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 79 peak regions and 10 molecular subtypes across 358 patients, 87 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'.
Amp Peak 3(2p16.1) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Amp Peak 4(2q31.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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' and 'METHLYATION_CNMF'.
Amp Peak 18(12p13.33) cnvs correlated to 'CN_CNMF'.
Amp Peak 22(15q26.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 23(17q25.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 24(18p11.32) cnvs correlated to 'CN_CNMF'.
Amp Peak 25(18q11.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 26(19q12) cnvs correlated to 'CN_CNMF'.
Amp Peak 28(20p12.2) cnvs correlated to 'CN_CNMF'.
Del Peak 1(1p36.32) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 2(1p13.2) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 4(2q22.1) cnvs correlated to 'CN_CNMF'.
Del Peak 5(2q36.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 7(3p13) cnvs correlated to 'CN_CNMF'.
Del Peak 8(3p12.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 9(4p15.31) cnvs correlated to 'CN_CNMF'.
Del Peak 11(4q32.3) cnvs correlated to 'CN_CNMF'.
Del Peak 12(4q35.2) cnvs correlated to 'CN_CNMF'.
Del Peak 13(5q11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 14(5q31.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 20(9p23) cnvs correlated to 'CN_CNMF'.
Del Peak 21(9p21.3) cnvs correlated to 'CN_CNMF'.
Del Peak 22(9q21.11) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 24(10q23.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 25(11p15.5) cnvs correlated to 'CN_CNMF' and 'RPPA_CHIERARCHICAL'.
Del Peak 36(17q11.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 39(19p13.3) cnvs correlated to 'CN_CNMF'.
Del Peak 40(19q13.33) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 41(19q13.43) cnvs correlated to 'CN_CNMF'.
Del Peak 43(21q22.3) cnvs correlated to 'CN_CNMF'.
Del Peak 45(Xp22.2) cnvs correlated to 'CN_CNMF'.
Del Peak 46(Xp21.1) cnvs correlated to 'CN_CNMF'.
Del Peak 47(Xp11.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 48(Xq22.3) 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 79 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 87 significant findings detected.


