Correlation between copy number variation genes and molecular subtypes

Overview

Introduction

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

Summary

Testing the association between copy number variation of 84 peak regions and 10 molecular subtypes across 397 patients, 117 significant findings detected with Q value < 0.25.

Amp Peak 2(1q21.2) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 3(2p16.1) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 4(2q31.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 6(3q26.33) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 8(5p15.33) cnvs correlated to 'CN_CNMF'.
Amp Peak 9(5p12) cnvs correlated to 'CN_CNMF'.
Amp Peak 13(7q21.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 19(12p13.33) cnvs correlated to 'CN_CNMF'.
Amp Peak 23(15q26.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Amp Peak 24(17q25.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 25(18p11.32) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 26(18q11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 27(19q12) cnvs correlated to 'CN_CNMF'.
Amp Peak 28(19q13.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 29(20p12.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 31(22q11.21) cnvs correlated to 'CN_CNMF'.
Del Peak 1(1p36.22) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 2(1p13.2) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 4(2q22.1) cnvs correlated to 'CN_CNMF'.
Del Peak 5(2q36.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 7(3p13) cnvs correlated to 'CN_CNMF'.
Del Peak 8(3p12.3) cnvs correlated to 'CN_CNMF'.
Del Peak 10(4p15.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 11(4q22.1) cnvs correlated to 'CN_CNMF'.
Del Peak 12(4q32.3) cnvs correlated to 'CN_CNMF'.
Del Peak 13(4q35.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Del Peak 14(5q11.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 15(5q31.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 16(6p25.3) cnvs correlated to 'MRNASEQ_CHIERARCHICAL'.
Del Peak 17(6q22.31) cnvs correlated to 'MRNASEQ_CNMF'.
Del Peak 19(7q11.22) cnvs correlated to 'CN_CNMF'.
Del Peak 22(9p23) cnvs correlated to 'CN_CNMF'.
Del Peak 23(9p21.3) cnvs correlated to 'CN_CNMF'.
Del Peak 24(9q21.11) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 25(10p15.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 26(10p15.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 27(10q23.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 28(11p15.5) cnvs correlated to 'CN_CNMF' and 'RPPA_CHIERARCHICAL'.
Del Peak 34(14q11.2) cnvs correlated to 'MRNASEQ_CHIERARCHICAL'.
Del Peak 40(17q11.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 43(19p13.3) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
Del Peak 44(19q13.33) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 46(21q22.3) cnvs correlated to 'CN_CNMF'.
Del Peak 48(22q13.32) cnvs correlated to 'MRNA_CNMF' and 'MRNA_CHIERARCHICAL'.
Del Peak 49(Xp22.2) cnvs correlated to 'CN_CNMF'.
Del Peak 50(Xp21.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 51(Xp11.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 52(Xq22.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 84 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 117 significant findings detected.


