (1.00)	5.42e-19 (3.92e-16)	1.81e-17 (1.3e-14)	0.117 (1.00)	0.033 (1.00)
Del Peak 36(17p12)	0 (0%)	232	6.93e-08 (4.57e-05)	2.79e-05 (0.0171)	2.01e-34 (1.48e-31)	6.04e-09 (4.03e-06)	0.103 (1.00)	0.0247 (1.00)	1.6e-08 (1.06e-05)	3.32e-06 (0.00211)	0.052 (1.00)	0.673 (1.00)
Del Peak 38(18p11 31)	0 (0%)	234	5.53e-13 (3.84e-10)	2.35e-09 (1.59e-06)	1.19e-41 (8.82e-39)	2.31e-15 (1.65e-12)	0.101 (1.00)	0.0305 (1.00)	1.4e-20 (1.02e-17)	5.08e-15 (3.58e-12)	0.0183 (1.00)	0.386 (1.00)
Del Peak 39(18q12 2)	0 (0%)	189	9.64e-10 (6.57e-07)	7.31e-08 (4.82e-05)	1.29e-49 (9.68e-47)	8.06e-18 (5.8e-15)	0.0431 (1.00)	0.028 (1.00)	2.84e-19 (2.05e-16)	1.22e-10 (8.36e-08)	0.00579 (1.00)	0.059 (1.00)
Del Peak 40(18q21 2)	0 (0%)	172	3.98e-10 (2.72e-07)	8.24e-08 (5.42e-05)	1.24e-50 (9.28e-48)	3.43e-15 (2.43e-12)	0.0134 (1.00)	0.0247 (1.00)	2.83e-15 (2.02e-12)	1.42e-09 (9.65e-07)	0.000657 (0.379)	0.126 (1.00)
Del Peak 41(18q22 1)	0 (0%)	177	2.43e-09 (1.64e-06)	2.07e-06 (0.00132)	9.55e-53 (7.16e-50)	1.37e-15 (9.77e-13)	0.0334 (1.00)	0.02 (1.00)	2.83e-15 (2.02e-12)	5.84e-09 (3.9e-06)	0.00128 (0.726)	0.171 (1.00)
Del Peak 1(1p36 11)	0 (0%)	353	7.45e-05 (0.0452)	0.00211 (1.00)	2.21e-13 (1.53e-10)	2.1e-05 (0.013)	0.0468 (1.00)	0.148 (1.00)	1.05e-05 (0.00655)	6.54e-05 (0.0397)	0.158 (1.00)	0.0183 (1.00)
Amp Peak 6(7p21 3)	0 (0%)	238	0.000636 (0.369)	0.00688 (1.00)	7.91e-22 (5.77e-19)	7.11e-06 (0.00448)	0.308 (1.00)	0.0266 (1.00)	6.87e-10 (4.69e-07)	3.15e-06 (0.002)	0.0224 (1.00)	0.00259 (1.00)
Amp Peak 12(11p15 5)	0 (0%)	446	4.31e-05 (0.0263)	0.00115 (0.656)	1.84e-06 (0.00118)	0.00344 (1.00)	0.0056 (1.00)	0.238 (1.00)	4.75e-05 (0.029)	7.68e-06 (0.00482)	0.352 (1.00)	0.00906 (1.00)
Amp Peak 23(20p11 23)	0 (0%)	274	0.0117 (1.00)	0.000401 (0.235)	5.56e-17 (3.98e-14)	0.0141 (1.00)	0.00142 (0.804)	0.178 (1.00)	1.06e-05 (0.00663)	2.29e-05 (0.0141)	0.353 (1.00)	0.425 (1.00)
Del Peak 11(4q22 1)	0 (0%)	377	0.0193 (1.00)	0.0507 (1.00)	1.25e-14 (8.77e-12)	7.66e-05 (0.0463)	0.767 (1.00)	0.77 (1.00)	7.1e-06 (0.00448)	0.00018 (0.108)	0.148 (1.00)	0.409 (1.00)
Del Peak 19(8p22)	0 (0%)	290	0.00109 (0.621)	0.0334 (1.00)	1.58e-37 (1.17e-34)	1.32e-06 (0.00085)	0.1 (1.00)	0.00225 (1.00)	1.05e-06 (0.000682)	0.000223 (0.133)	0.763 (1.00)	0.642 (1.00)
Amp Peak 2(2q33 1)	0 (0%)	452	0.048 (1.00)	0.0609 (1.00)	1.52e-06 (0.000978)	0.00502 (1.00)	0.596 (1.00)	0.901 (1.00)	0.000173 (0.103)	0.000166 (0.0994)	0.181 (1.00)	0.00129 (0.733)
Amp Peak 20(17q24 1)	0 (0%)	447	0.00963 (1.00)	0.00808 (1.00)	1.54e-08 (1.03e-05)	0.00035 (0.206)	0.124 (1.00)	0.00558 (1.00)	0.000201 (0.12)	0.00309 (1.00)	0.00127 (0.722)	0.0419 (1.00)
Del Peak 10(4p16 1)	0 (0%)	393	0.0524 (1.00)	0.424 (1.00)	1.65e-12 (1.14e-09)	0.00203 (1.00)	0.416 (1.00)	0.923 (1.00)	1.32e-06 (0.000853)	0.000143 (0.0861)	0.622 (1.00)	0.117 (1.00)
Del Peak 12(4q35 1)	0 (0%)	364	0.0161 (1.00)	0.185 (1.00)	1.25e-13 (8.69e-11)	0.000642 (0.372)	0.464 (1.00)	0.811 (1.00)	5.07e-05 (0.0309)	3.74e-05 (0.0229)	0.523 (1.00)	0.743 (1.00)
Del Peak 18(8p23 2)	0 (0%)	303	0.000586 (0.341)	0.0322 (1.00)	2.13e-34 (1.57e-31)	1.96e-06 (0.00125)	0.0964 (1.00)	0.00316 (1.00)	1.52e-05 (0.0094)	0.000561 (0.327)	0.802 (1.00)	0.399 (1.00)
Del Peak 26(10q25 2)	0 (0%)	435	0.312 (1.00)	0.116 (1.00)	3.06e-12 (2.11e-09)	0.105 (1.00)	0.00922 (1.00)	0.245 (1.00)	0.000239 (0.142)	0.000324 (0.191)	0.972 (1.00)	0.779 (1.00)
Del Peak 31(15q11 2)	0 (0%)	342	0.000687 (0.395)	0.0178 (1.00)	1.2e-23 (8.82e-21)	0.00572 (1.00)	0.35 (1.00)	0.359 (1.00)	1.41e-06 (0.000909)	1.38e-05 (0.00854)	0.478 (1.00)	0.111 (1.00)
Del Peak 32(15q21 1)	0 (0%)	348	0.00243 (1.00)	0.0767 (1.00)	2.43e-21 (1.77e-18)	0.00358 (1.00)	0.13 (1.00)	0.13 (1.00)	2.2e-07 (0.000144)	2.3e-05 (0.0141)	0.742 (1.00)	0.459 (1.00)
Del Peak 33(15q22 33)	0 (0%)	358	0.000645 (0.373)	0.00746 (1.00)	4.49e-23 (3.28e-20)	0.00084 (0.482)	0.661 (1.00)	0.463 (1.00)	5.81e-09 (3.89e-06)	5.5e-06 (0.00349)	0.865 (1.00)	0.117 (1.00)
Amp Peak 10(8q24 21)	0 (0%)	230	0.24 (1.00)	0.196 (1.00)	3.18e-35 (2.35e-32)	0.00429 (1.00)	0.0427 (1.00)	0.283 (1.00)	0.000294 (0.174)	0.0109 (1.00)	0.251 (1.00)	0.176 (1.00)
Amp Peak 18(16p11 2)	0 (0%)	414	0.0134 (1.00)	0.00695 (1.00)	1.33e-20 (9.68e-18)	0.00154 (0.867)	0.0915 (1.00)	0.0157 (1.00)	2.17e-05 (0.0134)	0.00369 (1.00)	0.811 (1.00)	0.11 (1.00)
Amp Peak 19(17q12)	0 (0%)	431	0.015 (1.00)	0.1 (1.00)	3.46e-09 (2.33e-06)	0.00726 (1.00)	0.23 (1.00)	0.0592 (1.00)	0.000424 (0.248)	0.00212 (1.00)	0.039 (1.00)	0.232 (1.00)
Del Peak 2(1p33)	0 (0%)	419	0.0103 (1.00)	0.0718 (1.00)	8.95e-13 (6.2e-10)	0.000371 (0.218)	0.801 (1.00)	0.574 (1.00)	0.0016 (0.898)	0.00208 (1.00)	0.532 (1.00)	0.0159 (1.00)
Del Peak 13(5q11 2)	0 (0%)	435	0.00191 (1.00)	0.48 (1.00)	2.13e-12 (1.47e-09)	0.00282 (1.00)	0.103 (1.00)	0.547 (1.00)	0.000317 (0.188)	0.00205 (1.00)	1 (1.00)	0.758 (1.00)
Del Peak 44(20p12 1)	0 (0%)	396	0.0234 (1.00)	0.0236 (1.00)	6.5e-15 (4.58e-12)	1.01e-05 (0.00632)	0.328 (1.00)	0.00712 (1.00)	0.0232 (1.00)	0.0151 (1.00)	0.223 (1.00)	0.976 (1.00)
Del Peak 45(20p12 1)	0 (0%)	396	0.0234 (1.00)	0.0236 (1.00)	6.5e-15 (4.58e-12)	1.01e-05 (0.00632)	0.328 (1.00)	0.00712 (1.00)	0.0232 (1.00)	0.0151 (1.00)	0.223 (1.00)	0.976 (1.00)
Amp Peak 1(1q31 1)	0 (0%)	441	0.444 (1.00)	0.813 (1.00)	0.000205 (0.122)	0.722 (1.00)	0.474 (1.00)	0.289 (1.00)	0.0893 (1.00)	0.32 (1.00)	0.765 (1.00)	0.944 (1.00)
Amp Peak 3(5p12)	0 (0%)	468	0.0978 (1.00)	0.974 (1.00)	6.55e-06 (0.00414)	0.794 (1.00)	0.0746 (1.00)	0.721 (1.00)	0.102 (1.00)	0.0189 (1.00)	0.889 (1.00)	0.347 (1.00)
Amp Peak 5(6p21 1)	0 (0%)	429	0.0263 (1.00)	0.00308 (1.00)	3.97e-14 (2.78e-11)	0.169 (1.00)	0.699 (1.00)	0.369 (1.00)	0.000931 (0.533)	0.0151 (1.00)	0.531 (1.00)	0.00678 (1.00)
Amp Peak 7(8p11 23)	0 (0%)	379	0.573 (1.00)	0.4 (1.00)	2.83e-23 (2.07e-20)	0.304 (1.00)	0.826 (1.00)	0.5 (1.00)	0.235 (1.00)	0.781 (1.00)	0.0154 (1.00)	0.0772 (1.00)
Amp Peak 8(8p11 21)	0 (0%)	337	0.306 (1.00)	0.256 (1.00)	3.33e-31 (2.45e-28)	0.237 (1.00)	0.378 (1.00)	0.394 (1.00)	0.41 (1.00)	0.735 (1.00)	0.0815 (1.00)	0.201 (1.00)
