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 76 peak regions and 12 molecular subtypes across 589 patients, 207 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 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.
Amp Peak 3(5p12) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_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', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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' and 'MRNASEQ_CNMF'.
Amp Peak 10(8q24.21) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'MRNASEQ_CNMF'.
Amp Peak 12(11p15.5) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 14(13q12.13) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Amp Peak 15(13q12.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Amp Peak 16(13q22.1) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Amp Peak 18(16p11.2) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 19(17q12) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 20(17q24.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_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 'CN_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
Amp Peak 24(20q11.21) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Amp Peak 25(20q12) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 26(20q13.32) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 27(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_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 11(4q22.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 12(4q35.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 13(5q11.2) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
Del Peak 14(5q22.2) cnvs correlated to 'CN_CNMF'.
Del Peak 18(8p23.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 19(8p23.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 20(8p22) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 21(8q11.1) 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' and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 28(12p13.1) cnvs correlated to 'CN_CNMF'.
Del Peak 29(12q21.31) cnvs correlated to 'CN_CNMF'.
Del Peak 30(14q11.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 31(14q31.1) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 32(14q31.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 33(15q11.2) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 34(15q21.1) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 35(15q22.33) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 38(17p12) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 40(18p11.31) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 41(18q12.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 42(18q21.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 43(18q22.1) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 44(19p13.3) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 45(19q13.43) cnvs correlated to 'CN_CNMF'.
Del Peak 46(20p12.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 47(20p12.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 48(21q11.2) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
Del Peak 49(22q13.32) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 76 regions and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 207 significant findings detected.


