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 72 peak regions and 8 molecular subtypes across 322 patients, 107 significant findings detected with Q value < 0.25.

Amp Peak 1(1q21.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
Amp Peak 2(2q11.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 3(2q31.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 4(2q32.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 5(3q26.33) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 6(5p15.33) cnvs correlated to 'CN_CNMF'.
Amp Peak 7(5p12) cnvs correlated to 'CN_CNMF'.
Amp Peak 8(6p12.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 10(7p11.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 11(7q22.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 13(8q11.21) cnvs correlated to 'CN_CNMF'.
Amp Peak 14(8q24.21) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 19(11q13.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 20(12p13.33) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 21(12q15) cnvs correlated to 'CN_CNMF'.
Amp Peak 22(13q22.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 23(14q11.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 24(15q26.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 25(17q12) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 26(18p11.31) cnvs correlated to 'CN_CNMF'.
Amp Peak 28(20q11.22) cnvs correlated to 'CN_CNMF'.
Amp Peak 29(Xq28) cnvs correlated to 'CN_CNMF'.
Del Peak 1(1p36.13) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Del Peak 2(1p13.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.
Del Peak 4(2q22.1) cnvs correlated to 'MIRSEQ_CHIERARCHICAL'.
Del Peak 5(2q36.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 6(3p24.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 7(3p14.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 8(3p12.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 9(4p16.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 10(4p15.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 11(4q22.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 12(4q35.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 13(5q11.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 14(5q35.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 15(6p25.3) cnvs correlated to 'METHLYATION_CNMF'.
Del Peak 18(8p23.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 19(9p23) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 20(9p21.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 21(9q21.11) cnvs correlated to 'CN_CNMF'.
Del Peak 23(10p15.3) cnvs correlated to 'CN_CNMF'.
Del Peak 24(10p11.21) cnvs correlated to 'CN_CNMF'.
Del Peak 26(11p15.4) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 27(11q23.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 29(13q12.11) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 30(13q14.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 32(14q32.32) cnvs correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 34(16q12.1) cnvs correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
Del Peak 35(16q23.3) cnvs correlated to 'MRNASEQ_CHIERARCHICAL'.
Del Peak 37(18q21.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 38(18q23) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 40(19q13.43) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 41(Xp21.3) cnvs correlated to 'CN_CNMF'.
Del Peak 42(Xp11.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 43(Xq21.33) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 72 regions and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 107 significant findings detected.


