Correlation between copy number variation genes and molecular subtypes

Overview

Introduction

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

Summary

Testing the association between copy number variation of 70 peak regions and 12 molecular subtypes across 559 patients, 82 significant findings detected with Q value < 0.25.

Amp Peak 1(1p34.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 2(1q21.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 3(1q42.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 4(2p23.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 5(2q31.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 6(3q26.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 8(4q13.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 9(5p15.33) cnvs correlated to 'CN_CNMF'.
Amp Peak 10(6p22.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 11(7q36.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 12(8p11.21) cnvs correlated to 'CN_CNMF'.
Amp Peak 13(8q24.21) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'MRNASEQ_CNMF'.
Amp Peak 14(10p15.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 16(11q14.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 17(12p13.33) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 18(12p12.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 20(15q26.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 22(18q11.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 23(19p13.12) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', and 'RPPA_CHIERARCHICAL'.
Amp Peak 24(19q12) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 25(19q13.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 26(20p13) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'METHLYATION_CNMF'.
Amp Peak 27(20q11.21) cnvs correlated to 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Amp Peak 28(20q13.33) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'METHLYATION_CNMF'.
Amp Peak 29(22q12.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 30(Xp11.23) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 31(Xq28) cnvs correlated to 'CN_CNMF'.
Del Peak 1(1p36.11) cnvs correlated to 'CN_CNMF'.
Del Peak 2(1q32.3) cnvs correlated to 'CN_CNMF'.
Del Peak 5(2q37.3) cnvs correlated to 'CN_CNMF'.
Del Peak 6(3p26.2) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'METHLYATION_CNMF'.
Del Peak 9(5q11.2) cnvs correlated to 'CN_CNMF'.
Del Peak 10(5q13.2) cnvs correlated to 'CN_CNMF'.
Del Peak 11(6q27) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 12(7p22.1) cnvs correlated to 'CN_CNMF'.
Del Peak 13(8p23.3) cnvs correlated to 'CN_CNMF'.
Del Peak 14(8p21.2) cnvs correlated to 'CN_CNMF'.
Del Peak 15(9p24.3) cnvs correlated to 'MRNA_CNMF'.
Del Peak 16(9q21.11) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 17(9q34.13) cnvs correlated to 'CN_CNMF'.
Del Peak 20(10q26.3) cnvs correlated to 'CN_CNMF'.
Del Peak 21(11p15.5) cnvs correlated to 'CN_CNMF'.
Del Peak 23(12q23.1) cnvs correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.
Del Peak 24(12q24.33) cnvs correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.
Del Peak 25(13q14.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'RPPA_CNMF'.
Del Peak 27(15q15.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 29(16q22.1) cnvs correlated to 'CN_CNMF'.
Del Peak 30(16q23.1) cnvs correlated to 'CN_CNMF'.
Del Peak 32(17q11.2) cnvs correlated to 'CN_CNMF'.
Del Peak 36(19q13.43) 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 70 regions and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 82 significant findings detected.


