Correlation between copy number variation genes and molecular subtypes

Overview

Introduction

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

Summary

Testing the association between copy number variation of 84 peak regions and 10 molecular subtypes across 397 patients, 99 significant findings detected with Q value < 0.25.

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

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 84 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 99 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 24(9q21 11)	191 (48%)	206	0.000177 (0.134)	4.92e-05 (0.0382)	5.97e-11 (4.97e-08)	1.14e-06 (0.000931)	0.653 (1.00)	0.239 (1.00)	4.44e-06 (0.00357)	2.4e-07 (0.000196)	0.0643 (1.00)	0.000283 (0.211)
Amp Peak 6(3q26 33)	364 (92%)	33	0.000427 (0.314)	1.71e-05 (0.0135)	7.05e-12 (5.88e-09)	6.69e-07 (0.000545)	0.193 (1.00)	0.0776 (1.00)	3.81e-05 (0.0297)	0.000164 (0.125)	0.238 (1.00)	1.37e-05 (0.0109)
Del Peak 1(1p36 22)	172 (43%)	225	1.43e-06 (0.00116)	1.78e-08 (1.47e-05)	1.61e-28 (1.36e-25)	2.1e-14 (1.76e-11)	0.412 (1.00)	0.0262 (1.00)	1.09e-09 (9.05e-07)	1.35e-08 (1.12e-05)	0.0227 (1.00)	0.00387 (1.00)
Del Peak 5(2q36 2)	132 (33%)	265	0.000236 (0.178)	4.76e-05 (0.037)	1.7e-12 (1.42e-09)	2.14e-06 (0.00174)	0.177 (1.00)	0.126 (1.00)	8.49e-05 (0.0653)	6.15e-06 (0.00494)	0.986 (1.00)	0.587 (1.00)
Del Peak 2(1p13 2)	172 (43%)	225	0.000237 (0.178)	0.00055 (0.4)	1.23e-15 (1.03e-12)	5.74e-09 (4.75e-06)	0.119 (1.00)	0.0712 (1.00)	2.35e-05 (0.0185)	7.07e-05 (0.0545)	0.165 (1.00)	0.0246 (1.00)
Del Peak 40(17q11 2)	96 (24%)	301	1.26e-05 (0.01)	6.44e-05 (0.0497)	3.04e-08 (2.51e-05)	0.0177 (1.00)	0.495 (1.00)	0.378 (1.00)	0.000122 (0.0932)	7.16e-06 (0.00574)	0.426 (1.00)	0.0683 (1.00)
Amp Peak 3(2p16 1)	216 (54%)	181	0.000305 (0.227)	0.00165 (1.00)	3.18e-13 (2.66e-10)	5.83e-05 (0.045)	0.95 (1.00)	0.643 (1.00)	0.000333 (0.247)	0.00113 (0.799)	0.79 (1.00)	0.043 (1.00)
Del Peak 27(10q23 31)	203 (51%)	194	0.0392 (1.00)	0.00386 (1.00)	2.17e-05 (0.017)	2.08e-06 (0.00169)	0.36 (1.00)	0.39 (1.00)	0.000104 (0.0793)	2.63e-05 (0.0206)	0.541 (1.00)	0.0173 (1.00)
Del Peak 14(5q11 2)	290 (73%)	107	0.842 (1.00)	0.303 (1.00)	2.03e-12 (1.7e-09)	0.000192 (0.145)	0.959 (1.00)	0.244 (1.00)	0.248 (1.00)	0.56 (1.00)	0.953 (1.00)	8.06e-05 (0.0621)
Del Peak 26(10p15 1)	168 (42%)	229	0.0722 (1.00)	0.484 (1.00)	0.000162 (0.123)	4.03e-06 (0.00325)	0.469 (1.00)	0.353 (1.00)	0.000259 (0.194)	0.0131 (1.00)	0.0442 (1.00)	0.00516 (1.00)
Amp Peak 4(2q31 2)	132 (33%)	265	0.0207 (1.00)	0.000948 (0.675)	6.52e-06 (0.00523)	1.99e-07 (0.000163)	0.724 (1.00)	0.887 (1.00)	0.000801 (0.575)	0.000932 (0.665)	0.426 (1.00)	0.37 (1.00)
Amp Peak 13(7q21 2)	209 (53%)	188	0.101 (1.00)	0.25 (1.00)	5.34e-10 (4.44e-07)	1.27e-05 (0.0101)	0.0573 (1.00)	0.389 (1.00)	0.0165 (1.00)	0.0221 (1.00)	0.122 (1.00)	0.0892 (1.00)
Amp Peak 23(15q26 3)	139 (35%)	258	0.151 (1.00)	0.021 (1.00)	1.56e-05 (0.0123)	9.39e-06 (0.0075)	0.354 (1.00)	0.0183 (1.00)	0.000622 (0.45)	0.00426 (1.00)	0.0241 (1.00)	0.000437 (0.321)
Amp Peak 24(17q25 1)	191 (48%)	206	0.0177 (1.00)	0.0608 (1.00)	6.01e-07 (0.00049)	2.17e-05 (0.017)	0.267 (1.00)	0.292 (1.00)	0.0274 (1.00)	0.00807 (1.00)	0.611 (1.00)	0.893 (1.00)
Amp Peak 25(18p11 32)	137 (35%)	260	0.0958 (1.00)	0.00981 (1.00)	2.48e-05 (0.0195)	0.000126 (0.096)	0.231 (1.00)	0.451 (1.00)	0.41 (1.00)	0.121 (1.00)	0.66 (1.00)	0.135 (1.00)
Amp Peak 29(20p12 2)	211 (53%)	186	0.000987 (0.698)	0.0043 (1.00)	8.92e-08 (7.34e-05)	0.000161 (0.123)	0.967 (1.00)	0.221 (1.00)	0.15 (1.00)	0.0134 (1.00)	0.611 (1.00)	0.279 (1.00)
Del Peak 13(4q35 2)	253 (64%)	144	0.1 (1.00)	0.206 (1.00)	2.84e-06 (0.0023)	0.000124 (0.0944)	0.455 (1.00)	0.47 (1.00)	0.00532 (1.00)	0.107 (1.00)	0.63 (1.00)	0.309 (1.00)