Amp Peak 9(8q12 1)	0 (0%)	266	0.0798 (1.00)	0.118 (1.00)	1.91e-36 (1.41e-33)	0.0153 (1.00)	0.0183 (1.00)	0.0546 (1.00)	0.000512 (0.299)	0.00729 (1.00)	0.102 (1.00)	0.146 (1.00)
Amp Peak 21(19p13 2)	0 (0%)	478	0.0439 (1.00)	0.377 (1.00)	8.87e-08 (5.83e-05)	0.0317 (1.00)	0.932 (1.00)	0.39 (1.00)	0.329 (1.00)	0.418 (1.00)	0.274 (1.00)	0.131 (1.00)
Amp Peak 22(19q12)	0 (0%)	453	0.0308 (1.00)	0.0107 (1.00)	6.23e-08 (4.12e-05)	0.251 (1.00)	0.258 (1.00)	0.326 (1.00)	0.0747 (1.00)	0.0789 (1.00)	0.71 (1.00)	0.49 (1.00)
Amp Peak 28(Xq28)	0 (0%)	454	0.345 (1.00)	0.581 (1.00)	1.72e-06 (0.0011)	0.1 (1.00)	0.00335 (1.00)	0.0093 (1.00)	0.171 (1.00)	0.024 (1.00)	0.99 (1.00)	0.783 (1.00)
Del Peak 3(1p13 2)	0 (0%)	418	0.189 (1.00)	0.0923 (1.00)	3.38e-09 (2.28e-06)	0.0153 (1.00)	0.937 (1.00)	0.702 (1.00)	0.0132 (1.00)	0.00062 (0.361)	0.756 (1.00)	0.351 (1.00)
Del Peak 14(5q22 2)	0 (0%)	403	0.00141 (0.797)	0.0581 (1.00)	2.23e-09 (1.51e-06)	0.114 (1.00)	0.388 (1.00)	0.922 (1.00)	0.00168 (0.942)	0.169 (1.00)	0.771 (1.00)	0.854 (1.00)
Del Peak 20(8p11 21)	0 (0%)	451	0.0111 (1.00)	0.126 (1.00)	4.85e-07 (0.000317)	0.341 (1.00)	0.0853 (1.00)	0.0903 (1.00)	0.0621 (1.00)	0.0497 (1.00)	0.162 (1.00)	0.4 (1.00)
Del Peak 23(10p15 3)	0 (0%)	473	0.246 (1.00)	0.417 (1.00)	1.38e-07 (9.02e-05)	0.0288 (1.00)	0.023 (1.00)	0.158 (1.00)	0.0122 (1.00)	0.0576 (1.00)	0.71 (1.00)	0.302 (1.00)
Del Peak 24(10q21 1)	0 (0%)	457	0.2 (1.00)	0.111 (1.00)	3.13e-11 (2.16e-08)	0.15 (1.00)	0.0871 (1.00)	0.133 (1.00)	0.0728 (1.00)	0.0438 (1.00)	0.691 (1.00)	0.577 (1.00)
Del Peak 25(10q23 31)	0 (0%)	430	0.135 (1.00)	0.496 (1.00)	9.09e-08 (5.96e-05)	0.155 (1.00)	0.033 (1.00)	0.242 (1.00)	0.00262 (1.00)	0.0685 (1.00)	0.762 (1.00)	0.365 (1.00)
Del Peak 28(12p13 1)	0 (0%)	498	0.00697 (1.00)	0.0173 (1.00)	3.89e-08 (2.58e-05)	0.429 (1.00)	0.977 (1.00)	0.732 (1.00)	0.0571 (1.00)	0.423 (1.00)	0.446 (1.00)	0.919 (1.00)
Del Peak 29(12q21 2)	0 (0%)	495	0.172 (1.00)	0.0294 (1.00)	5.52e-07 (0.000359)	0.348 (1.00)	0.901 (1.00)	0.546 (1.00)	0.0351 (1.00)	0.294 (1.00)	0.521 (1.00)	0.979 (1.00)
Del Peak 42(19p13 3)	0 (0%)	483	0.0887 (1.00)	0.684 (1.00)	1.35e-05 (0.00841)	0.825 (1.00)	0.636 (1.00)	0.666 (1.00)	0.0329 (1.00)	0.00869 (1.00)	0.579 (1.00)	0.911 (1.00)
Del Peak 43(19q13 43)	0 (0%)	507	0.951 (1.00)	0.698 (1.00)	0.00011 (0.0667)	0.6 (1.00)	0.0859 (1.00)	0.937 (1.00)	0.00935 (1.00)	0.00916 (1.00)	0.255 (1.00)	0.502 (1.00)
Del Peak 46(21q11 2)	0 (0%)	380	0.00177 (0.993)	0.126 (1.00)	4.07e-09 (2.73e-06)	0.0109 (1.00)	0.584 (1.00)	0.213 (1.00)	0.000647 (0.374)	0.00527 (1.00)	0.234 (1.00)	0.0494 (1.00)
Del Peak 47(22q13 32)	0 (0%)	371	0.0226 (1.00)	0.00461 (1.00)	9.83e-15 (6.9e-12)	0.0299 (1.00)	0.473 (1.00)	0.617 (1.00)	0.000824 (0.473)	0.0349 (1.00)	0.696 (1.00)	0.0115 (1.00)
Amp Peak 4(5q22 3)	0 (0%)	516	0.894 (1.00)	1 (1.00)	0.0037 (1.00)	0.32 (1.00)	0.676 (1.00)	0.815 (1.00)	0.248 (1.00)	0.02 (1.00)	0.46 (1.00)	0.894 (1.00)
Amp Peak 11(10q22 3)	0 (0%)	540	0.903 (1.00)	0.145 (1.00)	0.655 (1.00)	0.56 (1.00)	0.263 (1.00)	0.85 (1.00)	0.579 (1.00)	0.187 (1.00)	0.587 (1.00)	0.281 (1.00)
Amp Peak 13(12p13 32)	0 (0%)	431	0.181 (1.00)	0.786 (1.00)	0.252 (1.00)	0.137 (1.00)	0.768 (1.00)	0.813 (1.00)	0.205 (1.00)	0.348 (1.00)	0.676 (1.00)	0.886 (1.00)
Amp Peak 17(15q26 1)	0 (0%)	532	0.526 (1.00)	0.394 (1.00)	0.249 (1.00)	0.842 (1.00)	0.105 (1.00)	0.308 (1.00)	0.191 (1.00)	0.241 (1.00)	0.926 (1.00)	1 (1.00)
Del Peak 4(2p12)	0 (0%)	555	1 (1.00)	0.435 (1.00)	0.00194 (1.00)	0.0111 (1.00)	0.187 (1.00)	1 (1.00)	0.173 (1.00)	0.738 (1.00)	0.0165 (1.00)	0.0215 (1.00)
Del Peak 5(2q22 1)	0 (0%)	542	0.927 (1.00)	0.851 (1.00)	0.146 (1.00)	0.833 (1.00)	0.0998 (1.00)	0.901 (1.00)	0.974 (1.00)	0.797 (1.00)	0.316 (1.00)	0.272 (1.00)
Del Peak 6(2q37 2)	0 (0%)	545	0.924 (1.00)	0.691 (1.00)	0.285 (1.00)	0.833 (1.00)	0.278 (1.00)	0.162 (1.00)	0.56 (1.00)	0.0948 (1.00)	0.244 (1.00)	0.364 (1.00)
Del Peak 7(3p26 3)	0 (0%)	491	0.105 (1.00)	0.819 (1.00)	0.163 (1.00)	0.357 (1.00)	0.856 (1.00)	0.824 (1.00)	0.28 (1.00)	0.0366 (1.00)	0.277 (1.00)	0.728 (1.00)
Del Peak 8(3p14 2)	0 (0%)	471	0.475 (1.00)	0.9 (1.00)	0.932 (1.00)	0.597 (1.00)	0.565 (1.00)	0.674 (1.00)	0.553 (1.00)	0.663 (1.00)	0.0595 (1.00)	0.918 (1.00)
Del Peak 9(3q26 31)	0 (0%)	519	0.297 (1.00)	0.554 (1.00)	0.448 (1.00)	0.373 (1.00)	0.145 (1.00)	0.51 (1.00)	0.308 (1.00)	0.0516 (1.00)	0.0934 (1.00)	0.123 (1.00)
Del Peak 15(6p25 3)	0 (0%)	497	0.84 (1.00)	0.599 (1.00)	0.0849 (1.00)	0.262 (1.00)	0.176 (1.00)	0.94 (1.00)	0.961 (1.00)	0.385 (1.00)	0.61 (1.00)	0.957 (1.00)
Del Peak 16(6q26)	0 (0%)	485	0.886 (1.00)	0.698 (1.00)	0.0401 (1.00)	0.762 (1.00)	0.0542 (1.00)	0.451 (1.00)	0.919 (1.00)	0.948 (1.00)	0.223 (1.00)	0.507 (1.00)
Del Peak 17(7q31 1)	0 (0%)	560	0.103 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.589 (1.00)	0.273 (1.00)	0.66 (1.00)	0.714 (1.00)	0.235 (1.00)	0.498 (1.00)
Del Peak 21(8q11 1)	0 (0%)	531	0.272 (1.00)	0.687 (1.00)	0.00266 (1.00)	0.661 (1.00)	0.396 (1.00)	0.568 (1.00)	0.315 (1.00)	0.32 (1.00)	0.0819 (1.00)	0.0193 (1.00)
Del Peak 22(9p24 2)	0 (0%)	497	0.256 (1.00)	0.15 (1.00)	0.00178 (0.997)	0.0506 (1.00)	0.532 (1.00)	0.592 (1.00)	0.0295 (1.00)	0.00241 (1.00)	0.296 (1.00)	0.243 (1.00)
Del Peak 27(11q22 3)	0 (0%)	471	0.585 (1.00)	0.53 (1.00)	0.0385 (1.00)	0.125 (1.00)	0.437 (1.00)	0.147 (1.00)	0.0365 (1.00)	0.524 (1.00)	0.657 (1.00)	0.363 (1.00)
Del Peak 34(16p13 3)	0 (0%)	517	0.142 (1.00)	0.382 (1.00)	0.215 (1.00)	0.676 (1.00)	0.669 (1.00)	0.789 (1.00)	0.927 (1.00)	0.176 (1.00)	0.637 (1.00)	0.595 (1.00)
Del Peak 35(16q23 1)	0 (0%)	503	0.0646 (1.00)	0.00115 (0.654)	0.179 (1.00)	0.327 (1.00)	0.18 (1.00)	0.925 (1.00)	0.271 (1.00)	0.23 (1.00)	0.805 (1.00)	0.632 (1.00)
Del Peak 37(17q24 3)	0 (0%)	491	0.905 (1.00)	0.876 (1.00)	0.0296 (1.00)	0.528 (1.00)	1 (1.00)	0.523 (1.00)	0.184 (1.00)	0.0781 (1.00)	0.919 (1.00)	0.425 (1.00)

