Correlation between copy number variation genes and molecular subtypes

Colon Adenocarcinoma (Primary solid tumor)

22 February 2013 | analyses__2013_02_22

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variation genes and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1VX0DQH

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 68 peak regions and 10 molecular subtypes across 413 patients, 143 significant findings detected with Q value < 0.25.

Amp Peak 1(2q33.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 2(5p13.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 4(6p21.1) cnvs correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.
Amp Peak 5(8p11.23) cnvs correlated to 'CN_CNMF'.
Amp Peak 6(8p11.21) cnvs correlated to 'CN_CNMF'.
Amp Peak 7(8q12.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 8(8q24.21) cnvs correlated to 'CN_CNMF'.
Amp Peak 9(11p15.5) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 11(13q12.13) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 12(13q22.1) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 13(16p11.2) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 14(16q12.1) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 15(17q12) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Amp Peak 16(17q24.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 17(19p13.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 19(20p12.3) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 20(20p11.23) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 21(20p11.21) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 22(20q11.21) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 23(20q12) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 24(20q13.32) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 1(1p36.11) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 2(1p33) cnvs correlated to 'CN_CNMF'.
Del Peak 3(1p13.1) cnvs correlated to 'CN_CNMF'.
Del Peak 4(1q43) cnvs correlated to 'CN_CNMF'.
Del Peak 6(3p26.1) cnvs correlated to 'CN_CNMF'.
Del Peak 9(4p16.2) cnvs correlated to 'CN_CNMF'.
Del Peak 10(4q22.1) cnvs correlated to 'MRNA_CNMF' and 'CN_CNMF'.
Del Peak 11(4q35.1) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', and 'METHLYATION_CNMF'.
Del Peak 12(5q11.2) cnvs correlated to 'CN_CNMF'.
Del Peak 13(5q21.3) cnvs correlated to 'CN_CNMF'.
Del Peak 14(5q23.1) cnvs correlated to 'CN_CNMF'.
Del Peak 15(6p25.3) cnvs correlated to 'CN_CNMF'.
Del Peak 18(8p23.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 19(8p22) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 20(8p11.22) cnvs correlated to 'CN_CNMF'.
Del Peak 21(8p11.21) cnvs correlated to 'CN_CNMF'.
Del Peak 22(9p21.3) cnvs correlated to 'CN_CNMF'.
Del Peak 23(10p15.3) cnvs correlated to 'CN_CNMF'.
Del Peak 24(10q21.1) cnvs correlated to 'CN_CNMF'.
Del Peak 25(10q23.31) cnvs correlated to 'CN_CNMF'.
Del Peak 26(10q25.2) cnvs correlated to 'CN_CNMF'.
Del Peak 27(12p13.2) cnvs correlated to 'CN_CNMF'.
Del Peak 28(13q14.13) cnvs correlated to 'CN_CNMF'.
Del Peak 29(14q32.11) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 30(15q11.2) cnvs correlated to 'MRNA_CNMF' and 'CN_CNMF'.
Del Peak 31(15q21.1) cnvs correlated to 'CN_CNMF'.
Del Peak 32(15q22.33) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 35(17p12) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 37(18p11.31) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 38(18q12.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 39(18q21.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 40(18q22.1) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 42(20p12.1) cnvs correlated to 'CN_CNMF'.
Del Peak 43(21q11.2) cnvs correlated to 'CN_CNMF'.
Del Peak 44(22q13.32) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 68 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 143 significant findings detected.