Del Peak 15(5q31 1)	308 (78%)	89	0.332 (1.00)	0.228 (1.00)	5.7e-09 (4.72e-06)	3e-05 (0.0235)	0.272 (1.00)	0.166 (1.00)	0.294 (1.00)	0.445 (1.00)	0.709 (1.00)	0.000462 (0.339)
Del Peak 25(10p15 3)	178 (45%)	219	0.373 (1.00)	0.442 (1.00)	4.8e-05 (0.0373)	9.6e-05 (0.0736)	0.329 (1.00)	0.443 (1.00)	0.00383 (1.00)	0.0165 (1.00)	0.122 (1.00)	0.00273 (1.00)
Del Peak 28(11p15 5)	183 (46%)	214	0.000689 (0.497)	0.0528 (1.00)	1.28e-06 (0.00104)	0.0352 (1.00)	0.000764 (0.549)	2.02e-05 (0.0159)	0.02 (1.00)	0.0362 (1.00)	0.0436 (1.00)	0.0754 (1.00)
Del Peak 44(19q13 33)	106 (27%)	291	0.617 (1.00)	0.0694 (1.00)	0.000167 (0.126)	0.000187 (0.141)	0.244 (1.00)	0.719 (1.00)	0.436 (1.00)	0.212 (1.00)	0.438 (1.00)	0.126 (1.00)
Del Peak 48(22q13 32)	95 (24%)	302	0.000281 (0.21)	8.68e-05 (0.0667)	0.0172 (1.00)	0.351 (1.00)	0.543 (1.00)	0.0759 (1.00)	0.0575 (1.00)	0.162 (1.00)	0.0961 (1.00)	0.0162 (1.00)
Del Peak 50(Xp21 1)	127 (32%)	270	0.354 (1.00)	0.148 (1.00)	5.39e-05 (0.0417)	0.00024 (0.18)	0.344 (1.00)	0.681 (1.00)	0.0779 (1.00)	0.00716 (1.00)	0.321 (1.00)	0.0974 (1.00)
Del Peak 51(Xp11 3)	125 (31%)	272	0.062 (1.00)	0.175 (1.00)	9.19e-06 (0.00735)	4.09e-05 (0.0319)	0.0923 (1.00)	0.124 (1.00)	0.0142 (1.00)	0.0175 (1.00)	0.0635 (1.00)	0.193 (1.00)
Del Peak 52(Xq22 3)	95 (24%)	302	0.00853 (1.00)	0.105 (1.00)	1.91e-05 (0.015)	0.000249 (0.187)	0.663 (1.00)	0.92 (1.00)	0.0513 (1.00)	0.485 (1.00)	0.535 (1.00)	0.942 (1.00)
Amp Peak 2(1q21 2)	205 (52%)	192	0.0419 (1.00)	0.00618 (1.00)	1.98e-07 (0.000163)	0.00113 (0.798)	0.16 (1.00)	0.0492 (1.00)	0.000685 (0.495)	0.000488 (0.357)	0.178 (1.00)	0.0377 (1.00)
Amp Peak 8(5p15 33)	314 (79%)	83	0.853 (1.00)	0.867 (1.00)	1.07e-05 (0.00852)	0.0129 (1.00)	0.405 (1.00)	0.502 (1.00)	0.387 (1.00)	0.328 (1.00)	0.71 (1.00)	0.18 (1.00)
Amp Peak 9(5p12)	261 (66%)	136	0.919 (1.00)	0.514 (1.00)	7.58e-10 (6.29e-07)	0.00874 (1.00)	0.563 (1.00)	1 (1.00)	0.0635 (1.00)	0.586 (1.00)	0.0397 (1.00)	0.116 (1.00)
Amp Peak 19(12p13 33)	198 (50%)	199	0.0102 (1.00)	0.0571 (1.00)	1.23e-05 (0.00977)	0.000492 (0.359)	0.313 (1.00)	0.729 (1.00)	0.000575 (0.418)	0.00518 (1.00)	0.583 (1.00)	0.539 (1.00)
Amp Peak 26(18q11 2)	126 (32%)	271	0.000456 (0.334)	0.00227 (1.00)	1.37e-05 (0.0108)	0.000342 (0.253)	0.272 (1.00)	0.74 (1.00)	0.00438 (1.00)	0.000578 (0.419)	0.32 (1.00)	0.012 (1.00)
Amp Peak 27(19q12)	167 (42%)	230	0.455 (1.00)	0.249 (1.00)	4.07e-06 (0.00328)	0.182 (1.00)	0.231 (1.00)	0.0287 (1.00)	0.193 (1.00)	0.082 (1.00)	0.951 (1.00)	0.609 (1.00)
Amp Peak 28(19q13 2)	170 (43%)	227	0.715 (1.00)	1 (1.00)	0.000195 (0.147)	0.0708 (1.00)	0.356 (1.00)	0.117 (1.00)	0.626 (1.00)	0.053 (1.00)	0.872 (1.00)	0.454 (1.00)
Amp Peak 31(22q11 21)	199 (50%)	198	0.111 (1.00)	0.123 (1.00)	0.000296 (0.22)	0.000477 (0.349)	0.888 (1.00)	0.349 (1.00)	0.0671 (1.00)	0.0677 (1.00)	0.727 (1.00)	0.103 (1.00)
Del Peak 4(2q22 1)	105 (26%)	292	0.255 (1.00)	0.318 (1.00)	0.000271 (0.203)	0.0198 (1.00)	0.667 (1.00)	0.0777 (1.00)	0.188 (1.00)	0.231 (1.00)	0.648 (1.00)	0.551 (1.00)
Del Peak 7(3p13)	340 (86%)	57	0.419 (1.00)	0.549 (1.00)	2.67e-06 (0.00216)	0.000858 (0.613)	0.882 (1.00)	0.0379 (1.00)	0.369 (1.00)	0.0134 (1.00)	0.926 (1.00)	0.0046 (1.00)
Del Peak 8(3p12 3)	332 (84%)	65	0.258 (1.00)	0.342 (1.00)	3.03e-05 (0.0236)	0.00259 (1.00)	1 (1.00)	0.092 (1.00)	0.24 (1.00)	0.0162 (1.00)	0.894 (1.00)	0.00899 (1.00)
Del Peak 10(4p15 2)	239 (60%)	158	0.000807 (0.579)	0.00171 (1.00)	6.52e-06 (0.00523)	0.000341 (0.252)	0.662 (1.00)	0.0343 (1.00)	0.0883 (1.00)	0.0514 (1.00)	0.325 (1.00)	0.921 (1.00)
Del Peak 11(4q22 1)	217 (55%)	180	0.00685 (1.00)	0.0579 (1.00)	0.000102 (0.0782)	0.00829 (1.00)	0.123 (1.00)	0.381 (1.00)	0.0252 (1.00)	0.00636 (1.00)	0.219 (1.00)	0.242 (1.00)
Del Peak 12(4q32 3)	248 (62%)	149	0.00967 (1.00)	0.0253 (1.00)	3.5e-07 (0.000286)	0.000596 (0.432)	0.101 (1.00)	0.523 (1.00)	0.0057 (1.00)	0.036 (1.00)	0.344 (1.00)	0.0974 (1.00)