'Amp Peak 1(1q31.1)' versus 'CN_CNMF'

P value = 0.000205 (Fisher's exact test), Q value = 0.12

Table S1. Gene #1: 'Amp Peak 1(1q31.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 1(1Q31.1) CNV	59	34	26	15
AMP PEAK 1(1Q31.1) WILD-TYPE	141	200	74	26

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1q31.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 2(2q33.1)' versus 'CN_CNMF'

P value = 1.52e-06 (Fisher's exact test), Q value = 0.00098

Table S2. Gene #2: 'Amp Peak 2(2q33.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 2(2Q33.1) CNV	59	27	21	16
AMP PEAK 2(2Q33.1) WILD-TYPE	141	207	79	25

Figure S2. Get High-res Image Gene #2: 'Amp Peak 2(2q33.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 2(2q33.1)' versus 'MRNASEQ_CNMF'

P value = 0.000173 (Fisher's exact test), Q value = 0.1

Table S3. Gene #2: 'Amp Peak 2(2q33.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	81	56	66
AMP PEAK 2(2Q33.1) CNV	6	30	13	5
AMP PEAK 2(2Q33.1) WILD-TYPE	32	51	43	61

Figure S3. Get High-res Image Gene #2: 'Amp Peak 2(2q33.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 2(2q33.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000166 (Fisher's exact test), Q value = 0.099

Table S4. Gene #2: 'Amp Peak 2(2q33.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	67	79
AMP PEAK 2(2Q33.1) CNV	21	5	28
AMP PEAK 2(2Q33.1) WILD-TYPE	74	62	51

Figure S4. Get High-res Image Gene #2: 'Amp Peak 2(2q33.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 3(5p12)' versus 'CN_CNMF'

P value = 6.55e-06 (Fisher's exact test), Q value = 0.0041

Table S5. Gene #3: 'Amp Peak 3(5p12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 3(5P12) CNV	51	21	24	11
AMP PEAK 3(5P12) WILD-TYPE	149	213	76	30

Figure S5. Get High-res Image Gene #3: 'Amp Peak 3(5p12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 5(6p21.1)' versus 'CN_CNMF'

P value = 3.97e-14 (Fisher's exact test), Q value = 2.8e-11

Table S6. Gene #5: 'Amp Peak 5(6p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 5(6P21.1) CNV	83	22	27	14
AMP PEAK 5(6P21.1) WILD-TYPE	117	212	73	27

Figure S6. Get High-res Image Gene #5: 'Amp Peak 5(6p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 6(7p21.3)' versus 'CN_CNMF'

P value = 7.91e-22 (Fisher's exact test), Q value = 5.8e-19

Table S7. Gene #6: 'Amp Peak 6(7p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 6(7P21.3) CNV	157	81	66	33
AMP PEAK 6(7P21.3) WILD-TYPE	43	153	34	8

Figure S7. Get High-res Image Gene #6: 'Amp Peak 6(7p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 6(7p21.3)' versus 'METHLYATION_CNMF'

P value = 7.11e-06 (Fisher's exact test), Q value = 0.0045

Table S8. Gene #6: 'Amp Peak 6(7p21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
AMP PEAK 6(7P21.3) CNV	112	58	51
AMP PEAK 6(7P21.3) WILD-TYPE	31	55	40

Figure S8. Get High-res Image Gene #6: 'Amp Peak 6(7p21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 6(7p21.3)' versus 'MRNASEQ_CNMF'

P value = 6.87e-10 (Fisher's exact test), Q value = 4.7e-07

Table S9. Gene #6: 'Amp Peak 6(7p21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	81	56	66
AMP PEAK 6(7P21.3) CNV	27	67	38	20
AMP PEAK 6(7P21.3) WILD-TYPE	11	14	18	46

Figure S9. Get High-res Image Gene #6: 'Amp Peak 6(7p21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 6(7p21.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.15e-06 (Fisher's exact test), Q value = 0.002

Table S10. Gene #6: 'Amp Peak 6(7p21.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	67	79
AMP PEAK 6(7P21.3) CNV	64	26	62
AMP PEAK 6(7P21.3) WILD-TYPE	31	41	17

Figure S10. Get High-res Image Gene #6: 'Amp Peak 6(7p21.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 7(8p11.23)' versus 'CN_CNMF'

P value = 2.83e-23 (Fisher's exact test), Q value = 2.1e-20

Table S11. Gene #7: 'Amp Peak 7(8p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 7(8P11.23) CNV	56	44	76	20
AMP PEAK 7(8P11.23) WILD-TYPE	144	190	24	21

Figure S11. Get High-res Image Gene #7: 'Amp Peak 7(8p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 3.33e-31 (Fisher's exact test), Q value = 2.5e-28

Table S12. Gene #8: 'Amp Peak 8(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 8(8P11.21) CNV	75	51	89	23
AMP PEAK 8(8P11.21) WILD-TYPE	125	183	11	18

Figure S12. Get High-res Image Gene #8: 'Amp Peak 8(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 9(8q12.1)' versus 'CN_CNMF'

P value = 1.91e-36 (Fisher's exact test), Q value = 1.4e-33

Table S13. Gene #9: 'Amp Peak 9(8q12.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 9(8Q12.1) CNV	109	69	97	34
AMP PEAK 9(8Q12.1) WILD-TYPE	91	165	3	7

Figure S13. Get High-res Image Gene #9: 'Amp Peak 9(8q12.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 10(8q24.21)' versus 'CN_CNMF'

P value = 3.18e-35 (Fisher's exact test), Q value = 2.3e-32

Table S14. Gene #10: 'Amp Peak 10(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 10(8Q24.21) CNV	129	82	99	35
AMP PEAK 10(8Q24.21) WILD-TYPE	71	152	1	6

Figure S14. Get High-res Image Gene #10: 'Amp Peak 10(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 10(8q24.21)' versus 'MRNASEQ_CNMF'

P value = 0.000294 (Fisher's exact test), Q value = 0.17

Table S15. Gene #10: 'Amp Peak 10(8q24.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	81	56	66
AMP PEAK 10(8Q24.21) CNV	20	65	31	33
AMP PEAK 10(8Q24.21) WILD-TYPE	18	16	25	33

Figure S15. Get High-res Image Gene #10: 'Amp Peak 10(8q24.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 12(11p15.5)' versus 'MRNA_CNMF'

P value = 4.31e-05 (Fisher's exact test), Q value = 0.026

Table S16. Gene #12: 'Amp Peak 12(11p15.5)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	62	69	39
AMP PEAK 12(11P15.5) CNV	3	21	24	3
AMP PEAK 12(11P15.5) WILD-TYPE	42	41	45	36

Figure S16. Get High-res Image Gene #12: 'Amp Peak 12(11p15.5)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 12(11p15.5)' versus 'CN_CNMF'

P value = 1.84e-06 (Fisher's exact test), Q value = 0.0012

Table S17. Gene #12: 'Amp Peak 12(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 12(11P15.5) CNV	58	31	21	19
AMP PEAK 12(11P15.5) WILD-TYPE	142	203	79	22

Figure S17. Get High-res Image Gene #12: 'Amp Peak 12(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 12(11p15.5)' versus 'MRNASEQ_CNMF'

P value = 4.75e-05 (Fisher's exact test), Q value = 0.029

Table S18. Gene #12: 'Amp Peak 12(11p15.5)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	81	56	66
AMP PEAK 12(11P15.5) CNV	6	28	11	3
AMP PEAK 12(11P15.5) WILD-TYPE	32	53	45	63

Figure S18. Get High-res Image Gene #12: 'Amp Peak 12(11p15.5)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 12(11p15.5)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.68e-06 (Fisher's exact test), Q value = 0.0048

Table S19. Gene #12: 'Amp Peak 12(11p15.5)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	67	79
AMP PEAK 12(11P15.5) CNV	17	3	28
AMP PEAK 12(11P15.5) WILD-TYPE	78	64	51

Figure S19. Get High-res Image Gene #12: 'Amp Peak 12(11p15.5)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 14(13q12.13)' versus 'MRNA_CNMF'

P value = 3.25e-08 (Fisher's exact test), Q value = 2.2e-05

Table S20. Gene #14: 'Amp Peak 14(13q12.13)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	62	69	39
AMP PEAK 14(13Q12.13) CNV	20	49	57	14
AMP PEAK 14(13Q12.13) WILD-TYPE	25	13	12	25

Figure S20. Get High-res Image Gene #14: 'Amp Peak 14(13q12.13)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 14(13q12.13)' versus 'MRNA_CHIERARCHICAL'

P value = 1.57e-06 (Fisher's exact test), Q value = 0.001

Table S21. Gene #14: 'Amp Peak 14(13q12.13)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	61	114	40
AMP PEAK 14(13Q12.13) CNV	24	82	34
AMP PEAK 14(13Q12.13) WILD-TYPE	37	32	6

Figure S21. Get High-res Image Gene #14: 'Amp Peak 14(13q12.13)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 14(13q12.13)' versus 'CN_CNMF'

P value = 6.42e-44 (Fisher's exact test), Q value = 4.8e-41

Table S22. Gene #14: 'Amp Peak 14(13q12.13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 14(13Q12.13) CNV	194	86	66	25
AMP PEAK 14(13Q12.13) WILD-TYPE	6	148	34	16

Figure S22. Get High-res Image Gene #14: 'Amp Peak 14(13q12.13)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 14(13q12.13)' versus 'METHLYATION_CNMF'

P value = 8.91e-11 (Fisher's exact test), Q value = 6.1e-08

Table S23. Gene #14: 'Amp Peak 14(13q12.13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
AMP PEAK 14(13Q12.13) CNV	122	55	50
AMP PEAK 14(13Q12.13) WILD-TYPE	21	58	41

Figure S23. Get High-res Image Gene #14: 'Amp Peak 14(13q12.13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 14(13q12.13)' versus 'MRNASEQ_CNMF'

P value = 8e-11 (Fisher's exact test), Q value = 5.5e-08

Table S24. Gene #14: 'Amp Peak 14(13q12.13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	81	56	66
AMP PEAK 14(13Q12.13) CNV	29	67	37	19
AMP PEAK 14(13Q12.13) WILD-TYPE	9	14	19	47

Figure S24. Get High-res Image Gene #14: 'Amp Peak 14(13q12.13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 14(13q12.13)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.97e-07 (Fisher's exact test), Q value = 0.00032

Table S25. Gene #14: 'Amp Peak 14(13q12.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	67	79
AMP PEAK 14(13Q12.13) CNV	64	25	63
AMP PEAK 14(13Q12.13) WILD-TYPE	31	42	16

Figure S25. Get High-res Image Gene #14: 'Amp Peak 14(13q12.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 15(13q12.2)' versus 'MRNA_CNMF'

P value = 9.96e-07 (Fisher's exact test), Q value = 0.00065

Table S26. Gene #15: 'Amp Peak 15(13q12.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	62	69	39
AMP PEAK 15(13Q12.2) CNV	20	48	55	15
AMP PEAK 15(13Q12.2) WILD-TYPE	25	14	14	24

Figure S26. Get High-res Image Gene #15: 'Amp Peak 15(13q12.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 15(13q12.2)' versus 'MRNA_CHIERARCHICAL'

P value = 1.97e-05 (Fisher's exact test), Q value = 0.012

Table S27. Gene #15: 'Amp Peak 15(13q12.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	61	114	40
AMP PEAK 15(13Q12.2) CNV	25	80	33
AMP PEAK 15(13Q12.2) WILD-TYPE	36	34	7

Figure S27. Get High-res Image Gene #15: 'Amp Peak 15(13q12.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 15(13q12.2)' versus 'CN_CNMF'

P value = 2.2e-45 (Fisher's exact test), Q value = 1.6e-42

Table S28. Gene #15: 'Amp Peak 15(13q12.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 15(13Q12.2) CNV	194	83	64	25
AMP PEAK 15(13Q12.2) WILD-TYPE	6	151	36	16

Figure S28. Get High-res Image Gene #15: 'Amp Peak 15(13q12.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 15(13q12.2)' versus 'METHLYATION_CNMF'

P value = 2.31e-11 (Fisher's exact test), Q value = 1.6e-08

Table S29. Gene #15: 'Amp Peak 15(13q12.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
AMP PEAK 15(13Q12.2) CNV	122	53	50
AMP PEAK 15(13Q12.2) WILD-TYPE	21	60	41

Figure S29. Get High-res Image Gene #15: 'Amp Peak 15(13q12.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 15(13q12.2)' versus 'MRNASEQ_CNMF'