		Molecular subtypes	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
Amp Peak 25(20q12)	0 (0%)	138	1.06e-14 (9.2e-12)	4.18e-14 (3.62e-11)	1.08e-36 (9.7e-34)	4.84e-17 (4.25e-14)	0.0112 (1.00)	0.00555 (1.00)	1.76e-16 (1.55e-13)	2.08e-19 (1.84e-16)	0.00736 (1.00)	0.0543 (1.00)	2.72e-13 (2.33e-10)	6.6e-05 (0.0493)
Amp Peak 26(20q13 32)	0 (0%)	135	7.8e-14 (6.73e-11)	2.02e-12 (1.71e-09)	7.3e-37 (6.55e-34)	4.58e-16 (4e-13)	0.0142 (1.00)	0.0044 (1.00)	1.76e-16 (1.55e-13)	2.08e-19 (1.84e-16)	0.015 (1.00)	0.114 (1.00)	3.19e-12 (2.7e-09)	6.6e-05 (0.0493)
Del Peak 40(18p11 31)	0 (0%)	239	5.8e-12 (4.9e-09)	6.24e-10 (5.23e-07)	1.03e-44 (9.31e-42)	4.9e-18 (4.32e-15)	0.0417 (1.00)	0.0305 (1.00)	2.25e-16 (1.97e-13)	2.42e-15 (2.11e-12)	0.00459 (1.00)	0.651 (1.00)	1e-14 (8.7e-12)	0.000237 (0.169)
Del Peak 41(18q12 2)	0 (0%)	194	1.01e-09 (8.38e-07)	4.59e-09 (3.79e-06)	1.14e-52 (1.03e-49)	1.59e-20 (1.41e-17)	0.0342 (1.00)	0.028 (1.00)	1.77e-15 (1.54e-12)	4.76e-13 (4.07e-10)	0.000883 (0.604)	0.0891 (1.00)	6.25e-15 (5.44e-12)	0.00022 (0.158)
Del Peak 42(18q21 2)	0 (0%)	177	3.72e-10 (3.12e-07)	1.64e-08 (1.35e-05)	5.32e-54 (4.85e-51)	1.14e-17 (1e-14)	0.0149 (1.00)	0.0247 (1.00)	1.68e-13 (1.44e-10)	3.46e-13 (2.96e-10)	7.08e-05 (0.0526)	0.178 (1.00)	7.99e-13 (6.81e-10)	0.000697 (0.483)
Del Peak 43(18q22 1)	0 (0%)	182	2.01e-09 (1.67e-06)	1.23e-07 (9.94e-05)	4.47e-56 (4.07e-53)	3.8e-18 (3.35e-15)	0.0313 (1.00)	0.02 (1.00)	3.84e-13 (3.28e-10)	1.07e-12 (9.07e-10)	6.66e-05 (0.0496)	0.377 (1.00)	2.13e-13 (1.82e-10)	0.027 (1.00)
Amp Peak 14(13q12 13)	0 (0%)	208	1.92e-07 (0.000155)	4.12e-06 (0.00324)	5.16e-41 (4.66e-38)	1.05e-11 (8.87e-09)	0.0221 (1.00)	0.064 (1.00)	1.94e-07 (0.000156)	1.13e-08 (9.31e-06)	0.00043 (0.302)	0.438 (1.00)	9.89e-10 (8.21e-07)	0.00135 (0.9)
Amp Peak 15(13q12 2)	0 (0%)	213	4.65e-06 (0.00365)	5.25e-05 (0.0393)	6.93e-43 (6.26e-40)	2.31e-12 (1.95e-09)	0.0243 (1.00)	0.169 (1.00)	2.74e-07 (0.000219)	4.66e-09 (3.84e-06)	0.00114 (0.767)	0.497 (1.00)	2.74e-09 (2.26e-06)	0.0125 (1.00)
Amp Peak 16(13q22 1)	0 (0%)	208	9.73e-06 (0.00755)	0.000193 (0.14)	2.14e-39 (1.92e-36)	3.91e-10 (3.28e-07)	0.115 (1.00)	0.174 (1.00)	4.91e-07 (0.000392)	2.12e-08 (1.74e-05)	0.000941 (0.641)	0.248 (1.00)	1.21e-07 (9.75e-05)	0.041 (1.00)
Amp Peak 24(20q11 21)	0 (0%)	140	1.19e-13 (1.02e-10)	9.59e-13 (8.15e-10)	4.45e-36 (3.99e-33)	1.99e-18 (1.75e-15)	0.00688 (1.00)	0.0103 (1.00)	4.46e-17 (3.92e-14)	2.24e-20 (1.99e-17)	0.0173 (1.00)	0.164 (1.00)	9.09e-13 (7.74e-10)	0.000733 (0.508)
Del Peak 19(8p23 2)	0 (0%)	312	0.000258 (0.183)	0.000146 (0.107)	3.44e-51 (3.13e-48)	1.01e-07 (8.2e-05)	0.15 (1.00)	0.00316 (1.00)	2.6e-06 (0.00206)	8.32e-07 (0.000661)	0.219 (1.00)	0.0901 (1.00)	7.67e-06 (0.00597)	0.00566 (1.00)
Del Peak 30(14q11 2)	0 (0%)	396	3.66e-05 (0.0276)	5.71e-06 (0.00447)	1.81e-40 (1.63e-37)	5e-05 (0.0376)	0.00366 (1.00)	0.186 (1.00)	4e-06 (0.00315)	9.43e-05 (0.0697)	0.0609 (1.00)	0.6 (1.00)	7.63e-07 (0.000608)	0.076 (1.00)
Del Peak 38(17p12)	0 (0%)	240	8.38e-08 (6.8e-05)	2.2e-05 (0.0168)	9.96e-35 (8.91e-32)	5.81e-09 (4.79e-06)	0.00858 (1.00)	0.0247 (1.00)	1.5e-07 (0.000121)	1.89e-09 (1.56e-06)	0.0157 (1.00)	0.0543 (1.00)	2.48e-08 (2.02e-05)	0.156 (1.00)
Amp Peak 12(11p15 5)	0 (0%)	457	0.000202 (0.146)	0.000684 (0.476)	4.8e-05 (0.0361)	0.00191 (1.00)	0.0294 (1.00)	0.238 (1.00)	9.96e-05 (0.0735)	5.09e-05 (0.0382)	0.437 (1.00)	0.973 (1.00)	0.000195 (0.141)	2.57e-06 (0.00203)
Del Peak 31(14q31 1)	0 (0%)	391	0.000773 (0.533)	0.000257 (0.183)	4.82e-38 (4.34e-35)	0.000105 (0.0774)	0.000694 (0.482)	0.0357 (1.00)	1.56e-05 (0.012)	0.000244 (0.174)	0.266 (1.00)	0.572 (1.00)	3.16e-07 (0.000252)	0.0778 (1.00)
Amp Peak 6(7p21 3)	0 (0%)	245	0.0023 (1.00)	0.000932 (0.636)	5.48e-20 (4.86e-17)	3.32e-06 (0.00262)	0.0305 (1.00)	0.0266 (1.00)	3.18e-08 (2.59e-05)	2.22e-07 (0.000178)	0.0065 (1.00)	0.00219 (1.00)	3.58e-06 (0.00282)	0.303 (1.00)
Del Peak 1(1p36 11)	0 (0%)	365	0.000114 (0.084)	0.00379 (1.00)	7.78e-13 (6.63e-10)	4.56e-06 (0.00358)	0.0596 (1.00)	0.148 (1.00)	0.000172 (0.125)	0.000138 (0.101)	0.45 (1.00)	0.876 (1.00)	0.0142 (1.00)	0.0241 (1.00)
Del Peak 18(8p23 3)	0 (0%)	312	0.00168 (1.00)	0.000518 (0.364)	3.05e-47 (2.77e-44)	4.19e-07 (0.000335)	0.0792 (1.00)	0.00533 (1.00)	7.5e-06 (0.00584)	2.34e-06 (0.00185)	0.175 (1.00)	0.184 (1.00)	1.62e-05 (0.0124)	0.00856 (1.00)
Del Peak 20(8p22)	0 (0%)	299	0.00118 (0.794)	0.000857 (0.587)	5.79e-54 (5.27e-51)	7.97e-08 (6.47e-05)	0.109 (1.00)	0.00225 (1.00)	1.15e-05 (0.00891)	1.49e-06 (0.00118)	0.273 (1.00)	0.0369 (1.00)	2.24e-05 (0.0171)	0.00119 (0.796)
Del Peak 32(14q31 1)	0 (0%)	387	0.00123 (0.824)	0.000653 (0.457)	1.62e-37 (1.45e-34)	4.57e-05 (0.0345)	0.00106 (0.717)	0.0472 (1.00)	1.12e-05 (0.00867)	7.35e-05 (0.0546)	0.402 (1.00)	0.682 (1.00)	1.15e-07 (9.27e-05)	0.107 (1.00)
Del Peak 35(15q22 33)	0 (0%)	369	0.000199 (0.144)	0.00116 (0.781)	5.8e-21 (5.17e-18)	0.00187 (1.00)	0.586 (1.00)	0.463 (1.00)	3.29e-05 (0.0249)	6.57e-06 (0.00513)	0.792 (1.00)	0.466 (1.00)	2.58e-05 (0.0196)	0.202 (1.00)
Amp Peak 20(17q24 1)	0 (0%)	458	0.0257 (1.00)	0.00126 (0.84)	1.9e-10 (1.6e-07)	0.000341 (0.241)	0.0805 (1.00)	0.00558 (1.00)	0.00314 (1.00)	0.000186 (0.135)	0.000148 (0.108)	0.163 (1.00)	0.414 (1.00)	0.248 (1.00)
Del Peak 33(15q11 2)	0 (0%)	353	0.000821 (0.565)	0.00487 (1.00)	3.16e-21 (2.82e-18)	0.00498 (1.00)	0.213 (1.00)	0.359 (1.00)	0.000148 (0.108)	2.46e-05 (0.0187)	0.392 (1.00)	0.149 (1.00)	4.91e-06 (0.00384)	0.648 (1.00)
Amp Peak 10(8q24 21)	0 (0%)	237	0.239 (1.00)	0.000227 (0.162)	2.31e-45 (2.09e-42)	0.0028 (1.00)	0.0214 (1.00)	0.283 (1.00)	1.63e-05 (0.0125)	0.000792 (0.545)	0.18 (1.00)	0.173 (1.00)	0.00134 (0.894)	0.111 (1.00)
Amp Peak 18(16p11 2)	0 (0%)	427	0.0179 (1.00)	0.00574 (1.00)	1.6e-20 (1.43e-17)	0.000541 (0.379)	0.0141 (1.00)	0.0157 (1.00)	1.37e-05 (0.0106)	2.59e-05 (0.0197)	0.576 (1.00)	0.838 (1.00)	0.000407 (0.287)	0.122 (1.00)
Amp Peak 23(20p11 23)	0 (0%)	283	0.00346 (1.00)	0.00265 (1.00)	1.69e-08 (1.39e-05)	0.0196 (1.00)	0.00588 (1.00)	0.226 (1.00)	0.000164 (0.119)	0.000695 (0.482)	0.311 (1.00)	0.226 (1.00)	0.000142 (0.104)	0.165 (1.00)
Del Peak 10(4p16 1)	0 (0%)	402	0.0654 (1.00)	0.437 (1.00)	7.65e-14 (6.61e-11)	0.0015 (0.995)	0.402 (1.00)	0.923 (1.00)	0.00477 (1.00)	2.3e-05 (0.0175)	0.438 (1.00)	0.073 (1.00)	0.00025 (0.178)	0.188 (1.00)
Del Peak 12(4q35 1)	0 (0%)	374	0.021 (1.00)	0.17 (1.00)	2.24e-14 (1.94e-11)	6.21e-05 (0.0465)	0.295 (1.00)	0.888 (1.00)	0.00174 (1.00)	0.00669 (1.00)	0.325 (1.00)	0.0368 (1.00)	7.68e-05 (0.0569)	0.0112 (1.00)
Del Peak 34(15q21 1)	0 (0%)	360	0.000836 (0.574)	0.0239 (1.00)	4.96e-19 (4.39e-16)	0.0107 (1.00)	0.106 (1.00)	0.13 (1.00)	0.00025 (0.178)	0.000673 (0.469)	0.655 (1.00)	0.267 (1.00)	0.000104 (0.0768)	0.599 (1.00)
Amp Peak 2(2q33 1)	0 (0%)	462	0.0883 (1.00)	0.000319 (0.227)	0.00034 (0.241)	0.00322 (1.00)	0.229 (1.00)	0.901 (1.00)	0.00186 (1.00)	0.0177 (1.00)	0.0684 (1.00)	0.0243 (1.00)	0.17 (1.00)	0.129 (1.00)
Amp Peak 3(5p12)	0 (0%)	480	0.0977 (1.00)	0.435 (1.00)	2.48e-06 (0.00196)	0.851 (1.00)	0.00103 (0.697)	0.721 (1.00)	0.000844 (0.579)	0.000635 (0.444)	0.914 (1.00)	0.683 (1.00)	5.42e-05 (0.0406)	0.129 (1.00)
Amp Peak 9(8q12 1)	0 (0%)	274	0.143 (1.00)	0.000749 (0.518)	4.53e-44 (4.1e-41)	0.0248 (1.00)	0.0219 (1.00)	0.0546 (1.00)	2.55e-05 (0.0194)	0.00929 (1.00)	0.165 (1.00)	0.165 (1.00)	0.00572 (1.00)	0.0305 (1.00)
Amp Peak 19(17q12)	0 (0%)	442	0.0443 (1.00)	0.0276 (1.00)	8.55e-10 (7.12e-07)	0.00329 (1.00)	0.136 (1.00)	0.0592 (1.00)	0.0011 (0.745)	2.93e-05 (0.0221)	0.00639 (1.00)	0.183 (1.00)	0.264 (1.00)	0.288 (1.00)
Del Peak 2(1p33)	0 (0%)	432	0.0306 (1.00)	0.0913 (1.00)	7.12e-12 (6.01e-09)	0.000353 (0.249)	0.859 (1.00)	0.574 (1.00)	0.0065 (1.00)	0.00344 (1.00)	0.585 (1.00)	0.157 (1.00)	0.00955 (1.00)	0.00219 (1.00)
Del Peak 11(4q22 1)	0 (0%)	385	0.0216 (1.00)	0.031 (1.00)	2.06e-14 (1.79e-11)	1.79e-05 (0.0137)	0.541 (1.00)	0.77 (1.00)	0.00123 (0.822)	0.0124 (1.00)	0.0339 (1.00)	0.00687 (1.00)	0.00263 (1.00)	0.0392 (1.00)
Del Peak 13(5q11 2)	0 (0%)	446	0.0006 (0.42)	0.00466 (1.00)	3.45e-11 (2.9e-08)	0.00121 (0.81)	0.0205 (1.00)	0.547 (1.00)	0.0312 (1.00)	0.0203 (1.00)	0.839 (1.00)	0.0282 (1.00)	6.68e-06 (0.00521)	0.00364 (1.00)
Del Peak 26(10q25 2)	0 (0%)	447	0.318 (1.00)	0.162 (1.00)	6.62e-09 (5.45e-06)	0.0399 (1.00)	0.00431 (1.00)	0.245 (1.00)	0.00163 (1.00)	0.000241 (0.172)	0.991 (1.00)	0.00305 (1.00)	0.00155 (1.00)	0.036 (1.00)
Del Peak 44(19p13 3)	0 (0%)	496	0.117 (1.00)	0.151 (1.00)	2.61e-05 (0.0198)	0.657 (1.00)	0.88 (1.00)	0.666 (1.00)	0.371 (1.00)	0.317 (1.00)	0.517 (1.00)	9.99e-05 (0.0736)	0.0206 (1.00)	0.0148 (1.00)
Del Peak 46(20p12 1)	0 (0%)	408	0.0197 (1.00)	0.0203 (1.00)	6.56e-10 (5.49e-07)	1.27e-05 (0.00984)	0.741 (1.00)	0.00712 (1.00)	0.0251 (1.00)	0.00489 (1.00)	0.0873 (1.00)	0.103 (1.00)	0.0964 (1.00)	0.0827 (1.00)
Del Peak 47(20p12 1)	0 (0%)	408	0.0197 (1.00)	0.0203 (1.00)	6.56e-10 (5.49e-07)	1.27e-05 (0.00984)	0.741 (1.00)	0.00712 (1.00)	0.0251 (1.00)	0.00489 (1.00)	0.0873 (1.00)	0.103 (1.00)	0.0964 (1.00)	0.0827 (1.00)
Del Peak 48(21q11 2)	0 (0%)	389	0.0224 (1.00)	0.0216 (1.00)	5.74e-08 (4.68e-05)	0.00779 (1.00)	0.574 (1.00)	0.213 (1.00)	0.00148 (0.986)	0.00401 (1.00)	0.0413 (1.00)	0.336 (1.00)	0.00022 (0.158)	0.0832 (1.00)
Del Peak 49(22q13 32)	0 (0%)	378	0.00476 (1.00)	0.00578 (1.00)	1.15e-13 (9.93e-11)	0.0165 (1.00)	0.469 (1.00)	0.617 (1.00)	0.046 (1.00)	0.029 (1.00)	0.936 (1.00)	0.638 (1.00)	0.000177 (0.128)	0.502 (1.00)
Amp Peak 1(1q31 1)	0 (0%)	452	0.584 (1.00)	0.308 (1.00)	1.38e-05 (0.0106)	0.476 (1.00)	0.369 (1.00)	0.289 (1.00)	0.89 (1.00)	0.134 (1.00)	0.441 (1.00)	0.61 (1.00)	0.0229 (1.00)	0.962 (1.00)
Amp Peak 5(6p21 1)	0 (0%)	440	0.0224 (1.00)	0.00184 (1.00)	8.62e-15 (7.5e-12)	0.122 (1.00)	0.575 (1.00)	0.369 (1.00)	0.0351 (1.00)	0.0743 (1.00)	0.252 (1.00)	0.216 (1.00)	0.00588 (1.00)	0.206 (1.00)
Amp Peak 7(8p11 23)	0 (0%)	387	0.396 (1.00)	0.0486 (1.00)	8.55e-14 (7.37e-11)	0.373 (1.00)	0.732 (1.00)	0.5 (1.00)	0.109 (1.00)	0.142 (1.00)	0.0174 (1.00)	0.139 (1.00)	0.103 (1.00)	0.202 (1.00)
Amp Peak 8(8p11 21)	0 (0%)	345	0.173 (1.00)	0.00854 (1.00)	5.41e-25 (4.83e-22)	0.279 (1.00)	0.7 (1.00)	0.394 (1.00)	0.0435 (1.00)	0.158 (1.00)	0.103 (1.00)	0.147 (1.00)	0.446 (1.00)	0.399 (1.00)
Amp Peak 21(19p13 2)	0 (0%)	489	0.108 (1.00)	0.437 (1.00)	2.1e-07 (0.000169)	0.0101 (1.00)	0.663 (1.00)	0.39 (1.00)	0.0592 (1.00)	0.165 (1.00)	0.232 (1.00)	0.219 (1.00)	0.155 (1.00)	0.106 (1.00)
Amp Peak 22(19q12)	0 (0%)	465	0.0281 (1.00)	0.039 (1.00)	7.1e-08 (5.77e-05)	0.129 (1.00)	0.0809 (1.00)	0.326 (1.00)	0.0514 (1.00)	0.145 (1.00)	0.352 (1.00)	0.903 (1.00)	0.294 (1.00)	0.257 (1.00)
Amp Peak 27(Xq28)	0 (0%)	465	0.436 (1.00)	0.884 (1.00)	7.38e-05 (0.0547)	0.0816 (1.00)	0.00174 (1.00)	0.0093 (1.00)	0.095 (1.00)	0.0257 (1.00)	0.913 (1.00)	0.972 (1.00)	0.0397 (1.00)	0.596 (1.00)
Del Peak 3(1p13 2)	0 (0%)	430	0.288 (1.00)	0.129 (1.00)	7.04e-09 (5.79e-06)	0.0109 (1.00)	0.567 (1.00)	0.702 (1.00)	0.00632 (1.00)	0.00264 (1.00)	0.654 (1.00)	0.382 (1.00)	0.038 (1.00)	0.131 (1.00)
Del Peak 14(5q22 2)	0 (0%)	414	0.00106 (0.72)	0.0314 (1.00)	6.39e-10 (5.35e-07)	0.072 (1.00)	0.17 (1.00)	0.922 (1.00)	0.11 (1.00)	0.153 (1.00)	0.52 (1.00)	0.0214 (1.00)	0.000914 (0.624)	0.0518 (1.00)
Del Peak 21(8q11 1)	0 (0%)	544	0.58 (1.00)	0.557 (1.00)	0.000212 (0.152)	0.565 (1.00)	0.344 (1.00)	0.568 (1.00)	0.155 (1.00)	0.137 (1.00)	0.128 (1.00)	0.11 (1.00)	0.519 (1.00)	0.453 (1.00)
Del Peak 23(10p15 3)	0 (0%)	486	0.232 (1.00)	0.169 (1.00)	7.77e-06 (0.00604)	0.0283 (1.00)	0.0205 (1.00)	0.158 (1.00)	0.0241 (1.00)	0.000661 (0.462)	0.704 (1.00)	0.289 (1.00)	0.0621 (1.00)	0.0143 (1.00)
Del Peak 24(10q21 1)	0 (0%)	469	0.171 (1.00)	0.12 (1.00)	8.52e-10 (7.1e-07)	0.0993 (1.00)	0.0728 (1.00)	0.133 (1.00)	0.0164 (1.00)	0.0203 (1.00)	0.754 (1.00)	0.301 (1.00)	0.0233 (1.00)	0.252 (1.00)
Del Peak 25(10q23 31)	0 (0%)	441	0.136 (1.00)	0.52 (1.00)	4.43e-07 (0.000354)	0.157 (1.00)	0.061 (1.00)	0.242 (1.00)	0.00214 (1.00)	0.00417 (1.00)	0.723 (1.00)	0.0133 (1.00)	0.000965 (0.656)	0.00806 (1.00)
Del Peak 28(12p13 1)	0 (0%)	510	0.00599 (1.00)	0.0142 (1.00)	7.01e-10 (5.85e-07)	0.389 (1.00)	0.892 (1.00)	0.732 (1.00)	0.423 (1.00)	0.487 (1.00)	0.695 (1.00)	0.376 (1.00)	0.0192 (1.00)	0.168 (1.00)
Del Peak 29(12q21 31)	0 (0%)	510	0.0629 (1.00)	0.0677 (1.00)	2.72e-08 (2.22e-05)	0.144 (1.00)	0.574 (1.00)	0.591 (1.00)	0.0277 (1.00)	0.00261 (1.00)	0.718 (1.00)	0.979 (1.00)	0.0793 (1.00)	0.0291 (1.00)
Del Peak 45(19q13 43)	0 (0%)	521	0.72 (1.00)	0.219 (1.00)	9.24e-05 (0.0684)	0.298 (1.00)	0.165 (1.00)	0.937 (1.00)	0.477 (1.00)	0.143 (1.00)	0.225 (1.00)	0.13 (1.00)	0.121 (1.00)	0.577 (1.00)
Amp Peak 4(5q22 3)	0 (0%)	529	0.565 (1.00)	0.887 (1.00)	0.00619 (1.00)	0.243 (1.00)	0.662 (1.00)	0.815 (1.00)	0.15 (1.00)	0.0205 (1.00)	0.459 (1.00)	0.314 (1.00)	0.171 (1.00)	0.909 (1.00)
Amp Peak 11(10q22 3)	0 (0%)	553	1 (1.00)	0.182 (1.00)	0.779 (1.00)	0.616 (1.00)	0.297 (1.00)	0.85 (1.00)	0.779 (1.00)	0.206 (1.00)	0.435 (1.00)	0.563 (1.00)	0.00602 (1.00)	0.482 (1.00)
Amp Peak 13(12p13 32)	0 (0%)	445	0.556 (1.00)	0.787 (1.00)	0.104 (1.00)	0.0491 (1.00)	0.478 (1.00)	0.813 (1.00)	0.817 (1.00)	0.888 (1.00)	0.668 (1.00)	0.517 (1.00)	0.443 (1.00)	0.311 (1.00)
Amp Peak 17(15q26 1)	0 (0%)	545	0.527 (1.00)	0.0629 (1.00)	0.0709 (1.00)	0.77 (1.00)	0.0985 (1.00)	0.276 (1.00)	0.188 (1.00)	0.686 (1.00)	0.628 (1.00)	1 (1.00)	0.771 (1.00)	1 (1.00)
Del Peak 4(2p12)	0 (0%)	569	1 (1.00)	0.81 (1.00)	0.00169 (1.00)	0.00775 (1.00)	0.296 (1.00)	1 (1.00)	0.74 (1.00)	0.732 (1.00)	0.0108 (1.00)	0.0615 (1.00)	1 (1.00)	0.705 (1.00)
Del Peak 5(2q22 1)	0 (0%)	555	0.926 (1.00)	0.311 (1.00)	0.172 (1.00)	0.9 (1.00)	0.339 (1.00)	0.901 (1.00)	0.248 (1.00)	0.591 (1.00)	0.58 (1.00)	0.121 (1.00)	0.71 (1.00)	0.916 (1.00)
Del Peak 6(2q37 2)	0 (0%)	559	0.911 (1.00)	0.863 (1.00)	0.539 (1.00)	0.886 (1.00)	0.924 (1.00)	0.162 (1.00)	0.372 (1.00)	0.112 (1.00)	0.613 (1.00)	0.37 (1.00)	0.208 (1.00)	0.393 (1.00)
Del Peak 7(3p26 3)	0 (0%)	503	0.358 (1.00)	0.753 (1.00)	0.0414 (1.00)	0.354 (1.00)	0.562 (1.00)	0.824 (1.00)	0.259 (1.00)	0.769 (1.00)	0.692 (1.00)	0.135 (1.00)	0.0382 (1.00)	0.106 (1.00)
Del Peak 8(3p14 2)	0 (0%)	482	0.62 (1.00)	0.991 (1.00)	0.614 (1.00)	0.623 (1.00)	0.501 (1.00)	0.674 (1.00)	0.963 (1.00)	0.795 (1.00)	0.261 (1.00)	0.153 (1.00)	0.0947 (1.00)	0.754 (1.00)
Del Peak 9(3q26 31)	0 (0%)	530	0.544 (1.00)	0.788 (1.00)	0.0634 (1.00)	0.532 (1.00)	0.331 (1.00)	0.51 (1.00)	0.592 (1.00)	0.583 (1.00)	0.229 (1.00)	0.402 (1.00)	0.379 (1.00)	0.0396 (1.00)
Del Peak 15(6p25 3)	0 (0%)	511	0.907 (1.00)	0.553 (1.00)	0.4 (1.00)	0.318 (1.00)	0.0472 (1.00)	0.94 (1.00)	0.5 (1.00)	0.528 (1.00)	0.641 (1.00)	0.868 (1.00)	0.397 (1.00)	0.425 (1.00)
Del Peak 16(6q26)	0 (0%)	499	0.777 (1.00)	0.331 (1.00)	0.373 (1.00)	0.863 (1.00)	0.0471 (1.00)	0.451 (1.00)	0.687 (1.00)	0.866 (1.00)	0.423 (1.00)	0.612 (1.00)	0.424 (1.00)	0.316 (1.00)
Del Peak 17(7q31 1)	0 (0%)	574	0.292 (1.00)	0.933 (1.00)	1 (1.00)	1 (1.00)	0.873 (1.00)	0.273 (1.00)	0.712 (1.00)	1 (1.00)	0.158 (1.00)	0.488 (1.00)	0.257 (1.00)	0.761 (1.00)
Del Peak 22(9p24 2)	0 (0%)	510	0.452 (1.00)	0.299 (1.00)	0.0068 (1.00)	0.0481 (1.00)	0.564 (1.00)	0.592 (1.00)	0.233 (1.00)	0.341 (1.00)	0.27 (1.00)	0.0851 (1.00)	0.0434 (1.00)	0.26 (1.00)
Del Peak 27(11q22 3)	0 (0%)	484	0.478 (1.00)	0.0658 (1.00)	0.0743 (1.00)	0.075 (1.00)	0.26 (1.00)	0.147 (1.00)	1 (1.00)	0.963 (1.00)	0.818 (1.00)	0.742 (1.00)	0.268 (1.00)	0.545 (1.00)
Del Peak 36(16p13 3)	0 (0%)	530	0.139 (1.00)	0.119 (1.00)	0.808 (1.00)	0.617 (1.00)	0.49 (1.00)	0.789 (1.00)	0.444 (1.00)	0.117 (1.00)	0.638 (1.00)	0.233 (1.00)	0.734 (1.00)	0.544 (1.00)
Del Peak 37(16q23 1)	0 (0%)	515	0.0439 (1.00)	0.00729 (1.00)	0.311 (1.00)	0.252 (1.00)	0.221 (1.00)	0.925 (1.00)	0.408 (1.00)	0.567 (1.00)	0.726 (1.00)	0.495 (1.00)	0.556 (1.00)	0.361 (1.00)
Del Peak 39(17q24 3)	0 (0%)	503	1 (1.00)	0.224 (1.00)	0.0198 (1.00)	0.548 (1.00)	0.947 (1.00)	0.523 (1.00)	0.371 (1.00)	0.713 (1.00)	0.83 (1.00)	0.524 (1.00)	0.0331 (1.00)	0.671 (1.00)

