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 70 peak regions and 10 molecular subtypes across 563 patients, 117 significant findings detected with Q value < 0.25.

Amp Peak 1(1p36.21) cnvs correlated to 'CN_CNMF'.
Amp Peak 2(1q32.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 3(1q44) cnvs correlated to 'CN_CNMF'.
Amp Peak 4(2p24.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 5(3q26.33) cnvs correlated to 'CN_CNMF'.
Amp Peak 7(4q12) cnvs correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.
Amp Peak 8(7p11.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 9(7q11.21) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'MIR_CHIERARCHICAL', and 'CN_CNMF'.
Amp Peak 10(7q21.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', and 'CN_CNMF'.
Amp Peak 11(7q31.2) cnvs correlated to 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', and 'CN_CNMF'.
Amp Peak 12(7q36.1) cnvs correlated to 'MRNA_CNMF', 'MIR_CHIERARCHICAL', and 'CN_CNMF'.
Amp Peak 13(8q24.21) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', and 'CN_CNMF'.
Amp Peak 15(12p13.32) cnvs correlated to 'CN_CNMF'.
Amp Peak 16(12q14.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 17(12q15) cnvs correlated to 'CN_CNMF'.
Amp Peak 21(17q25.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 22(19p13.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'RPPA_CHIERARCHICAL'.
Amp Peak 23(19q12) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'RPPA_CHIERARCHICAL'.
Del Peak 7(2q22.1) cnvs correlated to 'CN_CNMF'.
Del Peak 9(3p21.1) cnvs correlated to 'CN_CNMF'.
Del Peak 10(3q13.31) cnvs correlated to 'CN_CNMF'.
Del Peak 11(3q22.1) cnvs correlated to 'CN_CNMF'.
Del Peak 14(4q34.3) cnvs correlated to 'CN_CNMF'.
Del Peak 15(5q35.3) cnvs correlated to 'MRNA_CNMF', 'MIR_CHIERARCHICAL', and 'CN_CNMF'.
Del Peak 16(6q22.31) cnvs correlated to 'CN_CNMF'.
Del Peak 17(6q26) cnvs correlated to 'CN_CNMF'.
Del Peak 19(9p21.3) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', and 'CN_CNMF'.
Del Peak 21(10p15.3) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', and 'CN_CNMF'.
Del Peak 22(10p13) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', and 'RPPA_CNMF'.
Del Peak 23(10p11.23) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', and 'CN_CNMF'.
Del Peak 24(10q23.31) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', and 'CN_CNMF'.
Del Peak 25(10q26.3) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', and 'CN_CNMF'.
Del Peak 26(11p15.5) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', and 'METHLYATION_CNMF'.
Del Peak 27(11p11.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', and 'CN_CNMF'.
Del Peak 28(11q14.1) cnvs correlated to 'MRNA_CNMF' and 'CN_CNMF'.
Del Peak 30(12q12) cnvs correlated to 'CN_CNMF'.
Del Peak 31(12q15) cnvs correlated to 'MRNA_CNMF' and 'CN_CNMF'.
Del Peak 32(13q14.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', and 'CN_CNMF'.
Del Peak 33(14q13.1) cnvs correlated to 'MRNA_CNMF' and 'CN_CNMF'.
Del Peak 34(14q24.2) cnvs correlated to 'MRNA_CNMF' and 'CN_CNMF'.
Del Peak 35(14q31.3) cnvs correlated to 'MRNA_CNMF' and 'CN_CNMF'.
Del Peak 36(15q14) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', and 'MRNASEQ_CNMF'.
Del Peak 39(17p13.2) cnvs correlated to 'CN_CNMF'.
Del Peak 40(17p13.1) cnvs correlated to 'MRNA_CNMF' and 'CN_CNMF'.
Del Peak 41(17q11.2) cnvs correlated to 'MRNA_CNMF' and 'CN_CNMF'.
Del Peak 43(19q13.41) cnvs correlated to 'MRNA_CHIERARCHICAL'.
Del Peak 44(21q22.3) cnvs correlated to 'MIR_CNMF'.
Del Peak 46(Xp22.2) cnvs correlated to 'CN_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 70 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	MIR CNMF	MIR CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ 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
Amp Peak 8(7p11 2)	0 (0%)	69	3.62e-11 (2.46e-08)	3.18e-11 (2.17e-08)	3.48e-07 (0.000226)	2.34e-13 (1.6e-10)	1.23e-20 (8.56e-18)	1.32e-06 (0.000844)	8.62e-06 (0.00538)	5.85e-05 (0.0356)	1.11e-05 (0.00686)	0.000357 (0.208)
Amp Peak 9(7q11 21)	0 (0%)	111	9.85e-06 (0.00614)	4.88e-07 (0.000315)	4.69e-06 (0.00295)	7.42e-09 (4.96e-06)	1.72e-09 (1.15e-06)	0.00585 (1.00)	0.00417 (1.00)	0.336 (1.00)	0.004 (1.00)	0.00143 (0.801)
Del Peak 22(10p13)	0 (0%)	104	3.17e-07 (0.000206)	9.94e-06 (0.00618)	0.00282 (1.00)	1.28e-07 (8.44e-05)	1.11e-15 (7.68e-13)	0.035 (1.00)	0.000132 (0.0792)	0.00458 (1.00)	0.0885 (1.00)	0.41 (1.00)
Del Peak 26(11p15 5)	0 (0%)	436	3.9e-10 (2.62e-07)	1.15e-06 (0.000737)	0.23 (1.00)	1.5e-06 (0.000956)	2.1e-15 (1.44e-12)	0.000309 (0.181)	0.268 (1.00)	0.0938 (1.00)	0.00119 (0.677)	0.263 (1.00)
Del Peak 36(15q14)	0 (0%)	412	1.46e-06 (0.000933)	7.39e-08 (4.88e-05)	0.00977 (1.00)	1.31e-06 (0.00084)	4.09e-07 (0.000265)	0.00231 (1.00)	0.0699 (1.00)	0.0241 (1.00)	0.000352 (0.205)	0.158 (1.00)
Amp Peak 10(7q21 2)	0 (0%)	95	1.02e-05 (0.00635)	4.54e-05 (0.0278)	0.0107 (1.00)	1.92e-06 (0.00122)	1.06e-10 (7.19e-08)	0.00363 (1.00)	0.0179 (1.00)	0.0964 (1.00)	0.0618 (1.00)	0.00474 (1.00)
Amp Peak 13(8q24 21)	0 (0%)	499	1.69e-07 (0.000111)	0.000183 (0.108)	0.0397 (1.00)	8.34e-05 (0.0506)	3.51e-06 (0.00222)	0.0699 (1.00)	0.104 (1.00)	0.00574 (1.00)	0.131 (1.00)	0.345 (1.00)
Amp Peak 22(19p13 2)	0 (0%)	323	2.33e-12 (1.59e-09)	2.56e-07 (0.000167)	0.248 (1.00)	0.00825 (1.00)	1.86e-20 (1.29e-17)	0.017 (1.00)	0.0116 (1.00)	1.32e-05 (0.00816)	0.164 (1.00)	0.0199 (1.00)
Amp Peak 23(19q12)	0 (0%)	360	1.29e-10 (8.73e-08)	3.97e-08 (2.63e-05)	0.218 (1.00)	0.00449 (1.00)	1.5e-15 (1.03e-12)	0.0553 (1.00)	0.0174 (1.00)	0.000213 (0.125)	0.0823 (1.00)	0.0438 (1.00)
Del Peak 21(10p15 3)	0 (0%)	106	1.64e-06 (0.00104)	0.000166 (0.0989)	0.0133 (1.00)	1.85e-07 (0.000121)	1.45e-14 (9.97e-12)	0.035 (1.00)	0.00523 (1.00)	0.0278 (1.00)	0.0147 (1.00)	0.41 (1.00)
Del Peak 23(10p11 23)	0 (0%)	100	2.94e-10 (1.98e-07)	9.54e-07 (0.000613)	0.00054 (0.314)	1.26e-08 (8.38e-06)	9.85e-17 (6.84e-14)	0.027 (1.00)	0.000786 (0.453)	0.0175 (1.00)	0.0443 (1.00)	0.084 (1.00)
Del Peak 24(10q23 31)	0 (0%)	64	4.77e-07 (0.000308)	0.000124 (0.0745)	0.00781 (1.00)	7.23e-05 (0.0439)	1.19e-16 (8.24e-14)	0.196 (1.00)	0.0105 (1.00)	0.131 (1.00)	0.369 (1.00)	0.16 (1.00)
Del Peak 27(11p11 2)	0 (0%)	462	5.47e-08 (3.62e-05)	0.000192 (0.113)	0.921 (1.00)	2.44e-05 (0.015)	2.18e-13 (1.49e-10)	0.000701 (0.405)	0.825 (1.00)	0.576 (1.00)	0.051 (1.00)	0.706 (1.00)
Amp Peak 11(7q31 2)	0 (0%)	103	0.000978 (0.559)	0.00013 (0.0782)	0.00207 (1.00)	0.000144 (0.0859)	2.21e-07 (0.000144)	0.0107 (1.00)	0.103 (1.00)	0.183 (1.00)	0.256 (1.00)	0.00355 (1.00)
Amp Peak 12(7q36 1)	0 (0%)	98	4.64e-05 (0.0283)	0.000671 (0.388)	0.059 (1.00)	4.59e-05 (0.0281)	1.41e-05 (0.00873)	0.00363 (1.00)	0.227 (1.00)	0.249 (1.00)	0.0292 (1.00)	0.00467 (1.00)
Del Peak 15(5q35 3)	0 (0%)	509	4.89e-06 (0.00308)	0.00216 (1.00)	0.00156 (0.872)	2.27e-05 (0.014)	5.69e-05 (0.0347)	0.00732 (1.00)	0.84 (1.00)	0.407 (1.00)	0.208 (1.00)	0.841 (1.00)
Del Peak 19(9p21 3)	0 (0%)	155	6.36e-06 (0.00398)	0.000114 (0.0691)	0.554 (1.00)	0.00153 (0.856)	3.77e-10 (2.54e-07)	0.0417 (1.00)	0.0878 (1.00)	0.0182 (1.00)	0.0274 (1.00)	0.00319 (1.00)
Del Peak 25(10q26 3)	0 (0%)	63	1.16e-07 (7.63e-05)	0.000142 (0.0852)	0.0777 (1.00)	0.00043 (0.251)	1.89e-13 (1.3e-10)	0.0145 (1.00)	0.117 (1.00)	0.0761 (1.00)	0.25 (1.00)	0.378 (1.00)
Del Peak 32(13q14 2)	0 (0%)	327	1.62e-07 (0.000106)	0.000164 (0.0973)	0.109 (1.00)	0.08 (1.00)	1.1e-15 (7.63e-13)	0.0328 (1.00)	0.794 (1.00)	0.107 (1.00)	0.0921 (1.00)	0.193 (1.00)
Amp Peak 7(4q12)	0 (0%)	459	0.00185 (1.00)	0.000115 (0.0696)	0.479 (1.00)	0.0527 (1.00)	4.31e-07 (0.000279)	0.384 (1.00)	0.272 (1.00)	0.664 (1.00)	0.0487 (1.00)	0.403 (1.00)
Del Peak 28(11q14 1)	0 (0%)	468	2.65e-07 (0.000173)	0.048 (1.00)	0.936 (1.00)	0.00783 (1.00)	1.3e-16 (9e-14)	0.259 (1.00)	0.552 (1.00)	0.5 (1.00)	0.0908 (1.00)	0.793 (1.00)
Del Peak 31(12q15)	0 (0%)	486	0.000124 (0.0745)	0.000563 (0.327)	0.247 (1.00)	0.0467 (1.00)	5.4e-07 (0.000347)	0.514 (1.00)	0.527 (1.00)	0.724 (1.00)	0.585 (1.00)	0.943 (1.00)