		Molecular subtypes	MRNA CNMF	MRNA CHIERARCHICAL	MIR CNMF	MIR CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact 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	Fisher's exact test	Fisher's exact test
Amp Peak 27(20q11 21)	326 (58%)	233	0.00553 (1.00)	3.68e-08 (2.97e-05)	0.185 (1.00)	0.000105 (0.0808)	1.01e-22 (8.5e-20)	8.1e-13 (6.74e-10)	0.18 (1.00)	0.0246 (1.00)	0.000329 (0.25)	0.0458 (1.00)	0.551 (1.00)	0.897 (1.00)
Amp Peak 13(8q24 21)	439 (79%)	120	1.05e-07 (8.43e-05)	1.24e-05 (0.00981)	0.229 (1.00)	0.00313 (1.00)	2.87e-19 (2.41e-16)	0.0047 (1.00)	0.918 (1.00)	0.631 (1.00)	1.62e-06 (0.00129)	0.00146 (1.00)	0.204 (1.00)	0.0269 (1.00)
Amp Peak 23(19p13 12)	301 (54%)	258	0.000624 (0.468)	0.000463 (0.349)	0.0461 (1.00)	0.052 (1.00)	1.97e-14 (1.64e-11)	3.88e-06 (0.00308)	4.82e-05 (0.0376)	0.000193 (0.148)	0.184 (1.00)	0.162 (1.00)	0.587 (1.00)	0.761 (1.00)
Amp Peak 26(20p13)	300 (54%)	259	0.186 (1.00)	0.000126 (0.0967)	0.201 (1.00)	0.0141 (1.00)	9.8e-12 (8.13e-09)	2.23e-09 (1.83e-06)	0.569 (1.00)	0.448 (1.00)	0.0317 (1.00)	0.0785 (1.00)	0.248 (1.00)	0.845 (1.00)
Amp Peak 28(20q13 33)	387 (69%)	172	0.00761 (1.00)	3.75e-05 (0.0294)	0.599 (1.00)	0.00326 (1.00)	1.21e-15 (1.01e-12)	2.8e-08 (2.26e-05)	0.62 (1.00)	0.347 (1.00)	0.0247 (1.00)	0.0702 (1.00)	0.432 (1.00)	0.416 (1.00)
Del Peak 6(3p26 2)	206 (37%)	353	0.083 (1.00)	6.13e-05 (0.0477)	0.00412 (1.00)	0.0222 (1.00)	9.31e-05 (0.0719)	5.51e-05 (0.0429)	0.728 (1.00)	0.238 (1.00)	0.00138 (1.00)	0.0109 (1.00)	0.579 (1.00)	0.796 (1.00)
Del Peak 25(13q14 2)	348 (62%)	211	0.0259 (1.00)	0.516 (1.00)	0.723 (1.00)	0.683 (1.00)	1.11e-06 (0.000885)	9.8e-06 (0.00777)	0.000301 (0.229)	0.00813 (1.00)	0.0309 (1.00)	0.247 (1.00)	0.221 (1.00)	1 (1.00)
Amp Peak 2(1q21 3)	350 (63%)	209	0.211 (1.00)	0.0621 (1.00)	0.687 (1.00)	0.15 (1.00)	7.18e-12 (5.96e-09)	4.81e-05 (0.0376)	0.0483 (1.00)	0.0541 (1.00)	0.658 (1.00)	0.126 (1.00)	0.907 (1.00)	0.86 (1.00)
Amp Peak 3(1q42 2)	304 (54%)	255	0.023 (1.00)	0.0325 (1.00)	0.941 (1.00)	0.0063 (1.00)	3.15e-10 (2.59e-07)	9.54e-05 (0.0735)	0.102 (1.00)	0.11 (1.00)	0.426 (1.00)	0.62 (1.00)	0.177 (1.00)	0.439 (1.00)
Amp Peak 14(10p15 3)	239 (43%)	320	0.758 (1.00)	0.092 (1.00)	0.0698 (1.00)	0.255 (1.00)	4.44e-11 (3.67e-08)	0.000103 (0.0794)	0.368 (1.00)	0.316 (1.00)	0.285 (1.00)	0.378 (1.00)	0.671 (1.00)	0.475 (1.00)
Amp Peak 17(12p13 33)	311 (56%)	248	0.0361 (1.00)	0.00326 (1.00)	0.29 (1.00)	0.0108 (1.00)	1.1e-09 (8.99e-07)	1.36e-05 (0.0107)	0.148 (1.00)	0.288 (1.00)	0.00977 (1.00)	0.054 (1.00)	0.523 (1.00)	0.612 (1.00)
Amp Peak 18(12p12 1)	294 (53%)	265	0.273 (1.00)	0.013 (1.00)	0.843 (1.00)	0.0968 (1.00)	2.05e-12 (1.71e-09)	1.01e-06 (0.000812)	0.766 (1.00)	0.0386 (1.00)	0.0267 (1.00)	0.0935 (1.00)	0.177 (1.00)	0.133 (1.00)
Amp Peak 24(19q12)	309 (55%)	250	0.0736 (1.00)	0.0235 (1.00)	0.0402 (1.00)	0.147 (1.00)	2.89e-26 (2.43e-23)	3.63e-10 (2.98e-07)	0.0574 (1.00)	0.771 (1.00)	0.409 (1.00)	0.391 (1.00)	0.361 (1.00)	0.784 (1.00)
Amp Peak 25(19q13 2)	235 (42%)	324	0.957 (1.00)	0.0425 (1.00)	0.654 (1.00)	0.307 (1.00)	6.25e-10 (5.12e-07)	0.000201 (0.153)	0.609 (1.00)	0.376 (1.00)	0.473 (1.00)	0.774 (1.00)	0.977 (1.00)	0.611 (1.00)
Amp Peak 30(Xp11 23)	162 (29%)	397	0.759 (1.00)	0.257 (1.00)	0.298 (1.00)	0.308 (1.00)	3.27e-06 (0.0026)	1.46e-05 (0.0115)	0.808 (1.00)	0.106 (1.00)	0.34 (1.00)	0.402 (1.00)	0.205 (1.00)	0.0203 (1.00)
Del Peak 11(6q27)	362 (65%)	197	0.509 (1.00)	0.0229 (1.00)	0.216 (1.00)	0.0651 (1.00)	8e-09 (6.52e-06)	1.62e-05 (0.0128)	0.849 (1.00)	0.748 (1.00)	0.000522 (0.393)	0.0556 (1.00)	0.598 (1.00)	0.075 (1.00)
Del Peak 16(9q21 11)	268 (48%)	291	0.0107 (1.00)	0.00136 (1.00)	0.139 (1.00)	0.00112 (0.836)	4.16e-15 (3.48e-12)	3.98e-07 (0.00032)	0.0737 (1.00)	0.79 (1.00)	0.00135 (1.00)	0.568 (1.00)	0.074 (1.00)	0.507 (1.00)
Del Peak 23(12q23 1)	193 (35%)	366	0.0032 (1.00)	0.000204 (0.156)	0.0409 (1.00)	0.0174 (1.00)	4.4e-08 (3.55e-05)	0.0261 (1.00)	0.603 (1.00)	0.518 (1.00)	0.0912 (1.00)	0.0166 (1.00)	0.132 (1.00)	0.0221 (1.00)
Del Peak 24(12q24 33)	213 (38%)	346	0.00195 (1.00)	2.63e-06 (0.00209)	0.216 (1.00)	0.0891 (1.00)	1.14e-11 (9.42e-09)	0.0505 (1.00)	0.299 (1.00)	0.214 (1.00)	0.208 (1.00)	0.0189 (1.00)	0.0175 (1.00)	0.0162 (1.00)
Del Peak 27(15q15 1)	351 (63%)	208	0.0423 (1.00)	0.000469 (0.353)	0.0111 (1.00)	0.00626 (1.00)	1.75e-10 (1.44e-07)	7.64e-05 (0.0593)	0.0265 (1.00)	0.162 (1.00)	0.0219 (1.00)	0.0736 (1.00)	0.246 (1.00)	0.407 (1.00)
Del Peak 36(19q13 43)	277 (50%)	282	0.0199 (1.00)	0.0612 (1.00)	0.0603 (1.00)	0.164 (1.00)	0.000298 (0.227)	0.000107 (0.0821)	0.17 (1.00)	0.328 (1.00)	0.517 (1.00)	0.182 (1.00)	0.472 (1.00)	0.18 (1.00)
Amp Peak 1(1p34 3)	277 (50%)	282	0.179 (1.00)	0.84 (1.00)	0.148 (1.00)	0.134 (1.00)	1.18e-06 (0.000944)	0.119 (1.00)	0.149 (1.00)	0.846 (1.00)	0.455 (1.00)	0.386 (1.00)	0.0286 (1.00)	0.423 (1.00)
Amp Peak 4(2p23 2)	235 (42%)	324	0.341 (1.00)	0.0263 (1.00)	0.582 (1.00)	0.0135 (1.00)	2.67e-08 (2.16e-05)	0.00279 (1.00)	0.315 (1.00)	0.463 (1.00)	0.0855 (1.00)	0.333 (1.00)	0.939 (1.00)	0.611 (1.00)
Amp Peak 5(2q31 2)	245 (44%)	314	0.0779 (1.00)	0.00222 (1.00)	0.0744 (1.00)	0.052 (1.00)	9.18e-10 (7.52e-07)	0.000382 (0.289)	0.0604 (1.00)	0.776 (1.00)	0.184 (1.00)	0.136 (1.00)	0.522 (1.00)	0.346 (1.00)
Amp Peak 6(3q26 2)	465 (83%)	94	0.00679 (1.00)	0.00101 (0.756)	0.989 (1.00)	0.454 (1.00)	1.02e-08 (8.31e-06)	0.108 (1.00)	0.969 (1.00)	0.115 (1.00)	0.0435 (1.00)	0.133 (1.00)	0.163 (1.00)	0.302 (1.00)
Amp Peak 8(4q13 3)	105 (19%)	454	0.914 (1.00)	0.133 (1.00)	0.354 (1.00)	0.175 (1.00)	1.59e-05 (0.0125)	0.125 (1.00)	0.567 (1.00)	0.115 (1.00)	0.459 (1.00)	0.717 (1.00)	0.804 (1.00)	0.948 (1.00)
Amp Peak 9(5p15 33)	295 (53%)	264	0.884 (1.00)	0.485 (1.00)	0.625 (1.00)	0.54 (1.00)	4.22e-07 (0.000338)	0.341 (1.00)	0.581 (1.00)	0.376 (1.00)	0.162 (1.00)	0.608 (1.00)	0.00672 (1.00)	0.425 (1.00)
Amp Peak 10(6p22 3)	287 (51%)	272	0.132 (1.00)	0.0154 (1.00)	0.249 (1.00)	0.156 (1.00)	1.67e-07 (0.000134)	0.0327 (1.00)	0.0249 (1.00)	0.0142 (1.00)	0.793 (1.00)	0.662 (1.00)	0.176 (1.00)	0.74 (1.00)
Amp Peak 11(7q36 3)	300 (54%)	259	0.0439 (1.00)	0.515 (1.00)	0.262 (1.00)	0.588 (1.00)	1.65e-06 (0.00132)	0.211 (1.00)	0.164 (1.00)	0.528 (1.00)	0.987 (1.00)	1 (1.00)	0.103 (1.00)	0.325 (1.00)
Amp Peak 12(8p11 21)	196 (35%)	363	0.105 (1.00)	0.00242 (1.00)	0.102 (1.00)	0.292 (1.00)	2.11e-05 (0.0166)	0.0122 (1.00)	0.131 (1.00)	0.598 (1.00)	0.271 (1.00)	0.105 (1.00)	0.844 (1.00)	0.385 (1.00)
Amp Peak 16(11q14 1)	247 (44%)	312	0.00682 (1.00)	0.0904 (1.00)	0.847 (1.00)	0.294 (1.00)	9.58e-09 (7.8e-06)	0.021 (1.00)	0.319 (1.00)	0.125 (1.00)	0.013 (1.00)	0.0644 (1.00)	0.125 (1.00)	0.968 (1.00)
Amp Peak 20(15q26 3)	156 (28%)	403	0.0786 (1.00)	0.955 (1.00)	0.503 (1.00)	0.689 (1.00)	5.92e-10 (4.86e-07)	0.646 (1.00)	0.851 (1.00)	0.0803 (1.00)	0.233 (1.00)	0.673 (1.00)	0.0967 (1.00)	0.173 (1.00)
Amp Peak 22(18q11 2)	137 (25%)	422	0.952 (1.00)	0.198 (1.00)	0.976 (1.00)	0.527 (1.00)	2.9e-06 (0.0023)	0.000456 (0.345)	0.109 (1.00)	0.341 (1.00)	0.103 (1.00)	0.0226 (1.00)	0.282 (1.00)	0.397 (1.00)
Amp Peak 29(22q12 2)	88 (16%)	471	0.602 (1.00)	0.739 (1.00)	0.0836 (1.00)	0.359 (1.00)	8.03e-05 (0.0622)	0.00187 (1.00)	0.983 (1.00)	0.108 (1.00)	0.275 (1.00)	0.289 (1.00)	0.0839 (1.00)	0.0166 (1.00)
