Correlation between copy number variation genes and molecular subtypes

Colon Adenocarcinoma (Primary solid tumor)

23 September 2013 | analyses__2013_09_23

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variation genes and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1QV3JTQ

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 63 peak regions and 12 molecular subtypes across 427 patients, 193 significant findings detected with Q value < 0.25.

Amp Peak 2(5p13.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 4(6p21.1) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 5(8p11.23) cnvs correlated to 'CN_CNMF'.
Amp Peak 6(8p11.21) cnvs correlated to 'CN_CNMF'.
Amp Peak 7(8q12.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 8(8q24.21) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 9(11p15.5) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 10(12p13.33) cnvs correlated to 'CN_CNMF'.
Amp Peak 11(13q12.13) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Amp Peak 12(13q22.1) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Amp Peak 13(16p11.2) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 14(16q12.1) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Amp Peak 15(17q12) cnvs correlated to 'CN_CNMF'.
Amp Peak 16(17q24.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 19(20p11.23) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 20(20q11.21) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Amp Peak 21(20q12) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Amp Peak 22(20q13.12) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 1(1p36.11) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 2(1p33) cnvs correlated to 'CN_CNMF'.
Del Peak 4(3p26.1) cnvs correlated to 'CN_CNMF'.
Del Peak 7(4p16.1) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 8(4q22.1) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 9(4q35.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 10(5q11.2) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 11(5q21.3) cnvs correlated to 'CN_CNMF'.
Del Peak 12(5q23.1) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 16(8p23.3) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 17(8p22) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 18(8p11.22) cnvs correlated to 'CN_CNMF'.
Del Peak 19(8p11.21) cnvs correlated to 'CN_CNMF'.
Del Peak 21(10p15.3) cnvs correlated to 'CN_CNMF'.
Del Peak 22(10q21.1) cnvs correlated to 'CN_CNMF'.
Del Peak 23(10q23.31) cnvs correlated to 'CN_CNMF'.
Del Peak 24(10q25.2) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
Del Peak 26(14q32.11) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 27(15q11.2) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 28(15q21.1) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 29(15q22.33) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 32(17p12) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 34(18p11.31) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 35(18q12.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 36(18q21.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 37(18q22.1) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 39(20p12.1) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 40(21q11.2) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
Del Peak 41(22q13.32) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 63 regions and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 193 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 22(20q13 12)	0 (0%)	117	3.87e-10 (2.63e-07)	7.28e-12 (5.1e-09)	3.63e-41 (2.72e-38)	3.72e-11 (2.58e-08)	0.000237 (0.138)	1.3e-05 (0.00821)	1.62e-13 (1.15e-10)	1.27e-15 (9.26e-13)	0.79 (1.00)	0.00028 (0.161)	5.84e-13 (4.13e-10)	0.163 (1.00)
Amp Peak 20(20q11 21)	0 (0%)	121	3.87e-10 (2.63e-07)	7.28e-12 (5.1e-09)	5.06e-42 (3.8e-39)	1.91e-12 (1.35e-09)	0.00073 (0.398)	0.000108 (0.0652)	2.4e-15 (1.74e-12)	3.41e-17 (2.49e-14)	0.821 (1.00)	0.000103 (0.0621)	2.18e-12 (1.53e-09)	0.143 (1.00)
Amp Peak 21(20q12)	0 (0%)	120	4.29e-11 (2.97e-08)	4.99e-12 (3.51e-09)	1.74e-41 (1.31e-38)	1.68e-11 (1.17e-08)	0.000512 (0.285)	2.18e-05 (0.0137)	3.88e-14 (2.79e-11)	2.6e-16 (1.89e-13)	0.774 (1.00)	0.000125 (0.0751)	1.94e-13 (1.38e-10)	0.14 (1.00)
Del Peak 26(14q32 11)	0 (0%)	292	1.58e-06 (0.00103)	3.23e-05 (0.0202)	1.67e-21 (1.24e-18)	0.000294 (0.168)	0.000199 (0.117)	0.0236 (1.00)	0.000757 (0.411)	7.38e-05 (0.045)	0.164 (1.00)	0.00017 (0.101)	6.78e-05 (0.0415)	0.141 (1.00)
Del Peak 32(17p12)	0 (0%)	192	2.47e-08 (1.66e-05)	4.97e-07 (0.000327)	3.53e-33 (2.65e-30)	1.08e-10 (7.37e-08)	0.00726 (1.00)	7.42e-05 (0.0451)	3.83e-11 (2.66e-08)	3.31e-11 (2.3e-08)	0.597 (1.00)	0.0261 (1.00)	8.13e-11 (5.6e-08)	0.026 (1.00)
Del Peak 34(18p11 31)	0 (0%)	198	6.87e-12 (4.82e-09)	7.49e-10 (5.08e-07)	3.11e-44 (2.34e-41)	4.14e-15 (2.99e-12)	0.00042 (0.238)	0.00104 (0.548)	5.06e-18 (3.71e-15)	7.54e-18 (5.53e-15)	0.876 (1.00)	0.0025 (1.00)	6.5e-14 (4.67e-11)	0.0188 (1.00)
Del Peak 35(18q12 2)	0 (0%)	171	1.09e-11 (7.65e-09)	2.66e-10 (1.82e-07)	7.34e-47 (5.54e-44)	1.24e-17 (9.1e-15)	0.00224 (1.00)	0.000421 (0.238)	2.22e-17 (1.62e-14)	1.43e-18 (1.05e-15)	0.943 (1.00)	0.00272 (1.00)	9.9e-15 (7.15e-12)	0.106 (1.00)
Del Peak 36(18q21 2)	0 (0%)	158	3.37e-11 (2.34e-08)	1.46e-10 (9.98e-08)	1.2e-44 (9.03e-42)	6.6e-14 (4.73e-11)	0.001 (0.53)	0.000225 (0.132)	3.56e-13 (2.52e-10)	1.06e-13 (7.59e-11)	0.444 (1.00)	0.0704 (1.00)	1.38e-13 (9.83e-11)	0.0664 (1.00)
Del Peak 37(18q22 1)	0 (0%)	158	8.76e-11 (6.03e-08)	8.34e-10 (5.63e-07)	3.76e-47 (2.84e-44)	3.75e-14 (2.7e-11)	0.00247 (1.00)	0.000224 (0.131)	3.56e-13 (2.52e-10)	1.06e-13 (7.59e-11)	0.584 (1.00)	0.0491 (1.00)	3.5e-14 (2.52e-11)	0.0644 (1.00)
Amp Peak 11(13q12 13)	0 (0%)	167	1.58e-06 (0.00103)	2.07e-06 (0.00134)	3.21e-32 (2.4e-29)	1.41e-05 (0.00891)	0.00491 (1.00)	0.0124 (1.00)	1.07e-06 (7e-04)	2.75e-09 (1.85e-06)	0.563 (1.00)	0.0181 (1.00)	2.83e-07 (0.000188)	0.692 (1.00)
Del Peak 17(8p22)	0 (0%)	237	0.00264 (1.00)	0.000174 (0.103)	2.78e-26 (2.08e-23)	4.13e-08 (2.76e-05)	0.00799 (1.00)	0.00013 (0.0778)	5.24e-05 (0.0323)	3.41e-06 (0.00221)	0.485 (1.00)	0.298 (1.00)	3.34e-07 (0.000221)	0.386 (1.00)
Del Peak 29(15q22 33)	0 (0%)	279	0.000273 (0.157)	0.000835 (0.451)	8.89e-20 (6.56e-17)	0.000136 (0.0811)	0.0436 (1.00)	0.0512 (1.00)	3.82e-07 (0.000252)	1.77e-08 (1.19e-05)	0.687 (1.00)	8.91e-05 (0.054)	0.000119 (0.0717)	0.333 (1.00)
Amp Peak 9(11p15 5)	0 (0%)	338	6.09e-06 (0.0039)	0.000343 (0.195)	9.35e-06 (0.00594)	8.76e-06 (0.00558)	0.0028 (1.00)	0.00358 (1.00)	0.00186 (0.953)	0.000461 (0.258)	0.182 (1.00)	7.62e-05 (0.0463)	0.00157 (0.81)	2e-05 (0.0126)
Amp Peak 12(13q22 1)	0 (0%)	163	0.000586 (0.323)	4.41e-05 (0.0273)	7.99e-31 (5.97e-28)	8.28e-06 (0.00529)	0.0148 (1.00)	0.0444 (1.00)	1.31e-06 (0.000853)	2.87e-08 (1.92e-05)	0.45 (1.00)	0.0332 (1.00)	4.33e-06 (0.00279)	0.978 (1.00)
Amp Peak 14(16q12 1)	0 (0%)	324	0.000126 (0.0757)	2.53e-05 (0.0159)	1.52e-20 (1.12e-17)	0.0499 (1.00)	0.082 (1.00)	0.081 (1.00)	0.000479 (0.268)	3.69e-05 (0.0229)	0.963 (1.00)	0.000191 (0.113)	0.000155 (0.0919)	0.241 (1.00)
Del Peak 1(1p36 11)	0 (0%)	275	0.00015 (0.0893)	0.00247 (1.00)	1.82e-13 (1.3e-10)	6.08e-05 (0.0373)	0.00567 (1.00)	0.0238 (1.00)	3.98e-05 (0.0247)	3.29e-05 (0.0205)	0.45 (1.00)	0.017 (1.00)	0.000156 (0.0929)	0.00279 (1.00)
Del Peak 8(4q22 1)	0 (0%)	295	0.000383 (0.218)	0.00214 (1.00)	1.38e-13 (9.83e-11)	0.000212 (0.124)	0.072 (1.00)	0.391 (1.00)	3.91e-06 (0.00252)	7.21e-07 (0.000472)	0.455 (1.00)	0.0129 (1.00)	0.000984 (0.521)	0.313 (1.00)
Del Peak 9(4q35 1)	0 (0%)	285	0.00098 (0.52)	0.00363 (1.00)	3.74e-15 (2.71e-12)	1.28e-05 (0.00812)	0.0146 (1.00)	0.146 (1.00)	1.5e-05 (0.00949)	2.05e-05 (0.0129)	0.351 (1.00)	0.0286 (1.00)	5.93e-06 (0.00381)	0.64 (1.00)
Del Peak 16(8p23 3)	0 (0%)	251	0.0114 (1.00)	6.76e-05 (0.0414)	6.52e-21 (4.84e-18)	3.21e-07 (0.000212)	0.00453 (1.00)	0.00096 (0.511)	0.000534 (0.296)	2.72e-06 (0.00176)	0.218 (1.00)	0.152 (1.00)	2.15e-07 (0.000143)	0.331 (1.00)
Del Peak 7(4p16 1)	0 (0%)	301	0.000733 (0.399)	0.00397 (1.00)	1.11e-12 (7.8e-10)	0.00234 (1.00)	0.0222 (1.00)	0.0866 (1.00)	3.17e-06 (0.00205)	2.56e-07 (0.00017)	0.381 (1.00)	0.0542 (1.00)	0.000229 (0.134)	0.511 (1.00)
Del Peak 10(5q11 2)	0 (0%)	333	0.00115 (0.6)	0.00127 (0.663)	8.17e-10 (5.52e-07)	0.0231 (1.00)	0.000855 (0.46)	0.0118 (1.00)	4.77e-05 (0.0294)	7.09e-05 (0.0433)	0.594 (1.00)	0.366 (1.00)	0.000273 (0.157)	0.511 (1.00)