		Molecular subtypes	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL
	nCNV (%)	nWild-Type	Chi-square test	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
Amp Peak 14(8q24 21)	232 (72%)	90	5.76e-08 (3.07e-05)	0.000106 (0.0515)	0.231 (1.00)	0.58 (1.00)	0.000102 (0.05)	0.000135 (0.0654)	0.0442 (1.00)	0.000169 (0.0817)
Amp Peak 1(1q21 2)	76 (24%)	246	1.21e-07 (6.4e-05)	2.63e-08 (1.42e-05)	0.838 (1.00)	0.359 (1.00)	0.000509 (0.24)	0.00316 (1.00)	0.000103 (0.0502)	0.272 (1.00)
Del Peak 30(13q14 2)	137 (43%)	185	3.1e-07 (0.000163)	5.88e-07 (0.000306)	0.661 (1.00)	0.26 (1.00)	5.7e-05 (0.0283)	6.46e-05 (0.032)	0.0431 (1.00)	0.568 (1.00)
Del Peak 34(16q12 1)	54 (17%)	268	0.0731 (1.00)	1.13e-07 (5.97e-05)	0.399 (1.00)	0.0768 (1.00)	7.1e-08 (3.78e-05)	3.91e-07 (0.000205)	0.00037 (0.175)	0.00585 (1.00)
Amp Peak 5(3q26 33)	242 (75%)	80	1.29e-09 (7.09e-07)	3.26e-05 (0.0163)	0.435 (1.00)	0.263 (1.00)	0.000829 (0.382)	0.000288 (0.137)	0.00356 (1.00)	0.406 (1.00)
Del Peak 1(1p36 13)	68 (21%)	254	1.48e-10 (8.22e-08)	5.38e-15 (3.05e-12)	0.00322 (1.00)	0.84 (1.00)	3.03e-05 (0.0152)	0.000716 (0.332)	0.0131 (1.00)	0.0668 (1.00)
Del Peak 2(1p13 2)	81 (25%)	241	2.77e-10 (1.53e-07)	8.62e-10 (4.73e-07)	0.00301 (1.00)	0.0475 (1.00)	0.00546 (1.00)	0.0927 (1.00)	0.000181 (0.0869)	0.97 (1.00)
Del Peak 14(5q35 3)	127 (39%)	195	4.01e-15 (2.28e-12)	4.25e-14 (2.4e-11)	0.243 (1.00)	0.187 (1.00)	0.0146 (1.00)	0.000477 (0.225)	0.13 (1.00)	0.663 (1.00)
Del Peak 27(11q23 1)	153 (48%)	169	1.37e-14 (7.76e-12)	8.45e-07 (0.000435)	0.358 (1.00)	0.453 (1.00)	0.000815 (0.377)	0.00023 (0.11)	0.207 (1.00)	0.182 (1.00)
Del Peak 32(14q32 32)	49 (15%)	273	0.285 (1.00)	1.42e-07 (7.5e-05)	0.317 (1.00)	0.507 (1.00)	0.000242 (0.116)	9.8e-05 (0.048)	0.115 (1.00)	0.126 (1.00)
Amp Peak 2(2q11 2)	69 (21%)	253	3.48e-06 (0.00178)	1.71e-08 (9.26e-06)	0.935 (1.00)	0.188 (1.00)	0.0119 (1.00)	0.0807 (1.00)	0.045 (1.00)	0.429 (1.00)
Amp Peak 3(2q31 2)	67 (21%)	255	8.38e-10 (4.61e-07)	9.37e-09 (5.09e-06)	0.117 (1.00)	0.359 (1.00)	0.318 (1.00)	0.11 (1.00)	0.367 (1.00)	0.0818 (1.00)
Amp Peak 4(2q32 2)	59 (18%)	263	7.97e-07 (0.000411)	5.3e-08 (2.84e-05)	0.0495 (1.00)	0.427 (1.00)	0.169 (1.00)	0.0513 (1.00)	0.0433 (1.00)	0.129 (1.00)
Amp Peak 10(7p11 2)	137 (43%)	185	1.91e-08 (1.03e-05)	6.87e-07 (0.000356)	0.935 (1.00)	0.75 (1.00)	0.5 (1.00)	0.923 (1.00)	0.405 (1.00)	0.197 (1.00)
Amp Peak 11(7q22 1)	114 (35%)	208	3.1e-11 (1.73e-08)	5.46e-08 (2.91e-05)	0.617 (1.00)	1 (1.00)	0.235 (1.00)	0.335 (1.00)	0.0689 (1.00)	0.101 (1.00)
Amp Peak 20(12p13 33)	109 (34%)	213	5.52e-11 (3.07e-08)	1.28e-05 (0.0065)	0.0836 (1.00)	0.413 (1.00)	0.00912 (1.00)	0.00101 (0.462)	0.00247 (1.00)	0.814 (1.00)
Amp Peak 22(13q22 1)	68 (21%)	254	4.16e-07 (0.000218)	8.43e-05 (0.0416)	0.00708 (1.00)	0.335 (1.00)	0.233 (1.00)	0.0924 (1.00)	0.551 (1.00)	0.409 (1.00)
Amp Peak 25(17q12)	56 (17%)	266	4.94e-05 (0.0246)	0.000112 (0.0541)	0.944 (1.00)	0.961 (1.00)	0.0168 (1.00)	0.0308 (1.00)	0.0253 (1.00)	0.399 (1.00)
Del Peak 5(2q36 2)	96 (30%)	226	0.000122 (0.0591)	5.69e-06 (0.0029)	0.248 (1.00)	0.269 (1.00)	0.000636 (0.298)	0.00125 (0.571)	0.0614 (1.00)	0.0106 (1.00)
Del Peak 6(3p24 1)	239 (74%)	83	3.25e-27 (1.87e-24)	3.93e-08 (2.11e-05)	0.183 (1.00)	0.247 (1.00)	0.0707 (1.00)	0.369 (1.00)	0.404 (1.00)	0.0983 (1.00)
Del Peak 7(3p14 2)	242 (75%)	80	3.41e-27 (1.96e-24)	5.71e-07 (0.000298)	0.137 (1.00)	0.603 (1.00)	0.115 (1.00)	0.161 (1.00)	0.895 (1.00)	0.122 (1.00)
Del Peak 8(3p12 2)	228 (71%)	94	3.11e-25 (1.79e-22)	4.04e-09 (2.2e-06)	0.843 (1.00)	0.784 (1.00)	0.241 (1.00)	0.463 (1.00)	0.541 (1.00)	0.122 (1.00)
Del Peak 9(4p16 3)	137 (43%)	185	1.38e-14 (7.8e-12)	1.5e-05 (0.00756)	0.0156 (1.00)	0.711 (1.00)	0.307 (1.00)	0.161 (1.00)	0.111 (1.00)	0.594 (1.00)
Del Peak 10(4p15 2)	138 (43%)	184	7.36e-16 (4.2e-13)	5.98e-07 (0.000311)	0.0207 (1.00)	0.326 (1.00)	0.0406 (1.00)	0.0129 (1.00)	0.0214 (1.00)	0.687 (1.00)
Del Peak 11(4q22 1)	102 (32%)	220	5.42e-12 (3.04e-09)	6.5e-07 (0.000337)	0.0244 (1.00)	0.769 (1.00)	0.371 (1.00)	0.205 (1.00)	0.293 (1.00)	0.71 (1.00)
Del Peak 12(4q35 2)	131 (41%)	191	4e-08 (2.14e-05)	2.97e-05 (0.0149)	0.00405 (1.00)	0.602 (1.00)	0.275 (1.00)	0.353 (1.00)	0.296 (1.00)	0.292 (1.00)
Del Peak 13(5q11 2)	134 (42%)	188	1.65e-16 (9.45e-14)	1.35e-12 (7.57e-10)	0.0952 (1.00)	0.786 (1.00)	0.0401 (1.00)	0.000767 (0.355)	0.076 (1.00)	0.397 (1.00)
Del Peak 18(8p23 2)	183 (57%)	139	4.99e-12 (2.8e-09)	3.84e-05 (0.0191)	0.524 (1.00)	0.237 (1.00)	0.0166 (1.00)	0.00353 (1.00)	0.0584 (1.00)	0.00355 (1.00)
Del Peak 19(9p23)	151 (47%)	171	6.45e-13 (3.63e-10)	5.42e-09 (2.95e-06)	0.174 (1.00)	0.845 (1.00)	0.74 (1.00)	0.493 (1.00)	0.652 (1.00)	0.225 (1.00)
Del Peak 20(9p21 3)	189 (59%)	133	3.52e-10 (1.94e-07)	2.83e-09 (1.54e-06)	0.399 (1.00)	0.646 (1.00)	0.39 (1.00)	0.462 (1.00)	0.958 (1.00)	0.62 (1.00)
Del Peak 26(11p15 4)	102 (32%)	220	3.91e-06 (0.002)	0.000523 (0.246)	0.426 (1.00)	0.598 (1.00)	0.00228 (1.00)	0.0071 (1.00)	0.00335 (1.00)	0.196 (1.00)
Del Peak 29(13q12 11)	145 (45%)	177	8.03e-11 (4.46e-08)	7.28e-07 (0.000377)	0.594 (1.00)	0.474 (1.00)	0.053 (1.00)	0.0289 (1.00)	0.693 (1.00)	0.319 (1.00)
Del Peak 37(18q21 2)	170 (53%)	152	3.21e-14 (1.82e-11)	1.69e-09 (9.24e-07)	0.497 (1.00)	0.495 (1.00)	0.00268 (1.00)	0.0073 (1.00)	0.0133 (1.00)	0.0318 (1.00)
Del Peak 38(18q23)	182 (57%)	140	2.42e-16 (1.38e-13)	1.38e-11 (7.7e-09)	0.136 (1.00)	0.217 (1.00)	0.00216 (0.972)	0.00333 (1.00)	0.0151 (1.00)	0.0359 (1.00)
Del Peak 40(19q13 43)	64 (20%)	258	9.26e-05 (0.0454)	6.93e-05 (0.0342)	0.671 (1.00)	0.138 (1.00)	0.584 (1.00)	0.262 (1.00)	0.0578 (1.00)	0.774 (1.00)
Del Peak 42(Xp11 3)	108 (34%)	214	9.69e-08 (5.15e-05)	5.8e-05 (0.0288)	0.139 (1.00)	0.005 (1.00)	0.211 (1.00)	0.0598 (1.00)	0.176 (1.00)	0.21 (1.00)
Del Peak 43(Xq21 33)	55 (17%)	267	1.07e-06 (0.000548)	0.00166 (0.752)	0.0322 (1.00)	0.701 (1.00)	0.00131 (0.594)	0.0123 (1.00)	0.000324 (0.154)	0.00524 (1.00)
Amp Peak 6(5p15 33)	147 (46%)	175	9.05e-11 (5.02e-08)	0.0256 (1.00)	0.437 (1.00)	0.513 (1.00)	0.683 (1.00)	0.32 (1.00)	0.665 (1.00)	0.179 (1.00)
Amp Peak 7(5p12)	122 (38%)	200	1.83e-10 (1.01e-07)	0.0182 (1.00)	0.823 (1.00)	0.86 (1.00)	0.9 (1.00)	0.388 (1.00)	0.819 (1.00)	0.676 (1.00)
Amp Peak 8(6p12 1)	64 (20%)	258	1.65e-05 (0.00829)	0.0028 (1.00)	0.952 (1.00)	0.676 (1.00)	0.983 (1.00)	0.802 (1.00)	0.744 (1.00)	0.666 (1.00)
Amp Peak 13(8q11 21)	189 (59%)	133	1.02e-06 (0.000525)	0.0111 (1.00)	0.902 (1.00)	0.764 (1.00)	0.00113 (0.515)	0.000664 (0.31)	0.0666 (1.00)	0.0023 (1.00)
Amp Peak 19(11q13 3)	146 (45%)	176	1.04e-23 (5.94e-21)	0.000897 (0.412)	0.904 (1.00)	0.263 (1.00)	0.361 (1.00)	0.504 (1.00)	0.723 (1.00)	0.81 (1.00)
Amp Peak 21(12q15)	63 (20%)	259	3.77e-08 (2.03e-05)	0.00842 (1.00)	0.425 (1.00)	0.0996 (1.00)	0.09 (1.00)	0.0459 (1.00)	0.486 (1.00)	0.666 (1.00)
Amp Peak 23(14q11 2)	88 (27%)	234	7.37e-06 (0.00375)	0.0239 (1.00)	0.636 (1.00)	0.845 (1.00)	0.053 (1.00)	0.384 (1.00)	0.00616 (1.00)	0.126 (1.00)
Amp Peak 24(15q26 3)	71 (22%)	251	0.000106 (0.0517)	0.217 (1.00)	0.504 (1.00)	0.932 (1.00)	0.923 (1.00)	0.416 (1.00)	0.44 (1.00)	0.265 (1.00)
Amp Peak 26(18p11 31)	103 (32%)	219	4.38e-07 (0.000229)	0.00306 (1.00)	0.873 (1.00)	0.735 (1.00)	0.238 (1.00)	0.169 (1.00)	0.759 (1.00)	0.73 (1.00)
Amp Peak 28(20q11 22)	145 (45%)	177	0.000225 (0.108)	0.0222 (1.00)	0.436 (1.00)	0.559 (1.00)	0.0128 (1.00)	0.0854 (1.00)	0.715 (1.00)	0.0965 (1.00)
Amp Peak 29(Xq28)	98 (30%)	224	3.96e-08 (2.13e-05)	0.0032 (1.00)	0.561 (1.00)	0.578 (1.00)	0.188 (1.00)	0.463 (1.00)	0.338 (1.00)	0.209 (1.00)
Del Peak 4(2q22 1)	66 (20%)	256	0.0906 (1.00)	0.00648 (1.00)	0.855 (1.00)	0.338 (1.00)	0.0513 (1.00)	0.0292 (1.00)	0.0954 (1.00)	0.000186 (0.0894)
Del Peak 15(6p25 3)	64 (20%)	258	0.00338 (1.00)	0.00033 (0.156)	0.0346 (1.00)	0.0862 (1.00)	0.00752 (1.00)	0.38 (1.00)	0.0054 (1.00)	0.625 (1.00)
Del Peak 21(9q21 11)	61 (19%)	261	2.24e-07 (0.000118)	0.000962 (0.441)	0.574 (1.00)	0.821 (1.00)	0.882 (1.00)	0.673 (1.00)	0.831 (1.00)	0.0214 (1.00)
Del Peak 23(10p15 3)	108 (34%)	214	1.84e-05 (0.00926)	0.0293 (1.00)	0.929 (1.00)	0.218 (1.00)	0.327 (1.00)	0.307 (1.00)	0.621 (1.00)	0.473 (1.00)
Del Peak 24(10p11 21)	101 (31%)	221	8.15e-06 (0.00413)	0.145 (1.00)	0.603 (1.00)	0.0924 (1.00)	0.702 (1.00)	0.975 (1.00)	0.942 (1.00)	0.67 (1.00)
Del Peak 35(16q23 3)	64 (20%)	258	0.074 (1.00)	0.000839 (0.386)	0.133 (1.00)	0.0394 (1.00)	0.000601 (0.282)	8.88e-05 (0.0437)	0.0333 (1.00)	0.0641 (1.00)
Del Peak 41(Xp21 3)	106 (33%)	216	7.73e-06 (0.00393)	0.00532 (1.00)	0.139 (1.00)	0.0371 (1.00)	0.275 (1.00)	0.0415 (1.00)	0.121 (1.00)	0.834 (1.00)
Amp Peak 9(6q12)	59 (18%)	263	0.000695 (0.323)	0.0138 (1.00)	0.878 (1.00)	0.527 (1.00)	1 (1.00)	0.822 (1.00)	0.705 (1.00)	0.929 (1.00)
Amp Peak 12(8p11 23)	102 (32%)	220	0.0409 (1.00)	0.0369 (1.00)	0.673 (1.00)	0.413 (1.00)	0.15 (1.00)	0.0182 (1.00)	0.0121 (1.00)	0.00753 (1.00)
Amp Peak 15(9p23)	76 (24%)	246	0.00248 (1.00)	0.786 (1.00)	1 (1.00)	0.647 (1.00)	0.0993 (1.00)	0.227 (1.00)	0.438 (1.00)	0.728 (1.00)
Amp Peak 16(9p13 3)	90 (28%)	232	0.00223 (0.999)	0.222 (1.00)	0.587 (1.00)	0.165 (1.00)	0.00708 (1.00)	0.0379 (1.00)	0.107 (1.00)	0.0574 (1.00)
Amp Peak 17(11p13)	63 (20%)	259	0.0177 (1.00)	0.0971 (1.00)	0.343 (1.00)	0.033 (1.00)	0.631 (1.00)	0.163 (1.00)	0.682 (1.00)	0.965 (1.00)
Amp Peak 18(11p11 2)	63 (20%)	259	0.14 (1.00)	0.533 (1.00)	0.203 (1.00)	0.336 (1.00)	0.626 (1.00)	0.148 (1.00)	0.671 (1.00)	0.339 (1.00)
Amp Peak 27(18q11 2)	71 (22%)	251	0.0131 (1.00)	0.033 (1.00)	0.468 (1.00)	0.552 (1.00)	1 (1.00)	0.689 (1.00)	0.49 (1.00)	0.451 (1.00)
Del Peak 3(2q21 2)	40 (12%)	282	0.289 (1.00)	0.0278 (1.00)	0.734 (1.00)	0.947 (1.00)	0.0154 (1.00)	0.00564 (1.00)	0.00349 (1.00)	0.093 (1.00)
Del Peak 16(7q31 1)	49 (15%)	273	0.00197 (0.887)	0.0261 (1.00)	0.563 (1.00)	0.624 (1.00)	0.363 (1.00)	0.609 (1.00)	0.167 (1.00)	0.279 (1.00)
Del Peak 17(7q36 1)	80 (25%)	242	0.0292 (1.00)	0.33 (1.00)	0.251 (1.00)	0.367 (1.00)	0.957 (1.00)	0.674 (1.00)	0.339 (1.00)	0.0237 (1.00)
Del Peak 22(9q34 3)	53 (16%)	269	0.000667 (0.311)	0.0316 (1.00)	0.374 (1.00)	0.116 (1.00)	0.851 (1.00)	0.409 (1.00)	0.473 (1.00)	0.278 (1.00)
Del Peak 25(10q23 31)	83 (26%)	239	0.00454 (1.00)	0.00416 (1.00)	0.865 (1.00)	0.699 (1.00)	0.0249 (1.00)	0.0128 (1.00)	0.276 (1.00)	0.761 (1.00)
Del Peak 28(12q24 33)	38 (12%)	284	0.0127 (1.00)	0.0646 (1.00)	0.0245 (1.00)	0.57 (1.00)	0.859 (1.00)	0.775 (1.00)	0.492 (1.00)	0.11 (1.00)
Del Peak 31(14q11 2)	46 (14%)	276	0.0264 (1.00)	0.00616 (1.00)	0.519 (1.00)	0.317 (1.00)	0.463 (1.00)	0.329 (1.00)	0.0897 (1.00)	0.0487 (1.00)
Del Peak 33(15q15 1)	76 (24%)	246	0.00392 (1.00)	0.501 (1.00)	0.381 (1.00)	0.137 (1.00)	0.0233 (1.00)	0.0488 (1.00)	0.367 (1.00)	0.255 (1.00)
Del Peak 36(17q25 3)	41 (13%)	281	0.0479 (1.00)	0.123 (1.00)	0.128 (1.00)	0.875 (1.00)	0.037 (1.00)	0.0612 (1.00)	0.0072 (1.00)	0.0403 (1.00)
Del Peak 39(19p13 3)	110 (34%)	212	0.00186 (0.843)	0.0368 (1.00)	0.852 (1.00)	0.0758 (1.00)	0.0876 (1.00)	0.761 (1.00)	0.758 (1.00)	0.774 (1.00)