Amp Peak 31(Xq28)	222 (40%)	337	0.241 (1.00)	0.392 (1.00)	0.832 (1.00)	0.117 (1.00)	2.43e-05 (0.019)	0.15 (1.00)	0.521 (1.00)	0.425 (1.00)	0.476 (1.00)	0.621 (1.00)	0.799 (1.00)	0.569 (1.00)
Del Peak 1(1p36 11)	264 (47%)	295	0.952 (1.00)	0.804 (1.00)	0.0385 (1.00)	0.326 (1.00)	5.76e-05 (0.0448)	0.182 (1.00)	0.189 (1.00)	0.486 (1.00)	0.936 (1.00)	0.81 (1.00)	0.324 (1.00)	0.0681 (1.00)
Del Peak 2(1q32 3)	92 (16%)	467	0.0848 (1.00)	0.518 (1.00)	0.477 (1.00)	0.11 (1.00)	6.56e-09 (5.35e-06)	0.284 (1.00)	0.982 (1.00)	0.104 (1.00)	0.244 (1.00)	0.372 (1.00)	0.848 (1.00)	0.877 (1.00)
Del Peak 5(2q37 3)	172 (31%)	387	0.0103 (1.00)	0.00158 (1.00)	0.716 (1.00)	0.00146 (1.00)	3.05e-05 (0.0239)	0.0428 (1.00)	0.562 (1.00)	0.667 (1.00)	0.0276 (1.00)	0.0296 (1.00)	0.00457 (1.00)	0.0106 (1.00)
Del Peak 9(5q11 2)	335 (60%)	224	0.694 (1.00)	0.144 (1.00)	0.425 (1.00)	0.206 (1.00)	2.74e-08 (2.21e-05)	0.000791 (0.592)	0.897 (1.00)	0.881 (1.00)	0.209 (1.00)	0.424 (1.00)	0.0328 (1.00)	0.0145 (1.00)
Del Peak 10(5q13 2)	398 (71%)	161	0.702 (1.00)	0.738 (1.00)	0.888 (1.00)	0.809 (1.00)	7.51e-13 (6.25e-10)	0.0601 (1.00)	0.956 (1.00)	0.821 (1.00)	0.407 (1.00)	0.135 (1.00)	0.134 (1.00)	0.032 (1.00)
Del Peak 12(7p22 1)	243 (43%)	316	0.569 (1.00)	0.0224 (1.00)	0.678 (1.00)	0.66 (1.00)	2.92e-14 (2.43e-11)	0.854 (1.00)	0.756 (1.00)	0.744 (1.00)	0.37 (1.00)	0.115 (1.00)	0.788 (1.00)	0.904 (1.00)
Del Peak 13(8p23 3)	375 (67%)	184	0.0571 (1.00)	0.00845 (1.00)	0.629 (1.00)	0.0185 (1.00)	1.1e-10 (9.09e-08)	0.0567 (1.00)	0.831 (1.00)	0.665 (1.00)	0.925 (1.00)	0.417 (1.00)	0.309 (1.00)	0.174 (1.00)
Del Peak 14(8p21 2)	392 (70%)	167	0.0388 (1.00)	0.0146 (1.00)	0.233 (1.00)	0.00956 (1.00)	1.05e-08 (8.49e-06)	0.37 (1.00)	0.432 (1.00)	0.978 (1.00)	0.321 (1.00)	0.615 (1.00)	0.84 (1.00)	1 (1.00)
Del Peak 15(9p24 3)	247 (44%)	312	0.000117 (0.0896)	0.0803 (1.00)	0.772 (1.00)	0.00914 (1.00)	0.0119 (1.00)	0.000361 (0.273)	0.732 (1.00)	0.338 (1.00)	0.0629 (1.00)	0.392 (1.00)	0.0638 (1.00)	0.0232 (1.00)
Del Peak 17(9q34 13)	330 (59%)	229	0.0193 (1.00)	0.0144 (1.00)	1 (1.00)	0.0188 (1.00)	1.15e-08 (9.36e-06)	0.00984 (1.00)	0.448 (1.00)	0.277 (1.00)	0.229 (1.00)	0.284 (1.00)	0.0578 (1.00)	0.155 (1.00)
Del Peak 20(10q26 3)	186 (33%)	373	0.00841 (1.00)	0.0553 (1.00)	0.25 (1.00)	0.405 (1.00)	8.82e-05 (0.0682)	0.104 (1.00)	0.317 (1.00)	0.0113 (1.00)	0.0636 (1.00)	0.055 (1.00)	0.00607 (1.00)	0.094 (1.00)
Del Peak 21(11p15 5)	334 (60%)	225	0.0499 (1.00)	0.306 (1.00)	0.729 (1.00)	0.0477 (1.00)	2.91e-11 (2.4e-08)	0.0167 (1.00)	0.916 (1.00)	0.792 (1.00)	0.9 (1.00)	0.334 (1.00)	0.0763 (1.00)	0.00977 (1.00)
Del Peak 29(16q22 1)	441 (79%)	118	0.363 (1.00)	0.319 (1.00)	0.0303 (1.00)	0.925 (1.00)	9.04e-05 (0.0698)	0.454 (1.00)	0.482 (1.00)	0.306 (1.00)	0.528 (1.00)	0.0792 (1.00)	0.505 (1.00)	0.188 (1.00)
Del Peak 30(16q23 1)	434 (78%)	125	0.11 (1.00)	0.105 (1.00)	0.143 (1.00)	0.32 (1.00)	3.93e-05 (0.0307)	0.49 (1.00)	0.434 (1.00)	0.397 (1.00)	0.563 (1.00)	0.231 (1.00)	0.101 (1.00)	0.0265 (1.00)
Del Peak 32(17q11 2)	456 (82%)	103	0.95 (1.00)	0.0627 (1.00)	0.735 (1.00)	0.477 (1.00)	0.000195 (0.149)	0.000733 (0.549)	0.671 (1.00)	0.103 (1.00)	0.705 (1.00)	0.315 (1.00)	0.077 (1.00)	0.294 (1.00)
Amp Peak 7(4p16 3)	152 (27%)	407	0.955 (1.00)	0.0338 (1.00)	0.0518 (1.00)	0.694 (1.00)	0.00123 (0.913)	0.00705 (1.00)	0.335 (1.00)	0.888 (1.00)	0.348 (1.00)	0.35 (1.00)	0.444 (1.00)	0.179 (1.00)
Amp Peak 15(10q22 3)	175 (31%)	384	0.443 (1.00)	0.327 (1.00)	0.607 (1.00)	0.0601 (1.00)	0.227 (1.00)	0.973 (1.00)	0.704 (1.00)	0.955 (1.00)	0.219 (1.00)	0.403 (1.00)	0.0934 (1.00)	0.576 (1.00)
Amp Peak 19(14q11 2)	142 (25%)	417	0.00478 (1.00)	0.0765 (1.00)	0.323 (1.00)	0.00145 (1.00)	0.0909 (1.00)	0.14 (1.00)	0.229 (1.00)	0.169 (1.00)	0.422 (1.00)	0.159 (1.00)	0.305 (1.00)	0.31 (1.00)
Amp Peak 21(17q25 3)	205 (37%)	354	0.453 (1.00)	0.261 (1.00)	0.913 (1.00)	0.123 (1.00)	0.0162 (1.00)	0.944 (1.00)	0.214 (1.00)	0.211 (1.00)	0.0216 (1.00)	0.0427 (1.00)	0.508 (1.00)	0.148 (1.00)
Del Peak 3(2p25 3)	117 (21%)	442	0.973 (1.00)	0.982 (1.00)	0.454 (1.00)	0.489 (1.00)	0.306 (1.00)	0.587 (1.00)	0.0516 (1.00)	0.109 (1.00)	0.269 (1.00)	0.799 (1.00)	0.914 (1.00)	1 (1.00)
Del Peak 4(2q22 1)	132 (24%)	427	0.0722 (1.00)	0.13 (1.00)	0.867 (1.00)	0.15 (1.00)	0.0526 (1.00)	0.251 (1.00)	0.368 (1.00)	0.697 (1.00)	0.723 (1.00)	0.235 (1.00)	0.618 (1.00)	0.106 (1.00)
Del Peak 7(4q22 1)	373 (67%)	186	0.0283 (1.00)	0.328 (1.00)	0.927 (1.00)	0.00966 (1.00)	0.0279 (1.00)	0.521 (1.00)	0.0172 (1.00)	0.0581 (1.00)	0.131 (1.00)	0.42 (1.00)	0.0797 (1.00)	0.0697 (1.00)
Del Peak 8(4q34 3)	404 (72%)	155	0.0165 (1.00)	0.135 (1.00)	0.0222 (1.00)	0.0134 (1.00)	0.183 (1.00)	0.475 (1.00)	0.592 (1.00)	0.296 (1.00)	0.0313 (1.00)	0.0911 (1.00)	0.37 (1.00)	0.241 (1.00)
Del Peak 18(10p15 3)	118 (21%)	441	0.138 (1.00)	0.0407 (1.00)	0.0968 (1.00)	0.0865 (1.00)	0.0994 (1.00)	0.412 (1.00)	0.372 (1.00)	0.0779 (1.00)	0.0834 (1.00)	0.0149 (1.00)	0.267 (1.00)	0.118 (1.00)
Del Peak 19(10q23 31)	215 (38%)	344	0.238 (1.00)	0.981 (1.00)	0.000556 (0.418)	0.0125 (1.00)	0.0019 (1.00)	0.00115 (0.86)	0.197 (1.00)	0.0155 (1.00)	0.865 (1.00)	0.103 (1.00)	0.0405 (1.00)	0.351 (1.00)
Del Peak 22(11q25)	193 (35%)	366	0.81 (1.00)	0.211 (1.00)	0.175 (1.00)	0.38 (1.00)	0.141 (1.00)	0.483 (1.00)	0.468 (1.00)	0.56 (1.00)	0.635 (1.00)	0.367 (1.00)	0.732 (1.00)	0.199 (1.00)
Del Peak 26(14q23 2)	292 (52%)	267	0.109 (1.00)	0.6 (1.00)	0.823 (1.00)	0.802 (1.00)	0.00227 (1.00)	0.381 (1.00)	0.202 (1.00)	0.499 (1.00)	0.891 (1.00)	0.133 (1.00)	0.483 (1.00)	0.423 (1.00)
Del Peak 28(16p13 3)	297 (53%)	262	0.542 (1.00)	0.0773 (1.00)	0.167 (1.00)	0.462 (1.00)	0.0856 (1.00)	0.685 (1.00)	0.645 (1.00)	0.0862 (1.00)	0.772 (1.00)	0.634 (1.00)	0.148 (1.00)	0.636 (1.00)
Del Peak 31(17p12)	472 (84%)	87	0.322 (1.00)	0.719 (1.00)	0.619 (1.00)	0.591 (1.00)	0.697 (1.00)	0.332 (1.00)	0.967 (1.00)	0.355 (1.00)	0.205 (1.00)	0.556 (1.00)	0.491 (1.00)	0.237 (1.00)
Del Peak 33(18q23)	364 (65%)	195	0.666 (1.00)	0.82 (1.00)	0.566 (1.00)	0.379 (1.00)	0.0022 (1.00)	0.673 (1.00)	0.465 (1.00)	0.786 (1.00)	0.139 (1.00)	0.104 (1.00)	0.637 (1.00)	0.336 (1.00)
Del Peak 34(19p13 3)	492 (88%)	67	0.257 (1.00)	0.00399 (1.00)	0.943 (1.00)	0.462 (1.00)	0.0096 (1.00)	0.0228 (1.00)	0.619 (1.00)	0.179 (1.00)	0.314 (1.00)	0.00187 (1.00)	0.403 (1.00)	0.28 (1.00)
Del Peak 35(19q13 33)	290 (52%)	269	0.000675 (0.506)	0.0101 (1.00)	0.0634 (1.00)	0.138 (1.00)	0.0362 (1.00)	0.00165 (1.00)	0.156 (1.00)	0.0548 (1.00)	0.0045 (1.00)	0.0316 (1.00)	0.408 (1.00)	0.454 (1.00)
Del Peak 37(21q22 3)	218 (39%)	341	0.235 (1.00)	0.359 (1.00)	0.705 (1.00)	0.241 (1.00)	0.855 (1.00)	0.306 (1.00)	0.858 (1.00)	0.901 (1.00)	0.14 (1.00)	0.233 (1.00)	0.458 (1.00)	0.861 (1.00)
Del Peak 38(22q13 32)	483 (86%)	76	0.125 (1.00)	0.0621 (1.00)	0.0229 (1.00)	0.0717 (1.00)	0.0592 (1.00)	0.102 (1.00)	0.0288 (1.00)	0.356 (1.00)	0.0956 (1.00)	0.0272 (1.00)	0.0286 (1.00)	0.503 (1.00)
Del Peak 39(Xp21 1)	356 (64%)	203	0.296 (1.00)	0.98 (1.00)	0.12 (1.00)	0.643 (1.00)	0.051 (1.00)	0.0126 (1.00)	0.119 (1.00)	0.0349 (1.00)	0.577 (1.00)	0.803 (1.00)	0.943 (1.00)	0.222 (1.00)