		Molecular subtypes	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
Del Peak 1(1p36 22)	0 (0%)	225	1.43e-06 (0.00115)	1.78e-08 (1.47e-05)	1.61e-28 (1.36e-25)	2.1e-14 (1.76e-11)	0.412 (1.00)	0.0262 (1.00)	8.67e-14 (7.25e-11)	9.45e-15 (7.92e-12)	0.000838 (0.586)	1.83e-05 (0.0143)
Del Peak 24(9q21 11)	0 (0%)	206	0.000177 (0.132)	4.92e-05 (0.0376)	5.97e-11 (4.96e-08)	1.14e-06 (0.000923)	0.653 (1.00)	0.239 (1.00)	4.4e-09 (3.64e-06)	1.63e-09 (1.35e-06)	0.000958 (0.664)	0.000184 (0.137)
Amp Peak 6(3q26 33)	0 (0%)	33	0.000427 (0.306)	1.71e-05 (0.0134)	7.05e-12 (5.86e-09)	6.69e-07 (0.000541)	0.193 (1.00)	0.0776 (1.00)	1.26e-06 (0.00101)	5.04e-05 (0.0384)	0.148 (1.00)	3.07e-06 (0.00245)
Del Peak 5(2q36 2)	0 (0%)	265	0.000236 (0.174)	4.76e-05 (0.0364)	1.7e-12 (1.41e-09)	2.14e-06 (0.00172)	0.177 (1.00)	0.126 (1.00)	6.61e-07 (0.000535)	2.98e-08 (2.45e-05)	0.885 (1.00)	0.163 (1.00)
Amp Peak 3(2p16 1)	0 (0%)	181	0.000305 (0.222)	0.00165 (1.00)	3.18e-13 (2.66e-10)	5.83e-05 (0.0443)	0.95 (1.00)	0.643 (1.00)	1.88e-05 (0.0146)	7.55e-05 (0.0573)	0.887 (1.00)	0.0171 (1.00)
Del Peak 2(1p13 2)	0 (0%)	225	0.000237 (0.175)	0.00055 (0.391)	1.23e-15 (1.03e-12)	5.74e-09 (4.73e-06)	0.119 (1.00)	0.0712 (1.00)	5.56e-07 (0.000451)	1.96e-07 (0.00016)	0.127 (1.00)	0.000788 (0.553)
Del Peak 40(17q11 2)	0 (0%)	301	1.26e-05 (0.00991)	6.44e-05 (0.049)	3.04e-08 (2.5e-05)	0.0177 (1.00)	0.495 (1.00)	0.378 (1.00)	1.48e-06 (0.00119)	4.83e-08 (3.95e-05)	0.143 (1.00)	0.0373 (1.00)
Amp Peak 4(2q31 2)	0 (0%)	265	0.0207 (1.00)	0.000948 (0.659)	6.52e-06 (0.00517)	1.99e-07 (0.000162)	0.724 (1.00)	0.887 (1.00)	0.000194 (0.144)	0.000248 (0.182)	0.37 (1.00)	0.511 (1.00)
Del Peak 26(10p15 1)	0 (0%)	229	0.0722 (1.00)	0.484 (1.00)	0.000162 (0.121)	4.03e-06 (0.00321)	0.469 (1.00)	0.353 (1.00)	0.000161 (0.121)	0.00143 (0.974)	0.0107 (1.00)	9.09e-06 (0.00719)
Del Peak 27(10q23 31)	0 (0%)	194	0.0392 (1.00)	0.00386 (1.00)	2.17e-05 (0.0168)	2.08e-06 (0.00167)	0.36 (1.00)	0.39 (1.00)	8.54e-06 (0.00677)	7.23e-07 (0.000584)	0.219 (1.00)	0.0644 (1.00)
Amp Peak 2(1q21 2)	0 (0%)	192	0.0419 (1.00)	0.00618 (1.00)	1.98e-07 (0.000162)	0.00113 (0.777)	0.16 (1.00)	0.0492 (1.00)	1.87e-05 (0.0146)	4.11e-05 (0.0316)	0.0393 (1.00)	0.00181 (1.00)
Amp Peak 13(7q21 2)	0 (0%)	188	0.101 (1.00)	0.25 (1.00)	5.34e-10 (4.43e-07)	1.27e-05 (0.00999)	0.0573 (1.00)	0.389 (1.00)	0.000661 (0.468)	0.000185 (0.138)	0.0358 (1.00)	0.0527 (1.00)
Amp Peak 23(15q26 3)	0 (0%)	258	0.151 (1.00)	0.021 (1.00)	1.56e-05 (0.0122)	9.39e-06 (0.00741)	0.354 (1.00)	0.0183 (1.00)	0.000334 (0.242)	0.00253 (1.00)	0.0159 (1.00)	0.00123 (0.838)
Amp Peak 24(17q25 1)	0 (0%)	206	0.0177 (1.00)	0.0608 (1.00)	6.01e-07 (0.000487)	2.17e-05 (0.0168)	0.267 (1.00)	0.292 (1.00)	0.0039 (1.00)	0.000165 (0.123)	0.796 (1.00)	0.0783 (1.00)
Amp Peak 26(18q11 2)	0 (0%)	271	0.000456 (0.327)	0.00227 (1.00)	1.37e-05 (0.0107)	0.000342 (0.248)	0.272 (1.00)	0.74 (1.00)	0.000841 (0.587)	5.04e-06 (0.00401)	0.402 (1.00)	0.00539 (1.00)
Del Peak 13(4q35 2)	0 (0%)	144	0.1 (1.00)	0.206 (1.00)	2.84e-06 (0.00227)	0.000124 (0.0933)	0.455 (1.00)	0.47 (1.00)	0.000143 (0.108)	0.0105 (1.00)	0.44 (1.00)	0.0957 (1.00)
Del Peak 25(10p15 3)	0 (0%)	219	0.373 (1.00)	0.442 (1.00)	4.8e-05 (0.0368)	9.6e-05 (0.0727)	0.329 (1.00)	0.443 (1.00)	0.00156 (1.00)	0.000554 (0.393)	0.0549 (1.00)	4.45e-05 (0.0342)
Amp Peak 25(18p11 32)	0 (0%)	260	0.0958 (1.00)	0.00981 (1.00)	2.48e-05 (0.0192)	0.000126 (0.0949)	0.231 (1.00)	0.451 (1.00)	0.131 (1.00)	0.0402 (1.00)	0.898 (1.00)	0.0209 (1.00)
Amp Peak 29(20p12 2)	0 (0%)	186	0.000987 (0.68)	0.0043 (1.00)	8.92e-08 (7.3e-05)	0.000161 (0.121)	0.967 (1.00)	0.221 (1.00)	0.0408 (1.00)	0.00273 (1.00)	0.259 (1.00)	0.0945 (1.00)
Del Peak 10(4p15 2)	0 (0%)	158	0.000807 (0.566)	0.00171 (1.00)	6.52e-06 (0.00517)	0.000341 (0.247)	0.662 (1.00)	0.0343 (1.00)	0.0138 (1.00)	0.00689 (1.00)	0.302 (1.00)	0.864 (1.00)
Del Peak 14(5q11 2)	0 (0%)	107	0.842 (1.00)	0.303 (1.00)	2.03e-12 (1.69e-09)	0.000192 (0.143)	0.959 (1.00)	0.244 (1.00)	0.0104 (1.00)	0.0858 (1.00)	0.987 (1.00)	0.00113 (0.777)
Del Peak 15(5q31 1)	0 (0%)	89	0.332 (1.00)	0.228 (1.00)	5.7e-09 (4.71e-06)	3e-05 (0.0232)	0.272 (1.00)	0.166 (1.00)	0.0582 (1.00)	0.0639 (1.00)	0.684 (1.00)	0.00713 (1.00)
Del Peak 28(11p15 5)	0 (0%)	214	0.000689 (0.486)	0.0528 (1.00)	1.28e-06 (0.00103)	0.0352 (1.00)	0.000764 (0.538)	2.02e-05 (0.0157)	0.00293 (1.00)	0.031 (1.00)	0.00193 (1.00)	0.0459 (1.00)
Del Peak 43(19p13 3)	0 (0%)	224	0.334 (1.00)	0.0231 (1.00)	1.38e-05 (0.0108)	0.145 (1.00)	0.0588 (1.00)	0.251 (1.00)	0.284 (1.00)	0.0283 (1.00)	0.000224 (0.166)	0.00297 (1.00)
Del Peak 44(19q13 33)	0 (0%)	291	0.617 (1.00)	0.0694 (1.00)	0.000167 (0.125)	0.000187 (0.139)	0.244 (1.00)	0.719 (1.00)	0.0819 (1.00)	0.0398 (1.00)	0.0341 (1.00)	0.334 (1.00)
Del Peak 48(22q13 32)	0 (0%)	302	0.000281 (0.205)	8.68e-05 (0.0658)	0.0172 (1.00)	0.351 (1.00)	0.543 (1.00)	0.0759 (1.00)	0.119 (1.00)	0.1 (1.00)	0.0185 (1.00)	0.0144 (1.00)
Del Peak 50(Xp21 1)	0 (0%)	270	0.354 (1.00)	0.148 (1.00)	5.39e-05 (0.0411)	0.00024 (0.177)	0.344 (1.00)	0.681 (1.00)	0.137 (1.00)	0.00706 (1.00)	0.538 (1.00)	0.163 (1.00)
Del Peak 51(Xp11 3)	0 (0%)	272	0.062 (1.00)	0.175 (1.00)	9.19e-06 (0.00726)	4.09e-05 (0.0315)	0.0923 (1.00)	0.124 (1.00)	0.0631 (1.00)	0.00391 (1.00)	0.131 (1.00)	0.138 (1.00)
Del Peak 52(Xq22 3)	0 (0%)	302	0.00853 (1.00)	0.105 (1.00)	1.91e-05 (0.0148)	0.000249 (0.183)	0.663 (1.00)	0.92 (1.00)	0.0422 (1.00)	0.438 (1.00)	0.276 (1.00)	0.797 (1.00)
Amp Peak 8(5p15 33)	0 (0%)	83	0.853 (1.00)	0.867 (1.00)	1.07e-05 (0.00841)	0.0129 (1.00)	0.405 (1.00)	0.502 (1.00)	0.262 (1.00)	0.487 (1.00)	0.45 (1.00)	0.735 (1.00)
Amp Peak 9(5p12)	0 (0%)	136	0.919 (1.00)	0.514 (1.00)	7.58e-10 (6.28e-07)	0.00874 (1.00)	0.563 (1.00)	1 (1.00)	0.225 (1.00)	0.21 (1.00)	0.792 (1.00)	0.236 (1.00)
Amp Peak 19(12p13 33)	0 (0%)	199	0.0102 (1.00)	0.0571 (1.00)	1.23e-05 (0.00965)	0.000492 (0.352)	0.313 (1.00)	0.729 (1.00)	0.000418 (0.301)	0.0103 (1.00)	0.837 (1.00)	0.218 (1.00)
Amp Peak 27(19q12)	0 (0%)	230	0.455 (1.00)	0.249 (1.00)	4.07e-06 (0.00324)	0.182 (1.00)	0.231 (1.00)	0.0287 (1.00)	0.00823 (1.00)	0.13 (1.00)	0.913 (1.00)	0.37 (1.00)
Amp Peak 28(19q13 2)	0 (0%)	227	0.715 (1.00)	1 (1.00)	0.000195 (0.144)	0.0708 (1.00)	0.356 (1.00)	0.117 (1.00)	0.106 (1.00)	0.085 (1.00)	0.77 (1.00)	0.246 (1.00)
Amp Peak 31(22q11 21)	0 (0%)	198	0.111 (1.00)	0.123 (1.00)	0.000296 (0.216)	0.000477 (0.342)	0.888 (1.00)	0.349 (1.00)	0.0122 (1.00)	0.0463 (1.00)	0.751 (1.00)	0.027 (1.00)
Del Peak 4(2q22 1)	0 (0%)	292	0.255 (1.00)	0.318 (1.00)	0.000271 (0.198)	0.0198 (1.00)	0.667 (1.00)	0.0777 (1.00)	0.0219 (1.00)	0.0165 (1.00)	0.512 (1.00)	0.226 (1.00)
Del Peak 7(3p13)	0 (0%)	57	0.419 (1.00)	0.549 (1.00)	2.67e-06 (0.00214)	0.000858 (0.598)	0.882 (1.00)	0.0379 (1.00)	0.0756 (1.00)	0.0171 (1.00)	0.432 (1.00)	0.00134 (0.915)
Del Peak 8(3p12 3)	0 (0%)	65	0.258 (1.00)	0.342 (1.00)	3.03e-05 (0.0233)	0.00259 (1.00)	1 (1.00)	0.092 (1.00)	0.12 (1.00)	0.0235 (1.00)	0.701 (1.00)	0.00577 (1.00)
Del Peak 11(4q22 1)	0 (0%)	180	0.00685 (1.00)	0.0579 (1.00)	0.000102 (0.0771)	0.00829 (1.00)	0.123 (1.00)	0.381 (1.00)	0.00473 (1.00)	0.00722 (1.00)	0.35 (1.00)	0.168 (1.00)
Del Peak 12(4q32 3)	0 (0%)	149	0.00967 (1.00)	0.0253 (1.00)	3.5e-07 (0.000285)	0.000596 (0.422)	0.101 (1.00)	0.523 (1.00)	0.0012 (0.819)	0.00455 (1.00)	0.663 (1.00)	0.242 (1.00)