Del Peak 27(15q11 2)	0 (0%)	264	0.000468 (0.262)	0.00159 (0.817)	8.07e-21 (5.98e-18)	0.00442 (1.00)	0.0415 (1.00)	0.07 (1.00)	5.1e-06 (0.00328)	6.06e-07 (0.000399)	0.99 (1.00)	0.00394 (1.00)	5.77e-05 (0.0355)	0.917 (1.00)
Del Peak 28(15q21 1)	0 (0%)	274	0.0261 (1.00)	0.0142 (1.00)	3.06e-17 (2.24e-14)	0.00424 (1.00)	0.00959 (1.00)	0.0657 (1.00)	1.56e-05 (0.00983)	6.81e-07 (0.000447)	0.815 (1.00)	0.00219 (1.00)	0.000428 (0.241)	0.955 (1.00)
Del Peak 41(22q13 32)	0 (0%)	282	0.000892 (0.477)	0.000232 (0.135)	4.07e-15 (2.94e-12)	0.00137 (0.715)	0.0792 (1.00)	0.218 (1.00)	0.000457 (0.257)	2.81e-05 (0.0175)	0.38 (1.00)	0.00263 (1.00)	8.33e-06 (0.00532)	0.474 (1.00)
Amp Peak 4(6p21 1)	0 (0%)	335	0.196 (1.00)	0.000191 (0.113)	8.94e-10 (6.03e-07)	0.0374 (1.00)	0.505 (1.00)	0.178 (1.00)	0.0226 (1.00)	0.000426 (0.241)	0.858 (1.00)	0.165 (1.00)	0.00149 (0.771)	0.705 (1.00)
Amp Peak 13(16p11 2)	0 (0%)	310	0.00114 (0.597)	0.000129 (0.0774)	1.44e-19 (1.06e-16)	0.022 (1.00)	0.0218 (1.00)	0.033 (1.00)	0.00101 (0.534)	0.000256 (0.148)	0.933 (1.00)	0.00257 (1.00)	0.000488 (0.272)	0.426 (1.00)
Amp Peak 16(17q24 1)	0 (0%)	332	0.0504 (1.00)	0.0263 (1.00)	3.39e-10 (2.31e-07)	0.000341 (0.194)	0.0579 (1.00)	0.00527 (1.00)	0.000551 (0.305)	0.000306 (0.175)	0.00916 (1.00)	0.213 (1.00)	0.0345 (1.00)	0.147 (1.00)
Amp Peak 19(20p11 23)	0 (0%)	219	0.0933 (1.00)	0.000725 (0.396)	9.01e-11 (6.18e-08)	0.0767 (1.00)	0.00595 (1.00)	0.186 (1.00)	0.000246 (0.142)	0.000272 (0.157)	0.453 (1.00)	0.0846 (1.00)	0.00198 (1.00)	0.98 (1.00)
Del Peak 12(5q23 1)	0 (0%)	317	0.0497 (1.00)	0.0242 (1.00)	7.91e-11 (5.46e-08)	0.0234 (1.00)	0.00895 (1.00)	0.15 (1.00)	0.000231 (0.134)	9.59e-05 (0.058)	0.873 (1.00)	0.792 (1.00)	0.00386 (1.00)	0.268 (1.00)
Amp Peak 8(8q24 21)	0 (0%)	181	0.563 (1.00)	0.0685 (1.00)	7.42e-21 (5.51e-18)	0.000339 (0.193)	0.0294 (1.00)	0.0104 (1.00)	0.0055 (1.00)	0.0124 (1.00)	0.771 (1.00)	0.403 (1.00)	0.000854 (0.46)	0.0535 (1.00)
Del Peak 24(10q25 2)	0 (0%)	332	0.125 (1.00)	0.00187 (0.955)	8.89e-11 (6.11e-08)	0.00498 (1.00)	0.00337 (1.00)	0.319 (1.00)	0.000982 (0.521)	0.000922 (0.493)	0.922 (1.00)	0.104 (1.00)	1.27e-05 (0.00809)	0.806 (1.00)
Del Peak 39(20p12 1)	0 (0%)	347	0.0484 (1.00)	0.203 (1.00)	7.23e-06 (0.00463)	0.000455 (0.256)	0.668 (1.00)	0.278 (1.00)	0.00212 (1.00)	7.09e-05 (0.0433)	0.135 (1.00)	0.122 (1.00)	0.00503 (1.00)	0.158 (1.00)
Del Peak 40(21q11 2)	0 (0%)	297	0.0264 (1.00)	0.0387 (1.00)	5.95e-11 (4.11e-08)	0.0289 (1.00)	0.182 (1.00)	0.455 (1.00)	0.000607 (0.334)	0.000651 (0.357)	0.905 (1.00)	0.12 (1.00)	0.000184 (0.109)	0.151 (1.00)
Amp Peak 2(5p13 2)	0 (0%)	344	0.38 (1.00)	0.268 (1.00)	2.93e-05 (0.0183)	0.595 (1.00)	0.00595 (1.00)	0.724 (1.00)	0.0343 (1.00)	0.00182 (0.934)	0.788 (1.00)	0.101 (1.00)	0.0478 (1.00)	0.507 (1.00)
Amp Peak 5(8p11 23)	0 (0%)	277	0.302 (1.00)	0.126 (1.00)	3.13e-25 (2.33e-22)	0.522 (1.00)	0.652 (1.00)	0.733 (1.00)	0.491 (1.00)	0.179 (1.00)	0.288 (1.00)	0.366 (1.00)	0.319 (1.00)	0.978 (1.00)
Amp Peak 6(8p11 21)	0 (0%)	248	0.444 (1.00)	0.0716 (1.00)	3.21e-19 (2.36e-16)	0.386 (1.00)	0.152 (1.00)	0.00672 (1.00)	0.541 (1.00)	0.124 (1.00)	0.635 (1.00)	0.503 (1.00)	0.269 (1.00)	0.658 (1.00)
Amp Peak 7(8q12 1)	0 (0%)	206	0.489 (1.00)	0.0389 (1.00)	2.41e-20 (1.78e-17)	0.00299 (1.00)	0.0059 (1.00)	0.00068 (0.373)	0.0127 (1.00)	0.00517 (1.00)	0.378 (1.00)	0.639 (1.00)	0.000576 (0.318)	0.0736 (1.00)
Amp Peak 10(12p13 33)	0 (0%)	323	0.537 (1.00)	0.801 (1.00)	0.000176 (0.104)	0.235 (1.00)	0.426 (1.00)	0.958 (1.00)	0.343 (1.00)	0.925 (1.00)	0.503 (1.00)	0.827 (1.00)	0.677 (1.00)	0.553 (1.00)
Amp Peak 15(17q12)	0 (0%)	323	0.0538 (1.00)	0.075 (1.00)	4.15e-08 (2.77e-05)	0.000517 (0.287)	0.131 (1.00)	0.00276 (1.00)	0.00079 (0.427)	0.00323 (1.00)	0.0376 (1.00)	0.176 (1.00)	0.0282 (1.00)	0.287 (1.00)
Del Peak 2(1p33)	0 (0%)	319	0.0223 (1.00)	0.376 (1.00)	1.12e-08 (7.54e-06)	0.00141 (0.737)	0.455 (1.00)	0.395 (1.00)	0.0112 (1.00)	0.00477 (1.00)	0.601 (1.00)	0.00154 (0.795)	0.00642 (1.00)	0.000955 (0.509)
Del Peak 4(3p26 1)	0 (0%)	365	0.399 (1.00)	0.281 (1.00)	4.05e-05 (0.0251)	0.0937 (1.00)	0.852 (1.00)	0.861 (1.00)	0.199 (1.00)	0.0127 (1.00)	0.686 (1.00)	0.105 (1.00)	0.00151 (0.783)	0.558 (1.00)
Del Peak 11(5q21 3)	0 (0%)	307	0.0661 (1.00)	0.0105 (1.00)	2.27e-11 (1.58e-08)	0.00944 (1.00)	0.0329 (1.00)	0.0971 (1.00)	0.00147 (0.765)	0.00087 (0.466)	0.933 (1.00)	0.718 (1.00)	0.0282 (1.00)	0.15 (1.00)
Del Peak 18(8p11 22)	0 (0%)	344	0.402 (1.00)	0.137 (1.00)	6.26e-10 (4.25e-07)	0.0384 (1.00)	0.0139 (1.00)	0.00534 (1.00)	0.0779 (1.00)	0.00662 (1.00)	0.814 (1.00)	0.148 (1.00)	0.0151 (1.00)	0.0481 (1.00)
Del Peak 19(8p11 21)	0 (0%)	383	0.0251 (1.00)	0.355 (1.00)	6.26e-07 (0.000411)	0.604 (1.00)	0.0515 (1.00)	0.024 (1.00)	0.342 (1.00)	0.0188 (1.00)	0.343 (1.00)	0.174 (1.00)	0.0844 (1.00)	0.287 (1.00)
Del Peak 21(10p15 3)	0 (0%)	358	0.115 (1.00)	0.102 (1.00)	1.05e-06 (0.000687)	0.013 (1.00)	0.0242 (1.00)	0.104 (1.00)	0.0674 (1.00)	0.00735 (1.00)	0.63 (1.00)	0.00547 (1.00)	0.00533 (1.00)	0.355 (1.00)
Del Peak 22(10q21 1)	0 (0%)	343	0.00335 (1.00)	0.00888 (1.00)	7.55e-10 (5.11e-07)	0.0834 (1.00)	0.0371 (1.00)	0.144 (1.00)	0.0779 (1.00)	0.0447 (1.00)	0.971 (1.00)	0.158 (1.00)	0.00705 (1.00)	0.745 (1.00)
Del Peak 23(10q23 31)	0 (0%)	330	0.146 (1.00)	0.0306 (1.00)	1.68e-07 (0.000112)	0.0649 (1.00)	0.093 (1.00)	0.375 (1.00)	0.0137 (1.00)	0.109 (1.00)	0.745 (1.00)	0.0254 (1.00)	0.000774 (0.42)	0.453 (1.00)
Amp Peak 1(2q33 1)	0 (0%)	344	0.166 (1.00)	0.0365 (1.00)	0.00165 (0.848)	0.054 (1.00)	0.054 (1.00)	0.0652 (1.00)	0.0141 (1.00)	0.0339 (1.00)	0.224 (1.00)	0.099 (1.00)	0.191 (1.00)	0.343 (1.00)
Amp Peak 3(5q22 3)	0 (0%)	386	0.915 (1.00)	0.677 (1.00)	0.00873 (1.00)	0.798 (1.00)	0.385 (1.00)	0.494 (1.00)	0.152 (1.00)	0.0105 (1.00)	0.902 (1.00)	1 (1.00)	0.153 (1.00)	0.417 (1.00)
Amp Peak 17(19p13 2)	0 (0%)	359	0.0674 (1.00)	0.0263 (1.00)	0.000707 (0.386)	0.0533 (1.00)	0.697 (1.00)	0.341 (1.00)	0.344 (1.00)	0.124 (1.00)	0.364 (1.00)	0.018 (1.00)	0.017 (1.00)	0.335 (1.00)
Amp Peak 18(19q13 11)	0 (0%)	342	0.181 (1.00)	0.0232 (1.00)	0.00409 (1.00)	0.161 (1.00)	0.0545 (1.00)	0.688 (1.00)	0.0841 (1.00)	0.0122 (1.00)	0.466 (1.00)	0.0971 (1.00)	0.0481 (1.00)	0.27 (1.00)
Del Peak 3(2q37 2)	0 (0%)	406	0.805 (1.00)	0.0652 (1.00)	0.656 (1.00)	0.288 (1.00)	0.367 (1.00)	0.208 (1.00)	0.944 (1.00)	0.167 (1.00)	0.245 (1.00)	0.36 (1.00)	1 (1.00)	0.787 (1.00)
Del Peak 5(3p14 2)	0 (0%)	349	0.554 (1.00)	0.556 (1.00)	0.00798 (1.00)	0.418 (1.00)	0.631 (1.00)	0.29 (1.00)	0.236 (1.00)	0.0255 (1.00)	0.456 (1.00)	0.761 (1.00)	0.00533 (1.00)	0.645 (1.00)
Del Peak 6(3q26 31)	0 (0%)	385	0.559 (1.00)	0.646 (1.00)	0.00554 (1.00)	0.246 (1.00)	0.497 (1.00)	0.369 (1.00)	0.113 (1.00)	0.24 (1.00)	0.32 (1.00)	0.569 (1.00)	0.00968 (1.00)	0.0187 (1.00)
Del Peak 13(6p25 3)	0 (0%)	373	0.852 (1.00)	0.756 (1.00)	0.0211 (1.00)	0.0772 (1.00)	0.0595 (1.00)	0.828 (1.00)	0.666 (1.00)	0.37 (1.00)	0.746 (1.00)	0.45 (1.00)	0.118 (1.00)	0.584 (1.00)
Del Peak 14(6q26)	0 (0%)	367	0.524 (1.00)	0.258 (1.00)	0.227 (1.00)	0.38 (1.00)	0.14 (1.00)	0.355 (1.00)	0.655 (1.00)	0.726 (1.00)	0.715 (1.00)	0.106 (1.00)	0.321 (1.00)	0.423 (1.00)
Del Peak 15(7q31 1)	0 (0%)	416	1 (1.00)	0.504 (1.00)	0.366 (1.00)	0.797 (1.00)	0.278 (1.00)	0.219 (1.00)	0.51 (1.00)	0.131 (1.00)	0.923 (1.00)	0.619 (1.00)	0.877 (1.00)	0.837 (1.00)
Del Peak 20(9p21 3)	0 (0%)	370	0.563 (1.00)	0.0923 (1.00)	0.000495 (0.276)	0.178 (1.00)	0.69 (1.00)	0.214 (1.00)	0.155 (1.00)	0.152 (1.00)	0.727 (1.00)	0.685 (1.00)	0.0714 (1.00)	0.684 (1.00)
Del Peak 25(13q14 13)	0 (0%)	409	0.275 (1.00)	0.876 (1.00)	0.166 (1.00)	0.18 (1.00)	0.24 (1.00)	0.34 (1.00)	0.211 (1.00)	1 (1.00)	0.688 (1.00)	0.905 (1.00)	0.632 (1.00)	0.787 (1.00)
Del Peak 30(16p13 3)	0 (0%)	381	0.303 (1.00)	0.338 (1.00)	0.249 (1.00)	0.261 (1.00)	0.367 (1.00)	0.913 (1.00)	0.0901 (1.00)	0.165 (1.00)	0.93 (1.00)	0.563 (1.00)	0.146 (1.00)	0.375 (1.00)
Del Peak 31(16q23 1)	0 (0%)	376	0.269 (1.00)	0.00608 (1.00)	0.255 (1.00)	0.268 (1.00)	0.154 (1.00)	0.821 (1.00)	0.293 (1.00)	0.0218 (1.00)	0.591 (1.00)	0.708 (1.00)	1 (1.00)	0.758 (1.00)
Del Peak 33(17q24 3)	0 (0%)	366	0.0956 (1.00)	0.707 (1.00)	0.0166 (1.00)	0.00849 (1.00)	0.73 (1.00)	0.338 (1.00)	0.0278 (1.00)	0.0293 (1.00)	0.798 (1.00)	0.664 (1.00)	0.0209 (1.00)	0.162 (1.00)
Del Peak 38(19p13 3)	0 (0%)	369	0.131 (1.00)	0.0385 (1.00)	0.000866 (0.465)	0.342 (1.00)	0.981 (1.00)	0.0676 (1.00)	0.0355 (1.00)	0.0179 (1.00)	0.446 (1.00)	0.551 (1.00)	0.0214 (1.00)	0.15 (1.00)