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

P value = 1.21e-07 (Chi-square test), Q value = 6.4e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
AMP PEAK 1(1Q21.2) MUTATED	26	12	21	10	2	3	2
AMP PEAK 1(1Q21.2) WILD-TYPE	40	29	25	75	20	7	50

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1q21.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 2.63e-08 (Chi-square test), Q value = 1.4e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
AMP PEAK 1(1Q21.2) MUTATED	8	13	4	10	31	1	0	4
AMP PEAK 1(1Q21.2) WILD-TYPE	35	34	35	35	27	50	4	15

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

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

P value = 0.000509 (Fisher's exact test), Q value = 0.24

Table S3. Gene #1: 'Amp Peak 1(1q21.2) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	91	90
AMP PEAK 1(1Q21.2) MUTATED	41	16	12
AMP PEAK 1(1Q21.2) WILD-TYPE	77	75	78

Figure S3. Get High-res Image Gene #1: 'Amp Peak 1(1q21.2) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

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

P value = 0.000103 (Fisher's exact test), Q value = 0.05

Table S4. Gene #1: 'Amp Peak 1(1q21.2) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	127	93
AMP PEAK 1(1Q21.2) MUTATED	11	44	21
AMP PEAK 1(1Q21.2) WILD-TYPE	90	83	72

Figure S4. Get High-res Image Gene #1: 'Amp Peak 1(1q21.2) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

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

P value = 3.48e-06 (Chi-square test), Q value = 0.0018

Table S5. Gene #2: 'Amp Peak 2(2q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
AMP PEAK 2(2Q11.2) MUTATED	19	14	20	5	4	1	6
AMP PEAK 2(2Q11.2) WILD-TYPE	47	27	26	80	18	9	46

Figure S5. Get High-res Image Gene #2: 'Amp Peak 2(2q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 2(2q11.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.71e-08 (Chi-square test), Q value = 9.3e-06

Table S6. Gene #2: 'Amp Peak 2(2q11.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
AMP PEAK 2(2Q11.2) MUTATED	19	9	4	1	26	5	1	2
AMP PEAK 2(2Q11.2) WILD-TYPE	24	38	35	44	32	46	3	17

Figure S6. Get High-res Image Gene #2: 'Amp Peak 2(2q11.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 3(2q31.2) mutation analysis' versus 'CN_CNMF'

P value = 8.38e-10 (Chi-square test), Q value = 4.6e-07

Table S7. Gene #3: 'Amp Peak 3(2q31.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
AMP PEAK 3(2Q31.2) MUTATED	23	15	20	3	2	0	4
AMP PEAK 3(2Q31.2) WILD-TYPE	43	26	26	82	20	10	48

Figure S7. Get High-res Image Gene #3: 'Amp Peak 3(2q31.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 3(2q31.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 9.37e-09 (Chi-square test), Q value = 5.1e-06

Table S8. Gene #3: 'Amp Peak 3(2q31.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
AMP PEAK 3(2Q31.2) MUTATED	13	8	5	2	30	5	1	1
AMP PEAK 3(2Q31.2) WILD-TYPE	30	39	34	43	28	46	3	18

Figure S8. Get High-res Image Gene #3: 'Amp Peak 3(2q31.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 4(2q32.2) mutation analysis' versus 'CN_CNMF'