Del Peak 16(6p25 3)	0 (0%)	297	0.22 (1.00)	0.11 (1.00)	0.00878 (1.00)	0.00143 (0.971)	0.393 (1.00)	0.013 (1.00)	0.00219 (1.00)	0.000305 (0.222)	0.179 (1.00)	0.0797 (1.00)
Del Peak 17(6q22 31)	0 (0%)	302	0.0192 (1.00)	0.00224 (1.00)	0.00513 (1.00)	0.000818 (0.573)	0.629 (1.00)	0.354 (1.00)	0.000249 (0.183)	0.000587 (0.416)	0.374 (1.00)	0.218 (1.00)
Del Peak 19(7q11 22)	0 (0%)	360	0.908 (1.00)	0.405 (1.00)	4.4e-05 (0.0338)	0.829 (1.00)	0.958 (1.00)	0.75 (1.00)	0.0465 (1.00)	0.0493 (1.00)	0.61 (1.00)	0.358 (1.00)
Del Peak 22(9p23)	0 (0%)	139	0.00561 (1.00)	0.00291 (1.00)	1.97e-10 (1.64e-07)	0.104 (1.00)	0.146 (1.00)	0.208 (1.00)	0.00281 (1.00)	0.0746 (1.00)	0.0991 (1.00)	0.0328 (1.00)
Del Peak 23(9p21 3)	0 (0%)	95	0.372 (1.00)	0.172 (1.00)	4.99e-07 (0.000406)	0.409 (1.00)	0.695 (1.00)	0.388 (1.00)	0.0535 (1.00)	0.472 (1.00)	0.351 (1.00)	0.421 (1.00)
Del Peak 34(14q11 2)	0 (0%)	257	0.0546 (1.00)	0.293 (1.00)	0.163 (1.00)	0.437 (1.00)	0.206 (1.00)	0.159 (1.00)	0.000386 (0.278)	9.8e-05 (0.0741)	0.183 (1.00)	0.493 (1.00)
Del Peak 46(21q22 3)	0 (0%)	173	0.957 (1.00)	0.193 (1.00)	2.13e-08 (1.75e-05)	0.00206 (1.00)	0.396 (1.00)	0.0991 (1.00)	0.13 (1.00)	0.0131 (1.00)	0.0589 (1.00)	0.161 (1.00)
Del Peak 49(Xp22 2)	0 (0%)	271	0.599 (1.00)	0.351 (1.00)	0.000249 (0.183)	0.0101 (1.00)	0.277 (1.00)	0.783 (1.00)	0.236 (1.00)	0.103 (1.00)	0.179 (1.00)	0.235 (1.00)
Amp Peak 1(1p34 2)	0 (0%)	334	0.028 (1.00)	0.481 (1.00)	0.000892 (0.621)	0.644 (1.00)	0.363 (1.00)	0.619 (1.00)	0.0242 (1.00)	0.0572 (1.00)	0.088 (1.00)	0.669 (1.00)
Amp Peak 5(3p11 1)	0 (0%)	317	0.0748 (1.00)	0.844 (1.00)	0.744 (1.00)	0.957 (1.00)	0.214 (1.00)	0.0013 (0.887)	0.239 (1.00)	0.541 (1.00)	0.845 (1.00)	0.602 (1.00)
Amp Peak 7(4q12)	0 (0%)	304	0.679 (1.00)	0.759 (1.00)	0.000353 (0.255)	0.124 (1.00)	0.356 (1.00)	0.131 (1.00)	0.221 (1.00)	0.106 (1.00)	0.178 (1.00)	0.393 (1.00)
Amp Peak 10(6p12 1)	0 (0%)	267	0.557 (1.00)	0.383 (1.00)	0.0018 (1.00)	0.168 (1.00)	0.962 (1.00)	0.3 (1.00)	0.106 (1.00)	0.522 (1.00)	0.27 (1.00)	0.267 (1.00)
Amp Peak 11(6q12)	0 (0%)	280	1 (1.00)	0.873 (1.00)	0.00114 (0.781)	0.0454 (1.00)	0.348 (1.00)	0.408 (1.00)	0.19 (1.00)	0.42 (1.00)	0.198 (1.00)	0.0784 (1.00)
Amp Peak 12(7p11 2)	0 (0%)	204	0.186 (1.00)	0.0939 (1.00)	0.00097 (0.669)	0.00366 (1.00)	0.687 (1.00)	0.801 (1.00)	0.0273 (1.00)	0.000542 (0.386)	0.634 (1.00)	0.0644 (1.00)
Amp Peak 14(8p11 23)	0 (0%)	213	0.00812 (1.00)	0.168 (1.00)	0.0254 (1.00)	0.0352 (1.00)	0.192 (1.00)	0.0988 (1.00)	0.363 (1.00)	0.537 (1.00)	0.135 (1.00)	0.371 (1.00)
Amp Peak 15(8q24 21)	0 (0%)	117	0.871 (1.00)	0.644 (1.00)	0.554 (1.00)	0.969 (1.00)	0.917 (1.00)	0.708 (1.00)	0.995 (1.00)	0.509 (1.00)	0.866 (1.00)	0.497 (1.00)
Amp Peak 16(9p24 1)	0 (0%)	324	0.375 (1.00)	0.0295 (1.00)	0.000354 (0.255)	0.177 (1.00)	0.0017 (1.00)	0.00501 (1.00)	0.00699 (1.00)	0.000767 (0.539)	0.117 (1.00)	0.0167 (1.00)
Amp Peak 17(9p13 3)	0 (0%)	288	0.17 (1.00)	0.373 (1.00)	0.043 (1.00)	0.0387 (1.00)	0.0708 (1.00)	0.00898 (1.00)	0.0114 (1.00)	0.00149 (1.00)	0.823 (1.00)	0.555 (1.00)
Amp Peak 18(11q13 3)	0 (0%)	254	0.0697 (1.00)	0.0306 (1.00)	0.00486 (1.00)	0.000518 (0.37)	0.19 (1.00)	0.0358 (1.00)	0.0123 (1.00)	0.124 (1.00)	0.0454 (1.00)	0.00669 (1.00)
Amp Peak 20(12q15)	0 (0%)	253	0.312 (1.00)	0.527 (1.00)	0.00531 (1.00)	0.00136 (0.927)	0.764 (1.00)	0.524 (1.00)	0.0588 (1.00)	0.0807 (1.00)	1 (1.00)	0.437 (1.00)
Amp Peak 21(13q34)	0 (0%)	326	0.964 (1.00)	0.0489 (1.00)	0.0384 (1.00)	0.182 (1.00)	0.87 (1.00)	0.0834 (1.00)	0.578 (1.00)	0.809 (1.00)	0.155 (1.00)	0.381 (1.00)
Amp Peak 22(14q13 3)	0 (0%)	276	0.345 (1.00)	0.246 (1.00)	0.127 (1.00)	0.0969 (1.00)	0.57 (1.00)	0.00826 (1.00)	0.0675 (1.00)	0.0164 (1.00)	0.0032 (1.00)	0.532 (1.00)
Amp Peak 30(20q11 21)	0 (0%)	168	0.991 (1.00)	0.844 (1.00)	0.00052 (0.371)	0.0132 (1.00)	0.669 (1.00)	0.588 (1.00)	0.585 (1.00)	0.757 (1.00)	0.941 (1.00)	0.373 (1.00)
Amp Peak 32(Xq28)	0 (0%)	291	0.633 (1.00)	0.636 (1.00)	0.039 (1.00)	0.0815 (1.00)	0.0701 (1.00)	0.069 (1.00)	0.109 (1.00)	0.0781 (1.00)	0.518 (1.00)	0.303 (1.00)
Del Peak 3(2p25 3)	0 (0%)	360	0.0461 (1.00)	0.179 (1.00)	0.0773 (1.00)	0.37 (1.00)	0.11 (1.00)	0.838 (1.00)	0.319 (1.00)	0.128 (1.00)	0.0533 (1.00)	0.0247 (1.00)
Del Peak 6(3p25 3)	0 (0%)	84	0.54 (1.00)	0.176 (1.00)	0.0278 (1.00)	0.00221 (1.00)	0.637 (1.00)	0.18 (1.00)	0.078 (1.00)	0.0433 (1.00)	0.602 (1.00)	0.0597 (1.00)
Del Peak 9(3q11 1)	0 (0%)	338	0.759 (1.00)	0.478 (1.00)	0.117 (1.00)	0.0538 (1.00)	0.765 (1.00)	0.282 (1.00)	0.885 (1.00)	0.803 (1.00)	0.289 (1.00)	0.887 (1.00)
Del Peak 18(6q26)	0 (0%)	294	0.0659 (1.00)	0.00298 (1.00)	0.00234 (1.00)	0.000727 (0.512)	0.921 (1.00)	0.69 (1.00)	0.00204 (1.00)	0.00223 (1.00)	0.184 (1.00)	0.085 (1.00)
Del Peak 20(7q36 3)	0 (0%)	316	0.187 (1.00)	0.112 (1.00)	0.00095 (0.659)	0.274 (1.00)	1 (1.00)	0.315 (1.00)	0.00254 (1.00)	0.0054 (1.00)	0.028 (1.00)	0.166 (1.00)
Del Peak 21(8p23 2)	0 (0%)	130	0.864 (1.00)	0.459 (1.00)	0.000961 (0.665)	0.173 (1.00)	0.345 (1.00)	0.141 (1.00)	0.494 (1.00)	0.0421 (1.00)	0.68 (1.00)	0.0705 (1.00)
Del Peak 29(11q22 1)	0 (0%)	279	0.493 (1.00)	0.288 (1.00)	0.0053 (1.00)	0.0314 (1.00)	0.103 (1.00)	0.995 (1.00)	0.13 (1.00)	0.263 (1.00)	0.382 (1.00)	0.849 (1.00)
Del Peak 30(11q25)	0 (0%)	254	0.798 (1.00)	0.429 (1.00)	0.0746 (1.00)	0.333 (1.00)	0.113 (1.00)	0.908 (1.00)	0.134 (1.00)	0.104 (1.00)	0.49 (1.00)	1 (1.00)
Del Peak 31(12q24 31)	0 (0%)	334	0.965 (1.00)	0.332 (1.00)	0.426 (1.00)	0.435 (1.00)	0.323 (1.00)	0.207 (1.00)	0.849 (1.00)	0.808 (1.00)	0.0766 (1.00)	0.362 (1.00)
Del Peak 32(13q12 11)	0 (0%)	137	0.0547 (1.00)	0.611 (1.00)	0.0344 (1.00)	0.164 (1.00)	0.907 (1.00)	0.268 (1.00)	0.73 (1.00)	0.286 (1.00)	0.812 (1.00)	0.681 (1.00)
Del Peak 33(13q14 2)	0 (0%)	126	0.0512 (1.00)	0.0962 (1.00)	0.00096 (0.665)	0.053 (1.00)	0.707 (1.00)	0.682 (1.00)	0.108 (1.00)	0.121 (1.00)	0.893 (1.00)	0.672 (1.00)
Del Peak 35(15q12)	0 (0%)	266	0.725 (1.00)	0.228 (1.00)	0.45 (1.00)	0.347 (1.00)	0.0717 (1.00)	0.00798 (1.00)	0.215 (1.00)	0.149 (1.00)	0.024 (1.00)	0.189 (1.00)
Del Peak 36(15q21 1)	0 (0%)	273	0.643 (1.00)	0.242 (1.00)	0.298 (1.00)	0.969 (1.00)	0.138 (1.00)	0.00763 (1.00)	0.299 (1.00)	0.104 (1.00)	0.0265 (1.00)	0.199 (1.00)
Del Peak 37(16p13 3)	0 (0%)	249	0.239 (1.00)	0.245 (1.00)	0.00525 (1.00)	0.197 (1.00)	0.149 (1.00)	0.606 (1.00)	0.371 (1.00)	0.268 (1.00)	0.427 (1.00)	0.401 (1.00)
Del Peak 38(16q23 1)	0 (0%)	231	0.942 (1.00)	0.659 (1.00)	0.0863 (1.00)	0.271 (1.00)	0.354 (1.00)	0.761 (1.00)	0.198 (1.00)	0.203 (1.00)	0.931 (1.00)	0.56 (1.00)
Del Peak 39(17p11 2)	0 (0%)	195	0.194 (1.00)	0.401 (1.00)	0.00185 (1.00)	0.161 (1.00)	0.15 (1.00)	0.0182 (1.00)	0.0446 (1.00)	0.0798 (1.00)	0.183 (1.00)	0.165 (1.00)
Del Peak 41(17q25 3)	0 (0%)	321	0.00515 (1.00)	0.0421 (1.00)	0.000405 (0.292)	0.0446 (1.00)	0.622 (1.00)	0.994 (1.00)	0.146 (1.00)	0.00187 (1.00)	0.529 (1.00)	0.223 (1.00)
Del Peak 42(18q23)	0 (0%)	218	0.508 (1.00)	0.788 (1.00)	0.502 (1.00)	0.898 (1.00)	0.801 (1.00)	0.397 (1.00)	0.524 (1.00)	0.0228 (1.00)	0.942 (1.00)	0.444 (1.00)
Del Peak 45(21q21 1)	0 (0%)	208	0.481 (1.00)	0.135 (1.00)	0.0117 (1.00)	0.0293 (1.00)	0.585 (1.00)	0.89 (1.00)	0.373 (1.00)	0.533 (1.00)	0.0379 (1.00)	0.0275 (1.00)
Del Peak 47(22q11 21)	0 (0%)	329	0.0904 (1.00)	0.0093 (1.00)	0.0672 (1.00)	0.0841 (1.00)	0.145 (1.00)	0.129 (1.00)	0.645 (1.00)	0.329 (1.00)	0.0583 (1.00)	0.0974 (1.00)