P value = 2.13e-10 (Fisher's exact test), Q value = 1.5e-07

Table S30. Gene #15: 'Amp Peak 15(13q12.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	81	56	66
AMP PEAK 15(13Q12.2) CNV	29	66	37	19
AMP PEAK 15(13Q12.2) WILD-TYPE	9	15	19	47

Figure S30. Get High-res Image Gene #15: 'Amp Peak 15(13q12.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 15(13q12.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.08e-06 (Fisher's exact test), Q value = 7e-04

Table S31. Gene #15: 'Amp Peak 15(13q12.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	67	79
AMP PEAK 15(13Q12.2) CNV	64	25	62
AMP PEAK 15(13Q12.2) WILD-TYPE	31	42	17

Figure S31. Get High-res Image Gene #15: 'Amp Peak 15(13q12.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 16(13q22.1)' versus 'MRNA_CNMF'

P value = 7.58e-06 (Fisher's exact test), Q value = 0.0048

Table S32. Gene #16: 'Amp Peak 16(13q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	62	69	39
AMP PEAK 16(13Q22.1) CNV	21	47	54	15
AMP PEAK 16(13Q22.1) WILD-TYPE	24	15	15	24

Figure S32. Get High-res Image Gene #16: 'Amp Peak 16(13q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 16(13q22.1)' versus 'MRNA_CHIERARCHICAL'

P value = 7.24e-05 (Fisher's exact test), Q value = 0.044

Table S33. Gene #16: 'Amp Peak 16(13q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	61	114	40
AMP PEAK 16(13Q22.1) CNV	25	81	31
AMP PEAK 16(13Q22.1) WILD-TYPE	36	33	9

Figure S33. Get High-res Image Gene #16: 'Amp Peak 16(13q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 16(13q22.1)' versus 'CN_CNMF'

P value = 7.69e-42 (Fisher's exact test), Q value = 5.7e-39

Table S34. Gene #16: 'Amp Peak 16(13q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 16(13Q22.1) CNV	193	88	66	24
AMP PEAK 16(13Q22.1) WILD-TYPE	7	146	34	17

Figure S34. Get High-res Image Gene #16: 'Amp Peak 16(13q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 16(13q22.1)' versus 'METHLYATION_CNMF'

P value = 2.99e-09 (Fisher's exact test), Q value = 2e-06

Table S35. Gene #16: 'Amp Peak 16(13q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
AMP PEAK 16(13Q22.1) CNV	121	58	51
AMP PEAK 16(13Q22.1) WILD-TYPE	22	55	40

Figure S35. Get High-res Image Gene #16: 'Amp Peak 16(13q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 16(13q22.1)' versus 'MRNASEQ_CNMF'

P value = 9.82e-10 (Fisher's exact test), Q value = 6.7e-07

Table S36. Gene #16: 'Amp Peak 16(13q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	81	56	66
AMP PEAK 16(13Q22.1) CNV	30	69	35	23
AMP PEAK 16(13Q22.1) WILD-TYPE	8	12	21	43

Figure S36. Get High-res Image Gene #16: 'Amp Peak 16(13q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 16(13q22.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.36e-07 (Fisher's exact test), Q value = 0.00035

Table S37. Gene #16: 'Amp Peak 16(13q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	67	79
AMP PEAK 16(13Q22.1) CNV	65	27	65
AMP PEAK 16(13Q22.1) WILD-TYPE	30	40	14

Figure S37. Get High-res Image Gene #16: 'Amp Peak 16(13q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 18(16p11.2)' versus 'CN_CNMF'

P value = 1.33e-20 (Fisher's exact test), Q value = 9.7e-18

Table S38. Gene #18: 'Amp Peak 18(16p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 18(16P11.2) CNV	101	22	25	13
AMP PEAK 18(16P11.2) WILD-TYPE	99	212	75	28

Figure S38. Get High-res Image Gene #18: 'Amp Peak 18(16p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 18(16p11.2)' versus 'MRNASEQ_CNMF'

P value = 2.17e-05 (Fisher's exact test), Q value = 0.013

Table S39. Gene #18: 'Amp Peak 18(16p11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	81	56	66
AMP PEAK 18(16P11.2) CNV	9	34	16	5
AMP PEAK 18(16P11.2) WILD-TYPE	29	47	40	61

Figure S39. Get High-res Image Gene #18: 'Amp Peak 18(16p11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 19(17q12)' versus 'CN_CNMF'

P value = 3.46e-09 (Fisher's exact test), Q value = 2.3e-06

Table S40. Gene #19: 'Amp Peak 19(17q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 19(17Q12) CNV	69	27	36	12
AMP PEAK 19(17Q12) WILD-TYPE	131	207	64	29

Figure S40. Get High-res Image Gene #19: 'Amp Peak 19(17q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 19(17q12)' versus 'MRNASEQ_CNMF'

P value = 0.000424 (Fisher's exact test), Q value = 0.25

Table S41. Gene #19: 'Amp Peak 19(17q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	81	56	66
AMP PEAK 19(17Q12) CNV	8	33	10	8
AMP PEAK 19(17Q12) WILD-TYPE	30	48	46	58

Figure S41. Get High-res Image Gene #19: 'Amp Peak 19(17q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 20(17q24.1)' versus 'CN_CNMF'

P value = 1.54e-08 (Fisher's exact test), Q value = 1e-05

Table S42. Gene #20: 'Amp Peak 20(17q24.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 20(17Q24.1) CNV	67	24	29	8
AMP PEAK 20(17Q24.1) WILD-TYPE	133	210	71	33

Figure S42. Get High-res Image Gene #20: 'Amp Peak 20(17q24.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 20(17q24.1)' versus 'METHLYATION_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.21

Table S43. Gene #20: 'Amp Peak 20(17q24.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
AMP PEAK 20(17Q24.1) CNV	47	20	11
AMP PEAK 20(17Q24.1) WILD-TYPE	96	93	80

Figure S43. Get High-res Image Gene #20: 'Amp Peak 20(17q24.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 20(17q24.1)' versus 'MRNASEQ_CNMF'

P value = 0.000201 (Fisher's exact test), Q value = 0.12

Table S44. Gene #20: 'Amp Peak 20(17q24.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	81	56	66
AMP PEAK 20(17Q24.1) CNV	9	32	7	8
AMP PEAK 20(17Q24.1) WILD-TYPE	29	49	49	58

Figure S44. Get High-res Image Gene #20: 'Amp Peak 20(17q24.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 21(19p13.2)' versus 'CN_CNMF'

P value = 8.87e-08 (Fisher's exact test), Q value = 5.8e-05

Table S45. Gene #21: 'Amp Peak 21(19p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 21(19P13.2) CNV	54	16	17	10
AMP PEAK 21(19P13.2) WILD-TYPE	146	218	83	31

Figure S45. Get High-res Image Gene #21: 'Amp Peak 21(19p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 22(19q12)' versus 'CN_CNMF'

P value = 6.23e-08 (Fisher's exact test), Q value = 4.1e-05

Table S46. Gene #22: 'Amp Peak 22(19q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 22(19Q12) CNV	68	25	19	10
AMP PEAK 22(19Q12) WILD-TYPE	132	209	81	31

Figure S46. Get High-res Image Gene #22: 'Amp Peak 22(19q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 23(20p11.23)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000401 (Fisher's exact test), Q value = 0.23

Table S47. Gene #23: 'Amp Peak 23(20p11.23)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	61	114	40
AMP PEAK 23(20P11.23) CNV	18	66	25
AMP PEAK 23(20P11.23) WILD-TYPE	43	48	15

Figure S47. Get High-res Image Gene #23: 'Amp Peak 23(20p11.23)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 23(20p11.23)' versus 'CN_CNMF'

P value = 5.56e-17 (Fisher's exact test), Q value = 4e-14

Table S48. Gene #23: 'Amp Peak 23(20p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 23(20P11.23) CNV	120	85	55	41
AMP PEAK 23(20P11.23) WILD-TYPE	80	149	45	0

Figure S48. Get High-res Image Gene #23: 'Amp Peak 23(20p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 23(20p11.23)' versus 'MRNASEQ_CNMF'

P value = 1.06e-05 (Fisher's exact test), Q value = 0.0066

Table S49. Gene #23: 'Amp Peak 23(20p11.23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	81	56	66
AMP PEAK 23(20P11.23) CNV	21	54	26	17
AMP PEAK 23(20P11.23) WILD-TYPE	17	27	30	49

Figure S49. Get High-res Image Gene #23: 'Amp Peak 23(20p11.23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 23(20p11.23)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.29e-05 (Fisher's exact test), Q value = 0.014

Table S50. Gene #23: 'Amp Peak 23(20p11.23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	67	79
AMP PEAK 23(20P11.23) CNV	49	18	51
AMP PEAK 23(20P11.23) WILD-TYPE	46	49	28

Figure S50. Get High-res Image Gene #23: 'Amp Peak 23(20p11.23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 24(20p11.21)' versus 'MRNA_CNMF'

P value = 0.000239 (Fisher's exact test), Q value = 0.14

Table S51. Gene #24: 'Amp Peak 24(20p11.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	62	69	39
AMP PEAK 24(20P11.21) CNV	17	42	49	16
AMP PEAK 24(20P11.21) WILD-TYPE	28	20	20	23

Figure S51. Get High-res Image Gene #24: 'Amp Peak 24(20p11.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 24(20p11.21)' versus 'MRNA_CHIERARCHICAL'

P value = 1.54e-06 (Fisher's exact test), Q value = 0.00099

Table S52. Gene #24: 'Amp Peak 24(20p11.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	61	114	40
AMP PEAK 24(20P11.21) CNV	19	74	31
AMP PEAK 24(20P11.21) WILD-TYPE	42	40	9

Figure S52. Get High-res Image Gene #24: 'Amp Peak 24(20p11.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 24(20p11.21)' versus 'CN_CNMF'

P value = 8.57e-23 (Fisher's exact test), Q value = 6.3e-20

Table S53. Gene #24: 'Amp Peak 24(20p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 24(20P11.21) CNV	150	88	60	41
AMP PEAK 24(20P11.21) WILD-TYPE	50	146	40	0

Figure S53. Get High-res Image Gene #24: 'Amp Peak 24(20p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 24(20p11.21)' versus 'METHLYATION_CNMF'

P value = 6.98e-06 (Fisher's exact test), Q value = 0.0044

Table S54. Gene #24: 'Amp Peak 24(20p11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
AMP PEAK 24(20P11.21) CNV	107	55	45
AMP PEAK 24(20P11.21) WILD-TYPE	36	58	46

Figure S54. Get High-res Image Gene #24: 'Amp Peak 24(20p11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 24(20p11.21)' versus 'MRNASEQ_CNMF'

P value = 4.83e-09 (Fisher's exact test), Q value = 3.2e-06

Table S55. Gene #24: 'Amp Peak 24(20p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	81	56	66
AMP PEAK 24(20P11.21) CNV	22	63	33	17
AMP PEAK 24(20P11.21) WILD-TYPE	16	18	23	49

Figure S55. Get High-res Image Gene #24: 'Amp Peak 24(20p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 24(20p11.21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.8e-09 (Fisher's exact test), Q value = 2.6e-06

Table S56. Gene #24: 'Amp Peak 24(20p11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	67	79
AMP PEAK 24(20P11.21) CNV	56	18	61
AMP PEAK 24(20P11.21) WILD-TYPE	39	49	18

Figure S56. Get High-res Image Gene #24: 'Amp Peak 24(20p11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 25(20q11.21)' versus 'MRNA_CNMF'