P value = 7.97e-07 (Chi-square test), Q value = 0.00041

Table S9. Gene #4: 'Amp Peak 4(2q32.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
AMP PEAK 4(2Q32.2) MUTATED	20	13	16	2	3	1	4
AMP PEAK 4(2Q32.2) WILD-TYPE	46	28	30	83	19	9	48

Figure S9. Get High-res Image Gene #4: 'Amp Peak 4(2q32.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 4(2q32.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.3e-08 (Chi-square test), Q value = 2.8e-05

Table S10. Gene #4: 'Amp Peak 4(2q32.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
AMP PEAK 4(2Q32.2) MUTATED	13	4	5	2	26	3	1	2
AMP PEAK 4(2Q32.2) WILD-TYPE	30	43	34	43	32	48	3	17

Figure S10. Get High-res Image Gene #4: 'Amp Peak 4(2q32.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

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

P value = 1.29e-09 (Chi-square test), Q value = 7.1e-07

Table S11. Gene #5: 'Amp Peak 5(3q26.33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
AMP PEAK 5(3Q26.33) MUTATED	54	35	46	41	18	8	40
AMP PEAK 5(3Q26.33) WILD-TYPE	12	6	0	44	4	2	12

Figure S11. Get High-res Image Gene #5: 'Amp Peak 5(3q26.33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 5(3q26.33) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.26e-05 (Chi-square test), Q value = 0.016

Table S12. Gene #5: 'Amp Peak 5(3q26.33) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
AMP PEAK 5(3Q26.33) MUTATED	34	38	25	36	55	30	2	9
AMP PEAK 5(3Q26.33) WILD-TYPE	9	9	14	9	3	21	2	10

Figure S12. Get High-res Image Gene #5: 'Amp Peak 5(3q26.33) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 5(3q26.33) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000288 (Fisher's exact test), Q value = 0.14

Table S13. Gene #5: 'Amp Peak 5(3q26.33) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	84	120
AMP PEAK 5(3Q26.33) MUTATED	75	50	101
AMP PEAK 5(3Q26.33) WILD-TYPE	20	34	19

Figure S13. Get High-res Image Gene #5: 'Amp Peak 5(3q26.33) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 6(5p15.33) mutation analysis' versus 'CN_CNMF'

P value = 9.05e-11 (Chi-square test), Q value = 5e-08

Table S14. Gene #6: 'Amp Peak 6(5p15.33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
AMP PEAK 6(5P15.33) MUTATED	37	27	22	25	22	3	11
AMP PEAK 6(5P15.33) WILD-TYPE	29	14	24	60	0	7	41

Figure S14. Get High-res Image Gene #6: 'Amp Peak 6(5p15.33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 7(5p12) mutation analysis' versus 'CN_CNMF'

P value = 1.83e-10 (Chi-square test), Q value = 1e-07

Table S15. Gene #7: 'Amp Peak 7(5p12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
AMP PEAK 7(5P12) MUTATED	26	21	21	17	22	2	13
AMP PEAK 7(5P12) WILD-TYPE	40	20	25	68	0	8	39

Figure S15. Get High-res Image Gene #7: 'Amp Peak 7(5p12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 8(6p12.1) mutation analysis' versus 'CN_CNMF'

P value = 1.65e-05 (Chi-square test), Q value = 0.0083

Table S16. Gene #8: 'Amp Peak 8(6p12.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
AMP PEAK 8(6P12.1) MUTATED	19	18	10	6	5	2	4
AMP PEAK 8(6P12.1) WILD-TYPE	47	23	36	79	17	8	48

Figure S16. Get High-res Image Gene #8: 'Amp Peak 8(6p12.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 10(7p11.2) mutation analysis' versus 'CN_CNMF'

P value = 1.91e-08 (Chi-square test), Q value = 1e-05

Table S17. Gene #10: 'Amp Peak 10(7p11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
AMP PEAK 10(7P11.2) MUTATED	36	32	22	20	11	1	15
AMP PEAK 10(7P11.2) WILD-TYPE	30	9	24	65	11	9	37

Figure S17. Get High-res Image Gene #10: 'Amp Peak 10(7p11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 10(7p11.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 6.87e-07 (Chi-square test), Q value = 0.00036

Table S18. Gene #10: 'Amp Peak 10(7p11.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
AMP PEAK 10(7P11.2) MUTATED	27	24	21	3	31	15	1	9
AMP PEAK 10(7P11.2) WILD-TYPE	16	23	18	42	27	36	3	10

Figure S18. Get High-res Image Gene #10: 'Amp Peak 10(7p11.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 11(7q22.1) mutation analysis' versus 'CN_CNMF'

P value = 3.1e-11 (Chi-square test), Q value = 1.7e-08

Table S19. Gene #11: 'Amp Peak 11(7q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
AMP PEAK 11(7Q22.1) MUTATED	42	17	25	13	9	0	8
AMP PEAK 11(7Q22.1) WILD-TYPE	24	24	21	72	13	10	44

Figure S19. Get High-res Image Gene #11: 'Amp Peak 11(7q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 11(7q22.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.46e-08 (Chi-square test), Q value = 2.9e-05

Table S20. Gene #11: 'Amp Peak 11(7q22.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
AMP PEAK 11(7Q22.1) MUTATED	16	11	15	6	40	11	2	5
AMP PEAK 11(7Q22.1) WILD-TYPE	27	36	24	39	18	40	2	14

Figure S20. Get High-res Image Gene #11: 'Amp Peak 11(7q22.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 13(8q11.21) mutation analysis' versus 'CN_CNMF'

P value = 1.02e-06 (Chi-square test), Q value = 0.00052

Table S21. Gene #13: 'Amp Peak 13(8q11.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
AMP PEAK 13(8Q11.21) MUTATED	43	34	17	35	16	9	35
AMP PEAK 13(8Q11.21) WILD-TYPE	23	7	29	50	6	1	17

Figure S21. Get High-res Image Gene #13: 'Amp Peak 13(8q11.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 14(8q24.21) mutation analysis' versus 'CN_CNMF'

P value = 5.76e-08 (Chi-square test), Q value = 3.1e-05

Table S22. Gene #14: 'Amp Peak 14(8q24.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
AMP PEAK 14(8Q24.21) MUTATED	59	36	28	42	18	10	39
AMP PEAK 14(8Q24.21) WILD-TYPE	7	5	18	43	4	0	13

Figure S22. Get High-res Image Gene #14: 'Amp Peak 14(8q24.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 14(8q24.21) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000106 (Chi-square test), Q value = 0.052

Table S23. Gene #14: 'Amp Peak 14(8q24.21) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
AMP PEAK 14(8Q24.21) MUTATED	30	42	32	20	40	33	4	16
AMP PEAK 14(8Q24.21) WILD-TYPE	13	5	7	25	18	18	0	3

Figure S23. Get High-res Image Gene #14: 'Amp Peak 14(8q24.21) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 14(8q24.21) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000102 (Fisher's exact test), Q value = 0.05

Table S24. Gene #14: 'Amp Peak 14(8q24.21) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	91	90
AMP PEAK 14(8Q24.21) MUTATED	69	77	68
AMP PEAK 14(8Q24.21) WILD-TYPE	49	14	22

Figure S24. Get High-res Image Gene #14: 'Amp Peak 14(8q24.21) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Amp Peak 14(8q24.21) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000135 (Fisher's exact test), Q value = 0.065

Table S25. Gene #14: 'Amp Peak 14(8q24.21) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	84	120
AMP PEAK 14(8Q24.21) MUTATED	79	65	70
AMP PEAK 14(8Q24.21) WILD-TYPE	16	19	50

Figure S25. Get High-res Image Gene #14: 'Amp Peak 14(8q24.21) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 14(8q24.21) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000169 (Fisher's exact test), Q value = 0.082

Table S26. Gene #14: 'Amp Peak 14(8q24.21) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	181	130	10
AMP PEAK 14(8Q24.21) MUTATED	114	109	8
AMP PEAK 14(8Q24.21) WILD-TYPE	67	21	2

Figure S26. Get High-res Image Gene #14: 'Amp Peak 14(8q24.21) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 19(11q13.3) mutation analysis' versus 'CN_CNMF'

P value = 1.04e-23 (Chi-square test), Q value = 5.9e-21

Table S27. Gene #19: 'Amp Peak 19(11q13.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
AMP PEAK 19(11Q13.3) MUTATED	66	17	22	11	10	2	18
AMP PEAK 19(11Q13.3) WILD-TYPE	0	24	24	74	12	8	34

Figure S27. Get High-res Image Gene #19: 'Amp Peak 19(11q13.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 20(12p13.33) mutation analysis' versus 'CN_CNMF'