		Molecular subtypes	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
Del Peak 22(9q21 11)	174 (49%)	184	0.000177 (0.127)	4.92e-05 (0.0363)	2.03e-07 (0.000157)	1.42e-06 (0.00108)	0.571 (1.00)	0.24 (1.00)	4.44e-06 (0.00337)	2.4e-07 (0.000185)	0.0445 (1.00)	3.16e-05 (0.0235)
Amp Peak 6(3q26 33)	330 (92%)	28	0.000427 (0.299)	1.71e-05 (0.0129)	1.63e-09 (1.27e-06)	0.000113 (0.0818)	0.213 (1.00)	0.0944 (1.00)	3.81e-05 (0.0283)	0.000164 (0.118)	0.205 (1.00)	9.11e-05 (0.0662)
Del Peak 1(1p36 32)	155 (43%)	203	1.28e-06 (0.000976)	1.29e-08 (1e-05)	3.34e-28 (2.64e-25)	4.78e-16 (3.77e-13)	0.419 (1.00)	0.00421 (1.00)	1.02e-10 (8.04e-08)	6.75e-09 (5.26e-06)	0.0237 (1.00)	0.00103 (0.699)
Del Peak 5(2q36 2)	116 (32%)	242	0.000236 (0.168)	4.76e-05 (0.0352)	5.32e-12 (4.19e-09)	0.000352 (0.248)	0.138 (1.00)	0.113 (1.00)	8.49e-05 (0.0619)	6.15e-06 (0.00466)	0.944 (1.00)	0.624 (1.00)
Del Peak 2(1p13 2)	156 (44%)	202	0.000237 (0.169)	0.00055 (0.382)	6.47e-14 (5.1e-11)	6.52e-09 (5.09e-06)	0.107 (1.00)	0.115 (1.00)	2.35e-05 (0.0175)	7.07e-05 (0.0517)	0.196 (1.00)	0.00967 (1.00)
Del Peak 36(17q11 2)	89 (25%)	269	1.26e-05 (0.00949)	6.44e-05 (0.0473)	9.35e-09 (7.27e-06)	0.0579 (1.00)	0.45 (1.00)	0.577 (1.00)	0.000122 (0.0881)	7.16e-06 (0.00542)	0.406 (1.00)	0.0154 (1.00)
Amp Peak 3(2p16 1)	194 (54%)	164	0.000305 (0.215)	0.00165 (1.00)	2.41e-09 (1.88e-06)	7e-05 (0.0513)	0.967 (1.00)	0.741 (1.00)	0.000333 (0.235)	0.00113 (0.764)	0.879 (1.00)	0.0312 (1.00)
Del Peak 24(10q23 31)	184 (51%)	174	0.0392 (1.00)	0.00386 (1.00)	0.00019 (0.136)	6.42e-05 (0.0472)	0.283 (1.00)	0.303 (1.00)	0.000104 (0.0752)	2.63e-05 (0.0196)	0.46 (1.00)	0.0277 (1.00)
Amp Peak 22(15q26 3)	128 (36%)	230	0.151 (1.00)	0.021 (1.00)	5.63e-07 (0.000433)	1.78e-05 (0.0134)	0.312 (1.00)	0.0162 (1.00)	0.000622 (0.429)	0.00426 (1.00)	0.0175 (1.00)	7.14e-05 (0.0521)
Del Peak 13(5q11 2)	265 (74%)	93	0.842 (1.00)	0.303 (1.00)	5.71e-10 (4.47e-07)	0.000266 (0.188)	1 (1.00)	0.237 (1.00)	0.248 (1.00)	0.56 (1.00)	0.888 (1.00)	0.000162 (0.116)
Amp Peak 4(2q31 2)	121 (34%)	237	0.0207 (1.00)	0.000948 (0.643)	6.74e-05 (0.0494)	4.94e-06 (0.00375)	0.738 (1.00)	0.912 (1.00)	0.000801 (0.548)	0.000932 (0.633)	0.465 (1.00)	0.252 (1.00)
Amp Peak 12(7q21 2)	188 (53%)	170	0.101 (1.00)	0.25 (1.00)	3.36e-10 (2.64e-07)	8.35e-06 (0.00631)	0.0408 (1.00)	0.215 (1.00)	0.0165 (1.00)	0.0221 (1.00)	0.247 (1.00)	0.0377 (1.00)
Amp Peak 23(17q25 1)	171 (48%)	187	0.0177 (1.00)	0.0608 (1.00)	1.87e-06 (0.00143)	0.000148 (0.107)	0.297 (1.00)	0.323 (1.00)	0.0274 (1.00)	0.00807 (1.00)	0.756 (1.00)	0.742 (1.00)
Del Peak 8(3p12 1)	280 (78%)	78	0.322 (1.00)	0.0413 (1.00)	1.46e-07 (0.000113)	2.79e-05 (0.0207)	0.688 (1.00)	0.109 (1.00)	0.155 (1.00)	0.00235 (1.00)	0.174 (1.00)	0.101 (1.00)
Del Peak 14(5q31 1)	277 (77%)	81	0.332 (1.00)	0.228 (1.00)	6.21e-07 (0.000477)	3.25e-05 (0.0241)	0.352 (1.00)	0.209 (1.00)	0.254 (1.00)	0.401 (1.00)	0.593 (1.00)	0.00832 (1.00)
Del Peak 25(11p15 5)	173 (48%)	185	0.000689 (0.474)	0.0528 (1.00)	6.04e-05 (0.0445)	0.0117 (1.00)	0.000449 (0.314)	2.34e-05 (0.0175)	0.02 (1.00)	0.0362 (1.00)	0.0253 (1.00)	0.0291 (1.00)
Del Peak 40(19q13 33)	96 (27%)	262	0.617 (1.00)	0.0694 (1.00)	4.76e-05 (0.0352)	0.000249 (0.177)	0.272 (1.00)	0.635 (1.00)	0.436 (1.00)	0.212 (1.00)	0.34 (1.00)	0.119 (1.00)
Del Peak 47(Xp11 3)	116 (32%)	242	0.062 (1.00)	0.175 (1.00)	2.82e-06 (0.00215)	5.16e-05 (0.038)	0.0823 (1.00)	0.0774 (1.00)	0.0142 (1.00)	0.0175 (1.00)	0.133 (1.00)	0.199 (1.00)
Amp Peak 1(1p34 2)	58 (16%)	300	0.028 (1.00)	0.481 (1.00)	0.000273 (0.193)	0.71 (1.00)	0.419 (1.00)	0.668 (1.00)	0.0484 (1.00)	0.241 (1.00)	0.299 (1.00)	0.494 (1.00)
Amp Peak 2(1q21 2)	186 (52%)	172	0.0419 (1.00)	0.00618 (1.00)	7.32e-07 (0.000561)	0.00128 (0.865)	0.155 (1.00)	0.0576 (1.00)	0.000685 (0.472)	0.000488 (0.34)	0.305 (1.00)	0.0562 (1.00)
Amp Peak 8(5p15 33)	281 (78%)	77	0.853 (1.00)	0.867 (1.00)	8.38e-06 (0.00632)	0.0036 (1.00)	0.498 (1.00)	0.422 (1.00)	0.387 (1.00)	0.328 (1.00)	0.841 (1.00)	0.263 (1.00)
Amp Peak 9(5p12)	236 (66%)	122	0.919 (1.00)	0.514 (1.00)	1.38e-09 (1.08e-06)	0.00666 (1.00)	0.669 (1.00)	1 (1.00)	0.0635 (1.00)	0.586 (1.00)	0.0413 (1.00)	0.219 (1.00)
Amp Peak 18(12p13 33)	177 (49%)	181	0.0102 (1.00)	0.0571 (1.00)	0.000255 (0.18)	0.0112 (1.00)	0.353 (1.00)	0.711 (1.00)	0.000575 (0.399)	0.00518 (1.00)	0.674 (1.00)	0.429 (1.00)
Amp Peak 24(18p11 32)	122 (34%)	236	0.0602 (1.00)	0.00628 (1.00)	0.000148 (0.106)	0.0328 (1.00)	0.226 (1.00)	0.844 (1.00)	0.607 (1.00)	0.177 (1.00)	0.526 (1.00)	0.163 (1.00)
Amp Peak 25(18q11 2)	115 (32%)	243	0.000456 (0.318)	0.00227 (1.00)	0.000231 (0.164)	0.00415 (1.00)	0.252 (1.00)	0.771 (1.00)	0.00438 (1.00)	0.000578 (0.4)	0.369 (1.00)	0.00926 (1.00)
Amp Peak 26(19q12)	149 (42%)	209	0.455 (1.00)	0.249 (1.00)	0.000111 (0.0804)	0.445 (1.00)	0.274 (1.00)	0.0244 (1.00)	0.193 (1.00)	0.082 (1.00)	0.949 (1.00)	0.686 (1.00)
Amp Peak 28(20p12 2)	193 (54%)	165	0.000987 (0.668)	0.0043 (1.00)	4.62e-08 (3.58e-05)	0.00141 (0.949)	0.95 (1.00)	0.293 (1.00)	0.15 (1.00)	0.0134 (1.00)	0.488 (1.00)	0.246 (1.00)
Del Peak 4(2q22 1)	96 (27%)	262	0.255 (1.00)	0.318 (1.00)	0.000217 (0.155)	0.0216 (1.00)	0.653 (1.00)	0.21 (1.00)	0.188 (1.00)	0.231 (1.00)	0.683 (1.00)	0.46 (1.00)
Del Peak 7(3p13)	310 (87%)	48	0.419 (1.00)	0.549 (1.00)	9.68e-05 (0.0703)	0.00211 (1.00)	0.91 (1.00)	0.0127 (1.00)	0.369 (1.00)	0.0134 (1.00)	0.872 (1.00)	0.00826 (1.00)
Del Peak 9(4p15 31)	219 (61%)	139	0.000807 (0.551)	0.00171 (1.00)	1.21e-05 (0.00912)	0.00406 (1.00)	0.675 (1.00)	0.0454 (1.00)	0.0883 (1.00)	0.0514 (1.00)	0.403 (1.00)	1 (1.00)
Del Peak 11(4q32 3)	226 (63%)	132	0.00967 (1.00)	0.0253 (1.00)	2.97e-07 (0.000229)	0.0112 (1.00)	0.102 (1.00)	0.585 (1.00)	0.0057 (1.00)	0.036 (1.00)	0.438 (1.00)	0.144 (1.00)
Del Peak 12(4q35 2)	229 (64%)	129	0.1 (1.00)	0.206 (1.00)	1.07e-06 (0.00082)	0.00259 (1.00)	0.455 (1.00)	0.561 (1.00)	0.00532 (1.00)	0.107 (1.00)	0.671 (1.00)	0.338 (1.00)
Del Peak 20(9p23)	234 (65%)	124	0.00561 (1.00)	0.00291 (1.00)	1.21e-07 (9.35e-05)	0.109 (1.00)	0.134 (1.00)	0.185 (1.00)	0.0261 (1.00)	0.0876 (1.00)	1 (1.00)	0.0901 (1.00)
Del Peak 21(9p21 3)	272 (76%)	86	0.372 (1.00)	0.172 (1.00)	3.23e-06 (0.00246)	0.517 (1.00)	0.679 (1.00)	0.379 (1.00)	0.164 (1.00)	0.846 (1.00)	0.865 (1.00)	0.337 (1.00)
Del Peak 39(19p13 3)	163 (46%)	195	0.334 (1.00)	0.0231 (1.00)	0.000227 (0.162)	0.14 (1.00)	0.0928 (1.00)	0.404 (1.00)	0.16 (1.00)	0.0124 (1.00)	0.0179 (1.00)	0.0478 (1.00)
Del Peak 41(19q13 43)	96 (27%)	262	0.644 (1.00)	0.207 (1.00)	9.08e-05 (0.0661)	0.000797 (0.546)	0.466 (1.00)	0.47 (1.00)	0.465 (1.00)	0.154 (1.00)	0.216 (1.00)	0.308 (1.00)
Del Peak 43(21q22 3)	205 (57%)	153	0.957 (1.00)	0.193 (1.00)	2.21e-08 (1.72e-05)	0.00109 (0.737)	0.478 (1.00)	0.14 (1.00)	0.564 (1.00)	0.302 (1.00)	0.00871 (1.00)	0.474 (1.00)
Del Peak 45(Xp22 2)	114 (32%)	244	0.599 (1.00)	0.351 (1.00)	1.57e-05 (0.0118)	0.0164 (1.00)	0.343 (1.00)	0.664 (1.00)	0.14 (1.00)	0.122 (1.00)	0.195 (1.00)	0.267 (1.00)