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

P value = 1.38e-05 (Fisher's exact test), Q value = 0.011

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	186	241	147	15
AMP PEAK 1(1Q31.1) CNV	56	34	39	8
AMP PEAK 1(1Q31.1) WILD-TYPE	130	207	108	7

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 'MRNA_CHIERARCHICAL'

P value = 0.000319 (Fisher's exact test), Q value = 0.23

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	50	63	60
AMP PEAK 2(2Q33.1) CNV	13	3	6	18
AMP PEAK 2(2Q33.1) WILD-TYPE	29	47	57	42

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

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

P value = 0.00034 (Fisher's exact test), Q value = 0.24

Table S3. Gene #2: 'Amp Peak 2(2q33.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
AMP PEAK 2(2Q33.1) CNV	53	33	35	6
AMP PEAK 2(2Q33.1) WILD-TYPE	133	208	112	9

Figure S3. Get High-res Image Gene #2: 'Amp Peak 2(2q33.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 2.48e-06 (Fisher's exact test), Q value = 0.002

Table S4. Gene #3: 'Amp Peak 3(5p12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
AMP PEAK 3(5P12) CNV	51	22	31	5
AMP PEAK 3(5P12) WILD-TYPE	135	219	116	10

Figure S4. Get High-res Image Gene #3: 'Amp Peak 3(5p12)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 5.42e-05 (Fisher's exact test), Q value = 0.041

Table S5. Gene #3: 'Amp Peak 3(5p12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
AMP PEAK 3(5P12) CNV	26	6	19
AMP PEAK 3(5P12) WILD-TYPE	74	103	66

Figure S5. Get High-res Image Gene #3: 'Amp Peak 3(5p12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 8.62e-15 (Fisher's exact test), Q value = 7.5e-12

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	186	241	147	15
AMP PEAK 5(6P21.1) CNV	78	22	45	4
AMP PEAK 5(6P21.1) WILD-TYPE	108	219	102	11

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 = 5.48e-20 (Fisher's exact test), Q value = 4.9e-17

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	186	241	147	15
AMP PEAK 6(7P21.3) CNV	145	86	101	12
AMP PEAK 6(7P21.3) WILD-TYPE	41	155	46	3

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 = 3.32e-06 (Fisher's exact test), Q value = 0.0026

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	116	91
AMP PEAK 6(7P21.3) CNV	121	58	51
AMP PEAK 6(7P21.3) WILD-TYPE	35	58	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 = 3.18e-08 (Fisher's exact test), Q value = 2.6e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	103	116
AMP PEAK 6(7P21.3) CNV	67	81	49
AMP PEAK 6(7P21.3) WILD-TYPE	28	22	67

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 = 2.22e-07 (Fisher's exact test), Q value = 0.00018

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	94	136
AMP PEAK 6(7P21.3) CNV	66	69	62
AMP PEAK 6(7P21.3) WILD-TYPE	18	25	74

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

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

P value = 3.58e-06 (Fisher's exact test), Q value = 0.0028

Table S11. Gene #6: 'Amp Peak 6(7p21.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
AMP PEAK 6(7P21.3) CNV	72	49	65
AMP PEAK 6(7P21.3) WILD-TYPE	28	60	20

Figure S11. Get High-res Image Gene #6: 'Amp Peak 6(7p21.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 8.55e-14 (Fisher's exact test), Q value = 7.4e-11

Table S12. Gene #7: 'Amp Peak 7(8p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
AMP PEAK 7(8P11.23) CNV	57	50	85	10
AMP PEAK 7(8P11.23) WILD-TYPE	129	191	62	5

Figure S12. 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 = 5.41e-25 (Fisher's exact test), Q value = 4.8e-22

Table S13. Gene #8: 'Amp Peak 8(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
AMP PEAK 8(8P11.21) CNV	69	54	111	10
AMP PEAK 8(8P11.21) WILD-TYPE	117	187	36	5

Figure S13. 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 = 4.53e-44 (Fisher's exact test), Q value = 4.1e-41

Table S14. Gene #9: 'Amp Peak 9(8q12.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
AMP PEAK 9(8Q12.1) CNV	94	68	141	12
AMP PEAK 9(8Q12.1) WILD-TYPE	92	173	6	3

Figure S14. Get High-res Image Gene #9: 'Amp Peak 9(8q12.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 2.55e-05 (Fisher's exact test), Q value = 0.019

Table S15. Gene #9: 'Amp Peak 9(8q12.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	103	116
AMP PEAK 9(8Q12.1) CNV	59	70	45
AMP PEAK 9(8Q12.1) WILD-TYPE	36	33	71

Figure S15. Get High-res Image Gene #9: 'Amp Peak 9(8q12.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 0.000227 (Fisher's exact test), Q value = 0.16

Table S16. Gene #10: 'Amp Peak 10(8q24.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	50	63	60
AMP PEAK 10(8Q24.21) CNV	30	18	31	43
AMP PEAK 10(8Q24.21) WILD-TYPE	12	32	32	17

Figure S16. Get High-res Image Gene #10: 'Amp Peak 10(8q24.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

P value = 2.31e-45 (Fisher's exact test), Q value = 2.1e-42

Table S17. Gene #10: 'Amp Peak 10(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
AMP PEAK 10(8Q24.21) CNV	115	80	146	11
AMP PEAK 10(8Q24.21) WILD-TYPE	71	161	1	4

Figure S17. 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 = 1.63e-05 (Fisher's exact test), Q value = 0.013

Table S18. Gene #10: 'Amp Peak 10(8q24.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	103	116
AMP PEAK 10(8Q24.21) CNV	63	77	52
AMP PEAK 10(8Q24.21) WILD-TYPE	32	26	64

Figure S18. 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 = 0.000202 (Fisher's exact test), Q value = 0.15

Table S19. Gene #12: 'Amp Peak 12(11p15.5)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
AMP PEAK 12(11P15.5) CNV	3	20	24	4
AMP PEAK 12(11P15.5) WILD-TYPE	40	42	45	37

Figure S19. 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 = 4.8e-05 (Fisher's exact test), Q value = 0.036

Table S20. Gene #12: 'Amp Peak 12(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
AMP PEAK 12(11P15.5) CNV	50	32	44	6
AMP PEAK 12(11P15.5) WILD-TYPE	136	209	103	9

Figure S20. 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 = 9.96e-05 (Fisher's exact test), Q value = 0.073

Table S21. Gene #12: 'Amp Peak 12(11p15.5)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	103	116
AMP PEAK 12(11P15.5) CNV	21	35	12
AMP PEAK 12(11P15.5) WILD-TYPE	74	68	104

Figure S21. 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 = 5.09e-05 (Fisher's exact test), Q value = 0.038

Table S22. Gene #12: 'Amp Peak 12(11p15.5)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	94	136
AMP PEAK 12(11P15.5) CNV	24	30	14
AMP PEAK 12(11P15.5) WILD-TYPE	60	64	122

Figure S22. Get High-res Image Gene #12: 'Amp Peak 12(11p15.5)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 0.000195 (Fisher's exact test), Q value = 0.14

Table S23. Gene #12: 'Amp Peak 12(11p15.5)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
AMP PEAK 12(11P15.5) CNV	30	10	23
AMP PEAK 12(11P15.5) WILD-TYPE	70	99	62

Figure S23. Get High-res Image Gene #12: 'Amp Peak 12(11p15.5)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 2.57e-06 (Fisher's exact test), Q value = 0.002

Table S24. Gene #12: 'Amp Peak 12(11p15.5)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	105	115	41
AMP PEAK 12(11P15.5) CNV	20	19	17	7
AMP PEAK 12(11P15.5) WILD-TYPE	13	86	98	34

Figure S24. Get High-res Image Gene #12: 'Amp Peak 12(11p15.5)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 1.92e-07 (Fisher's exact test), Q value = 0.00015

Table S25. Gene #14: 'Amp Peak 14(13q12.13)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
AMP PEAK 14(13Q12.13) CNV	19	48	57	16
AMP PEAK 14(13Q12.13) WILD-TYPE	24	14	12	25

Figure S25. 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 = 4.12e-06 (Fisher's exact test), Q value = 0.0032

Table S26. Gene #14: 'Amp Peak 14(13q12.13)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	50	63	60
AMP PEAK 14(13Q12.13) CNV	36	36	25	43
AMP PEAK 14(13Q12.13) WILD-TYPE	6	14	38	17

Figure S26. 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 = 5.16e-41 (Fisher's exact test), Q value = 4.7e-38

Table S27. Gene #14: 'Amp Peak 14(13q12.13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
AMP PEAK 14(13Q12.13) CNV	180	91	100	10
AMP PEAK 14(13Q12.13) WILD-TYPE	6	150	47	5

Figure S27. 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 = 1.05e-11 (Fisher's exact test), Q value = 8.9e-09

Table S28. Gene #14: 'Amp Peak 14(13q12.13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	116	91
AMP PEAK 14(13Q12.13) CNV	133	56	49
AMP PEAK 14(13Q12.13) WILD-TYPE	23	60	42

Figure S28. 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 = 1.94e-07 (Fisher's exact test), Q value = 0.00016

Table S29. Gene #14: 'Amp Peak 14(13q12.13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	103	116
AMP PEAK 14(13Q12.13) CNV	66	84	54
AMP PEAK 14(13Q12.13) WILD-TYPE	29	19	62

Figure S29. 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 = 1.13e-08 (Fisher's exact test), Q value = 9.3e-06

Table S30. Gene #14: 'Amp Peak 14(13q12.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	94	136
AMP PEAK 14(13Q12.13) CNV	67	74	63
AMP PEAK 14(13Q12.13) WILD-TYPE	17	20	73

Figure S30. Get High-res Image Gene #14: 'Amp Peak 14(13q12.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 9.89e-10 (Fisher's exact test), Q value = 8.2e-07

Table S31. Gene #14: 'Amp Peak 14(13q12.13)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
AMP PEAK 14(13Q12.13) CNV	85	49	64
AMP PEAK 14(13Q12.13) WILD-TYPE	15	60	21

Figure S31. Get High-res Image Gene #14: 'Amp Peak 14(13q12.13)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 4.65e-06 (Fisher's exact test), Q value = 0.0036

Table S32. Gene #15: 'Amp Peak 15(13q12.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
AMP PEAK 15(13Q12.2) CNV	19	47	55	17
AMP PEAK 15(13Q12.2) WILD-TYPE	24	15	14	24

Figure S32. 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 = 5.25e-05 (Fisher's exact test), Q value = 0.039

Table S33. Gene #15: 'Amp Peak 15(13q12.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	50	63	60
AMP PEAK 15(13Q12.2) CNV	35	35	26	42
AMP PEAK 15(13Q12.2) WILD-TYPE	7	15	37	18