Del Peak 33(14q13 1)	0 (0%)	388	8.84e-06 (0.00552)	0.0129 (1.00)	0.618 (1.00)	0.421 (1.00)	3.36e-30 (2.34e-27)	0.108 (1.00)	0.577 (1.00)	0.367 (1.00)	0.291 (1.00)	0.742 (1.00)
Del Peak 34(14q24 2)	0 (0%)	393	1.61e-07 (0.000106)	0.00516 (1.00)	0.0656 (1.00)	0.871 (1.00)	7.68e-39 (5.36e-36)	0.0503 (1.00)	0.457 (1.00)	0.275 (1.00)	0.0497 (1.00)	0.142 (1.00)
Del Peak 35(14q31 3)	0 (0%)	407	6.25e-09 (4.18e-06)	0.00555 (1.00)	0.422 (1.00)	0.835 (1.00)	8.42e-41 (5.89e-38)	0.00996 (1.00)	0.515 (1.00)	0.108 (1.00)	0.222 (1.00)	0.0846 (1.00)
Del Peak 40(17p13 1)	0 (0%)	468	0.000167 (0.0991)	0.453 (1.00)	0.88 (1.00)	0.605 (1.00)	1.42e-15 (9.77e-13)	0.133 (1.00)	0.709 (1.00)	0.447 (1.00)	0.645 (1.00)	0.295 (1.00)
Del Peak 41(17q11 2)	0 (0%)	492	7.43e-06 (0.00465)	0.000862 (0.495)	0.00192 (1.00)	0.00959 (1.00)	5.32e-07 (0.000343)	0.496 (1.00)	0.00594 (1.00)	0.00512 (1.00)	0.539 (1.00)	0.104 (1.00)
Amp Peak 1(1p36 21)	0 (0%)	474	0.399 (1.00)	0.839 (1.00)	0.179 (1.00)	0.0074 (1.00)	1.63e-08 (1.09e-05)	0.473 (1.00)	0.048 (1.00)	0.0531 (1.00)	0.0967 (1.00)	0.0808 (1.00)
Amp Peak 2(1q32 1)	0 (0%)	410	0.91 (1.00)	0.545 (1.00)	0.239 (1.00)	0.097 (1.00)	1.76e-08 (1.17e-05)	0.623 (1.00)	0.84 (1.00)	0.335 (1.00)	0.475 (1.00)	0.095 (1.00)
Amp Peak 3(1q44)	0 (0%)	467	0.156 (1.00)	0.739 (1.00)	0.403 (1.00)	0.441 (1.00)	8.32e-09 (5.55e-06)	0.931 (1.00)	0.426 (1.00)	0.177 (1.00)	0.775 (1.00)	0.439 (1.00)
Amp Peak 4(2p24 3)	0 (0%)	517	0.026 (1.00)	0.0372 (1.00)	0.748 (1.00)	0.385 (1.00)	0.000238 (0.139)	0.0574 (1.00)	0.209 (1.00)	0.112 (1.00)	0.93 (1.00)	1 (1.00)
Amp Peak 5(3q26 33)	0 (0%)	455	0.0157 (1.00)	0.14 (1.00)	0.9 (1.00)	0.724 (1.00)	3.56e-06 (0.00225)	0.00452 (1.00)	0.0685 (1.00)	0.358 (1.00)	0.546 (1.00)	0.321 (1.00)
Amp Peak 15(12p13 32)	0 (0%)	482	0.468 (1.00)	0.875 (1.00)	0.716 (1.00)	0.812 (1.00)	1.96e-05 (0.0121)	0.278 (1.00)	0.411 (1.00)	0.553 (1.00)	0.442 (1.00)	0.151 (1.00)
Amp Peak 16(12q14 1)	0 (0%)	432	0.0651 (1.00)	0.397 (1.00)	0.309 (1.00)	0.121 (1.00)	1.7e-09 (1.14e-06)	0.525 (1.00)	0.0452 (1.00)	0.338 (1.00)	0.0335 (1.00)	0.0543 (1.00)
Amp Peak 17(12q15)	0 (0%)	471	0.462 (1.00)	0.624 (1.00)	0.751 (1.00)	0.515 (1.00)	2.83e-07 (0.000184)	0.563 (1.00)	0.273 (1.00)	0.649 (1.00)	0.333 (1.00)	0.349 (1.00)
Amp Peak 21(17q25 1)	0 (0%)	485	0.0141 (1.00)	0.232 (1.00)	0.402 (1.00)	0.709 (1.00)	5.98e-05 (0.0364)	0.937 (1.00)	0.13 (1.00)	0.292 (1.00)	1 (1.00)	0.417 (1.00)
Del Peak 7(2q22 1)	0 (0%)	519	0.00176 (0.984)	0.213 (1.00)	0.437 (1.00)	0.0651 (1.00)	1.6e-06 (0.00102)	0.00338 (1.00)	0.478 (1.00)	0.86 (1.00)	0.181 (1.00)	0.21 (1.00)
Del Peak 9(3p21 1)	0 (0%)	511	0.231 (1.00)	0.603 (1.00)	0.911 (1.00)	0.104 (1.00)	0.000187 (0.11)	0.252 (1.00)	0.134 (1.00)	0.855 (1.00)	0.461 (1.00)	0.0959 (1.00)
Del Peak 10(3q13 31)	0 (0%)	508	0.566 (1.00)	0.865 (1.00)	0.98 (1.00)	0.708 (1.00)	5.68e-06 (0.00357)	0.405 (1.00)	0.87 (1.00)	0.797 (1.00)	1 (1.00)	0.0547 (1.00)
Del Peak 11(3q22 1)	0 (0%)	508	0.829 (1.00)	0.252 (1.00)	0.617 (1.00)	0.378 (1.00)	0.000235 (0.138)	0.198 (1.00)	0.859 (1.00)	0.892 (1.00)	1 (1.00)	0.103 (1.00)
Del Peak 14(4q34 3)	0 (0%)	473	0.00309 (1.00)	0.0159 (1.00)	0.088 (1.00)	0.0519 (1.00)	0.000153 (0.0909)	0.152 (1.00)	0.0967 (1.00)	0.283 (1.00)	0.125 (1.00)	0.96 (1.00)
Del Peak 16(6q22 31)	0 (0%)	410	0.797 (1.00)	0.96 (1.00)	0.554 (1.00)	0.029 (1.00)	9.83e-11 (6.67e-08)	0.311 (1.00)	0.204 (1.00)	0.192 (1.00)	0.796 (1.00)	0.426 (1.00)
Del Peak 17(6q26)	0 (0%)	390	0.768 (1.00)	0.236 (1.00)	0.866 (1.00)	0.125 (1.00)	1.08e-06 (0.000693)	0.617 (1.00)	0.0166 (1.00)	0.0111 (1.00)	0.761 (1.00)	0.292 (1.00)
Del Peak 30(12q12)	0 (0%)	487	0.00831 (1.00)	0.00296 (1.00)	0.188 (1.00)	0.0064 (1.00)	0.000175 (0.103)	0.299 (1.00)	0.137 (1.00)	0.489 (1.00)	0.941 (1.00)	0.868 (1.00)
Del Peak 39(17p13 2)	0 (0%)	478	0.00121 (0.684)	0.869 (1.00)	0.926 (1.00)	0.8 (1.00)	2e-10 (1.35e-07)	0.376 (1.00)	0.632 (1.00)	0.487 (1.00)	0.587 (1.00)	0.261 (1.00)
Del Peak 43(19q13 41)	0 (0%)	464	0.00103 (0.587)	1.23e-05 (0.0076)	0.0018 (1.00)	0.00108 (0.616)	0.0012 (0.68)	0.778 (1.00)	0.0401 (1.00)	0.574 (1.00)	0.02 (1.00)	0.0941 (1.00)
Del Peak 44(21q22 3)	0 (0%)	504	0.00118 (0.669)	0.0168 (1.00)	0.000108 (0.0652)	0.00239 (1.00)	0.14 (1.00)	0.0685 (1.00)	0.39 (1.00)	0.121 (1.00)	1 (1.00)	0.119 (1.00)
Del Peak 46(Xp22 2)	0 (0%)	440	0.00431 (1.00)	0.00119 (0.677)	0.155 (1.00)	0.209 (1.00)	6.6e-10 (4.44e-07)	0.00951 (1.00)	0.605 (1.00)	0.253 (1.00)	0.337 (1.00)	0.644 (1.00)
Amp Peak 6(4p16 3)	0 (0%)	517	0.348 (1.00)	0.852 (1.00)	0.828 (1.00)	0.403 (1.00)	0.465 (1.00)	0.529 (1.00)	0.636 (1.00)	0.53 (1.00)	0.941 (1.00)	0.759 (1.00)
Amp Peak 14(11p13)	0 (0%)	537	0.718 (1.00)	0.588 (1.00)	0.324 (1.00)	0.769 (1.00)	0.452 (1.00)	0.181 (1.00)	0.265 (1.00)	0.112 (1.00)	0.602 (1.00)	1 (1.00)
Amp Peak 18(13q34)	0 (0%)	533	0.169 (1.00)	0.691 (1.00)	0.17 (1.00)	0.115 (1.00)	0.014 (1.00)		0.0677 (1.00)	0.186 (1.00)	0.368 (1.00)	1 (1.00)
Amp Peak 19(14q32 33)	0 (0%)	529	0.368 (1.00)	0.434 (1.00)	0.0211 (1.00)	0.943 (1.00)	0.794 (1.00)	0.903 (1.00)	0.0394 (1.00)	0.275 (1.00)	0.0429 (1.00)	0.884 (1.00)
Amp Peak 20(17p13 2)	0 (0%)	518	0.00312 (1.00)	0.00458 (1.00)	0.0751 (1.00)	0.221 (1.00)	0.00696 (1.00)	0.865 (1.00)	0.0545 (1.00)	0.63 (1.00)	0.615 (1.00)	0.281 (1.00)
Amp Peak 24(21q21 1)	0 (0%)	496	0.00429 (1.00)	0.0716 (1.00)	0.108 (1.00)	0.0796 (1.00)	0.000771 (0.445)	0.879 (1.00)	0.669 (1.00)	0.83 (1.00)	0.0967 (1.00)	0.0663 (1.00)
Del Peak 1(1p36 32)	0 (0%)	464	0.797 (1.00)	0.0418 (1.00)	0.503 (1.00)	0.233 (1.00)	0.614 (1.00)	0.339 (1.00)	0.545 (1.00)	0.561 (1.00)	0.252 (1.00)	0.0437 (1.00)
Del Peak 2(1p36 23)	0 (0%)	428	0.133 (1.00)	0.107 (1.00)	0.369 (1.00)	0.33 (1.00)	0.00118 (0.671)	0.306 (1.00)	0.279 (1.00)	0.725 (1.00)	0.0632 (1.00)	0.103 (1.00)
Del Peak 3(1p32 3)	0 (0%)	503	0.248 (1.00)	0.299 (1.00)	0.97 (1.00)	0.871 (1.00)	0.0973 (1.00)	0.822 (1.00)	0.706 (1.00)	0.63 (1.00)	0.803 (1.00)	0.159 (1.00)
Del Peak 4(1p22 1)	0 (0%)	516	0.833 (1.00)	0.979 (1.00)	0.761 (1.00)	0.228 (1.00)	0.176 (1.00)	0.579 (1.00)	0.888 (1.00)	0.372 (1.00)	1 (1.00)	0.015 (1.00)
Del Peak 5(1q42 11)	0 (0%)	516	0.309 (1.00)	0.409 (1.00)	0.402 (1.00)	0.679 (1.00)	0.619 (1.00)	0.412 (1.00)	0.161 (1.00)	0.00286 (1.00)	0.686 (1.00)	0.647 (1.00)
Del Peak 6(1q44)	0 (0%)	531	0.729 (1.00)	0.555 (1.00)	0.685 (1.00)	0.315 (1.00)	0.612 (1.00)	0.187 (1.00)	0.799 (1.00)	0.335 (1.00)	0.539 (1.00)	0.904 (1.00)
Del Peak 8(2q37 1)	0 (0%)	507	0.0601 (1.00)	0.023 (1.00)	0.239 (1.00)	0.00097 (0.556)	0.00684 (1.00)	0.0265 (1.00)	0.647 (1.00)	0.72 (1.00)	0.181 (1.00)	0.687 (1.00)
Del Peak 12(3q29)	0 (0%)	499	0.0674 (1.00)	0.191 (1.00)	0.612 (1.00)	0.984 (1.00)	0.00683 (1.00)	0.259 (1.00)	0.379 (1.00)	0.684 (1.00)	0.954 (1.00)	0.731 (1.00)
Del Peak 13(4p16 3)	0 (0%)	485	0.0176 (1.00)	0.0695 (1.00)	0.35 (1.00)	0.178 (1.00)	0.0582 (1.00)	1 (1.00)	0.832 (1.00)	0.71 (1.00)	0.872 (1.00)	0.818 (1.00)
Del Peak 18(8p23 2)	0 (0%)	496	0.517 (1.00)	0.13 (1.00)	0.256 (1.00)	0.355 (1.00)	0.0382 (1.00)	0.892 (1.00)	0.951 (1.00)	0.946 (1.00)	0.62 (1.00)	0.159 (1.00)
Del Peak 20(9q34 2)	0 (0%)	492	0.19 (1.00)	0.116 (1.00)	0.84 (1.00)	0.401 (1.00)	0.292 (1.00)	0.652 (1.00)	0.113 (1.00)	0.241 (1.00)	0.442 (1.00)	0.0569 (1.00)
Del Peak 29(12p13 1)	0 (0%)	488	0.0112 (1.00)	0.013 (1.00)	0.129 (1.00)	0.056 (1.00)	0.077 (1.00)	0.669 (1.00)	0.875 (1.00)	0.522 (1.00)	0.944 (1.00)	0.566 (1.00)
Del Peak 37(16p12 2)	0 (0%)	474	0.389 (1.00)	0.248 (1.00)	0.0617 (1.00)	0.578 (1.00)	0.0942 (1.00)	0.243 (1.00)	0.405 (1.00)	0.535 (1.00)	0.443 (1.00)	0.422 (1.00)
Del Peak 38(16q23 3)	0 (0%)	468	0.0364 (1.00)	0.61 (1.00)	0.752 (1.00)	1 (1.00)	0.0045 (1.00)	0.752 (1.00)	0.0385 (1.00)	0.0802 (1.00)	0.528 (1.00)	0.468 (1.00)
Del Peak 42(18q22 3)	0 (0%)	484	0.192 (1.00)	0.205 (1.00)	0.498 (1.00)	0.421 (1.00)	0.00203 (1.00)	0.0928 (1.00)	0.0315 (1.00)	0.00134 (0.753)	0.159 (1.00)	0.697 (1.00)
Del Peak 45(22q13 32)	0 (0%)	355	0.749 (1.00)	0.305 (1.00)	0.0194 (1.00)	0.088 (1.00)	0.000804 (0.462)	0.774 (1.00)	0.915 (1.00)	0.941 (1.00)	0.0721 (1.00)	0.923 (1.00)