Del Peak 46(Xp21 1)	118 (33%)	240	0.354 (1.00)	0.148 (1.00)	2e-05 (0.015)	0.00181 (1.00)	0.381 (1.00)	0.57 (1.00)	0.0779 (1.00)	0.00716 (1.00)	0.407 (1.00)	0.109 (1.00)
Del Peak 48(Xq22 3)	91 (25%)	267	0.00853 (1.00)	0.105 (1.00)	1.03e-05 (0.00777)	0.000861 (0.586)	0.745 (1.00)	0.935 (1.00)	0.0513 (1.00)	0.485 (1.00)	0.716 (1.00)	0.954 (1.00)
Amp Peak 5(3p11 1)	73 (20%)	285	0.0748 (1.00)	0.844 (1.00)	0.673 (1.00)	0.826 (1.00)	0.202 (1.00)	0.000831 (0.567)	0.0555 (1.00)	0.444 (1.00)	0.41 (1.00)	0.947 (1.00)
Amp Peak 7(4q12)	85 (24%)	273	0.679 (1.00)	0.759 (1.00)	0.00548 (1.00)	0.284 (1.00)	0.312 (1.00)	0.0883 (1.00)	0.555 (1.00)	0.75 (1.00)	0.185 (1.00)	0.577 (1.00)
Amp Peak 10(6q12)	107 (30%)	251	1 (1.00)	0.873 (1.00)	0.069 (1.00)	0.26 (1.00)	0.349 (1.00)	0.496 (1.00)	0.395 (1.00)	0.236 (1.00)	0.595 (1.00)	0.155 (1.00)
Amp Peak 11(7p11 2)	174 (49%)	184	0.186 (1.00)	0.0939 (1.00)	0.00168 (1.00)	0.00254 (1.00)	0.642 (1.00)	0.85 (1.00)	0.076 (1.00)	0.0148 (1.00)	0.7 (1.00)	0.123 (1.00)
Amp Peak 13(8p11 23)	168 (47%)	190	0.00812 (1.00)	0.168 (1.00)	0.113 (1.00)	0.1 (1.00)	0.217 (1.00)	0.0871 (1.00)	0.00631 (1.00)	0.72 (1.00)	0.135 (1.00)	0.62 (1.00)
Amp Peak 14(8q24 21)	248 (69%)	110	0.871 (1.00)	0.644 (1.00)	0.339 (1.00)	0.589 (1.00)	0.958 (1.00)	0.768 (1.00)	0.734 (1.00)	0.428 (1.00)	0.491 (1.00)	0.932 (1.00)
Amp Peak 15(9p24 1)	67 (19%)	291	0.375 (1.00)	0.0295 (1.00)	0.000586 (0.405)	0.228 (1.00)	0.00176 (1.00)	0.00573 (1.00)	0.0413 (1.00)	0.00294 (1.00)	0.561 (1.00)	0.39 (1.00)
Amp Peak 16(9p13 3)	98 (27%)	260	0.17 (1.00)	0.373 (1.00)	0.0107 (1.00)	0.388 (1.00)	0.0779 (1.00)	0.00937 (1.00)	0.022 (1.00)	0.188 (1.00)	0.408 (1.00)	0.889 (1.00)
Amp Peak 17(11q13 3)	131 (37%)	227	0.0697 (1.00)	0.0306 (1.00)	0.0256 (1.00)	0.00148 (0.992)	0.184 (1.00)	0.0641 (1.00)	0.0125 (1.00)	0.139 (1.00)	0.15 (1.00)	0.33 (1.00)
Amp Peak 19(12q15)	132 (37%)	226	0.312 (1.00)	0.527 (1.00)	0.00874 (1.00)	0.0105 (1.00)	0.806 (1.00)	0.409 (1.00)	0.105 (1.00)	0.0491 (1.00)	0.565 (1.00)	0.926 (1.00)
Amp Peak 20(13q34)	64 (18%)	294	0.964 (1.00)	0.0489 (1.00)	0.396 (1.00)	0.166 (1.00)	0.824 (1.00)	0.196 (1.00)	0.803 (1.00)	0.407 (1.00)	0.0724 (1.00)	0.251 (1.00)
Amp Peak 21(14q13 3)	110 (31%)	248	0.345 (1.00)	0.246 (1.00)	0.528 (1.00)	0.47 (1.00)	0.509 (1.00)	0.0202 (1.00)	0.617 (1.00)	0.0847 (1.00)	0.0167 (1.00)	0.081 (1.00)
Amp Peak 27(19q13 2)	157 (44%)	201	0.473 (1.00)	0.909 (1.00)	0.000447 (0.313)	0.25 (1.00)	0.318 (1.00)	0.131 (1.00)	0.454 (1.00)	0.0336 (1.00)	0.975 (1.00)	0.286 (1.00)
Amp Peak 29(20q11 21)	206 (58%)	152	0.991 (1.00)	0.844 (1.00)	0.00275 (1.00)	0.0388 (1.00)	0.743 (1.00)	0.697 (1.00)	0.593 (1.00)	0.549 (1.00)	0.937 (1.00)	0.615 (1.00)
Amp Peak 30(22q11 21)	177 (49%)	181	0.111 (1.00)	0.123 (1.00)	0.0146 (1.00)	0.00291 (1.00)	0.874 (1.00)	0.339 (1.00)	0.0671 (1.00)	0.0677 (1.00)	0.816 (1.00)	0.132 (1.00)
Amp Peak 31(Xq28)	92 (26%)	266	0.644 (1.00)	0.515 (1.00)	0.24 (1.00)	0.0981 (1.00)	0.0546 (1.00)	0.0722 (1.00)	0.143 (1.00)	0.225 (1.00)	0.754 (1.00)	0.804 (1.00)
Del Peak 3(2p25 3)	34 (9%)	324	0.0461 (1.00)	0.179 (1.00)	0.0899 (1.00)	0.367 (1.00)	0.11 (1.00)	0.789 (1.00)	0.32 (1.00)	0.226 (1.00)	0.105 (1.00)	0.0641 (1.00)
Del Peak 6(3p25 3)	285 (80%)	73	0.54 (1.00)	0.176 (1.00)	0.0292 (1.00)	0.00407 (1.00)	0.624 (1.00)	0.212 (1.00)	0.327 (1.00)	0.00876 (1.00)	0.655 (1.00)	0.0137 (1.00)
Del Peak 10(4q22 1)	199 (56%)	159	0.00685 (1.00)	0.0579 (1.00)	0.000473 (0.33)	0.0405 (1.00)	0.147 (1.00)	0.346 (1.00)	0.0252 (1.00)	0.00636 (1.00)	0.37 (1.00)	0.134 (1.00)
Del Peak 15(6p25 3)	90 (25%)	268	0.22 (1.00)	0.11 (1.00)	0.0169 (1.00)	0.000692 (0.475)	0.542 (1.00)	0.00967 (1.00)	0.01 (1.00)	0.0204 (1.00)	0.238 (1.00)	0.179 (1.00)
Del Peak 16(6q26)	93 (26%)	265	0.0659 (1.00)	0.00298 (1.00)	0.00901 (1.00)	0.00168 (1.00)	0.885 (1.00)	0.866 (1.00)	0.0687 (1.00)	0.141 (1.00)	0.226 (1.00)	0.108 (1.00)
Del Peak 17(7q11 22)	35 (10%)	323	0.908 (1.00)	0.405 (1.00)	0.000385 (0.271)	0.394 (1.00)	0.958 (1.00)	0.8 (1.00)	0.0463 (1.00)	0.0644 (1.00)	0.804 (1.00)	0.526 (1.00)
Del Peak 18(7q36 1)	73 (20%)	285	0.393 (1.00)	0.569 (1.00)	0.0143 (1.00)	0.381 (1.00)	1 (1.00)	0.286 (1.00)	0.115 (1.00)	0.388 (1.00)	0.361 (1.00)	0.828 (1.00)
Del Peak 19(8p23 2)	243 (68%)	115	0.864 (1.00)	0.459 (1.00)	0.00493 (1.00)	0.295 (1.00)	0.382 (1.00)	0.196 (1.00)	0.157 (1.00)	0.072 (1.00)	0.451 (1.00)	0.167 (1.00)
Del Peak 23(10p15 3)	160 (45%)	198	0.373 (1.00)	0.442 (1.00)	0.0015 (1.00)	0.000931 (0.633)	0.407 (1.00)	0.391 (1.00)	0.00383 (1.00)	0.0165 (1.00)	0.104 (1.00)	0.00185 (1.00)
Del Peak 26(11q22 1)	108 (30%)	250	0.493 (1.00)	0.288 (1.00)	0.00281 (1.00)	0.0775 (1.00)	0.0868 (1.00)	0.975 (1.00)	0.245 (1.00)	0.423 (1.00)	0.278 (1.00)	0.0526 (1.00)
Del Peak 27(11q25)	131 (37%)	227	0.798 (1.00)	0.429 (1.00)	0.0229 (1.00)	0.381 (1.00)	0.109 (1.00)	0.867 (1.00)	0.447 (1.00)	0.406 (1.00)	0.185 (1.00)	0.171 (1.00)
Del Peak 28(12q24 31)	57 (16%)	301	0.965 (1.00)	0.332 (1.00)	0.598 (1.00)	0.303 (1.00)	0.359 (1.00)	0.203 (1.00)	0.9 (1.00)	0.689 (1.00)	0.118 (1.00)	0.302 (1.00)
Del Peak 29(13q12 11)	240 (67%)	118	0.0547 (1.00)	0.611 (1.00)	0.0338 (1.00)	0.156 (1.00)	1 (1.00)	0.193 (1.00)	0.7 (1.00)	0.214 (1.00)	0.958 (1.00)	0.987 (1.00)
Del Peak 30(13q14 2)	251 (70%)	107	0.0512 (1.00)	0.0962 (1.00)	0.00073 (0.501)	0.129 (1.00)	0.85 (1.00)	0.547 (1.00)	0.0281 (1.00)	0.147 (1.00)	0.654 (1.00)	0.543 (1.00)
Del Peak 31(14q11 2)	130 (36%)	228	0.0546 (1.00)	0.293 (1.00)	0.0383 (1.00)	0.321 (1.00)	0.243 (1.00)	0.152 (1.00)	0.00265 (1.00)	0.00213 (1.00)	0.333 (1.00)	0.172 (1.00)
Del Peak 32(15q12)	122 (34%)	236	0.725 (1.00)	0.228 (1.00)	0.334 (1.00)	0.317 (1.00)	0.0697 (1.00)	0.00674 (1.00)	0.132 (1.00)	0.356 (1.00)	0.0996 (1.00)	0.738 (1.00)
Del Peak 33(16p13 3)	129 (36%)	229	0.239 (1.00)	0.245 (1.00)	0.00318 (1.00)	0.362 (1.00)	0.135 (1.00)	0.496 (1.00)	0.531 (1.00)	0.247 (1.00)	0.643 (1.00)	0.164 (1.00)
Del Peak 34(16q23 1)	144 (40%)	214	0.942 (1.00)	0.659 (1.00)	0.0506 (1.00)	0.312 (1.00)	0.336 (1.00)	0.861 (1.00)	0.205 (1.00)	0.0264 (1.00)	0.441 (1.00)	0.581 (1.00)
Del Peak 35(17p11 2)	185 (52%)	173	0.194 (1.00)	0.401 (1.00)	0.004 (1.00)	0.136 (1.00)	0.135 (1.00)	0.0101 (1.00)	0.368 (1.00)	0.86 (1.00)	0.0697 (1.00)	0.022 (1.00)
Del Peak 37(17q25 3)	68 (19%)	290	0.00493 (1.00)	0.022 (1.00)	0.000468 (0.327)	0.0796 (1.00)	0.782 (1.00)	0.972 (1.00)	0.0423 (1.00)	0.000553 (0.384)	0.581 (1.00)	0.0108 (1.00)
Del Peak 38(18q23)	164 (46%)	194	0.508 (1.00)	0.788 (1.00)	0.517 (1.00)	0.97 (1.00)	0.858 (1.00)	0.325 (1.00)	0.23 (1.00)	0.115 (1.00)	0.804 (1.00)	0.536 (1.00)
Del Peak 42(21q11 2)	176 (49%)	182	0.558 (1.00)	0.223 (1.00)	0.0058 (1.00)	0.0647 (1.00)	0.966 (1.00)	0.904 (1.00)	0.908 (1.00)	0.485 (1.00)	0.203 (1.00)	0.233 (1.00)
Del Peak 44(22q11 21)	62 (17%)	296	0.0904 (1.00)	0.0093 (1.00)	0.172 (1.00)	0.342 (1.00)	0.125 (1.00)	0.114 (1.00)	0.598 (1.00)	0.748 (1.00)	0.149 (1.00)	0.101 (1.00)

