Correlation between copy number variation genes and molecular subtypes

Lung Squamous Cell Carcinoma (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/C12B8WCV

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 82 peak regions and 12 molecular subtypes across 489 patients, 191 significant findings detected with Q value < 0.25.

Amp Peak 1(1q21.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 2(2p16.1) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
Amp Peak 3(2q31.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Amp Peak 5(3q26.33) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 6(4q12) cnvs correlated to 'CN_CNMF'.
Amp Peak 7(5p15.33) cnvs correlated to 'CN_CNMF'.
Amp Peak 8(5p12) cnvs correlated to 'CN_CNMF'.
Amp Peak 9(6p12.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 10(6q12) cnvs correlated to 'CN_CNMF'.
Amp Peak 11(7p11.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 12(7q21.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 15(9p13.3) cnvs correlated to 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 16(11q13.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 17(12p13.33) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 18(12q15) cnvs correlated to 'CN_CNMF'.
Amp Peak 21(15q26.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 22(17q25.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 23(18p11.32) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 24(18q11.2) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 25(19q12) cnvs correlated to 'CN_CNMF'.
Amp Peak 26(19q13.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 27(20p12.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 28(20q11.21) cnvs correlated to 'CN_CNMF'.
Amp Peak 29(22q11.21) cnvs correlated to 'MRNASEQ_CNMF'.
Del Peak 1(1p36.32) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 2(1p13.1) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 4(2q22.1) cnvs correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 5(2q37.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 7(3p13) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 8(3p12.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 10(4p15.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Del Peak 11(4q22.1) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 12(4q32.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 13(4q35.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 14(5q11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 15(6p25.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 16(6q22.31) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 17(6q26) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 20(8p23.2) cnvs correlated to 'CN_CNMF'.
Del Peak 21(9p23) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 22(9p21.3) cnvs correlated to 'CN_CNMF'.
Del Peak 23(9p21.1) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 24(9q21.11) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 25(10p15.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 26(10p15.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 27(10q23.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 28(11p15.5) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', and 'RPPA_CHIERARCHICAL'.
Del Peak 29(11q22.1) cnvs correlated to 'CN_CNMF'.
Del Peak 34(14q11.2) cnvs correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 39(17p11.2) cnvs correlated to 'CN_CNMF'.
Del Peak 40(17q11.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 44(19q13.32) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 46(21q22.3) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
Del Peak 48(22q13.32) cnvs correlated to 'MRNA_CNMF'.
Del Peak 49(Xp22.2) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 50(Xp21.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 51(Xp11.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 52(Xq22.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 82 regions and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 191 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
Del Peak 1(1p36 32)	0 (0%)	277	1.49e-06 (0.00136)	1.22e-07 (0.000114)	7.51e-35 (7.39e-32)	1.96e-19 (1.92e-16)	0.373 (1.00)	0.0129 (1.00)	3.79e-20 (3.72e-17)	1.06e-20 (1.04e-17)	2.12e-06 (0.00192)	1.11e-05 (0.0097)	0.00232 (1.00)	3.84e-07 (0.000356)
Del Peak 2(1p13 1)	0 (0%)	281	0.000956 (0.726)	6.31e-05 (0.053)	3.83e-20 (3.76e-17)	2.04e-12 (1.98e-09)	0.0391 (1.00)	0.0673 (1.00)	2.36e-11 (2.28e-08)	1.66e-13 (1.62e-10)	4.79e-08 (4.52e-05)	6.69e-06 (0.00592)	0.00558 (1.00)	5.63e-06 (0.00499)
Del Peak 24(9q21 11)	0 (0%)	247	8.38e-05 (0.0698)	1.96e-05 (0.017)	5.61e-13 (5.45e-10)	1.41e-09 (1.35e-06)	0.653 (1.00)	0.239 (1.00)	2.45e-15 (2.4e-12)	6.64e-15 (6.49e-12)	1.4e-05 (0.0122)	5.56e-08 (5.24e-05)	0.000947 (0.72)	0.0462 (1.00)
Amp Peak 5(3q26 33)	0 (0%)	47	0.000425 (0.333)	1.03e-05 (0.009)	3.91e-15 (3.83e-12)	7.78e-09 (7.41e-06)	0.193 (1.00)	0.0776 (1.00)	1.98e-10 (1.91e-07)	4.02e-08 (3.8e-05)	6.45e-07 (0.000595)	1.01e-06 (0.000928)	0.0181 (1.00)	0.00124 (0.928)
Amp Peak 22(17q25 1)	0 (0%)	258	0.0133 (1.00)	0.0338 (1.00)	1.54e-13 (1.5e-10)	2.45e-08 (2.31e-05)	0.479 (1.00)	0.249 (1.00)	3.01e-06 (0.0027)	1.21e-07 (0.000113)	0.000281 (0.224)	0.0148 (1.00)	1.19e-05 (0.0104)	4.66e-06 (0.00415)
Amp Peak 24(18q11 2)	0 (0%)	344	0.000151 (0.123)	0.0114 (1.00)	6.51e-09 (6.21e-06)	1.91e-05 (0.0165)	0.197 (1.00)	0.711 (1.00)	7.51e-06 (0.00663)	7.26e-07 (0.000668)	0.00692 (1.00)	0.00236 (1.00)	0.000182 (0.147)	0.000111 (0.0917)
Del Peak 5(2q37 1)	0 (0%)	335	0.00257 (1.00)	0.00342 (1.00)	4.19e-09 (4.01e-06)	7.61e-07 (0.000699)	0.523 (1.00)	0.234 (1.00)	2.07e-06 (0.00188)	7.02e-06 (0.0062)	2.81e-05 (0.0241)	0.594 (1.00)	1.46e-05 (0.0127)	0.000193 (0.156)
Amp Peak 2(2p16 1)	0 (0%)	221	0.00212 (1.00)	0.000275 (0.22)	4.35e-14 (4.25e-11)	2.79e-06 (0.00251)	0.95 (1.00)	0.643 (1.00)	9.21e-10 (8.86e-07)	4.83e-07 (0.000446)	8.41e-05 (0.0699)	0.000554 (0.428)	0.00124 (0.932)	0.000529 (0.412)
Del Peak 25(10p15 3)	0 (0%)	272	0.403 (1.00)	0.572 (1.00)	1.33e-07 (0.000124)	8.77e-10 (8.45e-07)	0.312 (1.00)	0.39 (1.00)	3.92e-05 (0.0332)	4.28e-06 (0.00382)	1.89e-06 (0.00171)	1.14e-05 (0.00993)	0.0246 (1.00)	0.0139 (1.00)
Del Peak 26(10p15 1)	0 (0%)	284	0.109 (1.00)	0.633 (1.00)	1.83e-06 (0.00166)	2.6e-10 (2.52e-07)	0.469 (1.00)	0.353 (1.00)	1.59e-06 (0.00144)	2.33e-06 (0.0021)	1.58e-06 (0.00144)	3.6e-06 (0.00322)	0.173 (1.00)	0.00975 (1.00)
Del Peak 40(17q11 2)	0 (0%)	367	3.03e-05 (0.0259)	0.000101 (0.0837)	1.55e-06 (0.00142)	4.56e-05 (0.0384)	0.495 (1.00)	0.378 (1.00)	7.33e-09 (6.98e-06)	3.86e-09 (3.69e-06)	0.275 (1.00)	0.0053 (1.00)	0.0124 (1.00)	0.00178 (1.00)
Amp Peak 1(1q21 2)	0 (0%)	239	0.0448 (1.00)	0.0304 (1.00)	3.22e-12 (3.13e-09)	7.11e-07 (0.000655)	0.16 (1.00)	0.0492 (1.00)	1.48e-07 (0.000138)	4.92e-10 (4.74e-07)	0.00106 (0.798)	3.03e-05 (0.0259)	0.026 (1.00)	0.0201 (1.00)
Amp Peak 3(2q31 2)	0 (0%)	324	0.0154 (1.00)	0.0275 (1.00)	2.93e-06 (0.00264)	5.78e-06 (0.00512)	0.826 (1.00)	0.812 (1.00)	4.83e-06 (0.00429)	4.17e-05 (0.0353)	0.0392 (1.00)	0.62 (1.00)	0.000309 (0.246)	0.00191 (1.00)
Del Peak 12(4q32 3)	0 (0%)	171	0.0113 (1.00)	0.0203 (1.00)	5.63e-09 (5.38e-06)	7.36e-05 (0.0616)	0.101 (1.00)	0.523 (1.00)	4.7e-06 (0.00418)	8.9e-05 (0.0739)	0.000385 (0.303)	0.00947 (1.00)	0.0059 (1.00)	7.55e-05 (0.0629)
Del Peak 13(4q35 2)	0 (0%)	169	0.0987 (1.00)	0.396 (1.00)	7.6e-08 (7.14e-05)	3.56e-05 (0.0302)	0.455 (1.00)	0.47 (1.00)	3.97e-06 (0.00355)	0.000174 (0.142)	0.00261 (1.00)	0.0434 (1.00)	0.0442 (1.00)	0.000197 (0.159)
Del Peak 27(10q23 31)	0 (0%)	237	0.0148 (1.00)	0.0131 (1.00)	4.34e-08 (4.1e-05)	2.36e-07 (0.00022)	0.36 (1.00)	0.39 (1.00)	6.5e-08 (6.12e-05)	9.78e-10 (9.4e-07)	0.00477 (1.00)	0.00309 (1.00)	3.37e-05 (0.0286)	0.00543 (1.00)
Del Peak 50(Xp21 1)	0 (0%)	333	0.386 (1.00)	0.414 (1.00)	3.82e-07 (0.000354)	1.29e-05 (0.0112)	0.197 (1.00)	0.702 (1.00)	0.000869 (0.662)	0.00122 (0.917)	2.01e-05 (0.0174)	0.0544 (1.00)	0.000246 (0.197)	8.65e-09 (8.21e-06)
Del Peak 51(Xp11 3)	0 (0%)	336	0.11 (1.00)	0.414 (1.00)	1.22e-07 (0.000114)	4.05e-06 (0.00362)	0.0923 (1.00)	0.124 (1.00)	0.000787 (0.601)	0.000352 (0.278)	1.38e-06 (0.00126)	0.0455 (1.00)	3.21e-05 (0.0274)	1.47e-08 (1.39e-05)
Amp Peak 12(7q21 2)	0 (0%)	233	0.175 (1.00)	0.116 (1.00)	4.52e-13 (4.4e-10)	3.42e-06 (0.00307)	0.0573 (1.00)	0.389 (1.00)	5.62e-06 (0.00499)	1.09e-05 (0.00951)	0.00292 (1.00)	0.0251 (1.00)	0.00411 (1.00)	0.00127 (0.949)
Amp Peak 17(12p13 33)	0 (0%)	241	0.0263 (1.00)	0.0936 (1.00)	4.56e-07 (0.000422)	7.03e-05 (0.0588)	0.313 (1.00)	0.729 (1.00)	2.13e-08 (2.02e-05)	4.59e-05 (0.0386)	0.0121 (1.00)	0.0205 (1.00)	0.134 (1.00)	0.0263 (1.00)
Amp Peak 21(15q26 3)	0 (0%)	316	0.253 (1.00)	0.0414 (1.00)	2.65e-06 (0.00239)	0.000229 (0.185)	0.354 (1.00)	0.0183 (1.00)	2.47e-05 (0.0212)	0.000219 (0.177)	0.00716 (1.00)	0.0017 (1.00)	0.0126 (1.00)	0.0356 (1.00)
Del Peak 7(3p13)	0 (0%)	70	0.298 (1.00)	0.949 (1.00)	1.25e-06 (0.00114)	0.000314 (0.25)	0.775 (1.00)	0.0387 (1.00)	0.00143 (1.00)	0.00684 (1.00)	4.76e-05 (0.0401)	0.0118 (1.00)	0.00403 (1.00)	5.83e-05 (0.049)
Del Peak 15(6p25 3)	0 (0%)	364	0.319 (1.00)	0.0462 (1.00)	0.000114 (0.0935)	0.000102 (0.0844)	0.393 (1.00)	0.013 (1.00)	2.82e-06 (0.00254)	6.82e-08 (6.41e-05)	0.0926 (1.00)	0.0201 (1.00)	0.0767 (1.00)	0.00767 (1.00)
Del Peak 17(6q26)	0 (0%)	360	0.0421 (1.00)	0.0154 (1.00)	2.95e-05 (0.0252)	0.000115 (0.0949)	0.921 (1.00)	0.69 (1.00)	0.000276 (0.22)	0.000219 (0.177)	0.0208 (1.00)	0.029 (1.00)	0.0211 (1.00)	0.0159 (1.00)
Del Peak 4(2q22 1)	0 (0%)	368	0.208 (1.00)	0.245 (1.00)	1.69e-05 (0.0147)	0.000358 (0.282)	0.546 (1.00)	0.0829 (1.00)	0.00785 (1.00)	0.000962 (0.729)	0.000126 (0.104)	0.029 (1.00)	0.000293 (0.233)	0.0191 (1.00)
Del Peak 10(4p15 2)	0 (0%)	190	0.000325 (0.258)	0.00153 (1.00)	2.32e-09 (2.22e-06)	6.04e-06 (0.00535)	0.662 (1.00)	0.0343 (1.00)	9.06e-05 (0.0751)	0.000341 (0.27)	0.00352 (1.00)	0.974 (1.00)	0.005 (1.00)	0.00059 (0.454)
Del Peak 14(5q11 2)	0 (0%)	136	0.706 (1.00)	0.656 (1.00)	2.55e-11 (2.47e-08)	0.0001 (0.0832)	0.959 (1.00)	0.244 (1.00)	0.00353 (1.00)	0.00878 (1.00)	0.0237 (1.00)	3.21e-05 (0.0274)	0.00364 (1.00)	0.000523 (0.407)
Del Peak 28(11p15 5)	0 (0%)	259	0.000261 (0.209)	0.0341 (1.00)	1.39e-07 (0.000129)	0.0237 (1.00)	0.000764 (0.584)	2.02e-05 (0.0174)	0.0109 (1.00)	0.0322 (1.00)	0.0124 (1.00)	0.213 (1.00)	0.0203 (1.00)	0.0195 (1.00)
Del Peak 52(Xq22 3)	0 (0%)	370	0.00842 (1.00)	0.015 (1.00)	2.71e-07 (0.000252)	1.02e-05 (0.00897)	0.663 (1.00)	0.92 (1.00)	0.00195 (1.00)	0.0514 (1.00)	3.57e-05 (0.0303)	0.624 (1.00)	0.000444 (0.348)	0.013 (1.00)
