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 12 molecular subtypes across 416 patients, 122 significant findings detected with Q value < 0.25.

Amp Peak 1(1p34.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 2(1q21.2) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 3(2p16.1) cnvs correlated to 'MRNA_CHIERARCHICAL', '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 12(7q21.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 15(9p24.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 18(12p13.33) cnvs correlated to 'CN_CNMF'.
Amp Peak 22(15q26.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 23(17q25.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 24(18p11.32) cnvs correlated to 'CN_CNMF'.
Amp Peak 25(18q11.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 26(19q12) cnvs correlated to 'CN_CNMF'.
Amp Peak 27(19q13.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 28(20p12.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 29(20q11.21) 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', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 2(1p13.1) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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'.
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' and 'MRNASEQ_CNMF'.
Del Peak 14(5q11.2) cnvs correlated to 'CN_CNMF'.
Del Peak 15(5q31.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 17(6q22.31) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 18(6q26) cnvs correlated to 'CN_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(9p21.1) cnvs correlated to 'CN_CNMF'.
Del Peak 25(9q21.11) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 26(10p15.3) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 27(10p15.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 28(10q23.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 29(11p15.5) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', and 'RPPA_CHIERARCHICAL'.
Del Peak 35(14q11.2) cnvs correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 40(17p11.2) cnvs correlated to 'CN_CNMF'.
Del Peak 41(17q11.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 42(17q25.3) cnvs correlated to 'CN_CNMF'.
Del Peak 44(19p13.3) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
Del Peak 45(19q13.33) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 46(19q13.43) cnvs correlated to 'CN_CNMF'.
Del Peak 48(21q22.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 50(22q13.32) cnvs correlated to 'MRNA_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 51(Xp22.2) cnvs correlated to 'CN_CNMF'.
Del Peak 52(Xp11.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 53(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 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 122 significant findings detected.