Del Peak 19(7q11 22)	37 (9%)	360	0.908 (1.00)	0.405 (1.00)	4.4e-05 (0.0342)	0.829 (1.00)	0.958 (1.00)	0.75 (1.00)	0.0463 (1.00)	0.0644 (1.00)	0.837 (1.00)	0.524 (1.00)
Del Peak 22(9p23)	258 (65%)	139	0.00561 (1.00)	0.00291 (1.00)	1.97e-10 (1.64e-07)	0.104 (1.00)	0.146 (1.00)	0.208 (1.00)	0.0261 (1.00)	0.0876 (1.00)	0.986 (1.00)	0.0652 (1.00)
Del Peak 23(9p21 3)	302 (76%)	95	0.372 (1.00)	0.172 (1.00)	4.99e-07 (0.000408)	0.409 (1.00)	0.695 (1.00)	0.388 (1.00)	0.164 (1.00)	0.846 (1.00)	0.852 (1.00)	0.296 (1.00)
Del Peak 43(19p13 3)	173 (44%)	224	0.334 (1.00)	0.0231 (1.00)	1.38e-05 (0.0109)	0.145 (1.00)	0.0588 (1.00)	0.251 (1.00)	0.16 (1.00)	0.0124 (1.00)	0.0229 (1.00)	0.0692 (1.00)
Del Peak 46(21q22 3)	224 (56%)	173	0.957 (1.00)	0.193 (1.00)	2.13e-08 (1.75e-05)	0.00206 (1.00)	0.396 (1.00)	0.0991 (1.00)	0.564 (1.00)	0.302 (1.00)	0.00395 (1.00)	0.347 (1.00)
Del Peak 49(Xp22 2)	126 (32%)	271	0.599 (1.00)	0.351 (1.00)	0.000249 (0.187)	0.0101 (1.00)	0.277 (1.00)	0.783 (1.00)	0.14 (1.00)	0.122 (1.00)	0.122 (1.00)	0.244 (1.00)
Amp Peak 1(1p34 2)	63 (16%)	334	0.028 (1.00)	0.481 (1.00)	0.000892 (0.637)	0.644 (1.00)	0.363 (1.00)	0.619 (1.00)	0.0484 (1.00)	0.241 (1.00)	0.222 (1.00)	0.654 (1.00)
Amp Peak 5(3p11 1)	80 (20%)	317	0.0748 (1.00)	0.844 (1.00)	0.744 (1.00)	0.957 (1.00)	0.214 (1.00)	0.0013 (0.913)	0.0555 (1.00)	0.444 (1.00)	0.382 (1.00)	0.772 (1.00)
Amp Peak 7(4q12)	93 (23%)	304	0.679 (1.00)	0.759 (1.00)	0.000353 (0.261)	0.124 (1.00)	0.356 (1.00)	0.131 (1.00)	0.555 (1.00)	0.75 (1.00)	0.163 (1.00)	0.439 (1.00)
Amp Peak 10(6p12 1)	130 (33%)	267	0.557 (1.00)	0.383 (1.00)	0.0018 (1.00)	0.168 (1.00)	0.962 (1.00)	0.3 (1.00)	0.178 (1.00)	0.841 (1.00)	0.933 (1.00)	0.464 (1.00)
Amp Peak 11(6q12)	117 (29%)	280	1 (1.00)	0.873 (1.00)	0.00114 (0.802)	0.0454 (1.00)	0.348 (1.00)	0.408 (1.00)	0.395 (1.00)	0.236 (1.00)	0.595 (1.00)	0.214 (1.00)
Amp Peak 12(7p11 2)	193 (49%)	204	0.186 (1.00)	0.0939 (1.00)	0.00097 (0.687)	0.00366 (1.00)	0.687 (1.00)	0.801 (1.00)	0.076 (1.00)	0.0148 (1.00)	0.46 (1.00)	0.157 (1.00)
Amp Peak 14(8p11 23)	184 (46%)	213	0.00812 (1.00)	0.168 (1.00)	0.0254 (1.00)	0.0352 (1.00)	0.192 (1.00)	0.0988 (1.00)	0.00631 (1.00)	0.72 (1.00)	0.131 (1.00)	0.771 (1.00)
Amp Peak 15(8q24 21)	280 (71%)	117	0.871 (1.00)	0.644 (1.00)	0.554 (1.00)	0.969 (1.00)	0.917 (1.00)	0.708 (1.00)	0.734 (1.00)	0.428 (1.00)	0.392 (1.00)	0.935 (1.00)
Amp Peak 16(9p24 1)	73 (18%)	324	0.375 (1.00)	0.0295 (1.00)	0.000354 (0.261)	0.177 (1.00)	0.0017 (1.00)	0.00501 (1.00)	0.0413 (1.00)	0.00294 (1.00)	0.461 (1.00)	0.236 (1.00)
Amp Peak 17(9p13 3)	109 (27%)	288	0.17 (1.00)	0.373 (1.00)	0.043 (1.00)	0.0387 (1.00)	0.0708 (1.00)	0.00898 (1.00)	0.022 (1.00)	0.188 (1.00)	0.411 (1.00)	0.973 (1.00)
Amp Peak 18(11q13 3)	143 (36%)	254	0.0697 (1.00)	0.0306 (1.00)	0.00486 (1.00)	0.000518 (0.377)	0.19 (1.00)	0.0358 (1.00)	0.0125 (1.00)	0.139 (1.00)	0.142 (1.00)	0.214 (1.00)
Amp Peak 20(12q15)	144 (36%)	253	0.312 (1.00)	0.527 (1.00)	0.00531 (1.00)	0.00136 (0.956)	0.764 (1.00)	0.524 (1.00)	0.105 (1.00)	0.0491 (1.00)	0.509 (1.00)	0.93 (1.00)
Amp Peak 21(13q34)	71 (18%)	326	0.964 (1.00)	0.0489 (1.00)	0.0384 (1.00)	0.182 (1.00)	0.87 (1.00)	0.0834 (1.00)	0.803 (1.00)	0.407 (1.00)	0.0664 (1.00)	0.216 (1.00)
Amp Peak 22(14q13 3)	121 (30%)	276	0.345 (1.00)	0.246 (1.00)	0.127 (1.00)	0.0969 (1.00)	0.57 (1.00)	0.00826 (1.00)	0.617 (1.00)	0.0847 (1.00)	0.0275 (1.00)	0.0972 (1.00)
Amp Peak 30(20q11 21)	229 (58%)	168	0.991 (1.00)	0.844 (1.00)	0.00052 (0.379)	0.0132 (1.00)	0.669 (1.00)	0.588 (1.00)	0.593 (1.00)	0.549 (1.00)	0.904 (1.00)	0.519 (1.00)
Amp Peak 32(Xq28)	106 (27%)	291	0.633 (1.00)	0.636 (1.00)	0.039 (1.00)	0.0815 (1.00)	0.0701 (1.00)	0.069 (1.00)	0.136 (1.00)	0.165 (1.00)	0.502 (1.00)	0.734 (1.00)