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

P value = 1.98e-07 (Fisher's exact test), Q value = 0.00016

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
AMP PEAK 2(1Q21.2) CNV	57	92	56
AMP PEAK 2(1Q21.2) WILD-TYPE	86	37	69

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

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

P value = 1.87e-05 (Fisher's exact test), Q value = 0.015

Table S2. Gene #2: 'Amp Peak 2(1q21.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	102	111	55
AMP PEAK 2(1Q21.2) CNV	27	72	55	25
AMP PEAK 2(1Q21.2) WILD-TYPE	50	30	56	30

Figure S2. Get High-res Image Gene #2: 'Amp Peak 2(1q21.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 4.11e-05 (Fisher's exact test), Q value = 0.032

Table S3. Gene #2: 'Amp Peak 2(1q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	70	168
AMP PEAK 2(1Q21.2) CNV	74	35	70
AMP PEAK 2(1Q21.2) WILD-TYPE	33	35	98

Figure S3. Get High-res Image Gene #2: 'Amp Peak 2(1q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 3(2p16.1)' versus 'MRNA_CNMF'

P value = 0.000305 (Fisher's exact test), Q value = 0.22

Table S4. Gene #3: 'Amp Peak 3(2p16.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	50	30	31
AMP PEAK 3(2P16.1) CNV	19	40	12	15
AMP PEAK 3(2P16.1) WILD-TYPE	24	10	18	16

Figure S4. Get High-res Image Gene #3: 'Amp Peak 3(2p16.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 3(2p16.1)' versus 'CN_CNMF'

P value = 3.18e-13 (Fisher's exact test), Q value = 2.7e-10

Table S5. Gene #3: 'Amp Peak 3(2p16.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
AMP PEAK 3(2P16.1) CNV	49	102	65
AMP PEAK 3(2P16.1) WILD-TYPE	94	27	60

Figure S5. Get High-res Image Gene #3: 'Amp Peak 3(2p16.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 3(2p16.1)' versus 'METHLYATION_CNMF'

P value = 5.83e-05 (Fisher's exact test), Q value = 0.044

Table S6. Gene #3: 'Amp Peak 3(2p16.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	83	69
AMP PEAK 3(2P16.1) CNV	43	61	31
AMP PEAK 3(2P16.1) WILD-TYPE	55	22	38

Figure S6. Get High-res Image Gene #3: 'Amp Peak 3(2p16.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 3(2p16.1)' versus 'MRNASEQ_CNMF'

P value = 1.88e-05 (Fisher's exact test), Q value = 0.015

Table S7. Gene #3: 'Amp Peak 3(2p16.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	102	111	55
AMP PEAK 3(2P16.1) CNV	29	71	64	21
AMP PEAK 3(2P16.1) WILD-TYPE	48	31	47	34

Figure S7. Get High-res Image Gene #3: 'Amp Peak 3(2p16.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 3(2p16.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.55e-05 (Fisher's exact test), Q value = 0.057

Table S8. Gene #3: 'Amp Peak 3(2p16.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	70	168
AMP PEAK 3(2P16.1) CNV	75	37	73
AMP PEAK 3(2P16.1) WILD-TYPE	32	33	95

Figure S8. Get High-res Image Gene #3: 'Amp Peak 3(2p16.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 4(2q31.2)' versus 'CN_CNMF'

P value = 6.52e-06 (Fisher's exact test), Q value = 0.0052

Table S9. Gene #4: 'Amp Peak 4(2q31.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
AMP PEAK 4(2Q31.2) CNV	30	63	39
AMP PEAK 4(2Q31.2) WILD-TYPE	113	66	86

Figure S9. Get High-res Image Gene #4: 'Amp Peak 4(2q31.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 4(2q31.2)' versus 'METHLYATION_CNMF'

P value = 1.99e-07 (Fisher's exact test), Q value = 0.00016

Table S10. Gene #4: 'Amp Peak 4(2q31.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	83	69
AMP PEAK 4(2Q31.2) CNV	23	48	14
AMP PEAK 4(2Q31.2) WILD-TYPE	75	35	55

Figure S10. Get High-res Image Gene #4: 'Amp Peak 4(2q31.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 4(2q31.2)' versus 'MRNASEQ_CNMF'

P value = 0.000194 (Fisher's exact test), Q value = 0.14

Table S11. Gene #4: 'Amp Peak 4(2q31.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	102	111	55
AMP PEAK 4(2Q31.2) CNV	20	53	31	14
AMP PEAK 4(2Q31.2) WILD-TYPE	57	49	80	41

Figure S11. Get High-res Image Gene #4: 'Amp Peak 4(2q31.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 4(2q31.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000248 (Fisher's exact test), Q value = 0.18

Table S12. Gene #4: 'Amp Peak 4(2q31.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	70	168
AMP PEAK 4(2Q31.2) CNV	53	22	43
AMP PEAK 4(2Q31.2) WILD-TYPE	54	48	125

Figure S12. Get High-res Image Gene #4: 'Amp Peak 4(2q31.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 6(3q26.33)' versus 'MRNA_CHIERARCHICAL'

P value = 1.71e-05 (Fisher's exact test), Q value = 0.013

Table S13. Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	54	72
AMP PEAK 6(3Q26.33) CNV	19	54	67
AMP PEAK 6(3Q26.33) WILD-TYPE	9	0	5

Figure S13. Get High-res Image Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 6(3q26.33)' versus 'CN_CNMF'

P value = 7.05e-12 (Fisher's exact test), Q value = 5.9e-09

Table S14. Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
AMP PEAK 6(3Q26.33) CNV	113	129	122
AMP PEAK 6(3Q26.33) WILD-TYPE	30	0	3

Figure S14. Get High-res Image Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 6(3q26.33)' versus 'METHLYATION_CNMF'

P value = 6.69e-07 (Fisher's exact test), Q value = 0.00054

Table S15. Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	83	69
AMP PEAK 6(3Q26.33) CNV	79	83	67
AMP PEAK 6(3Q26.33) WILD-TYPE	19	0	2

Figure S15. Get High-res Image Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 6(3q26.33)' versus 'MRNASEQ_CNMF'

P value = 1.26e-06 (Fisher's exact test), Q value = 0.001

Table S16. Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	102	111	55
AMP PEAK 6(3Q26.33) CNV	73	102	100	42
AMP PEAK 6(3Q26.33) WILD-TYPE	4	0	11	13

Figure S16. Get High-res Image Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 6(3q26.33)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.04e-05 (Fisher's exact test), Q value = 0.038

Table S17. Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	70	168
AMP PEAK 6(3Q26.33) CNV	107	63	147
AMP PEAK 6(3Q26.33) WILD-TYPE	0	7	21

Figure S17. Get High-res Image Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 6(3q26.33)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.07e-06 (Fisher's exact test), Q value = 0.0024

Table S18. Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	181	73
AMP PEAK 6(3Q26.33) CNV	111	155	73
AMP PEAK 6(3Q26.33) WILD-TYPE	2	26	0

Figure S18. Get High-res Image Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 8(5p15.33)' versus 'CN_CNMF'

P value = 1.07e-05 (Fisher's exact test), Q value = 0.0084

Table S19. Gene #8: 'Amp Peak 8(5p15.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
AMP PEAK 8(5P15.33) CNV	99	100	115
AMP PEAK 8(5P15.33) WILD-TYPE	44	29	10

Figure S19. Get High-res Image Gene #8: 'Amp Peak 8(5p15.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 9(5p12)' versus 'CN_CNMF'