		Molecular subtypes	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
Del Peak 1(1p36 22)	0 (0%)	236	1.49e-06 (0.00144)	6.89e-08 (6.77e-05)	1.69e-26 (1.7e-23)	4.55e-15 (4.58e-12)	0.412 (1.00)	0.0262 (1.00)	8.67e-14 (8.69e-11)	9.45e-15 (9.48e-12)	0.000838 (0.721)	1.83e-05 (0.0172)	9.29e-06 (0.00877)	0.00595 (1.00)
Del Peak 25(9q21 11)	0 (0%)	217	8.38e-05 (0.077)	1.96e-05 (0.0183)	6.02e-10 (5.99e-07)	1.64e-06 (0.00158)	0.653 (1.00)	0.239 (1.00)	4.4e-09 (4.37e-06)	1.63e-09 (1.62e-06)	0.000958 (0.818)	0.000184 (0.166)	0.0172 (1.00)	0.000158 (0.143)
Del Peak 2(1p13 1)	0 (0%)	239	0.000956 (0.818)	6.31e-05 (0.0582)	4.33e-16 (4.36e-13)	5.81e-07 (0.000567)	0.0391 (1.00)	0.0673 (1.00)	2.33e-06 (0.00224)	6.91e-07 (0.000671)	0.0473 (1.00)	0.00022 (0.197)	1.59e-05 (0.0149)	0.0267 (1.00)
Del Peak 5(2q36 2)	0 (0%)	280	0.000141 (0.128)	4.34e-05 (0.0401)	6.14e-13 (6.15e-10)	1.12e-06 (0.00109)	0.177 (1.00)	0.126 (1.00)	6.61e-07 (0.000642)	2.98e-08 (2.95e-05)	0.885 (1.00)	0.163 (1.00)	3.47e-05 (0.0322)	0.272 (1.00)
Amp Peak 6(3q26 33)	0 (0%)	35	0.00118 (0.996)	3.91e-06 (0.00373)	3.55e-15 (3.57e-12)	2.84e-06 (0.00273)	0.141 (1.00)	0.0852 (1.00)	1.32e-06 (0.00128)	9.29e-05 (0.085)	0.218 (1.00)	4.12e-06 (0.00393)	0.0693 (1.00)	0.00343 (1.00)
Amp Peak 3(2p16 1)	0 (0%)	191	0.00212 (1.00)	0.000275 (0.244)	6.52e-14 (6.53e-11)	6.98e-06 (0.00662)	0.95 (1.00)	0.643 (1.00)	1.88e-05 (0.0176)	7.55e-05 (0.0695)	0.887 (1.00)	0.0171 (1.00)	0.0183 (1.00)	0.477 (1.00)
Del Peak 41(17q11 2)	0 (0%)	316	3.03e-05 (0.0281)	0.000101 (0.0923)	2.73e-09 (2.71e-06)	0.0107 (1.00)	0.495 (1.00)	0.378 (1.00)	1.48e-06 (0.00143)	4.83e-08 (4.75e-05)	0.143 (1.00)	0.0373 (1.00)	0.112 (1.00)	0.795 (1.00)
Amp Peak 4(2q31 2)	0 (0%)	277	0.0154 (1.00)	0.0275 (1.00)	6.32e-07 (0.000615)	3.95e-07 (0.000386)	0.724 (1.00)	0.887 (1.00)	0.000194 (0.174)	0.000248 (0.221)	0.37 (1.00)	0.511 (1.00)	0.0772 (1.00)	0.309 (1.00)
Del Peak 27(10p15 1)	0 (0%)	243	0.109 (1.00)	0.633 (1.00)	0.000162 (0.146)	2.68e-05 (0.0249)	0.469 (1.00)	0.353 (1.00)	0.000161 (0.145)	0.00143 (1.00)	0.0107 (1.00)	9.09e-06 (0.00859)	0.00157 (1.00)	0.0151 (1.00)
Del Peak 28(10q23 31)	0 (0%)	200	0.0148 (1.00)	0.0131 (1.00)	1.64e-05 (0.0154)	6.74e-06 (0.0064)	0.36 (1.00)	0.39 (1.00)	8.54e-06 (0.00808)	7.23e-07 (0.000701)	0.219 (1.00)	0.0644 (1.00)	0.116 (1.00)	0.543 (1.00)
Amp Peak 2(1q21 2)	0 (0%)	203	0.0448 (1.00)	0.0304 (1.00)	1.8e-08 (1.78e-05)	0.0043 (1.00)	0.16 (1.00)	0.0492 (1.00)	1.87e-05 (0.0175)	4.11e-05 (0.0381)	0.0393 (1.00)	0.00181 (1.00)	0.00803 (1.00)	0.273 (1.00)
Amp Peak 12(7q21 2)	0 (0%)	198	0.175 (1.00)	0.116 (1.00)	1.34e-11 (1.34e-08)	4.52e-06 (0.00431)	0.0573 (1.00)	0.389 (1.00)	0.000661 (0.573)	0.000185 (0.167)	0.0358 (1.00)	0.0527 (1.00)	0.0112 (1.00)	0.0121 (1.00)
Amp Peak 23(17q25 1)	0 (0%)	219	0.0133 (1.00)	0.0338 (1.00)	7.84e-09 (7.77e-06)	5.4e-05 (0.0498)	0.479 (1.00)	0.249 (1.00)	0.00285 (1.00)	9.13e-05 (0.0837)	0.772 (1.00)	0.0601 (1.00)	0.0455 (1.00)	0.154 (1.00)
Del Peak 29(11p15 5)	0 (0%)	226	0.000261 (0.231)	0.0341 (1.00)	4.67e-06 (0.00445)	0.023 (1.00)	0.000764 (0.659)	2.02e-05 (0.0189)	0.00293 (1.00)	0.031 (1.00)	0.00193 (1.00)	0.0459 (1.00)	0.0485 (1.00)	0.307 (1.00)
Amp Peak 22(15q26 3)	0 (0%)	273	0.253 (1.00)	0.0414 (1.00)	1.93e-06 (0.00186)	1.56e-05 (0.0147)	0.354 (1.00)	0.0183 (1.00)	0.000334 (0.294)	0.00253 (1.00)	0.0159 (1.00)	0.00123 (1.00)	0.00291 (1.00)	0.0151 (1.00)
Amp Peak 25(18q11 2)	0 (0%)	286	0.000339 (0.299)	0.0146 (1.00)	1.06e-07 (0.000104)	0.000618 (0.537)	0.272 (1.00)	0.74 (1.00)	0.000841 (0.723)	5.04e-06 (0.00479)	0.402 (1.00)	0.00539 (1.00)	0.00133 (1.00)	0.0819 (1.00)
Del Peak 13(4q35 2)	0 (0%)	146	0.0987 (1.00)	0.396 (1.00)	1.83e-07 (0.00018)	0.000424 (0.371)	0.455 (1.00)	0.47 (1.00)	0.000143 (0.13)	0.0105 (1.00)	0.44 (1.00)	0.0957 (1.00)	0.00104 (0.887)	0.288 (1.00)
Del Peak 15(5q31 1)	0 (0%)	94	0.273 (1.00)	0.47 (1.00)	1.56e-10 (1.56e-07)	8.05e-05 (0.074)	0.272 (1.00)	0.166 (1.00)	0.0582 (1.00)	0.0639 (1.00)	0.684 (1.00)	0.00713 (1.00)	0.12 (1.00)	0.115 (1.00)
Del Peak 17(6q22 31)	0 (0%)	314	0.0278 (1.00)	0.0123 (1.00)	9.32e-05 (0.0852)	0.00145 (1.00)	0.629 (1.00)	0.354 (1.00)	0.000249 (0.222)	0.000587 (0.51)	0.374 (1.00)	0.218 (1.00)	0.596 (1.00)	0.0427 (1.00)
Del Peak 26(10p15 3)	0 (0%)	231	0.318 (1.00)	0.493 (1.00)	4.61e-05 (0.0426)	0.000476 (0.416)	0.329 (1.00)	0.443 (1.00)	0.00156 (1.00)	0.000554 (0.482)	0.0549 (1.00)	4.45e-05 (0.0412)	0.00213 (1.00)	0.0295 (1.00)
Del Peak 35(14q11 2)	0 (0%)	273	0.0724 (1.00)	0.237 (1.00)	0.0692 (1.00)	0.438 (1.00)	0.206 (1.00)	0.159 (1.00)	0.000386 (0.339)	9.8e-05 (0.0894)	0.183 (1.00)	0.493 (1.00)	0.0223 (1.00)	0.000203 (0.182)
Del Peak 44(19p13 3)	0 (0%)	236	0.206 (1.00)	0.00433 (1.00)	2.55e-05 (0.0237)	0.209 (1.00)	0.0588 (1.00)	0.251 (1.00)	0.284 (1.00)	0.0283 (1.00)	0.000224 (0.2)	0.00297 (1.00)	0.237 (1.00)	0.0314 (1.00)
Del Peak 45(19q13 33)	0 (0%)	307	0.525 (1.00)	0.212 (1.00)	1.01e-06 (0.000979)	9.24e-05 (0.0846)	0.244 (1.00)	0.719 (1.00)	0.0819 (1.00)	0.0398 (1.00)	0.0341 (1.00)	0.334 (1.00)	0.148 (1.00)	0.65 (1.00)
Del Peak 48(21q22 3)	0 (0%)	184	0.876 (1.00)	0.189 (1.00)	1.82e-08 (1.8e-05)	0.000126 (0.114)	0.396 (1.00)	0.0991 (1.00)	0.13 (1.00)	0.0131 (1.00)	0.0589 (1.00)	0.161 (1.00)	0.0433 (1.00)	0.851 (1.00)
Del Peak 50(22q13 32)	0 (0%)	319	0.00022 (0.197)	0.00221 (1.00)	0.19 (1.00)	0.414 (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)	0.0194 (1.00)	0.000155 (0.141)
Del Peak 52(Xp11 3)	0 (0%)	287	0.11 (1.00)	0.414 (1.00)	2.49e-06 (0.00239)	1.46e-05 (0.0137)	0.0923 (1.00)	0.124 (1.00)	0.0631 (1.00)	0.00391 (1.00)	0.131 (1.00)	0.138 (1.00)	0.00181 (1.00)	0.125 (1.00)
Del Peak 53(Xq22 3)	0 (0%)	316	0.00842 (1.00)	0.015 (1.00)	3.76e-08 (3.71e-05)	0.000179 (0.161)	0.663 (1.00)	0.92 (1.00)	0.0422 (1.00)	0.438 (1.00)	0.276 (1.00)	0.797 (1.00)	0.0408 (1.00)	0.331 (1.00)
Amp Peak 1(1p34 2)	0 (0%)	349	0.0264 (1.00)	0.231 (1.00)	2.57e-07 (0.000252)	0.273 (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)	0.341 (1.00)	0.0594 (1.00)
Amp Peak 8(5p15 33)	0 (0%)	87	0.852 (1.00)	0.983 (1.00)	3.61e-06 (0.00345)	0.00694 (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)	1 (1.00)	0.902 (1.00)
Amp Peak 9(5p12)	0 (0%)	145	0.961 (1.00)	0.857 (1.00)	6.93e-09 (6.86e-06)	0.0036 (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)	0.104 (1.00)	0.0258 (1.00)
Amp Peak 15(9p24 1)	0 (0%)	342	0.188 (1.00)	0.0431 (1.00)	0.000198 (0.178)	0.278 (1.00)	0.0017 (1.00)	0.00501 (1.00)	0.00699 (1.00)	0.000767 (0.661)	0.117 (1.00)	0.0167 (1.00)	0.429 (1.00)	0.197 (1.00)
Amp Peak 18(12p13 33)	0 (0%)	210	0.0263 (1.00)	0.0936 (1.00)	3.83e-06 (0.00366)	0.00104 (0.886)	0.313 (1.00)	0.729 (1.00)	0.000418 (0.368)	0.0103 (1.00)	0.837 (1.00)	0.218 (1.00)	0.0123 (1.00)	0.37 (1.00)
Amp Peak 24(18p11 32)	0 (0%)	272	0.0831 (1.00)	0.021 (1.00)	2.88e-06 (0.00276)	0.00072 (0.622)	0.231 (1.00)	0.451 (1.00)	0.131 (1.00)	0.0402 (1.00)	0.898 (1.00)	0.0209 (1.00)	0.0353 (1.00)	0.69 (1.00)
Amp Peak 26(19q12)	0 (0%)	243	0.438 (1.00)	0.693 (1.00)	4.94e-06 (0.0047)	0.189 (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)	0.0616 (1.00)	0.51 (1.00)
Amp Peak 27(19q13 2)	0 (0%)	239	0.678 (1.00)	0.86 (1.00)	0.00025 (0.222)	0.101 (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)	0.302 (1.00)	0.574 (1.00)
Amp Peak 28(20p12 2)	0 (0%)	193	0.00106 (0.898)	0.0142 (1.00)	6.62e-09 (6.57e-06)	0.000419 (0.368)	0.967 (1.00)	0.221 (1.00)	0.0408 (1.00)	0.00273 (1.00)	0.259 (1.00)	0.0945 (1.00)	0.172 (1.00)	0.551 (1.00)
Amp Peak 29(20q11 21)	0 (0%)	175	0.86 (1.00)	0.948 (1.00)	0.000192 (0.173)	0.0234 (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)	0.228 (1.00)	0.937 (1.00)
Del Peak 4(2q22 1)	0 (0%)	309	0.208 (1.00)	0.245 (1.00)	0.000112 (0.102)	0.0327 (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)	0.000892 (0.765)	0.779 (1.00)