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

P value = 0.000273 (Fisher's exact test), Q value = 0.19

Table S1. Gene #1: 'Amp Peak 1(1p34.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
AMP PEAK 1(1P34.2) MUTATED	17	9	32
AMP PEAK 1(1P34.2) WILD-TYPE	112	103	85

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1p34.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 7.32e-07 (Fisher's exact test), Q value = 0.00056

Table S2. Gene #2: 'Amp Peak 2(1q21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
AMP PEAK 2(1Q21.2) MUTATED	52	81	53
AMP PEAK 2(1Q21.2) WILD-TYPE	77	31	64

Figure S2. Get High-res Image Gene #2: 'Amp Peak 2(1q21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

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

Table S3. Gene #3: 'Amp Peak 3(2p16.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

Figure S3. Get High-res Image Gene #3: 'Amp Peak 3(2p16.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

P value = 2.41e-09 (Fisher's exact test), Q value = 1.9e-06

Table S4. Gene #3: 'Amp Peak 3(2p16.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
AMP PEAK 3(2P16.1) MUTATED	48	86	60
AMP PEAK 3(2P16.1) WILD-TYPE	81	26	57

Figure S4. Get High-res Image Gene #3: 'Amp Peak 3(2p16.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 7e-05 (Fisher's exact test), Q value = 0.051

Table S5. Gene #3: 'Amp Peak 3(2p16.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	75	59
AMP PEAK 3(2P16.1) MUTATED	41	56	25
AMP PEAK 3(2P16.1) WILD-TYPE	49	19	34

Figure S5. Get High-res Image Gene #3: 'Amp Peak 3(2p16.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 0.000333 (Fisher's exact test), Q value = 0.23