P value = 7.58e-10 (Fisher's exact test), Q value = 6.3e-07

Table S20. Gene #9: 'Amp Peak 9(5p12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
AMP PEAK 9(5P12) CNV	70	84	107
AMP PEAK 9(5P12) WILD-TYPE	73	45	18

Figure S20. Get High-res Image Gene #9: 'Amp Peak 9(5p12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 13(7q21.2)' versus 'CN_CNMF'

P value = 5.34e-10 (Fisher's exact test), Q value = 4.4e-07

Table S21. Gene #13: 'Amp Peak 13(7q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
AMP PEAK 13(7Q21.2) CNV	51	96	62
AMP PEAK 13(7Q21.2) WILD-TYPE	92	33	63

Figure S21. Get High-res Image Gene #13: 'Amp Peak 13(7q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 13(7q21.2)' versus 'METHLYATION_CNMF'

P value = 1.27e-05 (Fisher's exact test), Q value = 0.01

Table S22. Gene #13: 'Amp Peak 13(7q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	83	69
AMP PEAK 13(7Q21.2) CNV	35	58	30
AMP PEAK 13(7Q21.2) WILD-TYPE	63	25	39

Figure S22. Get High-res Image Gene #13: 'Amp Peak 13(7q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 13(7q21.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000185 (Fisher's exact test), Q value = 0.14

Table S23. Gene #13: 'Amp Peak 13(7q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	70	168
AMP PEAK 13(7Q21.2) CNV	74	33	75
AMP PEAK 13(7Q21.2) WILD-TYPE	33	37	93

Figure S23. Get High-res Image Gene #13: 'Amp Peak 13(7q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 19(12p13.33)' versus 'CN_CNMF'

P value = 1.23e-05 (Fisher's exact test), Q value = 0.0097

Table S24. Gene #19: 'Amp Peak 19(12p13.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
AMP PEAK 19(12P13.33) CNV	51	83	64
AMP PEAK 19(12P13.33) WILD-TYPE	92	46	61

Figure S24. Get High-res Image Gene #19: 'Amp Peak 19(12p13.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 23(15q26.3)' versus 'CN_CNMF'

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

Table S25. Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
AMP PEAK 23(15Q26.3) CNV	30	61	48
AMP PEAK 23(15Q26.3) WILD-TYPE	113	68	77

Figure S25. Get High-res Image Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 23(15q26.3)' versus 'METHLYATION_CNMF'

P value = 9.39e-06 (Fisher's exact test), Q value = 0.0074

Table S26. Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	83	69
AMP PEAK 23(15Q26.3) CNV	16	40	27
AMP PEAK 23(15Q26.3) WILD-TYPE	82	43	42

Figure S26. Get High-res Image Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 23(15q26.3)' versus 'MRNASEQ_CNMF'

P value = 0.000334 (Fisher's exact test), Q value = 0.24

Table S27. Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	102	111	55
AMP PEAK 23(15Q26.3) CNV	17	52	33	17
AMP PEAK 23(15Q26.3) WILD-TYPE	60	50	78	38

Figure S27. Get High-res Image Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 24(17q25.1)' versus 'CN_CNMF'

P value = 6.01e-07 (Fisher's exact test), Q value = 0.00049

Table S28. Gene #24: 'Amp Peak 24(17q25.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
AMP PEAK 24(17Q25.1) CNV	46	83	62
AMP PEAK 24(17Q25.1) WILD-TYPE	97	46	63

Figure S28. Get High-res Image Gene #24: 'Amp Peak 24(17q25.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 24(17q25.1)' versus 'METHLYATION_CNMF'

P value = 2.17e-05 (Fisher's exact test), Q value = 0.017

Table S29. Gene #24: 'Amp Peak 24(17q25.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	83	69
AMP PEAK 24(17Q25.1) CNV	34	55	25
AMP PEAK 24(17Q25.1) WILD-TYPE	64	28	44

Figure S29. Get High-res Image Gene #24: 'Amp Peak 24(17q25.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 24(17q25.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000165 (Fisher's exact test), Q value = 0.12

Table S30. Gene #24: 'Amp Peak 24(17q25.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	70	168
AMP PEAK 24(17Q25.1) CNV	67	32	62
AMP PEAK 24(17Q25.1) WILD-TYPE	40	38	106

Figure S30. Get High-res Image Gene #24: 'Amp Peak 24(17q25.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 25(18p11.32)' versus 'CN_CNMF'

P value = 2.48e-05 (Fisher's exact test), Q value = 0.019

Table S31. Gene #25: 'Amp Peak 25(18p11.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
AMP PEAK 25(18P11.32) CNV	32	63	42
AMP PEAK 25(18P11.32) WILD-TYPE	111	66	83

Figure S31. Get High-res Image Gene #25: 'Amp Peak 25(18p11.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 25(18p11.32)' versus 'METHLYATION_CNMF'

P value = 0.000126 (Fisher's exact test), Q value = 0.095

Table S32. Gene #25: 'Amp Peak 25(18p11.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	83	69
AMP PEAK 25(18P11.32) CNV	18	38	28
AMP PEAK 25(18P11.32) WILD-TYPE	80	45	41

Figure S32. Get High-res Image Gene #25: 'Amp Peak 25(18p11.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

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

Table S33. Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
AMP PEAK 26(18Q11.2) CNV	26	57	43
AMP PEAK 26(18Q11.2) WILD-TYPE	117	72	82

Figure S33. Get High-res Image Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 0.000342 (Fisher's exact test), Q value = 0.25

Table S34. Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	83	69
AMP PEAK 26(18Q11.2) CNV	17	37	21
AMP PEAK 26(18Q11.2) WILD-TYPE	81	46	48

Figure S34. Get High-res Image Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 5.04e-06 (Fisher's exact test), Q value = 0.004

Table S35. Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	70	168
AMP PEAK 26(18Q11.2) CNV	46	31	32
AMP PEAK 26(18Q11.2) WILD-TYPE	61	39	136

Figure S35. Get High-res Image Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 4.07e-06 (Fisher's exact test), Q value = 0.0032

Table S36. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
AMP PEAK 27(19Q12) CNV	45	77	45
AMP PEAK 27(19Q12) WILD-TYPE	98	52	80

Figure S36. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 28(19q13.2)' versus 'CN_CNMF'

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

Table S37. Gene #28: 'Amp Peak 28(19q13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
AMP PEAK 28(19Q13.2) CNV	48	74	48
AMP PEAK 28(19Q13.2) WILD-TYPE	95	55	77

Figure S37. Get High-res Image Gene #28: 'Amp Peak 28(19q13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 29(20p12.2)' versus 'CN_CNMF'

P value = 8.92e-08 (Fisher's exact test), Q value = 7.3e-05

Table S38. Gene #29: 'Amp Peak 29(20p12.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
AMP PEAK 29(20P12.2) CNV	53	92	66
AMP PEAK 29(20P12.2) WILD-TYPE	90	37	59

Figure S38. Get High-res Image Gene #29: 'Amp Peak 29(20p12.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 29(20p12.2)' versus 'METHLYATION_CNMF'

P value = 0.000161 (Fisher's exact test), Q value = 0.12

Table S39. Gene #29: 'Amp Peak 29(20p12.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	83	69
AMP PEAK 29(20P12.2) CNV	42	60	33
AMP PEAK 29(20P12.2) WILD-TYPE	56	23	36

Figure S39. Get High-res Image Gene #29: 'Amp Peak 29(20p12.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 31(22q11.21)' versus 'CN_CNMF'

P value = 0.000296 (Fisher's exact test), Q value = 0.22

Table S40. Gene #31: 'Amp Peak 31(22q11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
AMP PEAK 31(22Q11.21) CNV	54	80	65
AMP PEAK 31(22Q11.21) WILD-TYPE	89	49	60

Figure S40. Get High-res Image Gene #31: 'Amp Peak 31(22q11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 1(1p36.22)' versus 'MRNA_CNMF'

P value = 1.43e-06 (Fisher's exact test), Q value = 0.0011

Table S41. Gene #33: 'Del Peak 1(1p36.22)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	50	30	31
DEL PEAK 1(1P36.22) CNV	9	37	13	10
DEL PEAK 1(1P36.22) WILD-TYPE	34	13	17	21

Figure S41. Get High-res Image Gene #33: 'Del Peak 1(1p36.22)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 1(1p36.22)' versus 'MRNA_CHIERARCHICAL'

P value = 1.78e-08 (Fisher's exact test), Q value = 1.5e-05

Table S42. Gene #33: 'Del Peak 1(1p36.22)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	54	72
DEL PEAK 1(1P36.22) CNV	11	41	17
DEL PEAK 1(1P36.22) WILD-TYPE	17	13	55

Figure S42. Get High-res Image Gene #33: 'Del Peak 1(1p36.22)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

P value = 1.61e-28 (Fisher's exact test), Q value = 1.4e-25

Table S43. Gene #33: 'Del Peak 1(1p36.22)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
DEL PEAK 1(1P36.22) CNV	34	107	31
DEL PEAK 1(1P36.22) WILD-TYPE	109	22	94

Figure S43. Get High-res Image Gene #33: 'Del Peak 1(1p36.22)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 1(1p36.22)' versus 'METHLYATION_CNMF'