'Amp Peak 2(5p13.2)' versus 'CN_CNMF'

P value = 2.93e-05 (Fisher's exact test), Q value = 0.018

Table S1. Gene #2: 'Amp Peak 2(5p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
AMP PEAK 2(5P13.2) CNV	50	20	13
AMP PEAK 2(5P13.2) WILD-TYPE	134	176	34

Figure S1. Get High-res Image Gene #2: 'Amp Peak 2(5p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 4(6p21.1)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000191 (Fisher's exact test), Q value = 0.11

Table S2. Gene #4: 'Amp Peak 4(6p21.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
AMP PEAK 4(6P21.1) CNV	8	3	19
AMP PEAK 4(6P21.1) WILD-TYPE	48	40	28

Figure S2. Get High-res Image Gene #4: 'Amp Peak 4(6p21.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 4(6p21.1)' versus 'CN_CNMF'

P value = 8.94e-10 (Fisher's exact test), Q value = 6e-07

Table S3. Gene #4: 'Amp Peak 4(6p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
AMP PEAK 4(6P21.1) CNV	66	18	8
AMP PEAK 4(6P21.1) WILD-TYPE	118	178	39

Figure S3. Get High-res Image Gene #4: 'Amp Peak 4(6p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 4(6p21.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000426 (Fisher's exact test), Q value = 0.24

Table S4. Gene #4: 'Amp Peak 4(6p21.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	77	74
AMP PEAK 4(6P21.1) CNV	26	6	16
AMP PEAK 4(6P21.1) WILD-TYPE	54	71	58

Figure S4. Get High-res Image Gene #4: 'Amp Peak 4(6p21.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 5(8p11.23)' versus 'CN_CNMF'

P value = 3.13e-25 (Fisher's exact test), Q value = 2.3e-22

Table S5. Gene #5: 'Amp Peak 5(8p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
AMP PEAK 5(8P11.23) CNV	61	42	47
AMP PEAK 5(8P11.23) WILD-TYPE	123	154	0

Figure S5. Get High-res Image Gene #5: 'Amp Peak 5(8p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 6(8p11.21)' versus 'CN_CNMF'

P value = 3.21e-19 (Fisher's exact test), Q value = 2.4e-16

Table S6. Gene #6: 'Amp Peak 6(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
AMP PEAK 6(8P11.21) CNV	83	51	45
AMP PEAK 6(8P11.21) WILD-TYPE	101	145	2

Figure S6. Get High-res Image Gene #6: 'Amp Peak 6(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 7(8q12.1)' versus 'CN_CNMF'

P value = 2.41e-20 (Fisher's exact test), Q value = 1.8e-17

Table S7. Gene #7: 'Amp Peak 7(8q12.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
AMP PEAK 7(8Q12.1) CNV	116	60	45
AMP PEAK 7(8Q12.1) WILD-TYPE	68	136	2

Figure S7. Get High-res Image Gene #7: 'Amp Peak 7(8q12.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 7.42e-21 (Fisher's exact test), Q value = 5.5e-18

Table S8. Gene #8: 'Amp Peak 8(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
AMP PEAK 8(8Q24.21) CNV	130	70	46
AMP PEAK 8(8Q24.21) WILD-TYPE	54	126	1

Figure S8. Get High-res Image Gene #8: 'Amp Peak 8(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 0.000339 (Fisher's exact test), Q value = 0.19

Table S9. Gene #8: 'Amp Peak 8(8q24.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
AMP PEAK 8(8Q24.21) CNV	85	42	39
AMP PEAK 8(8Q24.21) WILD-TYPE	29	46	29

Figure S9. Get High-res Image Gene #8: 'Amp Peak 8(8q24.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 9(11p15.5)' versus 'MRNA_CNMF'

P value = 6.09e-06 (Fisher's exact test), Q value = 0.0039

Table S10. Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
AMP PEAK 9(11P15.5) CNV	1	18	3	12
AMP PEAK 9(11P15.5) WILD-TYPE	34	43	26	9

Figure S10. Get High-res Image Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 9(11p15.5)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000343 (Fisher's exact test), Q value = 0.19

Table S11. Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
AMP PEAK 9(11P15.5) CNV	14	2	18
AMP PEAK 9(11P15.5) WILD-TYPE	42	41	29

Figure S11. Get High-res Image Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 9(11p15.5)' versus 'CN_CNMF'

P value = 9.35e-06 (Fisher's exact test), Q value = 0.0059

Table S12. Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
AMP PEAK 9(11P15.5) CNV	58	23	8
AMP PEAK 9(11P15.5) WILD-TYPE	126	173	39

Figure S12. Get High-res Image Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 9(11p15.5)' versus 'METHLYATION_CNMF'

P value = 8.76e-06 (Fisher's exact test), Q value = 0.0056

Table S13. Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
AMP PEAK 9(11P15.5) CNV	36	5	11
AMP PEAK 9(11P15.5) WILD-TYPE	78	83	57

Figure S13. Get High-res Image Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 9(11p15.5)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.62e-05 (Fisher's exact test), Q value = 0.046

Table S14. Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	174	143
AMP PEAK 9(11P15.5) CNV	4	45	35
AMP PEAK 9(11P15.5) WILD-TYPE	76	129	108

Figure S14. Get High-res Image Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 9(11p15.5)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.013

Table S15. Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	21	86	113
AMP PEAK 9(11P15.5) CNV	12	16	12
AMP PEAK 9(11P15.5) WILD-TYPE	9	70	101

Figure S15. Get High-res Image Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 10(12p13.33)' versus 'CN_CNMF'

P value = 0.000176 (Fisher's exact test), Q value = 0.1

Table S16. Gene #10: 'Amp Peak 10(12p13.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
AMP PEAK 10(12P13.33) CNV	30	53	21
AMP PEAK 10(12P13.33) WILD-TYPE	154	143	26

Figure S16. Get High-res Image Gene #10: 'Amp Peak 10(12p13.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 11(13q12.13)' versus 'MRNA_CNMF'

P value = 1.58e-06 (Fisher's exact test), Q value = 0.001

Table S17. Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
AMP PEAK 11(13Q12.13) CNV	15	51	10	16
AMP PEAK 11(13Q12.13) WILD-TYPE	20	10	19	5

Figure S17. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 11(13q12.13)' versus 'MRNA_CHIERARCHICAL'

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

Table S18. Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
AMP PEAK 11(13Q12.13) CNV	39	14	39
AMP PEAK 11(13Q12.13) WILD-TYPE	17	29	8

Figure S18. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 11(13q12.13)' versus 'CN_CNMF'

P value = 3.21e-32 (Fisher's exact test), Q value = 2.4e-29

Table S19. Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
AMP PEAK 11(13Q12.13) CNV	165	63	32
AMP PEAK 11(13Q12.13) WILD-TYPE	19	133	15

Figure S19. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 11(13q12.13)' versus 'METHLYATION_CNMF'

P value = 1.41e-05 (Fisher's exact test), Q value = 0.0089

Table S20. Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
AMP PEAK 11(13Q12.13) CNV	88	42	35
AMP PEAK 11(13Q12.13) WILD-TYPE	26	46	33

Figure S20. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 11(13q12.13)' versus 'MRNASEQ_CNMF'

P value = 1.07e-06 (Fisher's exact test), Q value = 7e-04

Table S21. Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	70	57	61
AMP PEAK 11(13Q12.13) CNV	29	54	33	19
AMP PEAK 11(13Q12.13) WILD-TYPE	14	16	24	42

Figure S21. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 11(13q12.13)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.75e-09 (Fisher's exact test), Q value = 1.8e-06

Table S22. Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	77	74
AMP PEAK 11(13Q12.13) CNV	60	23	52
AMP PEAK 11(13Q12.13) WILD-TYPE	20	54	22

Figure S22. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 11(13q12.13)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.83e-07 (Fisher's exact test), Q value = 0.00019

Table S23. Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
AMP PEAK 11(13Q12.13) CNV	62	29	43
AMP PEAK 11(13Q12.13) WILD-TYPE	17	49	20

Figure S23. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 12(13q22.1)' versus 'MRNA_CHIERARCHICAL'

P value = 4.41e-05 (Fisher's exact test), Q value = 0.027

Table S24. Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
AMP PEAK 12(13Q22.1) CNV	39	15	37
AMP PEAK 12(13Q22.1) WILD-TYPE	17	28	10

Figure S24. Get High-res Image Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 12(13q22.1)' versus 'CN_CNMF'

P value = 7.99e-31 (Fisher's exact test), Q value = 6e-28

Table S25. Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
AMP PEAK 12(13Q22.1) CNV	165	66	33
AMP PEAK 12(13Q22.1) WILD-TYPE	19	130	14

Figure S25. Get High-res Image Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 12(13q22.1)' versus 'METHLYATION_CNMF'

P value = 8.28e-06 (Fisher's exact test), Q value = 0.0053

Table S26. Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
AMP PEAK 12(13Q22.1) CNV	90	44	35
AMP PEAK 12(13Q22.1) WILD-TYPE	24	44	33

Figure S26. Get High-res Image Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 12(13q22.1)' versus 'MRNASEQ_CNMF'

P value = 1.31e-06 (Fisher's exact test), Q value = 0.00085

Table S27. Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	70	57	61
AMP PEAK 12(13Q22.1) CNV	29	57	32	22
AMP PEAK 12(13Q22.1) WILD-TYPE	14	13	25	39

Figure S27. Get High-res Image Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 12(13q22.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.87e-08 (Fisher's exact test), Q value = 1.9e-05

Table S28. Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	77	74
AMP PEAK 12(13Q22.1) CNV	60	26	54
AMP PEAK 12(13Q22.1) WILD-TYPE	20	51	20

Figure S28. Get High-res Image Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 12(13q22.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.33e-06 (Fisher's exact test), Q value = 0.0028

Table S29. Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
AMP PEAK 12(13Q22.1) CNV	63	33	43
AMP PEAK 12(13Q22.1) WILD-TYPE	16	45	20

Figure S29. Get High-res Image Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 13(16p11.2)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000129 (Fisher's exact test), Q value = 0.077

Table S30. Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
AMP PEAK 13(16P11.2) CNV	13	6	25
AMP PEAK 13(16P11.2) WILD-TYPE	43	37	22

Figure S30. Get High-res Image Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 13(16p11.2)' versus 'CN_CNMF'

P value = 1.44e-19 (Fisher's exact test), Q value = 1.1e-16

Table S31. Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
AMP PEAK 13(16P11.2) CNV	92	18	7
AMP PEAK 13(16P11.2) WILD-TYPE	92	178	40

Figure S31. Get High-res Image Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 13(16p11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000256 (Fisher's exact test), Q value = 0.15

Table S32. Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	77	74
AMP PEAK 13(16P11.2) CNV	30	8	16
AMP PEAK 13(16P11.2) WILD-TYPE	50	69	58

Figure S32. Get High-res Image Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 14(16q12.1)' versus 'MRNA_CNMF'

P value = 0.000126 (Fisher's exact test), Q value = 0.076

Table S33. Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
AMP PEAK 14(16Q12.1) CNV	4	22	2	11
AMP PEAK 14(16Q12.1) WILD-TYPE	31	39	27	10

Figure S33. Get High-res Image Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 14(16q12.1)' versus 'MRNA_CHIERARCHICAL'

P value = 2.53e-05 (Fisher's exact test), Q value = 0.016

Table S34. Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
AMP PEAK 14(16Q12.1) CNV	13	3	23
AMP PEAK 14(16Q12.1) WILD-TYPE	43	40	24

Figure S34. Get High-res Image Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 14(16q12.1)' versus 'CN_CNMF'