P value = 4.15e-15 (Fisher's exact test), Q value = 2.9e-12

Table S57. Gene #25: 'Amp Peak 25(20q11.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	62	69	39
AMP PEAK 25(20Q11.21) CNV	19	61	63	21
AMP PEAK 25(20Q11.21) WILD-TYPE	26	1	6	18

Figure S57. Get High-res Image Gene #25: 'Amp Peak 25(20q11.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 25(20q11.21)' versus 'MRNA_CHIERARCHICAL'

P value = 7.48e-14 (Fisher's exact test), Q value = 5.2e-11

Table S58. Gene #25: 'Amp Peak 25(20q11.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	61	114	40
AMP PEAK 25(20Q11.21) CNV	24	103	37
AMP PEAK 25(20Q11.21) WILD-TYPE	37	11	3

Figure S58. Get High-res Image Gene #25: 'Amp Peak 25(20q11.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 25(20q11.21)' versus 'CN_CNMF'

P value = 1.54e-42 (Fisher's exact test), Q value = 1.1e-39

Table S59. Gene #25: 'Amp Peak 25(20q11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 25(20Q11.21) CNV	199	116	83	41
AMP PEAK 25(20Q11.21) WILD-TYPE	1	118	17	0

Figure S59. Get High-res Image Gene #25: 'Amp Peak 25(20q11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 25(20q11.21)' versus 'METHLYATION_CNMF'

P value = 2.13e-16 (Fisher's exact test), Q value = 1.5e-13

Table S60. Gene #25: 'Amp Peak 25(20q11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
AMP PEAK 25(20Q11.21) CNV	139	65	62
AMP PEAK 25(20Q11.21) WILD-TYPE	4	48	29

Figure S60. Get High-res Image Gene #25: 'Amp Peak 25(20q11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 25(20q11.21)' versus 'MRNASEQ_CNMF'

P value = 1.59e-19 (Fisher's exact test), Q value = 1.2e-16

Table S61. Gene #25: 'Amp Peak 25(20q11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	81	56	66
AMP PEAK 25(20Q11.21) CNV	31	80	45	22
AMP PEAK 25(20Q11.21) WILD-TYPE	7	1	11	44

Figure S61. Get High-res Image Gene #25: 'Amp Peak 25(20q11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 25(20q11.21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.25e-18 (Fisher's exact test), Q value = 3.8e-15

Table S62. Gene #25: 'Amp Peak 25(20q11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	67	79
AMP PEAK 25(20Q11.21) CNV	75	25	78
AMP PEAK 25(20Q11.21) WILD-TYPE	20	42	1

Figure S62. Get High-res Image Gene #25: 'Amp Peak 25(20q11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 26(20q12)' versus 'MRNA_CNMF'

P value = 3.23e-16 (Fisher's exact test), Q value = 2.3e-13

Table S63. Gene #26: 'Amp Peak 26(20q12)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	62	69	39
AMP PEAK 26(20Q12) CNV	18	61	63	20
AMP PEAK 26(20Q12) WILD-TYPE	27	1	6	19

Figure S63. Get High-res Image Gene #26: 'Amp Peak 26(20q12)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 26(20q12)' versus 'MRNA_CHIERARCHICAL'

P value = 3.27e-15 (Fisher's exact test), Q value = 2.3e-12

Table S64. Gene #26: 'Amp Peak 26(20q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	61	114	40
AMP PEAK 26(20Q12) CNV	22	103	37
AMP PEAK 26(20Q12) WILD-TYPE	39	11	3

Figure S64. Get High-res Image Gene #26: 'Amp Peak 26(20q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 26(20q12)' versus 'CN_CNMF'

P value = 5.84e-43 (Fisher's exact test), Q value = 4.3e-40

Table S65. Gene #26: 'Amp Peak 26(20q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 26(20Q12) CNV	199	116	85	41
AMP PEAK 26(20Q12) WILD-TYPE	1	118	15	0

Figure S65. Get High-res Image Gene #26: 'Amp Peak 26(20q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 26(20q12)' versus 'METHLYATION_CNMF'

P value = 3.56e-15 (Fisher's exact test), Q value = 2.5e-12

Table S66. Gene #26: 'Amp Peak 26(20q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
AMP PEAK 26(20Q12) CNV	139	68	63
AMP PEAK 26(20Q12) WILD-TYPE	4	45	28

Figure S66. Get High-res Image Gene #26: 'Amp Peak 26(20q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 26(20q12)' versus 'MRNASEQ_CNMF'

P value = 5.42e-19 (Fisher's exact test), Q value = 3.9e-16

Table S67. Gene #26: 'Amp Peak 26(20q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	81	56	66
AMP PEAK 26(20Q12) CNV	31	80	46	23
AMP PEAK 26(20Q12) WILD-TYPE	7	1	10	43

Figure S67. Get High-res Image Gene #26: 'Amp Peak 26(20q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 26(20q12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.81e-17 (Fisher's exact test), Q value = 1.3e-14

Table S68. Gene #26: 'Amp Peak 26(20q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	67	79
AMP PEAK 26(20Q12) CNV	76	26	78
AMP PEAK 26(20Q12) WILD-TYPE	19	41	1

Figure S68. Get High-res Image Gene #26: 'Amp Peak 26(20q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 27(20q13.32)' versus 'MRNA_CNMF'

P value = 2.88e-15 (Fisher's exact test), Q value = 2e-12

Table S69. Gene #27: 'Amp Peak 27(20q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	62	69	39
AMP PEAK 27(20Q13.32) CNV	19	61	64	22
AMP PEAK 27(20Q13.32) WILD-TYPE	26	1	5	17

Figure S69. Get High-res Image Gene #27: 'Amp Peak 27(20q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 27(20q13.32)' versus 'MRNA_CHIERARCHICAL'

P value = 1.25e-13 (Fisher's exact test), Q value = 8.7e-11

Table S70. Gene #27: 'Amp Peak 27(20q13.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	61	114	40
AMP PEAK 27(20Q13.32) CNV	25	104	37
AMP PEAK 27(20Q13.32) WILD-TYPE	36	10	3

Figure S70. Get High-res Image Gene #27: 'Amp Peak 27(20q13.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 27(20q13.32)' versus 'CN_CNMF'

P value = 5.66e-43 (Fisher's exact test), Q value = 4.2e-40

Table S71. Gene #27: 'Amp Peak 27(20q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 27(20Q13.32) CNV	199	117	87	41
AMP PEAK 27(20Q13.32) WILD-TYPE	1	117	13	0

Figure S71. Get High-res Image Gene #27: 'Amp Peak 27(20q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 27(20q13.32)' versus 'METHLYATION_CNMF'

P value = 3.21e-14 (Fisher's exact test), Q value = 2.2e-11

Table S72. Gene #27: 'Amp Peak 27(20q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
AMP PEAK 27(20Q13.32) CNV	138	68	63
AMP PEAK 27(20Q13.32) WILD-TYPE	5	45	28

Figure S72. Get High-res Image Gene #27: 'Amp Peak 27(20q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 27(20q13.32)' versus 'MRNASEQ_CNMF'

P value = 5.42e-19 (Fisher's exact test), Q value = 3.9e-16

Table S73. Gene #27: 'Amp Peak 27(20q13.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	81	56	66
AMP PEAK 27(20Q13.32) CNV	31	80	46	23
AMP PEAK 27(20Q13.32) WILD-TYPE	7	1	10	43

Figure S73. Get High-res Image Gene #27: 'Amp Peak 27(20q13.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 27(20q13.32)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.81e-17 (Fisher's exact test), Q value = 1.3e-14

Table S74. Gene #27: 'Amp Peak 27(20q13.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	67	79
AMP PEAK 27(20Q13.32) CNV	76	26	78
AMP PEAK 27(20Q13.32) WILD-TYPE	19	41	1

Figure S74. Get High-res Image Gene #27: 'Amp Peak 27(20q13.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 28(Xq28)' versus 'CN_CNMF'

P value = 1.72e-06 (Fisher's exact test), Q value = 0.0011

Table S75. Gene #28: 'Amp Peak 28(Xq28)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 28(XQ28) CNV	51	25	32	13
AMP PEAK 28(XQ28) WILD-TYPE	149	209	68	28

Figure S75. Get High-res Image Gene #28: 'Amp Peak 28(Xq28)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 7.45e-05 (Fisher's exact test), Q value = 0.045

Table S76. Gene #29: 'Del Peak 1(1p36.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	62	69	39
DEL PEAK 1(1P36.11) CNV	15	36	34	6
DEL PEAK 1(1P36.11) WILD-TYPE	30	26	35	33

Figure S76. Get High-res Image Gene #29: 'Del Peak 1(1p36.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

P value = 2.21e-13 (Fisher's exact test), Q value = 1.5e-10

Table S77. Gene #29: 'Del Peak 1(1p36.11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 1(1P36.11) CNV	110	52	34	26
DEL PEAK 1(1P36.11) WILD-TYPE	90	182	66	15

Figure S77. Get High-res Image Gene #29: 'Del Peak 1(1p36.11)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 2.1e-05 (Fisher's exact test), Q value = 0.013

Table S78. Gene #29: 'Del Peak 1(1p36.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
DEL PEAK 1(1P36.11) CNV	72	26	29
DEL PEAK 1(1P36.11) WILD-TYPE	71	87	62

Figure S78. Get High-res Image Gene #29: 'Del Peak 1(1p36.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 1.05e-05 (Fisher's exact test), Q value = 0.0066

Table S79. Gene #29: 'Del Peak 1(1p36.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	81	56	66
DEL PEAK 1(1P36.11) CNV	15	40	27	9
DEL PEAK 1(1P36.11) WILD-TYPE	23	41	29	57

Figure S79. Get High-res Image Gene #29: 'Del Peak 1(1p36.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 6.54e-05 (Fisher's exact test), Q value = 0.04

Table S80. Gene #29: 'Del Peak 1(1p36.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	67	79
DEL PEAK 1(1P36.11) CNV	43	11	37
DEL PEAK 1(1P36.11) WILD-TYPE	52	56	42

Figure S80. Get High-res Image Gene #29: 'Del Peak 1(1p36.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 2(1p33)' versus 'CN_CNMF'

P value = 8.95e-13 (Fisher's exact test), Q value = 6.2e-10

Table S81. Gene #30: 'Del Peak 2(1p33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 2(1P33) CNV	83	37	14	22
DEL PEAK 2(1P33) WILD-TYPE	117	197	86	19

Figure S81. Get High-res Image Gene #30: 'Del Peak 2(1p33)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 2(1p33)' versus 'METHLYATION_CNMF'

P value = 0.000371 (Fisher's exact test), Q value = 0.22

Table S82. Gene #30: 'Del Peak 2(1p33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
DEL PEAK 2(1P33) CNV	53	17	25
DEL PEAK 2(1P33) WILD-TYPE	90	96	66

Figure S82. Get High-res Image Gene #30: 'Del Peak 2(1p33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 3.38e-09 (Fisher's exact test), Q value = 2.3e-06

Table S83. Gene #31: 'Del Peak 3(1p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 3(1P13.2) CNV	82	39	18	18
DEL PEAK 3(1P13.2) WILD-TYPE	118	195	82	23

Figure S83. Get High-res Image Gene #31: 'Del Peak 3(1p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 10(4p16.1)' versus 'CN_CNMF'

P value = 1.65e-12 (Fisher's exact test), Q value = 1.1e-09

Table S84. Gene #38: 'Del Peak 10(4p16.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 10(4P16.1) CNV	92	40	26	24
DEL PEAK 10(4P16.1) WILD-TYPE	108	194	74	17