P value = 2.1e-14 (Fisher's exact test), Q value = 1.8e-11

Table S44. Gene #33: 'Del Peak 1(1p36.22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	83	69
DEL PEAK 1(1P36.22) CNV	17	61	22
DEL PEAK 1(1P36.22) WILD-TYPE	81	22	47

Figure S44. Get High-res Image Gene #33: 'Del Peak 1(1p36.22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 1(1p36.22)' versus 'MRNASEQ_CNMF'

P value = 8.67e-14 (Fisher's exact test), Q value = 7.2e-11

Table S45. Gene #33: 'Del Peak 1(1p36.22)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	102	111	55
DEL PEAK 1(1P36.22) CNV	19	77	35	18
DEL PEAK 1(1P36.22) WILD-TYPE	58	25	76	37

Figure S45. Get High-res Image Gene #33: 'Del Peak 1(1p36.22)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 1(1p36.22)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.45e-15 (Fisher's exact test), Q value = 7.9e-12

Table S46. Gene #33: 'Del Peak 1(1p36.22)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	70	168
DEL PEAK 1(1P36.22) CNV	80	18	51
DEL PEAK 1(1P36.22) WILD-TYPE	27	52	117

Figure S46. Get High-res Image Gene #33: 'Del Peak 1(1p36.22)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 1(1p36.22)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.83e-05 (Fisher's exact test), Q value = 0.014

Table S47. Gene #33: 'Del Peak 1(1p36.22)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	181	73
DEL PEAK 1(1P36.22) CNV	42	66	49
DEL PEAK 1(1P36.22) WILD-TYPE	71	115	24

Figure S47. Get High-res Image Gene #33: 'Del Peak 1(1p36.22)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

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

Table S48. Gene #34: 'Del Peak 2(1p13.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	50	30	31
DEL PEAK 2(1P13.2) CNV	17	35	8	10
DEL PEAK 2(1P13.2) WILD-TYPE	26	15	22	21

Figure S48. Get High-res Image Gene #34: 'Del Peak 2(1p13.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

P value = 1.23e-15 (Fisher's exact test), Q value = 1e-12

Table S49. Gene #34: 'Del Peak 2(1p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
DEL PEAK 2(1P13.2) CNV	35	93	44
DEL PEAK 2(1P13.2) WILD-TYPE	108	36	81

Figure S49. Get High-res Image Gene #34: 'Del Peak 2(1p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 5.74e-09 (Fisher's exact test), Q value = 4.7e-06

Table S50. Gene #34: 'Del Peak 2(1p13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	83	69
DEL PEAK 2(1P13.2) CNV	20	54	28
DEL PEAK 2(1P13.2) WILD-TYPE	78	29	41

Figure S50. Get High-res Image Gene #34: 'Del Peak 2(1p13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 5.56e-07 (Fisher's exact test), Q value = 0.00045

Table S51. Gene #34: 'Del Peak 2(1p13.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	102	111	55
DEL PEAK 2(1P13.2) CNV	27	68	38	17
DEL PEAK 2(1P13.2) WILD-TYPE	50	34	73	38

Figure S51. Get High-res Image Gene #34: 'Del Peak 2(1p13.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 1.96e-07 (Fisher's exact test), Q value = 0.00016

Table S52. Gene #34: 'Del Peak 2(1p13.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	70	168
DEL PEAK 2(1P13.2) CNV	70	26	54
DEL PEAK 2(1P13.2) WILD-TYPE	37	44	114

Figure S52. Get High-res Image Gene #34: 'Del Peak 2(1p13.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 0.000271 (Fisher's exact test), Q value = 0.2

Table S53. Gene #36: 'Del Peak 4(2q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
DEL PEAK 4(2Q22.1) CNV	22	47	36
DEL PEAK 4(2Q22.1) WILD-TYPE	121	82	89

Figure S53. Get High-res Image Gene #36: 'Del Peak 4(2q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 5(2q36.2)' versus 'MRNA_CNMF'

P value = 0.000236 (Fisher's exact test), Q value = 0.17

Table S54. Gene #37: 'Del Peak 5(2q36.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	50	30	31
DEL PEAK 5(2Q36.2) CNV	9	26	3	12
DEL PEAK 5(2Q36.2) WILD-TYPE	34	24	27	19

Figure S54. Get High-res Image Gene #37: 'Del Peak 5(2q36.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 5(2q36.2)' versus 'MRNA_CHIERARCHICAL'

P value = 4.76e-05 (Fisher's exact test), Q value = 0.036

Table S55. Gene #37: 'Del Peak 5(2q36.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	54	72
DEL PEAK 5(2Q36.2) CNV	5	30	15
DEL PEAK 5(2Q36.2) WILD-TYPE	23	24	57

Figure S55. Get High-res Image Gene #37: 'Del Peak 5(2q36.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 5(2q36.2)' versus 'CN_CNMF'

P value = 1.7e-12 (Fisher's exact test), Q value = 1.4e-09

Table S56. Gene #37: 'Del Peak 5(2q36.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
DEL PEAK 5(2Q36.2) CNV	23	74	35
DEL PEAK 5(2Q36.2) WILD-TYPE	120	55	90

Figure S56. Get High-res Image Gene #37: 'Del Peak 5(2q36.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 5(2q36.2)' versus 'METHLYATION_CNMF'

P value = 2.14e-06 (Fisher's exact test), Q value = 0.0017

Table S57. Gene #37: 'Del Peak 5(2q36.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	83	69
DEL PEAK 5(2Q36.2) CNV	17	44	25
DEL PEAK 5(2Q36.2) WILD-TYPE	81	39	44

Figure S57. Get High-res Image Gene #37: 'Del Peak 5(2q36.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 5(2q36.2)' versus 'MRNASEQ_CNMF'

P value = 6.61e-07 (Fisher's exact test), Q value = 0.00054

Table S58. Gene #37: 'Del Peak 5(2q36.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	102	111	55
DEL PEAK 5(2Q36.2) CNV	27	53	30	6
DEL PEAK 5(2Q36.2) WILD-TYPE	50	49	81	49

Figure S58. Get High-res Image Gene #37: 'Del Peak 5(2q36.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 5(2q36.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.98e-08 (Fisher's exact test), Q value = 2.5e-05

Table S59. Gene #37: 'Del Peak 5(2q36.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	70	168
DEL PEAK 5(2Q36.2) CNV	60	19	37
DEL PEAK 5(2Q36.2) WILD-TYPE	47	51	131

Figure S59. Get High-res Image Gene #37: 'Del Peak 5(2q36.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 2.67e-06 (Fisher's exact test), Q value = 0.0021

Table S60. Gene #39: 'Del Peak 7(3p13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
DEL PEAK 7(3P13) CNV	105	119	116
DEL PEAK 7(3P13) WILD-TYPE	38	10	9

Figure S60. Get High-res Image Gene #39: 'Del Peak 7(3p13)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 3.03e-05 (Fisher's exact test), Q value = 0.023

Table S61. Gene #40: 'Del Peak 8(3p12.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
DEL PEAK 8(3P12.3) CNV	103	116	113
DEL PEAK 8(3P12.3) WILD-TYPE	40	13	12

Figure S61. Get High-res Image Gene #40: 'Del Peak 8(3p12.3)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 6.52e-06 (Fisher's exact test), Q value = 0.0052

Table S62. Gene #42: 'Del Peak 10(4p15.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
DEL PEAK 10(4P15.2) CNV	70	99	70
DEL PEAK 10(4P15.2) WILD-TYPE	73	30	55

Figure S62. Get High-res Image Gene #42: 'Del Peak 10(4p15.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 0.000341 (Fisher's exact test), Q value = 0.25

Table S63. Gene #42: 'Del Peak 10(4p15.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	83	69
DEL PEAK 10(4P15.2) CNV	44	61	44
DEL PEAK 10(4P15.2) WILD-TYPE	54	22	25

Figure S63. Get High-res Image Gene #42: 'Del Peak 10(4p15.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 0.000102 (Fisher's exact test), Q value = 0.077

Table S64. Gene #43: 'Del Peak 11(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
DEL PEAK 11(4Q22.1) CNV	65	90	62
DEL PEAK 11(4Q22.1) WILD-TYPE	78	39	63

Figure S64. Get High-res Image Gene #43: 'Del Peak 11(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 3.5e-07 (Fisher's exact test), Q value = 0.00028

Table S65. Gene #44: 'Del Peak 12(4q32.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
DEL PEAK 12(4Q32.3) CNV	72	104	72
DEL PEAK 12(4Q32.3) WILD-TYPE	71	25	53

Figure S65. Get High-res Image Gene #44: 'Del Peak 12(4q32.3)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 2.84e-06 (Fisher's exact test), Q value = 0.0023

Table S66. Gene #45: 'Del Peak 13(4q35.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
DEL PEAK 13(4Q35.2) CNV	76	104	73
DEL PEAK 13(4Q35.2) WILD-TYPE	67	25	52

Figure S66. Get High-res Image Gene #45: 'Del Peak 13(4q35.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 0.000124 (Fisher's exact test), Q value = 0.093

Table S67. Gene #45: 'Del Peak 13(4q35.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	83	69
DEL PEAK 13(4Q35.2) CNV	47	65	42
DEL PEAK 13(4Q35.2) WILD-TYPE	51	18	27

Figure S67. Get High-res Image Gene #45: 'Del Peak 13(4q35.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 0.000143 (Fisher's exact test), Q value = 0.11