Table S6. Gene #3: 'Amp Peak 3(2p16.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	60	80	79	38
AMP PEAK 3(2P16.1) MUTATED	23	58	44	17
AMP PEAK 3(2P16.1) WILD-TYPE	37	22	35	21

Figure S6. Get High-res Image Gene #3: 'Amp Peak 3(2p16.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 6.74e-05 (Fisher's exact test), Q value = 0.049

Table S7. Gene #4: 'Amp Peak 4(2q31.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
AMP PEAK 4(2Q31.2) MUTATED	29	55	37
AMP PEAK 4(2Q31.2) WILD-TYPE	100	57	80

Figure S7. Get High-res Image Gene #4: 'Amp Peak 4(2q31.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 4.94e-06 (Fisher's exact test), Q value = 0.0038

Table S8. Gene #4: 'Amp Peak 4(2q31.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	75	59
AMP PEAK 4(2Q31.2) MUTATED	26	42	10
AMP PEAK 4(2Q31.2) WILD-TYPE	64	33	49

Figure S8. Get High-res Image Gene #4: 'Amp Peak 4(2q31.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

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

Table S9. Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

Figure S9. Get High-res Image Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

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

Table S10. Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
AMP PEAK 6(3Q26.33) MUTATED	104	112	114
AMP PEAK 6(3Q26.33) WILD-TYPE	25	0	3

Figure S10. Get High-res Image Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 0.000113 (Fisher's exact test), Q value = 0.082

Table S11. Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	75	59
AMP PEAK 6(3Q26.33) MUTATED	76	75	57
AMP PEAK 6(3Q26.33) WILD-TYPE	14	0	2

Figure S11. Get High-res Image Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 3.81e-05 (Fisher's exact test), Q value = 0.028

Table S12. Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	60	80	79	38
AMP PEAK 6(3Q26.33) MUTATED	57	80	66	31
AMP PEAK 6(3Q26.33) WILD-TYPE	3	0	13	7

Figure S12. Get High-res Image Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 0.000164 (Fisher's exact test), Q value = 0.12

Table S13. Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	116	86	55
AMP PEAK 6(3Q26.33) MUTATED	100	86	48
AMP PEAK 6(3Q26.33) WILD-TYPE	16	0	7

Figure S13. Get High-res Image Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 9.11e-05 (Fisher's exact test), Q value = 0.066

Table S14. Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	173	108
AMP PEAK 6(3Q26.33) MUTATED	50	150	106
AMP PEAK 6(3Q26.33) WILD-TYPE	0	23	2

Figure S14. Get High-res Image Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 8.38e-06 (Fisher's exact test), Q value = 0.0063

Table S15. Gene #8: 'Amp Peak 8(5p15.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
AMP PEAK 8(5P15.33) MUTATED	89	84	108
AMP PEAK 8(5P15.33) WILD-TYPE	40	28	9

Figure S15. Get High-res Image Gene #8: 'Amp Peak 8(5p15.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 1.38e-09 (Fisher's exact test), Q value = 1.1e-06

Table S16. Gene #9: 'Amp Peak 9(5p12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
AMP PEAK 9(5P12) MUTATED	63	72	101
AMP PEAK 9(5P12) WILD-TYPE	66	40	16

Figure S16. Get High-res Image Gene #9: 'Amp Peak 9(5p12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 3.36e-10 (Fisher's exact test), Q value = 2.6e-07

Table S17. Gene #12: 'Amp Peak 12(7q21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
AMP PEAK 12(7Q21.2) MUTATED	44	85	59
AMP PEAK 12(7Q21.2) WILD-TYPE	85	27	58

Figure S17. Get High-res Image Gene #12: 'Amp Peak 12(7q21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 8.35e-06 (Fisher's exact test), Q value = 0.0063

Table S18. Gene #12: 'Amp Peak 12(7q21.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	75	59
AMP PEAK 12(7Q21.2) MUTATED	32	54	26
AMP PEAK 12(7Q21.2) WILD-TYPE	58	21	33

Figure S18. Get High-res Image Gene #12: 'Amp Peak 12(7q21.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 0.000255 (Fisher's exact test), Q value = 0.18

Table S19. Gene #18: 'Amp Peak 18(12p13.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
AMP PEAK 18(12P13.33) MUTATED	48	71	58
AMP PEAK 18(12P13.33) WILD-TYPE	81	41	59

Figure S19. Get High-res Image Gene #18: 'Amp Peak 18(12p13.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 5.63e-07 (Fisher's exact test), Q value = 0.00043

Table S20. Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
AMP PEAK 22(15Q26.3) MUTATED	25	58	45
AMP PEAK 22(15Q26.3) WILD-TYPE	104	54	72

Figure S20. Get High-res Image Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 1.78e-05 (Fisher's exact test), Q value = 0.013

Table S21. Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	75	59
AMP PEAK 22(15Q26.3) MUTATED	15	37	24
AMP PEAK 22(15Q26.3) WILD-TYPE	75	38	35

Figure S21. Get High-res Image Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 22(15q26.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.14e-05 (Fisher's exact test), Q value = 0.052

Table S22. Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	173	108
AMP PEAK 22(15Q26.3) MUTATED	28	46	49
AMP PEAK 22(15Q26.3) WILD-TYPE	22	127	59

Figure S22. Get High-res Image Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 1.87e-06 (Fisher's exact test), Q value = 0.0014

Table S23. Gene #23: 'Amp Peak 23(17q25.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
AMP PEAK 23(17Q25.1) MUTATED	40	71	60
AMP PEAK 23(17Q25.1) WILD-TYPE	89	41	57

Figure S23. Get High-res Image Gene #23: 'Amp Peak 23(17q25.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 0.000148 (Fisher's exact test), Q value = 0.11

Table S24. Gene #23: 'Amp Peak 23(17q25.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	75	59
AMP PEAK 23(17Q25.1) MUTATED	35	49	19
AMP PEAK 23(17Q25.1) WILD-TYPE	55	26	40

Figure S24. Get High-res Image Gene #23: 'Amp Peak 23(17q25.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 0.000148 (Fisher's exact test), Q value = 0.11

Table S25. Gene #24: 'Amp Peak 24(18p11.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
AMP PEAK 24(18P11.32) MUTATED	29	54	39
AMP PEAK 24(18P11.32) WILD-TYPE	100	58	78

Figure S25. Get High-res Image Gene #24: 'Amp Peak 24(18p11.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 0.000231 (Fisher's exact test), Q value = 0.16

Table S26. Gene #25: 'Amp Peak 25(18q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
AMP PEAK 25(18Q11.2) MUTATED	26	50	39
AMP PEAK 25(18Q11.2) WILD-TYPE	103	62	78

Figure S26. Get High-res Image Gene #25: 'Amp Peak 25(18q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 0.000111 (Fisher's exact test), Q value = 0.08

Table S27. Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
AMP PEAK 26(19Q12) MUTATED	42	65	42
AMP PEAK 26(19Q12) WILD-TYPE	87	47	75

Figure S27. Get High-res Image Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 4.62e-08 (Fisher's exact test), Q value = 3.6e-05

Table S28. Gene #28: 'Amp Peak 28(20p12.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
AMP PEAK 28(20P12.2) MUTATED	48	83	62
AMP PEAK 28(20P12.2) WILD-TYPE	81	29	55

Figure S28. Get High-res Image Gene #28: 'Amp Peak 28(20p12.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 1.28e-06 (Fisher's exact test), Q value = 0.00098