Amp Peak 23(18p11 32)	0 (0%)	319	0.0582 (1.00)	0.0147 (1.00)	2.38e-07 (0.000221)	2.17e-05 (0.0187)	0.261 (1.00)	0.735 (1.00)	0.0839 (1.00)	0.1 (1.00)	0.0311 (1.00)	0.0578 (1.00)	0.0219 (1.00)	0.0361 (1.00)
Amp Peak 27(20p12 2)	0 (0%)	221	0.00106 (0.798)	0.0142 (1.00)	5.15e-10 (4.96e-07)	0.000539 (0.418)	0.967 (1.00)	0.221 (1.00)	0.00307 (1.00)	0.000136 (0.111)	0.0107 (1.00)	0.398 (1.00)	0.0339 (1.00)	0.372 (1.00)
Del Peak 8(3p12 3)	0 (0%)	81	0.164 (1.00)	0.954 (1.00)	2.32e-05 (0.02)	0.000187 (0.151)	1 (1.00)	0.092 (1.00)	0.00452 (1.00)	0.00783 (1.00)	0.000542 (0.419)	0.0704 (1.00)	0.0306 (1.00)	0.00282 (1.00)
Del Peak 11(4q22 1)	0 (0%)	216	0.00688 (1.00)	0.0456 (1.00)	1.92e-06 (0.00175)	0.00169 (1.00)	0.123 (1.00)	0.381 (1.00)	0.00012 (0.0985)	0.00125 (0.935)	0.0298 (1.00)	0.0958 (1.00)	0.196 (1.00)	0.12 (1.00)
Del Peak 16(6q22 31)	0 (0%)	372	0.0278 (1.00)	0.0123 (1.00)	4.19e-05 (0.0354)	0.000726 (0.556)	0.629 (1.00)	0.354 (1.00)	0.000154 (0.126)	0.000571 (0.44)	0.0327 (1.00)	0.0398 (1.00)	0.0434 (1.00)	0.0264 (1.00)
Del Peak 21(9p23)	0 (0%)	172	0.0103 (1.00)	0.00676 (1.00)	3.09e-06 (0.00277)	0.0718 (1.00)	0.146 (1.00)	0.208 (1.00)	4.33e-05 (0.0365)	0.0144 (1.00)	0.00186 (1.00)	0.00151 (1.00)	0.0318 (1.00)	0.728 (1.00)
Del Peak 23(9p21 1)	0 (0%)	177	0.121 (1.00)	0.0364 (1.00)	9.11e-06 (0.008)	0.276 (1.00)	0.673 (1.00)	0.391 (1.00)	0.00011 (0.0905)	0.0108 (1.00)	0.267 (1.00)	0.0515 (1.00)	0.0527 (1.00)	0.416 (1.00)
Del Peak 34(14q11 2)	0 (0%)	322	0.0724 (1.00)	0.237 (1.00)	0.336 (1.00)	0.864 (1.00)	0.206 (1.00)	0.159 (1.00)	3.27e-05 (0.0278)	1.37e-07 (0.000128)	0.00508 (1.00)	0.103 (1.00)	0.422 (1.00)	0.243 (1.00)
Del Peak 44(19q13 32)	0 (0%)	348	0.749 (1.00)	0.247 (1.00)	1.13e-06 (0.00104)	2.32e-05 (0.02)	0.183 (1.00)	0.704 (1.00)	0.0038 (1.00)	0.0229 (1.00)	0.00795 (1.00)	0.767 (1.00)	0.152 (1.00)	0.0276 (1.00)
Del Peak 46(21q22 3)	0 (0%)	216	0.876 (1.00)	0.189 (1.00)	9.46e-08 (8.87e-05)	0.0191 (1.00)	0.396 (1.00)	0.0991 (1.00)	0.154 (1.00)	0.006 (1.00)	8.61e-05 (0.0716)	0.123 (1.00)	0.163 (1.00)	0.0263 (1.00)
Del Peak 49(Xp22 2)	0 (0%)	332	0.616 (1.00)	0.679 (1.00)	1.23e-05 (0.0107)	0.00111 (0.839)	0.354 (1.00)	0.8 (1.00)	0.0214 (1.00)	0.0339 (1.00)	0.000818 (0.624)	0.0869 (1.00)	0.000491 (0.384)	1.95e-06 (0.00177)
Amp Peak 6(4q12)	0 (0%)	378	0.809 (1.00)	0.2 (1.00)	0.00017 (0.138)	0.0861 (1.00)	0.356 (1.00)	0.131 (1.00)	0.101 (1.00)	0.0697 (1.00)	0.00308 (1.00)	0.455 (1.00)	0.0657 (1.00)	1 (1.00)
Amp Peak 7(5p15 33)	0 (0%)	112	0.852 (1.00)	0.983 (1.00)	3.16e-09 (3.03e-06)	0.0337 (1.00)	0.405 (1.00)	0.502 (1.00)	0.5 (1.00)	0.189 (1.00)	0.806 (1.00)	0.00869 (1.00)	0.428 (1.00)	0.237 (1.00)
Amp Peak 8(5p12)	0 (0%)	147	0.959 (1.00)	1 (1.00)	1.6e-08 (1.52e-05)	0.0402 (1.00)	0.217 (1.00)	0.988 (1.00)	0.511 (1.00)	0.947 (1.00)	0.946 (1.00)	0.0711 (1.00)	0.709 (1.00)	0.811 (1.00)
Amp Peak 9(6p12 1)	0 (0%)	329	0.551 (1.00)	0.737 (1.00)	1.48e-05 (0.0129)	0.0365 (1.00)	0.962 (1.00)	0.3 (1.00)	0.00127 (0.95)	0.251 (1.00)	0.593 (1.00)	0.107 (1.00)	0.0366 (1.00)	0.00435 (1.00)
Amp Peak 10(6q12)	0 (0%)	343	0.946 (1.00)	0.748 (1.00)	7.43e-05 (0.062)	0.00192 (1.00)	0.405 (1.00)	0.392 (1.00)	0.00602 (1.00)	0.0158 (1.00)	0.397 (1.00)	0.0974 (1.00)	0.288 (1.00)	0.00736 (1.00)
Amp Peak 11(7p11 2)	0 (0%)	244	0.164 (1.00)	0.0996 (1.00)	8.85e-06 (0.00779)	0.00298 (1.00)	0.687 (1.00)	0.801 (1.00)	0.00805 (1.00)	0.000385 (0.303)	0.0863 (1.00)	0.127 (1.00)	0.0238 (1.00)	0.0594 (1.00)
Amp Peak 15(9p13 3)	0 (0%)	354	0.124 (1.00)	0.838 (1.00)	0.00103 (0.778)	0.00131 (0.974)	0.0708 (1.00)	0.00898 (1.00)	0.000492 (0.384)	0.000184 (0.149)	0.0253 (1.00)	0.351 (1.00)	0.0811 (1.00)	0.0627 (1.00)
Amp Peak 16(11q13 3)	0 (0%)	311	0.0582 (1.00)	0.0872 (1.00)	0.000134 (0.11)	0.000629 (0.484)	0.19 (1.00)	0.0358 (1.00)	0.0134 (1.00)	0.0206 (1.00)	0.0022 (1.00)	0.111 (1.00)	0.0152 (1.00)	0.305 (1.00)
Amp Peak 18(12q15)	0 (0%)	316	0.235 (1.00)	0.326 (1.00)	3.26e-05 (0.0278)	0.00693 (1.00)	0.764 (1.00)	0.524 (1.00)	0.012 (1.00)	0.00319 (1.00)	0.647 (1.00)	0.412 (1.00)	0.0878 (1.00)	0.131 (1.00)
Amp Peak 25(19q12)	0 (0%)	277	0.438 (1.00)	0.693 (1.00)	8.3e-09 (7.9e-06)	0.00264 (1.00)	0.231 (1.00)	0.0287 (1.00)	0.0238 (1.00)	0.00647 (1.00)	0.311 (1.00)	0.586 (1.00)	0.0718 (1.00)	0.0572 (1.00)
Amp Peak 26(19q13 2)	0 (0%)	272	0.678 (1.00)	0.86 (1.00)	7.93e-07 (0.000728)	0.00221 (1.00)	0.356 (1.00)	0.117 (1.00)	0.0503 (1.00)	0.0031 (1.00)	0.445 (1.00)	0.535 (1.00)	0.284 (1.00)	0.222 (1.00)
Amp Peak 28(20q11 21)	0 (0%)	198	0.86 (1.00)	0.948 (1.00)	4.62e-07 (0.000427)	0.00646 (1.00)	0.669 (1.00)	0.588 (1.00)	0.706 (1.00)	0.436 (1.00)	0.139 (1.00)	0.0561 (1.00)	0.0517 (1.00)	0.652 (1.00)
Amp Peak 29(22q11 21)	0 (0%)	239	0.141 (1.00)	0.204 (1.00)	0.000374 (0.295)	0.00473 (1.00)	0.888 (1.00)	0.349 (1.00)	0.000284 (0.227)	0.00415 (1.00)	0.0157 (1.00)	0.311 (1.00)	0.00814 (1.00)	0.269 (1.00)
Del Peak 20(8p23 2)	0 (0%)	158	0.667 (1.00)	0.847 (1.00)	6.89e-05 (0.0578)	0.0334 (1.00)	0.345 (1.00)	0.141 (1.00)	0.173 (1.00)	0.0855 (1.00)	0.0973 (1.00)	0.117 (1.00)	0.644 (1.00)	0.0594 (1.00)
Del Peak 22(9p21 3)	0 (0%)	118	0.326 (1.00)	0.311 (1.00)	7.87e-06 (0.00693)	0.512 (1.00)	0.695 (1.00)	0.388 (1.00)	0.000539 (0.418)	0.387 (1.00)	0.217 (1.00)	0.17 (1.00)	0.0713 (1.00)	0.896 (1.00)
Del Peak 29(11q22 1)	0 (0%)	338	0.708 (1.00)	0.379 (1.00)	0.000171 (0.139)	0.00111 (0.835)	0.101 (1.00)	0.991 (1.00)	0.106 (1.00)	0.112 (1.00)	0.000537 (0.417)	0.569 (1.00)	0.0218 (1.00)	0.00303 (1.00)
Del Peak 39(17p11 2)	0 (0%)	231	0.217 (1.00)	0.0324 (1.00)	0.000255 (0.205)	0.699 (1.00)	0.15 (1.00)	0.0182 (1.00)	0.0734 (1.00)	0.0769 (1.00)	0.35 (1.00)	0.0494 (1.00)	0.941 (1.00)	1 (1.00)
Del Peak 48(22q13 32)	0 (0%)	364	0.00022 (0.177)	0.00221 (1.00)	0.109 (1.00)	0.0844 (1.00)	0.543 (1.00)	0.0759 (1.00)	0.00228 (1.00)	0.00291 (1.00)	0.0676 (1.00)	0.00175 (1.00)	0.715 (1.00)	0.372 (1.00)
Amp Peak 4(3p11 1)	0 (0%)	393	0.104 (1.00)	0.836 (1.00)	0.771 (1.00)	0.757 (1.00)	0.214 (1.00)	0.0013 (0.966)	0.312 (1.00)	0.331 (1.00)	0.24 (1.00)	0.579 (1.00)	0.738 (1.00)	0.251 (1.00)
Amp Peak 13(8p11 23)	0 (0%)	258	0.0137 (1.00)	0.467 (1.00)	0.000648 (0.497)	0.0237 (1.00)	0.192 (1.00)	0.0988 (1.00)	0.00963 (1.00)	0.716 (1.00)	0.658 (1.00)	0.149 (1.00)	0.656 (1.00)	0.183 (1.00)
Amp Peak 14(8q24 21)	0 (0%)	149	0.919 (1.00)	0.788 (1.00)	0.0255 (1.00)	0.319 (1.00)	0.917 (1.00)	0.708 (1.00)	0.878 (1.00)	0.991 (1.00)	0.544 (1.00)	0.484 (1.00)	0.229 (1.00)	1 (1.00)
Amp Peak 19(13q34)	0 (0%)	404	0.981 (1.00)	0.0207 (1.00)	0.214 (1.00)	0.521 (1.00)	0.87 (1.00)	0.0834 (1.00)	0.917 (1.00)	0.612 (1.00)	0.62 (1.00)	0.332 (1.00)	0.573 (1.00)	0.885 (1.00)
Amp Peak 20(14q13 3)	0 (0%)	338	0.316 (1.00)	0.194 (1.00)	0.0951 (1.00)	0.112 (1.00)	0.57 (1.00)	0.00826 (1.00)	0.0982 (1.00)	0.0256 (1.00)	0.0171 (1.00)	0.321 (1.00)	0.146 (1.00)	1 (1.00)
Amp Peak 30(Xq28)	0 (0%)	359	0.793 (1.00)	0.71 (1.00)	0.0184 (1.00)	0.0416 (1.00)	0.0701 (1.00)	0.069 (1.00)	0.0255 (1.00)	0.0368 (1.00)	0.00599 (1.00)	0.0978 (1.00)	0.0388 (1.00)	0.0177 (1.00)
Del Peak 3(2p25 3)	0 (0%)	443	0.0858 (1.00)	0.0152 (1.00)	0.169 (1.00)	0.267 (1.00)	0.11 (1.00)	0.838 (1.00)	0.329 (1.00)	0.0308 (1.00)	0.0262 (1.00)	0.14 (1.00)	0.168 (1.00)	0.319 (1.00)
Del Peak 6(3p25 3)	0 (0%)	104	0.674 (1.00)	0.63 (1.00)	0.00942 (1.00)	0.00125 (0.937)	0.637 (1.00)	0.18 (1.00)	0.0208 (1.00)	0.00844 (1.00)	0.000934 (0.711)	0.0141 (1.00)	0.152 (1.00)	0.015 (1.00)
Del Peak 9(3q11 1)	0 (0%)	412	0.762 (1.00)	0.625 (1.00)	0.3 (1.00)	0.949 (1.00)	0.765 (1.00)	0.282 (1.00)	0.753 (1.00)	0.866 (1.00)	0.769 (1.00)	0.493 (1.00)	0.426 (1.00)	0.227 (1.00)
Del Peak 18(7q11 22)	0 (0%)	443	0.802 (1.00)	0.106 (1.00)	0.000502 (0.392)	0.444 (1.00)	0.958 (1.00)	0.75 (1.00)	0.00636 (1.00)	0.124 (1.00)	0.882 (1.00)	0.862 (1.00)	0.784 (1.00)	1 (1.00)
Del Peak 19(7q36 3)	0 (0%)	386	0.17 (1.00)	0.131 (1.00)	0.000557 (0.43)	0.272 (1.00)	1 (1.00)	0.315 (1.00)	0.000659 (0.505)	0.0012 (0.903)	0.443 (1.00)	0.503 (1.00)	0.107 (1.00)	0.788 (1.00)
Del Peak 30(11q25)	0 (0%)	311	0.874 (1.00)	0.578 (1.00)	0.00367 (1.00)	0.0759 (1.00)	0.113 (1.00)	0.908 (1.00)	0.074 (1.00)	0.174 (1.00)	0.0123 (1.00)	0.568 (1.00)	0.107 (1.00)	0.0155 (1.00)
Del Peak 31(12q24 31)	0 (0%)	404	0.987 (1.00)	0.372 (1.00)	0.461 (1.00)	0.249 (1.00)	0.323 (1.00)	0.207 (1.00)	0.82 (1.00)	0.729 (1.00)	0.356 (1.00)	0.0879 (1.00)	0.55 (1.00)	1 (1.00)
Del Peak 32(13q12 11)	0 (0%)	170	0.0859 (1.00)	0.501 (1.00)	0.00855 (1.00)	0.148 (1.00)	0.891 (1.00)	0.16 (1.00)	0.728 (1.00)	0.261 (1.00)	0.77 (1.00)	0.386 (1.00)	0.0862 (1.00)	0.0801 (1.00)
Del Peak 33(13q14 2)	0 (0%)	157	0.0997 (1.00)	0.321 (1.00)	0.00861 (1.00)	0.0352 (1.00)	0.707 (1.00)	0.682 (1.00)	0.554 (1.00)	0.0734 (1.00)	0.147 (1.00)	0.305 (1.00)	0.0162 (1.00)	0.0129 (1.00)
Del Peak 35(15q12)	0 (0%)	325	0.47 (1.00)	0.469 (1.00)	0.0821 (1.00)	0.321 (1.00)	0.0344 (1.00)	0.0132 (1.00)	0.19 (1.00)	0.00448 (1.00)	0.00848 (1.00)	0.928 (1.00)	0.284 (1.00)	0.472 (1.00)
Del Peak 36(15q21 1)	0 (0%)	329	0.382 (1.00)	0.415 (1.00)	0.0155 (1.00)	0.293 (1.00)	0.138 (1.00)	0.00763 (1.00)	0.262 (1.00)	0.00598 (1.00)	0.00444 (1.00)	0.611 (1.00)	0.12 (1.00)	0.551 (1.00)
Del Peak 37(16p13 3)	0 (0%)	311	0.348 (1.00)	0.339 (1.00)	0.00721 (1.00)	0.058 (1.00)	0.149 (1.00)	0.606 (1.00)	0.776 (1.00)	0.108 (1.00)	0.0252 (1.00)	0.982 (1.00)	0.126 (1.00)	0.3 (1.00)
Del Peak 38(16q23 1)	0 (0%)	288	0.874 (1.00)	0.336 (1.00)	0.0359 (1.00)	0.362 (1.00)	0.354 (1.00)	0.761 (1.00)	0.147 (1.00)	0.149 (1.00)	0.0545 (1.00)	0.418 (1.00)	0.0018 (1.00)	0.00497 (1.00)
Del Peak 41(17q25 3)	0 (0%)	389	0.0046 (1.00)	0.015 (1.00)	0.00196 (1.00)	0.0291 (1.00)	0.622 (1.00)	0.994 (1.00)	0.00624 (1.00)	0.00192 (1.00)	0.884 (1.00)	0.0319 (1.00)	0.372 (1.00)	0.0138 (1.00)
Del Peak 42(18q23)	0 (0%)	262	0.454 (1.00)	0.217 (1.00)	0.0337 (1.00)	0.284 (1.00)	0.801 (1.00)	0.397 (1.00)	0.648 (1.00)	0.0728 (1.00)	0.237 (1.00)	0.662 (1.00)	0.1 (1.00)	0.374 (1.00)
Del Peak 43(19p13 3)	0 (0%)	268	0.223 (1.00)	0.00269 (1.00)	0.00298 (1.00)	0.834 (1.00)	0.0799 (1.00)	0.358 (1.00)	0.171 (1.00)	0.0501 (1.00)	0.0483 (1.00)	0.0022 (1.00)	0.424 (1.00)	0.576 (1.00)
Del Peak 45(21q21 1)	0 (0%)	253	0.571 (1.00)	0.395 (1.00)	0.000323 (0.256)	0.0832 (1.00)	0.585 (1.00)	0.89 (1.00)	0.394 (1.00)	0.0961 (1.00)	0.000467 (0.366)	0.0643 (1.00)	0.0175 (1.00)	0.0357 (1.00)
Del Peak 47(22q11 21)	0 (0%)	399	0.0298 (1.00)	0.16 (1.00)	0.227 (1.00)	0.299 (1.00)	0.145 (1.00)	0.129 (1.00)	0.581 (1.00)	0.542 (1.00)	0.312 (1.00)	1 (1.00)	0.33 (1.00)	0.3 (1.00)