Del Peak 7(3p13)	0 (0%)	61	0.304 (1.00)	0.987 (1.00)	6.21e-07 (0.000605)	0.000609 (0.529)	0.882 (1.00)	0.0379 (1.00)	0.0756 (1.00)	0.0171 (1.00)	0.432 (1.00)	0.00134 (1.00)	0.1 (1.00)	0.0425 (1.00)
Del Peak 8(3p12 3)	0 (0%)	70	0.164 (1.00)	0.954 (1.00)	1.47e-05 (0.0138)	0.0019 (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)	0.116 (1.00)	0.246 (1.00)
Del Peak 10(4p15 2)	0 (0%)	165	0.000325 (0.287)	0.00153 (1.00)	4.09e-07 (4e-04)	0.00088 (0.755)	0.662 (1.00)	0.0343 (1.00)	0.0138 (1.00)	0.00689 (1.00)	0.302 (1.00)	0.864 (1.00)	0.00495 (1.00)	0.412 (1.00)
Del Peak 11(4q22 1)	0 (0%)	188	0.00688 (1.00)	0.0456 (1.00)	1.43e-06 (0.00138)	0.0173 (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)	0.00308 (1.00)	0.571 (1.00)
Del Peak 12(4q32 3)	0 (0%)	152	0.0113 (1.00)	0.0203 (1.00)	3.01e-08 (2.96e-05)	0.00238 (1.00)	0.101 (1.00)	0.523 (1.00)	0.0012 (1.00)	0.00455 (1.00)	0.663 (1.00)	0.242 (1.00)	0.0101 (1.00)	0.317 (1.00)
Del Peak 14(5q11 2)	0 (0%)	111	0.706 (1.00)	0.656 (1.00)	2.04e-12 (2.04e-09)	0.000313 (0.277)	0.959 (1.00)	0.244 (1.00)	0.0104 (1.00)	0.0858 (1.00)	0.987 (1.00)	0.00113 (0.958)	0.232 (1.00)	0.139 (1.00)
Del Peak 18(6q26)	0 (0%)	306	0.0421 (1.00)	0.0154 (1.00)	0.000219 (0.196)	0.00116 (0.982)	0.921 (1.00)	0.69 (1.00)	0.00204 (1.00)	0.00223 (1.00)	0.184 (1.00)	0.085 (1.00)	0.138 (1.00)	0.23 (1.00)
Del Peak 19(7q11 22)	0 (0%)	377	0.802 (1.00)	0.106 (1.00)	6.68e-05 (0.0615)	0.687 (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)	0.4 (1.00)	0.886 (1.00)
Del Peak 22(9p23)	0 (0%)	143	0.0103 (1.00)	0.00676 (1.00)	2.72e-10 (2.71e-07)	0.0448 (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)	0.125 (1.00)	0.043 (1.00)
Del Peak 23(9p21 3)	0 (0%)	98	0.326 (1.00)	0.311 (1.00)	1.46e-07 (0.000143)	0.325 (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)	0.337 (1.00)	0.241 (1.00)
Del Peak 24(9p21 1)	0 (0%)	148	0.121 (1.00)	0.0364 (1.00)	8.75e-08 (8.59e-05)	0.1 (1.00)	0.673 (1.00)	0.391 (1.00)	0.0177 (1.00)	0.204 (1.00)	0.0873 (1.00)	0.0938 (1.00)	0.653 (1.00)	0.16 (1.00)
Del Peak 40(17p11 2)	0 (0%)	202	0.217 (1.00)	0.0324 (1.00)	0.000167 (0.15)	0.102 (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)	0.32 (1.00)	0.0761 (1.00)
Del Peak 42(17q25 3)	0 (0%)	333	0.0046 (1.00)	0.015 (1.00)	1.43e-05 (0.0135)	0.0983 (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)	0.348 (1.00)	0.814 (1.00)
Del Peak 46(19q13 43)	0 (0%)	309	0.619 (1.00)	0.491 (1.00)	8.08e-06 (0.00765)	0.000848 (0.728)	0.446 (1.00)	0.543 (1.00)	0.0902 (1.00)	0.02 (1.00)	0.077 (1.00)	0.437 (1.00)	0.477 (1.00)	0.607 (1.00)
Del Peak 51(Xp22 2)	0 (0%)	285	0.636 (1.00)	0.51 (1.00)	3.12e-05 (0.0289)	0.0174 (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)	0.0509 (1.00)	0.241 (1.00)
Amp Peak 5(3p11 1)	0 (0%)	332	0.104 (1.00)	0.836 (1.00)	0.863 (1.00)	0.788 (1.00)	0.214 (1.00)	0.0013 (1.00)	0.239 (1.00)	0.541 (1.00)	0.845 (1.00)	0.602 (1.00)	0.339 (1.00)	0.0999 (1.00)
Amp Peak 7(4q12)	0 (0%)	318	0.809 (1.00)	0.2 (1.00)	0.00214 (1.00)	0.118 (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)	0.069 (1.00)	0.149 (1.00)
Amp Peak 10(6p12 1)	0 (0%)	281	0.551 (1.00)	0.737 (1.00)	0.000939 (0.804)	0.385 (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)	0.0885 (1.00)	0.0596 (1.00)
Amp Peak 11(7p11 2)	0 (0%)	214	0.164 (1.00)	0.0996 (1.00)	0.000543 (0.474)	0.00576 (1.00)	0.687 (1.00)	0.801 (1.00)	0.0273 (1.00)	0.000542 (0.474)	0.634 (1.00)	0.0644 (1.00)	0.276 (1.00)	0.164 (1.00)
Amp Peak 13(8p11 23)	0 (0%)	223	0.0137 (1.00)	0.467 (1.00)	0.157 (1.00)	0.0813 (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)	0.862 (1.00)	0.664 (1.00)
Amp Peak 14(8q24 21)	0 (0%)	125	0.919 (1.00)	0.788 (1.00)	0.226 (1.00)	0.91 (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)	0.887 (1.00)	0.925 (1.00)
Amp Peak 16(9p13 3)	0 (0%)	301	0.23 (1.00)	0.641 (1.00)	0.00415 (1.00)	0.116 (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)	0.197 (1.00)	0.628 (1.00)
Amp Peak 17(11q13 3)	0 (0%)	265	0.0582 (1.00)	0.0872 (1.00)	0.00348 (1.00)	0.000474 (0.415)	0.19 (1.00)	0.0358 (1.00)	0.0123 (1.00)	0.124 (1.00)	0.0454 (1.00)	0.00669 (1.00)	0.00124 (1.00)	0.403 (1.00)
Amp Peak 19(12q15)	0 (0%)	270	0.235 (1.00)	0.326 (1.00)	0.00174 (1.00)	0.00255 (1.00)	0.764 (1.00)	0.524 (1.00)	0.0588 (1.00)	0.0807 (1.00)	1 (1.00)	0.437 (1.00)	0.0316 (1.00)	0.593 (1.00)
Amp Peak 20(13q34)	0 (0%)	342	0.981 (1.00)	0.0207 (1.00)	0.138 (1.00)	0.533 (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)	0.222 (1.00)	0.794 (1.00)
Amp Peak 21(14q13 3)	0 (0%)	286	0.316 (1.00)	0.194 (1.00)	0.108 (1.00)	0.147 (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)	0.204 (1.00)	0.00575 (1.00)
Amp Peak 30(22q11 21)	0 (0%)	210	0.141 (1.00)	0.204 (1.00)	0.00184 (1.00)	0.000296 (0.262)	0.888 (1.00)	0.349 (1.00)	0.0104 (1.00)	0.0345 (1.00)	0.751 (1.00)	0.027 (1.00)	0.666 (1.00)	0.852 (1.00)
Amp Peak 31(Xq28)	0 (0%)	307	0.793 (1.00)	0.71 (1.00)	0.0894 (1.00)	0.215 (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)	0.073 (1.00)	0.128 (1.00)
Del Peak 3(2p25 3)	0 (0%)	377	0.0858 (1.00)	0.0152 (1.00)	0.394 (1.00)	0.424 (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)	0.123 (1.00)	0.311 (1.00)
Del Peak 6(3p25 3)	0 (0%)	88	0.674 (1.00)	0.63 (1.00)	0.0138 (1.00)	0.00194 (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)	0.533 (1.00)	0.302 (1.00)
Del Peak 9(3q11 1)	0 (0%)	355	0.762 (1.00)	0.625 (1.00)	0.122 (1.00)	0.259 (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)	0.938 (1.00)	0.385 (1.00)
Del Peak 16(6p25 3)	0 (0%)	313	0.319 (1.00)	0.0462 (1.00)	0.0212 (1.00)	0.000974 (0.831)	0.393 (1.00)	0.013 (1.00)	0.00219 (1.00)	0.000305 (0.27)	0.179 (1.00)	0.0797 (1.00)	0.438 (1.00)	0.0956 (1.00)
Del Peak 20(7q36 3)	0 (0%)	332	0.17 (1.00)	0.131 (1.00)	0.000708 (0.612)	0.178 (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)	0.0247 (1.00)	0.0251 (1.00)
Del Peak 21(8p23 2)	0 (0%)	134	0.667 (1.00)	0.847 (1.00)	0.000531 (0.464)	0.206 (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)	0.117 (1.00)	0.469 (1.00)
Del Peak 30(11q22 1)	0 (0%)	290	0.708 (1.00)	0.379 (1.00)	0.00114 (0.966)	0.0101 (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)	0.727 (1.00)	0.411 (1.00)
Del Peak 31(11q25)	0 (0%)	264	0.874 (1.00)	0.578 (1.00)	0.00925 (1.00)	0.273 (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)	0.622 (1.00)	0.684 (1.00)
Del Peak 32(12q24 32)	0 (0%)	344	0.467 (1.00)	0.266 (1.00)	0.717 (1.00)	0.954 (1.00)	0.396 (1.00)	0.597 (1.00)	0.944 (1.00)	0.895 (1.00)	0.472 (1.00)	0.803 (1.00)	0.971 (1.00)	0.464 (1.00)
Del Peak 33(13q12 11)	0 (0%)	143	0.104 (1.00)	0.463 (1.00)	0.0231 (1.00)	0.18 (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)	0.964 (1.00)	0.0516 (1.00)
Del Peak 34(13q14 2)	0 (0%)	134	0.0997 (1.00)	0.321 (1.00)	0.00111 (0.939)	0.0629 (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)	0.392 (1.00)	0.0294 (1.00)
Del Peak 36(15q12)	0 (0%)	280	0.47 (1.00)	0.469 (1.00)	0.468 (1.00)	0.142 (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)	0.102 (1.00)	0.357 (1.00)
Del Peak 37(15q21 1)	0 (0%)	287	0.382 (1.00)	0.415 (1.00)	0.498 (1.00)	0.71 (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)	0.00528 (1.00)	0.286 (1.00)
Del Peak 38(16p13 3)	0 (0%)	263	0.348 (1.00)	0.339 (1.00)	0.00958 (1.00)	0.145 (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)	0.438 (1.00)	0.0287 (1.00)
Del Peak 39(16q23 1)	0 (0%)	243	0.874 (1.00)	0.336 (1.00)	0.218 (1.00)	0.145 (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)	0.0464 (1.00)	0.393 (1.00)
Del Peak 43(18q23)	0 (0%)	230	0.454 (1.00)	0.217 (1.00)	0.0441 (1.00)	0.961 (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)	0.937 (1.00)	0.332 (1.00)
Del Peak 47(21q21 1)	0 (0%)	218	0.571 (1.00)	0.395 (1.00)	0.000633 (0.548)	0.00268 (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)	0.0195 (1.00)	0.048 (1.00)
Del Peak 49(22q11 21)	0 (0%)	346	0.0298 (1.00)	0.16 (1.00)	0.173 (1.00)	0.123 (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)	0.304 (1.00)	0.383 (1.00)