'Amp Peak 1(1p36.21)' versus 'CN_CNMF'

P value = 1.63e-08 (Fisher's exact test), Q value = 1.1e-05

Table S1. Gene #1: 'Amp Peak 1(1p36.21)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
AMP PEAK 1(1P36.21) CNV	50	20	19
AMP PEAK 1(1P36.21) WILD-TYPE	111	194	169

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1p36.21)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 2(1q32.1)' versus 'CN_CNMF'

P value = 1.76e-08 (Fisher's exact test), Q value = 1.2e-05

Table S2. Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
AMP PEAK 2(1Q32.1) CNV	73	43	37
AMP PEAK 2(1Q32.1) WILD-TYPE	88	171	151

Figure S2. Get High-res Image Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 3(1q44)' versus 'CN_CNMF'

P value = 8.32e-09 (Fisher's exact test), Q value = 5.6e-06

Table S3. Gene #3: 'Amp Peak 3(1q44)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
AMP PEAK 3(1Q44) CNV	53	21	22
AMP PEAK 3(1Q44) WILD-TYPE	108	193	166

Figure S3. Get High-res Image Gene #3: 'Amp Peak 3(1q44)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 4(2p24.3)' versus 'CN_CNMF'

P value = 0.000238 (Fisher's exact test), Q value = 0.14

Table S4. Gene #4: 'Amp Peak 4(2p24.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
AMP PEAK 4(2P24.3) CNV	24	7	15
AMP PEAK 4(2P24.3) WILD-TYPE	137	207	173

Figure S4. Get High-res Image Gene #4: 'Amp Peak 4(2p24.3)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 3.56e-06 (Fisher's exact test), Q value = 0.0022

Table S5. Gene #5: 'Amp Peak 5(3q26.33)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
AMP PEAK 5(3Q26.33) CNV	52	25	31
AMP PEAK 5(3Q26.33) WILD-TYPE	109	189	157