P value = 1.52e-20 (Fisher's exact test), Q value = 1.1e-17

Table S35. Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
AMP PEAK 14(16Q12.1) CNV	85	12	6
AMP PEAK 14(16Q12.1) WILD-TYPE	99	184	41

Figure S35. Get High-res Image Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 14(16q12.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.69e-05 (Fisher's exact test), Q value = 0.023

Table S36. Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	77	74
AMP PEAK 14(16Q12.1) CNV	29	6	12
AMP PEAK 14(16Q12.1) WILD-TYPE	51	71	62

Figure S36. Get High-res Image Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 14(16q12.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000191 (Fisher's exact test), Q value = 0.11

Table S37. Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	174	143
AMP PEAK 14(16Q12.1) CNV	7	45	46
AMP PEAK 14(16Q12.1) WILD-TYPE	73	129	97

Figure S37. Get High-res Image Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 14(16q12.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000155 (Fisher's exact test), Q value = 0.092

Table S38. Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
AMP PEAK 14(16Q12.1) CNV	27	7	20
AMP PEAK 14(16Q12.1) WILD-TYPE	52	71	43

Figure S38. Get High-res Image Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 15(17q12)' versus 'CN_CNMF'

P value = 4.15e-08 (Fisher's exact test), Q value = 2.8e-05

Table S39. Gene #15: 'Amp Peak 15(17q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
AMP PEAK 15(17Q12) CNV	67	23	14
AMP PEAK 15(17Q12) WILD-TYPE	117	173	33

Figure S39. Get High-res Image Gene #15: 'Amp Peak 15(17q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 16(17q24.1)' versus 'CN_CNMF'

P value = 3.39e-10 (Fisher's exact test), Q value = 2.3e-07

Table S40. Gene #16: 'Amp Peak 16(17q24.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
AMP PEAK 16(17Q24.1) CNV	66	17	12
AMP PEAK 16(17Q24.1) WILD-TYPE	118	179	35

Figure S40. Get High-res Image Gene #16: 'Amp Peak 16(17q24.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 16(17q24.1)' versus 'METHLYATION_CNMF'

P value = 0.000341 (Fisher's exact test), Q value = 0.19

Table S41. Gene #16: 'Amp Peak 16(17q24.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
AMP PEAK 16(17Q24.1) CNV	41	16	8
AMP PEAK 16(17Q24.1) WILD-TYPE	73	72	60

Figure S41. Get High-res Image Gene #16: 'Amp Peak 16(17q24.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 16(17q24.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000306 (Fisher's exact test), Q value = 0.18

Table S42. Gene #16: 'Amp Peak 16(17q24.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	77	74
AMP PEAK 16(17Q24.1) CNV	22	7	26
AMP PEAK 16(17Q24.1) WILD-TYPE	58	70	48

Figure S42. Get High-res Image Gene #16: 'Amp Peak 16(17q24.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 19(20p11.23)' versus 'CN_CNMF'

P value = 9.01e-11 (Fisher's exact test), Q value = 6.2e-08

Table S43. Gene #19: 'Amp Peak 19(20p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
AMP PEAK 19(20P11.23) CNV	119	61	28
AMP PEAK 19(20P11.23) WILD-TYPE	65	135	19

Figure S43. Get High-res Image Gene #19: 'Amp Peak 19(20p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 19(20p11.23)' versus 'MRNASEQ_CNMF'

P value = 0.000246 (Fisher's exact test), Q value = 0.14

Table S44. Gene #19: 'Amp Peak 19(20p11.23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	70	57	61
AMP PEAK 19(20P11.23) CNV	24	42	24	15
AMP PEAK 19(20P11.23) WILD-TYPE	19	28	33	46

Figure S44. Get High-res Image Gene #19: 'Amp Peak 19(20p11.23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 19(20p11.23)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000272 (Fisher's exact test), Q value = 0.16

Table S45. Gene #19: 'Amp Peak 19(20p11.23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	77	74
AMP PEAK 19(20P11.23) CNV	41	21	43
AMP PEAK 19(20P11.23) WILD-TYPE	39	56	31

Figure S45. Get High-res Image Gene #19: 'Amp Peak 19(20p11.23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 3.87e-10 (Fisher's exact test), Q value = 2.6e-07

Table S46. Gene #20: 'Amp Peak 20(20q11.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
AMP PEAK 20(20Q11.21) CNV	13	58	16	18
AMP PEAK 20(20Q11.21) WILD-TYPE	22	3	13	3

Figure S46. Get High-res Image Gene #20: 'Amp Peak 20(20q11.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

P value = 7.28e-12 (Fisher's exact test), Q value = 5.1e-09

Table S47. Gene #20: 'Amp Peak 20(20q11.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
AMP PEAK 20(20Q11.21) CNV	50	13	42
AMP PEAK 20(20Q11.21) WILD-TYPE	6	30	5

Figure S47. Get High-res Image Gene #20: 'Amp Peak 20(20q11.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

P value = 5.06e-42 (Fisher's exact test), Q value = 3.8e-39

Table S48. Gene #20: 'Amp Peak 20(20q11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
AMP PEAK 20(20Q11.21) CNV	181	81	44
AMP PEAK 20(20Q11.21) WILD-TYPE	3	115	3

Figure S48. Get High-res Image Gene #20: 'Amp Peak 20(20q11.21)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 1.91e-12 (Fisher's exact test), Q value = 1.3e-09

Table S49. Gene #20: 'Amp Peak 20(20q11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
AMP PEAK 20(20Q11.21) CNV	107	46	42
AMP PEAK 20(20Q11.21) WILD-TYPE	7	42	26

Figure S49. Get High-res Image Gene #20: 'Amp Peak 20(20q11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 20(20q11.21)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000108 (Fisher's exact test), Q value = 0.065

Table S50. Gene #20: 'Amp Peak 20(20q11.21)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	56	63	180
AMP PEAK 20(20Q11.21) CNV	13	29	53	133
AMP PEAK 20(20Q11.21) WILD-TYPE	13	27	10	47

Figure S50. Get High-res Image Gene #20: 'Amp Peak 20(20q11.21)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

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

P value = 2.4e-15 (Fisher's exact test), Q value = 1.7e-12

Table S51. Gene #20: 'Amp Peak 20(20q11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	70	57	61
AMP PEAK 20(20Q11.21) CNV	31	68	42	20
AMP PEAK 20(20Q11.21) WILD-TYPE	12	2	15	41

Figure S51. Get High-res Image Gene #20: 'Amp Peak 20(20q11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 3.41e-17 (Fisher's exact test), Q value = 2.5e-14

Table S52. Gene #20: 'Amp Peak 20(20q11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	77	74
AMP PEAK 20(20Q11.21) CNV	69	25	67
AMP PEAK 20(20Q11.21) WILD-TYPE	11	52	7

Figure S52. Get High-res Image Gene #20: 'Amp Peak 20(20q11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 20(20q11.21)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000103 (Fisher's exact test), Q value = 0.062

Table S53. Gene #20: 'Amp Peak 20(20q11.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	174	143
AMP PEAK 20(20Q11.21) CNV	43	125	116
AMP PEAK 20(20Q11.21) WILD-TYPE	37	49	27

Figure S53. Get High-res Image Gene #20: 'Amp Peak 20(20q11.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 2.18e-12 (Fisher's exact test), Q value = 1.5e-09

Table S54. Gene #20: 'Amp Peak 20(20q11.21)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
AMP PEAK 20(20Q11.21) CNV	74	34	51
AMP PEAK 20(20Q11.21) WILD-TYPE	5	44	12

Figure S54. Get High-res Image Gene #20: 'Amp Peak 20(20q11.21)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 21(20q12)' versus 'MRNA_CNMF'

P value = 4.29e-11 (Fisher's exact test), Q value = 3e-08

Table S55. Gene #21: 'Amp Peak 21(20q12)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
AMP PEAK 21(20Q12) CNV	12	58	15	18
AMP PEAK 21(20Q12) WILD-TYPE	23	3	14	3

Figure S55. Get High-res Image Gene #21: 'Amp Peak 21(20q12)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 21(20q12)' versus 'MRNA_CHIERARCHICAL'

P value = 4.99e-12 (Fisher's exact test), Q value = 3.5e-09

Table S56. Gene #21: 'Amp Peak 21(20q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
AMP PEAK 21(20Q12) CNV	49	12	42
AMP PEAK 21(20Q12) WILD-TYPE	7	31	5

Figure S56. Get High-res Image Gene #21: 'Amp Peak 21(20q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 21(20q12)' versus 'CN_CNMF'

P value = 1.74e-41 (Fisher's exact test), Q value = 1.3e-38

Table S57. Gene #21: 'Amp Peak 21(20q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
AMP PEAK 21(20Q12) CNV	181	82	44
AMP PEAK 21(20Q12) WILD-TYPE	3	114	3

Figure S57. Get High-res Image Gene #21: 'Amp Peak 21(20q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 21(20q12)' versus 'METHLYATION_CNMF'

P value = 1.68e-11 (Fisher's exact test), Q value = 1.2e-08

Table S58. Gene #21: 'Amp Peak 21(20q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
AMP PEAK 21(20Q12) CNV	107	48	43
AMP PEAK 21(20Q12) WILD-TYPE	7	40	25

Figure S58. Get High-res Image Gene #21: 'Amp Peak 21(20q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 21(20q12)' versus 'RPPA_CHIERARCHICAL'

P value = 2.18e-05 (Fisher's exact test), Q value = 0.014

Table S59. Gene #21: 'Amp Peak 21(20q12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	56	63	180
AMP PEAK 21(20Q12) CNV	13	29	55	132
AMP PEAK 21(20Q12) WILD-TYPE	13	27	8	48

Figure S59. Get High-res Image Gene #21: 'Amp Peak 21(20q12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 21(20q12)' versus 'MRNASEQ_CNMF'

P value = 3.88e-14 (Fisher's exact test), Q value = 2.8e-11

Table S60. Gene #21: 'Amp Peak 21(20q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	70	57	61
AMP PEAK 21(20Q12) CNV	31	68	43	22
AMP PEAK 21(20Q12) WILD-TYPE	12	2	14	39

Figure S60. Get High-res Image Gene #21: 'Amp Peak 21(20q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 21(20q12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.6e-16 (Fisher's exact test), Q value = 1.9e-13

Table S61. Gene #21: 'Amp Peak 21(20q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	77	74
AMP PEAK 21(20Q12) CNV	70	27	67
AMP PEAK 21(20Q12) WILD-TYPE	10	50	7

Figure S61. Get High-res Image Gene #21: 'Amp Peak 21(20q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 21(20q12)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000125 (Fisher's exact test), Q value = 0.075

Table S62. Gene #21: 'Amp Peak 21(20q12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	174	143
AMP PEAK 21(20Q12) CNV	44	124	117
AMP PEAK 21(20Q12) WILD-TYPE	36	50	26

Figure S62. Get High-res Image Gene #21: 'Amp Peak 21(20q12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 21(20q12)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.94e-13 (Fisher's exact test), Q value = 1.4e-10

Table S63. Gene #21: 'Amp Peak 21(20q12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
AMP PEAK 21(20Q12) CNV	75	34	52
AMP PEAK 21(20Q12) WILD-TYPE	4	44	11

Figure S63. Get High-res Image Gene #21: 'Amp Peak 21(20q12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 22(20q13.12)' versus 'MRNA_CNMF'

P value = 3.87e-10 (Fisher's exact test), Q value = 2.6e-07

Table S64. Gene #22: 'Amp Peak 22(20q13.12)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
AMP PEAK 22(20Q13.12) CNV	13	58	16	18
AMP PEAK 22(20Q13.12) WILD-TYPE	22	3	13	3

Figure S64. Get High-res Image Gene #22: 'Amp Peak 22(20q13.12)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 22(20q13.12)' versus 'MRNA_CHIERARCHICAL'

P value = 7.28e-12 (Fisher's exact test), Q value = 5.1e-09

Table S65. Gene #22: 'Amp Peak 22(20q13.12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
AMP PEAK 22(20Q13.12) CNV	50	13	42
AMP PEAK 22(20Q13.12) WILD-TYPE	6	30	5

Figure S65. Get High-res Image Gene #22: 'Amp Peak 22(20q13.12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 22(20q13.12)' versus 'CN_CNMF'

P value = 3.63e-41 (Fisher's exact test), Q value = 2.7e-38

Table S66. Gene #22: 'Amp Peak 22(20q13.12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
AMP PEAK 22(20Q13.12) CNV	181	84	45
AMP PEAK 22(20Q13.12) WILD-TYPE	3	112	2

Figure S66. Get High-res Image Gene #22: 'Amp Peak 22(20q13.12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 22(20q13.12)' versus 'METHLYATION_CNMF'

P value = 3.72e-11 (Fisher's exact test), Q value = 2.6e-08

Table S67. Gene #22: 'Amp Peak 22(20q13.12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
AMP PEAK 22(20Q13.12) CNV	107	49	43
AMP PEAK 22(20Q13.12) WILD-TYPE	7	39	25