'Amp Peak 1(1p34.2)' versus 'CN_CNMF'

P value = 2.57e-07 (Fisher's exact test), Q value = 0.00025

Table S1. Gene #1: 'Amp Peak 1(1p34.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
AMP PEAK 1(1P34.2) CNV	18	7	42
AMP PEAK 1(1P34.2) WILD-TYPE	132	117	100

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1p34.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

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

Table S2. Gene #2: 'Amp Peak 2(1q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
AMP PEAK 2(1Q21.2) CNV	63	91	59
AMP PEAK 2(1Q21.2) WILD-TYPE	87	33	83

Figure S2. 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 = 0.018

Table S3. 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 S3. 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 = 0.038

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

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

P value = 0.000275 (Fisher's exact test), Q value = 0.24

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	22	56	23	53
AMP PEAK 3(2P16.1) CNV	7	42	15	22
AMP PEAK 3(2P16.1) WILD-TYPE	15	14	8	31

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

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

P value = 6.52e-14 (Fisher's exact test), Q value = 6.5e-11

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
AMP PEAK 3(2P16.1) CNV	55	101	69
AMP PEAK 3(2P16.1) WILD-TYPE	95	23	73

Figure S6. 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 = 6.98e-06 (Fisher's exact test), Q value = 0.0066

Table S7. Gene #3: 'Amp Peak 3(2p16.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	82	72
AMP PEAK 3(2P16.1) CNV	43	62	30
AMP PEAK 3(2P16.1) WILD-TYPE	53	20	42

Figure S7. 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 = 0.018

Table S8. 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 S8. 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 = 0.069

Table S9. 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 S9. 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 = 6.32e-07 (Fisher's exact test), Q value = 0.00061

Table S10. Gene #4: 'Amp Peak 4(2q31.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
AMP PEAK 4(2Q31.2) CNV	32	64	43
AMP PEAK 4(2Q31.2) WILD-TYPE	118	60	99

Figure S10. 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 = 3.95e-07 (Fisher's exact test), Q value = 0.00039

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	82	72
AMP PEAK 4(2Q31.2) CNV	24	47	14
AMP PEAK 4(2Q31.2) WILD-TYPE	72	35	58

Figure S11. 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 = 0.17

Table S12. 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 S12. 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 = 0.22

Table S13. 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 S13. 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 = 3.91e-06 (Fisher's exact test), Q value = 0.0037

Table S14. Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	22	56	23	53
AMP PEAK 6(3Q26.33) CNV	14	56	20	51
AMP PEAK 6(3Q26.33) WILD-TYPE	8	0	3	2

Figure S14. 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 = 3.55e-15 (Fisher's exact test), Q value = 3.6e-12

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
AMP PEAK 6(3Q26.33) CNV	116	124	141
AMP PEAK 6(3Q26.33) WILD-TYPE	34	0	1

Figure S15. 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 = 2.84e-06 (Fisher's exact test), Q value = 0.0027

Table S16. Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	82	72
AMP PEAK 6(3Q26.33) CNV	78	82	69
AMP PEAK 6(3Q26.33) WILD-TYPE	18	0	3

Figure S16. 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 = 1.32e-06 (Fisher's exact test), Q value = 0.0013

Table S17. 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	101	42
AMP PEAK 6(3Q26.33) WILD-TYPE	4	0	10	13

Figure S17. 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 = 9.29e-05 (Fisher's exact test), Q value = 0.085

Table S18. 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	148
AMP PEAK 6(3Q26.33) WILD-TYPE	0	7	20

Figure S18. 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 = 4.12e-06 (Fisher's exact test), Q value = 0.0039

Table S19. 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	156	73
AMP PEAK 6(3Q26.33) WILD-TYPE	2	25	0

Figure S19. 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 = 3.61e-06 (Fisher's exact test), Q value = 0.0035

Table S20. Gene #8: 'Amp Peak 8(5p15.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
AMP PEAK 8(5P15.33) CNV	103	96	130
AMP PEAK 8(5P15.33) WILD-TYPE	47	28	12

Figure S20. 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 = 6.93e-09 (Fisher's exact test), Q value = 6.9e-06

Table S21. Gene #9: 'Amp Peak 9(5p12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
AMP PEAK 9(5P12) CNV	73	81	117
AMP PEAK 9(5P12) WILD-TYPE	77	43	25

Figure S21. Get High-res Image Gene #9: 'Amp Peak 9(5p12)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 1.34e-11 (Fisher's exact test), Q value = 1.3e-08

Table S22. Gene #12: 'Amp Peak 12(7q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
AMP PEAK 12(7Q21.2) CNV	52	95	71
AMP PEAK 12(7Q21.2) WILD-TYPE	98	29	71

Figure S22. Get High-res Image Gene #12: 'Amp Peak 12(7q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 4.52e-06 (Fisher's exact test), Q value = 0.0043

Table S23. Gene #12: 'Amp Peak 12(7q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	82	72
AMP PEAK 12(7Q21.2) CNV	33	58	32
AMP PEAK 12(7Q21.2) WILD-TYPE	63	24	40

Figure S23. Get High-res Image Gene #12: 'Amp Peak 12(7q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 0.000185 (Fisher's exact test), Q value = 0.17

Table S24. Gene #12: 'Amp Peak 12(7q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	70	168
AMP PEAK 12(7Q21.2) CNV	74	33	75
AMP PEAK 12(7Q21.2) WILD-TYPE	33	37	93

Figure S24. Get High-res Image Gene #12: 'Amp Peak 12(7q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 15(9p24.1)' versus 'CN_CNMF'

P value = 0.000198 (Fisher's exact test), Q value = 0.18

Table S25. Gene #15: 'Amp Peak 15(9p24.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
AMP PEAK 15(9P24.1) CNV	28	34	12
AMP PEAK 15(9P24.1) WILD-TYPE	122	90	130

Figure S25. Get High-res Image Gene #15: 'Amp Peak 15(9p24.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 18(12p13.33)' versus 'CN_CNMF'

P value = 3.83e-06 (Fisher's exact test), Q value = 0.0037

Table S26. Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
AMP PEAK 18(12P13.33) CNV	54	82	70
AMP PEAK 18(12P13.33) WILD-TYPE	96	42	72

Figure S26. Get High-res Image Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 22(15q26.3)' versus 'CN_CNMF'

P value = 1.93e-06 (Fisher's exact test), Q value = 0.0019

Table S27. Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
AMP PEAK 22(15Q26.3) CNV	31	62	50
AMP PEAK 22(15Q26.3) WILD-TYPE	119	62	92

Figure S27. Get High-res Image Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 22(15q26.3)' versus 'METHLYATION_CNMF'

P value = 1.56e-05 (Fisher's exact test), Q value = 0.015

Table S28. Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	82	72
AMP PEAK 22(15Q26.3) CNV	16	40	27
AMP PEAK 22(15Q26.3) WILD-TYPE	80	42	45

Figure S28. Get High-res Image Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 23(17q25.1)' versus 'CN_CNMF'

P value = 7.84e-09 (Fisher's exact test), Q value = 7.8e-06

Table S29. Gene #23: 'Amp Peak 23(17q25.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
AMP PEAK 23(17Q25.1) CNV	48	85	64
AMP PEAK 23(17Q25.1) WILD-TYPE	102	39	78

Figure S29. Get High-res Image Gene #23: 'Amp Peak 23(17q25.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 23(17q25.1)' versus 'METHLYATION_CNMF'