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

P value = 3.22e-12 (Fisher's exact test), Q value = 3.1e-09

Table S1. Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
AMP PEAK 1(1Q21.2) CNV	80	120	50
AMP PEAK 1(1Q21.2) WILD-TYPE	114	42	83

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 7.11e-07 (Fisher's exact test), Q value = 0.00065

Table S2. Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	99
AMP PEAK 1(1Q21.2) CNV	50	78	48
AMP PEAK 1(1Q21.2) WILD-TYPE	92	36	51

Figure S2. Get High-res Image Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 1.48e-07 (Fisher's exact test), Q value = 0.00014

Table S3. Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	118	143	142	75
AMP PEAK 1(1Q21.2) CNV	44	100	71	29
AMP PEAK 1(1Q21.2) WILD-TYPE	74	43	71	46

Figure S3. Get High-res Image Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 4.92e-10 (Fisher's exact test), Q value = 4.7e-07

Table S4. Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	140	245
AMP PEAK 1(1Q21.2) CNV	52	100	92
AMP PEAK 1(1Q21.2) WILD-TYPE	41	40	153

Figure S4. Get High-res Image Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 3.03e-05 (Fisher's exact test), Q value = 0.026

Table S5. Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	163	229
AMP PEAK 1(1Q21.2) CNV	53	70	114
AMP PEAK 1(1Q21.2) WILD-TYPE	18	93	115

Figure S5. Get High-res Image Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 2(2p16.1)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000275 (Fisher's exact test), Q value = 0.22

Table S6. Gene #2: 'Amp Peak 2(2p16.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	22	56	23	53
AMP PEAK 2(2P16.1) CNV	7	42	15	22
AMP PEAK 2(2P16.1) WILD-TYPE	15	14	8	31

Figure S6. Get High-res Image Gene #2: 'Amp Peak 2(2p16.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 2(2p16.1)' versus 'CN_CNMF'

P value = 4.35e-14 (Fisher's exact test), Q value = 4.2e-11

Table S7. Gene #2: 'Amp Peak 2(2p16.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
AMP PEAK 2(2P16.1) CNV	72	126	70
AMP PEAK 2(2P16.1) WILD-TYPE	122	36	63

Figure S7. Get High-res Image Gene #2: 'Amp Peak 2(2p16.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 2(2p16.1)' versus 'METHLYATION_CNMF'

P value = 2.79e-06 (Fisher's exact test), Q value = 0.0025

Table S8. Gene #2: 'Amp Peak 2(2p16.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	99
AMP PEAK 2(2P16.1) CNV	61	84	51
AMP PEAK 2(2P16.1) WILD-TYPE	81	30	48

Figure S8. Get High-res Image Gene #2: 'Amp Peak 2(2p16.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 2(2p16.1)' versus 'MRNASEQ_CNMF'

P value = 9.21e-10 (Fisher's exact test), Q value = 8.9e-07

Table S9. Gene #2: 'Amp Peak 2(2p16.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	118	143	142	75
AMP PEAK 2(2P16.1) CNV	51	106	81	24
AMP PEAK 2(2P16.1) WILD-TYPE	67	37	61	51

Figure S9. Get High-res Image Gene #2: 'Amp Peak 2(2p16.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 2(2p16.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.83e-07 (Fisher's exact test), Q value = 0.00045

Table S10. Gene #2: 'Amp Peak 2(2p16.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	140	245
AMP PEAK 2(2P16.1) CNV	53	101	108
AMP PEAK 2(2P16.1) WILD-TYPE	40	39	137

Figure S10. Get High-res Image Gene #2: 'Amp Peak 2(2p16.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 2(2p16.1)' versus 'MIRSEQ_CNMF'

P value = 8.41e-05 (Fisher's exact test), Q value = 0.07

Table S11. Gene #2: 'Amp Peak 2(2p16.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	130	124	64
AMP PEAK 2(2P16.1) CNV	80	88	49	39
AMP PEAK 2(2P16.1) WILD-TYPE	65	42	75	25

Figure S11. Get High-res Image Gene #2: 'Amp Peak 2(2p16.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 3(2q31.2)' versus 'CN_CNMF'

P value = 2.93e-06 (Fisher's exact test), Q value = 0.0026

Table S12. Gene #3: 'Amp Peak 3(2q31.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
AMP PEAK 3(2Q31.2) CNV	43	77	45
AMP PEAK 3(2Q31.2) WILD-TYPE	151	85	88

Figure S12. Get High-res Image Gene #3: 'Amp Peak 3(2q31.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 3(2q31.2)' versus 'METHLYATION_CNMF'

P value = 5.78e-06 (Fisher's exact test), Q value = 0.0051

Table S13. Gene #3: 'Amp Peak 3(2q31.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	99
AMP PEAK 3(2Q31.2) CNV	36	60	26
AMP PEAK 3(2Q31.2) WILD-TYPE	106	54	73

Figure S13. Get High-res Image Gene #3: 'Amp Peak 3(2q31.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 3(2q31.2)' versus 'MRNASEQ_CNMF'

P value = 4.83e-06 (Fisher's exact test), Q value = 0.0043

Table S14. Gene #3: 'Amp Peak 3(2q31.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	118	143	142	75
AMP PEAK 3(2Q31.2) CNV	30	72	45	15
AMP PEAK 3(2Q31.2) WILD-TYPE	88	71	97	60

Figure S14. Get High-res Image Gene #3: 'Amp Peak 3(2q31.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 3(2q31.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.17e-05 (Fisher's exact test), Q value = 0.035

Table S15. Gene #3: 'Amp Peak 3(2q31.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	140	245
AMP PEAK 3(2Q31.2) CNV	33	67	62
AMP PEAK 3(2Q31.2) WILD-TYPE	60	73	183

Figure S15. Get High-res Image Gene #3: 'Amp Peak 3(2q31.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 3(2q31.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000309 (Fisher's exact test), Q value = 0.25

Table S16. Gene #3: 'Amp Peak 3(2q31.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	111	91
AMP PEAK 3(2Q31.2) CNV	56	29	19
AMP PEAK 3(2Q31.2) WILD-TYPE	69	82	72

Figure S16. Get High-res Image Gene #3: 'Amp Peak 3(2q31.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 5(3q26.33)' versus 'MRNA_CHIERARCHICAL'

P value = 1.03e-05 (Fisher's exact test), Q value = 0.009

Table S17. Gene #5: 'Amp Peak 5(3q26.33)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	22	56	23	53
AMP PEAK 5(3Q26.33) CNV	14	56	20	50
AMP PEAK 5(3Q26.33) WILD-TYPE	8	0	3	3

Figure S17. Get High-res Image Gene #5: 'Amp Peak 5(3q26.33)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 5(3q26.33)' versus 'CN_CNMF'

P value = 3.91e-15 (Fisher's exact test), Q value = 3.8e-12

Table S18. Gene #5: 'Amp Peak 5(3q26.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
AMP PEAK 5(3Q26.33) CNV	151	162	129
AMP PEAK 5(3Q26.33) WILD-TYPE	43	0	4

Figure S18. Get High-res Image Gene #5: 'Amp Peak 5(3q26.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 5(3q26.33)' versus 'METHLYATION_CNMF'

P value = 7.78e-09 (Fisher's exact test), Q value = 7.4e-06

Table S19. Gene #5: 'Amp Peak 5(3q26.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	99
AMP PEAK 5(3Q26.33) CNV	113	114	93
AMP PEAK 5(3Q26.33) WILD-TYPE	29	0	6

Figure S19. Get High-res Image Gene #5: 'Amp Peak 5(3q26.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 5(3q26.33)' versus 'MRNASEQ_CNMF'

P value = 1.98e-10 (Fisher's exact test), Q value = 1.9e-07

Table S20. Gene #5: 'Amp Peak 5(3q26.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	118	143	142	75
AMP PEAK 5(3Q26.33) CNV	110	143	124	55
AMP PEAK 5(3Q26.33) WILD-TYPE	8	0	18	20

Figure S20. Get High-res Image Gene #5: 'Amp Peak 5(3q26.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 5(3q26.33)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.02e-08 (Fisher's exact test), Q value = 3.8e-05

Table S21. Gene #5: 'Amp Peak 5(3q26.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	140	245
AMP PEAK 5(3Q26.33) CNV	85	140	207
AMP PEAK 5(3Q26.33) WILD-TYPE	8	0	38