'Amp Peak 1(1p34.3) mutation analysis' versus 'CN_CNMF'

P value = 1.18e-06 (Fisher's exact test), Q value = 0.00094

Table S1. Gene #1: 'Amp Peak 1(1p34.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
AMP PEAK 1(1P34.3) MUTATED	53	116	108
AMP PEAK 1(1P34.3) WILD-TYPE	110	93	79

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1p34.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Amp Peak 2(1q21.3) mutation analysis' versus 'CN_CNMF'

P value = 7.18e-12 (Fisher's exact test), Q value = 6e-09

Table S2. Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
AMP PEAK 2(1Q21.3) MUTATED	80	116	154
AMP PEAK 2(1Q21.3) WILD-TYPE	83	93	33

Figure S2. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Amp Peak 2(1q21.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.81e-05 (Fisher's exact test), Q value = 0.038

Table S3. Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	171	220
AMP PEAK 2(1Q21.3) MUTATED	124	87	139
AMP PEAK 2(1Q21.3) WILD-TYPE	43	84	81

Figure S3. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

'Amp Peak 3(1q42.2) mutation analysis' versus 'CN_CNMF'

P value = 3.15e-10 (Fisher's exact test), Q value = 2.6e-07

Table S4. Gene #3: 'Amp Peak 3(1q42.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
AMP PEAK 3(1Q42.2) MUTATED	84	84	136
AMP PEAK 3(1Q42.2) WILD-TYPE	79	125	51

Figure S4. Get High-res Image Gene #3: 'Amp Peak 3(1q42.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Amp Peak 3(1q42.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 9.54e-05 (Fisher's exact test), Q value = 0.074

Table S5. Gene #3: 'Amp Peak 3(1q42.2) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	171	220
AMP PEAK 3(1Q42.2) MUTATED	114	83	107
AMP PEAK 3(1Q42.2) WILD-TYPE	53	88	113

Figure S5. Get High-res Image Gene #3: 'Amp Peak 3(1q42.2) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

'Amp Peak 4(2p23.2) mutation analysis' versus 'CN_CNMF'

P value = 2.67e-08 (Fisher's exact test), Q value = 2.2e-05

Table S6. Gene #4: 'Amp Peak 4(2p23.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
AMP PEAK 4(2P23.2) MUTATED	44	83	108
AMP PEAK 4(2P23.2) WILD-TYPE	119	126	79

Figure S6. Get High-res Image Gene #4: 'Amp Peak 4(2p23.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Amp Peak 5(2q31.2) mutation analysis' versus 'CN_CNMF'

P value = 9.18e-10 (Fisher's exact test), Q value = 7.5e-07

Table S7. Gene #5: 'Amp Peak 5(2q31.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
AMP PEAK 5(2Q31.2) MUTATED	39	100	106
AMP PEAK 5(2Q31.2) WILD-TYPE	124	109	81

Figure S7. Get High-res Image Gene #5: 'Amp Peak 5(2q31.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Amp Peak 6(3q26.2) mutation analysis' versus 'CN_CNMF'

P value = 1.02e-08 (Fisher's exact test), Q value = 8.3e-06

Table S8. Gene #6: 'Amp Peak 6(3q26.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
AMP PEAK 6(3Q26.2) MUTATED	111	182	172
AMP PEAK 6(3Q26.2) WILD-TYPE	52	27	15

Figure S8. Get High-res Image Gene #6: 'Amp Peak 6(3q26.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Amp Peak 8(4q13.3) mutation analysis' versus 'CN_CNMF'

P value = 1.59e-05 (Fisher's exact test), Q value = 0.013

Table S9. Gene #8: 'Amp Peak 8(4q13.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
AMP PEAK 8(4Q13.3) MUTATED	13	55	37
AMP PEAK 8(4Q13.3) WILD-TYPE	150	154	150

Figure S9. Get High-res Image Gene #8: 'Amp Peak 8(4q13.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Amp Peak 9(5p15.33) mutation analysis' versus 'CN_CNMF'