		Molecular subtypes	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
Amp Peak 23(20q12)	297 (72%)	116	8.46e-12 (5.35e-09)	6.36e-13 (4.1e-10)	6.28e-43 (4.24e-40)	1.58e-08 (9.5e-06)	0.00209 (1.00)	0.000289 (0.158)	2.29e-16 (1.51e-13)	2.45e-17 (1.62e-14)	0.406 (1.00)	0.948 (1.00)
Amp Peak 24(20q13 32)	300 (73%)	113	2.31e-10 (1.44e-07)	8.16e-14 (5.31e-11)	3.18e-43 (2.15e-40)	1.58e-08 (9.5e-06)	0.003 (1.00)	0.000213 (0.117)	1.37e-15 (8.96e-13)	5.93e-16 (3.89e-13)	0.414 (1.00)	0.96 (1.00)
Del Peak 35(17p12)	229 (55%)	184	9.32e-09 (5.64e-06)	1.22e-06 (0.000711)	2.81e-35 (1.89e-32)	1.8e-09 (1.11e-06)	0.0139 (1.00)	4.89e-05 (0.0275)	1.04e-07 (6.2e-05)	1.35e-08 (8.17e-06)	0.363 (1.00)	0.729 (1.00)
Amp Peak 11(13q12 13)	250 (61%)	163	1.56e-07 (9.25e-05)	3.33e-07 (0.000197)	5.04e-36 (3.39e-33)	0.00027 (0.148)	0.124 (1.00)	0.0178 (1.00)	8.19e-09 (4.97e-06)	3.17e-07 (0.000188)	0.459 (1.00)	0.798 (1.00)
Amp Peak 22(20q11 21)	296 (72%)	117	1e-10 (6.25e-08)	6.73e-13 (4.32e-10)	1.54e-43 (1.04e-40)	2.19e-09 (1.34e-06)	0.0128 (1.00)	0.0018 (0.913)	1e-15 (6.55e-13)	1.82e-16 (1.2e-13)	0.443 (1.00)	1 (1.00)
Del Peak 37(18p11 31)	220 (53%)	193	2.86e-12 (1.82e-09)	7.25e-09 (4.41e-06)	1.93e-42 (1.3e-39)	3.11e-13 (2.01e-10)	0.0101 (1.00)	0.000933 (0.492)	1.82e-11 (1.14e-08)	7.97e-13 (5.12e-10)	0.48 (1.00)	0.841 (1.00)
Del Peak 38(18q12 2)	247 (60%)	166	6.79e-12 (4.31e-09)	3.95e-09 (2.41e-06)	1.87e-45 (1.27e-42)	8.98e-16 (5.88e-13)	0.0487 (1.00)	0.00156 (0.799)	1.07e-09 (6.63e-07)	2.63e-14 (1.71e-11)	0.449 (1.00)	0.865 (1.00)
Del Peak 39(18q21 2)	260 (63%)	153	2.46e-11 (1.54e-08)	2.09e-09 (1.28e-06)	1.51e-45 (1.03e-42)	3.29e-12 (2.09e-09)	0.0111 (1.00)	0.00141 (0.724)	5.07e-09 (3.09e-06)	6.12e-13 (3.94e-10)	0.0517 (1.00)	0.901 (1.00)
Del Peak 40(18q22 1)	260 (63%)	153	8.41e-11 (5.25e-08)	1.12e-08 (6.75e-06)	1.58e-47 (1.07e-44)	2.02e-12 (1.29e-09)	0.0187 (1.00)	0.00103 (0.539)	1.52e-08 (9.15e-06)	6.77e-12 (4.3e-09)	0.0746 (1.00)	0.912 (1.00)
Amp Peak 12(13q22 1)	254 (62%)	159	0.000106 (0.0587)	1.22e-05 (0.007)	7.2e-33 (4.83e-30)	0.00051 (0.274)	0.203 (1.00)	0.0233 (1.00)	8.12e-07 (0.000475)	3.85e-06 (0.00222)	0.272 (1.00)	0.977 (1.00)
Del Peak 19(8p22)	185 (45%)	228	0.00111 (0.577)	0.00632 (1.00)	2.41e-30 (1.61e-27)	3.46e-07 (0.000205)	0.0715 (1.00)	0.000139 (0.077)	0.000387 (0.21)	0.000323 (0.176)	0.115 (1.00)	0.832 (1.00)
Del Peak 29(14q32 11)	133 (32%)	280	1.14e-05 (0.00655)	0.000242 (0.133)	1.61e-20 (1.07e-17)	0.000707 (0.378)	0.000835 (0.442)	0.00501 (1.00)	7.25e-05 (0.0406)	4.35e-05 (0.0246)	0.319 (1.00)	0.0612 (1.00)