Figure S21. Get High-res Image Gene #5: 'Amp Peak 5(3q26.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 5(3q26.33)' versus 'MIRSEQ_CNMF'

P value = 6.45e-07 (Fisher's exact test), Q value = 0.00059

Table S22. Gene #5: 'Amp Peak 5(3q26.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	130	124	64
AMP PEAK 5(3Q26.33) CNV	131	127	98	63
AMP PEAK 5(3Q26.33) WILD-TYPE	14	3	26	1

Figure S22. Get High-res Image Gene #5: 'Amp Peak 5(3q26.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 5(3q26.33)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.01e-06 (Fisher's exact test), Q value = 0.00093

Table S23. Gene #5: 'Amp Peak 5(3q26.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	163	229
AMP PEAK 5(3Q26.33) CNV	71	156	192
AMP PEAK 5(3Q26.33) WILD-TYPE	0	7	37

Figure S23. Get High-res Image Gene #5: 'Amp Peak 5(3q26.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 6(4q12)' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.14

Table S24. Gene #6: 'Amp Peak 6(4q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
AMP PEAK 6(4Q12) CNV	27	40	44
AMP PEAK 6(4Q12) WILD-TYPE	167	122	89

Figure S24. Get High-res Image Gene #6: 'Amp Peak 6(4q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 7(5p15.33)' versus 'CN_CNMF'

P value = 3.16e-09 (Fisher's exact test), Q value = 3e-06

Table S25. Gene #7: 'Amp Peak 7(5p15.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
AMP PEAK 7(5P15.33) CNV	135	116	126
AMP PEAK 7(5P15.33) WILD-TYPE	59	46	7

Figure S25. Get High-res Image Gene #7: 'Amp Peak 7(5p15.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 8(5p12)' versus 'CN_CNMF'

P value = 1.6e-08 (Fisher's exact test), Q value = 1.5e-05

Table S26. Gene #8: 'Amp Peak 8(5p12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
AMP PEAK 8(5P12) CNV	113	112	117
AMP PEAK 8(5P12) WILD-TYPE	81	50	16

Figure S26. Get High-res Image Gene #8: 'Amp Peak 8(5p12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 9(6p12.1)' versus 'CN_CNMF'

P value = 1.48e-05 (Fisher's exact test), Q value = 0.013

Table S27. Gene #9: 'Amp Peak 9(6p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
AMP PEAK 9(6P12.1) CNV	40	65	55
AMP PEAK 9(6P12.1) WILD-TYPE	154	97	78

Figure S27. Get High-res Image Gene #9: 'Amp Peak 9(6p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 10(6q12)' versus 'CN_CNMF'

P value = 7.43e-05 (Fisher's exact test), Q value = 0.062

Table S28. Gene #10: 'Amp Peak 10(6q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
AMP PEAK 10(6Q12) CNV	37	57	52
AMP PEAK 10(6Q12) WILD-TYPE	157	105	81

Figure S28. Get High-res Image Gene #10: 'Amp Peak 10(6q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 11(7p11.2)' versus 'CN_CNMF'

P value = 8.85e-06 (Fisher's exact test), Q value = 0.0078

Table S29. Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
AMP PEAK 11(7P11.2) CNV	80	106	59
AMP PEAK 11(7P11.2) WILD-TYPE	114	56	74

Figure S29. Get High-res Image Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 12(7q21.2)' versus 'CN_CNMF'

P value = 4.52e-13 (Fisher's exact test), Q value = 4.4e-10

Table S30. Gene #12: 'Amp Peak 12(7q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
AMP PEAK 12(7Q21.2) CNV	67	120	69
AMP PEAK 12(7Q21.2) WILD-TYPE	127	42	64

Figure S30. Get High-res Image Gene #12: 'Amp Peak 12(7q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 12(7q21.2)' versus 'METHLYATION_CNMF'

P value = 3.42e-06 (Fisher's exact test), Q value = 0.0031

Table S31. Gene #12: 'Amp Peak 12(7q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	99
AMP PEAK 12(7Q21.2) CNV	50	75	55
AMP PEAK 12(7Q21.2) WILD-TYPE	92	39	44

Figure S31. Get High-res Image Gene #12: 'Amp Peak 12(7q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 12(7q21.2)' versus 'MRNASEQ_CNMF'

P value = 5.62e-06 (Fisher's exact test), Q value = 0.005

Table S32. Gene #12: 'Amp Peak 12(7q21.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	118	143	142	75
AMP PEAK 12(7Q21.2) CNV	59	100	64	29
AMP PEAK 12(7Q21.2) WILD-TYPE	59	43	78	46

Figure S32. Get High-res Image Gene #12: 'Amp Peak 12(7q21.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 12(7q21.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.09e-05 (Fisher's exact test), Q value = 0.0095

Table S33. Gene #12: 'Amp Peak 12(7q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	140	245
AMP PEAK 12(7Q21.2) CNV	46	97	109
AMP PEAK 12(7Q21.2) WILD-TYPE	47	43	136

Figure S33. Get High-res Image Gene #12: 'Amp Peak 12(7q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 15(9p13.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000184 (Fisher's exact test), Q value = 0.15

Table S34. Gene #15: 'Amp Peak 15(9p13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	140	245
AMP PEAK 15(9P13.3) CNV	26	57	51
AMP PEAK 15(9P13.3) WILD-TYPE	67	83	194

Figure S34. Get High-res Image Gene #15: 'Amp Peak 15(9p13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 16(11q13.3)' versus 'CN_CNMF'

P value = 0.000134 (Fisher's exact test), Q value = 0.11

Table S35. Gene #16: 'Amp Peak 16(11q13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
AMP PEAK 16(11Q13.3) CNV	51	62	65
AMP PEAK 16(11Q13.3) WILD-TYPE	143	100	68

Figure S35. Get High-res Image Gene #16: 'Amp Peak 16(11q13.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 17(12p13.33)' versus 'CN_CNMF'

P value = 4.56e-07 (Fisher's exact test), Q value = 0.00042

Table S36. Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
AMP PEAK 17(12P13.33) CNV	71	105	72
AMP PEAK 17(12P13.33) WILD-TYPE	123	57	61

Figure S36. Get High-res Image Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 17(12p13.33)' versus 'METHLYATION_CNMF'

P value = 7.03e-05 (Fisher's exact test), Q value = 0.059

Table S37. Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	99
AMP PEAK 17(12P13.33) CNV	57	75	60
AMP PEAK 17(12P13.33) WILD-TYPE	85	39	39

Figure S37. Get High-res Image Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 17(12p13.33)' versus 'MRNASEQ_CNMF'

P value = 2.13e-08 (Fisher's exact test), Q value = 2e-05

Table S38. Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	118	143	142	75
AMP PEAK 17(12P13.33) CNV	40	93	84	25
AMP PEAK 17(12P13.33) WILD-TYPE	78	50	58	50

Figure S38. Get High-res Image Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 17(12p13.33)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.59e-05 (Fisher's exact test), Q value = 0.039

Table S39. Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	140	245
AMP PEAK 17(12P13.33) CNV	54	88	100
AMP PEAK 17(12P13.33) WILD-TYPE	39	52	145

Figure S39. Get High-res Image Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 18(12q15)' versus 'CN_CNMF'

P value = 3.26e-05 (Fisher's exact test), Q value = 0.028

Table S40. Gene #18: 'Amp Peak 18(12q15)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
AMP PEAK 18(12Q15) CNV	50	79	44
AMP PEAK 18(12Q15) WILD-TYPE	144	83	89

Figure S40. Get High-res Image Gene #18: 'Amp Peak 18(12q15)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 21(15q26.3)' versus 'CN_CNMF'

P value = 2.65e-06 (Fisher's exact test), Q value = 0.0024

Table S41. Gene #21: 'Amp Peak 21(15q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
AMP PEAK 21(15Q26.3) CNV	45	79	49
AMP PEAK 21(15Q26.3) WILD-TYPE	149	83	84

Figure S41. Get High-res Image Gene #21: 'Amp Peak 21(15q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 21(15q26.3)' versus 'METHLYATION_CNMF'

P value = 0.000229 (Fisher's exact test), Q value = 0.18

Table S42. Gene #21: 'Amp Peak 21(15q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	99
AMP PEAK 21(15Q26.3) CNV	32	53	36
AMP PEAK 21(15Q26.3) WILD-TYPE	110	61	63

Figure S42. Get High-res Image Gene #21: 'Amp Peak 21(15q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 21(15q26.3)' versus 'MRNASEQ_CNMF'

P value = 2.47e-05 (Fisher's exact test), Q value = 0.021

Table S43. Gene #21: 'Amp Peak 21(15q26.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	118	143	142	75
AMP PEAK 21(15Q26.3) CNV	28	73	45	22
AMP PEAK 21(15Q26.3) WILD-TYPE	90	70	97	53

Figure S43. Get High-res Image Gene #21: 'Amp Peak 21(15q26.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 21(15q26.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000219 (Fisher's exact test), Q value = 0.18

Table S44. Gene #21: 'Amp Peak 21(15q26.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	140	245
AMP PEAK 21(15Q26.3) CNV	27	69	72
AMP PEAK 21(15Q26.3) WILD-TYPE	66	71	173

Figure S44. Get High-res Image Gene #21: 'Amp Peak 21(15q26.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 22(17q25.1)' versus 'CN_CNMF'

P value = 1.54e-13 (Fisher's exact test), Q value = 1.5e-10

Table S45. Gene #22: 'Amp Peak 22(17q25.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
AMP PEAK 22(17Q25.1) CNV	54	110	67
AMP PEAK 22(17Q25.1) WILD-TYPE	140	52	66

Figure S45. Get High-res Image Gene #22: 'Amp Peak 22(17q25.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 22(17q25.1)' versus 'METHLYATION_CNMF'

P value = 2.45e-08 (Fisher's exact test), Q value = 2.3e-05

Table S46. Gene #22: 'Amp Peak 22(17q25.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	99
AMP PEAK 22(17Q25.1) CNV	40	73	51
AMP PEAK 22(17Q25.1) WILD-TYPE	102	41	48

Figure S46. Get High-res Image Gene #22: 'Amp Peak 22(17q25.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 22(17q25.1)' versus 'MRNASEQ_CNMF'

P value = 3.01e-06 (Fisher's exact test), Q value = 0.0027

Table S47. Gene #22: 'Amp Peak 22(17q25.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	118	143	142	75
AMP PEAK 22(17Q25.1) CNV	45	93	60	26
AMP PEAK 22(17Q25.1) WILD-TYPE	73	50	82	49

Figure S47. Get High-res Image Gene #22: 'Amp Peak 22(17q25.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 22(17q25.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.21e-07 (Fisher's exact test), Q value = 0.00011

Table S48. Gene #22: 'Amp Peak 22(17q25.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	140	245
AMP PEAK 22(17Q25.1) CNV	48	90	86
AMP PEAK 22(17Q25.1) WILD-TYPE	45	50	159

Figure S48. Get High-res Image Gene #22: 'Amp Peak 22(17q25.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 22(17q25.1)' versus 'MIRSEQ_CNMF'

P value = 0.000281 (Fisher's exact test), Q value = 0.22

Table S49. Gene #22: 'Amp Peak 22(17q25.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	130	124	64
AMP PEAK 22(17Q25.1) CNV	71	78	41	29
AMP PEAK 22(17Q25.1) WILD-TYPE	74	52	83	35

Figure S49. Get High-res Image Gene #22: 'Amp Peak 22(17q25.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 22(17q25.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.19e-05 (Fisher's exact test), Q value = 0.01

Table S50. Gene #22: 'Amp Peak 22(17q25.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	111	91
AMP PEAK 22(17Q25.1) CNV	79	38	36
AMP PEAK 22(17Q25.1) WILD-TYPE	46	73	55

Figure S50. Get High-res Image Gene #22: 'Amp Peak 22(17q25.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 22(17q25.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.66e-06 (Fisher's exact test), Q value = 0.0042

Table S51. Gene #22: 'Amp Peak 22(17q25.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	150	177
AMP PEAK 22(17Q25.1) CNV	91	62
AMP PEAK 22(17Q25.1) WILD-TYPE	59	115

Figure S51. Get High-res Image Gene #22: 'Amp Peak 22(17q25.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 23(18p11.32)' versus 'CN_CNMF'

P value = 2.38e-07 (Fisher's exact test), Q value = 0.00022

Table S52. Gene #23: 'Amp Peak 23(18p11.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
AMP PEAK 23(18P11.32) CNV	42	80	48
AMP PEAK 23(18P11.32) WILD-TYPE	152	82	85

Figure S52. Get High-res Image Gene #23: 'Amp Peak 23(18p11.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 23(18p11.32)' versus 'METHLYATION_CNMF'

P value = 2.17e-05 (Fisher's exact test), Q value = 0.019

Table S53. Gene #23: 'Amp Peak 23(18p11.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	99
AMP PEAK 23(18P11.32) CNV	30	49	46
AMP PEAK 23(18P11.32) WILD-TYPE	112	65	53

Figure S53. Get High-res Image Gene #23: 'Amp Peak 23(18p11.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 24(18q11.2)' versus 'MRNA_CNMF'

P value = 0.000151 (Fisher's exact test), Q value = 0.12

Table S54. Gene #24: 'Amp Peak 24(18q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	52	32	28
AMP PEAK 24(18Q11.2) CNV	7	25	5	15
AMP PEAK 24(18Q11.2) WILD-TYPE	35	27	27	13

Figure S54. Get High-res Image Gene #24: 'Amp Peak 24(18q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 24(18q11.2)' versus 'CN_CNMF'

P value = 6.51e-09 (Fisher's exact test), Q value = 6.2e-06

Table S55. Gene #24: 'Amp Peak 24(18q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
AMP PEAK 24(18Q11.2) CNV	32	75	38
AMP PEAK 24(18Q11.2) WILD-TYPE	162	87	95

Figure S55. Get High-res Image Gene #24: 'Amp Peak 24(18q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 24(18q11.2)' versus 'METHLYATION_CNMF'