Figure S67. Get High-res Image Gene #22: 'Amp Peak 22(20q13.12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 22(20q13.12)' versus 'RPPA_CNMF'

P value = 0.000237 (Fisher's exact test), Q value = 0.14

Table S68. Gene #22: 'Amp Peak 22(20q13.12)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	127	26	94
AMP PEAK 22(20Q13.12) CNV	64	96	21	51
AMP PEAK 22(20Q13.12) WILD-TYPE	14	31	5	43

Figure S68. Get High-res Image Gene #22: 'Amp Peak 22(20q13.12)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 22(20q13.12)' versus 'RPPA_CHIERARCHICAL'

P value = 1.3e-05 (Fisher's exact test), Q value = 0.0082

Table S69. Gene #22: 'Amp Peak 22(20q13.12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	56	63	180
AMP PEAK 22(20Q13.12) CNV	13	29	55	135
AMP PEAK 22(20Q13.12) WILD-TYPE	13	27	8	45

Figure S69. Get High-res Image Gene #22: 'Amp Peak 22(20q13.12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 22(20q13.12)' versus 'MRNASEQ_CNMF'

P value = 1.62e-13 (Fisher's exact test), Q value = 1.2e-10

Table S70. Gene #22: 'Amp Peak 22(20q13.12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	70	57	61
AMP PEAK 22(20Q13.12) CNV	31	68	43	23
AMP PEAK 22(20Q13.12) WILD-TYPE	12	2	14	38

Figure S70. Get High-res Image Gene #22: 'Amp Peak 22(20q13.12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 22(20q13.12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.27e-15 (Fisher's exact test), Q value = 9.3e-13

Table S71. Gene #22: 'Amp Peak 22(20q13.12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	77	74
AMP PEAK 22(20Q13.12) CNV	70	28	67
AMP PEAK 22(20Q13.12) WILD-TYPE	10	49	7

Figure S71. Get High-res Image Gene #22: 'Amp Peak 22(20q13.12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 22(20q13.12)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.16

Table S72. Gene #22: 'Amp Peak 22(20q13.12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	174	143
AMP PEAK 22(20Q13.12) CNV	45	126	117
AMP PEAK 22(20Q13.12) WILD-TYPE	35	48	26

Figure S72. Get High-res Image Gene #22: 'Amp Peak 22(20q13.12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 22(20q13.12)' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.84e-13 (Fisher's exact test), Q value = 4.1e-10

Table S73. Gene #22: 'Amp Peak 22(20q13.12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
AMP PEAK 22(20Q13.12) CNV	75	35	52
AMP PEAK 22(20Q13.12) WILD-TYPE	4	43	11

Figure S73. Get High-res Image Gene #22: 'Amp Peak 22(20q13.12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 0.00015 (Fisher's exact test), Q value = 0.089

Table S74. Gene #23: 'Del Peak 1(1p36.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 1(1P36.11) CNV	9	35	4	10
DEL PEAK 1(1P36.11) WILD-TYPE	26	26	25	11

Figure S74. Get High-res Image Gene #23: 'Del Peak 1(1p36.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

P value = 1.82e-13 (Fisher's exact test), Q value = 1.3e-10

Table S75. Gene #23: 'Del Peak 1(1p36.11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
DEL PEAK 1(1P36.11) CNV	101	35	16
DEL PEAK 1(1P36.11) WILD-TYPE	83	161	31

Figure S75. Get High-res Image Gene #23: 'Del Peak 1(1p36.11)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 6.08e-05 (Fisher's exact test), Q value = 0.037

Table S76. Gene #23: 'Del Peak 1(1p36.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
DEL PEAK 1(1P36.11) CNV	55	17	20
DEL PEAK 1(1P36.11) WILD-TYPE	59	71	48

Figure S76. Get High-res Image Gene #23: 'Del Peak 1(1p36.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 3.98e-05 (Fisher's exact test), Q value = 0.025

Table S77. Gene #23: 'Del Peak 1(1p36.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	70	57	61
DEL PEAK 1(1P36.11) CNV	14	36	22	8
DEL PEAK 1(1P36.11) WILD-TYPE	29	34	35	53

Figure S77. Get High-res Image Gene #23: 'Del Peak 1(1p36.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 3.29e-05 (Fisher's exact test), Q value = 0.02

Table S78. Gene #23: 'Del Peak 1(1p36.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	77	74
DEL PEAK 1(1P36.11) CNV	38	12	30
DEL PEAK 1(1P36.11) WILD-TYPE	42	65	44

Figure S78. Get High-res Image Gene #23: 'Del Peak 1(1p36.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 0.000156 (Fisher's exact test), Q value = 0.093

Table S79. Gene #23: 'Del Peak 1(1p36.11)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 1(1P36.11) CNV	36	13	26
DEL PEAK 1(1P36.11) WILD-TYPE	43	65	37

Figure S79. Get High-res Image Gene #23: 'Del Peak 1(1p36.11)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 1.12e-08 (Fisher's exact test), Q value = 7.5e-06

Table S80. Gene #24: 'Del Peak 2(1p33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
DEL PEAK 2(1P33) CNV	73	26	9
DEL PEAK 2(1P33) WILD-TYPE	111	170	38

Figure S80. Get High-res Image Gene #24: 'Del Peak 2(1p33)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 4(3p26.1)' versus 'CN_CNMF'

P value = 4.05e-05 (Fisher's exact test), Q value = 0.025

Table S81. Gene #26: 'Del Peak 4(3p26.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
DEL PEAK 4(3P26.1) CNV	43	15	4
DEL PEAK 4(3P26.1) WILD-TYPE	141	181	43

Figure S81. Get High-res Image Gene #26: 'Del Peak 4(3p26.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 7(4p16.1)' versus 'CN_CNMF'

P value = 1.11e-12 (Fisher's exact test), Q value = 7.8e-10

Table S82. Gene #29: 'Del Peak 7(4p16.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
DEL PEAK 7(4P16.1) CNV	88	27	11
DEL PEAK 7(4P16.1) WILD-TYPE	96	169	36

Figure S82. Get High-res Image Gene #29: 'Del Peak 7(4p16.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 7(4p16.1)' versus 'MRNASEQ_CNMF'

P value = 3.17e-06 (Fisher's exact test), Q value = 0.0021

Table S83. Gene #29: 'Del Peak 7(4p16.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	70	57	61
DEL PEAK 7(4P16.1) CNV	12	29	20	3
DEL PEAK 7(4P16.1) WILD-TYPE	31	41	37	58

Figure S83. Get High-res Image Gene #29: 'Del Peak 7(4p16.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 7(4p16.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.56e-07 (Fisher's exact test), Q value = 0.00017

Table S84. Gene #29: 'Del Peak 7(4p16.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	77	74
DEL PEAK 7(4P16.1) CNV	32	5	27
DEL PEAK 7(4P16.1) WILD-TYPE	48	72	47

Figure S84. Get High-res Image Gene #29: 'Del Peak 7(4p16.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 7(4p16.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000229 (Fisher's exact test), Q value = 0.13

Table S85. Gene #29: 'Del Peak 7(4p16.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 7(4P16.1) CNV	27	8	22
DEL PEAK 7(4P16.1) WILD-TYPE	52	70	41

Figure S85. Get High-res Image Gene #29: 'Del Peak 7(4p16.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 8(4q22.1)' versus 'MRNA_CNMF'

P value = 0.000383 (Fisher's exact test), Q value = 0.22

Table S86. Gene #30: 'Del Peak 8(4q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 8(4Q22.1) CNV	9	27	2	11
DEL PEAK 8(4Q22.1) WILD-TYPE	26	34	27	10

Figure S86. Get High-res Image Gene #30: 'Del Peak 8(4q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 8(4q22.1)' versus 'CN_CNMF'

P value = 1.38e-13 (Fisher's exact test), Q value = 9.8e-11

Table S87. Gene #30: 'Del Peak 8(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
DEL PEAK 8(4Q22.1) CNV	93	33	6
DEL PEAK 8(4Q22.1) WILD-TYPE	91	163	41

Figure S87. Get High-res Image Gene #30: 'Del Peak 8(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 8(4q22.1)' versus 'METHLYATION_CNMF'

P value = 0.000212 (Fisher's exact test), Q value = 0.12

Table S88. Gene #30: 'Del Peak 8(4q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
DEL PEAK 8(4Q22.1) CNV	46	13	23
DEL PEAK 8(4Q22.1) WILD-TYPE	68	75	45

Figure S88. Get High-res Image Gene #30: 'Del Peak 8(4q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 8(4q22.1)' versus 'MRNASEQ_CNMF'

P value = 3.91e-06 (Fisher's exact test), Q value = 0.0025

Table S89. Gene #30: 'Del Peak 8(4q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	70	57	61
DEL PEAK 8(4Q22.1) CNV	12	34	19	5
DEL PEAK 8(4Q22.1) WILD-TYPE	31	36	38	56

Figure S89. Get High-res Image Gene #30: 'Del Peak 8(4q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 8(4q22.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.21e-07 (Fisher's exact test), Q value = 0.00047

Table S90. Gene #30: 'Del Peak 8(4q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	77	74
DEL PEAK 8(4Q22.1) CNV	35	7	28
DEL PEAK 8(4Q22.1) WILD-TYPE	45	70	46

Figure S90. Get High-res Image Gene #30: 'Del Peak 8(4q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 9(4q35.1)' versus 'CN_CNMF'

P value = 3.74e-15 (Fisher's exact test), Q value = 2.7e-12

Table S91. Gene #31: 'Del Peak 9(4q35.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
DEL PEAK 9(4Q35.1) CNV	100	32	10
DEL PEAK 9(4Q35.1) WILD-TYPE	84	164	37

Figure S91. Get High-res Image Gene #31: 'Del Peak 9(4q35.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 9(4q35.1)' versus 'METHLYATION_CNMF'

P value = 1.28e-05 (Fisher's exact test), Q value = 0.0081

Table S92. Gene #31: 'Del Peak 9(4q35.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
DEL PEAK 9(4Q35.1) CNV	50	12	23
DEL PEAK 9(4Q35.1) WILD-TYPE	64	76	45

Figure S92. Get High-res Image Gene #31: 'Del Peak 9(4q35.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 9(4q35.1)' versus 'MRNASEQ_CNMF'

P value = 1.5e-05 (Fisher's exact test), Q value = 0.0095

Table S93. Gene #31: 'Del Peak 9(4q35.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	70	57	61
DEL PEAK 9(4Q35.1) CNV	14	36	18	7
DEL PEAK 9(4Q35.1) WILD-TYPE	29	34	39	54

Figure S93. Get High-res Image Gene #31: 'Del Peak 9(4q35.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 9(4q35.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.05e-05 (Fisher's exact test), Q value = 0.013

Table S94. Gene #31: 'Del Peak 9(4q35.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	77	74
DEL PEAK 9(4Q35.1) CNV	33	10	32
DEL PEAK 9(4Q35.1) WILD-TYPE	47	67	42

Figure S94. Get High-res Image Gene #31: 'Del Peak 9(4q35.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 9(4q35.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.93e-06 (Fisher's exact test), Q value = 0.0038

Table S95. Gene #31: 'Del Peak 9(4q35.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 9(4Q35.1) CNV	33	8	24
DEL PEAK 9(4Q35.1) WILD-TYPE	46	70	39

Figure S95. Get High-res Image Gene #31: 'Del Peak 9(4q35.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 10(5q11.2)' versus 'CN_CNMF'

P value = 8.17e-10 (Fisher's exact test), Q value = 5.5e-07

Table S96. Gene #32: 'Del Peak 10(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
DEL PEAK 10(5Q11.2) CNV	64	17	13
DEL PEAK 10(5Q11.2) WILD-TYPE	120	179	34

Figure S96. Get High-res Image Gene #32: 'Del Peak 10(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 10(5q11.2)' versus 'MRNASEQ_CNMF'

P value = 4.77e-05 (Fisher's exact test), Q value = 0.029

Table S97. Gene #32: 'Del Peak 10(5q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	70	57	61
DEL PEAK 10(5Q11.2) CNV	12	23	10	2
DEL PEAK 10(5Q11.2) WILD-TYPE	31	47	47	59

Figure S97. Get High-res Image Gene #32: 'Del Peak 10(5q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 10(5q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.09e-05 (Fisher's exact test), Q value = 0.043

Table S98. Gene #32: 'Del Peak 10(5q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	77	74
DEL PEAK 10(5Q11.2) CNV	23	4	20
DEL PEAK 10(5Q11.2) WILD-TYPE	57	73	54

Figure S98. Get High-res Image Gene #32: 'Del Peak 10(5q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 10(5q11.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000273 (Fisher's exact test), Q value = 0.16

Table S99. Gene #32: 'Del Peak 10(5q11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 10(5Q11.2) CNV	24	5	15
DEL PEAK 10(5Q11.2) WILD-TYPE	55	73	48