Amp Peak 9(11p15 5)	86 (21%)	327	9.39e-06 (0.0054)	0.00105 (0.549)	1.54e-09 (9.5e-07)	0.000612 (0.328)	0.0284 (1.00)	0.000782 (0.416)	5.54e-07 (0.000327)	9.85e-07 (0.000575)	0.117 (1.00)	0.201 (1.00)
Amp Peak 21(20p11 21)	230 (56%)	183	0.000783 (0.416)	7.25e-05 (0.0406)	4e-23 (2.67e-20)	0.00113 (0.586)	0.205 (1.00)	0.192 (1.00)	2.47e-06 (0.00143)	7.83e-10 (4.85e-07)	0.174 (1.00)	0.509 (1.00)
Del Peak 1(1p36 11)	150 (36%)	263	2.06e-05 (0.0118)	0.00879 (1.00)	6.32e-17 (4.17e-14)	0.000792 (0.42)	0.0124 (1.00)	0.00495 (1.00)	6.23e-05 (0.035)	3.64e-05 (0.0206)	0.409 (1.00)	0.0624 (1.00)
Del Peak 32(15q22 33)	145 (35%)	268	0.00028 (0.153)	0.00279 (1.00)	2.48e-21 (1.65e-18)	0.000435 (0.234)	0.0574 (1.00)	0.226 (1.00)	0.0142 (1.00)	3e-05 (0.0171)	0.949 (1.00)	0.365 (1.00)
Amp Peak 13(16p11 2)	116 (28%)	297	0.000402 (0.218)	0.000753 (0.401)	8.55e-19 (5.67e-16)	0.0212 (1.00)	0.229 (1.00)	0.0119 (1.00)	0.00177 (0.903)	1.14e-06 (0.000666)	0.771 (1.00)	0.809 (1.00)
Amp Peak 14(16q12 1)	102 (25%)	311	2.79e-05 (0.0159)	0.00094 (0.495)	1.67e-20 (1.11e-17)	0.0511 (1.00)	0.471 (1.00)	0.051 (1.00)	0.0011 (0.569)	1.45e-06 (0.000841)	0.902 (1.00)	0.93 (1.00)
Amp Peak 19(20p12 3)	184 (45%)	229	0.00263 (1.00)	0.00213 (1.00)	1.86e-12 (1.19e-09)	0.434 (1.00)	0.0139 (1.00)	0.548 (1.00)	0.000181 (0.0999)	1.53e-06 (0.000886)	0.597 (1.00)	0.195 (1.00)
Del Peak 11(4q35 1)	137 (33%)	276	4.76e-05 (0.0269)	0.00406 (1.00)	1.05e-13 (6.79e-11)	7.69e-05 (0.0429)	0.057 (1.00)	0.375 (1.00)	0.0158 (1.00)	0.0197 (1.00)	0.416 (1.00)	0.235 (1.00)
Amp Peak 4(6p21 1)	89 (22%)	324	0.268 (1.00)	0.000328 (0.178)	3.37e-09 (2.06e-06)	0.17 (1.00)	0.6 (1.00)	0.0999 (1.00)	0.0165 (1.00)	0.00373 (1.00)	0.776 (1.00)	0.258 (1.00)
Amp Peak 15(17q12)	101 (24%)	312	0.0671 (1.00)	0.153 (1.00)	7.53e-07 (0.000441)	0.0164 (1.00)	0.596 (1.00)	0.00103 (0.539)	0.000187 (0.103)	0.0136 (1.00)	0.0121 (1.00)	0.986 (1.00)
Amp Peak 20(20p11 23)	205 (50%)	208	0.0285 (1.00)	0.00203 (1.00)	1.26e-16 (8.32e-14)	0.105 (1.00)	0.199 (1.00)	0.513 (1.00)	0.0018 (0.913)	5.87e-07 (0.000344)	0.455 (1.00)	0.212 (1.00)
Del Peak 10(4q22 1)	126 (31%)	287	0.000453 (0.244)	0.00856 (1.00)	8.5e-12 (5.37e-09)	0.00207 (1.00)	0.118 (1.00)	0.371 (1.00)	0.0338 (1.00)	0.00372 (1.00)	0.21 (1.00)	0.518 (1.00)
Del Peak 18(8p23 3)	171 (41%)	242	0.00297 (1.00)	0.00648 (1.00)	6.84e-26 (4.58e-23)	3.61e-06 (0.00209)	0.0742 (1.00)	0.00141 (0.726)	0.00127 (0.653)	0.00198 (1.00)	0.154 (1.00)	0.848 (1.00)