P value = 1.91e-05 (Fisher's exact test), Q value = 0.017

Table S56. Gene #24: 'Amp Peak 24(18q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	99
AMP PEAK 24(18Q11.2) CNV	23	48	31
AMP PEAK 24(18Q11.2) WILD-TYPE	119	66	68

Figure S56. Get High-res Image Gene #24: 'Amp Peak 24(18q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 24(18q11.2)' versus 'MRNASEQ_CNMF'

P value = 7.51e-06 (Fisher's exact test), Q value = 0.0066

Table S57. Gene #24: 'Amp Peak 24(18q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	118	143	142	75
AMP PEAK 24(18Q11.2) CNV	26	60	46	9
AMP PEAK 24(18Q11.2) WILD-TYPE	92	83	96	66

Figure S57. Get High-res Image Gene #24: 'Amp Peak 24(18q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 24(18q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.26e-07 (Fisher's exact test), Q value = 0.00067

Table S58. Gene #24: 'Amp Peak 24(18q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	140	245
AMP PEAK 24(18Q11.2) CNV	37	58	46
AMP PEAK 24(18Q11.2) WILD-TYPE	56	82	199

Figure S58. Get High-res Image Gene #24: 'Amp Peak 24(18q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 24(18q11.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000182 (Fisher's exact test), Q value = 0.15

Table S59. Gene #24: 'Amp Peak 24(18q11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	111	91
AMP PEAK 24(18Q11.2) CNV	49	17	24
AMP PEAK 24(18Q11.2) WILD-TYPE	76	94	67

Figure S59. Get High-res Image Gene #24: 'Amp Peak 24(18q11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 24(18q11.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000111 (Fisher's exact test), Q value = 0.092

Table S60. Gene #24: 'Amp Peak 24(18q11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	150	177
AMP PEAK 24(18Q11.2) CNV	57	33
AMP PEAK 24(18Q11.2) WILD-TYPE	93	144

Figure S60. Get High-res Image Gene #24: 'Amp Peak 24(18q11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 25(19q12)' versus 'CN_CNMF'

P value = 8.3e-09 (Fisher's exact test), Q value = 7.9e-06

Table S61. Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
AMP PEAK 25(19Q12) CNV	58	100	54
AMP PEAK 25(19Q12) WILD-TYPE	136	62	79

Figure S61. Get High-res Image Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 26(19q13.2)' versus 'CN_CNMF'

P value = 7.93e-07 (Fisher's exact test), Q value = 0.00073

Table S62. Gene #26: 'Amp Peak 26(19q13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
AMP PEAK 26(19Q13.2) CNV	62	97	58
AMP PEAK 26(19Q13.2) WILD-TYPE	132	65	75

Figure S62. Get High-res Image Gene #26: 'Amp Peak 26(19q13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 27(20p12.2)' versus 'CN_CNMF'

P value = 5.15e-10 (Fisher's exact test), Q value = 5e-07

Table S63. Gene #27: 'Amp Peak 27(20p12.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
AMP PEAK 27(20P12.2) CNV	74	117	77
AMP PEAK 27(20P12.2) WILD-TYPE	120	45	56

Figure S63. Get High-res Image Gene #27: 'Amp Peak 27(20p12.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 27(20p12.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000136 (Fisher's exact test), Q value = 0.11

Table S64. Gene #27: 'Amp Peak 27(20p12.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	140	245
AMP PEAK 27(20P12.2) CNV	53	96	114
AMP PEAK 27(20P12.2) WILD-TYPE	40	44	131

Figure S64. Get High-res Image Gene #27: 'Amp Peak 27(20p12.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 28(20q11.21)' versus 'CN_CNMF'

P value = 4.62e-07 (Fisher's exact test), Q value = 0.00043

Table S65. Gene #28: 'Amp Peak 28(20q11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
AMP PEAK 28(20Q11.21) CNV	87	109	95
AMP PEAK 28(20Q11.21) WILD-TYPE	107	53	38

Figure S65. Get High-res Image Gene #28: 'Amp Peak 28(20q11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 29(22q11.21)' versus 'MRNASEQ_CNMF'

P value = 0.000284 (Fisher's exact test), Q value = 0.23

Table S66. Gene #29: 'Amp Peak 29(22q11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	118	143	142	75
AMP PEAK 29(22Q11.21) CNV	56	94	66	29
AMP PEAK 29(22Q11.21) WILD-TYPE	62	49	76	46

Figure S66. Get High-res Image Gene #29: 'Amp Peak 29(22q11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 1(1p36.32)' versus 'MRNA_CNMF'

P value = 1.49e-06 (Fisher's exact test), Q value = 0.0014

Table S67. Gene #31: 'Del Peak 1(1p36.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	52	32	28
DEL PEAK 1(1P36.32) CNV	9	38	14	8
DEL PEAK 1(1P36.32) WILD-TYPE	33	14	18	20

Figure S67. Get High-res Image Gene #31: 'Del Peak 1(1p36.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 1(1p36.32)' versus 'MRNA_CHIERARCHICAL'

P value = 1.22e-07 (Fisher's exact test), Q value = 0.00011

Table S68. Gene #31: 'Del Peak 1(1p36.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	22	56	23	53
DEL PEAK 1(1P36.32) CNV	8	42	7	12
DEL PEAK 1(1P36.32) WILD-TYPE	14	14	16	41

Figure S68. Get High-res Image Gene #31: 'Del Peak 1(1p36.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 1(1p36.32)' versus 'CN_CNMF'

P value = 7.51e-35 (Fisher's exact test), Q value = 7.4e-32

Table S69. Gene #31: 'Del Peak 1(1p36.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
DEL PEAK 1(1P36.32) CNV	53	133	26
DEL PEAK 1(1P36.32) WILD-TYPE	141	29	107

Figure S69. Get High-res Image Gene #31: 'Del Peak 1(1p36.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 1(1p36.32)' versus 'METHLYATION_CNMF'

P value = 1.96e-19 (Fisher's exact test), Q value = 1.9e-16

Table S70. Gene #31: 'Del Peak 1(1p36.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	99
DEL PEAK 1(1P36.32) CNV	26	85	38
DEL PEAK 1(1P36.32) WILD-TYPE	116	29	61

Figure S70. Get High-res Image Gene #31: 'Del Peak 1(1p36.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 1(1p36.32)' versus 'MRNASEQ_CNMF'

P value = 3.79e-20 (Fisher's exact test), Q value = 3.7e-17

Table S71. Gene #31: 'Del Peak 1(1p36.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	118	143	142	75
DEL PEAK 1(1P36.32) CNV	34	110	43	22
DEL PEAK 1(1P36.32) WILD-TYPE	84	33	99	53

Figure S71. Get High-res Image Gene #31: 'Del Peak 1(1p36.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 1(1p36.32)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.06e-20 (Fisher's exact test), Q value = 1e-17

Table S72. Gene #31: 'Del Peak 1(1p36.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	140	245
DEL PEAK 1(1P36.32) CNV	28	108	73
DEL PEAK 1(1P36.32) WILD-TYPE	65	32	172

Figure S72. Get High-res Image Gene #31: 'Del Peak 1(1p36.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 1(1p36.32)' versus 'MIRSEQ_CNMF'

P value = 2.12e-06 (Fisher's exact test), Q value = 0.0019

Table S73. Gene #31: 'Del Peak 1(1p36.32)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	130	124	64
DEL PEAK 1(1P36.32) CNV	61	62	34	43
DEL PEAK 1(1P36.32) WILD-TYPE	84	68	90	21

Figure S73. Get High-res Image Gene #31: 'Del Peak 1(1p36.32)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 1(1p36.32)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.11e-05 (Fisher's exact test), Q value = 0.0097

Table S74. Gene #31: 'Del Peak 1(1p36.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	163	229
DEL PEAK 1(1P36.32) CNV	49	65	86
DEL PEAK 1(1P36.32) WILD-TYPE	22	98	143

Figure S74. Get High-res Image Gene #31: 'Del Peak 1(1p36.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 1(1p36.32)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.84e-07 (Fisher's exact test), Q value = 0.00036

Table S75. Gene #31: 'Del Peak 1(1p36.32)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	150	177
DEL PEAK 1(1P36.32) CNV	86	52
DEL PEAK 1(1P36.32) WILD-TYPE	64	125

Figure S75. Get High-res Image Gene #31: 'Del Peak 1(1p36.32)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 6.31e-05 (Fisher's exact test), Q value = 0.053

Table S76. Gene #32: 'Del Peak 2(1p13.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	22	56	23	53
DEL PEAK 2(1P13.1) CNV	9	37	12	12
DEL PEAK 2(1P13.1) WILD-TYPE	13	19	11	41

Figure S76. Get High-res Image Gene #32: 'Del Peak 2(1p13.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

P value = 3.83e-20 (Fisher's exact test), Q value = 3.8e-17

Table S77. Gene #32: 'Del Peak 2(1p13.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
DEL PEAK 2(1P13.1) CNV	50	117	41
DEL PEAK 2(1P13.1) WILD-TYPE	144	45	92

Figure S77. Get High-res Image Gene #32: 'Del Peak 2(1p13.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 2.04e-12 (Fisher's exact test), Q value = 2e-09

Table S78. Gene #32: 'Del Peak 2(1p13.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	99
DEL PEAK 2(1P13.1) CNV	35	78	33
DEL PEAK 2(1P13.1) WILD-TYPE	107	36	66

Figure S78. Get High-res Image Gene #32: 'Del Peak 2(1p13.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 2.36e-11 (Fisher's exact test), Q value = 2.3e-08

Table S79. Gene #32: 'Del Peak 2(1p13.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	118	143	142	75
DEL PEAK 2(1P13.1) CNV	37	97	49	22
DEL PEAK 2(1P13.1) WILD-TYPE	81	46	93	53

Figure S79. Get High-res Image Gene #32: 'Del Peak 2(1p13.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 1.66e-13 (Fisher's exact test), Q value = 1.6e-10

Table S80. Gene #32: 'Del Peak 2(1p13.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	140	245
DEL PEAK 2(1P13.1) CNV	39	96	70
DEL PEAK 2(1P13.1) WILD-TYPE	54	44	175

Figure S80. Get High-res Image Gene #32: 'Del Peak 2(1p13.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 4.79e-08 (Fisher's exact test), Q value = 4.5e-05

Table S81. Gene #32: 'Del Peak 2(1p13.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	130	124	64
DEL PEAK 2(1P13.1) CNV	66	61	28	42
DEL PEAK 2(1P13.1) WILD-TYPE	79	69	96	22

Figure S81. Get High-res Image Gene #32: 'Del Peak 2(1p13.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

P value = 6.69e-06 (Fisher's exact test), Q value = 0.0059

Table S82. Gene #32: 'Del Peak 2(1p13.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	163	229
DEL PEAK 2(1P13.1) CNV	49	62	86
DEL PEAK 2(1P13.1) WILD-TYPE	22	101	143

Figure S82. Get High-res Image Gene #32: 'Del Peak 2(1p13.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 5.63e-06 (Fisher's exact test), Q value = 0.005

Table S83. Gene #32: 'Del Peak 2(1p13.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	150	177
DEL PEAK 2(1P13.1) CNV	82	52
DEL PEAK 2(1P13.1) WILD-TYPE	68	125

Figure S83. Get High-res Image Gene #32: 'Del Peak 2(1p13.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 4(2q22.1)' versus 'CN_CNMF'

P value = 1.69e-05 (Fisher's exact test), Q value = 0.015

Table S84. Gene #34: 'Del Peak 4(2q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
DEL PEAK 4(2Q22.1) CNV	29	59	33
DEL PEAK 4(2Q22.1) WILD-TYPE	165	103	100

Figure S84. Get High-res Image Gene #34: 'Del Peak 4(2q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 4(2q22.1)' versus 'MIRSEQ_CNMF'

P value = 0.000126 (Fisher's exact test), Q value = 0.1

Table S85. Gene #34: 'Del Peak 4(2q22.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	130	124	64
DEL PEAK 4(2Q22.1) CNV	47	34	14	21
DEL PEAK 4(2Q22.1) WILD-TYPE	98	96	110	43

Figure S85. Get High-res Image Gene #34: 'Del Peak 4(2q22.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 4(2q22.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000293 (Fisher's exact test), Q value = 0.23

Table S86. Gene #34: 'Del Peak 4(2q22.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	111	91
DEL PEAK 4(2Q22.1) CNV	45	20	13
DEL PEAK 4(2Q22.1) WILD-TYPE	80	91	78

Figure S86. Get High-res Image Gene #34: 'Del Peak 4(2q22.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 5(2q37.1)' versus 'CN_CNMF'

P value = 4.19e-09 (Fisher's exact test), Q value = 4e-06

Table S87. Gene #35: 'Del Peak 5(2q37.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
DEL PEAK 5(2Q37.1) CNV	39	81	34
DEL PEAK 5(2Q37.1) WILD-TYPE	155	81	99

Figure S87. Get High-res Image Gene #35: 'Del Peak 5(2q37.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 5(2q37.1)' versus 'METHLYATION_CNMF'

P value = 7.61e-07 (Fisher's exact test), Q value = 7e-04

Table S88. Gene #35: 'Del Peak 5(2q37.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	99
DEL PEAK 5(2Q37.1) CNV	25	55	34
DEL PEAK 5(2Q37.1) WILD-TYPE	117	59	65

Figure S88. Get High-res Image Gene #35: 'Del Peak 5(2q37.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 5(2q37.1)' versus 'MRNASEQ_CNMF'

P value = 2.07e-06 (Fisher's exact test), Q value = 0.0019

Table S89. Gene #35: 'Del Peak 5(2q37.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	118	143	142	75
DEL PEAK 5(2Q37.1) CNV	36	67	38	10
DEL PEAK 5(2Q37.1) WILD-TYPE	82	76	104	65

Figure S89. Get High-res Image Gene #35: 'Del Peak 5(2q37.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 5(2q37.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.02e-06 (Fisher's exact test), Q value = 0.0062

Table S90. Gene #35: 'Del Peak 5(2q37.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	140	245
DEL PEAK 5(2Q37.1) CNV	25	67	59
DEL PEAK 5(2Q37.1) WILD-TYPE	68	73	186