Figure S33. 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 = 6.93e-43 (Fisher's exact test), Q value = 6.3e-40

Table S34. Gene #15: 'Amp Peak 15(13q12.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
AMP PEAK 15(13Q12.2) CNV	180	87	99	10
AMP PEAK 15(13Q12.2) WILD-TYPE	6	154	48	5

Figure S34. 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-12 (Fisher's exact test), Q value = 2e-09

Table S35. Gene #15: 'Amp Peak 15(13q12.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	116	91
AMP PEAK 15(13Q12.2) CNV	133	54	49
AMP PEAK 15(13Q12.2) WILD-TYPE	23	62	42

Figure S35. 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 = 2.74e-07 (Fisher's exact test), Q value = 0.00022

Table S36. Gene #15: 'Amp Peak 15(13q12.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	103	116
AMP PEAK 15(13Q12.2) CNV	65	83	53
AMP PEAK 15(13Q12.2) WILD-TYPE	30	20	63

Figure S36. 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 = 4.66e-09 (Fisher's exact test), Q value = 3.8e-06

Table S37. Gene #15: 'Amp Peak 15(13q12.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	94	136
AMP PEAK 15(13Q12.2) CNV	67	73	61
AMP PEAK 15(13Q12.2) WILD-TYPE	17	21	75

Figure S37. Get High-res Image Gene #15: 'Amp Peak 15(13q12.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 2.74e-09 (Fisher's exact test), Q value = 2.3e-06

Table S38. Gene #15: 'Amp Peak 15(13q12.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
AMP PEAK 15(13Q12.2) CNV	83	48	64
AMP PEAK 15(13Q12.2) WILD-TYPE	17	61	21

Figure S38. Get High-res Image Gene #15: 'Amp Peak 15(13q12.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 9.73e-06 (Fisher's exact test), Q value = 0.0075

Table S39. Gene #16: 'Amp Peak 16(13q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
AMP PEAK 16(13Q22.1) CNV	19	47	54	17
AMP PEAK 16(13Q22.1) WILD-TYPE	24	15	15	24

Figure S39. 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 = 0.000193 (Fisher's exact test), Q value = 0.14

Table S40. Gene #16: 'Amp Peak 16(13q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	50	63	60
AMP PEAK 16(13Q22.1) CNV	33	35	26	43
AMP PEAK 16(13Q22.1) WILD-TYPE	9	15	37	17

Figure S40. 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 = 2.14e-39 (Fisher's exact test), Q value = 1.9e-36

Table S41. Gene #16: 'Amp Peak 16(13q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
AMP PEAK 16(13Q22.1) CNV	179	92	99	11
AMP PEAK 16(13Q22.1) WILD-TYPE	7	149	48	4

Figure S41. 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 = 3.91e-10 (Fisher's exact test), Q value = 3.3e-07

Table S42. Gene #16: 'Amp Peak 16(13q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	116	91
AMP PEAK 16(13Q22.1) CNV	132	59	50
AMP PEAK 16(13Q22.1) WILD-TYPE	24	57	41

Figure S42. 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 = 4.91e-07 (Fisher's exact test), Q value = 0.00039

Table S43. Gene #16: 'Amp Peak 16(13q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	103	116
AMP PEAK 16(13Q22.1) CNV	64	85	56
AMP PEAK 16(13Q22.1) WILD-TYPE	31	18	60

Figure S43. 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 = 2.12e-08 (Fisher's exact test), Q value = 1.7e-05

Table S44. Gene #16: 'Amp Peak 16(13q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	94	136
AMP PEAK 16(13Q22.1) CNV	65	76	64
AMP PEAK 16(13Q22.1) WILD-TYPE	19	18	72

Figure S44. Get High-res Image Gene #16: 'Amp Peak 16(13q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 1.21e-07 (Fisher's exact test), Q value = 9.8e-05

Table S45. Gene #16: 'Amp Peak 16(13q22.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
AMP PEAK 16(13Q22.1) CNV	83	53	65
AMP PEAK 16(13Q22.1) WILD-TYPE	17	56	20

Figure S45. Get High-res Image Gene #16: 'Amp Peak 16(13q22.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 1.6e-20 (Fisher's exact test), Q value = 1.4e-17

Table S46. Gene #18: 'Amp Peak 18(16p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
AMP PEAK 18(16P11.2) CNV	92	21	45	4
AMP PEAK 18(16P11.2) WILD-TYPE	94	220	102	11

Figure S46. 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 = 1.37e-05 (Fisher's exact test), Q value = 0.011

Table S47. Gene #18: 'Amp Peak 18(16p11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	103	116
AMP PEAK 18(16P11.2) CNV	29	36	12
AMP PEAK 18(16P11.2) WILD-TYPE	66	67	104

Figure S47. Get High-res Image Gene #18: 'Amp Peak 18(16p11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 2.59e-05 (Fisher's exact test), Q value = 0.02

Table S48. Gene #18: 'Amp Peak 18(16p11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	94	136
AMP PEAK 18(16P11.2) CNV	32	28	17
AMP PEAK 18(16P11.2) WILD-TYPE	52	66	119

Figure S48. Get High-res Image Gene #18: 'Amp Peak 18(16p11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 8.55e-10 (Fisher's exact test), Q value = 7.1e-07

Table S49. Gene #19: 'Amp Peak 19(17q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
AMP PEAK 19(17Q12) CNV	58	29	58	2
AMP PEAK 19(17Q12) WILD-TYPE	128	212	89	13

Figure S49. Get High-res Image Gene #19: 'Amp Peak 19(17q12)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 2.93e-05 (Fisher's exact test), Q value = 0.022

Table S50. Gene #19: 'Amp Peak 19(17q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	94	136
AMP PEAK 19(17Q12) CNV	25	35	17
AMP PEAK 19(17Q12) WILD-TYPE	59	59	119

Figure S50. Get High-res Image Gene #19: 'Amp Peak 19(17q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 1.9e-10 (Fisher's exact test), Q value = 1.6e-07

Table S51. Gene #20: 'Amp Peak 20(17q24.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
AMP PEAK 20(17Q24.1) CNV	57	24	50	0
AMP PEAK 20(17Q24.1) WILD-TYPE	129	217	97	15

Figure S51. 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 = 0.000341 (Fisher's exact test), Q value = 0.24

Table S52. Gene #20: 'Amp Peak 20(17q24.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	116	91
AMP PEAK 20(17Q24.1) CNV	51	21	11
AMP PEAK 20(17Q24.1) WILD-TYPE	105	95	80

Figure S52. Get High-res Image Gene #20: 'Amp Peak 20(17q24.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 0.000186 (Fisher's exact test), Q value = 0.13

Table S53. Gene #20: 'Amp Peak 20(17q24.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	94	136
AMP PEAK 20(17Q24.1) CNV	22	33	17
AMP PEAK 20(17Q24.1) WILD-TYPE	62	61	119

Figure S53. Get High-res Image Gene #20: 'Amp Peak 20(17q24.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 0.000148 (Fisher's exact test), Q value = 0.11

Table S54. Gene #20: 'Amp Peak 20(17q24.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	211	95	232
AMP PEAK 20(17Q24.1) CNV	61	8	50
AMP PEAK 20(17Q24.1) WILD-TYPE	150	87	182

Figure S54. Get High-res Image Gene #20: 'Amp Peak 20(17q24.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

P value = 2.1e-07 (Fisher's exact test), Q value = 0.00017

Table S55. Gene #21: 'Amp Peak 21(19p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
AMP PEAK 21(19P13.2) CNV	51	18	30	1
AMP PEAK 21(19P13.2) WILD-TYPE	135	223	117	14

Figure S55. 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 = 7.1e-08 (Fisher's exact test), Q value = 5.8e-05

Table S56. Gene #22: 'Amp Peak 22(19q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
AMP PEAK 22(19Q12) CNV	64	27	32	1
AMP PEAK 22(19Q12) WILD-TYPE	122	214	115	14

Figure S56. Get High-res Image Gene #22: 'Amp Peak 22(19q12)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 1.69e-08 (Fisher's exact test), Q value = 1.4e-05

Table S57. Gene #23: 'Amp Peak 23(20p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
AMP PEAK 23(20P11.23) CNV	111	95	85	15
AMP PEAK 23(20P11.23) WILD-TYPE	75	146	62	0

Figure S57. 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 = 0.000164 (Fisher's exact test), Q value = 0.12

Table S58. Gene #23: 'Amp Peak 23(20p11.23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	103	116
AMP PEAK 23(20P11.23) CNV	48	68	44
AMP PEAK 23(20P11.23) WILD-TYPE	47	35	72

Figure S58. Get High-res Image Gene #23: 'Amp Peak 23(20p11.23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 0.000142 (Fisher's exact test), Q value = 0.1

Table S59. Gene #23: 'Amp Peak 23(20p11.23)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
AMP PEAK 23(20P11.23) CNV	64	40	50
AMP PEAK 23(20P11.23) WILD-TYPE	36	69	35

Figure S59. Get High-res Image Gene #23: 'Amp Peak 23(20p11.23)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 24(20q11.21)' versus 'MRNA_CNMF'

P value = 1.19e-13 (Fisher's exact test), Q value = 1e-10

Table S60. Gene #24: 'Amp Peak 24(20q11.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
AMP PEAK 24(20Q11.21) CNV	18	60	63	23
AMP PEAK 24(20Q11.21) WILD-TYPE	25	2	6	18

Figure S60. Get High-res Image Gene #24: 'Amp Peak 24(20q11.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 24(20q11.21)' versus 'MRNA_CHIERARCHICAL'

P value = 9.59e-13 (Fisher's exact test), Q value = 8.2e-10

Table S61. Gene #24: 'Amp Peak 24(20q11.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	50	63	60
AMP PEAK 24(20Q11.21) CNV	39	43	26	56
AMP PEAK 24(20Q11.21) WILD-TYPE	3	7	37	4

Figure S61. Get High-res Image Gene #24: 'Amp Peak 24(20q11.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 24(20q11.21)' versus 'CN_CNMF'

P value = 4.45e-36 (Fisher's exact test), Q value = 4e-33

Table S62. Gene #24: 'Amp Peak 24(20q11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
AMP PEAK 24(20Q11.21) CNV	184	124	126	15
AMP PEAK 24(20Q11.21) WILD-TYPE	2	117	21	0

Figure S62. Get High-res Image Gene #24: 'Amp Peak 24(20q11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 24(20q11.21)' versus 'METHLYATION_CNMF'

P value = 1.99e-18 (Fisher's exact test), Q value = 1.8e-15

Table S63. Gene #24: 'Amp Peak 24(20q11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	116	91
AMP PEAK 24(20Q11.21) CNV	152	66	61
AMP PEAK 24(20Q11.21) WILD-TYPE	4	50	30

Figure S63. Get High-res Image Gene #24: 'Amp Peak 24(20q11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 24(20q11.21)' versus 'MRNASEQ_CNMF'

P value = 4.46e-17 (Fisher's exact test), Q value = 3.9e-14

Table S64. Gene #24: 'Amp Peak 24(20q11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	103	116
AMP PEAK 24(20Q11.21) CNV	76	101	59
AMP PEAK 24(20Q11.21) WILD-TYPE	19	2	57

Figure S64. Get High-res Image Gene #24: 'Amp Peak 24(20q11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 24(20q11.21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.24e-20 (Fisher's exact test), Q value = 2e-17

Table S65. Gene #24: 'Amp Peak 24(20q11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	94	136
AMP PEAK 24(20Q11.21) CNV	76	92	68
AMP PEAK 24(20Q11.21) WILD-TYPE	8	2	68

Figure S65. Get High-res Image Gene #24: 'Amp Peak 24(20q11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 24(20q11.21)' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.09e-13 (Fisher's exact test), Q value = 7.7e-10

Table S66. Gene #24: 'Amp Peak 24(20q11.21)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
AMP PEAK 24(20Q11.21) CNV	94	59	75
AMP PEAK 24(20Q11.21) WILD-TYPE	6	50	10

Figure S66. Get High-res Image Gene #24: 'Amp Peak 24(20q11.21)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 25(20q12)' versus 'MRNA_CNMF'

P value = 1.06e-14 (Fisher's exact test), Q value = 9.2e-12

Table S67. Gene #25: 'Amp Peak 25(20q12)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
AMP PEAK 25(20Q12) CNV	17	60	63	22
AMP PEAK 25(20Q12) WILD-TYPE	26	2	6	19

Figure S67. Get High-res Image Gene #25: 'Amp Peak 25(20q12)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 25(20q12)' versus 'MRNA_CHIERARCHICAL'

P value = 4.18e-14 (Fisher's exact test), Q value = 3.6e-11

Table S68. Gene #25: 'Amp Peak 25(20q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	50	63	60
AMP PEAK 25(20Q12) CNV	39	43	24	56
AMP PEAK 25(20Q12) WILD-TYPE	3	7	39	4

Figure S68. Get High-res Image Gene #25: 'Amp Peak 25(20q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 25(20q12)' versus 'CN_CNMF'

P value = 1.08e-36 (Fisher's exact test), Q value = 9.7e-34

Table S69. Gene #25: 'Amp Peak 25(20q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
AMP PEAK 25(20Q12) CNV	184	124	128	15
AMP PEAK 25(20Q12) WILD-TYPE	2	117	19	0

Figure S69. Get High-res Image Gene #25: 'Amp Peak 25(20q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 25(20q12)' versus 'METHLYATION_CNMF'

P value = 4.84e-17 (Fisher's exact test), Q value = 4.3e-14

Table S70. Gene #25: 'Amp Peak 25(20q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	116	91
AMP PEAK 25(20Q12) CNV	152	69	62
AMP PEAK 25(20Q12) WILD-TYPE	4	47	29

Figure S70. Get High-res Image Gene #25: 'Amp Peak 25(20q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 25(20q12)' versus 'MRNASEQ_CNMF'