Del Peak 30(15q11 2)	160 (39%)	253	0.000129 (0.0715)	0.00753 (1.00)	1.2e-21 (7.98e-19)	0.00432 (1.00)	0.0381 (1.00)	0.343 (1.00)	0.0106 (1.00)	0.00378 (1.00)	0.877 (1.00)	0.893 (1.00)
Del Peak 44(22q13 32)	138 (33%)	275	0.00152 (0.782)	0.0016 (0.818)	9.76e-13 (6.26e-10)	0.0049 (1.00)	0.364 (1.00)	0.21 (1.00)	0.0684 (1.00)	1.99e-05 (0.0114)	0.394 (1.00)	0.069 (1.00)
Amp Peak 1(2q33 1)	79 (19%)	334	0.0607 (1.00)	0.0703 (1.00)	3.05e-05 (0.0173)	0.258 (1.00)	0.367 (1.00)	0.0366 (1.00)	0.288 (1.00)	0.0196 (1.00)	0.277 (1.00)	0.258 (1.00)
Amp Peak 2(5p13 2)	81 (20%)	332	0.34 (1.00)	0.493 (1.00)	0.000202 (0.111)	0.15 (1.00)	0.438 (1.00)	0.638 (1.00)	0.545 (1.00)	0.313 (1.00)	0.927 (1.00)	0.581 (1.00)
Amp Peak 5(8p11 23)	144 (35%)	269	0.27 (1.00)	0.105 (1.00)	2.99e-13 (1.93e-10)	0.868 (1.00)	0.784 (1.00)	0.367 (1.00)	0.11 (1.00)	0.141 (1.00)	0.179 (1.00)	0.189 (1.00)
Amp Peak 6(8p11 21)	173 (42%)	240	0.245 (1.00)	0.0914 (1.00)	4.51e-10 (2.8e-07)	0.886 (1.00)	0.241 (1.00)	0.0213 (1.00)	0.0217 (1.00)	0.0565 (1.00)	0.502 (1.00)	0.218 (1.00)
Amp Peak 7(8q12 1)	215 (52%)	198	0.209 (1.00)	0.0394 (1.00)	9.31e-12 (5.87e-09)	0.0383 (1.00)	0.0552 (1.00)	0.00111 (0.574)	0.0398 (1.00)	0.00204 (1.00)	0.126 (1.00)	0.295 (1.00)
Amp Peak 8(8q24 21)	239 (58%)	174	0.279 (1.00)	0.12 (1.00)	7.86e-14 (5.12e-11)	0.0102 (1.00)	0.177 (1.00)	0.00618 (1.00)	0.0334 (1.00)	0.00704 (1.00)	0.404 (1.00)	0.215 (1.00)
Amp Peak 16(17q24 1)	92 (22%)	321	0.0919 (1.00)	0.0498 (1.00)	1.61e-08 (9.61e-06)	0.0123 (1.00)	0.162 (1.00)	0.00318 (1.00)	0.00221 (1.00)	0.00207 (1.00)	0.00254 (1.00)	0.781 (1.00)
Amp Peak 17(19p13 2)	65 (16%)	348	0.0942 (1.00)	0.067 (1.00)	4.82e-05 (0.0271)	0.283 (1.00)	0.948 (1.00)	0.753 (1.00)	0.463 (1.00)	0.0935 (1.00)	0.204 (1.00)	0.385 (1.00)
Del Peak 2(1p33)	107 (26%)	306	0.0151 (1.00)	0.542 (1.00)	1.09e-11 (6.85e-09)	0.00668 (1.00)	0.382 (1.00)	0.0363 (1.00)	0.293 (1.00)	0.153 (1.00)	0.893 (1.00)	0.0519 (1.00)
Del Peak 3(1p13 1)	103 (25%)	310	0.068 (1.00)	0.296 (1.00)	6.85e-10 (4.25e-07)	0.185 (1.00)	0.384 (1.00)	0.192 (1.00)	0.216 (1.00)	0.053 (1.00)	0.868 (1.00)	0.379 (1.00)
Del Peak 4(1q43)	44 (11%)	369	0.0721 (1.00)	0.176 (1.00)	6.98e-06 (0.00402)	0.105 (1.00)	0.719 (1.00)	0.666 (1.00)	0.53 (1.00)	0.284 (1.00)	0.335 (1.00)	0.301 (1.00)
Del Peak 6(3p26 1)	60 (15%)	353	0.372 (1.00)	0.357 (1.00)	0.00043 (0.232)	0.268 (1.00)	0.774 (1.00)	0.685 (1.00)	0.663 (1.00)	0.489 (1.00)	0.541 (1.00)	0.958 (1.00)