Figure S99. Get High-res Image Gene #32: 'Del Peak 10(5q11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 11(5q21.3)' versus 'CN_CNMF'

P value = 2.27e-11 (Fisher's exact test), Q value = 1.6e-08

Table S100. Gene #33: 'Del Peak 11(5q21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
DEL PEAK 11(5Q21.3) CNV	79	24	17
DEL PEAK 11(5Q21.3) WILD-TYPE	105	172	30

Figure S100. Get High-res Image Gene #33: 'Del Peak 11(5q21.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 12(5q23.1)' versus 'CN_CNMF'

P value = 7.91e-11 (Fisher's exact test), Q value = 5.5e-08

Table S101. Gene #34: 'Del Peak 12(5q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
DEL PEAK 12(5Q23.1) CNV	73	21	16
DEL PEAK 12(5Q23.1) WILD-TYPE	111	175	31

Figure S101. Get High-res Image Gene #34: 'Del Peak 12(5q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 12(5q23.1)' versus 'MRNASEQ_CNMF'

P value = 0.000231 (Fisher's exact test), Q value = 0.13

Table S102. Gene #34: 'Del Peak 12(5q23.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	70	57	61
DEL PEAK 12(5Q23.1) CNV	13	29	11	6
DEL PEAK 12(5Q23.1) WILD-TYPE	30	41	46	55

Figure S102. Get High-res Image Gene #34: 'Del Peak 12(5q23.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 12(5q23.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.59e-05 (Fisher's exact test), Q value = 0.058

Table S103. Gene #34: 'Del Peak 12(5q23.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	77	74
DEL PEAK 12(5Q23.1) CNV	26	7	26
DEL PEAK 12(5Q23.1) WILD-TYPE	54	70	48

Figure S103. Get High-res Image Gene #34: 'Del Peak 12(5q23.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 16(8p23.3)' versus 'MRNA_CHIERARCHICAL'

P value = 6.76e-05 (Fisher's exact test), Q value = 0.041

Table S104. Gene #38: 'Del Peak 16(8p23.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
DEL PEAK 16(8P23.3) CNV	19	11	32
DEL PEAK 16(8P23.3) WILD-TYPE	37	32	15

Figure S104. Get High-res Image Gene #38: 'Del Peak 16(8p23.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 16(8p23.3)' versus 'CN_CNMF'

P value = 6.52e-21 (Fisher's exact test), Q value = 4.8e-18

Table S105. Gene #38: 'Del Peak 16(8p23.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
DEL PEAK 16(8P23.3) CNV	120	35	21
DEL PEAK 16(8P23.3) WILD-TYPE	64	161	26

Figure S105. Get High-res Image Gene #38: 'Del Peak 16(8p23.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 16(8p23.3)' versus 'METHLYATION_CNMF'

P value = 3.21e-07 (Fisher's exact test), Q value = 0.00021

Table S106. Gene #38: 'Del Peak 16(8p23.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
DEL PEAK 16(8P23.3) CNV	68	20	24
DEL PEAK 16(8P23.3) WILD-TYPE	46	68	44

Figure S106. Get High-res Image Gene #38: 'Del Peak 16(8p23.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 16(8p23.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.72e-06 (Fisher's exact test), Q value = 0.0018

Table S107. Gene #38: 'Del Peak 16(8p23.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	77	74
DEL PEAK 16(8P23.3) CNV	44	14	35
DEL PEAK 16(8P23.3) WILD-TYPE	36	63	39

Figure S107. Get High-res Image Gene #38: 'Del Peak 16(8p23.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 16(8p23.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.15e-07 (Fisher's exact test), Q value = 0.00014

Table S108. Gene #38: 'Del Peak 16(8p23.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 16(8P23.3) CNV	46	14	32
DEL PEAK 16(8P23.3) WILD-TYPE	33	64	31

Figure S108. Get High-res Image Gene #38: 'Del Peak 16(8p23.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 17(8p22)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000174 (Fisher's exact test), Q value = 0.1

Table S109. Gene #39: 'Del Peak 17(8p22)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
DEL PEAK 17(8P22) CNV	25	9	30
DEL PEAK 17(8P22) WILD-TYPE	31	34	17

Figure S109. Get High-res Image Gene #39: 'Del Peak 17(8p22)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 17(8p22)' versus 'CN_CNMF'

P value = 2.78e-26 (Fisher's exact test), Q value = 2.1e-23

Table S110. Gene #39: 'Del Peak 17(8p22)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
DEL PEAK 17(8P22) CNV	131	35	24
DEL PEAK 17(8P22) WILD-TYPE	53	161	23

Figure S110. Get High-res Image Gene #39: 'Del Peak 17(8p22)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 17(8p22)' versus 'METHLYATION_CNMF'

P value = 4.13e-08 (Fisher's exact test), Q value = 2.8e-05

Table S111. Gene #39: 'Del Peak 17(8p22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
DEL PEAK 17(8P22) CNV	75	23	26
DEL PEAK 17(8P22) WILD-TYPE	39	65	42

Figure S111. Get High-res Image Gene #39: 'Del Peak 17(8p22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 17(8p22)' versus 'RPPA_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.078

Table S112. Gene #39: 'Del Peak 17(8p22)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	56	63	180
DEL PEAK 17(8P22) CNV	5	15	38	82
DEL PEAK 17(8P22) WILD-TYPE	21	41	25	98

Figure S112. Get High-res Image Gene #39: 'Del Peak 17(8p22)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 17(8p22)' versus 'MRNASEQ_CNMF'

P value = 5.24e-05 (Fisher's exact test), Q value = 0.032

Table S113. Gene #39: 'Del Peak 17(8p22)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	70	57	61
DEL PEAK 17(8P22) CNV	20	43	27	13
DEL PEAK 17(8P22) WILD-TYPE	23	27	30	48

Figure S113. Get High-res Image Gene #39: 'Del Peak 17(8p22)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 17(8p22)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.41e-06 (Fisher's exact test), Q value = 0.0022

Table S114. Gene #39: 'Del Peak 17(8p22)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	77	74
DEL PEAK 17(8P22) CNV	47	17	39
DEL PEAK 17(8P22) WILD-TYPE	33	60	35

Figure S114. Get High-res Image Gene #39: 'Del Peak 17(8p22)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 17(8p22)' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.34e-07 (Fisher's exact test), Q value = 0.00022

Table S115. Gene #39: 'Del Peak 17(8p22)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 17(8P22) CNV	50	18	36
DEL PEAK 17(8P22) WILD-TYPE	29	60	27

Figure S115. Get High-res Image Gene #39: 'Del Peak 17(8p22)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 18(8p11.22)' versus 'CN_CNMF'

P value = 6.26e-10 (Fisher's exact test), Q value = 4.2e-07

Table S116. Gene #40: 'Del Peak 18(8p11.22)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
DEL PEAK 18(8P11.22) CNV	61	21	1
DEL PEAK 18(8P11.22) WILD-TYPE	123	175	46

Figure S116. Get High-res Image Gene #40: 'Del Peak 18(8p11.22)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 19(8p11.21)' versus 'CN_CNMF'

P value = 6.26e-07 (Fisher's exact test), Q value = 0.00041

Table S117. Gene #41: 'Del Peak 19(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
DEL PEAK 19(8P11.21) CNV	35	9	0
DEL PEAK 19(8P11.21) WILD-TYPE	149	187	47

Figure S117. Get High-res Image Gene #41: 'Del Peak 19(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 21(10p15.3)' versus 'CN_CNMF'

P value = 1.05e-06 (Fisher's exact test), Q value = 0.00069

Table S118. Gene #43: 'Del Peak 21(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
DEL PEAK 21(10P15.3) CNV	47	13	9
DEL PEAK 21(10P15.3) WILD-TYPE	137	183	38

Figure S118. Get High-res Image Gene #43: 'Del Peak 21(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 22(10q21.1)' versus 'CN_CNMF'

P value = 7.55e-10 (Fisher's exact test), Q value = 5.1e-07

Table S119. Gene #44: 'Del Peak 22(10q21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
DEL PEAK 22(10Q21.1) CNV	60	14	10
DEL PEAK 22(10Q21.1) WILD-TYPE	124	182	37

Figure S119. Get High-res Image Gene #44: 'Del Peak 22(10q21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 23(10q23.31)' versus 'CN_CNMF'

P value = 1.68e-07 (Fisher's exact test), Q value = 0.00011

Table S120. Gene #45: 'Del Peak 23(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
DEL PEAK 23(10Q23.31) CNV	64	22	11
DEL PEAK 23(10Q23.31) WILD-TYPE	120	174	36

Figure S120. Get High-res Image Gene #45: 'Del Peak 23(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 24(10q25.2)' versus 'CN_CNMF'

P value = 8.89e-11 (Fisher's exact test), Q value = 6.1e-08

Table S121. Gene #46: 'Del Peak 24(10q25.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
DEL PEAK 24(10Q25.2) CNV	68	17	10
DEL PEAK 24(10Q25.2) WILD-TYPE	116	179	37

Figure S121. Get High-res Image Gene #46: 'Del Peak 24(10q25.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 24(10q25.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.27e-05 (Fisher's exact test), Q value = 0.0081

Table S122. Gene #46: 'Del Peak 24(10q25.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 24(10Q25.2) CNV	26	4	17
DEL PEAK 24(10Q25.2) WILD-TYPE	53	74	46

Figure S122. Get High-res Image Gene #46: 'Del Peak 24(10q25.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 26(14q32.11)' versus 'MRNA_CNMF'

P value = 1.58e-06 (Fisher's exact test), Q value = 0.001

Table S123. Gene #48: 'Del Peak 26(14q32.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 26(14Q32.11) CNV	8	36	2	10
DEL PEAK 26(14Q32.11) WILD-TYPE	27	25	27	11

Figure S123. Get High-res Image Gene #48: 'Del Peak 26(14q32.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 26(14q32.11)' versus 'MRNA_CHIERARCHICAL'

P value = 3.23e-05 (Fisher's exact test), Q value = 0.02

Table S124. Gene #48: 'Del Peak 26(14q32.11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
DEL PEAK 26(14Q32.11) CNV	22	6	28
DEL PEAK 26(14Q32.11) WILD-TYPE	34	37	19

Figure S124. Get High-res Image Gene #48: 'Del Peak 26(14q32.11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 26(14q32.11)' versus 'CN_CNMF'

P value = 1.67e-21 (Fisher's exact test), Q value = 1.2e-18

Table S125. Gene #48: 'Del Peak 26(14q32.11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
DEL PEAK 26(14Q32.11) CNV	104	24	7
DEL PEAK 26(14Q32.11) WILD-TYPE	80	172	40

Figure S125. Get High-res Image Gene #48: 'Del Peak 26(14q32.11)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 26(14q32.11)' versus 'METHLYATION_CNMF'

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

Table S126. Gene #48: 'Del Peak 26(14q32.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
DEL PEAK 26(14Q32.11) CNV	47	14	17
DEL PEAK 26(14Q32.11) WILD-TYPE	67	74	51

Figure S126. Get High-res Image Gene #48: 'Del Peak 26(14q32.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 26(14q32.11)' versus 'RPPA_CNMF'

P value = 0.000199 (Fisher's exact test), Q value = 0.12

Table S127. Gene #48: 'Del Peak 26(14q32.11)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	127	26	94
DEL PEAK 26(14Q32.11) CNV	30	51	9	14
DEL PEAK 26(14Q32.11) WILD-TYPE	48	76	17	80

Figure S127. Get High-res Image Gene #48: 'Del Peak 26(14q32.11)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 26(14q32.11)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.38e-05 (Fisher's exact test), Q value = 0.045

Table S128. Gene #48: 'Del Peak 26(14q32.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	77	74
DEL PEAK 26(14Q32.11) CNV	31	8	24
DEL PEAK 26(14Q32.11) WILD-TYPE	49	69	50

Figure S128. Get High-res Image Gene #48: 'Del Peak 26(14q32.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 26(14q32.11)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.1

Table S129. Gene #48: 'Del Peak 26(14q32.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	174	143
DEL PEAK 26(14Q32.11) CNV	11	66	51
DEL PEAK 26(14Q32.11) WILD-TYPE	69	108	92

Figure S129. Get High-res Image Gene #48: 'Del Peak 26(14q32.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 26(14q32.11)' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.78e-05 (Fisher's exact test), Q value = 0.041

Table S130. Gene #48: 'Del Peak 26(14q32.11)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 26(14Q32.11) CNV	32	9	22
DEL PEAK 26(14Q32.11) WILD-TYPE	47	69	41

Figure S130. Get High-res Image Gene #48: 'Del Peak 26(14q32.11)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 27(15q11.2)' versus 'CN_CNMF'

P value = 8.07e-21 (Fisher's exact test), Q value = 6e-18

Table S131. Gene #49: 'Del Peak 27(15q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
DEL PEAK 27(15Q11.2) CNV	117	34	12
DEL PEAK 27(15Q11.2) WILD-TYPE	67	162	35