Figure S5. Get High-res Image Gene #5: 'Amp Peak 5(3q26.33)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 7(4q12)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000115 (Fisher's exact test), Q value = 0.07

Table S6. Gene #7: 'Amp Peak 7(4q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	166	213
AMP PEAK 7(4Q12) CNV	16	50	32
AMP PEAK 7(4Q12) WILD-TYPE	114	116	181

Figure S6. Get High-res Image Gene #7: 'Amp Peak 7(4q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 7(4q12)' versus 'CN_CNMF'

P value = 4.31e-07 (Fisher's exact test), Q value = 0.00028

Table S7. Gene #7: 'Amp Peak 7(4q12)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
AMP PEAK 7(4Q12) CNV	52	22	30
AMP PEAK 7(4Q12) WILD-TYPE	109	192	158

Figure S7. Get High-res Image Gene #7: 'Amp Peak 7(4q12)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 8(7p11.2)' versus 'MRNA_CNMF'

P value = 3.62e-11 (Fisher's exact test), Q value = 2.5e-08

Table S8. Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	94	152	116
AMP PEAK 8(7P11.2) CNV	139	66	147	91
AMP PEAK 8(7P11.2) WILD-TYPE	8	28	5	25

Figure S8. Get High-res Image Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 8(7p11.2)' versus 'MRNA_CHIERARCHICAL'

P value = 3.18e-11 (Fisher's exact test), Q value = 2.2e-08

Table S9. Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	166	213
AMP PEAK 8(7P11.2) CNV	124	119	200
AMP PEAK 8(7P11.2) WILD-TYPE	6	47	13

Figure S9. Get High-res Image Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 8(7p11.2)' versus 'MIR_CNMF'

P value = 3.48e-07 (Fisher's exact test), Q value = 0.00023

Table S10. Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	157	72	104
AMP PEAK 8(7P11.2) CNV	136	124	58	95
AMP PEAK 8(7P11.2) WILD-TYPE	3	33	14	9

Figure S10. Get High-res Image Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #3: 'MIR_CNMF'

'Amp Peak 8(7p11.2)' versus 'MIR_CHIERARCHICAL'

P value = 2.34e-13 (Fisher's exact test), Q value = 1.6e-10

Table S11. Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	179	130
AMP PEAK 8(7P11.2) CNV	153	172	88
AMP PEAK 8(7P11.2) WILD-TYPE	10	7	42

Figure S11. Get High-res Image Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Amp Peak 8(7p11.2)' versus 'CN_CNMF'

P value = 1.23e-20 (Fisher's exact test), Q value = 8.6e-18

Table S12. Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
AMP PEAK 8(7P11.2) CNV	149	213	132
AMP PEAK 8(7P11.2) WILD-TYPE	12	1	56

Figure S12. Get High-res Image Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 8(7p11.2)' versus 'METHLYATION_CNMF'

P value = 1.32e-06 (Fisher's exact test), Q value = 0.00084

Table S13. Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	27	16	27
AMP PEAK 8(7P11.2) CNV	38	27	16	16
AMP PEAK 8(7P11.2) WILD-TYPE	1	0	0	11

Figure S13. Get High-res Image Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'Amp Peak 8(7p11.2)' versus 'RPPA_CNMF'

P value = 8.62e-06 (Fisher's exact test), Q value = 0.0054

Table S14. Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	58	44	45
AMP PEAK 8(7P11.2) CNV	49	42	44	44
AMP PEAK 8(7P11.2) WILD-TYPE	5	16	0	1

Figure S14. Get High-res Image Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #7: 'RPPA_CNMF'

'Amp Peak 8(7p11.2)' versus 'RPPA_CHIERARCHICAL'

P value = 5.85e-05 (Fisher's exact test), Q value = 0.036

Table S15. Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	33	104
AMP PEAK 8(7P11.2) CNV	64	31	84
AMP PEAK 8(7P11.2) WILD-TYPE	0	2	20

Figure S15. Get High-res Image Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'Amp Peak 8(7p11.2)' versus 'MRNASEQ_CNMF'

P value = 1.11e-05 (Fisher's exact test), Q value = 0.0069

Table S16. Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	67	36
AMP PEAK 8(7P11.2) CNV	31	66	34
AMP PEAK 8(7P11.2) WILD-TYPE	13	1	2

Figure S16. Get High-res Image Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'Amp Peak 8(7p11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000357 (Fisher's exact test), Q value = 0.21

Table S17. Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	21	60
AMP PEAK 8(7P11.2) CNV	64	21	46
AMP PEAK 8(7P11.2) WILD-TYPE	2	0	14

Figure S17. Get High-res Image Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 9(7q11.21)' versus 'MRNA_CNMF'

P value = 9.85e-06 (Fisher's exact test), Q value = 0.0061

Table S18. Gene #9: 'Amp Peak 9(7q11.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	94	152	116
AMP PEAK 9(7Q11.21) CNV	133	62	124	84
AMP PEAK 9(7Q11.21) WILD-TYPE	14	32	28	32

Figure S18. Get High-res Image Gene #9: 'Amp Peak 9(7q11.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 9(7q11.21)' versus 'MRNA_CHIERARCHICAL'

P value = 4.88e-07 (Fisher's exact test), Q value = 0.00032

Table S19. Gene #9: 'Amp Peak 9(7q11.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	166	213
AMP PEAK 9(7Q11.21) CNV	109	108	186
AMP PEAK 9(7Q11.21) WILD-TYPE	21	58	27

Figure S19. Get High-res Image Gene #9: 'Amp Peak 9(7q11.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 9(7q11.21)' versus 'MIR_CNMF'

P value = 4.69e-06 (Fisher's exact test), Q value = 0.003

Table S20. Gene #9: 'Amp Peak 9(7q11.21)' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	157	72	104
AMP PEAK 9(7Q11.21) CNV	126	113	48	90
AMP PEAK 9(7Q11.21) WILD-TYPE	13	44	24	14

Figure S20. Get High-res Image Gene #9: 'Amp Peak 9(7q11.21)' versus Molecular Subtype #3: 'MIR_CNMF'

'Amp Peak 9(7q11.21)' versus 'MIR_CHIERARCHICAL'

P value = 7.42e-09 (Fisher's exact test), Q value = 5e-06

Table S21. Gene #9: 'Amp Peak 9(7q11.21)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	179	130
AMP PEAK 9(7Q11.21) CNV	143	155	79
AMP PEAK 9(7Q11.21) WILD-TYPE	20	24	51

Figure S21. Get High-res Image Gene #9: 'Amp Peak 9(7q11.21)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Amp Peak 9(7q11.21)' versus 'CN_CNMF'

P value = 1.72e-09 (Fisher's exact test), Q value = 1.2e-06

Table S22. Gene #9: 'Amp Peak 9(7q11.21)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
AMP PEAK 9(7Q11.21) CNV	144	186	122
AMP PEAK 9(7Q11.21) WILD-TYPE	17	28	66

Figure S22. Get High-res Image Gene #9: 'Amp Peak 9(7q11.21)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 10(7q21.2)' versus 'MRNA_CNMF'

P value = 1.02e-05 (Fisher's exact test), Q value = 0.0064

Table S23. Gene #10: 'Amp Peak 10(7q21.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	94	152	116
AMP PEAK 10(7Q21.2) CNV	131	62	135	91
AMP PEAK 10(7Q21.2) WILD-TYPE	16	32	17	25

Figure S23. Get High-res Image Gene #10: 'Amp Peak 10(7q21.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 10(7q21.2)' versus 'MRNA_CHIERARCHICAL'

P value = 4.54e-05 (Fisher's exact test), Q value = 0.028

Table S24. Gene #10: 'Amp Peak 10(7q21.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	166	213
AMP PEAK 10(7Q21.2) CNV	114	118	187
AMP PEAK 10(7Q21.2) WILD-TYPE	16	48	26

Figure S24. Get High-res Image Gene #10: 'Amp Peak 10(7q21.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 10(7q21.2)' versus 'MIR_CHIERARCHICAL'

P value = 1.92e-06 (Fisher's exact test), Q value = 0.0012

Table S25. Gene #10: 'Amp Peak 10(7q21.2)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	179	130
AMP PEAK 10(7Q21.2) CNV	140	160	87
AMP PEAK 10(7Q21.2) WILD-TYPE	23	19	43

Figure S25. Get High-res Image Gene #10: 'Amp Peak 10(7q21.2)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Amp Peak 10(7q21.2)' versus 'CN_CNMF'

P value = 1.06e-10 (Fisher's exact test), Q value = 7.2e-08

Table S26. Gene #10: 'Amp Peak 10(7q21.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
AMP PEAK 10(7Q21.2) CNV	145	196	127
AMP PEAK 10(7Q21.2) WILD-TYPE	16	18	61

Figure S26. Get High-res Image Gene #10: 'Amp Peak 10(7q21.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 11(7q31.2)' versus 'MRNA_CHIERARCHICAL'

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

Table S27. Gene #11: 'Amp Peak 11(7q31.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	166	213
AMP PEAK 11(7Q31.2) CNV	107	118	188
AMP PEAK 11(7Q31.2) WILD-TYPE	23	48	25

Figure S27. Get High-res Image Gene #11: 'Amp Peak 11(7q31.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 11(7q31.2)' versus 'MIR_CHIERARCHICAL'

P value = 0.000144 (Fisher's exact test), Q value = 0.086

Table S28. Gene #11: 'Amp Peak 11(7q31.2)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	179	130
AMP PEAK 11(7Q31.2) CNV	141	151	88
AMP PEAK 11(7Q31.2) WILD-TYPE	22	28	42

Figure S28. Get High-res Image Gene #11: 'Amp Peak 11(7q31.2)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Amp Peak 11(7q31.2)' versus 'CN_CNMF'