Table S68. Gene #45: 'Del Peak 13(4q35.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	102	111	55
DEL PEAK 13(4Q35.2) CNV	40	82	67	30
DEL PEAK 13(4Q35.2) WILD-TYPE	37	20	44	25

Figure S68. Get High-res Image Gene #45: 'Del Peak 13(4q35.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 2.03e-12 (Fisher's exact test), Q value = 1.7e-09

Table S69. Gene #46: 'Del Peak 14(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
DEL PEAK 14(5Q11.2) CNV	73	108	109
DEL PEAK 14(5Q11.2) WILD-TYPE	70	21	16

Figure S69. Get High-res Image Gene #46: 'Del Peak 14(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 0.000192 (Fisher's exact test), Q value = 0.14

Table S70. Gene #46: 'Del Peak 14(5q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	83	69
DEL PEAK 14(5Q11.2) CNV	57	69	56
DEL PEAK 14(5Q11.2) WILD-TYPE	41	14	13

Figure S70. Get High-res Image Gene #46: 'Del Peak 14(5q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 15(5q31.1)' versus 'CN_CNMF'

P value = 5.7e-09 (Fisher's exact test), Q value = 4.7e-06

Table S71. Gene #47: 'Del Peak 15(5q31.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
DEL PEAK 15(5Q31.1) CNV	86	111	111
DEL PEAK 15(5Q31.1) WILD-TYPE	57	18	14

Figure S71. Get High-res Image Gene #47: 'Del Peak 15(5q31.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 15(5q31.1)' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.023

Table S72. Gene #47: 'Del Peak 15(5q31.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	83	69
DEL PEAK 15(5Q31.1) CNV	63	71	63
DEL PEAK 15(5Q31.1) WILD-TYPE	35	12	6

Figure S72. Get High-res Image Gene #47: 'Del Peak 15(5q31.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 16(6p25.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000305 (Fisher's exact test), Q value = 0.22

Table S73. Gene #48: 'Del Peak 16(6p25.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	70	168
DEL PEAK 16(6P25.3) CNV	43	11	36
DEL PEAK 16(6P25.3) WILD-TYPE	64	59	132

Figure S73. Get High-res Image Gene #48: 'Del Peak 16(6p25.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 17(6q22.31)' versus 'MRNASEQ_CNMF'

P value = 0.000249 (Fisher's exact test), Q value = 0.18

Table S74. Gene #49: 'Del Peak 17(6q22.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	102	111	55
DEL PEAK 17(6Q22.31) CNV	9	38	19	14
DEL PEAK 17(6Q22.31) WILD-TYPE	68	64	92	41

Figure S74. Get High-res Image Gene #49: 'Del Peak 17(6q22.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 19(7q11.22)' versus 'CN_CNMF'

P value = 4.4e-05 (Fisher's exact test), Q value = 0.034

Table S75. Gene #51: 'Del Peak 19(7q11.22)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
DEL PEAK 19(7Q11.22) CNV	11	3	23
DEL PEAK 19(7Q11.22) WILD-TYPE	132	126	102

Figure S75. Get High-res Image Gene #51: 'Del Peak 19(7q11.22)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 22(9p23)' versus 'CN_CNMF'

P value = 1.97e-10 (Fisher's exact test), Q value = 1.6e-07

Table S76. Gene #54: 'Del Peak 22(9p23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
DEL PEAK 22(9P23) CNV	74	75	109
DEL PEAK 22(9P23) WILD-TYPE	69	54	16

Figure S76. Get High-res Image Gene #54: 'Del Peak 22(9p23)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 23(9p21.3)' versus 'CN_CNMF'

P value = 4.99e-07 (Fisher's exact test), Q value = 0.00041

Table S77. Gene #55: 'Del Peak 23(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
DEL PEAK 23(9P21.3) CNV	92	96	114
DEL PEAK 23(9P21.3) WILD-TYPE	51	33	11

Figure S77. Get High-res Image Gene #55: 'Del Peak 23(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 0.000177 (Fisher's exact test), Q value = 0.13

Table S78. Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	50	30	31
DEL PEAK 24(9Q21.11) CNV	28	12	19	15
DEL PEAK 24(9Q21.11) WILD-TYPE	15	38	11	16

Figure S78. Get High-res Image Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

P value = 4.92e-05 (Fisher's exact test), Q value = 0.038

Table S79. Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	54	72
DEL PEAK 24(9Q21.11) CNV	16	13	45
DEL PEAK 24(9Q21.11) WILD-TYPE	12	41	27

Figure S79. Get High-res Image Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

P value = 5.97e-11 (Fisher's exact test), Q value = 5e-08

Table S80. Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
DEL PEAK 24(9Q21.11) CNV	69	35	87
DEL PEAK 24(9Q21.11) WILD-TYPE	74	94	38

Figure S80. Get High-res Image Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 1.14e-06 (Fisher's exact test), Q value = 0.00092

Table S81. Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	83	69
DEL PEAK 24(9Q21.11) CNV	54	22	46
DEL PEAK 24(9Q21.11) WILD-TYPE	44	61	23

Figure S81. Get High-res Image Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 4.4e-09 (Fisher's exact test), Q value = 3.6e-06

Table S82. Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	102	111	55
DEL PEAK 24(9Q21.11) CNV	43	23	71	29
DEL PEAK 24(9Q21.11) WILD-TYPE	34	79	40	26

Figure S82. Get High-res Image Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 1.63e-09 (Fisher's exact test), Q value = 1.3e-06

Table S83. Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	70	168
DEL PEAK 24(9Q21.11) CNV	25	45	96
DEL PEAK 24(9Q21.11) WILD-TYPE	82	25	72

Figure S83. Get High-res Image Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 0.000184 (Fisher's exact test), Q value = 0.14

Table S84. Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	181	73
DEL PEAK 24(9Q21.11) CNV	65	91	20
DEL PEAK 24(9Q21.11) WILD-TYPE	48	90	53

Figure S84. Get High-res Image Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 4.8e-05 (Fisher's exact test), Q value = 0.037

Table S85. Gene #57: 'Del Peak 25(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
DEL PEAK 25(10P15.3) CNV	45	75	58
DEL PEAK 25(10P15.3) WILD-TYPE	98	54	67

Figure S85. Get High-res Image Gene #57: 'Del Peak 25(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 9.6e-05 (Fisher's exact test), Q value = 0.073

Table S86. Gene #57: 'Del Peak 25(10p15.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	83	69
DEL PEAK 25(10P15.3) CNV	34	54	27
DEL PEAK 25(10P15.3) WILD-TYPE	64	29	42

Figure S86. Get High-res Image Gene #57: 'Del Peak 25(10p15.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 4.45e-05 (Fisher's exact test), Q value = 0.034

Table S87. Gene #57: 'Del Peak 25(10p15.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	181	73
DEL PEAK 25(10P15.3) CNV	60	63	46
DEL PEAK 25(10P15.3) WILD-TYPE	53	118	27

Figure S87. Get High-res Image Gene #57: 'Del Peak 25(10p15.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 0.000162 (Fisher's exact test), Q value = 0.12

Table S88. Gene #58: 'Del Peak 26(10p15.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
DEL PEAK 26(10P15.1) CNV	43	71	54
DEL PEAK 26(10P15.1) WILD-TYPE	100	58	71

Figure S88. Get High-res Image Gene #58: 'Del Peak 26(10p15.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 4.03e-06 (Fisher's exact test), Q value = 0.0032

Table S89. Gene #58: 'Del Peak 26(10p15.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	83	69
DEL PEAK 26(10P15.1) CNV	32	55	23
DEL PEAK 26(10P15.1) WILD-TYPE	66	28	46

Figure S89. Get High-res Image Gene #58: 'Del Peak 26(10p15.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 0.000161 (Fisher's exact test), Q value = 0.12

Table S90. Gene #58: 'Del Peak 26(10p15.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	102	111	55
DEL PEAK 26(10P15.1) CNV	26	60	47	14
DEL PEAK 26(10P15.1) WILD-TYPE	51	42	64	41

Figure S90. Get High-res Image Gene #58: 'Del Peak 26(10p15.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 9.09e-06 (Fisher's exact test), Q value = 0.0072

Table S91. Gene #58: 'Del Peak 26(10p15.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	181	73
DEL PEAK 26(10P15.1) CNV	53	58	47
DEL PEAK 26(10P15.1) WILD-TYPE	60	123	26

Figure S91. Get High-res Image Gene #58: 'Del Peak 26(10p15.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 2.17e-05 (Fisher's exact test), Q value = 0.017

Table S92. Gene #59: 'Del Peak 27(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
DEL PEAK 27(10Q23.31) CNV	58	87	58
DEL PEAK 27(10Q23.31) WILD-TYPE	85	42	67

Figure S92. Get High-res Image Gene #59: 'Del Peak 27(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 2.08e-06 (Fisher's exact test), Q value = 0.0017

Table S93. Gene #59: 'Del Peak 27(10q23.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	83	69
DEL PEAK 27(10Q23.31) CNV	34	60	33
DEL PEAK 27(10Q23.31) WILD-TYPE	64	23	36

Figure S93. Get High-res Image Gene #59: 'Del Peak 27(10q23.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 8.54e-06 (Fisher's exact test), Q value = 0.0068

Table S94. Gene #59: 'Del Peak 27(10q23.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	102	111	55
DEL PEAK 27(10Q23.31) CNV	27	72	51	24
DEL PEAK 27(10Q23.31) WILD-TYPE	50	30	60	31