P value = 5.4e-05 (Fisher's exact test), Q value = 0.05

Table S30. Gene #23: 'Amp Peak 23(17q25.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	82	72
AMP PEAK 23(17Q25.1) CNV	32	53	27
AMP PEAK 23(17Q25.1) WILD-TYPE	64	29	45

Figure S30. Get High-res Image Gene #23: 'Amp Peak 23(17q25.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 23(17q25.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.13e-05 (Fisher's exact test), Q value = 0.084

Table S31. Gene #23: 'Amp Peak 23(17q25.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	70	168
AMP PEAK 23(17Q25.1) CNV	66	32	59
AMP PEAK 23(17Q25.1) WILD-TYPE	41	38	109

Figure S31. Get High-res Image Gene #23: 'Amp Peak 23(17q25.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 24(18p11.32)' versus 'CN_CNMF'

P value = 2.88e-06 (Fisher's exact test), Q value = 0.0028

Table S32. Gene #24: 'Amp Peak 24(18p11.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
AMP PEAK 24(18P11.32) CNV	36	65	43
AMP PEAK 24(18P11.32) WILD-TYPE	114	59	99

Figure S32. Get High-res Image Gene #24: 'Amp Peak 24(18p11.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 25(18q11.2)' versus 'CN_CNMF'

P value = 1.06e-07 (Fisher's exact test), Q value = 1e-04

Table S33. Gene #25: 'Amp Peak 25(18q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
AMP PEAK 25(18Q11.2) CNV	26	61	43
AMP PEAK 25(18Q11.2) WILD-TYPE	124	63	99

Figure S33. Get High-res Image Gene #25: 'Amp Peak 25(18q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 25(18q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.04e-06 (Fisher's exact test), Q value = 0.0048

Table S34. Gene #25: 'Amp Peak 25(18q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	70	168
AMP PEAK 25(18Q11.2) CNV	46	31	32
AMP PEAK 25(18Q11.2) WILD-TYPE	61	39	136

Figure S34. Get High-res Image Gene #25: 'Amp Peak 25(18q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 26(19q12)' versus 'CN_CNMF'

P value = 4.94e-06 (Fisher's exact test), Q value = 0.0047

Table S35. Gene #26: 'Amp Peak 26(19q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
AMP PEAK 26(19Q12) CNV	47	74	52
AMP PEAK 26(19Q12) WILD-TYPE	103	50	90

Figure S35. Get High-res Image Gene #26: 'Amp Peak 26(19q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 27(19q13.2)' versus 'CN_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.22

Table S36. Gene #27: 'Amp Peak 27(19q13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
AMP PEAK 27(19Q13.2) CNV	50	71	56
AMP PEAK 27(19Q13.2) WILD-TYPE	100	53	86

Figure S36. Get High-res Image Gene #27: 'Amp Peak 27(19q13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 28(20p12.2)' versus 'CN_CNMF'

P value = 6.62e-09 (Fisher's exact test), Q value = 6.6e-06

Table S37. Gene #28: 'Amp Peak 28(20p12.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
AMP PEAK 28(20P12.2) CNV	55	91	77
AMP PEAK 28(20P12.2) WILD-TYPE	95	33	65

Figure S37. Get High-res Image Gene #28: 'Amp Peak 28(20p12.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 29(20q11.21)' versus 'CN_CNMF'

P value = 0.000192 (Fisher's exact test), Q value = 0.17

Table S38. Gene #29: 'Amp Peak 29(20q11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
AMP PEAK 29(20Q11.21) CNV	67	83	91
AMP PEAK 29(20Q11.21) WILD-TYPE	83	41	51

Figure S38. Get High-res Image Gene #29: 'Amp Peak 29(20q11.21)' versus Molecular Subtype #3: 'CN_CNMF'

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

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

Table S39. Gene #32: 'Del Peak 1(1p36.22)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	52	32	28
DEL PEAK 1(1P36.22) CNV	9	38	14	8
DEL PEAK 1(1P36.22) WILD-TYPE	33	14	18	20

Figure S39. Get High-res Image Gene #32: 'Del Peak 1(1p36.22)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

P value = 6.89e-08 (Fisher's exact test), Q value = 6.8e-05

Table S40. Gene #32: 'Del Peak 1(1p36.22)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	22	56	23	53
DEL PEAK 1(1P36.22) CNV	8	42	8	11
DEL PEAK 1(1P36.22) WILD-TYPE	14	14	15	42

Figure S40. Get High-res Image Gene #32: 'Del Peak 1(1p36.22)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

P value = 1.69e-26 (Fisher's exact test), Q value = 1.7e-23

Table S41. Gene #32: 'Del Peak 1(1p36.22)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
DEL PEAK 1(1P36.22) CNV	40	103	37
DEL PEAK 1(1P36.22) WILD-TYPE	110	21	105

Figure S41. Get High-res Image Gene #32: 'Del Peak 1(1p36.22)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 4.55e-15 (Fisher's exact test), Q value = 4.6e-12

Table S42. Gene #32: 'Del Peak 1(1p36.22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	82	72
DEL PEAK 1(1P36.22) CNV	16	61	23
DEL PEAK 1(1P36.22) WILD-TYPE	80	21	49

Figure S42. Get High-res Image Gene #32: '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 = 8.7e-11

Table S43. Gene #32: '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 S43. Get High-res Image Gene #32: '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 = 9.5e-12

Table S44. Gene #32: '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 S44. Get High-res Image Gene #32: '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 = 0.017

Table S45. Gene #32: '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 S45. Get High-res Image Gene #32: 'Del Peak 1(1p36.22)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 9.29e-06 (Fisher's exact test), Q value = 0.0088

Table S46. Gene #32: 'Del Peak 1(1p36.22)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	72	41
DEL PEAK 1(1P36.22) CNV	44	20	30
DEL PEAK 1(1P36.22) WILD-TYPE	74	52	11

Figure S46. Get High-res Image Gene #32: 'Del Peak 1(1p36.22)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 6.31e-05 (Fisher's exact test), Q value = 0.058

Table S47. Gene #33: 'Del Peak 2(1p13.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S47. Get High-res Image Gene #33: 'Del Peak 2(1p13.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

P value = 4.33e-16 (Fisher's exact test), Q value = 4.4e-13

Table S48. Gene #33: 'Del Peak 2(1p13.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
DEL PEAK 2(1P13.1) CNV	36	90	51
DEL PEAK 2(1P13.1) WILD-TYPE	114	34	91

Figure S48. Get High-res Image Gene #33: 'Del Peak 2(1p13.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 5.81e-07 (Fisher's exact test), Q value = 0.00057

Table S49. Gene #33: 'Del Peak 2(1p13.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	82	72
DEL PEAK 2(1P13.1) CNV	21	50	27
DEL PEAK 2(1P13.1) WILD-TYPE	75	32	45

Figure S49. Get High-res Image Gene #33: 'Del Peak 2(1p13.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 2.33e-06 (Fisher's exact test), Q value = 0.0022

Table S50. Gene #33: 'Del Peak 2(1p13.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	102	111	55
DEL PEAK 2(1P13.1) CNV	26	66	38	17
DEL PEAK 2(1P13.1) WILD-TYPE	51	36	73	38

Figure S50. Get High-res Image Gene #33: 'Del Peak 2(1p13.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 6.91e-07 (Fisher's exact test), Q value = 0.00067

Table S51. Gene #33: 'Del Peak 2(1p13.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	70	168
DEL PEAK 2(1P13.1) CNV	68	26	53
DEL PEAK 2(1P13.1) WILD-TYPE	39	44	115

Figure S51. Get High-res Image Gene #33: 'Del Peak 2(1p13.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 0.00022 (Fisher's exact test), Q value = 0.2

Table S52. Gene #33: 'Del Peak 2(1p13.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	181	73
DEL PEAK 2(1P13.1) CNV	40	67	46
DEL PEAK 2(1P13.1) WILD-TYPE	73	114	27

Figure S52. Get High-res Image Gene #33: 'Del Peak 2(1p13.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 1.59e-05 (Fisher's exact test), Q value = 0.015

Table S53. Gene #33: 'Del Peak 2(1p13.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	72	41
DEL PEAK 2(1P13.1) CNV	45	17	28
DEL PEAK 2(1P13.1) WILD-TYPE	73	55	13

Figure S53. Get High-res Image Gene #33: 'Del Peak 2(1p13.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 0.000112 (Fisher's exact test), Q value = 0.1

Table S54. Gene #35: 'Del Peak 4(2q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
DEL PEAK 4(2Q22.1) CNV	23	47	37
DEL PEAK 4(2Q22.1) WILD-TYPE	127	77	105

Figure S54. Get High-res Image Gene #35: 'Del Peak 4(2q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 0.000141 (Fisher's exact test), Q value = 0.13

Table S55. Gene #36: 'Del Peak 5(2q36.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	52	32	28
DEL PEAK 5(2Q36.2) CNV	8	28	4	10
DEL PEAK 5(2Q36.2) WILD-TYPE	34	24	28	18