P value = 4.22e-07 (Fisher's exact test), Q value = 0.00034

Table S10. Gene #9: 'Amp Peak 9(5p15.33) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
AMP PEAK 9(5P15.33) MUTATED	57	125	113
AMP PEAK 9(5P15.33) WILD-TYPE	106	84	74

Figure S10. Get High-res Image Gene #9: 'Amp Peak 9(5p15.33) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Amp Peak 10(6p22.3) mutation analysis' versus 'CN_CNMF'

P value = 1.67e-07 (Fisher's exact test), Q value = 0.00013

Table S11. Gene #10: 'Amp Peak 10(6p22.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
AMP PEAK 10(6P22.3) MUTATED	54	126	107
AMP PEAK 10(6P22.3) WILD-TYPE	109	83	80

Figure S11. Get High-res Image Gene #10: 'Amp Peak 10(6p22.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Amp Peak 11(7q36.3) mutation analysis' versus 'CN_CNMF'

P value = 1.65e-06 (Fisher's exact test), Q value = 0.0013

Table S12. Gene #11: 'Amp Peak 11(7q36.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
AMP PEAK 11(7Q36.3) MUTATED	60	124	116
AMP PEAK 11(7Q36.3) WILD-TYPE	103	85	71

Figure S12. Get High-res Image Gene #11: 'Amp Peak 11(7q36.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Amp Peak 12(8p11.21) mutation analysis' versus 'CN_CNMF'

P value = 2.11e-05 (Fisher's exact test), Q value = 0.017

Table S13. Gene #12: 'Amp Peak 12(8p11.21) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
AMP PEAK 12(8P11.21) MUTATED	40	67	89
AMP PEAK 12(8P11.21) WILD-TYPE	123	142	98

Figure S13. Get High-res Image Gene #12: 'Amp Peak 12(8p11.21) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

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

P value = 1.05e-07 (Fisher's exact test), Q value = 8.4e-05

Table S14. Gene #13: 'Amp Peak 13(8q24.21) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	213	129
AMP PEAK 13(8Q24.21) MUTATED	142	183	113
AMP PEAK 13(8Q24.21) WILD-TYPE	73	30	16

Figure S14. Get High-res Image Gene #13: 'Amp Peak 13(8q24.21) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

P value = 1.24e-05 (Fisher's exact test), Q value = 0.0098

Table S15. Gene #13: 'Amp Peak 13(8q24.21) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	199	125
AMP PEAK 13(8Q24.21) MUTATED	205	140	93
AMP PEAK 13(8Q24.21) WILD-TYPE	28	59	32

Figure S15. Get High-res Image Gene #13: 'Amp Peak 13(8q24.21) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

P value = 2.87e-19 (Fisher's exact test), Q value = 2.4e-16

Table S16. Gene #13: 'Amp Peak 13(8q24.21) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
AMP PEAK 13(8Q24.21) MUTATED	106	203	130
AMP PEAK 13(8Q24.21) WILD-TYPE	57	6	57

Figure S16. Get High-res Image Gene #13: 'Amp Peak 13(8q24.21) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Amp Peak 13(8q24.21) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.62e-06 (Fisher's exact test), Q value = 0.0013

Table S17. Gene #13: 'Amp Peak 13(8q24.21) mutation analysis' versus Clinical Feature #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	70	91
AMP PEAK 13(8Q24.21) MUTATED	87	64	57
AMP PEAK 13(8Q24.21) WILD-TYPE	11	6	34

Figure S17. Get High-res Image Gene #13: 'Amp Peak 13(8q24.21) mutation analysis' versus Clinical Feature #9: 'MRNASEQ_CNMF'

'Amp Peak 14(10p15.3) mutation analysis' versus 'CN_CNMF'

P value = 4.44e-11 (Fisher's exact test), Q value = 3.7e-08

Table S18. Gene #14: 'Amp Peak 14(10p15.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
AMP PEAK 14(10P15.3) MUTATED	46	76	117
AMP PEAK 14(10P15.3) WILD-TYPE	117	133	70

Figure S18. Get High-res Image Gene #14: 'Amp Peak 14(10p15.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Amp Peak 14(10p15.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000103 (Fisher's exact test), Q value = 0.079

Table S19. Gene #14: 'Amp Peak 14(10p15.3) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	171	220
AMP PEAK 14(10P15.3) MUTATED	94	60	84
AMP PEAK 14(10P15.3) WILD-TYPE	73	111	136

Figure S19. Get High-res Image Gene #14: 'Amp Peak 14(10p15.3) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

'Amp Peak 16(11q14.1) mutation analysis' versus 'CN_CNMF'

P value = 9.58e-09 (Fisher's exact test), Q value = 7.8e-06

Table S20. Gene #16: 'Amp Peak 16(11q14.1) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
AMP PEAK 16(11Q14.1) MUTATED	48	125	74
AMP PEAK 16(11Q14.1) WILD-TYPE	115	84	113

Figure S20. Get High-res Image Gene #16: 'Amp Peak 16(11q14.1) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Amp Peak 17(12p13.33) mutation analysis' versus 'CN_CNMF'

P value = 1.1e-09 (Fisher's exact test), Q value = 9e-07

Table S21. Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
AMP PEAK 17(12P13.33) MUTATED	64	111	136
AMP PEAK 17(12P13.33) WILD-TYPE	99	98	51

Figure S21. Get High-res Image Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Amp Peak 17(12p13.33) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.36e-05 (Fisher's exact test), Q value = 0.011

Table S22. Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	171	220
AMP PEAK 17(12P13.33) MUTATED	117	92	102
AMP PEAK 17(12P13.33) WILD-TYPE	50	79	118

Figure S22. Get High-res Image Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

'Amp Peak 18(12p12.1) mutation analysis' versus 'CN_CNMF'

P value = 2.05e-12 (Fisher's exact test), Q value = 1.7e-09

Table S23. Gene #18: 'Amp Peak 18(12p12.1) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
AMP PEAK 18(12P12.1) MUTATED	59	98	137
AMP PEAK 18(12P12.1) WILD-TYPE	104	111	50

Figure S23. Get High-res Image Gene #18: 'Amp Peak 18(12p12.1) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Amp Peak 18(12p12.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.01e-06 (Fisher's exact test), Q value = 0.00081

Table S24. Gene #18: 'Amp Peak 18(12p12.1) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	171	220
AMP PEAK 18(12P12.1) MUTATED	116	80	98
AMP PEAK 18(12P12.1) WILD-TYPE	51	91	122

Figure S24. Get High-res Image Gene #18: 'Amp Peak 18(12p12.1) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

'Amp Peak 20(15q26.3) mutation analysis' versus 'CN_CNMF'

P value = 5.92e-10 (Fisher's exact test), Q value = 4.9e-07

Table S25. Gene #20: 'Amp Peak 20(15q26.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
AMP PEAK 20(15Q26.3) MUTATED	27	92	37
AMP PEAK 20(15Q26.3) WILD-TYPE	136	117	150

Figure S25. Get High-res Image Gene #20: 'Amp Peak 20(15q26.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Amp Peak 22(18q11.2) mutation analysis' versus 'CN_CNMF'

P value = 2.9e-06 (Fisher's exact test), Q value = 0.0023

Table S26. Gene #22: 'Amp Peak 22(18q11.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
AMP PEAK 22(18Q11.2) MUTATED	22	47	68
AMP PEAK 22(18Q11.2) WILD-TYPE	141	162	119

Figure S26. Get High-res Image Gene #22: 'Amp Peak 22(18q11.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Amp Peak 23(19p13.12) mutation analysis' versus 'CN_CNMF'

P value = 1.97e-14 (Fisher's exact test), Q value = 1.6e-11

Table S27. Gene #23: 'Amp Peak 23(19p13.12) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
AMP PEAK 23(19P13.12) MUTATED	68	89	144
AMP PEAK 23(19P13.12) WILD-TYPE	95	120	43

Figure S27. Get High-res Image Gene #23: 'Amp Peak 23(19p13.12) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Amp Peak 23(19p13.12) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.88e-06 (Fisher's exact test), Q value = 0.0031

Table S28. Gene #23: 'Amp Peak 23(19p13.12) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	171	220
AMP PEAK 23(19P13.12) MUTATED	114	71	115
AMP PEAK 23(19P13.12) WILD-TYPE	53	100	105

Figure S28. Get High-res Image Gene #23: 'Amp Peak 23(19p13.12) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

'Amp Peak 23(19p13.12) mutation analysis' versus 'RPPA_CNMF'