Del Peak 9(4p16 2)	121 (29%)	292	0.00074 (0.395)	0.0162 (1.00)	1.16e-12 (7.4e-10)	0.011 (1.00)	0.143 (1.00)	0.219 (1.00)	0.00561 (1.00)	0.00288 (1.00)	0.376 (1.00)	0.206 (1.00)
Del Peak 12(5q11 2)	91 (22%)	322	0.000991 (0.52)	0.00346 (1.00)	4.94e-09 (3.01e-06)	0.0339 (1.00)	0.392 (1.00)	0.0412 (1.00)	0.0103 (1.00)	0.0224 (1.00)	0.835 (1.00)	0.215 (1.00)
Del Peak 13(5q21 3)	117 (28%)	296	0.0606 (1.00)	0.0339 (1.00)	1.14e-09 (7.05e-07)	0.0359 (1.00)	0.203 (1.00)	0.232 (1.00)	0.00296 (1.00)	0.000972 (0.511)	0.654 (1.00)	0.36 (1.00)
Del Peak 14(5q23 1)	107 (26%)	306	0.0361 (1.00)	0.0403 (1.00)	1.57e-08 (9.44e-06)	0.087 (1.00)	0.196 (1.00)	0.28 (1.00)	0.00171 (0.87)	0.00547 (1.00)	0.622 (1.00)	0.246 (1.00)
Del Peak 15(6p25 3)	54 (13%)	359	0.697 (1.00)	0.48 (1.00)	0.000102 (0.0571)	0.0527 (1.00)	0.292 (1.00)	0.397 (1.00)	0.418 (1.00)	0.774 (1.00)	0.406 (1.00)	0.453 (1.00)
Del Peak 20(8p11 22)	80 (19%)	333	0.217 (1.00)	0.0856 (1.00)	8.88e-09 (5.38e-06)	0.0614 (1.00)	0.00867 (1.00)	0.0669 (1.00)	0.27 (1.00)	0.0915 (1.00)	0.359 (1.00)	0.831 (1.00)
Del Peak 21(8p11 21)	43 (10%)	370	0.0258 (1.00)	0.348 (1.00)	5.81e-07 (0.000342)	0.366 (1.00)	0.122 (1.00)	0.112 (1.00)	0.174 (1.00)	0.433 (1.00)	0.0997 (1.00)	0.549 (1.00)
Del Peak 22(9p21 3)	56 (14%)	357	0.627 (1.00)	0.341 (1.00)	4.51e-05 (0.0255)	0.204 (1.00)	0.474 (1.00)	0.245 (1.00)	0.0733 (1.00)	0.348 (1.00)	0.904 (1.00)	0.663 (1.00)
Del Peak 23(10p15 3)	68 (16%)	345	0.204 (1.00)	0.136 (1.00)	2.25e-08 (1.34e-05)	0.0291 (1.00)	0.113 (1.00)	0.146 (1.00)	0.174 (1.00)	0.336 (1.00)	0.68 (1.00)	0.566 (1.00)
Del Peak 24(10q21 1)	82 (20%)	331	0.00314 (1.00)	0.0191 (1.00)	2.24e-11 (1.4e-08)	0.194 (1.00)	0.167 (1.00)	0.0179 (1.00)	0.0116 (1.00)	0.00373 (1.00)	0.887 (1.00)	0.831 (1.00)
Del Peak 25(10q23 31)	94 (23%)	319	0.138 (1.00)	0.178 (1.00)	3.46e-07 (0.000205)	0.0801 (1.00)	0.269 (1.00)	0.599 (1.00)	0.0432 (1.00)	0.00351 (1.00)	0.885 (1.00)	0.985 (1.00)
Del Peak 26(10q25 2)	93 (23%)	320	0.116 (1.00)	0.00191 (0.968)	1.91e-11 (1.2e-08)	0.0139 (1.00)	0.0107 (1.00)	0.395 (1.00)	0.226 (1.00)	0.00101 (0.528)	0.921 (1.00)	0.593 (1.00)
Del Peak 27(12p13 2)	44 (11%)	369	0.0429 (1.00)	0.00554 (1.00)	9.87e-08 (5.88e-05)	0.207 (1.00)	0.415 (1.00)	0.815 (1.00)	0.308 (1.00)	0.419 (1.00)	0.695 (1.00)	0.973 (1.00)
Del Peak 28(13q14 13)	18 (4%)	395	0.392 (1.00)	0.478 (1.00)	0.000128 (0.0708)	0.153 (1.00)	0.6 (1.00)	0.17 (1.00)	0.122 (1.00)	1 (1.00)	0.614 (1.00)	0.834 (1.00)