Figure S84. Get High-res Image Gene #38: 'Del Peak 10(4p16.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 10(4p16.1)' versus 'MRNASEQ_CNMF'

P value = 1.32e-06 (Fisher's exact test), Q value = 0.00085

Table S85. Gene #38: 'Del Peak 10(4p16.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	81	56	66
DEL PEAK 10(4P16.1) CNV	15	28	27	5
DEL PEAK 10(4P16.1) WILD-TYPE	23	53	29	61

Figure S85. Get High-res Image Gene #38: 'Del Peak 10(4p16.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 10(4p16.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000143 (Fisher's exact test), Q value = 0.086

Table S86. Gene #38: 'Del Peak 10(4p16.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	67	79
DEL PEAK 10(4P16.1) CNV	38	8	29
DEL PEAK 10(4P16.1) WILD-TYPE	57	59	50

Figure S86. Get High-res Image Gene #38: 'Del Peak 10(4p16.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 11(4q22.1)' versus 'CN_CNMF'

P value = 1.25e-14 (Fisher's exact test), Q value = 8.8e-12

Table S87. Gene #39: 'Del Peak 11(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 11(4Q22.1) CNV	101	43	28	26
DEL PEAK 11(4Q22.1) WILD-TYPE	99	191	72	15

Figure S87. Get High-res Image Gene #39: 'Del Peak 11(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 11(4q22.1)' versus 'METHLYATION_CNMF'

P value = 7.66e-05 (Fisher's exact test), Q value = 0.046

Table S88. Gene #39: 'Del Peak 11(4q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
DEL PEAK 11(4Q22.1) CNV	64	22	34
DEL PEAK 11(4Q22.1) WILD-TYPE	79	91	57

Figure S88. Get High-res Image Gene #39: 'Del Peak 11(4q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 11(4q22.1)' versus 'MRNASEQ_CNMF'

P value = 7.1e-06 (Fisher's exact test), Q value = 0.0045

Table S89. Gene #39: 'Del Peak 11(4q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	81	56	66
DEL PEAK 11(4Q22.1) CNV	16	33	27	7
DEL PEAK 11(4Q22.1) WILD-TYPE	22	48	29	59

Figure S89. Get High-res Image Gene #39: 'Del Peak 11(4q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 11(4q22.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.11

Table S90. Gene #39: 'Del Peak 11(4q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	67	79
DEL PEAK 11(4Q22.1) CNV	42	10	31
DEL PEAK 11(4Q22.1) WILD-TYPE	53	57	48

Figure S90. Get High-res Image Gene #39: 'Del Peak 11(4q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 12(4q35.1)' versus 'CN_CNMF'

P value = 1.25e-13 (Fisher's exact test), Q value = 8.7e-11

Table S91. Gene #40: 'Del Peak 12(4q35.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 12(4Q35.1) CNV	105	46	35	25
DEL PEAK 12(4Q35.1) WILD-TYPE	95	188	65	16

Figure S91. Get High-res Image Gene #40: 'Del Peak 12(4q35.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 12(4q35.1)' versus 'MRNASEQ_CNMF'

P value = 5.07e-05 (Fisher's exact test), Q value = 0.031

Table S92. Gene #40: 'Del Peak 12(4q35.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	81	56	66
DEL PEAK 12(4Q35.1) CNV	17	37	28	10
DEL PEAK 12(4Q35.1) WILD-TYPE	21	44	28	56

Figure S92. Get High-res Image Gene #40: 'Del Peak 12(4q35.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 12(4q35.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.74e-05 (Fisher's exact test), Q value = 0.023

Table S93. Gene #40: 'Del Peak 12(4q35.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	67	79
DEL PEAK 12(4Q35.1) CNV	42	11	39
DEL PEAK 12(4Q35.1) WILD-TYPE	53	56	40

Figure S93. Get High-res Image Gene #40: 'Del Peak 12(4q35.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 13(5q11.2)' versus 'CN_CNMF'

P value = 2.13e-12 (Fisher's exact test), Q value = 1.5e-09

Table S94. Gene #41: 'Del Peak 13(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 13(5Q11.2) CNV	69	23	27	21
DEL PEAK 13(5Q11.2) WILD-TYPE	131	211	73	20

Figure S94. Get High-res Image Gene #41: 'Del Peak 13(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 13(5q11.2)' versus 'MRNASEQ_CNMF'

P value = 0.000317 (Fisher's exact test), Q value = 0.19

Table S95. Gene #41: 'Del Peak 13(5q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	81	56	66
DEL PEAK 13(5Q11.2) CNV	11	26	16	4
DEL PEAK 13(5Q11.2) WILD-TYPE	27	55	40	62

Figure S95. Get High-res Image Gene #41: 'Del Peak 13(5q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 14(5q22.2)' versus 'CN_CNMF'

P value = 2.23e-09 (Fisher's exact test), Q value = 1.5e-06

Table S96. Gene #42: 'Del Peak 14(5q22.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 14(5Q22.2) CNV	80	38	32	22
DEL PEAK 14(5Q22.2) WILD-TYPE	120	196	68	19

Figure S96. Get High-res Image Gene #42: 'Del Peak 14(5q22.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 2.13e-34 (Fisher's exact test), Q value = 1.6e-31

Table S97. Gene #46: 'Del Peak 18(8p23.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 18(8P23.2) CNV	135	42	77	18
DEL PEAK 18(8P23.2) WILD-TYPE	65	192	23	23

Figure S97. Get High-res Image Gene #46: 'Del Peak 18(8p23.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 1.96e-06 (Fisher's exact test), Q value = 0.0012

Table S98. Gene #46: 'Del Peak 18(8p23.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
DEL PEAK 18(8P23.2) CNV	89	35	38
DEL PEAK 18(8P23.2) WILD-TYPE	54	78	53

Figure S98. Get High-res Image Gene #46: 'Del Peak 18(8p23.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 1.52e-05 (Fisher's exact test), Q value = 0.0094

Table S99. Gene #46: 'Del Peak 18(8p23.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	81	56	66
DEL PEAK 18(8P23.2) CNV	20	48	30	14
DEL PEAK 18(8P23.2) WILD-TYPE	18	33	26	52

Figure S99. Get High-res Image Gene #46: 'Del Peak 18(8p23.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 19(8p22)' versus 'CN_CNMF'

P value = 1.58e-37 (Fisher's exact test), Q value = 1.2e-34

Table S100. Gene #47: 'Del Peak 19(8p22)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 19(8P22) CNV	142	44	80	19
DEL PEAK 19(8P22) WILD-TYPE	58	190	20	22

Figure S100. Get High-res Image Gene #47: 'Del Peak 19(8p22)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 19(8p22)' versus 'METHLYATION_CNMF'

P value = 1.32e-06 (Fisher's exact test), Q value = 0.00085

Table S101. Gene #47: 'Del Peak 19(8p22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
DEL PEAK 19(8P22) CNV	94	39	39
DEL PEAK 19(8P22) WILD-TYPE	49	74	52

Figure S101. Get High-res Image Gene #47: 'Del Peak 19(8p22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 19(8p22)' versus 'MRNASEQ_CNMF'

P value = 1.05e-06 (Fisher's exact test), Q value = 0.00068

Table S102. Gene #47: 'Del Peak 19(8p22)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	81	56	66
DEL PEAK 19(8P22) CNV	22	51	32	14
DEL PEAK 19(8P22) WILD-TYPE	16	30	24	52

Figure S102. Get High-res Image Gene #47: 'Del Peak 19(8p22)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 19(8p22)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000223 (Fisher's exact test), Q value = 0.13

Table S103. Gene #47: 'Del Peak 19(8p22)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	67	79
DEL PEAK 19(8P22) CNV	56	19	44
DEL PEAK 19(8P22) WILD-TYPE	39	48	35

Figure S103. Get High-res Image Gene #47: 'Del Peak 19(8p22)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 20(8p11.21)' versus 'CN_CNMF'

P value = 4.85e-07 (Fisher's exact test), Q value = 0.00032

Table S104. Gene #48: 'Del Peak 20(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 20(8P11.21) CNV	68	28	18	10
DEL PEAK 20(8P11.21) WILD-TYPE	132	206	82	31

Figure S104. Get High-res Image Gene #48: 'Del Peak 20(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 23(10p15.3)' versus 'CN_CNMF'

P value = 1.38e-07 (Fisher's exact test), Q value = 9e-05

Table S105. Gene #51: 'Del Peak 23(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 23(10P15.3) CNV	41	21	21	19
DEL PEAK 23(10P15.3) WILD-TYPE	159	213	79	22

Figure S105. Get High-res Image Gene #51: 'Del Peak 23(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 24(10q21.1)' versus 'CN_CNMF'

P value = 3.13e-11 (Fisher's exact test), Q value = 2.2e-08

Table S106. Gene #52: 'Del Peak 24(10q21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 24(10Q21.1) CNV	49	20	27	22
DEL PEAK 24(10Q21.1) WILD-TYPE	151	214	73	19

Figure S106. Get High-res Image Gene #52: 'Del Peak 24(10q21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 25(10q23.31)' versus 'CN_CNMF'

P value = 9.09e-08 (Fisher's exact test), Q value = 6e-05

Table S107. Gene #53: 'Del Peak 25(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 25(10Q23.31) CNV	55	35	32	23
DEL PEAK 25(10Q23.31) WILD-TYPE	145	199	68	18

Figure S107. Get High-res Image Gene #53: 'Del Peak 25(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 26(10q25.2)' versus 'CN_CNMF'

P value = 3.06e-12 (Fisher's exact test), Q value = 2.1e-09

Table S108. Gene #54: 'Del Peak 26(10q25.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 26(10Q25.2) CNV	56	30	26	28
DEL PEAK 26(10Q25.2) WILD-TYPE	144	204	74	13

Figure S108. Get High-res Image Gene #54: 'Del Peak 26(10q25.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 26(10q25.2)' versus 'MRNASEQ_CNMF'

P value = 0.000239 (Fisher's exact test), Q value = 0.14

Table S109. Gene #54: 'Del Peak 26(10q25.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	81	56	66
DEL PEAK 26(10Q25.2) CNV	11	26	17	4
DEL PEAK 26(10Q25.2) WILD-TYPE	27	55	39	62

Figure S109. Get High-res Image Gene #54: 'Del Peak 26(10q25.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 26(10q25.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000324 (Fisher's exact test), Q value = 0.19

Table S110. Gene #54: 'Del Peak 26(10q25.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	67	79
DEL PEAK 26(10Q25.2) CNV	28	5	25
DEL PEAK 26(10Q25.2) WILD-TYPE	67	62	54

Figure S110. Get High-res Image Gene #54: 'Del Peak 26(10q25.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 28(12p13.1)' versus 'CN_CNMF'

P value = 3.89e-08 (Fisher's exact test), Q value = 2.6e-05

Table S111. Gene #56: 'Del Peak 28(12p13.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 28(12P13.1) CNV	44	10	13	10
DEL PEAK 28(12P13.1) WILD-TYPE	156	224	87	31

Figure S111. Get High-res Image Gene #56: 'Del Peak 28(12p13.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 29(12q21.2)' versus 'CN_CNMF'

P value = 5.52e-07 (Fisher's exact test), Q value = 0.00036

Table S112. Gene #57: 'Del Peak 29(12q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 29(12Q21.2) CNV	45	13	12	10
DEL PEAK 29(12Q21.2) WILD-TYPE	155	221	88	31

Figure S112. Get High-res Image Gene #57: 'Del Peak 29(12q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 30(14q22.1)' versus 'MRNA_CNMF'