P value = 1.76e-16 (Fisher's exact test), Q value = 1.5e-13

Table S71. Gene #25: 'Amp Peak 25(20q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	103	116
AMP PEAK 25(20Q12) CNV	78	101	61
AMP PEAK 25(20Q12) WILD-TYPE	17	2	55

Figure S71. Get High-res Image Gene #25: 'Amp Peak 25(20q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 25(20q12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.08e-19 (Fisher's exact test), Q value = 1.8e-16

Table S72. Gene #25: 'Amp Peak 25(20q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	94	136
AMP PEAK 25(20Q12) CNV	77	92	71
AMP PEAK 25(20Q12) WILD-TYPE	7	2	65

Figure S72. Get High-res Image Gene #25: 'Amp Peak 25(20q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 25(20q12)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.72e-13 (Fisher's exact test), Q value = 2.3e-10

Table S73. Gene #25: 'Amp Peak 25(20q12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
AMP PEAK 25(20Q12) CNV	95	60	76
AMP PEAK 25(20Q12) WILD-TYPE	5	49	9

Figure S73. Get High-res Image Gene #25: 'Amp Peak 25(20q12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 25(20q12)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.6e-05 (Fisher's exact test), Q value = 0.049

Table S74. Gene #25: 'Amp Peak 25(20q12)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	105	115	41
AMP PEAK 25(20Q12) CNV	31	84	77	39
AMP PEAK 25(20Q12) WILD-TYPE	2	21	38	2

Figure S74. Get High-res Image Gene #25: 'Amp Peak 25(20q12)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 26(20q13.32)' versus 'MRNA_CNMF'

P value = 7.8e-14 (Fisher's exact test), Q value = 6.7e-11

Table S75. Gene #26: 'Amp Peak 26(20q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
AMP PEAK 26(20Q13.32) CNV	18	60	64	24
AMP PEAK 26(20Q13.32) WILD-TYPE	25	2	5	17

Figure S75. Get High-res Image Gene #26: 'Amp Peak 26(20q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 26(20q13.32)' versus 'MRNA_CHIERARCHICAL'

P value = 2.02e-12 (Fisher's exact test), Q value = 1.7e-09

Table S76. Gene #26: 'Amp Peak 26(20q13.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	50	63	60
AMP PEAK 26(20Q13.32) CNV	39	44	27	56
AMP PEAK 26(20Q13.32) WILD-TYPE	3	6	36	4

Figure S76. Get High-res Image Gene #26: 'Amp Peak 26(20q13.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 26(20q13.32)' versus 'CN_CNMF'

P value = 7.3e-37 (Fisher's exact test), Q value = 6.5e-34

Table S77. Gene #26: 'Amp Peak 26(20q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
AMP PEAK 26(20Q13.32) CNV	184	125	130	15
AMP PEAK 26(20Q13.32) WILD-TYPE	2	116	17	0

Figure S77. Get High-res Image Gene #26: 'Amp Peak 26(20q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 26(20q13.32)' versus 'METHLYATION_CNMF'

P value = 4.58e-16 (Fisher's exact test), Q value = 4e-13

Table S78. Gene #26: 'Amp Peak 26(20q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	116	91
AMP PEAK 26(20Q13.32) CNV	151	69	62
AMP PEAK 26(20Q13.32) WILD-TYPE	5	47	29

Figure S78. Get High-res Image Gene #26: 'Amp Peak 26(20q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 26(20q13.32)' versus 'MRNASEQ_CNMF'

P value = 1.76e-16 (Fisher's exact test), Q value = 1.5e-13

Table S79. Gene #26: 'Amp Peak 26(20q13.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	103	116
AMP PEAK 26(20Q13.32) CNV	78	101	61
AMP PEAK 26(20Q13.32) WILD-TYPE	17	2	55

Figure S79. Get High-res Image Gene #26: 'Amp Peak 26(20q13.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 26(20q13.32)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.08e-19 (Fisher's exact test), Q value = 1.8e-16

Table S80. Gene #26: 'Amp Peak 26(20q13.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	94	136
AMP PEAK 26(20Q13.32) CNV	77	92	71
AMP PEAK 26(20Q13.32) WILD-TYPE	7	2	65

Figure S80. Get High-res Image Gene #26: 'Amp Peak 26(20q13.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 26(20q13.32)' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.19e-12 (Fisher's exact test), Q value = 2.7e-09

Table S81. Gene #26: 'Amp Peak 26(20q13.32)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
AMP PEAK 26(20Q13.32) CNV	94	61	76
AMP PEAK 26(20Q13.32) WILD-TYPE	6	48	9

Figure S81. Get High-res Image Gene #26: 'Amp Peak 26(20q13.32)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 26(20q13.32)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.6e-05 (Fisher's exact test), Q value = 0.049

Table S82. Gene #26: 'Amp Peak 26(20q13.32)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	105	115	41
AMP PEAK 26(20Q13.32) CNV	31	84	77	39
AMP PEAK 26(20Q13.32) WILD-TYPE	2	21	38	2

Figure S82. Get High-res Image Gene #26: 'Amp Peak 26(20q13.32)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 27(Xq28)' versus 'CN_CNMF'

P value = 7.38e-05 (Fisher's exact test), Q value = 0.055

Table S83. Gene #27: 'Amp Peak 27(Xq28)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
AMP PEAK 27(XQ28) CNV	48	30	44	2
AMP PEAK 27(XQ28) WILD-TYPE	138	211	103	13

Figure S83. Get High-res Image Gene #27: 'Amp Peak 27(Xq28)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 0.000114 (Fisher's exact test), Q value = 0.084

Table S84. Gene #28: 'Del Peak 1(1p36.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
DEL PEAK 1(1P36.11) CNV	14	36	34	7
DEL PEAK 1(1P36.11) WILD-TYPE	29	26	35	34

Figure S84. Get High-res Image Gene #28: 'Del Peak 1(1p36.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

P value = 7.78e-13 (Fisher's exact test), Q value = 6.6e-10

Table S85. Gene #28: 'Del Peak 1(1p36.11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
DEL PEAK 1(1P36.11) CNV	100	53	59	12
DEL PEAK 1(1P36.11) WILD-TYPE	86	188	88	3

Figure S85. Get High-res Image Gene #28: 'Del Peak 1(1p36.11)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 4.56e-06 (Fisher's exact test), Q value = 0.0036

Table S86. Gene #28: 'Del Peak 1(1p36.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	116	91
DEL PEAK 1(1P36.11) CNV	78	25	29
DEL PEAK 1(1P36.11) WILD-TYPE	78	91	62

Figure S86. Get High-res Image Gene #28: 'Del Peak 1(1p36.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 0.000172 (Fisher's exact test), Q value = 0.13

Table S87. Gene #28: 'Del Peak 1(1p36.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	103	116
DEL PEAK 1(1P36.11) CNV	38	50	26
DEL PEAK 1(1P36.11) WILD-TYPE	57	53	90

Figure S87. Get High-res Image Gene #28: 'Del Peak 1(1p36.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 0.000138 (Fisher's exact test), Q value = 0.1

Table S88. Gene #28: 'Del Peak 1(1p36.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	94	136
DEL PEAK 1(1P36.11) CNV	41	41	32
DEL PEAK 1(1P36.11) WILD-TYPE	43	53	104

Figure S88. Get High-res Image Gene #28: 'Del Peak 1(1p36.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 7.12e-12 (Fisher's exact test), Q value = 6e-09

Table S89. Gene #29: 'Del Peak 2(1p33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
DEL PEAK 2(1P33) CNV	76	39	30	12
DEL PEAK 2(1P33) WILD-TYPE	110	202	117	3

Figure S89. Get High-res Image Gene #29: 'Del Peak 2(1p33)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 0.000353 (Fisher's exact test), Q value = 0.25

Table S90. Gene #29: 'Del Peak 2(1p33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	116	91
DEL PEAK 2(1P33) CNV	56	17	25
DEL PEAK 2(1P33) WILD-TYPE	100	99	66

Figure S90. Get High-res Image Gene #29: 'Del Peak 2(1p33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 7.04e-09 (Fisher's exact test), Q value = 5.8e-06

Table S91. Gene #30: 'Del Peak 3(1p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
DEL PEAK 3(1P13.2) CNV	77	42	31	9
DEL PEAK 3(1P13.2) WILD-TYPE	109	199	116	6

Figure S91. Get High-res Image Gene #30: 'Del Peak 3(1p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 7.65e-14 (Fisher's exact test), Q value = 6.6e-11

Table S92. Gene #37: 'Del Peak 10(4p16.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
DEL PEAK 10(4P16.1) CNV	91	43	41	12
DEL PEAK 10(4P16.1) WILD-TYPE	95	198	106	3

Figure S92. Get High-res Image Gene #37: 'Del Peak 10(4p16.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 2.3e-05 (Fisher's exact test), Q value = 0.018

Table S93. Gene #37: 'Del Peak 10(4p16.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	94	136
DEL PEAK 10(4P16.1) CNV	40	31	25
DEL PEAK 10(4P16.1) WILD-TYPE	44	63	111

Figure S93. Get High-res Image Gene #37: 'Del Peak 10(4p16.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 0.00025 (Fisher's exact test), Q value = 0.18

Table S94. Gene #37: 'Del Peak 10(4p16.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
DEL PEAK 10(4P16.1) CNV	40	18	31
DEL PEAK 10(4P16.1) WILD-TYPE	60	91	54

Figure S94. Get High-res Image Gene #37: 'Del Peak 10(4p16.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 2.06e-14 (Fisher's exact test), Q value = 1.8e-11

Table S95. Gene #38: 'Del Peak 11(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
DEL PEAK 11(4Q22.1) CNV	95	44	53	12
DEL PEAK 11(4Q22.1) WILD-TYPE	91	197	94	3

Figure S95. Get High-res Image Gene #38: 'Del Peak 11(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 1.79e-05 (Fisher's exact test), Q value = 0.014

Table S96. Gene #38: 'Del Peak 11(4q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	116	91
DEL PEAK 11(4Q22.1) CNV	71	22	34
DEL PEAK 11(4Q22.1) WILD-TYPE	85	94	57

Figure S96. Get High-res Image Gene #38: 'Del Peak 11(4q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 2.24e-14 (Fisher's exact test), Q value = 1.9e-11

Table S97. Gene #39: 'Del Peak 12(4q35.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
DEL PEAK 12(4Q35.1) CNV	99	46	59	11
DEL PEAK 12(4Q35.1) WILD-TYPE	87	195	88	4

Figure S97. Get High-res Image Gene #39: 'Del Peak 12(4q35.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 6.21e-05 (Fisher's exact test), Q value = 0.046

Table S98. Gene #39: 'Del Peak 12(4q35.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	116	91
DEL PEAK 12(4Q35.1) CNV	71	24	37
DEL PEAK 12(4Q35.1) WILD-TYPE	85	92	54

Figure S98. Get High-res Image Gene #39: 'Del Peak 12(4q35.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 7.68e-05 (Fisher's exact test), Q value = 0.057

Table S99. Gene #39: 'Del Peak 12(4q35.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
DEL PEAK 12(4Q35.1) CNV	49	23	34
DEL PEAK 12(4Q35.1) WILD-TYPE	51	86	51

Figure S99. Get High-res Image Gene #39: 'Del Peak 12(4q35.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 3.45e-11 (Fisher's exact test), Q value = 2.9e-08

Table S100. Gene #40: 'Del Peak 13(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
DEL PEAK 13(5Q11.2) CNV	62	24	50	7
DEL PEAK 13(5Q11.2) WILD-TYPE	124	217	97	8

Figure S100. Get High-res Image Gene #40: 'Del Peak 13(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 6.68e-06 (Fisher's exact test), Q value = 0.0052

Table S101. Gene #40: 'Del Peak 13(5q11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
DEL PEAK 13(5Q11.2) CNV	35	10	26
DEL PEAK 13(5Q11.2) WILD-TYPE	65	99	59

Figure S101. Get High-res Image Gene #40: 'Del Peak 13(5q11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 6.39e-10 (Fisher's exact test), Q value = 5.3e-07

Table S102. Gene #41: 'Del Peak 14(5q22.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
DEL PEAK 14(5Q22.2) CNV	70	38	57	10
DEL PEAK 14(5Q22.2) WILD-TYPE	116	203	90	5

Figure S102. Get High-res Image Gene #41: 'Del Peak 14(5q22.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 18(8p23.3)' versus 'CN_CNMF'

P value = 3.05e-47 (Fisher's exact test), Q value = 2.8e-44

Table S103. Gene #45: 'Del Peak 18(8p23.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
DEL PEAK 18(8P23.3) CNV	118	36	121	2
DEL PEAK 18(8P23.3) WILD-TYPE	68	205	26	13

Figure S103. Get High-res Image Gene #45: 'Del Peak 18(8p23.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 18(8p23.3)' versus 'METHLYATION_CNMF'

P value = 4.19e-07 (Fisher's exact test), Q value = 0.00033

Table S104. Gene #45: 'Del Peak 18(8p23.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	116	91
DEL PEAK 18(8P23.3) CNV	97	35	37
DEL PEAK 18(8P23.3) WILD-TYPE	59	81	54

Figure S104. Get High-res Image Gene #45: 'Del Peak 18(8p23.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 18(8p23.3)' versus 'MRNASEQ_CNMF'

P value = 7.5e-06 (Fisher's exact test), Q value = 0.0058

Table S105. Gene #45: 'Del Peak 18(8p23.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	103	116
DEL PEAK 18(8P23.3) CNV	56	55	33
DEL PEAK 18(8P23.3) WILD-TYPE	39	48	83

Figure S105. Get High-res Image Gene #45: 'Del Peak 18(8p23.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 18(8p23.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.34e-06 (Fisher's exact test), Q value = 0.0019

Table S106. Gene #45: 'Del Peak 18(8p23.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	94	136
DEL PEAK 18(8P23.3) CNV	53	50	41
DEL PEAK 18(8P23.3) WILD-TYPE	31	44	95