Figure S55. Get High-res Image Gene #36: 'Del Peak 5(2q36.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

P value = 4.34e-05 (Fisher's exact test), Q value = 0.04

Table S56. Gene #36: 'Del Peak 5(2q36.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	22	56	23	53
DEL PEAK 5(2Q36.2) CNV	4	31	7	8
DEL PEAK 5(2Q36.2) WILD-TYPE	18	25	16	45

Figure S56. Get High-res Image Gene #36: 'Del Peak 5(2q36.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

P value = 6.14e-13 (Fisher's exact test), Q value = 6.1e-10

Table S57. Gene #36: 'Del Peak 5(2q36.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
DEL PEAK 5(2Q36.2) CNV	26	73	37
DEL PEAK 5(2Q36.2) WILD-TYPE	124	51	105

Figure S57. Get High-res Image Gene #36: 'Del Peak 5(2q36.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 1.12e-06 (Fisher's exact test), Q value = 0.0011

Table S58. Gene #36: 'Del Peak 5(2q36.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	82	72
DEL PEAK 5(2Q36.2) CNV	17	45	24
DEL PEAK 5(2Q36.2) WILD-TYPE	79	37	48

Figure S58. Get High-res Image Gene #36: '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 = 0.00064

Table S59. Gene #36: '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 S59. Get High-res Image Gene #36: '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 = 2.9e-05

Table S60. Gene #36: '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 S60. Get High-res Image Gene #36: 'Del Peak 5(2q36.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 3.47e-05 (Fisher's exact test), Q value = 0.032

Table S61. Gene #36: 'Del Peak 5(2q36.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	72	41
DEL PEAK 5(2Q36.2) CNV	47	10	20
DEL PEAK 5(2Q36.2) WILD-TYPE	71	62	21

Figure S61. Get High-res Image Gene #36: 'Del Peak 5(2q36.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 6.21e-07 (Fisher's exact test), Q value = 0.00061

Table S62. Gene #38: 'Del Peak 7(3p13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
DEL PEAK 7(3P13) CNV	109	114	132
DEL PEAK 7(3P13) WILD-TYPE	41	10	10

Figure S62. Get High-res Image Gene #38: 'Del Peak 7(3p13)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 1.47e-05 (Fisher's exact test), Q value = 0.014

Table S63. Gene #39: 'Del Peak 8(3p12.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
DEL PEAK 8(3P12.3) CNV	107	111	128
DEL PEAK 8(3P12.3) WILD-TYPE	43	13	14

Figure S63. Get High-res Image Gene #39: 'Del Peak 8(3p12.3)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 4.09e-07 (Fisher's exact test), Q value = 4e-04

Table S64. Gene #41: 'Del Peak 10(4p15.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
DEL PEAK 10(4P15.2) CNV	72	98	81
DEL PEAK 10(4P15.2) WILD-TYPE	78	26	61

Figure S64. Get High-res Image Gene #41: 'Del Peak 10(4p15.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 1.43e-06 (Fisher's exact test), Q value = 0.0014

Table S65. Gene #42: 'Del Peak 11(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
DEL PEAK 11(4Q22.1) CNV	65	91	72
DEL PEAK 11(4Q22.1) WILD-TYPE	85	33	70

Figure S65. Get High-res Image Gene #42: 'Del Peak 11(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 3.01e-08 (Fisher's exact test), Q value = 3e-05

Table S66. Gene #43: 'Del Peak 12(4q32.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
DEL PEAK 12(4Q32.3) CNV	75	103	86
DEL PEAK 12(4Q32.3) WILD-TYPE	75	21	56

Figure S66. Get High-res Image Gene #43: 'Del Peak 12(4q32.3)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 1.83e-07 (Fisher's exact test), Q value = 0.00018

Table S67. Gene #44: 'Del Peak 13(4q35.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
DEL PEAK 13(4Q35.2) CNV	81	104	85
DEL PEAK 13(4Q35.2) WILD-TYPE	69	20	57

Figure S67. Get High-res Image Gene #44: 'Del Peak 13(4q35.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 0.000143 (Fisher's exact test), Q value = 0.13

Table S68. Gene #44: '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 #44: 'Del Peak 13(4q35.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

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

Table S69. Gene #45: 'Del Peak 14(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
DEL PEAK 14(5Q11.2) CNV	78	103	124
DEL PEAK 14(5Q11.2) WILD-TYPE	72	21	18

Figure S69. Get High-res Image Gene #45: 'Del Peak 14(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 1.56e-10 (Fisher's exact test), Q value = 1.6e-07

Table S70. Gene #46: 'Del Peak 15(5q31.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
DEL PEAK 15(5Q31.1) CNV	88	109	125
DEL PEAK 15(5Q31.1) WILD-TYPE	62	15	17

Figure S70. Get High-res Image Gene #46: 'Del Peak 15(5q31.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 8.05e-05 (Fisher's exact test), Q value = 0.074

Table S71. Gene #46: 'Del Peak 15(5q31.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	82	72
DEL PEAK 15(5Q31.1) CNV	62	70	65
DEL PEAK 15(5Q31.1) WILD-TYPE	34	12	7

Figure S71. Get High-res Image Gene #46: 'Del Peak 15(5q31.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 9.32e-05 (Fisher's exact test), Q value = 0.085

Table S72. Gene #48: 'Del Peak 17(6q22.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
DEL PEAK 17(6Q22.31) CNV	26	48	28
DEL PEAK 17(6Q22.31) WILD-TYPE	124	76	114

Figure S72. Get High-res Image Gene #48: 'Del Peak 17(6q22.31)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 0.000249 (Fisher's exact test), Q value = 0.22

Table S73. Gene #48: '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 S73. Get High-res Image Gene #48: 'Del Peak 17(6q22.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 18(6q26)' versus 'CN_CNMF'

P value = 0.000219 (Fisher's exact test), Q value = 0.2

Table S74. Gene #49: 'Del Peak 18(6q26)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
DEL PEAK 18(6Q26) CNV	32	50	28
DEL PEAK 18(6Q26) WILD-TYPE	118	74	114

Figure S74. Get High-res Image Gene #49: 'Del Peak 18(6q26)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 6.68e-05 (Fisher's exact test), Q value = 0.062

Table S75. Gene #50: 'Del Peak 19(7q11.22)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
DEL PEAK 19(7Q11.22) CNV	11	3	25
DEL PEAK 19(7Q11.22) WILD-TYPE	139	121	117

Figure S75. Get High-res Image Gene #50: 'Del Peak 19(7q11.22)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 2.72e-10 (Fisher's exact test), Q value = 2.7e-07

Table S76. Gene #53: 'Del Peak 22(9p23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
DEL PEAK 22(9P23) CNV	78	73	122
DEL PEAK 22(9P23) WILD-TYPE	72	51	20

Figure S76. Get High-res Image Gene #53: 'Del Peak 22(9p23)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 1.46e-07 (Fisher's exact test), Q value = 0.00014

Table S77. Gene #54: 'Del Peak 23(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
DEL PEAK 23(9P21.3) CNV	96	93	129
DEL PEAK 23(9P21.3) WILD-TYPE	54	31	13

Figure S77. Get High-res Image Gene #54: 'Del Peak 23(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 24(9p21.1)' versus 'CN_CNMF'

P value = 8.75e-08 (Fisher's exact test), Q value = 8.6e-05

Table S78. Gene #55: 'Del Peak 24(9p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
DEL PEAK 24(9P21.1) CNV	81	70	117
DEL PEAK 24(9P21.1) WILD-TYPE	69	54	25

Figure S78. Get High-res Image Gene #55: 'Del Peak 24(9p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 25(9q21.11)' versus 'MRNA_CNMF'

P value = 8.38e-05 (Fisher's exact test), Q value = 0.077

Table S79. Gene #56: 'Del Peak 25(9q21.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	52	32	28
DEL PEAK 25(9Q21.11) CNV	28	12	19	15
DEL PEAK 25(9Q21.11) WILD-TYPE	14	40	13	13

Figure S79. Get High-res Image Gene #56: 'Del Peak 25(9q21.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 25(9q21.11)' versus 'MRNA_CHIERARCHICAL'

P value = 1.96e-05 (Fisher's exact test), Q value = 0.018

Table S80. Gene #56: 'Del Peak 25(9q21.11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	22	56	23	53
DEL PEAK 25(9Q21.11) CNV	14	13	17	30
DEL PEAK 25(9Q21.11) WILD-TYPE	8	43	6	23

Figure S80. Get High-res Image Gene #56: 'Del Peak 25(9q21.11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 25(9q21.11)' versus 'CN_CNMF'