P value = 2.21e-07 (Fisher's exact test), Q value = 0.00014

Table S29. Gene #11: 'Amp Peak 11(7q31.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
AMP PEAK 11(7Q31.2) CNV	141	190	129
AMP PEAK 11(7Q31.2) WILD-TYPE	20	24	59

Figure S29. Get High-res Image Gene #11: 'Amp Peak 11(7q31.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 12(7q36.1)' versus 'MRNA_CNMF'

P value = 4.64e-05 (Fisher's exact test), Q value = 0.028

Table S30. Gene #12: 'Amp Peak 12(7q36.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	94	152	116
AMP PEAK 12(7Q36.1) CNV	131	62	132	92
AMP PEAK 12(7Q36.1) WILD-TYPE	16	32	20	24

Figure S30. Get High-res Image Gene #12: 'Amp Peak 12(7q36.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 12(7q36.1)' versus 'MIR_CHIERARCHICAL'

P value = 4.59e-05 (Fisher's exact test), Q value = 0.028

Table S31. Gene #12: 'Amp Peak 12(7q36.1)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	179	130
AMP PEAK 12(7Q36.1) CNV	138	158	89
AMP PEAK 12(7Q36.1) WILD-TYPE	25	21	41

Figure S31. Get High-res Image Gene #12: 'Amp Peak 12(7q36.1)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Amp Peak 12(7q36.1)' versus 'CN_CNMF'

P value = 1.41e-05 (Fisher's exact test), Q value = 0.0087

Table S32. Gene #12: 'Amp Peak 12(7q36.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
AMP PEAK 12(7Q36.1) CNV	139	191	135
AMP PEAK 12(7Q36.1) WILD-TYPE	22	23	53

Figure S32. Get High-res Image Gene #12: 'Amp Peak 12(7q36.1)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 13(8q24.21)' versus 'MRNA_CNMF'

P value = 1.69e-07 (Fisher's exact test), Q value = 0.00011

Table S33. Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	94	152	116
AMP PEAK 13(8Q24.21) CNV	8	24	6	19
AMP PEAK 13(8Q24.21) WILD-TYPE	139	70	146	97

Figure S33. Get High-res Image Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 13(8q24.21)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000183 (Fisher's exact test), Q value = 0.11

Table S34. Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	166	213
AMP PEAK 13(8Q24.21) CNV	9	33	15
AMP PEAK 13(8Q24.21) WILD-TYPE	121	133	198

Figure S34. Get High-res Image Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 13(8q24.21)' versus 'MIR_CHIERARCHICAL'

P value = 8.34e-05 (Fisher's exact test), Q value = 0.051

Table S35. Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	179	130
AMP PEAK 13(8Q24.21) CNV	12	13	29
AMP PEAK 13(8Q24.21) WILD-TYPE	151	166	101

Figure S35. Get High-res Image Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Amp Peak 13(8q24.21)' versus 'CN_CNMF'

P value = 3.51e-06 (Fisher's exact test), Q value = 0.0022

Table S36. Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
AMP PEAK 13(8Q24.21) CNV	31	8	25
AMP PEAK 13(8Q24.21) WILD-TYPE	130	206	163

Figure S36. Get High-res Image Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 15(12p13.32)' versus 'CN_CNMF'

P value = 1.96e-05 (Fisher's exact test), Q value = 0.012

Table S37. Gene #15: 'Amp Peak 15(12p13.32)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
AMP PEAK 15(12P13.32) CNV	41	18	22
AMP PEAK 15(12P13.32) WILD-TYPE	120	196	166

Figure S37. Get High-res Image Gene #15: 'Amp Peak 15(12p13.32)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 16(12q14.1)' versus 'CN_CNMF'

P value = 1.7e-09 (Fisher's exact test), Q value = 1.1e-06

Table S38. Gene #16: 'Amp Peak 16(12q14.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
AMP PEAK 16(12Q14.1) CNV	67	37	27
AMP PEAK 16(12Q14.1) WILD-TYPE	94	177	161

Figure S38. Get High-res Image Gene #16: 'Amp Peak 16(12q14.1)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 17(12q15)' versus 'CN_CNMF'

P value = 2.83e-07 (Fisher's exact test), Q value = 0.00018

Table S39. Gene #17: 'Amp Peak 17(12q15)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
AMP PEAK 17(12Q15) CNV	49	24	19
AMP PEAK 17(12Q15) WILD-TYPE	112	190	169

Figure S39. Get High-res Image Gene #17: 'Amp Peak 17(12q15)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 21(17q25.1)' versus 'CN_CNMF'

P value = 5.98e-05 (Fisher's exact test), Q value = 0.036

Table S40. Gene #21: 'Amp Peak 21(17q25.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
AMP PEAK 21(17Q25.1) CNV	39	18	21
AMP PEAK 21(17Q25.1) WILD-TYPE	122	196	167

Figure S40. Get High-res Image Gene #21: 'Amp Peak 21(17q25.1)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 22(19p13.2)' versus 'MRNA_CNMF'

P value = 2.33e-12 (Fisher's exact test), Q value = 1.6e-09

Table S41. Gene #22: 'Amp Peak 22(19p13.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	94	152	116
AMP PEAK 22(19P13.2) CNV	56	37	100	25
AMP PEAK 22(19P13.2) WILD-TYPE	91	57	52	91

Figure S41. Get High-res Image Gene #22: 'Amp Peak 22(19p13.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 22(19p13.2)' versus 'MRNA_CHIERARCHICAL'

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

Table S42. Gene #22: 'Amp Peak 22(19p13.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	166	213
AMP PEAK 22(19P13.2) CNV	78	47	93
AMP PEAK 22(19P13.2) WILD-TYPE	52	119	120

Figure S42. Get High-res Image Gene #22: 'Amp Peak 22(19p13.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 22(19p13.2)' versus 'CN_CNMF'

P value = 1.86e-20 (Fisher's exact test), Q value = 1.3e-17

Table S43. Gene #22: 'Amp Peak 22(19p13.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
AMP PEAK 22(19P13.2) CNV	47	145	48
AMP PEAK 22(19P13.2) WILD-TYPE	114	69	140

Figure S43. Get High-res Image Gene #22: 'Amp Peak 22(19p13.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 22(19p13.2)' versus 'RPPA_CHIERARCHICAL'

P value = 1.32e-05 (Fisher's exact test), Q value = 0.0082

Table S44. Gene #22: 'Amp Peak 22(19p13.2)' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	33	104
AMP PEAK 22(19P13.2) CNV	42	8	34
AMP PEAK 22(19P13.2) WILD-TYPE	22	25	70

Figure S44. Get High-res Image Gene #22: 'Amp Peak 22(19p13.2)' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'Amp Peak 23(19q12)' versus 'MRNA_CNMF'

P value = 1.29e-10 (Fisher's exact test), Q value = 8.7e-08

Table S45. Gene #23: 'Amp Peak 23(19q12)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	94	152	116
AMP PEAK 23(19Q12) CNV	55	29	83	17
AMP PEAK 23(19Q12) WILD-TYPE	92	65	69	99

Figure S45. Get High-res Image Gene #23: 'Amp Peak 23(19q12)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 23(19q12)' versus 'MRNA_CHIERARCHICAL'

P value = 3.97e-08 (Fisher's exact test), Q value = 2.6e-05

Table S46. Gene #23: 'Amp Peak 23(19q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	166	213
AMP PEAK 23(19Q12) CNV	64	32	88
AMP PEAK 23(19Q12) WILD-TYPE	66	134	125

Figure S46. Get High-res Image Gene #23: 'Amp Peak 23(19q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 23(19q12)' versus 'CN_CNMF'

P value = 1.5e-15 (Fisher's exact test), Q value = 1e-12

Table S47. Gene #23: 'Amp Peak 23(19q12)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
AMP PEAK 23(19Q12) CNV	38	123	42
AMP PEAK 23(19Q12) WILD-TYPE	123	91	146

Figure S47. Get High-res Image Gene #23: 'Amp Peak 23(19q12)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 23(19q12)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000213 (Fisher's exact test), Q value = 0.13

Table S48. Gene #23: 'Amp Peak 23(19q12)' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	33	104
AMP PEAK 23(19Q12) CNV	35	7	27
AMP PEAK 23(19Q12) WILD-TYPE	29	26	77

Figure S48. Get High-res Image Gene #23: 'Amp Peak 23(19q12)' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'Del Peak 7(2q22.1)' versus 'CN_CNMF'

P value = 1.6e-06 (Fisher's exact test), Q value = 0.001

Table S49. Gene #31: 'Del Peak 7(2q22.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
DEL PEAK 7(2Q22.1) CNV	26	4	14
DEL PEAK 7(2Q22.1) WILD-TYPE	135	210	174

Figure S49. Get High-res Image Gene #31: 'Del Peak 7(2q22.1)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 9(3p21.1)' versus 'CN_CNMF'

P value = 0.000187 (Fisher's exact test), Q value = 0.11

Table S50. Gene #33: 'Del Peak 9(3p21.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
DEL PEAK 9(3P21.1) CNV	23	7	22
DEL PEAK 9(3P21.1) WILD-TYPE	138	207	166

Figure S50. Get High-res Image Gene #33: 'Del Peak 9(3p21.1)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 10(3q13.31)' versus 'CN_CNMF'

P value = 5.68e-06 (Fisher's exact test), Q value = 0.0036

Table S51. Gene #34: 'Del Peak 10(3q13.31)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
DEL PEAK 10(3Q13.31) CNV	27	6	22
DEL PEAK 10(3Q13.31) WILD-TYPE	134	208	166

Figure S51. Get High-res Image Gene #34: 'Del Peak 10(3q13.31)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 11(3q22.1)' versus 'CN_CNMF'