Del Peak 3(2p25 3)	37 (9%)	360	0.0461 (1.00)	0.179 (1.00)	0.0773 (1.00)	0.37 (1.00)	0.11 (1.00)	0.838 (1.00)	0.32 (1.00)	0.226 (1.00)	0.096 (1.00)	0.0676 (1.00)
Del Peak 6(3p25 3)	313 (79%)	84	0.54 (1.00)	0.176 (1.00)	0.0278 (1.00)	0.00221 (1.00)	0.637 (1.00)	0.18 (1.00)	0.327 (1.00)	0.00876 (1.00)	0.759 (1.00)	0.00743 (1.00)
Del Peak 9(3q11 1)	59 (15%)	338	0.759 (1.00)	0.478 (1.00)	0.117 (1.00)	0.0538 (1.00)	0.765 (1.00)	0.282 (1.00)	0.925 (1.00)	0.674 (1.00)	0.74 (1.00)	0.891 (1.00)
Del Peak 16(6p25 3)	100 (25%)	297	0.22 (1.00)	0.11 (1.00)	0.00878 (1.00)	0.00143 (1.00)	0.393 (1.00)	0.013 (1.00)	0.01 (1.00)	0.0204 (1.00)	0.159 (1.00)	0.181 (1.00)
Del Peak 17(6q22 31)	95 (24%)	302	0.0192 (1.00)	0.00224 (1.00)	0.00513 (1.00)	0.000818 (0.586)	0.629 (1.00)	0.354 (1.00)	0.0217 (1.00)	0.0133 (1.00)	0.194 (1.00)	0.243 (1.00)
Del Peak 18(6q26)	103 (26%)	294	0.0659 (1.00)	0.00298 (1.00)	0.00234 (1.00)	0.000727 (0.523)	0.921 (1.00)	0.69 (1.00)	0.0687 (1.00)	0.141 (1.00)	0.149 (1.00)	0.0889 (1.00)
Del Peak 20(7q36 3)	81 (20%)	316	0.187 (1.00)	0.112 (1.00)	0.00095 (0.675)	0.274 (1.00)	1 (1.00)	0.315 (1.00)	0.0928 (1.00)	0.0698 (1.00)	0.138 (1.00)	0.163 (1.00)
Del Peak 21(8p23 2)	267 (67%)	130	0.864 (1.00)	0.459 (1.00)	0.000961 (0.682)	0.173 (1.00)	0.345 (1.00)	0.141 (1.00)	0.157 (1.00)	0.072 (1.00)	0.345 (1.00)	0.285 (1.00)
Del Peak 29(11q22 1)	118 (30%)	279	0.493 (1.00)	0.288 (1.00)	0.0053 (1.00)	0.0314 (1.00)	0.103 (1.00)	0.995 (1.00)	0.259 (1.00)	0.426 (1.00)	0.219 (1.00)	0.0584 (1.00)
Del Peak 30(11q25)	143 (36%)	254	0.798 (1.00)	0.429 (1.00)	0.0746 (1.00)	0.333 (1.00)	0.113 (1.00)	0.908 (1.00)	0.447 (1.00)	0.406 (1.00)	0.14 (1.00)	0.189 (1.00)
Del Peak 31(12q24 31)	63 (16%)	334	0.965 (1.00)	0.332 (1.00)	0.426 (1.00)	0.435 (1.00)	0.323 (1.00)	0.207 (1.00)	0.9 (1.00)	0.689 (1.00)	0.282 (1.00)	0.322 (1.00)
Del Peak 32(13q12 11)	260 (65%)	137	0.0547 (1.00)	0.611 (1.00)	0.0344 (1.00)	0.164 (1.00)	0.907 (1.00)	0.268 (1.00)	0.7 (1.00)	0.214 (1.00)	0.973 (1.00)	1 (1.00)
Del Peak 33(13q14 2)	271 (68%)	126	0.0512 (1.00)	0.0962 (1.00)	0.00096 (0.682)	0.053 (1.00)	0.707 (1.00)	0.682 (1.00)	0.0281 (1.00)	0.147 (1.00)	0.905 (1.00)	0.561 (1.00)
Del Peak 34(14q11 2)	140 (35%)	257	0.0546 (1.00)	0.293 (1.00)	0.163 (1.00)	0.437 (1.00)	0.206 (1.00)	0.159 (1.00)	0.00265 (1.00)	0.00213 (1.00)	0.252 (1.00)	0.274 (1.00)
Del Peak 35(15q12)	131 (33%)	266	0.725 (1.00)	0.228 (1.00)	0.45 (1.00)	0.347 (1.00)	0.0717 (1.00)	0.00798 (1.00)	0.132 (1.00)	0.356 (1.00)	0.0723 (1.00)	0.636 (1.00)
Del Peak 36(15q21 1)	124 (31%)	273	0.643 (1.00)	0.242 (1.00)	0.298 (1.00)	0.969 (1.00)	0.138 (1.00)	0.00763 (1.00)	0.156 (1.00)	0.354 (1.00)	0.228 (1.00)	0.318 (1.00)
Del Peak 37(16p13 3)	148 (37%)	249	0.239 (1.00)	0.245 (1.00)	0.00525 (1.00)	0.197 (1.00)	0.149 (1.00)	0.606 (1.00)	0.531 (1.00)	0.247 (1.00)	0.618 (1.00)	0.0677 (1.00)
Del Peak 38(16q23 1)	166 (42%)	231	0.942 (1.00)	0.659 (1.00)	0.0863 (1.00)	0.271 (1.00)	0.354 (1.00)	0.761 (1.00)	0.205 (1.00)	0.0264 (1.00)	0.535 (1.00)	0.337 (1.00)
Del Peak 39(17p11 2)	202 (51%)	195	0.194 (1.00)	0.401 (1.00)	0.00185 (1.00)	0.161 (1.00)	0.15 (1.00)	0.0182 (1.00)	0.368 (1.00)	0.86 (1.00)	0.0666 (1.00)	0.0313 (1.00)
Del Peak 41(17q25 3)	76 (19%)	321	0.00515 (1.00)	0.0421 (1.00)	0.000405 (0.299)	0.0446 (1.00)	0.622 (1.00)	0.994 (1.00)	0.13 (1.00)	0.0021 (1.00)	0.946 (1.00)	0.111 (1.00)
Del Peak 42(18q23)	179 (45%)	218	0.508 (1.00)	0.788 (1.00)	0.502 (1.00)	0.898 (1.00)	0.801 (1.00)	0.397 (1.00)	0.23 (1.00)	0.115 (1.00)	0.773 (1.00)	0.502 (1.00)
Del Peak 45(21q21 1)	189 (48%)	208	0.481 (1.00)	0.135 (1.00)	0.0117 (1.00)	0.0293 (1.00)	0.585 (1.00)	0.89 (1.00)	0.996 (1.00)	0.815 (1.00)	0.0562 (1.00)	0.0687 (1.00)
Del Peak 47(22q11 21)	68 (17%)	329	0.0904 (1.00)	0.0093 (1.00)	0.0672 (1.00)	0.0841 (1.00)	0.145 (1.00)	0.129 (1.00)	0.598 (1.00)	0.748 (1.00)	0.172 (1.00)	0.126 (1.00)