P value = 6.02e-10 (Fisher's exact test), Q value = 6e-07

Table S81. Gene #56: 'Del Peak 25(9q21.11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
DEL PEAK 25(9Q21.11) CNV	70	34	95
DEL PEAK 25(9Q21.11) WILD-TYPE	80	90	47

Figure S81. Get High-res Image Gene #56: 'Del Peak 25(9q21.11)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 25(9q21.11)' versus 'METHLYATION_CNMF'

P value = 1.64e-06 (Fisher's exact test), Q value = 0.0016

Table S82. Gene #56: 'Del Peak 25(9q21.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	82	72
DEL PEAK 25(9Q21.11) CNV	52	22	48
DEL PEAK 25(9Q21.11) WILD-TYPE	44	60	24

Figure S82. Get High-res Image Gene #56: 'Del Peak 25(9q21.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 25(9q21.11)' versus 'MRNASEQ_CNMF'

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

Table S83. Gene #56: 'Del Peak 25(9q21.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	102	111	55
DEL PEAK 25(9Q21.11) CNV	43	23	71	29
DEL PEAK 25(9Q21.11) WILD-TYPE	34	79	40	26

Figure S83. Get High-res Image Gene #56: 'Del Peak 25(9q21.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 25(9q21.11)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.63e-09 (Fisher's exact test), Q value = 1.6e-06

Table S84. Gene #56: 'Del Peak 25(9q21.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

Figure S84. Get High-res Image Gene #56: 'Del Peak 25(9q21.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 25(9q21.11)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000184 (Fisher's exact test), Q value = 0.17

Table S85. Gene #56: 'Del Peak 25(9q21.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	181	73
DEL PEAK 25(9Q21.11) CNV	65	91	20
DEL PEAK 25(9Q21.11) WILD-TYPE	48	90	53

Figure S85. Get High-res Image Gene #56: 'Del Peak 25(9q21.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 25(9q21.11)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000158 (Fisher's exact test), Q value = 0.14

Table S86. Gene #56: 'Del Peak 25(9q21.11)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	40	108
DEL PEAK 25(9Q21.11) CNV	35	11	68
DEL PEAK 25(9Q21.11) WILD-TYPE	48	29	40

Figure S86. Get High-res Image Gene #56: 'Del Peak 25(9q21.11)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 26(10p15.3)' versus 'CN_CNMF'

P value = 4.61e-05 (Fisher's exact test), Q value = 0.043

Table S87. Gene #57: 'Del Peak 26(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
DEL PEAK 26(10P15.3) CNV	48	73	64
DEL PEAK 26(10P15.3) WILD-TYPE	102	51	78

Figure S87. Get High-res Image Gene #57: 'Del Peak 26(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 26(10p15.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.45e-05 (Fisher's exact test), Q value = 0.041

Table S88. Gene #57: 'Del Peak 26(10p15.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	181	73
DEL PEAK 26(10P15.3) CNV	60	63	46
DEL PEAK 26(10P15.3) WILD-TYPE	53	118	27

Figure S88. Get High-res Image Gene #57: 'Del Peak 26(10p15.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 27(10p15.1)' versus 'CN_CNMF'

P value = 0.000162 (Fisher's exact test), Q value = 0.15

Table S89. Gene #58: 'Del Peak 27(10p15.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
DEL PEAK 27(10P15.1) CNV	46	69	58
DEL PEAK 27(10P15.1) WILD-TYPE	104	55	84

Figure S89. Get High-res Image Gene #58: 'Del Peak 27(10p15.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 27(10p15.1)' versus 'METHLYATION_CNMF'

P value = 2.68e-05 (Fisher's exact test), Q value = 0.025

Table S90. Gene #58: 'Del Peak 27(10p15.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	82	72
DEL PEAK 27(10P15.1) CNV	32	53	25
DEL PEAK 27(10P15.1) WILD-TYPE	64	29	47

Figure S90. Get High-res Image Gene #58: 'Del Peak 27(10p15.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 27(10p15.1)' versus 'MRNASEQ_CNMF'

P value = 0.000161 (Fisher's exact test), Q value = 0.15

Table S91. Gene #58: 'Del Peak 27(10p15.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	102	111	55
DEL PEAK 27(10P15.1) CNV	26	60	47	14
DEL PEAK 27(10P15.1) WILD-TYPE	51	42	64	41

Figure S91. Get High-res Image Gene #58: 'Del Peak 27(10p15.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 27(10p15.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.09e-06 (Fisher's exact test), Q value = 0.0086

Table S92. Gene #58: 'Del Peak 27(10p15.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	181	73
DEL PEAK 27(10P15.1) CNV	53	58	47
DEL PEAK 27(10P15.1) WILD-TYPE	60	123	26

Figure S92. Get High-res Image Gene #58: 'Del Peak 27(10p15.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 28(10q23.31)' versus 'CN_CNMF'

P value = 1.64e-05 (Fisher's exact test), Q value = 0.015

Table S93. Gene #59: 'Del Peak 28(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
DEL PEAK 28(10Q23.31) CNV	61	85	70
DEL PEAK 28(10Q23.31) WILD-TYPE	89	39	72

Figure S93. Get High-res Image Gene #59: 'Del Peak 28(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 28(10q23.31)' versus 'METHLYATION_CNMF'

P value = 6.74e-06 (Fisher's exact test), Q value = 0.0064

Table S94. Gene #59: 'Del Peak 28(10q23.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	82	72
DEL PEAK 28(10Q23.31) CNV	33	58	36
DEL PEAK 28(10Q23.31) WILD-TYPE	63	24	36

Figure S94. Get High-res Image Gene #59: 'Del Peak 28(10q23.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 28(10q23.31)' versus 'MRNASEQ_CNMF'

P value = 8.54e-06 (Fisher's exact test), Q value = 0.0081

Table S95. Gene #59: 'Del Peak 28(10q23.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	102	111	55
DEL PEAK 28(10Q23.31) CNV	27	72	51	24
DEL PEAK 28(10Q23.31) WILD-TYPE	50	30	60	31

Figure S95. Get High-res Image Gene #59: 'Del Peak 28(10q23.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 28(10q23.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.23e-07 (Fisher's exact test), Q value = 7e-04

Table S96. Gene #59: 'Del Peak 28(10q23.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	70	168
DEL PEAK 28(10Q23.31) CNV	75	36	63
DEL PEAK 28(10Q23.31) WILD-TYPE	32	34	105

Figure S96. Get High-res Image Gene #59: 'Del Peak 28(10q23.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 29(11p15.5)' versus 'MRNA_CNMF'

P value = 0.000261 (Fisher's exact test), Q value = 0.23

Table S97. Gene #60: 'Del Peak 29(11p15.5)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	52	32	28
DEL PEAK 29(11P15.5) CNV	30	20	9	18
DEL PEAK 29(11P15.5) WILD-TYPE	12	32	23	10

Figure S97. Get High-res Image Gene #60: 'Del Peak 29(11p15.5)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 29(11p15.5)' versus 'CN_CNMF'

P value = 4.67e-06 (Fisher's exact test), Q value = 0.0045

Table S98. Gene #60: 'Del Peak 29(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
DEL PEAK 29(11P15.5) CNV	49	54	87
DEL PEAK 29(11P15.5) WILD-TYPE	101	70	55

Figure S98. Get High-res Image Gene #60: 'Del Peak 29(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 29(11p15.5)' versus 'RPPA_CHIERARCHICAL'

P value = 2.02e-05 (Fisher's exact test), Q value = 0.019

Table S99. Gene #60: 'Del Peak 29(11p15.5)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	47	49	40
DEL PEAK 29(11P15.5) CNV	29	17	36	10
DEL PEAK 29(11P15.5) WILD-TYPE	29	30	13	30

Figure S99. Get High-res Image Gene #60: 'Del Peak 29(11p15.5)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 35(14q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.8e-05 (Fisher's exact test), Q value = 0.089

Table S100. Gene #66: 'Del Peak 35(14q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	70	168
DEL PEAK 35(14Q11.2) CNV	38	39	44
DEL PEAK 35(14Q11.2) WILD-TYPE	69	31	124

Figure S100. Get High-res Image Gene #66: 'Del Peak 35(14q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 35(14q11.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000203 (Fisher's exact test), Q value = 0.18

Table S101. Gene #66: 'Del Peak 35(14q11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	40	108
DEL PEAK 35(14Q11.2) CNV	16	21	45
DEL PEAK 35(14Q11.2) WILD-TYPE	67	19	63

Figure S101. Get High-res Image Gene #66: 'Del Peak 35(14q11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 40(17p11.2)' versus 'CN_CNMF'

P value = 0.000167 (Fisher's exact test), Q value = 0.15

Table S102. Gene #71: 'Del Peak 40(17p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
DEL PEAK 40(17P11.2) CNV	68	53	93
DEL PEAK 40(17P11.2) WILD-TYPE	82	71	49