P value = 0.000235 (Fisher's exact test), Q value = 0.14

Table S52. Gene #35: 'Del Peak 11(3q22.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
DEL PEAK 11(3Q22.1) CNV	24	8	23
DEL PEAK 11(3Q22.1) WILD-TYPE	137	206	165

Figure S52. Get High-res Image Gene #35: 'Del Peak 11(3q22.1)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 14(4q34.3)' versus 'CN_CNMF'

P value = 0.000153 (Fisher's exact test), Q value = 0.091

Table S53. Gene #38: 'Del Peak 14(4q34.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
DEL PEAK 14(4Q34.3) CNV	41	20	29
DEL PEAK 14(4Q34.3) WILD-TYPE	120	194	159

Figure S53. Get High-res Image Gene #38: 'Del Peak 14(4q34.3)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 15(5q35.3)' versus 'MRNA_CNMF'

P value = 4.89e-06 (Fisher's exact test), Q value = 0.0031

Table S54. Gene #39: 'Del Peak 15(5q35.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	94	152	116
DEL PEAK 15(5Q35.3) CNV	8	22	6	15
DEL PEAK 15(5Q35.3) WILD-TYPE	139	72	146	101

Figure S54. Get High-res Image Gene #39: 'Del Peak 15(5q35.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 15(5q35.3)' versus 'MIR_CHIERARCHICAL'

P value = 2.27e-05 (Fisher's exact test), Q value = 0.014

Table S55. Gene #39: 'Del Peak 15(5q35.3)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	179	130
DEL PEAK 15(5Q35.3) CNV	6	15	26
DEL PEAK 15(5Q35.3) WILD-TYPE	157	164	104

Figure S55. Get High-res Image Gene #39: 'Del Peak 15(5q35.3)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Del Peak 15(5q35.3)' versus 'CN_CNMF'

P value = 5.69e-05 (Fisher's exact test), Q value = 0.035

Table S56. Gene #39: 'Del Peak 15(5q35.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
DEL PEAK 15(5Q35.3) CNV	18	7	29
DEL PEAK 15(5Q35.3) WILD-TYPE	143	207	159

Figure S56. Get High-res Image Gene #39: 'Del Peak 15(5q35.3)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 9.83e-11 (Fisher's exact test), Q value = 6.7e-08

Table S57. Gene #40: 'Del Peak 16(6q22.31)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
DEL PEAK 16(6Q22.31) CNV	77	42	34
DEL PEAK 16(6Q22.31) WILD-TYPE	84	172	154

Figure S57. Get High-res Image Gene #40: 'Del Peak 16(6q22.31)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 1.08e-06 (Fisher's exact test), Q value = 0.00069

Table S58. Gene #41: 'Del Peak 17(6q26)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
DEL PEAK 17(6Q26) CNV	75	58	40
DEL PEAK 17(6Q26) WILD-TYPE	86	156	148

Figure S58. Get High-res Image Gene #41: 'Del Peak 17(6q26)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 19(9p21.3)' versus 'MRNA_CNMF'

P value = 6.36e-06 (Fisher's exact test), Q value = 0.004

Table S59. Gene #43: 'Del Peak 19(9p21.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	94	152	116
DEL PEAK 19(9P21.3) CNV	100	60	133	77
DEL PEAK 19(9P21.3) WILD-TYPE	47	34	19	39

Figure S59. Get High-res Image Gene #43: 'Del Peak 19(9p21.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 19(9p21.3)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000114 (Fisher's exact test), Q value = 0.069

Table S60. Gene #43: 'Del Peak 19(9p21.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	166	213
DEL PEAK 19(9P21.3) CNV	112	109	149
DEL PEAK 19(9P21.3) WILD-TYPE	18	57	64

Figure S60. Get High-res Image Gene #43: 'Del Peak 19(9p21.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 19(9p21.3)' versus 'CN_CNMF'

P value = 3.77e-10 (Fisher's exact test), Q value = 2.5e-07

Table S61. Gene #43: 'Del Peak 19(9p21.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
DEL PEAK 19(9P21.3) CNV	108	187	113
DEL PEAK 19(9P21.3) WILD-TYPE	53	27	75

Figure S61. Get High-res Image Gene #43: 'Del Peak 19(9p21.3)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 1.64e-06 (Fisher's exact test), Q value = 0.001

Table S62. Gene #45: 'Del Peak 21(10p15.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	94	152	116
DEL PEAK 21(10P15.3) CNV	129	60	134	85
DEL PEAK 21(10P15.3) WILD-TYPE	18	34	18	31

Figure S62. Get High-res Image Gene #45: 'Del Peak 21(10p15.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

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

Table S63. Gene #45: 'Del Peak 21(10p15.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	166	213
DEL PEAK 21(10P15.3) CNV	112	115	181
DEL PEAK 21(10P15.3) WILD-TYPE	18	51	32

Figure S63. Get High-res Image Gene #45: 'Del Peak 21(10p15.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

P value = 1.85e-07 (Fisher's exact test), Q value = 0.00012

Table S64. Gene #45: 'Del Peak 21(10p15.3)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	179	130
DEL PEAK 21(10P15.3) CNV	143	154	82
DEL PEAK 21(10P15.3) WILD-TYPE	20	25	48

Figure S64. Get High-res Image Gene #45: 'Del Peak 21(10p15.3)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

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

P value = 1.45e-14 (Fisher's exact test), Q value = 1e-11

Table S65. Gene #45: 'Del Peak 21(10p15.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
DEL PEAK 21(10P15.3) CNV	137	201	119
DEL PEAK 21(10P15.3) WILD-TYPE	24	13	69

Figure S65. Get High-res Image Gene #45: 'Del Peak 21(10p15.3)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 22(10p13)' versus 'MRNA_CNMF'

P value = 3.17e-07 (Fisher's exact test), Q value = 0.00021

Table S66. Gene #46: 'Del Peak 22(10p13)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	94	152	116
DEL PEAK 22(10P13) CNV	131	62	135	82
DEL PEAK 22(10P13) WILD-TYPE	16	32	17	34

Figure S66. Get High-res Image Gene #46: 'Del Peak 22(10p13)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 22(10p13)' versus 'MRNA_CHIERARCHICAL'

P value = 9.94e-06 (Fisher's exact test), Q value = 0.0062

Table S67. Gene #46: 'Del Peak 22(10p13)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	166	213
DEL PEAK 22(10P13) CNV	112	113	185
DEL PEAK 22(10P13) WILD-TYPE	18	53	28

Figure S67. Get High-res Image Gene #46: 'Del Peak 22(10p13)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 22(10p13)' versus 'MIR_CHIERARCHICAL'

P value = 1.28e-07 (Fisher's exact test), Q value = 8.4e-05

Table S68. Gene #46: 'Del Peak 22(10p13)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	179	130
DEL PEAK 22(10P13) CNV	145	154	83
DEL PEAK 22(10P13) WILD-TYPE	18	25	47

Figure S68. Get High-res Image Gene #46: 'Del Peak 22(10p13)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Del Peak 22(10p13)' versus 'CN_CNMF'

P value = 1.11e-15 (Fisher's exact test), Q value = 7.7e-13

Table S69. Gene #46: 'Del Peak 22(10p13)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
DEL PEAK 22(10P13) CNV	137	203	119
DEL PEAK 22(10P13) WILD-TYPE	24	11	69

Figure S69. Get High-res Image Gene #46: 'Del Peak 22(10p13)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 22(10p13)' versus 'RPPA_CNMF'

P value = 0.000132 (Fisher's exact test), Q value = 0.079

Table S70. Gene #46: 'Del Peak 22(10p13)' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	58	44	45
DEL PEAK 22(10P13) CNV	50	38	42	37
DEL PEAK 22(10P13) WILD-TYPE	4	20	2	8

Figure S70. Get High-res Image Gene #46: 'Del Peak 22(10p13)' versus Molecular Subtype #7: 'RPPA_CNMF'

'Del Peak 23(10p11.23)' versus 'MRNA_CNMF'

P value = 2.94e-10 (Fisher's exact test), Q value = 2e-07

Table S71. Gene #47: 'Del Peak 23(10p11.23)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	94	152	116
DEL PEAK 23(10P11.23) CNV	130	58	142	86
DEL PEAK 23(10P11.23) WILD-TYPE	17	36	10	30

Figure S71. Get High-res Image Gene #47: 'Del Peak 23(10p11.23)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 23(10p11.23)' versus 'MRNA_CHIERARCHICAL'

P value = 9.54e-07 (Fisher's exact test), Q value = 0.00061

Table S72. Gene #47: 'Del Peak 23(10p11.23)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	166	213
DEL PEAK 23(10P11.23) CNV	118	114	184
DEL PEAK 23(10P11.23) WILD-TYPE	12	52	29

Figure S72. Get High-res Image Gene #47: 'Del Peak 23(10p11.23)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 23(10p11.23)' versus 'MIR_CHIERARCHICAL'

P value = 1.26e-08 (Fisher's exact test), Q value = 8.4e-06

Table S73. Gene #47: 'Del Peak 23(10p11.23)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	179	130
DEL PEAK 23(10P11.23) CNV	145	159	83
DEL PEAK 23(10P11.23) WILD-TYPE	18	20	47

Figure S73. Get High-res Image Gene #47: 'Del Peak 23(10p11.23)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Del Peak 23(10p11.23)' versus 'CN_CNMF'

P value = 9.85e-17 (Fisher's exact test), Q value = 6.8e-14

Table S74. Gene #47: 'Del Peak 23(10p11.23)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
DEL PEAK 23(10P11.23) CNV	138	205	120
DEL PEAK 23(10P11.23) WILD-TYPE	23	9	68