Figure S94. Get High-res Image Gene #59: 'Del Peak 27(10q23.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 7.23e-07 (Fisher's exact test), Q value = 0.00058

Table S95. Gene #59: 'Del Peak 27(10q23.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	70	168
DEL PEAK 27(10Q23.31) CNV	75	36	63
DEL PEAK 27(10Q23.31) WILD-TYPE	32	34	105

Figure S95. Get High-res Image Gene #59: 'Del Peak 27(10q23.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 1.28e-06 (Fisher's exact test), Q value = 0.001

Table S96. Gene #60: 'Del Peak 28(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
DEL PEAK 28(11P15.5) CNV	49	53	81
DEL PEAK 28(11P15.5) WILD-TYPE	94	76	44

Figure S96. Get High-res Image Gene #60: '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 = 0.016

Table S97. Gene #60: '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 S97. Get High-res Image Gene #60: 'Del Peak 28(11p15.5)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 34(14q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.8e-05 (Fisher's exact test), Q value = 0.074

Table S98. Gene #66: 'Del Peak 34(14q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	70	168
DEL PEAK 34(14Q11.2) CNV	38	39	44
DEL PEAK 34(14Q11.2) WILD-TYPE	69	31	124

Figure S98. Get High-res Image Gene #66: 'Del Peak 34(14q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 40(17q11.2)' versus 'MRNA_CNMF'

P value = 1.26e-05 (Fisher's exact test), Q value = 0.0099

Table S99. Gene #72: 'Del Peak 40(17q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	50	30	31
DEL PEAK 40(17Q11.2) CNV	21	3	11	7
DEL PEAK 40(17Q11.2) WILD-TYPE	22	47	19	24

Figure S99. Get High-res Image Gene #72: 'Del Peak 40(17q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 40(17q11.2)' versus 'MRNA_CHIERARCHICAL'

P value = 6.44e-05 (Fisher's exact test), Q value = 0.049

Table S100. Gene #72: 'Del Peak 40(17q11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	54	72
DEL PEAK 40(17Q11.2) CNV	9	4	29
DEL PEAK 40(17Q11.2) WILD-TYPE	19	50	43

Figure S100. Get High-res Image Gene #72: 'Del Peak 40(17q11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 40(17q11.2)' versus 'CN_CNMF'

P value = 3.04e-08 (Fisher's exact test), Q value = 2.5e-05

Table S101. Gene #72: 'Del Peak 40(17q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
DEL PEAK 40(17Q11.2) CNV	40	10	46
DEL PEAK 40(17Q11.2) WILD-TYPE	103	119	79

Figure S101. Get High-res Image Gene #72: 'Del Peak 40(17q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 40(17q11.2)' versus 'MRNASEQ_CNMF'

P value = 1.48e-06 (Fisher's exact test), Q value = 0.0012

Table S102. Gene #72: 'Del Peak 40(17q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	102	111	55
DEL PEAK 40(17Q11.2) CNV	24	7	36	19
DEL PEAK 40(17Q11.2) WILD-TYPE	53	95	75	36

Figure S102. Get High-res Image Gene #72: 'Del Peak 40(17q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 40(17q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.83e-08 (Fisher's exact test), Q value = 4e-05

Table S103. Gene #72: 'Del Peak 40(17q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	70	168
DEL PEAK 40(17Q11.2) CNV	7	20	59
DEL PEAK 40(17Q11.2) WILD-TYPE	100	50	109

Figure S103. Get High-res Image Gene #72: 'Del Peak 40(17q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 43(19p13.3)' versus 'CN_CNMF'

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

Table S104. Gene #75: 'Del Peak 43(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
DEL PEAK 43(19P13.3) CNV	48	49	76
DEL PEAK 43(19P13.3) WILD-TYPE	95	80	49

Figure S104. Get High-res Image Gene #75: 'Del Peak 43(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 43(19p13.3)' versus 'MIRSEQ_CNMF'

P value = 0.000224 (Fisher's exact test), Q value = 0.17

Table S105. Gene #75: 'Del Peak 43(19p13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	133	166	68
DEL PEAK 43(19P13.3) CNV	71	72	16
DEL PEAK 43(19P13.3) WILD-TYPE	62	94	52

Figure S105. Get High-res Image Gene #75: 'Del Peak 43(19p13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 44(19q13.33)' versus 'CN_CNMF'

P value = 0.000167 (Fisher's exact test), Q value = 0.12

Table S106. Gene #76: 'Del Peak 44(19q13.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
DEL PEAK 44(19Q13.33) CNV	22	48	36
DEL PEAK 44(19Q13.33) WILD-TYPE	121	81	89

Figure S106. Get High-res Image Gene #76: 'Del Peak 44(19q13.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 44(19q13.33)' versus 'METHLYATION_CNMF'

P value = 0.000187 (Fisher's exact test), Q value = 0.14

Table S107. Gene #76: 'Del Peak 44(19q13.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	83	69
DEL PEAK 44(19Q13.33) CNV	12	30	23
DEL PEAK 44(19Q13.33) WILD-TYPE	86	53	46

Figure S107. Get High-res Image Gene #76: 'Del Peak 44(19q13.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 46(21q22.3)' versus 'CN_CNMF'

P value = 2.13e-08 (Fisher's exact test), Q value = 1.8e-05

Table S108. Gene #78: 'Del Peak 46(21q22.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
DEL PEAK 46(21Q22.3) CNV	53	91	80
DEL PEAK 46(21Q22.3) WILD-TYPE	90	38	45

Figure S108. Get High-res Image Gene #78: 'Del Peak 46(21q22.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 48(22q13.32)' versus 'MRNA_CNMF'

P value = 0.000281 (Fisher's exact test), Q value = 0.21

Table S109. Gene #80: 'Del Peak 48(22q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	50	30	31
DEL PEAK 48(22Q13.32) CNV	9	7	7	18
DEL PEAK 48(22Q13.32) WILD-TYPE	34	43	23	13

Figure S109. Get High-res Image Gene #80: 'Del Peak 48(22q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 48(22q13.32)' versus 'MRNA_CHIERARCHICAL'

P value = 8.68e-05 (Fisher's exact test), Q value = 0.066

Table S110. Gene #80: 'Del Peak 48(22q13.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	54	72
DEL PEAK 48(22Q13.32) CNV	17	9	15
DEL PEAK 48(22Q13.32) WILD-TYPE	11	45	57

Figure S110. Get High-res Image Gene #80: 'Del Peak 48(22q13.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 49(Xp22.2)' versus 'CN_CNMF'

P value = 0.000249 (Fisher's exact test), Q value = 0.18

Table S111. Gene #81: 'Del Peak 49(Xp22.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
DEL PEAK 49(XP22.2) CNV	28	53	45
DEL PEAK 49(XP22.2) WILD-TYPE	115	76	80

Figure S111. Get High-res Image Gene #81: 'Del Peak 49(Xp22.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 50(Xp21.1)' versus 'CN_CNMF'

P value = 5.39e-05 (Fisher's exact test), Q value = 0.041

Table S112. Gene #82: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
DEL PEAK 50(XP21.1) CNV	27	55	45
DEL PEAK 50(XP21.1) WILD-TYPE	116	74	80

Figure S112. Get High-res Image Gene #82: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 50(Xp21.1)' versus 'METHLYATION_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.18

Table S113. Gene #82: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	83	69
DEL PEAK 50(XP21.1) CNV	18	36	29
DEL PEAK 50(XP21.1) WILD-TYPE	80	47	40

Figure S113. Get High-res Image Gene #82: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 51(Xp11.3)' versus 'CN_CNMF'

P value = 9.19e-06 (Fisher's exact test), Q value = 0.0073

Table S114. Gene #83: 'Del Peak 51(Xp11.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
DEL PEAK 51(XP11.3) CNV	26	58	41
DEL PEAK 51(XP11.3) WILD-TYPE	117	71	84

Figure S114. Get High-res Image Gene #83: 'Del Peak 51(Xp11.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 51(Xp11.3)' versus 'METHLYATION_CNMF'

P value = 4.09e-05 (Fisher's exact test), Q value = 0.032

Table S115. Gene #83: 'Del Peak 51(Xp11.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	83	69
DEL PEAK 51(XP11.3) CNV	16	38	26
DEL PEAK 51(XP11.3) WILD-TYPE	82	45	43

Figure S115. Get High-res Image Gene #83: 'Del Peak 51(Xp11.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 52(Xq22.3)' versus 'CN_CNMF'

P value = 1.91e-05 (Fisher's exact test), Q value = 0.015

Table S116. Gene #84: 'Del Peak 52(Xq22.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	129	125
DEL PEAK 52(XQ22.3) CNV	18	31	46
DEL PEAK 52(XQ22.3) WILD-TYPE	125	98	79

Figure S116. Get High-res Image Gene #84: 'Del Peak 52(Xq22.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 52(Xq22.3)' versus 'METHLYATION_CNMF'

P value = 0.000249 (Fisher's exact test), Q value = 0.18

Table S117. Gene #84: 'Del Peak 52(Xq22.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	83	69
DEL PEAK 52(XQ22.3) CNV	10	20	25
DEL PEAK 52(XQ22.3) WILD-TYPE	88	63	44

Figure S117. Get High-res Image Gene #84: 'Del Peak 52(Xq22.3)' versus Molecular Subtype #4: 'METHLYATION_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 = 397
Number of copy number variation regions = 84
Number of molecular subtypes = 10
Exclude regions that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

[3] GISTIC_version2

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