Figure S102. Get High-res Image Gene #71: 'Del Peak 40(17p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 3.03e-05 (Fisher's exact test), Q value = 0.028

Table S103. Gene #72: 'Del Peak 41(17q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	52	32	28
DEL PEAK 41(17Q11.2) CNV	21	4	11	6
DEL PEAK 41(17Q11.2) WILD-TYPE	21	48	21	22

Figure S103. Get High-res Image Gene #72: 'Del Peak 41(17q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

P value = 0.000101 (Fisher's exact test), Q value = 0.092

Table S104. Gene #72: 'Del Peak 41(17q11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	22	56	23	53
DEL PEAK 41(17Q11.2) CNV	8	4	9	21
DEL PEAK 41(17Q11.2) WILD-TYPE	14	52	14	32

Figure S104. Get High-res Image Gene #72: 'Del Peak 41(17q11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

P value = 2.73e-09 (Fisher's exact test), Q value = 2.7e-06

Table S105. Gene #72: 'Del Peak 41(17q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
DEL PEAK 41(17Q11.2) CNV	39	8	53
DEL PEAK 41(17Q11.2) WILD-TYPE	111	116	89

Figure S105. Get High-res Image Gene #72: 'Del Peak 41(17q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 1.48e-06 (Fisher's exact test), Q value = 0.0014

Table S106. Gene #72: 'Del Peak 41(17q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	102	111	55
DEL PEAK 41(17Q11.2) CNV	24	7	36	19
DEL PEAK 41(17Q11.2) WILD-TYPE	53	95	75	36

Figure S106. Get High-res Image Gene #72: 'Del Peak 41(17q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 4.83e-08 (Fisher's exact test), Q value = 4.8e-05

Table S107. Gene #72: 'Del Peak 41(17q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	107	70	168
DEL PEAK 41(17Q11.2) CNV	7	20	59
DEL PEAK 41(17Q11.2) WILD-TYPE	100	50	109

Figure S107. Get High-res Image Gene #72: 'Del Peak 41(17q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 42(17q25.3)' versus 'CN_CNMF'

P value = 1.43e-05 (Fisher's exact test), Q value = 0.014

Table S108. Gene #73: 'Del Peak 42(17q25.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
DEL PEAK 42(17Q25.3) CNV	27	11	45
DEL PEAK 42(17Q25.3) WILD-TYPE	123	113	97

Figure S108. Get High-res Image Gene #73: 'Del Peak 42(17q25.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 44(19p13.3)' versus 'CN_CNMF'

P value = 2.55e-05 (Fisher's exact test), Q value = 0.024

Table S109. Gene #75: 'Del Peak 44(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
DEL PEAK 44(19P13.3) CNV	47	51	82
DEL PEAK 44(19P13.3) WILD-TYPE	103	73	60

Figure S109. Get High-res Image Gene #75: 'Del Peak 44(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 44(19p13.3)' versus 'MIRSEQ_CNMF'

P value = 0.000224 (Fisher's exact test), Q value = 0.2

Table S110. Gene #75: 'Del Peak 44(19p13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	133	166	68
DEL PEAK 44(19P13.3) CNV	71	72	16
DEL PEAK 44(19P13.3) WILD-TYPE	62	94	52

Figure S110. Get High-res Image Gene #75: 'Del Peak 44(19p13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 45(19q13.33)' versus 'CN_CNMF'

P value = 1.01e-06 (Fisher's exact test), Q value = 0.00098

Table S111. Gene #76: 'Del Peak 45(19q13.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
DEL PEAK 45(19Q13.33) CNV	20	51	38
DEL PEAK 45(19Q13.33) WILD-TYPE	130	73	104

Figure S111. Get High-res Image Gene #76: 'Del Peak 45(19q13.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 45(19q13.33)' versus 'METHLYATION_CNMF'

P value = 9.24e-05 (Fisher's exact test), Q value = 0.085

Table S112. Gene #76: 'Del Peak 45(19q13.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	82	72
DEL PEAK 45(19Q13.33) CNV	11	30	24
DEL PEAK 45(19Q13.33) WILD-TYPE	85	52	48

Figure S112. Get High-res Image Gene #76: 'Del Peak 45(19q13.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 46(19q13.43)' versus 'CN_CNMF'

P value = 8.08e-06 (Fisher's exact test), Q value = 0.0077

Table S113. Gene #77: 'Del Peak 46(19q13.43)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
DEL PEAK 46(19Q13.43) CNV	21	49	37
DEL PEAK 46(19Q13.43) WILD-TYPE	129	75	105

Figure S113. Get High-res Image Gene #77: 'Del Peak 46(19q13.43)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 48(21q22.3)' versus 'CN_CNMF'

P value = 1.82e-08 (Fisher's exact test), Q value = 1.8e-05

Table S114. Gene #79: 'Del Peak 48(21q22.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
DEL PEAK 48(21Q22.3) CNV	56	89	87
DEL PEAK 48(21Q22.3) WILD-TYPE	94	35	55

Figure S114. Get High-res Image Gene #79: 'Del Peak 48(21q22.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 48(21q22.3)' versus 'METHLYATION_CNMF'

P value = 0.000126 (Fisher's exact test), Q value = 0.11

Table S115. Gene #79: 'Del Peak 48(21q22.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	82	72
DEL PEAK 48(21Q22.3) CNV	38	58	42
DEL PEAK 48(21Q22.3) WILD-TYPE	58	24	30

Figure S115. Get High-res Image Gene #79: 'Del Peak 48(21q22.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 50(22q13.32)' versus 'MRNA_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.2

Table S116. Gene #81: 'Del Peak 50(22q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	52	32	28
DEL PEAK 50(22Q13.32) CNV	8	8	8	17
DEL PEAK 50(22Q13.32) WILD-TYPE	34	44	24	11

Figure S116. Get High-res Image Gene #81: 'Del Peak 50(22q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 50(22q13.32)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000155 (Fisher's exact test), Q value = 0.14

Table S117. Gene #81: 'Del Peak 50(22q13.32)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	40	108
DEL PEAK 50(22Q13.32) CNV	13	2	36
DEL PEAK 50(22Q13.32) WILD-TYPE	70	38	72

Figure S117. Get High-res Image Gene #81: 'Del Peak 50(22q13.32)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 51(Xp22.2)' versus 'CN_CNMF'

P value = 3.12e-05 (Fisher's exact test), Q value = 0.029

Table S118. Gene #82: 'Del Peak 51(Xp22.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
DEL PEAK 51(XP22.2) CNV	27	48	56
DEL PEAK 51(XP22.2) WILD-TYPE	123	76	86

Figure S118. Get High-res Image Gene #82: 'Del Peak 51(Xp22.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 52(Xp11.3)' versus 'CN_CNMF'

P value = 2.49e-06 (Fisher's exact test), Q value = 0.0024

Table S119. Gene #83: 'Del Peak 52(Xp11.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
DEL PEAK 52(XP11.3) CNV	25	54	50
DEL PEAK 52(XP11.3) WILD-TYPE	125	70	92

Figure S119. Get High-res Image Gene #83: 'Del Peak 52(Xp11.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 52(Xp11.3)' versus 'METHLYATION_CNMF'

P value = 1.46e-05 (Fisher's exact test), Q value = 0.014

Table S120. Gene #83: 'Del Peak 52(Xp11.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	82	72
DEL PEAK 52(XP11.3) CNV	15	39	26
DEL PEAK 52(XP11.3) WILD-TYPE	81	43	46

Figure S120. Get High-res Image Gene #83: 'Del Peak 52(Xp11.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 53(Xq22.3)' versus 'CN_CNMF'

P value = 3.76e-08 (Fisher's exact test), Q value = 3.7e-05

Table S121. Gene #84: 'Del Peak 53(Xq22.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	150	124	142
DEL PEAK 53(XQ22.3) CNV	15	30	55
DEL PEAK 53(XQ22.3) WILD-TYPE	135	94	87

Figure S121. Get High-res Image Gene #84: 'Del Peak 53(Xq22.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 53(Xq22.3)' versus 'METHLYATION_CNMF'

P value = 0.000179 (Fisher's exact test), Q value = 0.16

Table S122. Gene #84: 'Del Peak 53(Xq22.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	82	72
DEL PEAK 53(XQ22.3) CNV	9	21	25
DEL PEAK 53(XQ22.3) WILD-TYPE	87	61	47

Figure S122. Get High-res Image Gene #84: 'Del Peak 53(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 = 416
Number of copy number variation regions = 84
Number of molecular subtypes = 12
Exclude regions that fewer than K tumors have alterations, K = 3

Fisher's exact test

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

Q value calculation

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

References

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

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

[3] GISTIC_version2

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