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

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

Table S1. Gene #2: 'Amp Peak 2(1q21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S1. Get High-res Image Gene #2: 'Amp Peak 2(1q21.2) 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 = 0.23

Table S2. 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 S2. 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 = 3.18e-13 (Fisher's exact test), Q value = 2.7e-10

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

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

Figure S3. 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 = 5.83e-05 (Fisher's exact test), Q value = 0.045

Table S4. Gene #3: 'Amp Peak 3(2p16.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S4. 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 = 0.25

Table S5. 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 S5. 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 = 6.52e-06 (Fisher's exact test), Q value = 0.0052

Table S6. Gene #4: 'Amp Peak 4(2q31.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S6. 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 = 1.99e-07 (Fisher's exact test), Q value = 0.00016

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

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

Figure S7. 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 = 0.014

Table S8. 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 S8. 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 = 7.05e-12 (Fisher's exact test), Q value = 5.9e-09

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

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

Figure S9. 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 = 6.69e-07 (Fisher's exact test), Q value = 0.00055

Table S10. Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S10. 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 = 0.03

Table S11. 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 S11. 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 S12. 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 S12. 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 = 1.37e-05 (Fisher's exact test), Q value = 0.011

Table S13. Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	176	118
AMP PEAK 6(3Q26.33) MUTATED	53	151	116
AMP PEAK 6(3Q26.33) WILD-TYPE	0	25	2