Table S29. Gene #32: 'Del Peak 1(1p36.32) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	50	30	31
DEL PEAK 1(1P36.32) MUTATED	9	37	12	10
DEL PEAK 1(1P36.32) WILD-TYPE	34	13	18	21

Figure S29. Get High-res Image Gene #32: 'Del Peak 1(1p36.32) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

P value = 1.29e-08 (Fisher's exact test), Q value = 1e-05

Table S30. Gene #32: 'Del Peak 1(1p36.32) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	54	72
DEL PEAK 1(1P36.32) MUTATED	10	41	17
DEL PEAK 1(1P36.32) WILD-TYPE	18	13	55

Figure S30. Get High-res Image Gene #32: 'Del Peak 1(1p36.32) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

P value = 3.34e-28 (Fisher's exact test), Q value = 2.6e-25

Table S31. Gene #32: 'Del Peak 1(1p36.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
DEL PEAK 1(1P36.32) MUTATED	33	96	26
DEL PEAK 1(1P36.32) WILD-TYPE	96	16	91

Figure S31. Get High-res Image Gene #32: 'Del Peak 1(1p36.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 4.78e-16 (Fisher's exact test), Q value = 3.8e-13

Table S32. Gene #32: 'Del Peak 1(1p36.32) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	75	59
DEL PEAK 1(1P36.32) MUTATED	15	59	19
DEL PEAK 1(1P36.32) WILD-TYPE	75	16	40

Figure S32. Get High-res Image Gene #32: 'Del Peak 1(1p36.32) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 1.02e-10 (Fisher's exact test), Q value = 8e-08

Table S33. Gene #32: 'Del Peak 1(1p36.32) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	60	80	79	38
DEL PEAK 1(1P36.32) MUTATED	16	61	26	11
DEL PEAK 1(1P36.32) WILD-TYPE	44	19	53	27

Figure S33. Get High-res Image Gene #32: 'Del Peak 1(1p36.32) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 6.75e-09 (Fisher's exact test), Q value = 5.3e-06

Table S34. Gene #32: 'Del Peak 1(1p36.32) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	116	86	55
DEL PEAK 1(1P36.32) MUTATED	37	61	16
DEL PEAK 1(1P36.32) WILD-TYPE	79	25	39

Figure S34. Get High-res Image Gene #32: 'Del Peak 1(1p36.32) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

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

Table S35. Gene #33: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

Figure S35. Get High-res Image Gene #33: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

P value = 6.47e-14 (Fisher's exact test), Q value = 5.1e-11

Table S36. Gene #33: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
DEL PEAK 2(1P13.2) MUTATED	34	82	40
DEL PEAK 2(1P13.2) WILD-TYPE	95	30	77

Figure S36. Get High-res Image Gene #33: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 6.52e-09 (Fisher's exact test), Q value = 5.1e-06

Table S37. Gene #33: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	75	59
DEL PEAK 2(1P13.2) MUTATED	19	51	24
DEL PEAK 2(1P13.2) WILD-TYPE	71	24	35

Figure S37. Get High-res Image Gene #33: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 2.35e-05 (Fisher's exact test), Q value = 0.018

Table S38. Gene #33: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	60	80	79	38
DEL PEAK 2(1P13.2) MUTATED	23	53	25	12
DEL PEAK 2(1P13.2) WILD-TYPE	37	27	54	26

Figure S38. Get High-res Image Gene #33: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 7.07e-05 (Fisher's exact test), Q value = 0.052

Table S39. Gene #33: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	116	86	55
DEL PEAK 2(1P13.2) MUTATED	38	54	21
DEL PEAK 2(1P13.2) WILD-TYPE	78	32	34

Figure S39. Get High-res Image Gene #33: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 0.000217 (Fisher's exact test), Q value = 0.15

Table S40. Gene #35: 'Del Peak 4(2q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
DEL PEAK 4(2Q22.1) MUTATED	19	41	36
DEL PEAK 4(2Q22.1) WILD-TYPE	110	71	81

Figure S40. Get High-res Image Gene #35: 'Del Peak 4(2q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

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

Table S41. Gene #36: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

Figure S41. Get High-res Image Gene #36: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

P value = 4.76e-05 (Fisher's exact test), Q value = 0.035

Table S42. Gene #36: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

Figure S42. Get High-res Image Gene #36: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

P value = 5.32e-12 (Fisher's exact test), Q value = 4.2e-09

Table S43. Gene #36: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
DEL PEAK 5(2Q36.2) MUTATED	20	65	31
DEL PEAK 5(2Q36.2) WILD-TYPE	109	47	86

Figure S43. Get High-res Image Gene #36: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 0.000352 (Fisher's exact test), Q value = 0.25

Table S44. Gene #36: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	75	59
DEL PEAK 5(2Q36.2) MUTATED	19	38	19
DEL PEAK 5(2Q36.2) WILD-TYPE	71	37	40

Figure S44. Get High-res Image Gene #36: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 8.49e-05 (Fisher's exact test), Q value = 0.062

Table S45. Gene #36: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	60	80	79	38
DEL PEAK 5(2Q36.2) MUTATED	17	40	18	5
DEL PEAK 5(2Q36.2) WILD-TYPE	43	40	61	33

Figure S45. Get High-res Image Gene #36: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 6.15e-06 (Fisher's exact test), Q value = 0.0047

Table S46. Gene #36: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	116	86	55
DEL PEAK 5(2Q36.2) MUTATED	23	44	13
DEL PEAK 5(2Q36.2) WILD-TYPE	93	42	42

Figure S46. Get High-res Image Gene #36: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 9.68e-05 (Fisher's exact test), Q value = 0.07

Table S47. Gene #38: 'Del Peak 7(3p13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
DEL PEAK 7(3P13) MUTATED	98	104	108
DEL PEAK 7(3P13) WILD-TYPE	31	8	9

Figure S47. Get High-res Image Gene #38: 'Del Peak 7(3p13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 8(3p12.1) mutation analysis' versus 'CN_CNMF'

P value = 1.46e-07 (Fisher's exact test), Q value = 0.00011

Table S48. Gene #39: 'Del Peak 8(3p12.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
DEL PEAK 8(3P12.1) MUTATED	80	101	99
DEL PEAK 8(3P12.1) WILD-TYPE	49	11	18

Figure S48. Get High-res Image Gene #39: 'Del Peak 8(3p12.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 8(3p12.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.79e-05 (Fisher's exact test), Q value = 0.021

Table S49. Gene #39: 'Del Peak 8(3p12.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	75	59
DEL PEAK 8(3P12.1) MUTATED	59	66	55
DEL PEAK 8(3P12.1) WILD-TYPE	31	9	4

Figure S49. Get High-res Image Gene #39: 'Del Peak 8(3p12.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 9(4p15.31) mutation analysis' versus 'CN_CNMF'

P value = 1.21e-05 (Fisher's exact test), Q value = 0.0091

Table S50. Gene #40: 'Del Peak 9(4p15.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
DEL PEAK 9(4P15.31) MUTATED	65	88	66
DEL PEAK 9(4P15.31) WILD-TYPE	64	24	51

Figure S50. Get High-res Image Gene #40: 'Del Peak 9(4p15.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 11(4q32.3) mutation analysis' versus 'CN_CNMF'

P value = 2.97e-07 (Fisher's exact test), Q value = 0.00023

Table S51. Gene #42: 'Del Peak 11(4q32.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
DEL PEAK 11(4Q32.3) MUTATED	67	93	66
DEL PEAK 11(4Q32.3) WILD-TYPE	62	19	51