P value = 5.52e-11 (Chi-square test), Q value = 3.1e-08

Table S28. Gene #20: 'Amp Peak 20(12p13.33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
AMP PEAK 20(12P13.33) MUTATED	24	25	28	12	10	5	5
AMP PEAK 20(12P13.33) WILD-TYPE	42	16	18	73	12	5	47

Figure S28. Get High-res Image Gene #20: 'Amp Peak 20(12p13.33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 20(12p13.33) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.28e-05 (Chi-square test), Q value = 0.0065

Table S29. Gene #20: 'Amp Peak 20(12p13.33) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
AMP PEAK 20(12P13.33) MUTATED	20	20	5	14	34	12	0	3
AMP PEAK 20(12P13.33) WILD-TYPE	23	27	34	31	24	39	4	16

Figure S29. Get High-res Image Gene #20: 'Amp Peak 20(12p13.33) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 21(12q15) mutation analysis' versus 'CN_CNMF'

P value = 3.77e-08 (Chi-square test), Q value = 2e-05

Table S30. Gene #21: 'Amp Peak 21(12q15) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
AMP PEAK 21(12Q15) MUTATED	20	20	9	7	3	3	1
AMP PEAK 21(12Q15) WILD-TYPE	46	21	37	78	19	7	51

Figure S30. Get High-res Image Gene #21: 'Amp Peak 21(12q15) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 22(13q22.1) mutation analysis' versus 'CN_CNMF'

P value = 4.16e-07 (Chi-square test), Q value = 0.00022

Table S31. Gene #22: 'Amp Peak 22(13q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
AMP PEAK 22(13Q22.1) MUTATED	19	21	3	7	3	2	13
AMP PEAK 22(13Q22.1) WILD-TYPE	47	20	43	78	19	8	39

Figure S31. Get High-res Image Gene #22: 'Amp Peak 22(13q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 22(13q22.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.43e-05 (Chi-square test), Q value = 0.042

Table S32. Gene #22: 'Amp Peak 22(13q22.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
AMP PEAK 22(13Q22.1) MUTATED	7	23	7	10	12	3	0	5
AMP PEAK 22(13Q22.1) WILD-TYPE	36	24	32	35	46	48	4	14

Figure S32. Get High-res Image Gene #22: 'Amp Peak 22(13q22.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 23(14q11.2) mutation analysis' versus 'CN_CNMF'

P value = 7.37e-06 (Chi-square test), Q value = 0.0038

Table S33. Gene #23: 'Amp Peak 23(14q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
AMP PEAK 23(14Q11.2) MUTATED	20	23	15	8	7	4	11
AMP PEAK 23(14Q11.2) WILD-TYPE	46	18	31	77	15	6	41

Figure S33. Get High-res Image Gene #23: 'Amp Peak 23(14q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 24(15q26.3) mutation analysis' versus 'CN_CNMF'

P value = 0.000106 (Chi-square test), Q value = 0.052

Table S34. Gene #24: 'Amp Peak 24(15q26.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
AMP PEAK 24(15Q26.3) MUTATED	24	17	9	9	5	1	6
AMP PEAK 24(15Q26.3) WILD-TYPE	42	24	37	76	17	9	46

Figure S34. Get High-res Image Gene #24: 'Amp Peak 24(15q26.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 25(17q12) mutation analysis' versus 'CN_CNMF'

P value = 4.94e-05 (Chi-square test), Q value = 0.025

Table S35. Gene #25: 'Amp Peak 25(17q12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
AMP PEAK 25(17Q12) MUTATED	21	10	12	3	3	3	4
AMP PEAK 25(17Q12) WILD-TYPE	45	31	34	82	19	7	48

Figure S35. Get High-res Image Gene #25: 'Amp Peak 25(17q12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 25(17q12) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000112 (Chi-square test), Q value = 0.054

Table S36. Gene #25: 'Amp Peak 25(17q12) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
AMP PEAK 25(17Q12) MUTATED	10	8	2	4	22	4	0	2
AMP PEAK 25(17Q12) WILD-TYPE	33	39	37	41	36	47	4	17

Figure S36. Get High-res Image Gene #25: 'Amp Peak 25(17q12) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 26(18p11.31) mutation analysis' versus 'CN_CNMF'

P value = 4.38e-07 (Chi-square test), Q value = 0.00023

Table S37. Gene #26: 'Amp Peak 26(18p11.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
AMP PEAK 26(18P11.31) MUTATED	26	18	21	11	13	6	8
AMP PEAK 26(18P11.31) WILD-TYPE	40	23	25	74	9	4	44

Figure S37. Get High-res Image Gene #26: 'Amp Peak 26(18p11.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 28(20q11.22) mutation analysis' versus 'CN_CNMF'

P value = 0.000225 (Chi-square test), Q value = 0.11

Table S38. Gene #28: 'Amp Peak 28(20q11.22) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
AMP PEAK 28(20Q11.22) MUTATED	30	31	19	27	13	6	19
AMP PEAK 28(20Q11.22) WILD-TYPE	36	10	27	58	9	4	33

Figure S38. Get High-res Image Gene #28: 'Amp Peak 28(20q11.22) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 29(Xq28) mutation analysis' versus 'CN_CNMF'

P value = 3.96e-08 (Chi-square test), Q value = 2.1e-05

Table S39. Gene #29: 'Amp Peak 29(Xq28) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
AMP PEAK 29(XQ28) MUTATED	31	23	9	12	9	6	8
AMP PEAK 29(XQ28) WILD-TYPE	35	18	37	73	13	4	44

Figure S39. Get High-res Image Gene #29: 'Amp Peak 29(Xq28) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 1(1p36.13) mutation analysis' versus 'CN_CNMF'

P value = 1.48e-10 (Chi-square test), Q value = 8.2e-08

Table S40. Gene #30: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
DEL PEAK 1(1P36.13) MUTATED	14	14	26	10	0	0	4
DEL PEAK 1(1P36.13) WILD-TYPE	52	27	20	75	22	10	48

Figure S40. Get High-res Image Gene #30: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 1(1p36.13) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.38e-15 (Chi-square test), Q value = 3.1e-12

Table S41. Gene #30: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 1(1P36.13) MUTATED	6	4	8	5	36	1	2	2
DEL PEAK 1(1P36.13) WILD-TYPE	37	43	31	40	22	50	2	17

Figure S41. Get High-res Image Gene #30: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 1(1p36.13) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.03e-05 (Fisher's exact test), Q value = 0.015

Table S42. Gene #30: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	91	90
DEL PEAK 1(1P36.13) MUTATED	39	17	7
DEL PEAK 1(1P36.13) WILD-TYPE	79	74	83

Figure S42. Get High-res Image Gene #30: 'Del Peak 1(1p36.13) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

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

P value = 2.77e-10 (Chi-square test), Q value = 1.5e-07

Table S43. Gene #31: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
DEL PEAK 2(1P13.2) MUTATED	16	16	28	5	6	3	7
DEL PEAK 2(1P13.2) WILD-TYPE	50	25	18	80	16	7	45

Figure S43. Get High-res Image Gene #31: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 8.62e-10 (Chi-square test), Q value = 4.7e-07

Table S44. Gene #31: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 2(1P13.2) MUTATED	10	9	6	4	35	5	2	4
DEL PEAK 2(1P13.2) WILD-TYPE	33	38	33	41	23	46	2	15

Figure S44. Get High-res Image Gene #31: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

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

P value = 0.000181 (Fisher's exact test), Q value = 0.087

Table S45. Gene #31: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	127	93
DEL PEAK 2(1P13.2) MUTATED	16	48	17
DEL PEAK 2(1P13.2) WILD-TYPE	85	79	76

Figure S45. Get High-res Image Gene #31: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

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

P value = 0.000186 (Fisher's exact test), Q value = 0.089

Table S46. Gene #33: 'Del Peak 4(2q22.1) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	181	130	10
DEL PEAK 4(2Q22.1) MUTATED	45	15	6
DEL PEAK 4(2Q22.1) WILD-TYPE	136	115	4

Figure S46. Get High-res Image Gene #33: 'Del Peak 4(2q22.1) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

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

P value = 0.000122 (Chi-square test), Q value = 0.059

Table S47. Gene #34: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
DEL PEAK 5(2Q36.2) MUTATED	21	14	27	15	4	3	12
DEL PEAK 5(2Q36.2) WILD-TYPE	45	27	19	70	18	7	40

Figure S47. Get High-res Image Gene #34: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 5.69e-06 (Chi-square test), Q value = 0.0029