Figure S13. 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 = 1.07e-05 (Fisher's exact test), Q value = 0.0085

Table S14. Gene #8: 'Amp Peak 8(5p15.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S14. 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 = 7.58e-10 (Fisher's exact test), Q value = 6.3e-07

Table S15. Gene #9: 'Amp Peak 9(5p12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S15. Get High-res Image Gene #9: 'Amp Peak 9(5p12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

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

Table S16. Gene #13: 'Amp Peak 13(7q21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S16. Get High-res Image Gene #13: 'Amp Peak 13(7q21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

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

Table S17. Gene #13: 'Amp Peak 13(7q21.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S17. Get High-res Image Gene #13: 'Amp Peak 13(7q21.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 1.23e-05 (Fisher's exact test), Q value = 0.0098

Table S18. Gene #19: 'Amp Peak 19(12p13.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S18. Get High-res Image Gene #19: 'Amp Peak 19(12p13.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

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

Table S19. Gene #23: 'Amp Peak 23(15q26.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S19. Get High-res Image Gene #23: 'Amp Peak 23(15q26.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 9.39e-06 (Fisher's exact test), Q value = 0.0075

Table S20. Gene #23: 'Amp Peak 23(15q26.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S20. Get High-res Image Gene #23: 'Amp Peak 23(15q26.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

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

Table S21. Gene #24: 'Amp Peak 24(17q25.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S21. Get High-res Image Gene #24: 'Amp Peak 24(17q25.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

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

Table S22. Gene #24: 'Amp Peak 24(17q25.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S22. Get High-res Image Gene #24: 'Amp Peak 24(17q25.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

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

Table S23. Gene #25: 'Amp Peak 25(18p11.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S23. Get High-res Image Gene #25: 'Amp Peak 25(18p11.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 0.000126 (Fisher's exact test), Q value = 0.096

Table S24. Gene #25: 'Amp Peak 25(18p11.32) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S24. Get High-res Image Gene #25: 'Amp Peak 25(18p11.32) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

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

Table S25. Gene #26: 'Amp Peak 26(18q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S25. Get High-res Image Gene #26: 'Amp Peak 26(18q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 4.07e-06 (Fisher's exact test), Q value = 0.0033

Table S26. Gene #27: 'Amp Peak 27(19q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S26. Get High-res Image Gene #27: 'Amp Peak 27(19q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 0.000195 (Fisher's exact test), Q value = 0.15

Table S27. Gene #28: 'Amp Peak 28(19q13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S27. Get High-res Image Gene #28: 'Amp Peak 28(19q13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

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

Table S28. Gene #29: 'Amp Peak 29(20p12.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S28. Get High-res Image Gene #29: 'Amp Peak 29(20p12.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

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

Table S29. Gene #29: 'Amp Peak 29(20p12.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S29. Get High-res Image Gene #29: 'Amp Peak 29(20p12.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

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

Table S30. Gene #31: 'Amp Peak 31(22q11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S30. Get High-res Image Gene #31: 'Amp Peak 31(22q11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 1.43e-06 (Fisher's exact test), Q value = 0.0012

Table S31. Gene #33: 'Del Peak 1(1p36.22) 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(1P36.22) MUTATED	9	37	13	10
DEL PEAK 1(1P36.22) WILD-TYPE	34	13	17	21

Figure S31. Get High-res Image Gene #33: 'Del Peak 1(1p36.22) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

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

Table S32. Gene #33: 'Del Peak 1(1p36.22) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

Figure S32. Get High-res Image Gene #33: 'Del Peak 1(1p36.22) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

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

Table S33. Gene #33: 'Del Peak 1(1p36.22) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S33. Get High-res Image Gene #33: 'Del Peak 1(1p36.22) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

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

Table S34. Gene #33: 'Del Peak 1(1p36.22) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S34. Get High-res Image Gene #33: 'Del Peak 1(1p36.22) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 1.09e-09 (Fisher's exact test), Q value = 9e-07

Table S35. Gene #33: 'Del Peak 1(1p36.22) 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(1P36.22) MUTATED	16	60	27	12
DEL PEAK 1(1P36.22) WILD-TYPE	44	20	52	26

Figure S35. Get High-res Image Gene #33: 'Del Peak 1(1p36.22) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 1.35e-08 (Fisher's exact test), Q value = 1.1e-05

Table S36. Gene #33: 'Del Peak 1(1p36.22) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	116	86	55
DEL PEAK 1(1P36.22) MUTATED	36	61	18
DEL PEAK 1(1P36.22) WILD-TYPE	80	25	37

Figure S36. Get High-res Image Gene #33: 'Del Peak 1(1p36.22) 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 = 0.18

Table S37. Gene #34: '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 S37. Get High-res Image Gene #34: '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 = 1.23e-15 (Fisher's exact test), Q value = 1e-12

Table S38. Gene #34: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S38. Get High-res Image Gene #34: '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 = 5.74e-09 (Fisher's exact test), Q value = 4.8e-06

Table S39. Gene #34: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S39. Get High-res Image Gene #34: '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 S40. Gene #34: '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 S40. Get High-res Image Gene #34: '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 = 0.055

Table S41. Gene #34: '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 S41. Get High-res Image Gene #34: '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 = 0.000271 (Fisher's exact test), Q value = 0.2

Table S42. Gene #36: 'Del Peak 4(2q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S42. Get High-res Image Gene #36: '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 = 0.18

Table S43. Gene #37: '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 S43. Get High-res Image Gene #37: '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 = 0.037

Table S44. Gene #37: '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 S44. Get High-res Image Gene #37: '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 = 1.7e-12 (Fisher's exact test), Q value = 1.4e-09

Table S45. Gene #37: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S45. Get High-res Image Gene #37: '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 = 2.14e-06 (Fisher's exact test), Q value = 0.0017

Table S46. Gene #37: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S46. Get High-res Image Gene #37: '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 = 0.065