Figure S90. Get High-res Image Gene #35: 'Del Peak 5(2q37.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 5(2q37.1)' versus 'MIRSEQ_CNMF'

P value = 2.81e-05 (Fisher's exact test), Q value = 0.024

Table S91. Gene #35: 'Del Peak 5(2q37.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	130	124	64
DEL PEAK 5(2Q37.1) CNV	52	53	19	23
DEL PEAK 5(2Q37.1) WILD-TYPE	93	77	105	41

Figure S91. Get High-res Image Gene #35: 'Del Peak 5(2q37.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 5(2q37.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.46e-05 (Fisher's exact test), Q value = 0.013

Table S92. Gene #35: 'Del Peak 5(2q37.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	111	91
DEL PEAK 5(2Q37.1) CNV	58	24	19
DEL PEAK 5(2Q37.1) WILD-TYPE	67	87	72

Figure S92. Get High-res Image Gene #35: 'Del Peak 5(2q37.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 5(2q37.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000193 (Fisher's exact test), Q value = 0.16

Table S93. Gene #35: 'Del Peak 5(2q37.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	150	177
DEL PEAK 5(2Q37.1) CNV	62	39
DEL PEAK 5(2Q37.1) WILD-TYPE	88	138

Figure S93. Get High-res Image Gene #35: 'Del Peak 5(2q37.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 7(3p13)' versus 'CN_CNMF'

P value = 1.25e-06 (Fisher's exact test), Q value = 0.0011

Table S94. Gene #37: 'Del Peak 7(3p13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
DEL PEAK 7(3P13) CNV	147	153	119
DEL PEAK 7(3P13) WILD-TYPE	47	9	14

Figure S94. Get High-res Image Gene #37: 'Del Peak 7(3p13)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 7(3p13)' versus 'METHLYATION_CNMF'

P value = 0.000314 (Fisher's exact test), Q value = 0.25

Table S95. Gene #37: 'Del Peak 7(3p13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	99
DEL PEAK 7(3P13) CNV	109	107	88
DEL PEAK 7(3P13) WILD-TYPE	33	7	11

Figure S95. Get High-res Image Gene #37: 'Del Peak 7(3p13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 7(3p13)' versus 'MIRSEQ_CNMF'

P value = 4.76e-05 (Fisher's exact test), Q value = 0.04

Table S96. Gene #37: 'Del Peak 7(3p13)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	130	124	64
DEL PEAK 7(3P13) CNV	127	119	90	60
DEL PEAK 7(3P13) WILD-TYPE	18	11	34	4

Figure S96. Get High-res Image Gene #37: 'Del Peak 7(3p13)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 7(3p13)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.83e-05 (Fisher's exact test), Q value = 0.049

Table S97. Gene #37: 'Del Peak 7(3p13)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	150	177
DEL PEAK 7(3P13) CNV	141	139
DEL PEAK 7(3P13) WILD-TYPE	9	38

Figure S97. Get High-res Image Gene #37: 'Del Peak 7(3p13)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 8(3p12.3)' versus 'CN_CNMF'

P value = 2.32e-05 (Fisher's exact test), Q value = 0.02

Table S98. Gene #38: 'Del Peak 8(3p12.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
DEL PEAK 8(3P12.3) CNV	144	149	115
DEL PEAK 8(3P12.3) WILD-TYPE	50	13	18

Figure S98. Get High-res Image Gene #38: 'Del Peak 8(3p12.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 8(3p12.3)' versus 'METHLYATION_CNMF'

P value = 0.000187 (Fisher's exact test), Q value = 0.15

Table S99. Gene #38: 'Del Peak 8(3p12.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	99
DEL PEAK 8(3P12.3) CNV	105	106	84
DEL PEAK 8(3P12.3) WILD-TYPE	37	8	15

Figure S99. Get High-res Image Gene #38: 'Del Peak 8(3p12.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 10(4p15.2)' versus 'CN_CNMF'

P value = 2.32e-09 (Fisher's exact test), Q value = 2.2e-06

Table S100. Gene #40: 'Del Peak 10(4p15.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
DEL PEAK 10(4P15.2) CNV	93	129	77
DEL PEAK 10(4P15.2) WILD-TYPE	101	33	56

Figure S100. Get High-res Image Gene #40: 'Del Peak 10(4p15.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 10(4p15.2)' versus 'METHLYATION_CNMF'

P value = 6.04e-06 (Fisher's exact test), Q value = 0.0053

Table S101. Gene #40: 'Del Peak 10(4p15.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	99
DEL PEAK 10(4P15.2) CNV	66	86	66
DEL PEAK 10(4P15.2) WILD-TYPE	76	28	33

Figure S101. Get High-res Image Gene #40: 'Del Peak 10(4p15.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 10(4p15.2)' versus 'MRNASEQ_CNMF'

P value = 9.06e-05 (Fisher's exact test), Q value = 0.075

Table S102. Gene #40: 'Del Peak 10(4p15.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	118	143	142	75
DEL PEAK 10(4P15.2) CNV	76	107	73	38
DEL PEAK 10(4P15.2) WILD-TYPE	42	36	69	37

Figure S102. Get High-res Image Gene #40: 'Del Peak 10(4p15.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 1.92e-06 (Fisher's exact test), Q value = 0.0017

Table S103. Gene #41: 'Del Peak 11(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
DEL PEAK 11(4Q22.1) CNV	88	116	69
DEL PEAK 11(4Q22.1) WILD-TYPE	106	46	64

Figure S103. Get High-res Image Gene #41: 'Del Peak 11(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 0.00012 (Fisher's exact test), Q value = 0.098

Table S104. Gene #41: 'Del Peak 11(4q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	118	143	142	75
DEL PEAK 11(4Q22.1) CNV	65	99	73	29
DEL PEAK 11(4Q22.1) WILD-TYPE	53	44	69	46

Figure S104. Get High-res Image Gene #41: 'Del Peak 11(4q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 12(4q32.3)' versus 'CN_CNMF'

P value = 5.63e-09 (Fisher's exact test), Q value = 5.4e-06

Table S105. Gene #42: 'Del Peak 12(4q32.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
DEL PEAK 12(4Q32.3) CNV	102	134	82
DEL PEAK 12(4Q32.3) WILD-TYPE	92	28	51

Figure S105. Get High-res Image Gene #42: 'Del Peak 12(4q32.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 12(4q32.3)' versus 'METHLYATION_CNMF'

P value = 7.36e-05 (Fisher's exact test), Q value = 0.062

Table S106. Gene #42: 'Del Peak 12(4q32.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	99
DEL PEAK 12(4Q32.3) CNV	73	87	70
DEL PEAK 12(4Q32.3) WILD-TYPE	69	27	29

Figure S106. Get High-res Image Gene #42: 'Del Peak 12(4q32.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 12(4q32.3)' versus 'MRNASEQ_CNMF'

P value = 4.7e-06 (Fisher's exact test), Q value = 0.0042

Table S107. Gene #42: 'Del Peak 12(4q32.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	118	143	142	75
DEL PEAK 12(4Q32.3) CNV	78	114	84	35
DEL PEAK 12(4Q32.3) WILD-TYPE	40	29	58	40

Figure S107. Get High-res Image Gene #42: 'Del Peak 12(4q32.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 12(4q32.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.9e-05 (Fisher's exact test), Q value = 0.074

Table S108. Gene #42: 'Del Peak 12(4q32.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	140	245
DEL PEAK 12(4Q32.3) CNV	61	110	140
DEL PEAK 12(4Q32.3) WILD-TYPE	32	30	105

Figure S108. Get High-res Image Gene #42: 'Del Peak 12(4q32.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 12(4q32.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.55e-05 (Fisher's exact test), Q value = 0.063

Table S109. Gene #42: 'Del Peak 12(4q32.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	150	177
DEL PEAK 12(4Q32.3) CNV	114	97
DEL PEAK 12(4Q32.3) WILD-TYPE	36	80

Figure S109. Get High-res Image Gene #42: 'Del Peak 12(4q32.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 13(4q35.2)' versus 'CN_CNMF'

P value = 7.6e-08 (Fisher's exact test), Q value = 7.1e-05

Table S110. Gene #43: 'Del Peak 13(4q35.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
DEL PEAK 13(4Q35.2) CNV	106	133	81
DEL PEAK 13(4Q35.2) WILD-TYPE	88	29	52

Figure S110. Get High-res Image Gene #43: 'Del Peak 13(4q35.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 13(4q35.2)' versus 'METHLYATION_CNMF'

P value = 3.56e-05 (Fisher's exact test), Q value = 0.03

Table S111. Gene #43: 'Del Peak 13(4q35.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	99
DEL PEAK 13(4Q35.2) CNV	74	90	66
DEL PEAK 13(4Q35.2) WILD-TYPE	68	24	33

Figure S111. Get High-res Image Gene #43: 'Del Peak 13(4q35.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 13(4q35.2)' versus 'MRNASEQ_CNMF'

P value = 3.97e-06 (Fisher's exact test), Q value = 0.0035

Table S112. Gene #43: 'Del Peak 13(4q35.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	118	143	142	75
DEL PEAK 13(4Q35.2) CNV	75	115	87	35
DEL PEAK 13(4Q35.2) WILD-TYPE	43	28	55	40

Figure S112. Get High-res Image Gene #43: 'Del Peak 13(4q35.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 13(4q35.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000174 (Fisher's exact test), Q value = 0.14

Table S113. Gene #43: 'Del Peak 13(4q35.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	140	245
DEL PEAK 13(4Q35.2) CNV	60	110	142
DEL PEAK 13(4Q35.2) WILD-TYPE	33	30	103

Figure S113. Get High-res Image Gene #43: 'Del Peak 13(4q35.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 13(4q35.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000197 (Fisher's exact test), Q value = 0.16

Table S114. Gene #43: 'Del Peak 13(4q35.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	150	177
DEL PEAK 13(4Q35.2) CNV	113	98
DEL PEAK 13(4Q35.2) WILD-TYPE	37	79

Figure S114. Get High-res Image Gene #43: 'Del Peak 13(4q35.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 14(5q11.2)' versus 'CN_CNMF'

P value = 2.55e-11 (Fisher's exact test), Q value = 2.5e-08

Table S115. Gene #44: 'Del Peak 14(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
DEL PEAK 14(5Q11.2) CNV	106	134	113
DEL PEAK 14(5Q11.2) WILD-TYPE	88	28	20

Figure S115. Get High-res Image Gene #44: 'Del Peak 14(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 14(5q11.2)' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.083

Table S116. Gene #44: 'Del Peak 14(5q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	99
DEL PEAK 14(5Q11.2) CNV	84	92	79
DEL PEAK 14(5Q11.2) WILD-TYPE	58	22	20

Figure S116. Get High-res Image Gene #44: 'Del Peak 14(5q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 14(5q11.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.21e-05 (Fisher's exact test), Q value = 0.027

Table S117. Gene #44: 'Del Peak 14(5q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	163	229
DEL PEAK 14(5Q11.2) CNV	54	137	146
DEL PEAK 14(5Q11.2) WILD-TYPE	17	26	83

Figure S117. Get High-res Image Gene #44: 'Del Peak 14(5q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 15(6p25.3)' versus 'CN_CNMF'

P value = 0.000114 (Fisher's exact test), Q value = 0.094

Table S118. Gene #45: 'Del Peak 15(6p25.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
DEL PEAK 15(6P25.3) CNV	40	61	24
DEL PEAK 15(6P25.3) WILD-TYPE	154	101	109

Figure S118. Get High-res Image Gene #45: 'Del Peak 15(6p25.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 15(6p25.3)' versus 'METHLYATION_CNMF'

P value = 0.000102 (Fisher's exact test), Q value = 0.084

Table S119. Gene #45: 'Del Peak 15(6p25.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	99
DEL PEAK 15(6P25.3) CNV	25	47	23
DEL PEAK 15(6P25.3) WILD-TYPE	117	67	76

Figure S119. Get High-res Image Gene #45: 'Del Peak 15(6p25.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 15(6p25.3)' versus 'MRNASEQ_CNMF'

P value = 2.82e-06 (Fisher's exact test), Q value = 0.0025

Table S120. Gene #45: 'Del Peak 15(6p25.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	118	143	142	75
DEL PEAK 15(6P25.3) CNV	28	60	22	14
DEL PEAK 15(6P25.3) WILD-TYPE	90	83	120	61

Figure S120. Get High-res Image Gene #45: 'Del Peak 15(6p25.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 15(6p25.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.82e-08 (Fisher's exact test), Q value = 6.4e-05

Table S121. Gene #45: 'Del Peak 15(6p25.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	140	245
DEL PEAK 15(6P25.3) CNV	12	61	51
DEL PEAK 15(6P25.3) WILD-TYPE	81	79	194

Figure S121. Get High-res Image Gene #45: 'Del Peak 15(6p25.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 16(6q22.31)' versus 'CN_CNMF'

P value = 4.19e-05 (Fisher's exact test), Q value = 0.035

Table S122. Gene #46: 'Del Peak 16(6q22.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
DEL PEAK 16(6Q22.31) CNV	33	59	25
DEL PEAK 16(6Q22.31) WILD-TYPE	161	103	108

Figure S122. Get High-res Image Gene #46: 'Del Peak 16(6q22.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 16(6q22.31)' versus 'MRNASEQ_CNMF'

P value = 0.000154 (Fisher's exact test), Q value = 0.13

Table S123. Gene #46: 'Del Peak 16(6q22.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	118	143	142	75
DEL PEAK 16(6Q22.31) CNV	20	54	25	17
DEL PEAK 16(6Q22.31) WILD-TYPE	98	89	117	58

Figure S123. Get High-res Image Gene #46: 'Del Peak 16(6q22.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 17(6q26)' versus 'CN_CNMF'

P value = 2.95e-05 (Fisher's exact test), Q value = 0.025

Table S124. Gene #47: 'Del Peak 17(6q26)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
DEL PEAK 17(6Q26) CNV	37	64	28
DEL PEAK 17(6Q26) WILD-TYPE	157	98	105

Figure S124. Get High-res Image Gene #47: 'Del Peak 17(6q26)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 17(6q26)' versus 'METHLYATION_CNMF'