Table S48. Gene #34: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 5(2Q36.2) MUTATED	14	11	16	15	29	2	3	3
DEL PEAK 5(2Q36.2) WILD-TYPE	29	36	23	30	29	49	1	16

Figure S48. Get High-res Image Gene #34: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 6(3p24.1) mutation analysis' versus 'CN_CNMF'

P value = 3.25e-27 (Chi-square test), Q value = 1.9e-24

Table S49. Gene #35: 'Del Peak 6(3p24.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
DEL PEAK 6(3P24.1) MUTATED	62	34	42	23	22	8	48
DEL PEAK 6(3P24.1) WILD-TYPE	4	7	4	62	0	2	4

Figure S49. Get High-res Image Gene #35: 'Del Peak 6(3p24.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 6(3p24.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.93e-08 (Chi-square test), Q value = 2.1e-05

Table S50. Gene #35: 'Del Peak 6(3p24.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 6(3P24.1) MUTATED	39	42	28	20	51	29	4	14
DEL PEAK 6(3P24.1) WILD-TYPE	4	5	11	25	7	22	0	5

Figure S50. Get High-res Image Gene #35: 'Del Peak 6(3p24.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 7(3p14.2) mutation analysis' versus 'CN_CNMF'

P value = 3.41e-27 (Chi-square test), Q value = 2e-24

Table S51. Gene #36: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
DEL PEAK 7(3P14.2) MUTATED	62	35	43	24	21	9	48
DEL PEAK 7(3P14.2) WILD-TYPE	4	6	3	61	1	1	4

Figure S51. Get High-res Image Gene #36: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 7(3p14.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.71e-07 (Chi-square test), Q value = 3e-04

Table S52. Gene #36: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 7(3P14.2) MUTATED	41	41	27	23	51	30	4	14
DEL PEAK 7(3P14.2) WILD-TYPE	2	6	12	22	7	21	0	5

Figure S52. Get High-res Image Gene #36: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 8(3p12.2) mutation analysis' versus 'CN_CNMF'

P value = 3.11e-25 (Chi-square test), Q value = 1.8e-22

Table S53. Gene #37: 'Del Peak 8(3p12.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
DEL PEAK 8(3P12.2) MUTATED	59	34	44	20	20	9	42
DEL PEAK 8(3P12.2) WILD-TYPE	7	7	2	65	2	1	10

Figure S53. Get High-res Image Gene #37: 'Del Peak 8(3p12.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 8(3p12.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.04e-09 (Chi-square test), Q value = 2.2e-06

Table S54. Gene #37: 'Del Peak 8(3p12.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 8(3P12.2) MUTATED	38	38	27	18	53	26	4	13
DEL PEAK 8(3P12.2) WILD-TYPE	5	9	12	27	5	25	0	6

Figure S54. Get High-res Image Gene #37: 'Del Peak 8(3p12.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 9(4p16.3) mutation analysis' versus 'CN_CNMF'

P value = 1.38e-14 (Chi-square test), Q value = 7.8e-12

Table S55. Gene #38: 'Del Peak 9(4p16.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
DEL PEAK 9(4P16.3) MUTATED	44	25	34	13	4	2	15
DEL PEAK 9(4P16.3) WILD-TYPE	22	16	12	72	18	8	37

Figure S55. Get High-res Image Gene #38: 'Del Peak 9(4p16.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 9(4p16.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.5e-05 (Chi-square test), Q value = 0.0076

Table S56. Gene #38: 'Del Peak 9(4p16.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 9(4P16.3) MUTATED	20	17	17	13	41	11	3	9
DEL PEAK 9(4P16.3) WILD-TYPE	23	30	22	32	17	40	1	10

Figure S56. Get High-res Image Gene #38: 'Del Peak 9(4p16.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

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

P value = 7.36e-16 (Chi-square test), Q value = 4.2e-13

Table S57. Gene #39: 'Del Peak 10(4p15.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
DEL PEAK 10(4P15.2) MUTATED	41	25	38	13	4	2	15
DEL PEAK 10(4P15.2) WILD-TYPE	25	16	8	72	18	8	37

Figure S57. Get High-res Image Gene #39: 'Del Peak 10(4p15.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 5.98e-07 (Chi-square test), Q value = 0.00031

Table S58. Gene #39: 'Del Peak 10(4p15.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 10(4P15.2) MUTATED	20	15	17	13	44	12	3	7
DEL PEAK 10(4P15.2) WILD-TYPE	23	32	22	32	14	39	1	12

Figure S58. Get High-res Image Gene #39: 'Del Peak 10(4p15.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

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

P value = 5.42e-12 (Chi-square test), Q value = 3e-09

Table S59. Gene #40: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
DEL PEAK 11(4Q22.1) MUTATED	21	24	30	9	9	2	7
DEL PEAK 11(4Q22.1) WILD-TYPE	45	17	16	76	13	8	45

Figure S59. Get High-res Image Gene #40: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 6.5e-07 (Chi-square test), Q value = 0.00034

Table S60. Gene #40: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 11(4Q22.1) MUTATED	17	16	11	7	36	8	1	2
DEL PEAK 11(4Q22.1) WILD-TYPE	26	31	28	38	22	43	3	17

Figure S60. Get High-res Image Gene #40: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

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

P value = 4e-08 (Chi-square test), Q value = 2.1e-05

Table S61. Gene #41: 'Del Peak 12(4q35.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
DEL PEAK 12(4Q35.2) MUTATED	21	28	29	17	14	3	19
DEL PEAK 12(4Q35.2) WILD-TYPE	45	13	17	68	8	7	33

Figure S61. Get High-res Image Gene #41: 'Del Peak 12(4q35.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 2.97e-05 (Chi-square test), Q value = 0.015

Table S62. Gene #41: 'Del Peak 12(4q35.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 12(4Q35.2) MUTATED	17	25	19	9	36	12	0	6
DEL PEAK 12(4Q35.2) WILD-TYPE	26	22	20	36	22	39	4	13

Figure S62. Get High-res Image Gene #41: 'Del Peak 12(4q35.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

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

P value = 1.65e-16 (Chi-square test), Q value = 9.5e-14

Table S63. Gene #42: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
DEL PEAK 13(5Q11.2) MUTATED	32	32	33	8	13	2	14
DEL PEAK 13(5Q11.2) WILD-TYPE	34	9	13	77	9	8	38

Figure S63. Get High-res Image Gene #42: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 1.35e-12 (Chi-square test), Q value = 7.6e-10

Table S64. Gene #42: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 13(5Q11.2) MUTATED	30	27	8	6	41	11	1	6
DEL PEAK 13(5Q11.2) WILD-TYPE	13	20	31	39	17	40	3	13

Figure S64. Get High-res Image Gene #42: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 14(5q35.3) mutation analysis' versus 'CN_CNMF'

P value = 4.01e-15 (Chi-square test), Q value = 2.3e-12

Table S65. Gene #43: 'Del Peak 14(5q35.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
DEL PEAK 14(5Q35.3) MUTATED	26	29	34	10	14	2	12
DEL PEAK 14(5Q35.3) WILD-TYPE	40	12	12	75	8	8	40

Figure S65. Get High-res Image Gene #43: 'Del Peak 14(5q35.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 14(5q35.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.25e-14 (Chi-square test), Q value = 2.4e-11

Table S66. Gene #43: 'Del Peak 14(5q35.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 14(5Q35.3) MUTATED	33	24	5	8	37	8	0	6
DEL PEAK 14(5Q35.3) WILD-TYPE	10	23	34	37	21	43	4	13

Figure S66. Get High-res Image Gene #43: 'Del Peak 14(5q35.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 14(5q35.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000477 (Fisher's exact test), Q value = 0.23

Table S67. Gene #43: 'Del Peak 14(5q35.3) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	84	120
DEL PEAK 14(5Q35.3) MUTATED	39	20	61
DEL PEAK 14(5Q35.3) WILD-TYPE	56	64	59

Figure S67. Get High-res Image Gene #43: 'Del Peak 14(5q35.3) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 15(6p25.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.00033 (Chi-square test), Q value = 0.16

Table S68. Gene #44: 'Del Peak 15(6p25.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 15(6P25.3) MUTATED	7	9	5	6	26	6	1	3
DEL PEAK 15(6P25.3) WILD-TYPE	36	38	34	39	32	45	3	16

Figure S68. Get High-res Image Gene #44: 'Del Peak 15(6p25.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 18(8p23.2) mutation analysis' versus 'CN_CNMF'

P value = 4.99e-12 (Chi-square test), Q value = 2.8e-09

Table S69. Gene #47: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
DEL PEAK 18(8P23.2) MUTATED	54	31	17	24	17	5	35
DEL PEAK 18(8P23.2) WILD-TYPE	12	10	29	61	5	5	17