Table S47. Gene #37: '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 S47. Get High-res Image Gene #37: '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 = 0.0049

Table S48. Gene #37: '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 S48. Get High-res Image Gene #37: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 2.67e-06 (Fisher's exact test), Q value = 0.0022

Table S49. Gene #39: 'Del Peak 7(3p13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S49. Get High-res Image Gene #39: 'Del Peak 7(3p13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 3.03e-05 (Fisher's exact test), Q value = 0.024

Table S50. Gene #40: 'Del Peak 8(3p12.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S50. Get High-res Image Gene #40: 'Del Peak 8(3p12.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

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

Table S51. Gene #42: 'Del Peak 10(4p15.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S51. Get High-res Image Gene #42: 'Del Peak 10(4p15.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 0.000102 (Fisher's exact test), Q value = 0.078

Table S52. Gene #43: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S52. Get High-res Image Gene #43: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 3.5e-07 (Fisher's exact test), Q value = 0.00029

Table S53. Gene #44: 'Del Peak 12(4q32.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S53. Get High-res Image Gene #44: 'Del Peak 12(4q32.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

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

Table S54. Gene #45: 'Del Peak 13(4q35.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S54. Get High-res Image Gene #45: 'Del Peak 13(4q35.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 0.000124 (Fisher's exact test), Q value = 0.094

Table S55. Gene #45: 'Del Peak 13(4q35.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S55. Get High-res Image Gene #45: 'Del Peak 13(4q35.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

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

Table S56. Gene #46: 'Del Peak 14(5q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S56. Get High-res Image Gene #46: 'Del Peak 14(5q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 0.000192 (Fisher's exact test), Q value = 0.15

Table S57. Gene #46: 'Del Peak 14(5q11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S57. Get High-res Image Gene #46: 'Del Peak 14(5q11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 8.06e-05 (Fisher's exact test), Q value = 0.062

Table S58. Gene #46: 'Del Peak 14(5q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	176	118
DEL PEAK 14(5Q11.2) MUTATED	41	115	103
DEL PEAK 14(5Q11.2) WILD-TYPE	12	61	15

Figure S58. Get High-res Image Gene #46: 'Del Peak 14(5q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

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

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

Table S59. Gene #47: 'Del Peak 15(5q31.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S59. Get High-res Image Gene #47: 'Del Peak 15(5q31.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

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

Table S60. Gene #47: 'Del Peak 15(5q31.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S60. Get High-res Image Gene #47: 'Del Peak 15(5q31.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

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

Table S61. Gene #51: 'Del Peak 19(7q11.22) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S61. Get High-res Image Gene #51: 'Del Peak 19(7q11.22) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

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

Table S62. Gene #54: 'Del Peak 22(9p23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S62. Get High-res Image Gene #54: 'Del Peak 22(9p23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

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

Table S63. Gene #55: 'Del Peak 23(9p21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S63. Get High-res Image Gene #55: 'Del Peak 23(9p21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

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

Table S64. Gene #56: 'Del Peak 24(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 24(9Q21.11) MUTATED	28	12	19	15
DEL PEAK 24(9Q21.11) WILD-TYPE	15	38	11	16

Figure S64. Get High-res Image Gene #56: 'Del Peak 24(9q21.11) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

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

Table S65. Gene #56: 'Del Peak 24(9q21.11) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

Figure S65. Get High-res Image Gene #56: 'Del Peak 24(9q21.11) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

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

Table S66. Gene #56: 'Del Peak 24(9q21.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S66. Get High-res Image Gene #56: 'Del Peak 24(9q21.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 1.14e-06 (Fisher's exact test), Q value = 0.00093

Table S67. Gene #56: 'Del Peak 24(9q21.11) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S67. Get High-res Image Gene #56: 'Del Peak 24(9q21.11) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 4.44e-06 (Fisher's exact test), Q value = 0.0036

Table S68. Gene #56: 'Del Peak 24(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 24(9Q21.11) MUTATED	33	19	48	22
DEL PEAK 24(9Q21.11) WILD-TYPE	27	61	31	16

Figure S68. Get High-res Image Gene #56: 'Del Peak 24(9q21.11) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 2.4e-07 (Fisher's exact test), Q value = 2e-04

Table S69. Gene #56: 'Del Peak 24(9q21.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	116	86	55
DEL PEAK 24(9Q21.11) MUTATED	64	21	37
DEL PEAK 24(9Q21.11) WILD-TYPE	52	65	18

Figure S69. Get High-res Image Gene #56: 'Del Peak 24(9q21.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 0.000283 (Fisher's exact test), Q value = 0.21

Table S70. Gene #56: 'Del Peak 24(9q21.11) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	176	118
DEL PEAK 24(9Q21.11) MUTATED	13	90	67
DEL PEAK 24(9Q21.11) WILD-TYPE	40	86	51

Figure S70. Get High-res Image Gene #56: 'Del Peak 24(9q21.11) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

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

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

Table S71. Gene #57: 'Del Peak 25(10p15.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S71. Get High-res Image Gene #57: 'Del Peak 25(10p15.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 9.6e-05 (Fisher's exact test), Q value = 0.074

Table S72. Gene #57: 'Del Peak 25(10p15.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S72. Get High-res Image Gene #57: 'Del Peak 25(10p15.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

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

Table S73. Gene #58: 'Del Peak 26(10p15.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S73. Get High-res Image Gene #58: 'Del Peak 26(10p15.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 4.03e-06 (Fisher's exact test), Q value = 0.0033

Table S74. Gene #58: 'Del Peak 26(10p15.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S74. Get High-res Image Gene #58: 'Del Peak 26(10p15.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 0.000259 (Fisher's exact test), Q value = 0.19