P value = 0.000117 (Fisher's exact test), Q value = 0.071

Table S113. Gene #58: 'Del Peak 30(14q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	62	69	39
DEL PEAK 30(14Q22.1) CNV	10	31	30	5
DEL PEAK 30(14Q22.1) WILD-TYPE	35	31	39	34

Figure S113. Get High-res Image Gene #58: 'Del Peak 30(14q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 30(14q22.1)' versus 'MRNA_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.072

Table S114. Gene #58: 'Del Peak 30(14q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	61	114	40
DEL PEAK 30(14Q22.1) CNV	9	47	20
DEL PEAK 30(14Q22.1) WILD-TYPE	52	67	20

Figure S114. Get High-res Image Gene #58: 'Del Peak 30(14q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 30(14q22.1)' versus 'CN_CNMF'

P value = 1.95e-28 (Fisher's exact test), Q value = 1.4e-25

Table S115. Gene #58: 'Del Peak 30(14q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 30(14Q22.1) CNV	124	31	17	13
DEL PEAK 30(14Q22.1) WILD-TYPE	76	203	83	28

Figure S115. Get High-res Image Gene #58: 'Del Peak 30(14q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 30(14q22.1)' versus 'METHLYATION_CNMF'

P value = 8.14e-06 (Fisher's exact test), Q value = 0.0051

Table S116. Gene #58: 'Del Peak 30(14q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
DEL PEAK 30(14Q22.1) CNV	63	19	24
DEL PEAK 30(14Q22.1) WILD-TYPE	80	94	67

Figure S116. Get High-res Image Gene #58: 'Del Peak 30(14q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 30(14q22.1)' versus 'RPPA_CNMF'

P value = 0.000318 (Fisher's exact test), Q value = 0.19

Table S117. Gene #58: 'Del Peak 30(14q22.1)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	115	184	33	119
DEL PEAK 30(14Q22.1) CNV	39	78	7	24
DEL PEAK 30(14Q22.1) WILD-TYPE	76	106	26	95

Figure S117. Get High-res Image Gene #58: 'Del Peak 30(14q22.1)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 30(14q22.1)' versus 'MRNASEQ_CNMF'

P value = 4.09e-08 (Fisher's exact test), Q value = 2.7e-05

Table S118. Gene #58: 'Del Peak 30(14q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	81	56	66
DEL PEAK 30(14Q22.1) CNV	14	40	16	4
DEL PEAK 30(14Q22.1) WILD-TYPE	24	41	40	62

Figure S118. Get High-res Image Gene #58: 'Del Peak 30(14q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 30(14q22.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.08e-05 (Fisher's exact test), Q value = 0.019

Table S119. Gene #58: 'Del Peak 30(14q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	67	79
DEL PEAK 30(14Q22.1) CNV	34	7	33
DEL PEAK 30(14Q22.1) WILD-TYPE	61	60	46

Figure S119. Get High-res Image Gene #58: 'Del Peak 30(14q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 31(15q11.2)' versus 'CN_CNMF'

P value = 1.2e-23 (Fisher's exact test), Q value = 8.8e-21

Table S120. Gene #59: 'Del Peak 31(15q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 31(15Q11.2) CNV	122	41	40	30
DEL PEAK 31(15Q11.2) WILD-TYPE	78	193	60	11

Figure S120. Get High-res Image Gene #59: 'Del Peak 31(15q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 31(15q11.2)' versus 'MRNASEQ_CNMF'

P value = 1.41e-06 (Fisher's exact test), Q value = 0.00091

Table S121. Gene #59: 'Del Peak 31(15q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	81	56	66
DEL PEAK 31(15Q11.2) CNV	16	45	24	9
DEL PEAK 31(15Q11.2) WILD-TYPE	22	36	32	57

Figure S121. Get High-res Image Gene #59: 'Del Peak 31(15q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 31(15q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.38e-05 (Fisher's exact test), Q value = 0.0085

Table S122. Gene #59: 'Del Peak 31(15q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	67	79
DEL PEAK 31(15Q11.2) CNV	42	11	41
DEL PEAK 31(15Q11.2) WILD-TYPE	53	56	38

Figure S122. Get High-res Image Gene #59: 'Del Peak 31(15q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 32(15q21.1)' versus 'CN_CNMF'

P value = 2.43e-21 (Fisher's exact test), Q value = 1.8e-18

Table S123. Gene #60: 'Del Peak 32(15q21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 32(15Q21.1) CNV	117	41	40	29
DEL PEAK 32(15Q21.1) WILD-TYPE	83	193	60	12

Figure S123. Get High-res Image Gene #60: 'Del Peak 32(15q21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 32(15q21.1)' versus 'MRNASEQ_CNMF'

P value = 2.2e-07 (Fisher's exact test), Q value = 0.00014

Table S124. Gene #60: 'Del Peak 32(15q21.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	81	56	66
DEL PEAK 32(15Q21.1) CNV	16	44	21	7
DEL PEAK 32(15Q21.1) WILD-TYPE	22	37	35	59

Figure S124. Get High-res Image Gene #60: 'Del Peak 32(15q21.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 32(15q21.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.3e-05 (Fisher's exact test), Q value = 0.014

Table S125. Gene #60: 'Del Peak 32(15q21.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	67	79
DEL PEAK 32(15Q21.1) CNV	39	10	39
DEL PEAK 32(15Q21.1) WILD-TYPE	56	57	40

Figure S125. Get High-res Image Gene #60: 'Del Peak 32(15q21.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 33(15q22.33)' versus 'CN_CNMF'

P value = 4.49e-23 (Fisher's exact test), Q value = 3.3e-20

Table S126. Gene #61: 'Del Peak 33(15q22.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 33(15Q22.33) CNV	113	35	40	29
DEL PEAK 33(15Q22.33) WILD-TYPE	87	199	60	12

Figure S126. Get High-res Image Gene #61: 'Del Peak 33(15q22.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 33(15q22.33)' versus 'MRNASEQ_CNMF'

P value = 5.81e-09 (Fisher's exact test), Q value = 3.9e-06

Table S127. Gene #61: 'Del Peak 33(15q22.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	81	56	66
DEL PEAK 33(15Q22.33) CNV	15	44	24	5
DEL PEAK 33(15Q22.33) WILD-TYPE	23	37	32	61

Figure S127. Get High-res Image Gene #61: 'Del Peak 33(15q22.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 33(15q22.33)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.5e-06 (Fisher's exact test), Q value = 0.0035

Table S128. Gene #61: 'Del Peak 33(15q22.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	67	79
DEL PEAK 33(15Q22.33) CNV	40	9	39
DEL PEAK 33(15Q22.33) WILD-TYPE	55	58	40

Figure S128. Get High-res Image Gene #61: 'Del Peak 33(15q22.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 36(17p12)' versus 'MRNA_CNMF'

P value = 6.93e-08 (Fisher's exact test), Q value = 4.6e-05

Table S129. Gene #64: 'Del Peak 36(17p12)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	62	69	39
DEL PEAK 36(17P12) CNV	18	50	51	13
DEL PEAK 36(17P12) WILD-TYPE	27	12	18	26

Figure S129. Get High-res Image Gene #64: 'Del Peak 36(17p12)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 36(17p12)' versus 'MRNA_CHIERARCHICAL'

P value = 2.79e-05 (Fisher's exact test), Q value = 0.017

Table S130. Gene #64: 'Del Peak 36(17p12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	61	114	40
DEL PEAK 36(17P12) CNV	23	78	31
DEL PEAK 36(17P12) WILD-TYPE	38	36	9

Figure S130. Get High-res Image Gene #64: 'Del Peak 36(17p12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 36(17p12)' versus 'CN_CNMF'

P value = 2.01e-34 (Fisher's exact test), Q value = 1.5e-31

Table S131. Gene #64: 'Del Peak 36(17p12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 36(17P12) CNV	169	69	75	30
DEL PEAK 36(17P12) WILD-TYPE	31	165	25	11

Figure S131. Get High-res Image Gene #64: 'Del Peak 36(17p12)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 36(17p12)' versus 'METHLYATION_CNMF'

P value = 6.04e-09 (Fisher's exact test), Q value = 4e-06

Table S132. Gene #64: 'Del Peak 36(17p12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
DEL PEAK 36(17P12) CNV	112	50	44
DEL PEAK 36(17P12) WILD-TYPE	31	63	47

Figure S132. Get High-res Image Gene #64: 'Del Peak 36(17p12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 36(17p12)' versus 'MRNASEQ_CNMF'

P value = 1.6e-08 (Fisher's exact test), Q value = 1.1e-05

Table S133. Gene #64: 'Del Peak 36(17p12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	81	56	66
DEL PEAK 36(17P12) CNV	26	60	35	17
DEL PEAK 36(17P12) WILD-TYPE	12	21	21	49

Figure S133. Get High-res Image Gene #64: 'Del Peak 36(17p12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 36(17p12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.32e-06 (Fisher's exact test), Q value = 0.0021

Table S134. Gene #64: 'Del Peak 36(17p12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	67	79
DEL PEAK 36(17P12) CNV	58	22	58
DEL PEAK 36(17P12) WILD-TYPE	37	45	21

Figure S134. Get High-res Image Gene #64: 'Del Peak 36(17p12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 38(18p11.31)' versus 'MRNA_CNMF'

P value = 5.53e-13 (Fisher's exact test), Q value = 3.8e-10

Table S135. Gene #66: 'Del Peak 38(18p11.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	62	69	39
DEL PEAK 38(18P11.31) CNV	12	52	52	11
DEL PEAK 38(18P11.31) WILD-TYPE	33	10	17	28

Figure S135. Get High-res Image Gene #66: 'Del Peak 38(18p11.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 38(18p11.31)' versus 'MRNA_CHIERARCHICAL'

P value = 2.35e-09 (Fisher's exact test), Q value = 1.6e-06

Table S136. Gene #66: 'Del Peak 38(18p11.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	61	114	40
DEL PEAK 38(18P11.31) CNV	16	79	32
DEL PEAK 38(18P11.31) WILD-TYPE	45	35	8

Figure S136. Get High-res Image Gene #66: 'Del Peak 38(18p11.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 38(18p11.31)' versus 'CN_CNMF'

P value = 1.19e-41 (Fisher's exact test), Q value = 8.8e-39

Table S137. Gene #66: 'Del Peak 38(18p11.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 38(18P11.31) CNV	176	65	64	36
DEL PEAK 38(18P11.31) WILD-TYPE	24	169	36	5

Figure S137. Get High-res Image Gene #66: 'Del Peak 38(18p11.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 38(18p11.31)' versus 'METHLYATION_CNMF'

P value = 2.31e-15 (Fisher's exact test), Q value = 1.7e-12

Table S138. Gene #66: 'Del Peak 38(18p11.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
DEL PEAK 38(18P11.31) CNV	120	40	49
DEL PEAK 38(18P11.31) WILD-TYPE	23	73	42

Figure S138. Get High-res Image Gene #66: 'Del Peak 38(18p11.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 38(18p11.31)' versus 'MRNASEQ_CNMF'

P value = 1.4e-20 (Fisher's exact test), Q value = 1e-17

Table S139. Gene #66: 'Del Peak 38(18p11.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	81	56	66
DEL PEAK 38(18P11.31) CNV	23	71	36	8
DEL PEAK 38(18P11.31) WILD-TYPE	15	10	20	58

Figure S139. Get High-res Image Gene #66: 'Del Peak 38(18p11.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 38(18p11.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.08e-15 (Fisher's exact test), Q value = 3.6e-12