Figure S69. Get High-res Image Gene #47: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 18(8p23.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.84e-05 (Chi-square test), Q value = 0.019

Table S70. Gene #47: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 18(8P23.2) MUTATED	21	34	30	11	36	28	2	11
DEL PEAK 18(8P23.2) WILD-TYPE	22	13	9	34	22	23	2	8

Figure S70. Get High-res Image Gene #47: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 19(9p23) mutation analysis' versus 'CN_CNMF'

P value = 6.45e-13 (Chi-square test), Q value = 3.6e-10

Table S71. Gene #48: 'Del Peak 19(9p23) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
DEL PEAK 19(9P23) MUTATED	40	27	27	11	15	0	31
DEL PEAK 19(9P23) WILD-TYPE	26	14	19	74	7	10	21

Figure S71. Get High-res Image Gene #48: 'Del Peak 19(9p23) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 19(9p23) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.42e-09 (Chi-square test), Q value = 2.9e-06

Table S72. Gene #48: 'Del Peak 19(9p23) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 19(9P23) MUTATED	30	25	20	5	38	13	3	8
DEL PEAK 19(9P23) WILD-TYPE	13	22	19	40	20	38	1	11

Figure S72. Get High-res Image Gene #48: 'Del Peak 19(9p23) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 20(9p21.3) mutation analysis' versus 'CN_CNMF'

P value = 3.52e-10 (Chi-square test), Q value = 1.9e-07

Table S73. Gene #49: 'Del Peak 20(9p21.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
DEL PEAK 20(9P21.3) MUTATED	53	25	31	25	16	2	37
DEL PEAK 20(9P21.3) WILD-TYPE	13	16	15	60	6	8	15

Figure S73. Get High-res Image Gene #49: 'Del Peak 20(9p21.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 20(9p21.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.83e-09 (Chi-square test), Q value = 1.5e-06

Table S74. Gene #49: 'Del Peak 20(9p21.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 20(9P21.3) MUTATED	35	30	26	7	40	23	3	14
DEL PEAK 20(9P21.3) WILD-TYPE	8	17	13	38	18	28	1	5

Figure S74. Get High-res Image Gene #49: 'Del Peak 20(9p21.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 21(9q21.11) mutation analysis' versus 'CN_CNMF'

P value = 2.24e-07 (Chi-square test), Q value = 0.00012

Table S75. Gene #50: 'Del Peak 21(9q21.11) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
DEL PEAK 21(9Q21.11) MUTATED	25	12	5	6	9	0	4
DEL PEAK 21(9Q21.11) WILD-TYPE	41	29	41	79	13	10	48

Figure S75. Get High-res Image Gene #50: 'Del Peak 21(9q21.11) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 23(10p15.3) mutation analysis' versus 'CN_CNMF'

P value = 1.84e-05 (Chi-square test), Q value = 0.0093

Table S76. Gene #52: 'Del Peak 23(10p15.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
DEL PEAK 23(10P15.3) MUTATED	28	20	15	9	8	6	22
DEL PEAK 23(10P15.3) WILD-TYPE	38	21	31	76	14	4	30

Figure S76. Get High-res Image Gene #52: 'Del Peak 23(10p15.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 24(10p11.21) mutation analysis' versus 'CN_CNMF'

P value = 8.15e-06 (Chi-square test), Q value = 0.0041

Table S77. Gene #53: 'Del Peak 24(10p11.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
DEL PEAK 24(10P11.21) MUTATED	28	22	11	9	8	5	18
DEL PEAK 24(10P11.21) WILD-TYPE	38	19	35	76	14	5	34

Figure S77. Get High-res Image Gene #53: 'Del Peak 24(10p11.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 26(11p15.4) mutation analysis' versus 'CN_CNMF'

P value = 3.91e-06 (Chi-square test), Q value = 0.002

Table S78. Gene #55: 'Del Peak 26(11p15.4) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
DEL PEAK 26(11P15.4) MUTATED	37	13	18	16	9	1	8
DEL PEAK 26(11P15.4) WILD-TYPE	29	28	28	69	13	9	44

Figure S78. Get High-res Image Gene #55: 'Del Peak 26(11p15.4) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 26(11p15.4) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000523 (Chi-square test), Q value = 0.25

Table S79. Gene #55: 'Del Peak 26(11p15.4) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 26(11P15.4) MUTATED	17	14	9	13	32	8	1	3
DEL PEAK 26(11P15.4) WILD-TYPE	26	33	30	32	26	43	3	16

Figure S79. Get High-res Image Gene #55: 'Del Peak 26(11p15.4) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 27(11q23.1) mutation analysis' versus 'CN_CNMF'

P value = 1.37e-14 (Chi-square test), Q value = 7.8e-12

Table S80. Gene #56: 'Del Peak 27(11q23.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
DEL PEAK 27(11Q23.1) MUTATED	60	10	24	28	10	7	14
DEL PEAK 27(11Q23.1) WILD-TYPE	6	31	22	57	12	3	38

Figure S80. Get High-res Image Gene #56: 'Del Peak 27(11q23.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 27(11q23.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.45e-07 (Chi-square test), Q value = 0.00044

Table S81. Gene #56: 'Del Peak 27(11q23.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 27(11Q23.1) MUTATED	18	21	16	40	31	16	1	6
DEL PEAK 27(11Q23.1) WILD-TYPE	25	26	23	5	27	35	3	13

Figure S81. Get High-res Image Gene #56: 'Del Peak 27(11q23.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 27(11q23.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.11

Table S82. Gene #56: 'Del Peak 27(11q23.1) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	84	120
DEL PEAK 27(11Q23.1) MUTATED	37	33	76
DEL PEAK 27(11Q23.1) WILD-TYPE	58	51	44

Figure S82. Get High-res Image Gene #56: 'Del Peak 27(11q23.1) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 29(13q12.11) mutation analysis' versus 'CN_CNMF'

P value = 8.03e-11 (Chi-square test), Q value = 4.5e-08

Table S83. Gene #58: 'Del Peak 29(13q12.11) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
DEL PEAK 29(13Q12.11) MUTATED	35	24	36	14	14	3	19
DEL PEAK 29(13Q12.11) WILD-TYPE	31	17	10	71	8	7	33

Figure S83. Get High-res Image Gene #58: 'Del Peak 29(13q12.11) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 29(13q12.11) mutation analysis' versus 'METHLYATION_CNMF'

P value = 7.28e-07 (Chi-square test), Q value = 0.00038

Table S84. Gene #58: 'Del Peak 29(13q12.11) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 29(13Q12.11) MUTATED	31	22	15	13	39	12	1	6
DEL PEAK 29(13Q12.11) WILD-TYPE	12	25	24	32	19	39	3	13

Figure S84. Get High-res Image Gene #58: 'Del Peak 29(13q12.11) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 30(13q14.2) mutation analysis' versus 'CN_CNMF'

P value = 3.1e-07 (Chi-square test), Q value = 0.00016

Table S85. Gene #59: 'Del Peak 30(13q14.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
DEL PEAK 30(13Q14.2) MUTATED	32	18	35	22	13	4	13
DEL PEAK 30(13Q14.2) WILD-TYPE	34	23	11	63	9	6	39

Figure S85. Get High-res Image Gene #59: 'Del Peak 30(13q14.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 30(13q14.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.88e-07 (Chi-square test), Q value = 0.00031

Table S86. Gene #59: 'Del Peak 30(13q14.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 30(13Q14.2) MUTATED	32	17	13	23	31	10	0	4
DEL PEAK 30(13Q14.2) WILD-TYPE	11	30	26	22	27	41	4	15

Figure S86. Get High-res Image Gene #59: 'Del Peak 30(13q14.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 30(13q14.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 5.7e-05 (Fisher's exact test), Q value = 0.028

Table S87. Gene #59: 'Del Peak 30(13q14.2) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	91	90
DEL PEAK 30(13Q14.2) MUTATED	66	39	23
DEL PEAK 30(13Q14.2) WILD-TYPE	52	52	67

Figure S87. Get High-res Image Gene #59: 'Del Peak 30(13q14.2) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 30(13q14.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.46e-05 (Fisher's exact test), Q value = 0.032

Table S88. Gene #59: 'Del Peak 30(13q14.2) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	84	120
DEL PEAK 30(13Q14.2) MUTATED	38	22	68
DEL PEAK 30(13Q14.2) WILD-TYPE	57	62	52

Figure S88. Get High-res Image Gene #59: 'Del Peak 30(13q14.2) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 32(14q32.32) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.42e-07 (Chi-square test), Q value = 7.5e-05