Table S75. Gene #58: 'Del Peak 26(10p15.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	60	80	79	38
DEL PEAK 26(10P15.1) MUTATED	17	48	32	10
DEL PEAK 26(10P15.1) WILD-TYPE	43	32	47	28

Figure S75. Get High-res Image Gene #58: 'Del Peak 26(10p15.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

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

Table S76. Gene #59: 'Del Peak 27(10q23.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S76. Get High-res Image Gene #59: 'Del Peak 27(10q23.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

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

Table S77. Gene #59: 'Del Peak 27(10q23.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S77. Get High-res Image Gene #59: 'Del Peak 27(10q23.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 0.000104 (Fisher's exact test), Q value = 0.079

Table S78. Gene #59: 'Del Peak 27(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 27(10Q23.31) MUTATED	22	57	35	16
DEL PEAK 27(10Q23.31) WILD-TYPE	38	23	44	22

Figure S78. Get High-res Image Gene #59: 'Del Peak 27(10q23.31) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 2.63e-05 (Fisher's exact test), Q value = 0.021

Table S79. Gene #59: 'Del Peak 27(10q23.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

Figure S79. Get High-res Image Gene #59: 'Del Peak 27(10q23.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

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

Table S80. Gene #60: 'Del Peak 28(11p15.5) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S80. Get High-res Image Gene #60: 'Del Peak 28(11p15.5) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 28(11p15.5) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 2.02e-05 (Fisher's exact test), Q value = 0.016

Table S81. Gene #60: 'Del Peak 28(11p15.5) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	47	49	40
DEL PEAK 28(11P15.5) MUTATED	29	17	36	10
DEL PEAK 28(11P15.5) WILD-TYPE	29	30	13	30

Figure S81. Get High-res Image Gene #60: 'Del Peak 28(11p15.5) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

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

P value = 1.26e-05 (Fisher's exact test), Q value = 0.01

Table S82. Gene #72: 'Del Peak 40(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 40(17Q11.2) MUTATED	21	3	11	7
DEL PEAK 40(17Q11.2) WILD-TYPE	22	47	19	24

Figure S82. Get High-res Image Gene #72: 'Del Peak 40(17q11.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

P value = 6.44e-05 (Fisher's exact test), Q value = 0.05

Table S83. Gene #72: 'Del Peak 40(17q11.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

Figure S83. Get High-res Image Gene #72: 'Del Peak 40(17q11.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

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

Table S84. Gene #72: 'Del Peak 40(17q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S84. Get High-res Image Gene #72: 'Del Peak 40(17q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 0.000122 (Fisher's exact test), Q value = 0.093

Table S85. Gene #72: 'Del Peak 40(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 40(17Q11.2) MUTATED	20	6	23	13
DEL PEAK 40(17Q11.2) WILD-TYPE	40	74	56	25

Figure S85. Get High-res Image Gene #72: 'Del Peak 40(17q11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 7.16e-06 (Fisher's exact test), Q value = 0.0057

Table S86. Gene #72: 'Del Peak 40(17q11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	116	86	55
DEL PEAK 40(17Q11.2) MUTATED	39	6	17
DEL PEAK 40(17Q11.2) WILD-TYPE	77	80	38

Figure S86. Get High-res Image Gene #72: 'Del Peak 40(17q11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

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

Table S87. Gene #75: 'Del Peak 43(19p13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S87. Get High-res Image Gene #75: 'Del Peak 43(19p13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 0.000167 (Fisher's exact test), Q value = 0.13

Table S88. Gene #76: 'Del Peak 44(19q13.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S88. Get High-res Image Gene #76: 'Del Peak 44(19q13.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

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

Table S89. Gene #76: 'Del Peak 44(19q13.33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S89. Get High-res Image Gene #76: 'Del Peak 44(19q13.33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

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

Table S90. Gene #78: 'Del Peak 46(21q22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S90. Get High-res Image Gene #78: 'Del Peak 46(21q22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

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

Table S91. Gene #80: 'Del Peak 48(22q13.32) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

Figure S91. Get High-res Image Gene #80: 'Del Peak 48(22q13.32) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

P value = 8.68e-05 (Fisher's exact test), Q value = 0.067

Table S92. Gene #80: 'Del Peak 48(22q13.32) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

Figure S92. Get High-res Image Gene #80: 'Del Peak 48(22q13.32) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

P value = 0.000249 (Fisher's exact test), Q value = 0.19

Table S93. Gene #81: 'Del Peak 49(Xp22.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S93. Get High-res Image Gene #81: 'Del Peak 49(Xp22.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 5.39e-05 (Fisher's exact test), Q value = 0.042

Table S94. Gene #82: 'Del Peak 50(Xp21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S94. Get High-res Image Gene #82: 'Del Peak 50(Xp21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

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

Table S95. Gene #82: 'Del Peak 50(Xp21.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S95. Get High-res Image Gene #82: 'Del Peak 50(Xp21.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

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

Table S96. Gene #83: 'Del Peak 51(Xp11.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S96. Get High-res Image Gene #83: 'Del Peak 51(Xp11.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

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

Table S97. Gene #83: 'Del Peak 51(Xp11.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S97. Get High-res Image Gene #83: 'Del Peak 51(Xp11.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

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

Table S98. Gene #84: 'Del Peak 52(Xq22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

Figure S98. Get High-res Image Gene #84: 'Del Peak 52(Xq22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 0.000249 (Fisher's exact test), Q value = 0.19

Table S99. Gene #84: 'Del Peak 52(Xq22.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

Figure S99. Get High-res Image Gene #84: 'Del Peak 52(Xq22.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

Methods & Data

Input

Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
Molecular subtype file = LUSC-TP.transferedmergedcluster.txt
Number of patients = 397
Number of copy number variation regions = 84
Number of molecular subtypes = 10
Exclude regions that fewer than K tumors have alterations, K = 3

Fisher's exact test

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

Q value calculation

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

References

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

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

[3] GISTIC_version2

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