Figure S131. Get High-res Image Gene #49: 'Del Peak 27(15q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 27(15q11.2)' versus 'MRNASEQ_CNMF'

P value = 5.1e-06 (Fisher's exact test), Q value = 0.0033

Table S132. Gene #49: 'Del Peak 27(15q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	70	57	61
DEL PEAK 27(15Q11.2) CNV	15	37	23	7
DEL PEAK 27(15Q11.2) WILD-TYPE	28	33	34	54

Figure S132. Get High-res Image Gene #49: 'Del Peak 27(15q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 27(15q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.06e-07 (Fisher's exact test), Q value = 4e-04

Table S133. Gene #49: 'Del Peak 27(15q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	77	74
DEL PEAK 27(15Q11.2) CNV	40	10	32
DEL PEAK 27(15Q11.2) WILD-TYPE	40	67	42

Figure S133. Get High-res Image Gene #49: 'Del Peak 27(15q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 27(15q11.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.77e-05 (Fisher's exact test), Q value = 0.035

Table S134. Gene #49: 'Del Peak 27(15q11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 27(15Q11.2) CNV	40	15	29
DEL PEAK 27(15Q11.2) WILD-TYPE	39	63	34

Figure S134. Get High-res Image Gene #49: 'Del Peak 27(15q11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 28(15q21.1)' versus 'CN_CNMF'

P value = 3.06e-17 (Fisher's exact test), Q value = 2.2e-14

Table S135. Gene #50: 'Del Peak 28(15q21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
DEL PEAK 28(15Q21.1) CNV	108	34	11
DEL PEAK 28(15Q21.1) WILD-TYPE	76	162	36

Figure S135. Get High-res Image Gene #50: 'Del Peak 28(15q21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 28(15q21.1)' versus 'MRNASEQ_CNMF'

P value = 1.56e-05 (Fisher's exact test), Q value = 0.0098

Table S136. Gene #50: 'Del Peak 28(15q21.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	70	57	61
DEL PEAK 28(15Q21.1) CNV	14	34	20	6
DEL PEAK 28(15Q21.1) WILD-TYPE	29	36	37	55

Figure S136. Get High-res Image Gene #50: 'Del Peak 28(15q21.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 28(15q21.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.81e-07 (Fisher's exact test), Q value = 0.00045

Table S137. Gene #50: 'Del Peak 28(15q21.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	77	74
DEL PEAK 28(15Q21.1) CNV	37	8	29
DEL PEAK 28(15Q21.1) WILD-TYPE	43	69	45

Figure S137. Get High-res Image Gene #50: 'Del Peak 28(15q21.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 28(15q21.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000428 (Fisher's exact test), Q value = 0.24

Table S138. Gene #50: 'Del Peak 28(15q21.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 28(15Q21.1) CNV	35	14	27
DEL PEAK 28(15Q21.1) WILD-TYPE	44	64	36

Figure S138. Get High-res Image Gene #50: 'Del Peak 28(15q21.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 29(15q22.33)' versus 'MRNA_CNMF'

P value = 0.000273 (Fisher's exact test), Q value = 0.16

Table S139. Gene #51: 'Del Peak 29(15q22.33)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 29(15Q22.33) CNV	8	31	3	10
DEL PEAK 29(15Q22.33) WILD-TYPE	27	30	26	11

Figure S139. Get High-res Image Gene #51: 'Del Peak 29(15q22.33)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 29(15q22.33)' versus 'CN_CNMF'

P value = 8.89e-20 (Fisher's exact test), Q value = 6.6e-17

Table S140. Gene #51: 'Del Peak 29(15q22.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
DEL PEAK 29(15Q22.33) CNV	108	28	12
DEL PEAK 29(15Q22.33) WILD-TYPE	76	168	35

Figure S140. Get High-res Image Gene #51: 'Del Peak 29(15q22.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 29(15q22.33)' versus 'METHLYATION_CNMF'

P value = 0.000136 (Fisher's exact test), Q value = 0.081

Table S141. Gene #51: 'Del Peak 29(15q22.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
DEL PEAK 29(15Q22.33) CNV	54	17	23
DEL PEAK 29(15Q22.33) WILD-TYPE	60	71	45

Figure S141. Get High-res Image Gene #51: 'Del Peak 29(15q22.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 29(15q22.33)' versus 'MRNASEQ_CNMF'

P value = 3.82e-07 (Fisher's exact test), Q value = 0.00025

Table S142. Gene #51: 'Del Peak 29(15q22.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	70	57	61
DEL PEAK 29(15Q22.33) CNV	15	37	20	5
DEL PEAK 29(15Q22.33) WILD-TYPE	28	33	37	56

Figure S142. Get High-res Image Gene #51: 'Del Peak 29(15q22.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 29(15q22.33)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.77e-08 (Fisher's exact test), Q value = 1.2e-05

Table S143. Gene #51: 'Del Peak 29(15q22.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	77	74
DEL PEAK 29(15Q22.33) CNV	40	7	30
DEL PEAK 29(15Q22.33) WILD-TYPE	40	70	44

Figure S143. Get High-res Image Gene #51: 'Del Peak 29(15q22.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 29(15q22.33)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.91e-05 (Fisher's exact test), Q value = 0.054

Table S144. Gene #51: 'Del Peak 29(15q22.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	174	143
DEL PEAK 29(15Q22.33) CNV	13	61	63
DEL PEAK 29(15Q22.33) WILD-TYPE	67	113	80

Figure S144. Get High-res Image Gene #51: 'Del Peak 29(15q22.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 29(15q22.33)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000119 (Fisher's exact test), Q value = 0.072

Table S145. Gene #51: 'Del Peak 29(15q22.33)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 29(15Q22.33) CNV	35	13	28
DEL PEAK 29(15Q22.33) WILD-TYPE	44	65	35

Figure S145. Get High-res Image Gene #51: 'Del Peak 29(15q22.33)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 32(17p12)' versus 'MRNA_CNMF'

P value = 2.47e-08 (Fisher's exact test), Q value = 1.7e-05

Table S146. Gene #54: 'Del Peak 32(17p12)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 32(17P12) CNV	10	49	8	15
DEL PEAK 32(17P12) WILD-TYPE	25	12	21	6

Figure S146. Get High-res Image Gene #54: 'Del Peak 32(17p12)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 32(17p12)' versus 'MRNA_CHIERARCHICAL'

P value = 4.97e-07 (Fisher's exact test), Q value = 0.00033

Table S147. Gene #54: 'Del Peak 32(17p12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
DEL PEAK 32(17P12) CNV	36	10	36
DEL PEAK 32(17P12) WILD-TYPE	20	33	11

Figure S147. Get High-res Image Gene #54: 'Del Peak 32(17p12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 32(17p12)' versus 'CN_CNMF'

P value = 3.53e-33 (Fisher's exact test), Q value = 2.6e-30

Table S148. Gene #54: 'Del Peak 32(17p12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
DEL PEAK 32(17P12) CNV	156	49	30
DEL PEAK 32(17P12) WILD-TYPE	28	147	17

Figure S148. Get High-res Image Gene #54: 'Del Peak 32(17p12)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 32(17p12)' versus 'METHLYATION_CNMF'

P value = 1.08e-10 (Fisher's exact test), Q value = 7.4e-08

Table S149. Gene #54: 'Del Peak 32(17p12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
DEL PEAK 32(17P12) CNV	89	29	31
DEL PEAK 32(17P12) WILD-TYPE	25	59	37

Figure S149. Get High-res Image Gene #54: 'Del Peak 32(17p12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 32(17p12)' versus 'RPPA_CHIERARCHICAL'

P value = 7.42e-05 (Fisher's exact test), Q value = 0.045

Table S150. Gene #54: 'Del Peak 32(17p12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	56	63	180
DEL PEAK 32(17P12) CNV	8	19	43	106
DEL PEAK 32(17P12) WILD-TYPE	18	37	20	74

Figure S150. Get High-res Image Gene #54: 'Del Peak 32(17p12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 32(17p12)' versus 'MRNASEQ_CNMF'

P value = 3.83e-11 (Fisher's exact test), Q value = 2.7e-08

Table S151. Gene #54: 'Del Peak 32(17p12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	70	57	61
DEL PEAK 32(17P12) CNV	26	56	29	12
DEL PEAK 32(17P12) WILD-TYPE	17	14	28	49

Figure S151. Get High-res Image Gene #54: 'Del Peak 32(17p12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 32(17p12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.31e-11 (Fisher's exact test), Q value = 2.3e-08

Table S152. Gene #54: 'Del Peak 32(17p12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	77	74
DEL PEAK 32(17P12) CNV	51	17	55
DEL PEAK 32(17P12) WILD-TYPE	29	60	19

Figure S152. Get High-res Image Gene #54: 'Del Peak 32(17p12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 32(17p12)' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.13e-11 (Fisher's exact test), Q value = 5.6e-08

Table S153. Gene #54: 'Del Peak 32(17p12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 32(17P12) CNV	64	22	36
DEL PEAK 32(17P12) WILD-TYPE	15	56	27

Figure S153. Get High-res Image Gene #54: 'Del Peak 32(17p12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 34(18p11.31)' versus 'MRNA_CNMF'

P value = 6.87e-12 (Fisher's exact test), Q value = 4.8e-09

Table S154. Gene #56: 'Del Peak 34(18p11.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 34(18P11.31) CNV	6	50	7	15
DEL PEAK 34(18P11.31) WILD-TYPE	29	11	22	6

Figure S154. Get High-res Image Gene #56: 'Del Peak 34(18p11.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 34(18p11.31)' versus 'MRNA_CHIERARCHICAL'

P value = 7.49e-10 (Fisher's exact test), Q value = 5.1e-07

Table S155. Gene #56: 'Del Peak 34(18p11.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
DEL PEAK 34(18P11.31) CNV	36	6	36
DEL PEAK 34(18P11.31) WILD-TYPE	20	37	11

Figure S155. Get High-res Image Gene #56: 'Del Peak 34(18p11.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 34(18p11.31)' versus 'CN_CNMF'

P value = 3.11e-44 (Fisher's exact test), Q value = 2.3e-41

Table S156. Gene #56: 'Del Peak 34(18p11.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
DEL PEAK 34(18P11.31) CNV	163	39	27
DEL PEAK 34(18P11.31) WILD-TYPE	21	157	20

Figure S156. Get High-res Image Gene #56: 'Del Peak 34(18p11.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 34(18p11.31)' versus 'METHLYATION_CNMF'

P value = 4.14e-15 (Fisher's exact test), Q value = 3e-12

Table S157. Gene #56: 'Del Peak 34(18p11.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
DEL PEAK 34(18P11.31) CNV	92	22	34
DEL PEAK 34(18P11.31) WILD-TYPE	22	66	34

Figure S157. Get High-res Image Gene #56: 'Del Peak 34(18p11.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 34(18p11.31)' versus 'RPPA_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.24

Table S158. Gene #56: 'Del Peak 34(18p11.31)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	78	127	26	94
DEL PEAK 34(18P11.31) CNV	43	78	16	32
DEL PEAK 34(18P11.31) WILD-TYPE	35	49	10	62

Figure S158. Get High-res Image Gene #56: 'Del Peak 34(18p11.31)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 34(18p11.31)' versus 'MRNASEQ_CNMF'

P value = 5.06e-18 (Fisher's exact test), Q value = 3.7e-15

Table S159. Gene #56: 'Del Peak 34(18p11.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	70	57	61
DEL PEAK 34(18P11.31) CNV	23	61	31	7
DEL PEAK 34(18P11.31) WILD-TYPE	20	9	26	54

Figure S159. Get High-res Image Gene #56: 'Del Peak 34(18p11.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 34(18p11.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.54e-18 (Fisher's exact test), Q value = 5.5e-15

Table S160. Gene #56: 'Del Peak 34(18p11.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	77	74
DEL PEAK 34(18P11.31) CNV	57	10	55
DEL PEAK 34(18P11.31) WILD-TYPE	23	67	19

Figure S160. Get High-res Image Gene #56: 'Del Peak 34(18p11.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 34(18p11.31)' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.5e-14 (Fisher's exact test), Q value = 4.7e-11

Table S161. Gene #56: 'Del Peak 34(18p11.31)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 34(18P11.31) CNV	62	15	38
DEL PEAK 34(18P11.31) WILD-TYPE	17	63	25

Figure S161. Get High-res Image Gene #56: 'Del Peak 34(18p11.31)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 35(18q12.2)' versus 'MRNA_CNMF'

P value = 1.09e-11 (Fisher's exact test), Q value = 7.7e-09

Table S162. Gene #57: 'Del Peak 35(18q12.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 35(18Q12.2) CNV	8	53	9	16
DEL PEAK 35(18Q12.2) WILD-TYPE	27	8	20	5

Figure S162. Get High-res Image Gene #57: 'Del Peak 35(18q12.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 35(18q12.2)' versus 'MRNA_CHIERARCHICAL'