Table S89. Gene #61: 'Del Peak 32(14q32.32) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 32(14Q32.32) MUTATED	5	3	4	20	13	1	0	1
DEL PEAK 32(14Q32.32) WILD-TYPE	38	44	35	25	45	50	4	18

Figure S89. Get High-res Image Gene #61: 'Del Peak 32(14q32.32) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 32(14q32.32) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000242 (Fisher's exact test), Q value = 0.12

Table S90. Gene #61: 'Del Peak 32(14q32.32) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	91	90
DEL PEAK 32(14Q32.32) MUTATED	30	11	5
DEL PEAK 32(14Q32.32) WILD-TYPE	88	80	85

Figure S90. Get High-res Image Gene #61: 'Del Peak 32(14q32.32) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 32(14q32.32) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.8e-05 (Fisher's exact test), Q value = 0.048

Table S91. Gene #61: 'Del Peak 32(14q32.32) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	84	120
DEL PEAK 32(14Q32.32) MUTATED	11	4	31
DEL PEAK 32(14Q32.32) WILD-TYPE	84	80	89

Figure S91. Get High-res Image Gene #61: 'Del Peak 32(14q32.32) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 34(16q12.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.13e-07 (Chi-square test), Q value = 6e-05

Table S92. Gene #63: 'Del Peak 34(16q12.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 34(16Q12.1) MUTATED	8	1	5	21	13	2	1	1
DEL PEAK 34(16Q12.1) WILD-TYPE	35	46	34	24	45	49	3	18

Figure S92. Get High-res Image Gene #63: 'Del Peak 34(16q12.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 34(16q12.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 7.1e-08 (Fisher's exact test), Q value = 3.8e-05

Table S93. Gene #63: 'Del Peak 34(16q12.1) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	91	90
DEL PEAK 34(16Q12.1) MUTATED	38	9	4
DEL PEAK 34(16Q12.1) WILD-TYPE	80	82	86

Figure S93. Get High-res Image Gene #63: 'Del Peak 34(16q12.1) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 34(16q12.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.91e-07 (Fisher's exact test), Q value = 0.00021

Table S94. Gene #63: 'Del Peak 34(16q12.1) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	84	120
DEL PEAK 34(16Q12.1) MUTATED	7	6	38
DEL PEAK 34(16Q12.1) WILD-TYPE	88	78	82

Figure S94. Get High-res Image Gene #63: 'Del Peak 34(16q12.1) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 34(16q12.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.17

Table S95. Gene #63: 'Del Peak 34(16q12.1) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	127	93
DEL PEAK 34(16Q12.1) MUTATED	13	34	7
DEL PEAK 34(16Q12.1) WILD-TYPE	88	93	86

Figure S95. Get High-res Image Gene #63: 'Del Peak 34(16q12.1) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'Del Peak 35(16q23.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.88e-05 (Fisher's exact test), Q value = 0.044

Table S96. Gene #64: 'Del Peak 35(16q23.3) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	84	120
DEL PEAK 35(16Q23.3) MUTATED	11	9	38
DEL PEAK 35(16Q23.3) WILD-TYPE	84	75	82

Figure S96. Get High-res Image Gene #64: 'Del Peak 35(16q23.3) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 37(18q21.2) mutation analysis' versus 'CN_CNMF'

P value = 3.21e-14 (Chi-square test), Q value = 1.8e-11

Table S97. Gene #66: 'Del Peak 37(18q21.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
DEL PEAK 37(18Q21.2) MUTATED	43	35	21	14	15	6	36
DEL PEAK 37(18Q21.2) WILD-TYPE	23	6	25	71	7	4	16

Figure S97. Get High-res Image Gene #66: 'Del Peak 37(18q21.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 37(18q21.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.69e-09 (Chi-square test), Q value = 9.2e-07

Table S98. Gene #66: 'Del Peak 37(18q21.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 37(18Q21.2) MUTATED	30	35	22	4	34	24	4	8
DEL PEAK 37(18Q21.2) WILD-TYPE	13	12	17	41	24	27	0	11

Figure S98. Get High-res Image Gene #66: 'Del Peak 37(18q21.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 38(18q23) mutation analysis' versus 'CN_CNMF'

P value = 2.42e-16 (Chi-square test), Q value = 1.4e-13

Table S99. Gene #67: 'Del Peak 38(18q23) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
DEL PEAK 38(18Q23) MUTATED	45	37	28	14	15	5	38
DEL PEAK 38(18Q23) WILD-TYPE	21	4	18	71	7	5	14

Figure S99. Get High-res Image Gene #67: 'Del Peak 38(18q23) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 38(18q23) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.38e-11 (Chi-square test), Q value = 7.7e-09

Table S100. Gene #67: 'Del Peak 38(18q23) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 38(18Q23) MUTATED	31	40	23	5	39	23	3	8
DEL PEAK 38(18Q23) WILD-TYPE	12	7	16	40	19	28	1	11

Figure S100. Get High-res Image Gene #67: 'Del Peak 38(18q23) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 40(19q13.43) mutation analysis' versus 'CN_CNMF'

P value = 9.26e-05 (Chi-square test), Q value = 0.045

Table S101. Gene #69: 'Del Peak 40(19q13.43) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
DEL PEAK 40(19Q13.43) MUTATED	16	14	16	4	1	2	11
DEL PEAK 40(19Q13.43) WILD-TYPE	50	27	30	81	21	8	41

Figure S101. Get High-res Image Gene #69: 'Del Peak 40(19q13.43) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 40(19q13.43) mutation analysis' versus 'METHLYATION_CNMF'

P value = 6.93e-05 (Chi-square test), Q value = 0.034

Table S102. Gene #69: 'Del Peak 40(19q13.43) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 40(19Q13.43) MUTATED	7	14	9	3	22	3	0	1
DEL PEAK 40(19Q13.43) WILD-TYPE	36	33	30	42	36	48	4	18

Figure S102. Get High-res Image Gene #69: 'Del Peak 40(19q13.43) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 41(Xp21.3) mutation analysis' versus 'CN_CNMF'

P value = 7.73e-06 (Chi-square test), Q value = 0.0039

Table S103. Gene #70: 'Del Peak 41(Xp21.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
DEL PEAK 41(XP21.3) MUTATED	29	22	21	12	9	3	10
DEL PEAK 41(XP21.3) WILD-TYPE	37	19	25	73	13	7	42

Figure S103. Get High-res Image Gene #70: 'Del Peak 41(Xp21.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 42(Xp11.3) mutation analysis' versus 'CN_CNMF'

P value = 9.69e-08 (Chi-square test), Q value = 5.1e-05

Table S104. Gene #71: 'Del Peak 42(Xp11.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
DEL PEAK 42(XP11.3) MUTATED	30	22	24	11	9	4	8
DEL PEAK 42(XP11.3) WILD-TYPE	36	19	22	74	13	6	44

Figure S104. Get High-res Image Gene #71: 'Del Peak 42(Xp11.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 42(Xp11.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.8e-05 (Chi-square test), Q value = 0.029

Table S105. Gene #71: 'Del Peak 42(Xp11.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 42(XP11.3) MUTATED	15	18	13	7	34	8	2	6
DEL PEAK 42(XP11.3) WILD-TYPE	28	29	26	38	24	43	2	13

Figure S105. Get High-res Image Gene #71: 'Del Peak 42(Xp11.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 43(Xq21.33) mutation analysis' versus 'CN_CNMF'

P value = 1.07e-06 (Chi-square test), Q value = 0.00055

Table S106. Gene #72: 'Del Peak 43(Xq21.33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	66	41	46	85	22	10	52
DEL PEAK 43(XQ21.33) MUTATED	16	5	20	4	4	0	6
DEL PEAK 43(XQ21.33) WILD-TYPE	50	36	26	81	18	10	46

Figure S106. Get High-res Image Gene #72: 'Del Peak 43(Xq21.33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 43(Xq21.33) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000324 (Fisher's exact test), Q value = 0.15

Table S107. Gene #72: 'Del Peak 43(Xq21.33) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	127	93
DEL PEAK 43(XQ21.33) MUTATED	12	35	8
DEL PEAK 43(XQ21.33) WILD-TYPE	89	92	85

Figure S107. Get High-res Image Gene #72: 'Del Peak 43(Xq21.33) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_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 = HNSC-TP.transferedmergedcluster.txt
Number of patients = 322
Number of copy number variation regions = 72
Number of molecular subtypes = 8
Exclude regions that fewer than K tumors have alterations, K = 3

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[2] 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)

[3] 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)

[4] GISTIC_version2

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