Figure S106. Get High-res Image Gene #45: 'Del Peak 18(8p23.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 18(8p23.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.62e-05 (Fisher's exact test), Q value = 0.012

Table S107. Gene #45: 'Del Peak 18(8p23.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
DEL PEAK 18(8P23.3) CNV	60	32	45
DEL PEAK 18(8P23.3) WILD-TYPE	40	77	40

Figure S107. Get High-res Image Gene #45: 'Del Peak 18(8p23.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 19(8p23.2)' versus 'MRNA_CNMF'

P value = 0.000258 (Fisher's exact test), Q value = 0.18

Table S108. Gene #46: 'Del Peak 19(8p23.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
DEL PEAK 19(8P23.2) CNV	17	42	37	11
DEL PEAK 19(8P23.2) WILD-TYPE	26	20	32	30

Figure S108. Get High-res Image Gene #46: 'Del Peak 19(8p23.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 19(8p23.2)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000146 (Fisher's exact test), Q value = 0.11

Table S109. Gene #46: 'Del Peak 19(8p23.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	50	63	60
DEL PEAK 19(8P23.2) CNV	26	17	23	41
DEL PEAK 19(8P23.2) WILD-TYPE	16	33	40	19

Figure S109. Get High-res Image Gene #46: 'Del Peak 19(8p23.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 19(8p23.2)' versus 'CN_CNMF'

P value = 3.44e-51 (Fisher's exact test), Q value = 3.1e-48

Table S110. Gene #46: 'Del Peak 19(8p23.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
DEL PEAK 19(8P23.2) CNV	119	33	123	2
DEL PEAK 19(8P23.2) WILD-TYPE	67	208	24	13

Figure S110. Get High-res Image Gene #46: 'Del Peak 19(8p23.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 19(8p23.2)' versus 'METHLYATION_CNMF'

P value = 1.01e-07 (Fisher's exact test), Q value = 8.2e-05

Table S111. Gene #46: 'Del Peak 19(8p23.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	116	91
DEL PEAK 19(8P23.2) CNV	98	34	37
DEL PEAK 19(8P23.2) WILD-TYPE	58	82	54

Figure S111. Get High-res Image Gene #46: 'Del Peak 19(8p23.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 19(8p23.2)' versus 'MRNASEQ_CNMF'

P value = 2.6e-06 (Fisher's exact test), Q value = 0.0021

Table S112. Gene #46: 'Del Peak 19(8p23.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	103	116
DEL PEAK 19(8P23.2) CNV	56	56	32
DEL PEAK 19(8P23.2) WILD-TYPE	39	47	84

Figure S112. Get High-res Image Gene #46: 'Del Peak 19(8p23.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 19(8p23.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.32e-07 (Fisher's exact test), Q value = 0.00066

Table S113. Gene #46: 'Del Peak 19(8p23.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	94	136
DEL PEAK 19(8P23.2) CNV	55	48	41
DEL PEAK 19(8P23.2) WILD-TYPE	29	46	95

Figure S113. Get High-res Image Gene #46: 'Del Peak 19(8p23.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 19(8p23.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.67e-06 (Fisher's exact test), Q value = 0.006

Table S114. Gene #46: 'Del Peak 19(8p23.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
DEL PEAK 19(8P23.2) CNV	61	32	46
DEL PEAK 19(8P23.2) WILD-TYPE	39	77	39

Figure S114. Get High-res Image Gene #46: 'Del Peak 19(8p23.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 20(8p22)' versus 'CN_CNMF'

P value = 5.79e-54 (Fisher's exact test), Q value = 5.3e-51

Table S115. Gene #47: 'Del Peak 20(8p22)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
DEL PEAK 20(8P22) CNV	125	36	127	2
DEL PEAK 20(8P22) WILD-TYPE	61	205	20	13

Figure S115. Get High-res Image Gene #47: 'Del Peak 20(8p22)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 20(8p22)' versus 'METHLYATION_CNMF'

P value = 7.97e-08 (Fisher's exact test), Q value = 6.5e-05

Table S116. Gene #47: 'Del Peak 20(8p22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	116	91
DEL PEAK 20(8P22) CNV	103	38	38
DEL PEAK 20(8P22) WILD-TYPE	53	78	53

Figure S116. Get High-res Image Gene #47: 'Del Peak 20(8p22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 20(8p22)' versus 'MRNASEQ_CNMF'

P value = 1.15e-05 (Fisher's exact test), Q value = 0.0089

Table S117. Gene #47: 'Del Peak 20(8p22)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	103	116
DEL PEAK 20(8P22) CNV	57	59	36
DEL PEAK 20(8P22) WILD-TYPE	38	44	80

Figure S117. Get High-res Image Gene #47: 'Del Peak 20(8p22)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 20(8p22)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.49e-06 (Fisher's exact test), Q value = 0.0012

Table S118. Gene #47: 'Del Peak 20(8p22)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	94	136
DEL PEAK 20(8P22) CNV	57	50	45
DEL PEAK 20(8P22) WILD-TYPE	27	44	91

Figure S118. Get High-res Image Gene #47: 'Del Peak 20(8p22)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 20(8p22)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.24e-05 (Fisher's exact test), Q value = 0.017

Table S119. Gene #47: 'Del Peak 20(8p22)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
DEL PEAK 20(8P22) CNV	63	36	49
DEL PEAK 20(8P22) WILD-TYPE	37	73	36

Figure S119. Get High-res Image Gene #47: 'Del Peak 20(8p22)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 21(8q11.1)' versus 'CN_CNMF'

P value = 0.000212 (Fisher's exact test), Q value = 0.15

Table S120. Gene #48: 'Del Peak 21(8q11.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
DEL PEAK 21(8Q11.1) CNV	28	12	5	0
DEL PEAK 21(8Q11.1) WILD-TYPE	158	229	142	15

Figure S120. Get High-res Image Gene #48: 'Del Peak 21(8q11.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 7.77e-06 (Fisher's exact test), Q value = 0.006

Table S121. Gene #50: 'Del Peak 23(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
DEL PEAK 23(10P15.3) CNV	40	22	34	7
DEL PEAK 23(10P15.3) WILD-TYPE	146	219	113	8

Figure S121. Get High-res Image Gene #50: 'Del Peak 23(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 8.52e-10 (Fisher's exact test), Q value = 7.1e-07

Table S122. Gene #51: 'Del Peak 24(10q21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
DEL PEAK 24(10Q21.1) CNV	49	21	41	9
DEL PEAK 24(10Q21.1) WILD-TYPE	137	220	106	6

Figure S122. Get High-res Image Gene #51: 'Del Peak 24(10q21.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 4.43e-07 (Fisher's exact test), Q value = 0.00035

Table S123. Gene #52: 'Del Peak 25(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
DEL PEAK 25(10Q23.31) CNV	54	35	50	9
DEL PEAK 25(10Q23.31) WILD-TYPE	132	206	97	6

Figure S123. Get High-res Image Gene #52: 'Del Peak 25(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 6.62e-09 (Fisher's exact test), Q value = 5.4e-06

Table S124. Gene #53: 'Del Peak 26(10q25.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
DEL PEAK 26(10Q25.2) CNV	58	30	44	10
DEL PEAK 26(10Q25.2) WILD-TYPE	128	211	103	5

Figure S124. Get High-res Image Gene #53: 'Del Peak 26(10q25.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 0.000241 (Fisher's exact test), Q value = 0.17

Table S125. Gene #53: 'Del Peak 26(10q25.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	94	136
DEL PEAK 26(10Q25.2) CNV	31	23	18
DEL PEAK 26(10Q25.2) WILD-TYPE	53	71	118

Figure S125. Get High-res Image Gene #53: 'Del Peak 26(10q25.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 7.01e-10 (Fisher's exact test), Q value = 5.8e-07

Table S126. Gene #55: 'Del Peak 28(12p13.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
DEL PEAK 28(12P13.1) CNV	42	9	22	6
DEL PEAK 28(12P13.1) WILD-TYPE	144	232	125	9

Figure S126. Get High-res Image Gene #55: 'Del Peak 28(12p13.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 29(12q21.31)' versus 'CN_CNMF'

P value = 2.72e-08 (Fisher's exact test), Q value = 2.2e-05

Table S127. Gene #56: 'Del Peak 29(12q21.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
DEL PEAK 29(12Q21.31) CNV	40	11	22	6
DEL PEAK 29(12Q21.31) WILD-TYPE	146	230	125	9

Figure S127. Get High-res Image Gene #56: 'Del Peak 29(12q21.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 30(14q11.2)' versus 'MRNA_CNMF'

P value = 3.66e-05 (Fisher's exact test), Q value = 0.028

Table S128. Gene #57: 'Del Peak 30(14q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
DEL PEAK 30(14Q11.2) CNV	8	31	32	6
DEL PEAK 30(14Q11.2) WILD-TYPE	35	31	37	35

Figure S128. Get High-res Image Gene #57: 'Del Peak 30(14q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 30(14q11.2)' versus 'MRNA_CHIERARCHICAL'

P value = 5.71e-06 (Fisher's exact test), Q value = 0.0045

Table S129. Gene #57: 'Del Peak 30(14q11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	50	63	60
DEL PEAK 30(14Q11.2) CNV	21	21	7	28
DEL PEAK 30(14Q11.2) WILD-TYPE	21	29	56	32

Figure S129. Get High-res Image Gene #57: 'Del Peak 30(14q11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 30(14q11.2)' versus 'CN_CNMF'

P value = 1.81e-40 (Fisher's exact test), Q value = 1.6e-37

Table S130. Gene #57: 'Del Peak 30(14q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
DEL PEAK 30(14Q11.2) CNV	132	30	25	6
DEL PEAK 30(14Q11.2) WILD-TYPE	54	211	122	9

Figure S130. Get High-res Image Gene #57: 'Del Peak 30(14q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 30(14q11.2)' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.038

Table S131. Gene #57: 'Del Peak 30(14q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	116	91
DEL PEAK 30(14Q11.2) CNV	68	22	25
DEL PEAK 30(14Q11.2) WILD-TYPE	88	94	66

Figure S131. Get High-res Image Gene #57: 'Del Peak 30(14q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 30(14q11.2)' versus 'MRNASEQ_CNMF'

P value = 4e-06 (Fisher's exact test), Q value = 0.0031

Table S132. Gene #57: 'Del Peak 30(14q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	103	116
DEL PEAK 30(14Q11.2) CNV	25	52	23
DEL PEAK 30(14Q11.2) WILD-TYPE	70	51	93

Figure S132. Get High-res Image Gene #57: 'Del Peak 30(14q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 30(14q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.43e-05 (Fisher's exact test), Q value = 0.07

Table S133. Gene #57: 'Del Peak 30(14q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	94	136
DEL PEAK 30(14Q11.2) CNV	35	39	26
DEL PEAK 30(14Q11.2) WILD-TYPE	49	55	110

Figure S133. Get High-res Image Gene #57: 'Del Peak 30(14q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 30(14q11.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.63e-07 (Fisher's exact test), Q value = 0.00061

Table S134. Gene #57: 'Del Peak 30(14q11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
DEL PEAK 30(14Q11.2) CNV	49	17	31
DEL PEAK 30(14Q11.2) WILD-TYPE	51	92	54

Figure S134. Get High-res Image Gene #57: 'Del Peak 30(14q11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 31(14q31.1)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000257 (Fisher's exact test), Q value = 0.18

Table S135. Gene #58: 'Del Peak 31(14q31.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	50	63	60
DEL PEAK 31(14Q31.1) CNV	23	19	11	28
DEL PEAK 31(14Q31.1) WILD-TYPE	19	31	52	32

Figure S135. Get High-res Image Gene #58: 'Del Peak 31(14q31.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 31(14q31.1)' versus 'CN_CNMF'

P value = 4.82e-38 (Fisher's exact test), Q value = 4.3e-35

Table S136. Gene #58: 'Del Peak 31(14q31.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
DEL PEAK 31(14Q31.1) CNV	132	34	26	6
DEL PEAK 31(14Q31.1) WILD-TYPE	54	207	121	9

Figure S136. Get High-res Image Gene #58: 'Del Peak 31(14q31.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 31(14q31.1)' versus 'METHLYATION_CNMF'

P value = 0.000105 (Fisher's exact test), Q value = 0.077

Table S137. Gene #58: 'Del Peak 31(14q31.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	116	91
DEL PEAK 31(14Q31.1) CNV	68	23	25
DEL PEAK 31(14Q31.1) WILD-TYPE	88	93	66

Figure S137. Get High-res Image Gene #58: 'Del Peak 31(14q31.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 31(14q31.1)' versus 'MRNASEQ_CNMF'

P value = 1.56e-05 (Fisher's exact test), Q value = 0.012

Table S138. Gene #58: 'Del Peak 31(14q31.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	103	116
DEL PEAK 31(14Q31.1) CNV	24	49	22
DEL PEAK 31(14Q31.1) WILD-TYPE	71	54	94

Figure S138. Get High-res Image Gene #58: 'Del Peak 31(14q31.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 31(14q31.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000244 (Fisher's exact test), Q value = 0.17

Table S139. Gene #58: 'Del Peak 31(14q31.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	94	136
DEL PEAK 31(14Q31.1) CNV	32	38	25
DEL PEAK 31(14Q31.1) WILD-TYPE	52	56	111

Figure S139. Get High-res Image Gene #58: 'Del Peak 31(14q31.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 31(14q31.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.16e-07 (Fisher's exact test), Q value = 0.00025

Table S140. Gene #58: 'Del Peak 31(14q31.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
DEL PEAK 31(14Q31.1) CNV	49	16	30
DEL PEAK 31(14Q31.1) WILD-TYPE	51	93	55

Figure S140. Get High-res Image Gene #58: 'Del Peak 31(14q31.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 32(14q31.1)' versus 'CN_CNMF'

P value = 1.62e-37 (Fisher's exact test), Q value = 1.5e-34

Table S141. Gene #59: 'Del Peak 32(14q31.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
DEL PEAK 32(14Q31.1) CNV	133	35	28	6
DEL PEAK 32(14Q31.1) WILD-TYPE	53	206	119	9