Del Peak 31(15q21 1)	151 (37%)	262	0.007 (1.00)	0.0523 (1.00)	8.15e-18 (5.39e-15)	0.00747 (1.00)	0.0676 (1.00)	0.172 (1.00)	0.148 (1.00)	0.0069 (1.00)	0.979 (1.00)	0.621 (1.00)
Del Peak 42(20p12 1)	79 (19%)	334	0.0393 (1.00)	0.0347 (1.00)	1.38e-13 (8.93e-11)	0.00404 (1.00)	0.352 (1.00)	0.167 (1.00)	0.0158 (1.00)	0.188 (1.00)	0.0931 (1.00)	0.101 (1.00)
Del Peak 43(21q11 2)	125 (30%)	288	0.00822 (1.00)	0.0576 (1.00)	3.37e-09 (2.06e-06)	0.0302 (1.00)	0.587 (1.00)	0.554 (1.00)	0.0339 (1.00)	0.0491 (1.00)	0.923 (1.00)	0.47 (1.00)
Amp Peak 3(5q22 3)	40 (10%)	373	0.779 (1.00)	0.558 (1.00)	0.0293 (1.00)	0.875 (1.00)	0.192 (1.00)	0.459 (1.00)	0.185 (1.00)	0.0722 (1.00)	0.693 (1.00)	0.839 (1.00)
Amp Peak 10(12p13 33)	104 (25%)	309	0.61 (1.00)	0.223 (1.00)	0.0612 (1.00)	0.247 (1.00)	0.332 (1.00)	0.599 (1.00)	0.449 (1.00)	0.558 (1.00)	0.304 (1.00)	0.173 (1.00)
Amp Peak 18(19q13 11)	83 (20%)	330	0.249 (1.00)	0.00697 (1.00)	0.002 (1.00)	0.517 (1.00)	0.234 (1.00)	0.958 (1.00)	0.0249 (1.00)	0.00888 (1.00)	0.417 (1.00)	0.491 (1.00)
Del Peak 5(2q37 2)	21 (5%)	392	0.927 (1.00)	0.0138 (1.00)	0.977 (1.00)	0.701 (1.00)	0.0373 (1.00)	0.271 (1.00)	0.442 (1.00)	1 (1.00)	0.447 (1.00)	0.447 (1.00)
Del Peak 7(3p14 2)	75 (18%)	338	0.717 (1.00)	0.819 (1.00)	0.205 (1.00)	0.735 (1.00)	0.934 (1.00)	0.734 (1.00)	0.606 (1.00)	0.602 (1.00)	0.203 (1.00)	0.536 (1.00)
Del Peak 8(3q26 31)	39 (9%)	374	0.41 (1.00)	0.676 (1.00)	0.00818 (1.00)	0.497 (1.00)	0.111 (1.00)	0.109 (1.00)	0.157 (1.00)	0.703 (1.00)	0.15 (1.00)	0.939 (1.00)
Del Peak 16(6q26)	60 (15%)	353	0.356 (1.00)	0.193 (1.00)	0.157 (1.00)	0.356 (1.00)	0.0359 (1.00)	0.889 (1.00)	0.571 (1.00)	0.696 (1.00)	0.797 (1.00)	0.53 (1.00)
Del Peak 17(7q31 1)	11 (3%)	402	1 (1.00)	0.557 (1.00)	0.816 (1.00)	0.795 (1.00)	0.249 (1.00)	0.331 (1.00)	0.491 (1.00)	0.792 (1.00)	1 (1.00)	0.564 (1.00)
Del Peak 33(16p13 3)	45 (11%)	368	0.345 (1.00)	0.125 (1.00)	0.208 (1.00)	0.376 (1.00)	0.0298 (1.00)	0.886 (1.00)	0.428 (1.00)	0.473 (1.00)	0.842 (1.00)	0.739 (1.00)
Del Peak 34(16q23 1)	49 (12%)	364	0.283 (1.00)	0.0233 (1.00)	0.131 (1.00)	0.337 (1.00)	0.445 (1.00)	0.885 (1.00)	0.00919 (1.00)	0.00359 (1.00)	0.977 (1.00)	0.505 (1.00)
Del Peak 36(17q24 3)	59 (14%)	354	0.11 (1.00)	0.579 (1.00)	0.00348 (1.00)	0.0118 (1.00)	0.524 (1.00)	0.329 (1.00)	0.586 (1.00)	0.395 (1.00)	0.681 (1.00)	0.979 (1.00)
Del Peak 41(19p13 3)	57 (14%)	356	0.275 (1.00)	0.196 (1.00)	0.00362 (1.00)	0.565 (1.00)	0.387 (1.00)	0.149 (1.00)	0.0301 (1.00)	0.149 (1.00)	0.582 (1.00)	0.0166 (1.00)