Figure S51. Get High-res Image Gene #42: 'Del Peak 11(4q32.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 12(4q35.2) mutation analysis' versus 'CN_CNMF'

P value = 1.07e-06 (Fisher's exact test), Q value = 0.00082

Table S52. Gene #43: 'Del Peak 12(4q35.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
DEL PEAK 12(4Q35.2) MUTATED	70	93	66
DEL PEAK 12(4Q35.2) WILD-TYPE	59	19	51

Figure S52. Get High-res Image Gene #43: 'Del Peak 12(4q35.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 13(5q11.2) mutation analysis' versus 'CN_CNMF'

P value = 5.71e-10 (Fisher's exact test), Q value = 4.5e-07

Table S53. Gene #44: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
DEL PEAK 13(5Q11.2) MUTATED	69	96	100
DEL PEAK 13(5Q11.2) WILD-TYPE	60	16	17

Figure S53. Get High-res Image Gene #44: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 13(5q11.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000266 (Fisher's exact test), Q value = 0.19

Table S54. Gene #44: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	75	59
DEL PEAK 13(5Q11.2) MUTATED	54	62	51
DEL PEAK 13(5Q11.2) WILD-TYPE	36	13	8

Figure S54. Get High-res Image Gene #44: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 13(5q11.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S55. Gene #44: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	173	108
DEL PEAK 13(5Q11.2) MUTATED	39	115	95
DEL PEAK 13(5Q11.2) WILD-TYPE	11	58	13

Figure S55. Get High-res Image Gene #44: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 14(5q31.1) mutation analysis' versus 'CN_CNMF'

P value = 6.21e-07 (Fisher's exact test), Q value = 0.00048

Table S56. Gene #45: 'Del Peak 14(5q31.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
DEL PEAK 14(5Q31.1) MUTATED	79	97	101
DEL PEAK 14(5Q31.1) WILD-TYPE	50	15	16

Figure S56. Get High-res Image Gene #45: 'Del Peak 14(5q31.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 14(5q31.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.25e-05 (Fisher's exact test), Q value = 0.024

Table S57. Gene #45: 'Del Peak 14(5q31.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	75	59
DEL PEAK 14(5Q31.1) MUTATED	58	64	55
DEL PEAK 14(5Q31.1) WILD-TYPE	32	11	4

Figure S57. Get High-res Image Gene #45: 'Del Peak 14(5q31.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 20(9p23) mutation analysis' versus 'CN_CNMF'

P value = 1.21e-07 (Fisher's exact test), Q value = 9.4e-05

Table S58. Gene #51: 'Del Peak 20(9p23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
DEL PEAK 20(9P23) MUTATED	68	67	99
DEL PEAK 20(9P23) WILD-TYPE	61	45	18

Figure S58. Get High-res Image Gene #51: 'Del Peak 20(9p23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 21(9p21.3) mutation analysis' versus 'CN_CNMF'

P value = 3.23e-06 (Fisher's exact test), Q value = 0.0025

Table S59. Gene #52: 'Del Peak 21(9p21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
DEL PEAK 21(9P21.3) MUTATED	81	86	105
DEL PEAK 21(9P21.3) WILD-TYPE	48	26	12

Figure S59. Get High-res Image Gene #52: 'Del Peak 21(9p21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 22(9q21.11) mutation analysis' versus 'MRNA_CNMF'

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

Table S60. Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	50	30	31
DEL PEAK 22(9Q21.11) MUTATED	28	12	19	15
DEL PEAK 22(9Q21.11) WILD-TYPE	15	38	11	16

Figure S60. Get High-res Image Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 22(9q21.11) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 4.92e-05 (Fisher's exact test), Q value = 0.036

Table S61. Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	54	72
DEL PEAK 22(9Q21.11) MUTATED	16	13	45
DEL PEAK 22(9Q21.11) WILD-TYPE	12	41	27

Figure S61. Get High-res Image Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 22(9q21.11) mutation analysis' versus 'CN_CNMF'

P value = 2.03e-07 (Fisher's exact test), Q value = 0.00016

Table S62. Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
DEL PEAK 22(9Q21.11) MUTATED	62	34	78
DEL PEAK 22(9Q21.11) WILD-TYPE	67	78	39

Figure S62. Get High-res Image Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 22(9q21.11) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.42e-06 (Fisher's exact test), Q value = 0.0011

Table S63. Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	75	59
DEL PEAK 22(9Q21.11) MUTATED	49	19	40
DEL PEAK 22(9Q21.11) WILD-TYPE	41	56	19

Figure S63. Get High-res Image Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 22(9q21.11) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 4.44e-06 (Fisher's exact test), Q value = 0.0034

Table S64. Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	60	80	79	38
DEL PEAK 22(9Q21.11) MUTATED	33	19	48	22
DEL PEAK 22(9Q21.11) WILD-TYPE	27	61	31	16

Figure S64. Get High-res Image Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 22(9q21.11) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.4e-07 (Fisher's exact test), Q value = 0.00018

Table S65. Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	116	86	55
DEL PEAK 22(9Q21.11) MUTATED	64	21	37
DEL PEAK 22(9Q21.11) WILD-TYPE	52	65	18

Figure S65. Get High-res Image Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 22(9q21.11) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.16e-05 (Fisher's exact test), Q value = 0.023

Table S66. Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	173	108
DEL PEAK 22(9Q21.11) MUTATED	10	90	61
DEL PEAK 22(9Q21.11) WILD-TYPE	40	83	47

Figure S66. Get High-res Image Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 0.00019 (Fisher's exact test), Q value = 0.14

Table S67. Gene #55: 'Del Peak 24(10q23.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
DEL PEAK 24(10Q23.31) MUTATED	53	75	56
DEL PEAK 24(10Q23.31) WILD-TYPE	76	37	61

Figure S67. Get High-res Image Gene #55: 'Del Peak 24(10q23.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 24(10q23.31) mutation analysis' versus 'METHLYATION_CNMF'

P value = 6.42e-05 (Fisher's exact test), Q value = 0.047

Table S68. Gene #55: 'Del Peak 24(10q23.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	75	59
DEL PEAK 24(10Q23.31) MUTATED	33	53	30
DEL PEAK 24(10Q23.31) WILD-TYPE	57	22	29

Figure S68. Get High-res Image Gene #55: 'Del Peak 24(10q23.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 24(10q23.31) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000104 (Fisher's exact test), Q value = 0.075

Table S69. Gene #55: 'Del Peak 24(10q23.31) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	60	80	79	38
DEL PEAK 24(10Q23.31) MUTATED	22	57	35	16
DEL PEAK 24(10Q23.31) WILD-TYPE	38	23	44	22

Figure S69. Get High-res Image Gene #55: 'Del Peak 24(10q23.31) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 24(10q23.31) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.63e-05 (Fisher's exact test), Q value = 0.02

Table S70. Gene #55: 'Del Peak 24(10q23.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	116	86	55
DEL PEAK 24(10Q23.31) MUTATED	42	59	29
DEL PEAK 24(10Q23.31) WILD-TYPE	74	27	26

Figure S70. Get High-res Image Gene #55: 'Del Peak 24(10q23.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 25(11p15.5) mutation analysis' versus 'CN_CNMF'