Figure S141. Get High-res Image Gene #59: 'Del Peak 32(14q31.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 32(14q31.1)' versus 'METHLYATION_CNMF'

P value = 4.57e-05 (Fisher's exact test), Q value = 0.034

Table S142. Gene #59: 'Del Peak 32(14q31.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	116	91
DEL PEAK 32(14Q31.1) CNV	70	23	26
DEL PEAK 32(14Q31.1) WILD-TYPE	86	93	65

Figure S142. Get High-res Image Gene #59: 'Del Peak 32(14q31.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 32(14q31.1)' versus 'MRNASEQ_CNMF'

P value = 1.12e-05 (Fisher's exact test), Q value = 0.0087

Table S143. Gene #59: 'Del Peak 32(14q31.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	103	116
DEL PEAK 32(14Q31.1) CNV	26	50	22
DEL PEAK 32(14Q31.1) WILD-TYPE	69	53	94

Figure S143. Get High-res Image Gene #59: 'Del Peak 32(14q31.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 32(14q31.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.35e-05 (Fisher's exact test), Q value = 0.055

Table S144. Gene #59: 'Del Peak 32(14q31.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	94	136
DEL PEAK 32(14Q31.1) CNV	34	39	25
DEL PEAK 32(14Q31.1) WILD-TYPE	50	55	111

Figure S144. Get High-res Image Gene #59: 'Del Peak 32(14q31.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 32(14q31.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.15e-07 (Fisher's exact test), Q value = 9.3e-05

Table S145. Gene #59: 'Del Peak 32(14q31.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
DEL PEAK 32(14Q31.1) CNV	50	16	32
DEL PEAK 32(14Q31.1) WILD-TYPE	50	93	53

Figure S145. Get High-res Image Gene #59: 'Del Peak 32(14q31.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 33(15q11.2)' versus 'CN_CNMF'

P value = 3.16e-21 (Fisher's exact test), Q value = 2.8e-18

Table S146. Gene #60: 'Del Peak 33(15q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
DEL PEAK 33(15Q11.2) CNV	113	43	69	11
DEL PEAK 33(15Q11.2) WILD-TYPE	73	198	78	4

Figure S146. Get High-res Image Gene #60: 'Del Peak 33(15q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 33(15q11.2)' versus 'MRNASEQ_CNMF'

P value = 0.000148 (Fisher's exact test), Q value = 0.11

Table S147. Gene #60: 'Del Peak 33(15q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	103	116
DEL PEAK 33(15Q11.2) CNV	41	52	28
DEL PEAK 33(15Q11.2) WILD-TYPE	54	51	88

Figure S147. Get High-res Image Gene #60: 'Del Peak 33(15q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 33(15q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.46e-05 (Fisher's exact test), Q value = 0.019

Table S148. Gene #60: 'Del Peak 33(15q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	94	136
DEL PEAK 33(15Q11.2) CNV	46	41	34
DEL PEAK 33(15Q11.2) WILD-TYPE	38	53	102

Figure S148. Get High-res Image Gene #60: 'Del Peak 33(15q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 33(15q11.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.91e-06 (Fisher's exact test), Q value = 0.0038

Table S149. Gene #60: 'Del Peak 33(15q11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
DEL PEAK 33(15Q11.2) CNV	54	25	41
DEL PEAK 33(15Q11.2) WILD-TYPE	46	84	44

Figure S149. Get High-res Image Gene #60: 'Del Peak 33(15q11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 34(15q21.1)' versus 'CN_CNMF'

P value = 4.96e-19 (Fisher's exact test), Q value = 4.4e-16

Table S150. Gene #61: 'Del Peak 34(15q21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
DEL PEAK 34(15Q21.1) CNV	107	43	68	11
DEL PEAK 34(15Q21.1) WILD-TYPE	79	198	79	4

Figure S150. Get High-res Image Gene #61: 'Del Peak 34(15q21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 34(15q21.1)' versus 'MRNASEQ_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.18

Table S151. Gene #61: 'Del Peak 34(15q21.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	103	116
DEL PEAK 34(15Q21.1) CNV	36	51	27
DEL PEAK 34(15Q21.1) WILD-TYPE	59	52	89

Figure S151. Get High-res Image Gene #61: 'Del Peak 34(15q21.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 34(15q21.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000104 (Fisher's exact test), Q value = 0.077

Table S152. Gene #61: 'Del Peak 34(15q21.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
DEL PEAK 34(15Q21.1) CNV	49	25	39
DEL PEAK 34(15Q21.1) WILD-TYPE	51	84	46

Figure S152. Get High-res Image Gene #61: 'Del Peak 34(15q21.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 35(15q22.33)' versus 'MRNA_CNMF'

P value = 0.000199 (Fisher's exact test), Q value = 0.14

Table S153. Gene #62: 'Del Peak 35(15q22.33)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
DEL PEAK 35(15Q22.33) CNV	12	31	34	6
DEL PEAK 35(15Q22.33) WILD-TYPE	31	31	35	35

Figure S153. Get High-res Image Gene #62: 'Del Peak 35(15q22.33)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 35(15q22.33)' versus 'CN_CNMF'

P value = 5.8e-21 (Fisher's exact test), Q value = 5.2e-18

Table S154. Gene #62: 'Del Peak 35(15q22.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
DEL PEAK 35(15Q22.33) CNV	107	38	64	11
DEL PEAK 35(15Q22.33) WILD-TYPE	79	203	83	4

Figure S154. Get High-res Image Gene #62: 'Del Peak 35(15q22.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 35(15q22.33)' versus 'MRNASEQ_CNMF'

P value = 3.29e-05 (Fisher's exact test), Q value = 0.025

Table S155. Gene #62: 'Del Peak 35(15q22.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	103	116
DEL PEAK 35(15Q22.33) CNV	39	50	24
DEL PEAK 35(15Q22.33) WILD-TYPE	56	53	92

Figure S155. Get High-res Image Gene #62: 'Del Peak 35(15q22.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 35(15q22.33)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.57e-06 (Fisher's exact test), Q value = 0.0051

Table S156. Gene #62: 'Del Peak 35(15q22.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	94	136
DEL PEAK 35(15Q22.33) CNV	45	38	30
DEL PEAK 35(15Q22.33) WILD-TYPE	39	56	106

Figure S156. Get High-res Image Gene #62: 'Del Peak 35(15q22.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 35(15q22.33)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.58e-05 (Fisher's exact test), Q value = 0.02

Table S157. Gene #62: 'Del Peak 35(15q22.33)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
DEL PEAK 35(15Q22.33) CNV	48	23	40
DEL PEAK 35(15Q22.33) WILD-TYPE	52	86	45

Figure S157. Get High-res Image Gene #62: 'Del Peak 35(15q22.33)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 38(17p12)' versus 'MRNA_CNMF'

P value = 8.38e-08 (Fisher's exact test), Q value = 6.8e-05

Table S158. Gene #65: 'Del Peak 38(17p12)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
DEL PEAK 38(17P12) CNV	16	50	51	15
DEL PEAK 38(17P12) WILD-TYPE	27	12	18	26

Figure S158. Get High-res Image Gene #65: 'Del Peak 38(17p12)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 38(17p12)' versus 'MRNA_CHIERARCHICAL'

P value = 2.2e-05 (Fisher's exact test), Q value = 0.017

Table S159. Gene #65: 'Del Peak 38(17p12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	50	63	60
DEL PEAK 38(17P12) CNV	33	30	24	45
DEL PEAK 38(17P12) WILD-TYPE	9	20	39	15

Figure S159. Get High-res Image Gene #65: 'Del Peak 38(17p12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 38(17p12)' versus 'CN_CNMF'

P value = 9.96e-35 (Fisher's exact test), Q value = 8.9e-32

Table S160. Gene #65: 'Del Peak 38(17p12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
DEL PEAK 38(17P12) CNV	151	70	117	11
DEL PEAK 38(17P12) WILD-TYPE	35	171	30	4

Figure S160. Get High-res Image Gene #65: 'Del Peak 38(17p12)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 38(17p12)' versus 'METHLYATION_CNMF'

P value = 5.81e-09 (Fisher's exact test), Q value = 4.8e-06

Table S161. Gene #65: 'Del Peak 38(17p12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	116	91
DEL PEAK 38(17P12) CNV	120	51	43
DEL PEAK 38(17P12) WILD-TYPE	36	65	48

Figure S161. Get High-res Image Gene #65: 'Del Peak 38(17p12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 38(17p12)' versus 'MRNASEQ_CNMF'

P value = 1.5e-07 (Fisher's exact test), Q value = 0.00012

Table S162. Gene #65: 'Del Peak 38(17p12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	103	116
DEL PEAK 38(17P12) CNV	58	78	45
DEL PEAK 38(17P12) WILD-TYPE	37	25	71

Figure S162. Get High-res Image Gene #65: 'Del Peak 38(17p12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 38(17p12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.89e-09 (Fisher's exact test), Q value = 1.6e-06

Table S163. Gene #65: 'Del Peak 38(17p12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	94	136
DEL PEAK 38(17P12) CNV	62	68	51
DEL PEAK 38(17P12) WILD-TYPE	22	26	85

Figure S163. Get High-res Image Gene #65: 'Del Peak 38(17p12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 38(17p12)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.48e-08 (Fisher's exact test), Q value = 2e-05

Table S164. Gene #65: 'Del Peak 38(17p12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
DEL PEAK 38(17P12) CNV	79	43	53
DEL PEAK 38(17P12) WILD-TYPE	21	66	32

Figure S164. Get High-res Image Gene #65: 'Del Peak 38(17p12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 40(18p11.31)' versus 'MRNA_CNMF'

P value = 5.8e-12 (Fisher's exact test), Q value = 4.9e-09

Table S165. Gene #67: 'Del Peak 40(18p11.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
DEL PEAK 40(18P11.31) CNV	11	51	52	13
DEL PEAK 40(18P11.31) WILD-TYPE	32	11	17	28

Figure S165. Get High-res Image Gene #67: 'Del Peak 40(18p11.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 40(18p11.31)' versus 'MRNA_CHIERARCHICAL'

P value = 6.24e-10 (Fisher's exact test), Q value = 5.2e-07

Table S166. Gene #67: 'Del Peak 40(18p11.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	50	63	60
DEL PEAK 40(18P11.31) CNV	35	29	17	46
DEL PEAK 40(18P11.31) WILD-TYPE	7	21	46	14

Figure S166. Get High-res Image Gene #67: 'Del Peak 40(18p11.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 40(18p11.31)' versus 'CN_CNMF'

P value = 1.03e-44 (Fisher's exact test), Q value = 9.3e-42

Table S167. Gene #67: 'Del Peak 40(18p11.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
DEL PEAK 40(18P11.31) CNV	167	65	104	14
DEL PEAK 40(18P11.31) WILD-TYPE	19	176	43	1

Figure S167. Get High-res Image Gene #67: 'Del Peak 40(18p11.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 40(18p11.31)' versus 'METHLYATION_CNMF'

P value = 4.9e-18 (Fisher's exact test), Q value = 4.3e-15

Table S168. Gene #67: 'Del Peak 40(18p11.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	116	91
DEL PEAK 40(18P11.31) CNV	133	40	48
DEL PEAK 40(18P11.31) WILD-TYPE	23	76	43

Figure S168. Get High-res Image Gene #67: 'Del Peak 40(18p11.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 40(18p11.31)' versus 'MRNASEQ_CNMF'

P value = 2.25e-16 (Fisher's exact test), Q value = 2e-13

Table S169. Gene #67: 'Del Peak 40(18p11.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	103	116
DEL PEAK 40(18P11.31) CNV	61	89	37
DEL PEAK 40(18P11.31) WILD-TYPE	34	14	79

Figure S169. Get High-res Image Gene #67: 'Del Peak 40(18p11.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 40(18p11.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.42e-15 (Fisher's exact test), Q value = 2.1e-12

Table S170. Gene #67: 'Del Peak 40(18p11.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	94	136
DEL PEAK 40(18P11.31) CNV	66	75	46
DEL PEAK 40(18P11.31) WILD-TYPE	18	19	90

Figure S170. Get High-res Image Gene #67: 'Del Peak 40(18p11.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 40(18p11.31)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-14 (Fisher's exact test), Q value = 8.7e-12

Table S171. Gene #67: 'Del Peak 40(18p11.31)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
DEL PEAK 40(18P11.31) CNV	83	34	59
DEL PEAK 40(18P11.31) WILD-TYPE	17	75	26

Figure S171. Get High-res Image Gene #67: 'Del Peak 40(18p11.31)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 40(18p11.31)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000237 (Fisher's exact test), Q value = 0.17

Table S172. Gene #67: 'Del Peak 40(18p11.31)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	105	115	41
DEL PEAK 40(18P11.31) CNV	28	65	54	29
DEL PEAK 40(18P11.31) WILD-TYPE	5	40	61	12

Figure S172. Get High-res Image Gene #67: 'Del Peak 40(18p11.31)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 41(18q12.2)' versus 'MRNA_CNMF'

P value = 1.01e-09 (Fisher's exact test), Q value = 8.4e-07

Table S173. Gene #68: 'Del Peak 41(18q12.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
DEL PEAK 41(18Q12.2) CNV	17	54	56	17
DEL PEAK 41(18Q12.2) WILD-TYPE	26	8	13	24

Figure S173. Get High-res Image Gene #68: 'Del Peak 41(18q12.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 41(18q12.2)' versus 'MRNA_CHIERARCHICAL'

P value = 4.59e-09 (Fisher's exact test), Q value = 3.8e-06

Table S174. Gene #68: 'Del Peak 41(18q12.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	50	63	60
DEL PEAK 41(18Q12.2) CNV	37	32	24	51
DEL PEAK 41(18Q12.2) WILD-TYPE	5	18	39	9

Figure S174. Get High-res Image Gene #68: 'Del Peak 41(18q12.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 41(18q12.2)' versus 'CN_CNMF'