P value = 4.82e-05 (Fisher's exact test), Q value = 0.038

Table S29. Gene #23: 'Amp Peak 23(19p13.12) mutation analysis' versus Clinical Feature #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	124	204	70
AMP PEAK 23(19P13.12) MUTATED	57	131	26
AMP PEAK 23(19P13.12) WILD-TYPE	67	73	44

Figure S29. Get High-res Image Gene #23: 'Amp Peak 23(19p13.12) mutation analysis' versus Clinical Feature #7: 'RPPA_CNMF'

'Amp Peak 23(19p13.12) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 0.000193 (Fisher's exact test), Q value = 0.15

Table S30. Gene #23: 'Amp Peak 23(19p13.12) mutation analysis' versus Clinical Feature #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	65	141	94
AMP PEAK 23(19P13.12) MUTATED	56	36	57	65
AMP PEAK 23(19P13.12) WILD-TYPE	42	29	84	29

Figure S30. Get High-res Image Gene #23: 'Amp Peak 23(19p13.12) mutation analysis' versus Clinical Feature #8: 'RPPA_CHIERARCHICAL'

'Amp Peak 24(19q12) mutation analysis' versus 'CN_CNMF'

P value = 2.89e-26 (Fisher's exact test), Q value = 2.4e-23

Table S31. Gene #24: 'Amp Peak 24(19q12) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
AMP PEAK 24(19Q12) MUTATED	62	86	161
AMP PEAK 24(19Q12) WILD-TYPE	101	123	26

Figure S31. Get High-res Image Gene #24: 'Amp Peak 24(19q12) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Amp Peak 24(19q12) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.63e-10 (Fisher's exact test), Q value = 3e-07

Table S32. Gene #24: 'Amp Peak 24(19q12) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	171	220
AMP PEAK 24(19Q12) MUTATED	124	67	118
AMP PEAK 24(19Q12) WILD-TYPE	43	104	102

Figure S32. Get High-res Image Gene #24: 'Amp Peak 24(19q12) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

'Amp Peak 25(19q13.2) mutation analysis' versus 'CN_CNMF'

P value = 6.25e-10 (Fisher's exact test), Q value = 5.1e-07

Table S33. Gene #25: 'Amp Peak 25(19q13.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
AMP PEAK 25(19Q13.2) MUTATED	48	73	114
AMP PEAK 25(19Q13.2) WILD-TYPE	115	136	73

Figure S33. Get High-res Image Gene #25: 'Amp Peak 25(19q13.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Amp Peak 25(19q13.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000201 (Fisher's exact test), Q value = 0.15

Table S34. Gene #25: 'Amp Peak 25(19q13.2) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	171	220
AMP PEAK 25(19Q13.2) MUTATED	91	56	88
AMP PEAK 25(19Q13.2) WILD-TYPE	76	115	132

Figure S34. Get High-res Image Gene #25: 'Amp Peak 25(19q13.2) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

'Amp Peak 26(20p13) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000126 (Fisher's exact test), Q value = 0.097

Table S35. Gene #26: 'Amp Peak 26(20p13) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	199	125
AMP PEAK 26(20P13) MUTATED	120	128	51
AMP PEAK 26(20P13) WILD-TYPE	113	71	74

Figure S35. Get High-res Image Gene #26: 'Amp Peak 26(20p13) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 26(20p13) mutation analysis' versus 'CN_CNMF'

P value = 9.8e-12 (Fisher's exact test), Q value = 8.1e-09

Table S36. Gene #26: 'Amp Peak 26(20p13) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
AMP PEAK 26(20P13) MUTATED	66	95	139
AMP PEAK 26(20P13) WILD-TYPE	97	114	48

Figure S36. Get High-res Image Gene #26: 'Amp Peak 26(20p13) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Amp Peak 26(20p13) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.23e-09 (Fisher's exact test), Q value = 1.8e-06

Table S37. Gene #26: 'Amp Peak 26(20p13) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	171	220
AMP PEAK 26(20P13) MUTATED	123	78	98
AMP PEAK 26(20P13) WILD-TYPE	44	93	122

Figure S37. Get High-res Image Gene #26: 'Amp Peak 26(20p13) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

'Amp Peak 27(20q11.21) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 3.68e-08 (Fisher's exact test), Q value = 3e-05

Table S38. Gene #27: 'Amp Peak 27(20q11.21) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	199	125
AMP PEAK 27(20Q11.21) MUTATED	132	143	49
AMP PEAK 27(20Q11.21) WILD-TYPE	101	56	76

Figure S38. Get High-res Image Gene #27: 'Amp Peak 27(20q11.21) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 27(20q11.21) mutation analysis' versus 'MIR_CHIERARCHICAL'

P value = 0.000105 (Chi-square test), Q value = 0.081

Table S39. Gene #27: 'Amp Peak 27(20q11.21) mutation analysis' versus Clinical Feature #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	65	115	125	99	57	94
AMP PEAK 27(20Q11.21) MUTATED	37	54	71	50	39	73
AMP PEAK 27(20Q11.21) WILD-TYPE	28	61	54	49	18	21

Figure S39. Get High-res Image Gene #27: 'Amp Peak 27(20q11.21) mutation analysis' versus Clinical Feature #4: 'MIR_CHIERARCHICAL'

'Amp Peak 27(20q11.21) mutation analysis' versus 'CN_CNMF'

P value = 1.01e-22 (Fisher's exact test), Q value = 8.5e-20

Table S40. Gene #27: 'Amp Peak 27(20q11.21) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
AMP PEAK 27(20Q11.21) MUTATED	72	92	162
AMP PEAK 27(20Q11.21) WILD-TYPE	91	117	25

Figure S40. Get High-res Image Gene #27: 'Amp Peak 27(20q11.21) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Amp Peak 27(20q11.21) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.1e-13 (Fisher's exact test), Q value = 6.7e-10

Table S41. Gene #27: 'Amp Peak 27(20q11.21) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	171	220
AMP PEAK 27(20Q11.21) MUTATED	136	86	104
AMP PEAK 27(20Q11.21) WILD-TYPE	31	85	116

Figure S41. Get High-res Image Gene #27: 'Amp Peak 27(20q11.21) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

'Amp Peak 27(20q11.21) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000329 (Fisher's exact test), Q value = 0.25

Table S42. Gene #27: 'Amp Peak 27(20q11.21) mutation analysis' versus Clinical Feature #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	70	91
AMP PEAK 27(20Q11.21) MUTATED	60	29	66
AMP PEAK 27(20Q11.21) WILD-TYPE	38	41	25

Figure S42. Get High-res Image Gene #27: 'Amp Peak 27(20q11.21) mutation analysis' versus Clinical Feature #9: 'MRNASEQ_CNMF'

'Amp Peak 28(20q13.33) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 3.75e-05 (Fisher's exact test), Q value = 0.029

Table S43. Gene #28: 'Amp Peak 28(20q13.33) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	199	125
AMP PEAK 28(20Q13.33) MUTATED	157	158	70
AMP PEAK 28(20Q13.33) WILD-TYPE	76	41	55

Figure S43. Get High-res Image Gene #28: 'Amp Peak 28(20q13.33) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 28(20q13.33) mutation analysis' versus 'CN_CNMF'

P value = 1.21e-15 (Fisher's exact test), Q value = 1e-12

Table S44. Gene #28: 'Amp Peak 28(20q13.33) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
AMP PEAK 28(20Q13.33) MUTATED	82	138	167
AMP PEAK 28(20Q13.33) WILD-TYPE	81	71	20

Figure S44. Get High-res Image Gene #28: 'Amp Peak 28(20q13.33) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Amp Peak 28(20q13.33) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.8e-08 (Fisher's exact test), Q value = 2.3e-05

Table S45. Gene #28: 'Amp Peak 28(20q13.33) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	171	220
AMP PEAK 28(20Q13.33) MUTATED	144	106	137
AMP PEAK 28(20Q13.33) WILD-TYPE	23	65	83

Figure S45. Get High-res Image Gene #28: 'Amp Peak 28(20q13.33) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

'Amp Peak 29(22q12.2) mutation analysis' versus 'CN_CNMF'

P value = 8.03e-05 (Fisher's exact test), Q value = 0.062

Table S46. Gene #29: 'Amp Peak 29(22q12.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
AMP PEAK 29(22Q12.2) MUTATED	10	44	34
AMP PEAK 29(22Q12.2) WILD-TYPE	153	165	153