P value = 0.000115 (Fisher's exact test), Q value = 0.095

Table S125. Gene #47: 'Del Peak 17(6q26)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	99
DEL PEAK 17(6Q26) CNV	27	48	22
DEL PEAK 17(6Q26) WILD-TYPE	115	66	77

Figure S125. Get High-res Image Gene #47: 'Del Peak 17(6q26)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 17(6q26)' versus 'MRNASEQ_CNMF'

P value = 0.000276 (Fisher's exact test), Q value = 0.22

Table S126. Gene #47: 'Del Peak 17(6q26)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	118	143	142	75
DEL PEAK 17(6Q26) CNV	23	58	31	16
DEL PEAK 17(6Q26) WILD-TYPE	95	85	111	59

Figure S126. Get High-res Image Gene #47: 'Del Peak 17(6q26)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 17(6q26)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000219 (Fisher's exact test), Q value = 0.18

Table S127. Gene #47: 'Del Peak 17(6q26)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	140	245
DEL PEAK 17(6Q26) CNV	19	56	53
DEL PEAK 17(6Q26) WILD-TYPE	74	84	192

Figure S127. Get High-res Image Gene #47: 'Del Peak 17(6q26)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 20(8p23.2)' versus 'CN_CNMF'

P value = 6.89e-05 (Fisher's exact test), Q value = 0.058

Table S128. Gene #50: 'Del Peak 20(8p23.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
DEL PEAK 20(8P23.2) CNV	109	121	101
DEL PEAK 20(8P23.2) WILD-TYPE	85	41	32

Figure S128. Get High-res Image Gene #50: 'Del Peak 20(8p23.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 21(9p23)' versus 'CN_CNMF'

P value = 3.09e-06 (Fisher's exact test), Q value = 0.0028

Table S129. Gene #51: 'Del Peak 21(9p23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
DEL PEAK 21(9P23) CNV	111	97	109
DEL PEAK 21(9P23) WILD-TYPE	83	65	24

Figure S129. Get High-res Image Gene #51: 'Del Peak 21(9p23)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 21(9p23)' versus 'MRNASEQ_CNMF'

P value = 4.33e-05 (Fisher's exact test), Q value = 0.037

Table S130. Gene #51: 'Del Peak 21(9p23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	118	143	142	75
DEL PEAK 21(9P23) CNV	90	79	103	38
DEL PEAK 21(9P23) WILD-TYPE	28	64	39	37

Figure S130. Get High-res Image Gene #51: 'Del Peak 21(9p23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 22(9p21.3)' versus 'CN_CNMF'

P value = 7.87e-06 (Fisher's exact test), Q value = 0.0069

Table S131. Gene #52: 'Del Peak 22(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
DEL PEAK 22(9P21.3) CNV	130	122	119
DEL PEAK 22(9P21.3) WILD-TYPE	64	40	14

Figure S131. Get High-res Image Gene #52: 'Del Peak 22(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 23(9p21.1)' versus 'CN_CNMF'

P value = 9.11e-06 (Fisher's exact test), Q value = 0.008

Table S132. Gene #53: 'Del Peak 23(9p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
DEL PEAK 23(9P21.1) CNV	113	92	107
DEL PEAK 23(9P21.1) WILD-TYPE	81	70	26

Figure S132. Get High-res Image Gene #53: 'Del Peak 23(9p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 23(9p21.1)' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.09

Table S133. Gene #53: 'Del Peak 23(9p21.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	118	143	142	75
DEL PEAK 23(9P21.1) CNV	90	77	99	39
DEL PEAK 23(9P21.1) WILD-TYPE	28	66	43	36

Figure S133. Get High-res Image Gene #53: 'Del Peak 23(9p21.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 24(9q21.11)' versus 'MRNA_CNMF'

P value = 8.38e-05 (Fisher's exact test), Q value = 0.07

Table S134. Gene #54: 'Del Peak 24(9q21.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	52	32	28
DEL PEAK 24(9Q21.11) CNV	28	12	19	15
DEL PEAK 24(9Q21.11) WILD-TYPE	14	40	13	13

Figure S134. Get High-res Image Gene #54: 'Del Peak 24(9q21.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 24(9q21.11)' versus 'MRNA_CHIERARCHICAL'

P value = 1.96e-05 (Fisher's exact test), Q value = 0.017

Table S135. Gene #54: 'Del Peak 24(9q21.11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	22	56	23	53
DEL PEAK 24(9Q21.11) CNV	14	13	17	30
DEL PEAK 24(9Q21.11) WILD-TYPE	8	43	6	23

Figure S135. Get High-res Image Gene #54: 'Del Peak 24(9q21.11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 24(9q21.11)' versus 'CN_CNMF'

P value = 5.61e-13 (Fisher's exact test), Q value = 5.5e-10

Table S136. Gene #54: 'Del Peak 24(9q21.11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
DEL PEAK 24(9Q21.11) CNV	97	48	97
DEL PEAK 24(9Q21.11) WILD-TYPE	97	114	36

Figure S136. Get High-res Image Gene #54: 'Del Peak 24(9q21.11)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 24(9q21.11)' versus 'METHLYATION_CNMF'

P value = 1.41e-09 (Fisher's exact test), Q value = 1.4e-06

Table S137. Gene #54: 'Del Peak 24(9q21.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	99
DEL PEAK 24(9Q21.11) CNV	84	29	63
DEL PEAK 24(9Q21.11) WILD-TYPE	58	85	36

Figure S137. Get High-res Image Gene #54: 'Del Peak 24(9q21.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 24(9q21.11)' versus 'MRNASEQ_CNMF'

P value = 2.45e-15 (Fisher's exact test), Q value = 2.4e-12

Table S138. Gene #54: 'Del Peak 24(9q21.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	118	143	142	75
DEL PEAK 24(9Q21.11) CNV	78	31	90	37
DEL PEAK 24(9Q21.11) WILD-TYPE	40	112	52	38

Figure S138. Get High-res Image Gene #54: 'Del Peak 24(9q21.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 24(9q21.11)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.64e-15 (Fisher's exact test), Q value = 6.5e-12

Table S139. Gene #54: 'Del Peak 24(9q21.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	140	245
DEL PEAK 24(9Q21.11) CNV	60	30	146
DEL PEAK 24(9Q21.11) WILD-TYPE	33	110	99

Figure S139. Get High-res Image Gene #54: 'Del Peak 24(9q21.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 24(9q21.11)' versus 'MIRSEQ_CNMF'

P value = 1.4e-05 (Fisher's exact test), Q value = 0.012

Table S140. Gene #54: 'Del Peak 24(9q21.11)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	130	124	64
DEL PEAK 24(9Q21.11) CNV	62	78	71	17
DEL PEAK 24(9Q21.11) WILD-TYPE	83	52	53	47

Figure S140. Get High-res Image Gene #54: 'Del Peak 24(9q21.11)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 24(9q21.11)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.56e-08 (Fisher's exact test), Q value = 5.2e-05

Table S141. Gene #54: 'Del Peak 24(9q21.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	163	229
DEL PEAK 24(9Q21.11) CNV	17	104	107
DEL PEAK 24(9Q21.11) WILD-TYPE	54	59	122

Figure S141. Get High-res Image Gene #54: 'Del Peak 24(9q21.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 25(10p15.3)' versus 'CN_CNMF'

P value = 1.33e-07 (Fisher's exact test), Q value = 0.00012

Table S142. Gene #55: 'Del Peak 25(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
DEL PEAK 25(10P15.3) CNV	63	100	54
DEL PEAK 25(10P15.3) WILD-TYPE	131	62	79

Figure S142. Get High-res Image Gene #55: 'Del Peak 25(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 25(10p15.3)' versus 'METHLYATION_CNMF'

P value = 8.77e-10 (Fisher's exact test), Q value = 8.4e-07

Table S143. Gene #55: 'Del Peak 25(10p15.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	99
DEL PEAK 25(10P15.3) CNV	46	80	36
DEL PEAK 25(10P15.3) WILD-TYPE	96	34	63

Figure S143. Get High-res Image Gene #55: 'Del Peak 25(10p15.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 25(10p15.3)' versus 'MRNASEQ_CNMF'

P value = 3.92e-05 (Fisher's exact test), Q value = 0.033

Table S144. Gene #55: 'Del Peak 25(10p15.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	118	143	142	75
DEL PEAK 25(10P15.3) CNV	46	87	56	24
DEL PEAK 25(10P15.3) WILD-TYPE	72	56	86	51

Figure S144. Get High-res Image Gene #55: 'Del Peak 25(10p15.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 25(10p15.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.28e-06 (Fisher's exact test), Q value = 0.0038

Table S145. Gene #55: 'Del Peak 25(10p15.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	140	245
DEL PEAK 25(10P15.3) CNV	35	87	91
DEL PEAK 25(10P15.3) WILD-TYPE	58	53	154

Figure S145. Get High-res Image Gene #55: 'Del Peak 25(10p15.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 25(10p15.3)' versus 'MIRSEQ_CNMF'

P value = 1.89e-06 (Fisher's exact test), Q value = 0.0017

Table S146. Gene #55: 'Del Peak 25(10p15.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	130	124	64
DEL PEAK 25(10P15.3) CNV	67	67	34	42
DEL PEAK 25(10P15.3) WILD-TYPE	78	63	90	22

Figure S146. Get High-res Image Gene #55: 'Del Peak 25(10p15.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 25(10p15.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.14e-05 (Fisher's exact test), Q value = 0.0099

Table S147. Gene #55: 'Del Peak 25(10p15.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	163	229
DEL PEAK 25(10P15.3) CNV	50	72	88
DEL PEAK 25(10P15.3) WILD-TYPE	21	91	141

Figure S147. Get High-res Image Gene #55: 'Del Peak 25(10p15.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 26(10p15.1)' versus 'CN_CNMF'

P value = 1.83e-06 (Fisher's exact test), Q value = 0.0017

Table S148. Gene #56: 'Del Peak 26(10p15.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
DEL PEAK 26(10P15.1) CNV	62	94	49
DEL PEAK 26(10P15.1) WILD-TYPE	132	68	84

Figure S148. Get High-res Image Gene #56: 'Del Peak 26(10p15.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 26(10p15.1)' versus 'METHLYATION_CNMF'

P value = 2.6e-10 (Fisher's exact test), Q value = 2.5e-07

Table S149. Gene #56: 'Del Peak 26(10p15.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	99
DEL PEAK 26(10P15.1) CNV	45	78	30
DEL PEAK 26(10P15.1) WILD-TYPE	97	36	69

Figure S149. Get High-res Image Gene #56: 'Del Peak 26(10p15.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 26(10p15.1)' versus 'MRNASEQ_CNMF'

P value = 1.59e-06 (Fisher's exact test), Q value = 0.0014

Table S150. Gene #56: 'Del Peak 26(10p15.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	118	143	142	75
DEL PEAK 26(10P15.1) CNV	42	86	53	20
DEL PEAK 26(10P15.1) WILD-TYPE	76	57	89	55

Figure S150. Get High-res Image Gene #56: 'Del Peak 26(10p15.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 26(10p15.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.33e-06 (Fisher's exact test), Q value = 0.0021

Table S151. Gene #56: 'Del Peak 26(10p15.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	140	245
DEL PEAK 26(10P15.1) CNV	33	84	84
DEL PEAK 26(10P15.1) WILD-TYPE	60	56	161

Figure S151. Get High-res Image Gene #56: 'Del Peak 26(10p15.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 26(10p15.1)' versus 'MIRSEQ_CNMF'

P value = 1.58e-06 (Fisher's exact test), Q value = 0.0014

Table S152. Gene #56: 'Del Peak 26(10p15.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	130	124	64
DEL PEAK 26(10P15.1) CNV	65	61	31	41
DEL PEAK 26(10P15.1) WILD-TYPE	80	69	93	23

Figure S152. Get High-res Image Gene #56: 'Del Peak 26(10p15.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 26(10p15.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.6e-06 (Fisher's exact test), Q value = 0.0032

Table S153. Gene #56: 'Del Peak 26(10p15.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	163	229
DEL PEAK 26(10P15.1) CNV	49	68	81
DEL PEAK 26(10P15.1) WILD-TYPE	22	95	148

Figure S153. Get High-res Image Gene #56: 'Del Peak 26(10p15.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 27(10q23.31)' versus 'CN_CNMF'

P value = 4.34e-08 (Fisher's exact test), Q value = 4.1e-05

Table S154. Gene #57: 'Del Peak 27(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
DEL PEAK 27(10Q23.31) CNV	75	112	65
DEL PEAK 27(10Q23.31) WILD-TYPE	119	50	68

Figure S154. Get High-res Image Gene #57: 'Del Peak 27(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 27(10q23.31)' versus 'METHLYATION_CNMF'

P value = 2.36e-07 (Fisher's exact test), Q value = 0.00022

Table S155. Gene #57: 'Del Peak 27(10q23.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	99
DEL PEAK 27(10Q23.31) CNV	52	81	51
DEL PEAK 27(10Q23.31) WILD-TYPE	90	33	48

Figure S155. Get High-res Image Gene #57: 'Del Peak 27(10q23.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 27(10q23.31)' versus 'MRNASEQ_CNMF'

P value = 6.5e-08 (Fisher's exact test), Q value = 6.1e-05

Table S156. Gene #57: 'Del Peak 27(10q23.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	118	143	142	75
DEL PEAK 27(10Q23.31) CNV	51	103	61	30
DEL PEAK 27(10Q23.31) WILD-TYPE	67	40	81	45

Figure S156. Get High-res Image Gene #57: 'Del Peak 27(10q23.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 27(10q23.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.78e-10 (Fisher's exact test), Q value = 9.4e-07

Table S157. Gene #57: 'Del Peak 27(10q23.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	140	245
DEL PEAK 27(10Q23.31) CNV	47	102	96
DEL PEAK 27(10Q23.31) WILD-TYPE	46	38	149

Figure S157. Get High-res Image Gene #57: 'Del Peak 27(10q23.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 27(10q23.31)' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.37e-05 (Fisher's exact test), Q value = 0.029