P value = 2.66e-10 (Fisher's exact test), Q value = 1.8e-07

Table S163. Gene #57: 'Del Peak 35(18q12.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
DEL PEAK 35(18Q12.2) CNV	39	8	39
DEL PEAK 35(18Q12.2) WILD-TYPE	17	35	8

Figure S163. Get High-res Image Gene #57: 'Del Peak 35(18q12.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 35(18q12.2)' versus 'CN_CNMF'

P value = 7.34e-47 (Fisher's exact test), Q value = 5.5e-44

Table S164. Gene #57: 'Del Peak 35(18q12.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
DEL PEAK 35(18Q12.2) CNV	173	50	33
DEL PEAK 35(18Q12.2) WILD-TYPE	11	146	14

Figure S164. Get High-res Image Gene #57: 'Del Peak 35(18q12.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 35(18q12.2)' versus 'METHLYATION_CNMF'

P value = 1.24e-17 (Fisher's exact test), Q value = 9.1e-15

Table S165. Gene #57: 'Del Peak 35(18q12.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
DEL PEAK 35(18Q12.2) CNV	102	29	34
DEL PEAK 35(18Q12.2) WILD-TYPE	12	59	34

Figure S165. Get High-res Image Gene #57: 'Del Peak 35(18q12.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 35(18q12.2)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000421 (Fisher's exact test), Q value = 0.24

Table S166. Gene #57: 'Del Peak 35(18q12.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	56	63	180
DEL PEAK 35(18Q12.2) CNV	9	22	43	113
DEL PEAK 35(18Q12.2) WILD-TYPE	17	34	20	67

Figure S166. Get High-res Image Gene #57: 'Del Peak 35(18q12.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 35(18q12.2)' versus 'MRNASEQ_CNMF'

P value = 2.22e-17 (Fisher's exact test), Q value = 1.6e-14

Table S167. Gene #57: 'Del Peak 35(18q12.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	70	57	61
DEL PEAK 35(18Q12.2) CNV	27	63	36	10
DEL PEAK 35(18Q12.2) WILD-TYPE	16	7	21	51

Figure S167. Get High-res Image Gene #57: 'Del Peak 35(18q12.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 35(18q12.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.43e-18 (Fisher's exact test), Q value = 1.1e-15

Table S168. Gene #57: 'Del Peak 35(18q12.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	77	74
DEL PEAK 35(18Q12.2) CNV	62	14	60
DEL PEAK 35(18Q12.2) WILD-TYPE	18	63	14

Figure S168. Get High-res Image Gene #57: 'Del Peak 35(18q12.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 35(18q12.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.9e-15 (Fisher's exact test), Q value = 7.1e-12

Table S169. Gene #57: 'Del Peak 35(18q12.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 35(18Q12.2) CNV	69	21	42
DEL PEAK 35(18Q12.2) WILD-TYPE	10	57	21

Figure S169. Get High-res Image Gene #57: 'Del Peak 35(18q12.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 36(18q21.2)' versus 'MRNA_CNMF'

P value = 3.37e-11 (Fisher's exact test), Q value = 2.3e-08

Table S170. Gene #58: 'Del Peak 36(18q21.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 36(18Q21.2) CNV	8	53	10	16
DEL PEAK 36(18Q21.2) WILD-TYPE	27	8	19	5

Figure S170. Get High-res Image Gene #58: 'Del Peak 36(18q21.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 36(18q21.2)' versus 'MRNA_CHIERARCHICAL'

P value = 1.46e-10 (Fisher's exact test), Q value = 1e-07

Table S171. Gene #58: 'Del Peak 36(18q21.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
DEL PEAK 36(18Q21.2) CNV	40	8	39
DEL PEAK 36(18Q21.2) WILD-TYPE	16	35	8

Figure S171. Get High-res Image Gene #58: 'Del Peak 36(18q21.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 36(18q21.2)' versus 'CN_CNMF'

P value = 1.2e-44 (Fisher's exact test), Q value = 9e-42

Table S172. Gene #58: 'Del Peak 36(18q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
DEL PEAK 36(18Q21.2) CNV	175	58	36
DEL PEAK 36(18Q21.2) WILD-TYPE	9	138	11

Figure S172. Get High-res Image Gene #58: 'Del Peak 36(18q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 36(18q21.2)' versus 'METHLYATION_CNMF'

P value = 6.6e-14 (Fisher's exact test), Q value = 4.7e-11

Table S173. Gene #58: 'Del Peak 36(18q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
DEL PEAK 36(18Q21.2) CNV	103	38	36
DEL PEAK 36(18Q21.2) WILD-TYPE	11	50	32

Figure S173. Get High-res Image Gene #58: 'Del Peak 36(18q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 36(18q21.2)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000225 (Fisher's exact test), Q value = 0.13

Table S174. Gene #58: 'Del Peak 36(18q21.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	56	63	180
DEL PEAK 36(18Q21.2) CNV	10	24	46	120
DEL PEAK 36(18Q21.2) WILD-TYPE	16	32	17	60

Figure S174. Get High-res Image Gene #58: 'Del Peak 36(18q21.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 36(18q21.2)' versus 'MRNASEQ_CNMF'

P value = 3.56e-13 (Fisher's exact test), Q value = 2.5e-10

Table S175. Gene #58: 'Del Peak 36(18q21.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	70	57	61
DEL PEAK 36(18Q21.2) CNV	27	64	38	17
DEL PEAK 36(18Q21.2) WILD-TYPE	16	6	19	44

Figure S175. Get High-res Image Gene #58: 'Del Peak 36(18q21.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 36(18q21.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.06e-13 (Fisher's exact test), Q value = 7.6e-11

Table S176. Gene #58: 'Del Peak 36(18q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	77	74
DEL PEAK 36(18Q21.2) CNV	63	22	61
DEL PEAK 36(18Q21.2) WILD-TYPE	17	55	13

Figure S176. Get High-res Image Gene #58: 'Del Peak 36(18q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 36(18q21.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.38e-13 (Fisher's exact test), Q value = 9.8e-11

Table S177. Gene #58: 'Del Peak 36(18q21.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 36(18Q21.2) CNV	72	27	44
DEL PEAK 36(18Q21.2) WILD-TYPE	7	51	19

Figure S177. Get High-res Image Gene #58: 'Del Peak 36(18q21.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 37(18q22.1)' versus 'MRNA_CNMF'

P value = 8.76e-11 (Fisher's exact test), Q value = 6e-08

Table S178. Gene #59: 'Del Peak 37(18q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	61	29	21
DEL PEAK 37(18Q22.1) CNV	8	53	11	16
DEL PEAK 37(18Q22.1) WILD-TYPE	27	8	18	5

Figure S178. Get High-res Image Gene #59: 'Del Peak 37(18q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 37(18q22.1)' versus 'MRNA_CHIERARCHICAL'

P value = 8.34e-10 (Fisher's exact test), Q value = 5.6e-07

Table S179. Gene #59: 'Del Peak 37(18q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
DEL PEAK 37(18Q22.1) CNV	40	9	39
DEL PEAK 37(18Q22.1) WILD-TYPE	16	34	8

Figure S179. Get High-res Image Gene #59: 'Del Peak 37(18q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 37(18q22.1)' versus 'CN_CNMF'

P value = 3.76e-47 (Fisher's exact test), Q value = 2.8e-44

Table S180. Gene #59: 'Del Peak 37(18q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
DEL PEAK 37(18Q22.1) CNV	177	57	35
DEL PEAK 37(18Q22.1) WILD-TYPE	7	139	12

Figure S180. Get High-res Image Gene #59: 'Del Peak 37(18q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 37(18q22.1)' versus 'METHLYATION_CNMF'

P value = 3.75e-14 (Fisher's exact test), Q value = 2.7e-11

Table S181. Gene #59: 'Del Peak 37(18q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	88	68
DEL PEAK 37(18Q22.1) CNV	103	38	35
DEL PEAK 37(18Q22.1) WILD-TYPE	11	50	33

Figure S181. Get High-res Image Gene #59: 'Del Peak 37(18q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 37(18q22.1)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000224 (Fisher's exact test), Q value = 0.13

Table S182. Gene #59: 'Del Peak 37(18q22.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	56	63	180
DEL PEAK 37(18Q22.1) CNV	10	24	45	122
DEL PEAK 37(18Q22.1) WILD-TYPE	16	32	18	58

Figure S182. Get High-res Image Gene #59: 'Del Peak 37(18q22.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 37(18q22.1)' versus 'MRNASEQ_CNMF'

P value = 3.56e-13 (Fisher's exact test), Q value = 2.5e-10

Table S183. Gene #59: 'Del Peak 37(18q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	70	57	61
DEL PEAK 37(18Q22.1) CNV	27	64	38	17
DEL PEAK 37(18Q22.1) WILD-TYPE	16	6	19	44

Figure S183. Get High-res Image Gene #59: 'Del Peak 37(18q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 37(18q22.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.06e-13 (Fisher's exact test), Q value = 7.6e-11

Table S184. Gene #59: 'Del Peak 37(18q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	77	74
DEL PEAK 37(18Q22.1) CNV	63	22	61
DEL PEAK 37(18Q22.1) WILD-TYPE	17	55	13

Figure S184. Get High-res Image Gene #59: 'Del Peak 37(18q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 37(18q22.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.5e-14 (Fisher's exact test), Q value = 2.5e-11

Table S185. Gene #59: 'Del Peak 37(18q22.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 37(18Q22.1) CNV	72	26	44
DEL PEAK 37(18Q22.1) WILD-TYPE	7	52	19

Figure S185. Get High-res Image Gene #59: 'Del Peak 37(18q22.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 39(20p12.1)' versus 'CN_CNMF'

P value = 7.23e-06 (Fisher's exact test), Q value = 0.0046

Table S186. Gene #61: 'Del Peak 39(20p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
DEL PEAK 39(20P12.1) CNV	51	18	11
DEL PEAK 39(20P12.1) WILD-TYPE	133	178	36

Figure S186. Get High-res Image Gene #61: 'Del Peak 39(20p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 39(20p12.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.09e-05 (Fisher's exact test), Q value = 0.043

Table S187. Gene #61: 'Del Peak 39(20p12.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	77	74
DEL PEAK 39(20P12.1) CNV	23	4	20
DEL PEAK 39(20P12.1) WILD-TYPE	57	73	54

Figure S187. Get High-res Image Gene #61: 'Del Peak 39(20p12.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 40(21q11.2)' versus 'CN_CNMF'

P value = 5.95e-11 (Fisher's exact test), Q value = 4.1e-08

Table S188. Gene #62: 'Del Peak 40(21q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
DEL PEAK 40(21Q11.2) CNV	88	32	10
DEL PEAK 40(21Q11.2) WILD-TYPE	96	164	37

Figure S188. Get High-res Image Gene #62: 'Del Peak 40(21q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 40(21q11.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000184 (Fisher's exact test), Q value = 0.11

Table S189. Gene #62: 'Del Peak 40(21q11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 40(21Q11.2) CNV	34	11	22
DEL PEAK 40(21Q11.2) WILD-TYPE	45	67	41

Figure S189. Get High-res Image Gene #62: 'Del Peak 40(21q11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 41(22q13.32)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000232 (Fisher's exact test), Q value = 0.13

Table S190. Gene #63: 'Del Peak 41(22q13.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	43	47
DEL PEAK 41(22Q13.32) CNV	26	6	24
DEL PEAK 41(22Q13.32) WILD-TYPE	30	37	23

Figure S190. Get High-res Image Gene #63: 'Del Peak 41(22q13.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 41(22q13.32)' versus 'CN_CNMF'

P value = 4.07e-15 (Fisher's exact test), Q value = 2.9e-12

Table S191. Gene #63: 'Del Peak 41(22q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	196	47
DEL PEAK 41(22Q13.32) CNV	101	32	12
DEL PEAK 41(22Q13.32) WILD-TYPE	83	164	35

Figure S191. Get High-res Image Gene #63: 'Del Peak 41(22q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 41(22q13.32)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.81e-05 (Fisher's exact test), Q value = 0.018

Table S192. Gene #63: 'Del Peak 41(22q13.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	77	74
DEL PEAK 41(22Q13.32) CNV	33	10	31
DEL PEAK 41(22Q13.32) WILD-TYPE	47	67	43

Figure S192. Get High-res Image Gene #63: 'Del Peak 41(22q13.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 41(22q13.32)' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.33e-06 (Fisher's exact test), Q value = 0.0053

Table S193. Gene #63: 'Del Peak 41(22q13.32)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	78	63
DEL PEAK 41(22Q13.32) CNV	34	9	25
DEL PEAK 41(22Q13.32) WILD-TYPE	45	69	38

Figure S193. Get High-res Image Gene #63: 'Del Peak 41(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 = COAD-TP.transferedmergedcluster.txt
Number of patients = 427
Number of copy number variation regions = 63
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.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] 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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