Table S140. Gene #66: 'Del Peak 38(18p11.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	67	79
DEL PEAK 38(18P11.31) CNV	62	12	64
DEL PEAK 38(18P11.31) WILD-TYPE	33	55	15

Figure S140. Get High-res Image Gene #66: 'Del Peak 38(18p11.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 39(18q12.2)' versus 'MRNA_CNMF'

P value = 9.64e-10 (Fisher's exact test), Q value = 6.6e-07

Table S141. Gene #67: 'Del Peak 39(18q12.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	62	69	39
DEL PEAK 39(18Q12.2) CNV	19	54	56	15
DEL PEAK 39(18Q12.2) WILD-TYPE	26	8	13	24

Figure S141. Get High-res Image Gene #67: 'Del Peak 39(18q12.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 39(18q12.2)' versus 'MRNA_CHIERARCHICAL'

P value = 7.31e-08 (Fisher's exact test), Q value = 4.8e-05

Table S142. Gene #67: 'Del Peak 39(18q12.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	61	114	40
DEL PEAK 39(18Q12.2) CNV	23	87	34
DEL PEAK 39(18Q12.2) WILD-TYPE	38	27	6

Figure S142. Get High-res Image Gene #67: 'Del Peak 39(18q12.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 39(18q12.2)' versus 'CN_CNMF'

P value = 1.29e-49 (Fisher's exact test), Q value = 9.7e-47

Table S143. Gene #67: 'Del Peak 39(18q12.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 39(18Q12.2) CNV	187	76	86	37
DEL PEAK 39(18Q12.2) WILD-TYPE	13	158	14	4

Figure S143. Get High-res Image Gene #67: 'Del Peak 39(18q12.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 39(18q12.2)' versus 'METHLYATION_CNMF'

P value = 8.06e-18 (Fisher's exact test), Q value = 5.8e-15

Table S144. Gene #67: 'Del Peak 39(18q12.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
DEL PEAK 39(18Q12.2) CNV	132	51	52
DEL PEAK 39(18Q12.2) WILD-TYPE	11	62	39

Figure S144. Get High-res Image Gene #67: 'Del Peak 39(18q12.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 39(18q12.2)' versus 'MRNASEQ_CNMF'

P value = 2.84e-19 (Fisher's exact test), Q value = 2.1e-16

Table S145. Gene #67: 'Del Peak 39(18q12.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	81	56	66
DEL PEAK 39(18Q12.2) CNV	29	72	41	12
DEL PEAK 39(18Q12.2) WILD-TYPE	9	9	15	54

Figure S145. Get High-res Image Gene #67: 'Del Peak 39(18q12.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 39(18q12.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.22e-10 (Fisher's exact test), Q value = 8.4e-08

Table S146. Gene #67: 'Del Peak 39(18q12.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	67	79
DEL PEAK 39(18Q12.2) CNV	67	21	66
DEL PEAK 39(18Q12.2) WILD-TYPE	28	46	13

Figure S146. Get High-res Image Gene #67: 'Del Peak 39(18q12.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 40(18q21.2)' versus 'MRNA_CNMF'

P value = 3.98e-10 (Fisher's exact test), Q value = 2.7e-07

Table S147. Gene #68: 'Del Peak 40(18q21.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	62	69	39
DEL PEAK 40(18Q21.2) CNV	19	55	57	16
DEL PEAK 40(18Q21.2) WILD-TYPE	26	7	12	23

Figure S147. Get High-res Image Gene #68: 'Del Peak 40(18q21.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 40(18q21.2)' versus 'MRNA_CHIERARCHICAL'

P value = 8.24e-08 (Fisher's exact test), Q value = 5.4e-05

Table S148. Gene #68: 'Del Peak 40(18q21.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	61	114	40
DEL PEAK 40(18Q21.2) CNV	24	89	34
DEL PEAK 40(18Q21.2) WILD-TYPE	37	25	6

Figure S148. Get High-res Image Gene #68: 'Del Peak 40(18q21.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 40(18q21.2)' versus 'CN_CNMF'

P value = 1.24e-50 (Fisher's exact test), Q value = 9.3e-48

Table S149. Gene #68: 'Del Peak 40(18q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 40(18Q21.2) CNV	190	84	91	38
DEL PEAK 40(18Q21.2) WILD-TYPE	10	150	9	3

Figure S149. Get High-res Image Gene #68: 'Del Peak 40(18q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 40(18q21.2)' versus 'METHLYATION_CNMF'

P value = 3.43e-15 (Fisher's exact test), Q value = 2.4e-12

Table S150. Gene #68: 'Del Peak 40(18q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
DEL PEAK 40(18Q21.2) CNV	134	61	54
DEL PEAK 40(18Q21.2) WILD-TYPE	9	52	37

Figure S150. Get High-res Image Gene #68: 'Del Peak 40(18q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 40(18q21.2)' versus 'MRNASEQ_CNMF'

P value = 2.83e-15 (Fisher's exact test), Q value = 2e-12

Table S151. Gene #68: 'Del Peak 40(18q21.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	81	56	66
DEL PEAK 40(18Q21.2) CNV	29	73	42	18
DEL PEAK 40(18Q21.2) WILD-TYPE	9	8	14	48

Figure S151. Get High-res Image Gene #68: 'Del Peak 40(18q21.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 40(18q21.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.42e-09 (Fisher's exact test), Q value = 9.7e-07

Table S152. Gene #68: 'Del Peak 40(18q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	67	79
DEL PEAK 40(18Q21.2) CNV	69	25	68
DEL PEAK 40(18Q21.2) WILD-TYPE	26	42	11

Figure S152. Get High-res Image Gene #68: 'Del Peak 40(18q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 41(18q22.1)' versus 'MRNA_CNMF'

P value = 2.43e-09 (Fisher's exact test), Q value = 1.6e-06

Table S153. Gene #69: 'Del Peak 41(18q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	45	62	69	39
DEL PEAK 41(18Q22.1) CNV	19	55	56	17
DEL PEAK 41(18Q22.1) WILD-TYPE	26	7	13	22

Figure S153. Get High-res Image Gene #69: 'Del Peak 41(18q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 41(18q22.1)' versus 'MRNA_CHIERARCHICAL'

P value = 2.07e-06 (Fisher's exact test), Q value = 0.0013

Table S154. Gene #69: 'Del Peak 41(18q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	61	114	40
DEL PEAK 41(18Q22.1) CNV	26	87	34
DEL PEAK 41(18Q22.1) WILD-TYPE	35	27	6

Figure S154. Get High-res Image Gene #69: 'Del Peak 41(18q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 41(18q22.1)' versus 'CN_CNMF'

P value = 9.55e-53 (Fisher's exact test), Q value = 7.2e-50

Table S155. Gene #69: 'Del Peak 41(18q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 41(18Q22.1) CNV	190	80	89	39
DEL PEAK 41(18Q22.1) WILD-TYPE	10	154	11	2

Figure S155. Get High-res Image Gene #69: 'Del Peak 41(18q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 41(18q22.1)' versus 'METHLYATION_CNMF'

P value = 1.37e-15 (Fisher's exact test), Q value = 9.8e-13

Table S156. Gene #69: 'Del Peak 41(18q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
DEL PEAK 41(18Q22.1) CNV	133	59	52
DEL PEAK 41(18Q22.1) WILD-TYPE	10	54	39

Figure S156. Get High-res Image Gene #69: 'Del Peak 41(18q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 41(18q22.1)' versus 'MRNASEQ_CNMF'

P value = 2.83e-15 (Fisher's exact test), Q value = 2e-12

Table S157. Gene #69: 'Del Peak 41(18q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	81	56	66
DEL PEAK 41(18Q22.1) CNV	29	73	42	18
DEL PEAK 41(18Q22.1) WILD-TYPE	9	8	14	48

Figure S157. Get High-res Image Gene #69: 'Del Peak 41(18q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 41(18q22.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.84e-09 (Fisher's exact test), Q value = 3.9e-06

Table S158. Gene #69: 'Del Peak 41(18q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	67	79
DEL PEAK 41(18Q22.1) CNV	68	26	68
DEL PEAK 41(18Q22.1) WILD-TYPE	27	41	11

Figure S158. Get High-res Image Gene #69: 'Del Peak 41(18q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 42(19p13.3)' versus 'CN_CNMF'

P value = 1.35e-05 (Fisher's exact test), Q value = 0.0084

Table S159. Gene #70: 'Del Peak 42(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 42(19P13.3) CNV	44	17	21	10
DEL PEAK 42(19P13.3) WILD-TYPE	156	217	79	31

Figure S159. Get High-res Image Gene #70: 'Del Peak 42(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 43(19q13.43)' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.067

Table S160. Gene #71: 'Del Peak 43(19q13.43)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 43(19Q13.43) CNV	28	13	16	11
DEL PEAK 43(19Q13.43) WILD-TYPE	172	221	84	30

Figure S160. Get High-res Image Gene #71: 'Del Peak 43(19q13.43)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 44(20p12.1)' versus 'CN_CNMF'

P value = 6.5e-15 (Fisher's exact test), Q value = 4.6e-12

Table S161. Gene #72: 'Del Peak 44(20p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 44(20P12.1) CNV	96	46	37	0
DEL PEAK 44(20P12.1) WILD-TYPE	104	188	63	41

Figure S161. Get High-res Image Gene #72: 'Del Peak 44(20p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 44(20p12.1)' versus 'METHLYATION_CNMF'

P value = 1.01e-05 (Fisher's exact test), Q value = 0.0063

Table S162. Gene #72: 'Del Peak 44(20p12.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
DEL PEAK 44(20P12.1) CNV	63	21	20
DEL PEAK 44(20P12.1) WILD-TYPE	80	92	71

Figure S162. Get High-res Image Gene #72: 'Del Peak 44(20p12.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 45(20p12.1)' versus 'CN_CNMF'

P value = 6.5e-15 (Fisher's exact test), Q value = 4.6e-12

Table S163. Gene #73: 'Del Peak 45(20p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 45(20P12.1) CNV	96	46	37	0
DEL PEAK 45(20P12.1) WILD-TYPE	104	188	63	41

Figure S163. Get High-res Image Gene #73: 'Del Peak 45(20p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 45(20p12.1)' versus 'METHLYATION_CNMF'

P value = 1.01e-05 (Fisher's exact test), Q value = 0.0063

Table S164. Gene #73: 'Del Peak 45(20p12.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
DEL PEAK 45(20P12.1) CNV	63	21	20
DEL PEAK 45(20P12.1) WILD-TYPE	80	92	71

Figure S164. Get High-res Image Gene #73: 'Del Peak 45(20p12.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 46(21q11.2)' versus 'CN_CNMF'

P value = 4.07e-09 (Fisher's exact test), Q value = 2.7e-06

Table S165. Gene #74: 'Del Peak 46(21q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 46(21Q11.2) CNV	95	50	28	22
DEL PEAK 46(21Q11.2) WILD-TYPE	105	184	72	19

Figure S165. Get High-res Image Gene #74: 'Del Peak 46(21q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 47(22q13.32)' versus 'CN_CNMF'

P value = 9.83e-15 (Fisher's exact test), Q value = 6.9e-12

Table S166. Gene #75: 'Del Peak 47(22q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 47(22Q13.32) CNV	108	45	28	23
DEL PEAK 47(22Q13.32) WILD-TYPE	92	189	72	18

Figure S166. Get High-res Image Gene #75: 'Del Peak 47(22q13.32)' versus Molecular Subtype #3: '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 = COADREAD-TP.transferedmergedcluster.txt
Number of patients = 575
Number of copy number variation regions = 75
Number of molecular subtypes = 10
Exclude regions that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

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.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

[3] GISTIC_version2

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