P value = 1.14e-52 (Fisher's exact test), Q value = 1e-49

Table S175. Gene #68: 'Del Peak 41(18q12.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
DEL PEAK 41(18Q12.2) CNV	173	77	130	15
DEL PEAK 41(18Q12.2) WILD-TYPE	13	164	17	0

Figure S175. Get High-res Image Gene #68: 'Del Peak 41(18q12.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 41(18q12.2)' versus 'METHLYATION_CNMF'

P value = 1.59e-20 (Fisher's exact test), Q value = 1.4e-17

Table S176. Gene #68: 'Del Peak 41(18q12.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	116	91
DEL PEAK 41(18Q12.2) CNV	145	51	51
DEL PEAK 41(18Q12.2) WILD-TYPE	11	65	40

Figure S176. Get High-res Image Gene #68: 'Del Peak 41(18q12.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 41(18q12.2)' versus 'MRNASEQ_CNMF'

P value = 1.77e-15 (Fisher's exact test), Q value = 1.5e-12

Table S177. Gene #68: 'Del Peak 41(18q12.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	103	116
DEL PEAK 41(18Q12.2) CNV	67	94	47
DEL PEAK 41(18Q12.2) WILD-TYPE	28	9	69

Figure S177. Get High-res Image Gene #68: 'Del Peak 41(18q12.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 41(18q12.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.76e-13 (Fisher's exact test), Q value = 4.1e-10

Table S178. Gene #68: 'Del Peak 41(18q12.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	94	136
DEL PEAK 41(18Q12.2) CNV	71	78	59
DEL PEAK 41(18Q12.2) WILD-TYPE	13	16	77

Figure S178. Get High-res Image Gene #68: 'Del Peak 41(18q12.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 41(18q12.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.25e-15 (Fisher's exact test), Q value = 5.4e-12

Table S179. Gene #68: 'Del Peak 41(18q12.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
DEL PEAK 41(18Q12.2) CNV	90	44	66
DEL PEAK 41(18Q12.2) WILD-TYPE	10	65	19

Figure S179. Get High-res Image Gene #68: 'Del Peak 41(18q12.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 41(18q12.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.16

Table S180. Gene #68: 'Del Peak 41(18q12.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	105	115	41
DEL PEAK 41(18Q12.2) CNV	28	71	65	36
DEL PEAK 41(18Q12.2) WILD-TYPE	5	34	50	5

Figure S180. Get High-res Image Gene #68: 'Del Peak 41(18q12.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 42(18q21.2)' versus 'MRNA_CNMF'

P value = 3.72e-10 (Fisher's exact test), Q value = 3.1e-07

Table S181. Gene #69: 'Del Peak 42(18q21.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
DEL PEAK 42(18Q21.2) CNV	17	55	57	18
DEL PEAK 42(18Q21.2) WILD-TYPE	26	7	12	23

Figure S181. Get High-res Image Gene #69: 'Del Peak 42(18q21.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 42(18q21.2)' versus 'MRNA_CHIERARCHICAL'

P value = 1.64e-08 (Fisher's exact test), Q value = 1.3e-05

Table S182. Gene #69: 'Del Peak 42(18q21.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	50	63	60
DEL PEAK 42(18Q21.2) CNV	37	34	25	51
DEL PEAK 42(18Q21.2) WILD-TYPE	5	16	38	9

Figure S182. Get High-res Image Gene #69: 'Del Peak 42(18q21.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 42(18q21.2)' versus 'CN_CNMF'

P value = 5.32e-54 (Fisher's exact test), Q value = 4.8e-51

Table S183. Gene #69: 'Del Peak 42(18q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
DEL PEAK 42(18Q21.2) CNV	176	85	136	15
DEL PEAK 42(18Q21.2) WILD-TYPE	10	156	11	0

Figure S183. Get High-res Image Gene #69: 'Del Peak 42(18q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 42(18q21.2)' versus 'METHLYATION_CNMF'

P value = 1.14e-17 (Fisher's exact test), Q value = 1e-14

Table S184. Gene #69: 'Del Peak 42(18q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	116	91
DEL PEAK 42(18Q21.2) CNV	147	61	53
DEL PEAK 42(18Q21.2) WILD-TYPE	9	55	38

Figure S184. Get High-res Image Gene #69: 'Del Peak 42(18q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 42(18q21.2)' versus 'MRNASEQ_CNMF'

P value = 1.68e-13 (Fisher's exact test), Q value = 1.4e-10

Table S185. Gene #69: 'Del Peak 42(18q21.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	103	116
DEL PEAK 42(18Q21.2) CNV	71	95	54
DEL PEAK 42(18Q21.2) WILD-TYPE	24	8	62

Figure S185. Get High-res Image Gene #69: 'Del Peak 42(18q21.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 42(18q21.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.46e-13 (Fisher's exact test), Q value = 3e-10

Table S186. Gene #69: 'Del Peak 42(18q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	94	136
DEL PEAK 42(18Q21.2) CNV	74	81	65
DEL PEAK 42(18Q21.2) WILD-TYPE	10	13	71

Figure S186. Get High-res Image Gene #69: 'Del Peak 42(18q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 42(18q21.2)' versus 'MIRSEQ_CNMF'

P value = 7.08e-05 (Fisher's exact test), Q value = 0.053

Table S187. Gene #69: 'Del Peak 42(18q21.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	211	95	232
DEL PEAK 42(18Q21.2) CNV	169	55	153
DEL PEAK 42(18Q21.2) WILD-TYPE	42	40	79

Figure S187. Get High-res Image Gene #69: 'Del Peak 42(18q21.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 42(18q21.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.99e-13 (Fisher's exact test), Q value = 6.8e-10

Table S188. Gene #69: 'Del Peak 42(18q21.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
DEL PEAK 42(18Q21.2) CNV	92	52	68
DEL PEAK 42(18Q21.2) WILD-TYPE	8	57	17

Figure S188. Get High-res Image Gene #69: 'Del Peak 42(18q21.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 43(18q22.1)' versus 'MRNA_CNMF'

P value = 2.01e-09 (Fisher's exact test), Q value = 1.7e-06

Table S189. Gene #70: 'Del Peak 43(18q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	62	69	41
DEL PEAK 43(18Q22.1) CNV	17	55	56	19
DEL PEAK 43(18Q22.1) WILD-TYPE	26	7	13	22

Figure S189. Get High-res Image Gene #70: 'Del Peak 43(18q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 43(18q22.1)' versus 'MRNA_CHIERARCHICAL'

P value = 1.23e-07 (Fisher's exact test), Q value = 9.9e-05

Table S190. Gene #70: 'Del Peak 43(18q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	50	63	60
DEL PEAK 43(18Q22.1) CNV	37	32	27	51
DEL PEAK 43(18Q22.1) WILD-TYPE	5	18	36	9

Figure S190. Get High-res Image Gene #70: 'Del Peak 43(18q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 43(18q22.1)' versus 'CN_CNMF'

P value = 4.47e-56 (Fisher's exact test), Q value = 4.1e-53

Table S191. Gene #70: 'Del Peak 43(18q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
DEL PEAK 43(18Q22.1) CNV	177	81	134	15
DEL PEAK 43(18Q22.1) WILD-TYPE	9	160	13	0

Figure S191. Get High-res Image Gene #70: 'Del Peak 43(18q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 43(18q22.1)' versus 'METHLYATION_CNMF'

P value = 3.8e-18 (Fisher's exact test), Q value = 3.4e-15

Table S192. Gene #70: 'Del Peak 43(18q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	116	91
DEL PEAK 43(18Q22.1) CNV	146	59	51
DEL PEAK 43(18Q22.1) WILD-TYPE	10	57	40

Figure S192. Get High-res Image Gene #70: 'Del Peak 43(18q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 43(18q22.1)' versus 'MRNASEQ_CNMF'

P value = 3.84e-13 (Fisher's exact test), Q value = 3.3e-10

Table S193. Gene #70: 'Del Peak 43(18q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	103	116
DEL PEAK 43(18Q22.1) CNV	70	94	53
DEL PEAK 43(18Q22.1) WILD-TYPE	25	9	63

Figure S193. Get High-res Image Gene #70: 'Del Peak 43(18q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 43(18q22.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.07e-12 (Fisher's exact test), Q value = 9.1e-10

Table S194. Gene #70: 'Del Peak 43(18q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	94	136
DEL PEAK 43(18Q22.1) CNV	73	80	64
DEL PEAK 43(18Q22.1) WILD-TYPE	11	14	72

Figure S194. Get High-res Image Gene #70: 'Del Peak 43(18q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 43(18q22.1)' versus 'MIRSEQ_CNMF'

P value = 6.66e-05 (Fisher's exact test), Q value = 0.05

Table S195. Gene #70: 'Del Peak 43(18q22.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	211	95	232
DEL PEAK 43(18Q22.1) CNV	167	53	153
DEL PEAK 43(18Q22.1) WILD-TYPE	44	42	79

Figure S195. Get High-res Image Gene #70: 'Del Peak 43(18q22.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 43(18q22.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.13e-13 (Fisher's exact test), Q value = 1.8e-10

Table S196. Gene #70: 'Del Peak 43(18q22.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
DEL PEAK 43(18Q22.1) CNV	92	50	66
DEL PEAK 43(18Q22.1) WILD-TYPE	8	59	19

Figure S196. Get High-res Image Gene #70: 'Del Peak 43(18q22.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 44(19p13.3)' versus 'CN_CNMF'

P value = 2.61e-05 (Fisher's exact test), Q value = 0.02

Table S197. Gene #71: 'Del Peak 44(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
DEL PEAK 44(19P13.3) CNV	39	18	33	3
DEL PEAK 44(19P13.3) WILD-TYPE	147	223	114	12

Figure S197. Get High-res Image Gene #71: 'Del Peak 44(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 44(19p13.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.99e-05 (Fisher's exact test), Q value = 0.074

Table S198. Gene #71: 'Del Peak 44(19p13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	253	248
DEL PEAK 44(19P13.3) CNV	16	32	40
DEL PEAK 44(19P13.3) WILD-TYPE	21	221	208

Figure S198. Get High-res Image Gene #71: 'Del Peak 44(19p13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 45(19q13.43)' versus 'CN_CNMF'

P value = 9.24e-05 (Fisher's exact test), Q value = 0.068

Table S199. Gene #72: 'Del Peak 45(19q13.43)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
DEL PEAK 45(19Q13.43) CNV	26	12	27	3
DEL PEAK 45(19Q13.43) WILD-TYPE	160	229	120	12

Figure S199. Get High-res Image Gene #72: 'Del Peak 45(19q13.43)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 46(20p12.1)' versus 'CN_CNMF'

P value = 6.56e-10 (Fisher's exact test), Q value = 5.5e-07

Table S200. Gene #73: 'Del Peak 46(20p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
DEL PEAK 46(20P12.1) CNV	86	46	49	0
DEL PEAK 46(20P12.1) WILD-TYPE	100	195	98	15

Figure S200. Get High-res Image Gene #73: 'Del Peak 46(20p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 46(20p12.1)' versus 'METHLYATION_CNMF'

P value = 1.27e-05 (Fisher's exact test), Q value = 0.0098

Table S201. Gene #73: 'Del Peak 46(20p12.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	116	91
DEL PEAK 46(20P12.1) CNV	67	22	19
DEL PEAK 46(20P12.1) WILD-TYPE	89	94	72

Figure S201. Get High-res Image Gene #73: 'Del Peak 46(20p12.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 47(20p12.1)' versus 'CN_CNMF'

P value = 6.56e-10 (Fisher's exact test), Q value = 5.5e-07

Table S202. Gene #74: 'Del Peak 47(20p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
DEL PEAK 47(20P12.1) CNV	86	46	49	0
DEL PEAK 47(20P12.1) WILD-TYPE	100	195	98	15

Figure S202. Get High-res Image Gene #74: 'Del Peak 47(20p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 47(20p12.1)' versus 'METHLYATION_CNMF'

P value = 1.27e-05 (Fisher's exact test), Q value = 0.0098

Table S203. Gene #74: 'Del Peak 47(20p12.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	156	116	91
DEL PEAK 47(20P12.1) CNV	67	22	19
DEL PEAK 47(20P12.1) WILD-TYPE	89	94	72

Figure S203. Get High-res Image Gene #74: 'Del Peak 47(20p12.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 48(21q11.2)' versus 'CN_CNMF'

P value = 5.74e-08 (Fisher's exact test), Q value = 4.7e-05

Table S204. Gene #75: 'Del Peak 48(21q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
DEL PEAK 48(21Q11.2) CNV	88	51	53	8
DEL PEAK 48(21Q11.2) WILD-TYPE	98	190	94	7

Figure S204. Get High-res Image Gene #75: 'Del Peak 48(21q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 48(21q11.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.16

Table S205. Gene #75: 'Del Peak 48(21q11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
DEL PEAK 48(21Q11.2) CNV	50	25	29
DEL PEAK 48(21Q11.2) WILD-TYPE	50	84	56

Figure S205. Get High-res Image Gene #75: 'Del Peak 48(21q11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 49(22q13.32)' versus 'CN_CNMF'

P value = 1.15e-13 (Fisher's exact test), Q value = 9.9e-11

Table S206. Gene #76: 'Del Peak 49(22q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	186	241	147	15
DEL PEAK 49(22Q13.32) CNV	104	48	51	8
DEL PEAK 49(22Q13.32) WILD-TYPE	82	193	96	7

Figure S206. Get High-res Image Gene #76: 'Del Peak 49(22q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 49(22q13.32)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000177 (Fisher's exact test), Q value = 0.13

Table S207. Gene #76: 'Del Peak 49(22q13.32)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	109	85
DEL PEAK 49(22Q13.32) CNV	48	23	32
DEL PEAK 49(22Q13.32) WILD-TYPE	52	86	53

Figure S207. Get High-res Image Gene #76: 'Del Peak 49(22q13.32)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_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 = 589
Number of copy number variation regions = 76
Number of molecular subtypes = 12
Exclude regions that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

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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