Figure S46. Get High-res Image Gene #29: 'Amp Peak 29(22q12.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Amp Peak 30(Xp11.23) mutation analysis' versus 'CN_CNMF'

P value = 3.27e-06 (Fisher's exact test), Q value = 0.0026

Table S47. Gene #30: 'Amp Peak 30(Xp11.23) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
AMP PEAK 30(XP11.23) MUTATED	29	55	78
AMP PEAK 30(XP11.23) WILD-TYPE	134	154	109

Figure S47. Get High-res Image Gene #30: 'Amp Peak 30(Xp11.23) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Amp Peak 30(Xp11.23) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.46e-05 (Fisher's exact test), Q value = 0.011

Table S48. Gene #30: 'Amp Peak 30(Xp11.23) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	171	220
AMP PEAK 30(XP11.23) MUTATED	72	37	53
AMP PEAK 30(XP11.23) WILD-TYPE	95	134	167

Figure S48. Get High-res Image Gene #30: 'Amp Peak 30(Xp11.23) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

'Amp Peak 31(Xq28) mutation analysis' versus 'CN_CNMF'

P value = 2.43e-05 (Fisher's exact test), Q value = 0.019

Table S49. Gene #31: 'Amp Peak 31(Xq28) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
AMP PEAK 31(XQ28) MUTATED	42	102	78
AMP PEAK 31(XQ28) WILD-TYPE	121	107	109

Figure S49. Get High-res Image Gene #31: 'Amp Peak 31(Xq28) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Del Peak 1(1p36.11) mutation analysis' versus 'CN_CNMF'

P value = 5.76e-05 (Fisher's exact test), Q value = 0.045

Table S50. Gene #32: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
DEL PEAK 1(1P36.11) MUTATED	85	115	64
DEL PEAK 1(1P36.11) WILD-TYPE	78	94	123

Figure S50. Get High-res Image Gene #32: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Del Peak 2(1q32.3) mutation analysis' versus 'CN_CNMF'

P value = 6.56e-09 (Fisher's exact test), Q value = 5.4e-06

Table S51. Gene #33: 'Del Peak 2(1q32.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
DEL PEAK 2(1Q32.3) MUTATED	14	61	17
DEL PEAK 2(1Q32.3) WILD-TYPE	149	148	170

Figure S51. Get High-res Image Gene #33: 'Del Peak 2(1q32.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Del Peak 5(2q37.3) mutation analysis' versus 'CN_CNMF'

P value = 3.05e-05 (Fisher's exact test), Q value = 0.024

Table S52. Gene #36: 'Del Peak 5(2q37.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
DEL PEAK 5(2Q37.3) MUTATED	35	88	49
DEL PEAK 5(2Q37.3) WILD-TYPE	128	121	138

Figure S52. Get High-res Image Gene #36: 'Del Peak 5(2q37.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Del Peak 6(3p26.2) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 6.13e-05 (Fisher's exact test), Q value = 0.048

Table S53. Gene #37: 'Del Peak 6(3p26.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	199	125
DEL PEAK 6(3P26.2) MUTATED	88	90	27
DEL PEAK 6(3P26.2) WILD-TYPE	145	109	98

Figure S53. Get High-res Image Gene #37: 'Del Peak 6(3p26.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 6(3p26.2) mutation analysis' versus 'CN_CNMF'

P value = 9.31e-05 (Fisher's exact test), Q value = 0.072

Table S54. Gene #37: 'Del Peak 6(3p26.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
DEL PEAK 6(3P26.2) MUTATED	44	71	91
DEL PEAK 6(3P26.2) WILD-TYPE	119	138	96

Figure S54. Get High-res Image Gene #37: 'Del Peak 6(3p26.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Del Peak 6(3p26.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.51e-05 (Fisher's exact test), Q value = 0.043

Table S55. Gene #37: 'Del Peak 6(3p26.2) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	171	220
DEL PEAK 6(3P26.2) MUTATED	84	48	73
DEL PEAK 6(3P26.2) WILD-TYPE	83	123	147

Figure S55. Get High-res Image Gene #37: 'Del Peak 6(3p26.2) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

'Del Peak 9(5q11.2) mutation analysis' versus 'CN_CNMF'

P value = 2.74e-08 (Fisher's exact test), Q value = 2.2e-05

Table S56. Gene #40: 'Del Peak 9(5q11.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
DEL PEAK 9(5Q11.2) MUTATED	67	147	121
DEL PEAK 9(5Q11.2) WILD-TYPE	96	62	66

Figure S56. Get High-res Image Gene #40: 'Del Peak 9(5q11.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Del Peak 10(5q13.2) mutation analysis' versus 'CN_CNMF'

P value = 7.51e-13 (Fisher's exact test), Q value = 6.3e-10

Table S57. Gene #41: 'Del Peak 10(5q13.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
DEL PEAK 10(5Q13.2) MUTATED	84	181	133
DEL PEAK 10(5Q13.2) WILD-TYPE	79	28	54

Figure S57. Get High-res Image Gene #41: 'Del Peak 10(5q13.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Del Peak 11(6q27) mutation analysis' versus 'CN_CNMF'

P value = 8e-09 (Fisher's exact test), Q value = 6.5e-06

Table S58. Gene #42: 'Del Peak 11(6q27) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
DEL PEAK 11(6Q27) MUTATED	114	159	89
DEL PEAK 11(6Q27) WILD-TYPE	49	50	98

Figure S58. Get High-res Image Gene #42: 'Del Peak 11(6q27) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Del Peak 11(6q27) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.62e-05 (Fisher's exact test), Q value = 0.013

Table S59. Gene #42: 'Del Peak 11(6q27) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	171	220
DEL PEAK 11(6Q27) MUTATED	85	128	148
DEL PEAK 11(6Q27) WILD-TYPE	82	43	72

Figure S59. Get High-res Image Gene #42: 'Del Peak 11(6q27) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

'Del Peak 12(7p22.1) mutation analysis' versus 'CN_CNMF'

P value = 2.92e-14 (Fisher's exact test), Q value = 2.4e-11

Table S60. Gene #43: 'Del Peak 12(7p22.1) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
DEL PEAK 12(7P22.1) MUTATED	45	135	63
DEL PEAK 12(7P22.1) WILD-TYPE	118	74	124

Figure S60. Get High-res Image Gene #43: 'Del Peak 12(7p22.1) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Del Peak 13(8p23.3) mutation analysis' versus 'CN_CNMF'

P value = 1.1e-10 (Fisher's exact test), Q value = 9.1e-08

Table S61. Gene #44: 'Del Peak 13(8p23.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
DEL PEAK 13(8P23.3) MUTATED	75	163	137
DEL PEAK 13(8P23.3) WILD-TYPE	88	46	50

Figure S61. Get High-res Image Gene #44: 'Del Peak 13(8p23.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Del Peak 14(8p21.2) mutation analysis' versus 'CN_CNMF'

P value = 1.05e-08 (Fisher's exact test), Q value = 8.5e-06

Table S62. Gene #45: 'Del Peak 14(8p21.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
DEL PEAK 14(8P21.2) MUTATED	84	165	143
DEL PEAK 14(8P21.2) WILD-TYPE	79	44	44

Figure S62. Get High-res Image Gene #45: 'Del Peak 14(8p21.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Del Peak 15(9p24.3) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000117 (Fisher's exact test), Q value = 0.09

Table S63. Gene #46: 'Del Peak 15(9p24.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	213	129
DEL PEAK 15(9P24.3) MUTATED	110	70	66
DEL PEAK 15(9P24.3) WILD-TYPE	105	143	63

Figure S63. Get High-res Image Gene #46: 'Del Peak 15(9p24.3) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 16(9q21.11) mutation analysis' versus 'CN_CNMF'

P value = 4.16e-15 (Fisher's exact test), Q value = 3.5e-12

Table S64. Gene #47: 'Del Peak 16(9q21.11) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
DEL PEAK 16(9Q21.11) MUTATED	69	66	133
DEL PEAK 16(9Q21.11) WILD-TYPE	94	143	54

Figure S64. Get High-res Image Gene #47: 'Del Peak 16(9q21.11) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Del Peak 16(9q21.11) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.98e-07 (Fisher's exact test), Q value = 0.00032

Table S65. Gene #47: 'Del Peak 16(9q21.11) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	171	220
DEL PEAK 16(9Q21.11) MUTATED	109	65	94
DEL PEAK 16(9Q21.11) WILD-TYPE	58	106	126