Figure S74. Get High-res Image Gene #47: 'Del Peak 23(10p11.23)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 24(10q23.31)' versus 'MRNA_CNMF'

P value = 4.77e-07 (Fisher's exact test), Q value = 0.00031

Table S75. Gene #48: 'Del Peak 24(10q23.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	94	152	116
DEL PEAK 24(10Q23.31) CNV	136	72	147	94
DEL PEAK 24(10Q23.31) WILD-TYPE	11	22	5	22

Figure S75. Get High-res Image Gene #48: 'Del Peak 24(10q23.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 24(10q23.31)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000124 (Fisher's exact test), Q value = 0.074

Table S76. Gene #48: 'Del Peak 24(10q23.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	166	213
DEL PEAK 24(10Q23.31) CNV	123	132	194
DEL PEAK 24(10Q23.31) WILD-TYPE	7	34	19

Figure S76. Get High-res Image Gene #48: 'Del Peak 24(10q23.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 24(10q23.31)' versus 'MIR_CHIERARCHICAL'

P value = 7.23e-05 (Fisher's exact test), Q value = 0.044

Table S77. Gene #48: 'Del Peak 24(10q23.31)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	179	130
DEL PEAK 24(10Q23.31) CNV	150	167	101
DEL PEAK 24(10Q23.31) WILD-TYPE	13	12	29

Figure S77. Get High-res Image Gene #48: 'Del Peak 24(10q23.31)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Del Peak 24(10q23.31)' versus 'CN_CNMF'

P value = 1.19e-16 (Fisher's exact test), Q value = 8.2e-14

Table S78. Gene #48: 'Del Peak 24(10q23.31)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
DEL PEAK 24(10Q23.31) CNV	149	212	138
DEL PEAK 24(10Q23.31) WILD-TYPE	12	2	50

Figure S78. Get High-res Image Gene #48: 'Del Peak 24(10q23.31)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 25(10q26.3)' versus 'MRNA_CNMF'

P value = 1.16e-07 (Fisher's exact test), Q value = 7.6e-05

Table S79. Gene #49: 'Del Peak 25(10q26.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	94	152	116
DEL PEAK 25(10Q26.3) CNV	136	72	148	94
DEL PEAK 25(10Q26.3) WILD-TYPE	11	22	4	22

Figure S79. Get High-res Image Gene #49: 'Del Peak 25(10q26.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 25(10q26.3)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000142 (Fisher's exact test), Q value = 0.085

Table S80. Gene #49: 'Del Peak 25(10q26.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	166	213
DEL PEAK 25(10Q26.3) CNV	124	133	193
DEL PEAK 25(10Q26.3) WILD-TYPE	6	33	20

Figure S80. Get High-res Image Gene #49: 'Del Peak 25(10q26.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 25(10q26.3)' versus 'CN_CNMF'

P value = 1.89e-13 (Fisher's exact test), Q value = 1.3e-10

Table S81. Gene #49: 'Del Peak 25(10q26.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
DEL PEAK 25(10Q26.3) CNV	147	211	142
DEL PEAK 25(10Q26.3) WILD-TYPE	14	3	46

Figure S81. Get High-res Image Gene #49: 'Del Peak 25(10q26.3)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 26(11p15.5)' versus 'MRNA_CNMF'

P value = 3.9e-10 (Fisher's exact test), Q value = 2.6e-07

Table S82. Gene #50: 'Del Peak 26(11p15.5)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	94	152	116
DEL PEAK 26(11P15.5) CNV	32	43	13	32
DEL PEAK 26(11P15.5) WILD-TYPE	115	51	139	84

Figure S82. Get High-res Image Gene #50: 'Del Peak 26(11p15.5)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 26(11p15.5)' versus 'MRNA_CHIERARCHICAL'

P value = 1.15e-06 (Fisher's exact test), Q value = 0.00074

Table S83. Gene #50: 'Del Peak 26(11p15.5)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	166	213
DEL PEAK 26(11P15.5) CNV	14	60	46
DEL PEAK 26(11P15.5) WILD-TYPE	116	106	167

Figure S83. Get High-res Image Gene #50: 'Del Peak 26(11p15.5)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 26(11p15.5)' versus 'MIR_CHIERARCHICAL'

P value = 1.5e-06 (Fisher's exact test), Q value = 0.00096

Table S84. Gene #50: 'Del Peak 26(11p15.5)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	179	130
DEL PEAK 26(11P15.5) CNV	29	32	54
DEL PEAK 26(11P15.5) WILD-TYPE	134	147	76

Figure S84. Get High-res Image Gene #50: 'Del Peak 26(11p15.5)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Del Peak 26(11p15.5)' versus 'CN_CNMF'

P value = 2.1e-15 (Fisher's exact test), Q value = 1.4e-12

Table S85. Gene #50: 'Del Peak 26(11p15.5)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
DEL PEAK 26(11P15.5) CNV	63	13	51
DEL PEAK 26(11P15.5) WILD-TYPE	98	201	137

Figure S85. Get High-res Image Gene #50: 'Del Peak 26(11p15.5)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 26(11p15.5)' versus 'METHLYATION_CNMF'

P value = 0.000309 (Fisher's exact test), Q value = 0.18

Table S86. Gene #50: 'Del Peak 26(11p15.5)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	27	16	27
DEL PEAK 26(11P15.5) CNV	0	4	1	9
DEL PEAK 26(11P15.5) WILD-TYPE	39	23	15	18

Figure S86. Get High-res Image Gene #50: 'Del Peak 26(11p15.5)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'Del Peak 27(11p11.2)' versus 'MRNA_CNMF'

P value = 5.47e-08 (Fisher's exact test), Q value = 3.6e-05

Table S87. Gene #51: 'Del Peak 27(11p11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	94	152	116
DEL PEAK 27(11P11.2) CNV	26	35	10	24
DEL PEAK 27(11P11.2) WILD-TYPE	121	59	142	92

Figure S87. Get High-res Image Gene #51: 'Del Peak 27(11p11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 27(11p11.2)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000192 (Fisher's exact test), Q value = 0.11

Table S88. Gene #51: 'Del Peak 27(11p11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	166	213
DEL PEAK 27(11P11.2) CNV	13	47	35
DEL PEAK 27(11P11.2) WILD-TYPE	117	119	178

Figure S88. Get High-res Image Gene #51: 'Del Peak 27(11p11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 27(11p11.2)' versus 'MIR_CHIERARCHICAL'

P value = 2.44e-05 (Fisher's exact test), Q value = 0.015

Table S89. Gene #51: 'Del Peak 27(11p11.2)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	179	130
DEL PEAK 27(11P11.2) CNV	29	20	42
DEL PEAK 27(11P11.2) WILD-TYPE	134	159	88

Figure S89. Get High-res Image Gene #51: 'Del Peak 27(11p11.2)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Del Peak 27(11p11.2)' versus 'CN_CNMF'

P value = 2.18e-13 (Fisher's exact test), Q value = 1.5e-10

Table S90. Gene #51: 'Del Peak 27(11p11.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
DEL PEAK 27(11P11.2) CNV	55	10	36
DEL PEAK 27(11P11.2) WILD-TYPE	106	204	152

Figure S90. Get High-res Image Gene #51: 'Del Peak 27(11p11.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 28(11q14.1)' versus 'MRNA_CNMF'

P value = 2.65e-07 (Fisher's exact test), Q value = 0.00017

Table S91. Gene #52: 'Del Peak 28(11q14.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	94	152	116
DEL PEAK 28(11Q14.1) CNV	29	34	12	14
DEL PEAK 28(11Q14.1) WILD-TYPE	118	60	140	102

Figure S91. Get High-res Image Gene #52: 'Del Peak 28(11q14.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 28(11q14.1)' versus 'CN_CNMF'

P value = 1.3e-16 (Fisher's exact test), Q value = 9e-14

Table S92. Gene #52: 'Del Peak 28(11q14.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
DEL PEAK 28(11Q14.1) CNV	61	10	24
DEL PEAK 28(11Q14.1) WILD-TYPE	100	204	164

Figure S92. Get High-res Image Gene #52: 'Del Peak 28(11q14.1)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 30(12q12)' versus 'CN_CNMF'

P value = 0.000175 (Fisher's exact test), Q value = 0.1

Table S93. Gene #54: 'Del Peak 30(12q12)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
DEL PEAK 30(12Q12) CNV	35	15	26
DEL PEAK 30(12Q12) WILD-TYPE	126	199	162

Figure S93. Get High-res Image Gene #54: 'Del Peak 30(12q12)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 31(12q15)' versus 'MRNA_CNMF'

P value = 0.000124 (Fisher's exact test), Q value = 0.074

Table S94. Gene #55: 'Del Peak 31(12q15)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	94	152	116
DEL PEAK 31(12Q15) CNV	20	21	7	21
DEL PEAK 31(12Q15) WILD-TYPE	127	73	145	95

Figure S94. Get High-res Image Gene #55: 'Del Peak 31(12q15)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 31(12q15)' versus 'CN_CNMF'

P value = 5.4e-07 (Fisher's exact test), Q value = 0.00035

Table S95. Gene #55: 'Del Peak 31(12q15)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
DEL PEAK 31(12Q15) CNV	40	12	25
DEL PEAK 31(12Q15) WILD-TYPE	121	202	163

Figure S95. Get High-res Image Gene #55: 'Del Peak 31(12q15)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 32(13q14.2)' versus 'MRNA_CNMF'

P value = 1.62e-07 (Fisher's exact test), Q value = 0.00011

Table S96. Gene #56: 'Del Peak 32(13q14.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	94	152	116
DEL PEAK 32(13Q14.2) CNV	81	43	36	55
DEL PEAK 32(13Q14.2) WILD-TYPE	66	51	116	61