P value = 6.04e-05 (Fisher's exact test), Q value = 0.044

Table S71. Gene #56: 'Del Peak 25(11p15.5) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
DEL PEAK 25(11P15.5) MUTATED	47	51	75
DEL PEAK 25(11P15.5) WILD-TYPE	82	61	42

Figure S71. Get High-res Image Gene #56: 'Del Peak 25(11p15.5) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 25(11p15.5) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 2.34e-05 (Fisher's exact test), Q value = 0.017

Table S72. Gene #56: 'Del Peak 25(11p15.5) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	47	48	58	41
DEL PEAK 25(11P15.5) MUTATED	35	17	29	11
DEL PEAK 25(11P15.5) WILD-TYPE	12	31	29	30

Figure S72. Get High-res Image Gene #56: 'Del Peak 25(11p15.5) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 36(17q11.2) mutation analysis' versus 'MRNA_CNMF'

P value = 1.26e-05 (Fisher's exact test), Q value = 0.0095

Table S73. Gene #67: 'Del Peak 36(17q11.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	50	30	31
DEL PEAK 36(17Q11.2) MUTATED	21	3	11	7
DEL PEAK 36(17Q11.2) WILD-TYPE	22	47	19	24

Figure S73. Get High-res Image Gene #67: 'Del Peak 36(17q11.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 36(17q11.2) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 6.44e-05 (Fisher's exact test), Q value = 0.047

Table S74. Gene #67: 'Del Peak 36(17q11.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	54	72
DEL PEAK 36(17Q11.2) MUTATED	9	4	29
DEL PEAK 36(17Q11.2) WILD-TYPE	19	50	43

Figure S74. Get High-res Image Gene #67: 'Del Peak 36(17q11.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 36(17q11.2) mutation analysis' versus 'CN_CNMF'

P value = 9.35e-09 (Fisher's exact test), Q value = 7.3e-06

Table S75. Gene #67: 'Del Peak 36(17q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
DEL PEAK 36(17Q11.2) MUTATED	34	8	47
DEL PEAK 36(17Q11.2) WILD-TYPE	95	104	70

Figure S75. Get High-res Image Gene #67: 'Del Peak 36(17q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 36(17q11.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000122 (Fisher's exact test), Q value = 0.088

Table S76. Gene #67: 'Del Peak 36(17q11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	60	80	79	38
DEL PEAK 36(17Q11.2) MUTATED	20	6	23	13
DEL PEAK 36(17Q11.2) WILD-TYPE	40	74	56	25

Figure S76. Get High-res Image Gene #67: 'Del Peak 36(17q11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 36(17q11.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.16e-06 (Fisher's exact test), Q value = 0.0054

Table S77. Gene #67: 'Del Peak 36(17q11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	116	86	55
DEL PEAK 36(17Q11.2) MUTATED	39	6	17
DEL PEAK 36(17Q11.2) WILD-TYPE	77	80	38

Figure S77. Get High-res Image Gene #67: 'Del Peak 36(17q11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 39(19p13.3) mutation analysis' versus 'CN_CNMF'

P value = 0.000227 (Fisher's exact test), Q value = 0.16

Table S78. Gene #70: 'Del Peak 39(19p13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
DEL PEAK 39(19P13.3) MUTATED	46	46	71
DEL PEAK 39(19P13.3) WILD-TYPE	83	66	46

Figure S78. Get High-res Image Gene #70: 'Del Peak 39(19p13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 40(19q13.33) mutation analysis' versus 'CN_CNMF'

P value = 4.76e-05 (Fisher's exact test), Q value = 0.035

Table S79. Gene #71: 'Del Peak 40(19q13.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
DEL PEAK 40(19Q13.33) MUTATED	20	46	30
DEL PEAK 40(19Q13.33) WILD-TYPE	109	66	87

Figure S79. Get High-res Image Gene #71: 'Del Peak 40(19q13.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 40(19q13.33) mutation analysis' versus 'METHLYATION_CNMF'

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

Table S80. Gene #71: 'Del Peak 40(19q13.33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	75	59
DEL PEAK 40(19Q13.33) MUTATED	11	27	21
DEL PEAK 40(19Q13.33) WILD-TYPE	79	48	38

Figure S80. Get High-res Image Gene #71: 'Del Peak 40(19q13.33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 41(19q13.43) mutation analysis' versus 'CN_CNMF'

P value = 9.08e-05 (Fisher's exact test), Q value = 0.066

Table S81. Gene #72: 'Del Peak 41(19q13.43) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
DEL PEAK 41(19Q13.43) MUTATED	20	45	31
DEL PEAK 41(19Q13.43) WILD-TYPE	109	67	86

Figure S81. Get High-res Image Gene #72: 'Del Peak 41(19q13.43) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 43(21q22.3) mutation analysis' versus 'CN_CNMF'

P value = 2.21e-08 (Fisher's exact test), Q value = 1.7e-05

Table S82. Gene #74: 'Del Peak 43(21q22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
DEL PEAK 43(21Q22.3) MUTATED	48	82	75
DEL PEAK 43(21Q22.3) WILD-TYPE	81	30	42

Figure S82. Get High-res Image Gene #74: 'Del Peak 43(21q22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 45(Xp22.2) mutation analysis' versus 'CN_CNMF'

P value = 1.57e-05 (Fisher's exact test), Q value = 0.012

Table S83. Gene #76: 'Del Peak 45(Xp22.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
DEL PEAK 45(XP22.2) MUTATED	22	48	44
DEL PEAK 45(XP22.2) WILD-TYPE	107	64	73

Figure S83. Get High-res Image Gene #76: 'Del Peak 45(Xp22.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 46(Xp21.1) mutation analysis' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S84. Gene #77: 'Del Peak 46(Xp21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
DEL PEAK 46(XP21.1) MUTATED	24	51	43
DEL PEAK 46(XP21.1) WILD-TYPE	105	61	74

Figure S84. Get High-res Image Gene #77: 'Del Peak 46(Xp21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 47(Xp11.3) mutation analysis' versus 'CN_CNMF'

P value = 2.82e-06 (Fisher's exact test), Q value = 0.0021

Table S85. Gene #78: 'Del Peak 47(Xp11.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
DEL PEAK 47(XP11.3) MUTATED	22	52	42
DEL PEAK 47(XP11.3) WILD-TYPE	107	60	75

Figure S85. Get High-res Image Gene #78: 'Del Peak 47(Xp11.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 47(Xp11.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.16e-05 (Fisher's exact test), Q value = 0.038

Table S86. Gene #78: 'Del Peak 47(Xp11.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	75	59
DEL PEAK 47(XP11.3) MUTATED	15	36	22
DEL PEAK 47(XP11.3) WILD-TYPE	75	39	37

Figure S86. Get High-res Image Gene #78: 'Del Peak 47(Xp11.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 48(Xq22.3) mutation analysis' versus 'CN_CNMF'

P value = 1.03e-05 (Fisher's exact test), Q value = 0.0078

Table S87. Gene #79: 'Del Peak 48(Xq22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	129	112	117
DEL PEAK 48(XQ22.3) MUTATED	16	30	45
DEL PEAK 48(XQ22.3) WILD-TYPE	113	82	72

Figure S87. Get High-res Image Gene #79: 'Del Peak 48(Xq22.3) mutation analysis' versus Clinical Feature #3: '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 = LUSC-TP.transferedmergedcluster.txt
Number of patients = 358
Number of copy number variation regions = 79
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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