Figure S65. Get High-res Image Gene #47: 'Del Peak 16(9q21.11) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

'Del Peak 17(9q34.13) mutation analysis' versus 'CN_CNMF'

P value = 1.15e-08 (Fisher's exact test), Q value = 9.4e-06

Table S66. Gene #48: 'Del Peak 17(9q34.13) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
DEL PEAK 17(9Q34.13) MUTATED	82	105	143
DEL PEAK 17(9Q34.13) WILD-TYPE	81	104	44

Figure S66. Get High-res Image Gene #48: 'Del Peak 17(9q34.13) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Del Peak 20(10q26.3) mutation analysis' versus 'CN_CNMF'

P value = 8.82e-05 (Fisher's exact test), Q value = 0.068

Table S67. Gene #51: 'Del Peak 20(10q26.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
DEL PEAK 20(10Q26.3) MUTATED	34	87	65
DEL PEAK 20(10Q26.3) WILD-TYPE	129	122	122

Figure S67. Get High-res Image Gene #51: 'Del Peak 20(10q26.3) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Del Peak 21(11p15.5) mutation analysis' versus 'CN_CNMF'

P value = 2.91e-11 (Fisher's exact test), Q value = 2.4e-08

Table S68. Gene #52: 'Del Peak 21(11p15.5) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
DEL PEAK 21(11P15.5) MUTATED	72	162	100
DEL PEAK 21(11P15.5) WILD-TYPE	91	47	87

Figure S68. Get High-res Image Gene #52: 'Del Peak 21(11p15.5) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Del Peak 23(12q23.1) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000204 (Fisher's exact test), Q value = 0.16

Table S69. Gene #54: 'Del Peak 23(12q23.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	199	125
DEL PEAK 23(12Q23.1) MUTATED	97	47	48
DEL PEAK 23(12Q23.1) WILD-TYPE	136	152	77

Figure S69. Get High-res Image Gene #54: 'Del Peak 23(12q23.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 23(12q23.1) mutation analysis' versus 'CN_CNMF'

P value = 4.4e-08 (Fisher's exact test), Q value = 3.6e-05

Table S70. Gene #54: 'Del Peak 23(12q23.1) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
DEL PEAK 23(12Q23.1) MUTATED	43	104	46
DEL PEAK 23(12Q23.1) WILD-TYPE	120	105	141

Figure S70. Get High-res Image Gene #54: 'Del Peak 23(12q23.1) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Del Peak 24(12q24.33) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 2.63e-06 (Fisher's exact test), Q value = 0.0021

Table S71. Gene #55: 'Del Peak 24(12q24.33) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	199	125
DEL PEAK 24(12Q24.33) MUTATED	101	49	62
DEL PEAK 24(12Q24.33) WILD-TYPE	132	150	63

Figure S71. Get High-res Image Gene #55: 'Del Peak 24(12q24.33) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 24(12q24.33) mutation analysis' versus 'CN_CNMF'

P value = 1.14e-11 (Fisher's exact test), Q value = 9.4e-09

Table S72. Gene #55: 'Del Peak 24(12q24.33) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
DEL PEAK 24(12Q24.33) MUTATED	47	119	47
DEL PEAK 24(12Q24.33) WILD-TYPE	116	90	140

Figure S72. Get High-res Image Gene #55: 'Del Peak 24(12q24.33) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Del Peak 25(13q14.2) mutation analysis' versus 'CN_CNMF'

P value = 1.11e-06 (Fisher's exact test), Q value = 0.00089

Table S73. Gene #56: 'Del Peak 25(13q14.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
DEL PEAK 25(13Q14.2) MUTATED	79	156	113
DEL PEAK 25(13Q14.2) WILD-TYPE	84	53	74

Figure S73. Get High-res Image Gene #56: 'Del Peak 25(13q14.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Del Peak 25(13q14.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 9.8e-06 (Fisher's exact test), Q value = 0.0078

Table S74. Gene #56: 'Del Peak 25(13q14.2) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	171	220
DEL PEAK 25(13Q14.2) MUTATED	106	83	159
DEL PEAK 25(13Q14.2) WILD-TYPE	61	88	61

Figure S74. Get High-res Image Gene #56: 'Del Peak 25(13q14.2) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

'Del Peak 25(13q14.2) mutation analysis' versus 'RPPA_CNMF'

P value = 0.000301 (Fisher's exact test), Q value = 0.23

Table S75. Gene #56: 'Del Peak 25(13q14.2) mutation analysis' versus Clinical Feature #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	124	204	70
DEL PEAK 25(13Q14.2) MUTATED	64	146	37
DEL PEAK 25(13Q14.2) WILD-TYPE	60	58	33

Figure S75. Get High-res Image Gene #56: 'Del Peak 25(13q14.2) mutation analysis' versus Clinical Feature #7: 'RPPA_CNMF'

'Del Peak 27(15q15.1) mutation analysis' versus 'CN_CNMF'

P value = 1.75e-10 (Fisher's exact test), Q value = 1.4e-07

Table S76. Gene #58: 'Del Peak 27(15q15.1) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
DEL PEAK 27(15Q15.1) MUTATED	78	122	151
DEL PEAK 27(15Q15.1) WILD-TYPE	85	87	36

Figure S76. Get High-res Image Gene #58: 'Del Peak 27(15q15.1) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Del Peak 27(15q15.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 7.64e-05 (Fisher's exact test), Q value = 0.059

Table S77. Gene #58: 'Del Peak 27(15q15.1) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	171	220
DEL PEAK 27(15Q15.1) MUTATED	127	94	130
DEL PEAK 27(15Q15.1) WILD-TYPE	40	77	90

Figure S77. Get High-res Image Gene #58: 'Del Peak 27(15q15.1) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

'Del Peak 29(16q22.1) mutation analysis' versus 'CN_CNMF'

P value = 9.04e-05 (Fisher's exact test), Q value = 0.07

Table S78. Gene #60: 'Del Peak 29(16q22.1) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
DEL PEAK 29(16Q22.1) MUTATED	110	170	161
DEL PEAK 29(16Q22.1) WILD-TYPE	53	39	26

Figure S78. Get High-res Image Gene #60: 'Del Peak 29(16q22.1) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Del Peak 30(16q23.1) mutation analysis' versus 'CN_CNMF'

P value = 3.93e-05 (Fisher's exact test), Q value = 0.031

Table S79. Gene #61: 'Del Peak 30(16q23.1) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
DEL PEAK 30(16Q23.1) MUTATED	107	167	160
DEL PEAK 30(16Q23.1) WILD-TYPE	56	42	27

Figure S79. Get High-res Image Gene #61: 'Del Peak 30(16q23.1) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Del Peak 32(17q11.2) mutation analysis' versus 'CN_CNMF'

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

Table S80. Gene #63: 'Del Peak 32(17q11.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
DEL PEAK 32(17Q11.2) MUTATED	127	188	141
DEL PEAK 32(17Q11.2) WILD-TYPE	36	21	46

Figure S80. Get High-res Image Gene #63: 'Del Peak 32(17q11.2) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Del Peak 36(19q13.43) mutation analysis' versus 'CN_CNMF'

P value = 0.000298 (Fisher's exact test), Q value = 0.23

Table S81. Gene #67: 'Del Peak 36(19q13.43) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	209	187
DEL PEAK 36(19Q13.43) MUTATED	80	84	113
DEL PEAK 36(19Q13.43) WILD-TYPE	83	125	74

Figure S81. Get High-res Image Gene #67: 'Del Peak 36(19q13.43) mutation analysis' versus Clinical Feature #5: 'CN_CNMF'

'Del Peak 36(19q13.43) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000107 (Fisher's exact test), Q value = 0.082

Table S82. Gene #67: 'Del Peak 36(19q13.43) mutation analysis' versus Clinical Feature #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	171	220
DEL PEAK 36(19Q13.43) MUTATED	101	64	112
DEL PEAK 36(19Q13.43) WILD-TYPE	66	107	108

Figure S82. Get High-res Image Gene #67: 'Del Peak 36(19q13.43) mutation analysis' versus Clinical Feature #6: '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 = OV-TP.transferedmergedcluster.txt
Number of patients = 559
Number of copy number variation regions = 70
Number of molecular subtypes = 12
Exclude regions that fewer than K tumors have alterations, K = 3

Fisher's exact test

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

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

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

[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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