Figure S96. Get High-res Image Gene #56: 'Del Peak 32(13q14.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 32(13q14.2)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000164 (Fisher's exact test), Q value = 0.097

Table S97. Gene #56: 'Del Peak 32(13q14.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	166	213
DEL PEAK 32(13Q14.2) CNV	35	77	103
DEL PEAK 32(13Q14.2) WILD-TYPE	95	89	110

Figure S97. Get High-res Image Gene #56: 'Del Peak 32(13q14.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 32(13q14.2)' versus 'CN_CNMF'

P value = 1.1e-15 (Fisher's exact test), Q value = 7.6e-13

Table S98. Gene #56: 'Del Peak 32(13q14.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
DEL PEAK 32(13Q14.2) CNV	100	46	90
DEL PEAK 32(13Q14.2) WILD-TYPE	61	168	98

Figure S98. Get High-res Image Gene #56: 'Del Peak 32(13q14.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 33(14q13.1)' versus 'MRNA_CNMF'

P value = 8.84e-06 (Fisher's exact test), Q value = 0.0055

Table S99. Gene #57: 'Del Peak 33(14q13.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	94	152	116
DEL PEAK 33(14Q13.1) CNV	55	37	25	46
DEL PEAK 33(14Q13.1) WILD-TYPE	92	57	127	70

Figure S99. Get High-res Image Gene #57: 'Del Peak 33(14q13.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 33(14q13.1)' versus 'CN_CNMF'

P value = 3.36e-30 (Fisher's exact test), Q value = 2.3e-27

Table S100. Gene #57: 'Del Peak 33(14q13.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
DEL PEAK 33(14Q13.1) CNV	104	20	51
DEL PEAK 33(14Q13.1) WILD-TYPE	57	194	137

Figure S100. Get High-res Image Gene #57: 'Del Peak 33(14q13.1)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 34(14q24.2)' versus 'MRNA_CNMF'

P value = 1.61e-07 (Fisher's exact test), Q value = 0.00011

Table S101. Gene #58: 'Del Peak 34(14q24.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	94	152	116
DEL PEAK 34(14Q24.2) CNV	52	40	22	48
DEL PEAK 34(14Q24.2) WILD-TYPE	95	54	130	68

Figure S101. Get High-res Image Gene #58: 'Del Peak 34(14q24.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 34(14q24.2)' versus 'CN_CNMF'

P value = 7.68e-39 (Fisher's exact test), Q value = 5.4e-36

Table S102. Gene #58: 'Del Peak 34(14q24.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
DEL PEAK 34(14Q24.2) CNV	107	11	52
DEL PEAK 34(14Q24.2) WILD-TYPE	54	203	136

Figure S102. Get High-res Image Gene #58: 'Del Peak 34(14q24.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 35(14q31.3)' versus 'MRNA_CNMF'

P value = 6.25e-09 (Fisher's exact test), Q value = 4.2e-06

Table S103. Gene #59: 'Del Peak 35(14q31.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	94	152	116
DEL PEAK 35(14Q31.3) CNV	52	36	16	44
DEL PEAK 35(14Q31.3) WILD-TYPE	95	58	136	72

Figure S103. Get High-res Image Gene #59: 'Del Peak 35(14q31.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 35(14q31.3)' versus 'CN_CNMF'

P value = 8.42e-41 (Fisher's exact test), Q value = 5.9e-38

Table S104. Gene #59: 'Del Peak 35(14q31.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
DEL PEAK 35(14Q31.3) CNV	102	6	48
DEL PEAK 35(14Q31.3) WILD-TYPE	59	208	140

Figure S104. Get High-res Image Gene #59: 'Del Peak 35(14q31.3)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 36(15q14)' versus 'MRNA_CNMF'

P value = 1.46e-06 (Fisher's exact test), Q value = 0.00093

Table S105. Gene #60: 'Del Peak 36(15q14)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	94	152	116
DEL PEAK 36(15Q14) CNV	35	37	22	46
DEL PEAK 36(15Q14) WILD-TYPE	112	57	130	70

Figure S105. Get High-res Image Gene #60: 'Del Peak 36(15q14)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 36(15q14)' versus 'MRNA_CHIERARCHICAL'

P value = 7.39e-08 (Fisher's exact test), Q value = 4.9e-05

Table S106. Gene #60: 'Del Peak 36(15q14)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	166	213
DEL PEAK 36(15Q14) CNV	16	69	55
DEL PEAK 36(15Q14) WILD-TYPE	114	97	158

Figure S106. Get High-res Image Gene #60: 'Del Peak 36(15q14)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 36(15q14)' versus 'MIR_CHIERARCHICAL'

P value = 1.31e-06 (Fisher's exact test), Q value = 0.00084

Table S107. Gene #60: 'Del Peak 36(15q14)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	179	130
DEL PEAK 36(15Q14) CNV	24	52	54
DEL PEAK 36(15Q14) WILD-TYPE	139	127	76

Figure S107. Get High-res Image Gene #60: 'Del Peak 36(15q14)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Del Peak 36(15q14)' versus 'CN_CNMF'

P value = 4.09e-07 (Fisher's exact test), Q value = 0.00026

Table S108. Gene #60: 'Del Peak 36(15q14)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
DEL PEAK 36(15Q14) CNV	69	39	43
DEL PEAK 36(15Q14) WILD-TYPE	92	175	145

Figure S108. Get High-res Image Gene #60: 'Del Peak 36(15q14)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 36(15q14)' versus 'MRNASEQ_CNMF'

P value = 0.000352 (Fisher's exact test), Q value = 0.21

Table S109. Gene #60: 'Del Peak 36(15q14)' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	67	36
DEL PEAK 36(15Q14) CNV	24	14	7
DEL PEAK 36(15Q14) WILD-TYPE	20	53	29

Figure S109. Get High-res Image Gene #60: 'Del Peak 36(15q14)' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'Del Peak 39(17p13.2)' versus 'CN_CNMF'

P value = 2e-10 (Fisher's exact test), Q value = 1.4e-07

Table S110. Gene #63: 'Del Peak 39(17p13.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
DEL PEAK 39(17P13.2) CNV	43	8	34
DEL PEAK 39(17P13.2) WILD-TYPE	118	206	154

Figure S110. Get High-res Image Gene #63: 'Del Peak 39(17p13.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 40(17p13.1)' versus 'MRNA_CNMF'

P value = 0.000167 (Fisher's exact test), Q value = 0.099

Table S111. Gene #64: 'Del Peak 40(17p13.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	94	152	116
DEL PEAK 40(17P13.1) CNV	32	27	13	16
DEL PEAK 40(17P13.1) WILD-TYPE	115	67	139	100

Figure S111. Get High-res Image Gene #64: 'Del Peak 40(17p13.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 40(17p13.1)' versus 'CN_CNMF'

P value = 1.42e-15 (Fisher's exact test), Q value = 9.8e-13

Table S112. Gene #64: 'Del Peak 40(17p13.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
DEL PEAK 40(17P13.1) CNV	53	6	36
DEL PEAK 40(17P13.1) WILD-TYPE	108	208	152

Figure S112. Get High-res Image Gene #64: 'Del Peak 40(17p13.1)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 41(17q11.2)' versus 'MRNA_CNMF'

P value = 7.43e-06 (Fisher's exact test), Q value = 0.0047

Table S113. Gene #65: 'Del Peak 41(17q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	94	152	116
DEL PEAK 41(17Q11.2) CNV	35	10	12	5
DEL PEAK 41(17Q11.2) WILD-TYPE	112	84	140	111

Figure S113. Get High-res Image Gene #65: 'Del Peak 41(17q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 41(17q11.2)' versus 'CN_CNMF'

P value = 5.32e-07 (Fisher's exact test), Q value = 0.00034

Table S114. Gene #65: 'Del Peak 41(17q11.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
DEL PEAK 41(17Q11.2) CNV	31	8	32
DEL PEAK 41(17Q11.2) WILD-TYPE	130	206	156

Figure S114. Get High-res Image Gene #65: 'Del Peak 41(17q11.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 43(19q13.41)' versus 'MRNA_CHIERARCHICAL'

P value = 1.23e-05 (Fisher's exact test), Q value = 0.0076

Table S115. Gene #67: 'Del Peak 43(19q13.41)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	166	213
DEL PEAK 43(19Q13.41) CNV	12	49	31
DEL PEAK 43(19Q13.41) WILD-TYPE	118	117	182

Figure S115. Get High-res Image Gene #67: 'Del Peak 43(19q13.41)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 44(21q22.3)' versus 'MIR_CNMF'

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

Table S116. Gene #68: 'Del Peak 44(21q22.3)' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	157	72	104
DEL PEAK 44(21Q22.3) CNV	8	32	8	5
DEL PEAK 44(21Q22.3) WILD-TYPE	131	125	64	99

Figure S116. Get High-res Image Gene #68: 'Del Peak 44(21q22.3)' versus Molecular Subtype #3: 'MIR_CNMF'

'Del Peak 46(Xp22.2)' versus 'CN_CNMF'

P value = 6.6e-10 (Fisher's exact test), Q value = 4.4e-07

Table S117. Gene #70: 'Del Peak 46(Xp22.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	214	188
DEL PEAK 46(XP22.2) CNV	65	29	29
DEL PEAK 46(XP22.2) WILD-TYPE	96	185	159

Figure S117. Get High-res Image Gene #70: 'Del Peak 46(Xp22.2)' versus Molecular Subtype #5: 'CN_CNMF'

Methods & Data

Input

Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
Molecular subtype file = GBM-TP.transferedmergedcluster.txt
Number of patients = 563
Number of copy number variation regions = 70
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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