Table S158. Gene #57: 'Del Peak 27(10q23.31)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	111	91
DEL PEAK 27(10Q23.31) CNV	84	45	39
DEL PEAK 27(10Q23.31) WILD-TYPE	41	66	52

Figure S158. Get High-res Image Gene #57: 'Del Peak 27(10q23.31)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 28(11p15.5)' versus 'MRNA_CNMF'

P value = 0.000261 (Fisher's exact test), Q value = 0.21

Table S159. Gene #58: 'Del Peak 28(11p15.5)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	52	32	28
DEL PEAK 28(11P15.5) CNV	30	20	9	18
DEL PEAK 28(11P15.5) WILD-TYPE	12	32	23	10

Figure S159. Get High-res Image Gene #58: 'Del Peak 28(11p15.5)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 28(11p15.5)' versus 'CN_CNMF'

P value = 1.39e-07 (Fisher's exact test), Q value = 0.00013

Table S160. Gene #58: 'Del Peak 28(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
DEL PEAK 28(11P15.5) CNV	66	77	87
DEL PEAK 28(11P15.5) WILD-TYPE	128	85	46

Figure S160. Get High-res Image Gene #58: 'Del Peak 28(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 28(11p15.5)' versus 'RPPA_CHIERARCHICAL'

P value = 2.02e-05 (Fisher's exact test), Q value = 0.017

Table S161. Gene #58: 'Del Peak 28(11p15.5)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	47	49	40
DEL PEAK 28(11P15.5) CNV	29	17	36	10
DEL PEAK 28(11P15.5) WILD-TYPE	29	30	13	30

Figure S161. Get High-res Image Gene #58: 'Del Peak 28(11p15.5)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 29(11q22.1)' versus 'CN_CNMF'

P value = 0.000171 (Fisher's exact test), Q value = 0.14

Table S162. Gene #59: 'Del Peak 29(11q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
DEL PEAK 29(11Q22.1) CNV	40	65	46
DEL PEAK 29(11Q22.1) WILD-TYPE	154	97	87

Figure S162. Get High-res Image Gene #59: 'Del Peak 29(11q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 34(14q11.2)' versus 'MRNASEQ_CNMF'

P value = 3.27e-05 (Fisher's exact test), Q value = 0.028

Table S163. Gene #64: 'Del Peak 34(14q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	118	143	142	75
DEL PEAK 34(14Q11.2) CNV	27	53	68	17
DEL PEAK 34(14Q11.2) WILD-TYPE	91	90	74	58

Figure S163. Get High-res Image Gene #64: 'Del Peak 34(14q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 34(14q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.37e-07 (Fisher's exact test), Q value = 0.00013

Table S164. Gene #64: 'Del Peak 34(14q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	140	245
DEL PEAK 34(14Q11.2) CNV	53	52	60
DEL PEAK 34(14Q11.2) WILD-TYPE	40	88	185

Figure S164. Get High-res Image Gene #64: 'Del Peak 34(14q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 39(17p11.2)' versus 'CN_CNMF'

P value = 0.000255 (Fisher's exact test), Q value = 0.2

Table S165. Gene #69: 'Del Peak 39(17p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
DEL PEAK 39(17P11.2) CNV	86	83	89
DEL PEAK 39(17P11.2) WILD-TYPE	108	79	44

Figure S165. Get High-res Image Gene #69: 'Del Peak 39(17p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 40(17q11.2)' versus 'MRNA_CNMF'

P value = 3.03e-05 (Fisher's exact test), Q value = 0.026

Table S166. Gene #70: 'Del Peak 40(17q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	52	32	28
DEL PEAK 40(17Q11.2) CNV	21	4	11	6
DEL PEAK 40(17Q11.2) WILD-TYPE	21	48	21	22

Figure S166. Get High-res Image Gene #70: 'Del Peak 40(17q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 40(17q11.2)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000101 (Fisher's exact test), Q value = 0.084

Table S167. Gene #70: 'Del Peak 40(17q11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	22	56	23	53
DEL PEAK 40(17Q11.2) CNV	8	4	9	21
DEL PEAK 40(17Q11.2) WILD-TYPE	14	52	14	32

Figure S167. Get High-res Image Gene #70: 'Del Peak 40(17q11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 40(17q11.2)' versus 'CN_CNMF'

P value = 1.55e-06 (Fisher's exact test), Q value = 0.0014

Table S168. Gene #70: 'Del Peak 40(17q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
DEL PEAK 40(17Q11.2) CNV	55	19	48
DEL PEAK 40(17Q11.2) WILD-TYPE	139	143	85

Figure S168. Get High-res Image Gene #70: 'Del Peak 40(17q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 40(17q11.2)' versus 'METHLYATION_CNMF'

P value = 4.56e-05 (Fisher's exact test), Q value = 0.038

Table S169. Gene #70: 'Del Peak 40(17q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	99
DEL PEAK 40(17Q11.2) CNV	45	11	27
DEL PEAK 40(17Q11.2) WILD-TYPE	97	103	72

Figure S169. Get High-res Image Gene #70: 'Del Peak 40(17q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 40(17q11.2)' versus 'MRNASEQ_CNMF'

P value = 7.33e-09 (Fisher's exact test), Q value = 7e-06

Table S170. Gene #70: 'Del Peak 40(17q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	118	143	142	75
DEL PEAK 40(17Q11.2) CNV	44	11	42	24
DEL PEAK 40(17Q11.2) WILD-TYPE	74	132	100	51

Figure S170. Get High-res Image Gene #70: 'Del Peak 40(17q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 40(17q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.86e-09 (Fisher's exact test), Q value = 3.7e-06

Table S171. Gene #70: 'Del Peak 40(17q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	93	140	245
DEL PEAK 40(17Q11.2) CNV	25	11	85
DEL PEAK 40(17Q11.2) WILD-TYPE	68	129	160

Figure S171. Get High-res Image Gene #70: 'Del Peak 40(17q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 44(19q13.32)' versus 'CN_CNMF'

P value = 1.13e-06 (Fisher's exact test), Q value = 0.001

Table S172. Gene #74: 'Del Peak 44(19q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
DEL PEAK 44(19Q13.32) CNV	33	68	40
DEL PEAK 44(19Q13.32) WILD-TYPE	161	94	93

Figure S172. Get High-res Image Gene #74: 'Del Peak 44(19q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 44(19q13.32)' versus 'METHLYATION_CNMF'

P value = 2.32e-05 (Fisher's exact test), Q value = 0.02

Table S173. Gene #74: 'Del Peak 44(19q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	99
DEL PEAK 44(19Q13.32) CNV	22	42	38
DEL PEAK 44(19Q13.32) WILD-TYPE	120	72	61

Figure S173. Get High-res Image Gene #74: 'Del Peak 44(19q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 46(21q22.3)' versus 'CN_CNMF'

P value = 9.46e-08 (Fisher's exact test), Q value = 8.9e-05

Table S174. Gene #76: 'Del Peak 46(21q22.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
DEL PEAK 46(21Q22.3) CNV	78	110	85
DEL PEAK 46(21Q22.3) WILD-TYPE	116	52	48

Figure S174. Get High-res Image Gene #76: 'Del Peak 46(21q22.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 46(21q22.3)' versus 'MIRSEQ_CNMF'

P value = 8.61e-05 (Fisher's exact test), Q value = 0.072

Table S175. Gene #76: 'Del Peak 46(21q22.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	130	124	64
DEL PEAK 46(21Q22.3) CNV	95	83	50	33
DEL PEAK 46(21Q22.3) WILD-TYPE	50	47	74	31

Figure S175. Get High-res Image Gene #76: 'Del Peak 46(21q22.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 48(22q13.32)' versus 'MRNA_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.18

Table S176. Gene #78: 'Del Peak 48(22q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	52	32	28
DEL PEAK 48(22Q13.32) CNV	8	8	8	17
DEL PEAK 48(22Q13.32) WILD-TYPE	34	44	24	11

Figure S176. Get High-res Image Gene #78: 'Del Peak 48(22q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 49(Xp22.2)' versus 'CN_CNMF'

P value = 1.23e-05 (Fisher's exact test), Q value = 0.011

Table S177. Gene #79: 'Del Peak 49(Xp22.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
DEL PEAK 49(XP22.2) CNV	39	68	50
DEL PEAK 49(XP22.2) WILD-TYPE	155	94	83

Figure S177. Get High-res Image Gene #79: 'Del Peak 49(Xp22.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 49(Xp22.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.95e-06 (Fisher's exact test), Q value = 0.0018

Table S178. Gene #79: 'Del Peak 49(Xp22.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	150	177
DEL PEAK 49(XP22.2) CNV	70	38
DEL PEAK 49(XP22.2) WILD-TYPE	80	139

Figure S178. Get High-res Image Gene #79: 'Del Peak 49(Xp22.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 50(Xp21.1)' versus 'CN_CNMF'

P value = 3.82e-07 (Fisher's exact test), Q value = 0.00035

Table S179. Gene #80: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
DEL PEAK 50(XP21.1) CNV	36	72	48
DEL PEAK 50(XP21.1) WILD-TYPE	158	90	85

Figure S179. Get High-res Image Gene #80: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 50(Xp21.1)' versus 'METHLYATION_CNMF'

P value = 1.29e-05 (Fisher's exact test), Q value = 0.011

Table S180. Gene #80: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	99
DEL PEAK 50(XP21.1) CNV	25	48	39
DEL PEAK 50(XP21.1) WILD-TYPE	117	66	60

Figure S180. Get High-res Image Gene #80: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 50(Xp21.1)' versus 'MIRSEQ_CNMF'

P value = 2.01e-05 (Fisher's exact test), Q value = 0.017

Table S181. Gene #80: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	130	124	64
DEL PEAK 50(XP21.1) CNV	47	54	21	29
DEL PEAK 50(XP21.1) WILD-TYPE	98	76	103	35

Figure S181. Get High-res Image Gene #80: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 50(Xp21.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000246 (Fisher's exact test), Q value = 0.2

Table S182. Gene #80: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	111	91
DEL PEAK 50(XP21.1) CNV	57	24	25
DEL PEAK 50(XP21.1) WILD-TYPE	68	87	66

Figure S182. Get High-res Image Gene #80: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 50(Xp21.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.65e-09 (Fisher's exact test), Q value = 8.2e-06

Table S183. Gene #80: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	150	177
DEL PEAK 50(XP21.1) CNV	73	33
DEL PEAK 50(XP21.1) WILD-TYPE	77	144

Figure S183. Get High-res Image Gene #80: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 51(Xp11.3)' versus 'CN_CNMF'

P value = 1.22e-07 (Fisher's exact test), Q value = 0.00011

Table S184. Gene #81: 'Del Peak 51(Xp11.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
DEL PEAK 51(XP11.3) CNV	36	75	42
DEL PEAK 51(XP11.3) WILD-TYPE	158	87	91

Figure S184. Get High-res Image Gene #81: 'Del Peak 51(Xp11.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 51(Xp11.3)' versus 'METHLYATION_CNMF'

P value = 4.05e-06 (Fisher's exact test), Q value = 0.0036

Table S185. Gene #81: 'Del Peak 51(Xp11.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	99
DEL PEAK 51(XP11.3) CNV	24	51	35
DEL PEAK 51(XP11.3) WILD-TYPE	118	63	64

Figure S185. Get High-res Image Gene #81: 'Del Peak 51(Xp11.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 51(Xp11.3)' versus 'MIRSEQ_CNMF'

P value = 1.38e-06 (Fisher's exact test), Q value = 0.0013

Table S186. Gene #81: 'Del Peak 51(Xp11.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	130	124	64
DEL PEAK 51(XP11.3) CNV	44	53	19	31
DEL PEAK 51(XP11.3) WILD-TYPE	101	77	105	33

Figure S186. Get High-res Image Gene #81: 'Del Peak 51(Xp11.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 51(Xp11.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.21e-05 (Fisher's exact test), Q value = 0.027

Table S187. Gene #81: 'Del Peak 51(Xp11.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	111	91
DEL PEAK 51(XP11.3) CNV	58	23	22
DEL PEAK 51(XP11.3) WILD-TYPE	67	88	69

Figure S187. Get High-res Image Gene #81: 'Del Peak 51(Xp11.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 51(Xp11.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.47e-08 (Fisher's exact test), Q value = 1.4e-05

Table S188. Gene #81: 'Del Peak 51(Xp11.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	150	177
DEL PEAK 51(XP11.3) CNV	71	32
DEL PEAK 51(XP11.3) WILD-TYPE	79	145

Figure S188. Get High-res Image Gene #81: 'Del Peak 51(Xp11.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 52(Xq22.3)' versus 'CN_CNMF'

P value = 2.71e-07 (Fisher's exact test), Q value = 0.00025

Table S189. Gene #82: 'Del Peak 52(Xq22.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	194	162	133
DEL PEAK 52(XQ22.3) CNV	25	42	52
DEL PEAK 52(XQ22.3) WILD-TYPE	169	120	81

Figure S189. Get High-res Image Gene #82: 'Del Peak 52(Xq22.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 52(Xq22.3)' versus 'METHLYATION_CNMF'

P value = 1.02e-05 (Fisher's exact test), Q value = 0.009

Table S190. Gene #82: 'Del Peak 52(Xq22.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	114	99
DEL PEAK 52(XQ22.3) CNV	16	27	37
DEL PEAK 52(XQ22.3) WILD-TYPE	126	87	62

Figure S190. Get High-res Image Gene #82: 'Del Peak 52(Xq22.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 52(Xq22.3)' versus 'MIRSEQ_CNMF'

P value = 3.57e-05 (Fisher's exact test), Q value = 0.03

Table S191. Gene #82: 'Del Peak 52(Xq22.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	130	124	64
DEL PEAK 52(XQ22.3) CNV	41	45	13	16
DEL PEAK 52(XQ22.3) WILD-TYPE	104	85	111	48

Figure S191. Get High-res Image Gene #82: 'Del Peak 52(Xq22.3)' versus Molecular Subtype #9: 'MIRSEQ_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 = LUSC-TP.transferedmergedcluster.txt
Number of patients = 489
Number of copy number variation regions = 82
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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