'Amp Peak 1(2q33.1) mutation analysis' versus 'CN_CNMF'

P value = 3.05e-05 (Fisher's exact test), Q value = 0.017

Table S1. Gene #1: 'Amp Peak 1(2q33.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 1(2Q33.1) MUTATED	49	18	8	4
AMP PEAK 1(2Q33.1) WILD-TYPE	121	169	24	20

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(2q33.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 2(5p13.2) mutation analysis' versus 'CN_CNMF'

P value = 0.000202 (Fisher's exact test), Q value = 0.11

Table S2. Gene #2: 'Amp Peak 2(5p13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 2(5P13.2) MUTATED	46	20	10	5
AMP PEAK 2(5P13.2) WILD-TYPE	124	167	22	19

Figure S2. Get High-res Image Gene #2: 'Amp Peak 2(5p13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 4(6p21.1) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000328 (Fisher's exact test), Q value = 0.18

Table S3. Gene #4: 'Amp Peak 4(6p21.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	48	13	43
AMP PEAK 4(6P21.1) MUTATED	4	8	0	18
AMP PEAK 4(6P21.1) WILD-TYPE	40	40	13	25

Figure S3. Get High-res Image Gene #4: 'Amp Peak 4(6p21.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 4(6p21.1) mutation analysis' versus 'CN_CNMF'

P value = 3.37e-09 (Fisher's exact test), Q value = 2.1e-06

Table S4. Gene #4: 'Amp Peak 4(6p21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 4(6P21.1) MUTATED	61	16	8	4
AMP PEAK 4(6P21.1) WILD-TYPE	109	171	24	20

Figure S4. Get High-res Image Gene #4: 'Amp Peak 4(6p21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 5(8p11.23) mutation analysis' versus 'CN_CNMF'

P value = 2.99e-13 (Fisher's exact test), Q value = 1.9e-10

Table S5. Gene #5: 'Amp Peak 5(8p11.23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 5(8P11.23) MUTATED	56	47	17	24
AMP PEAK 5(8P11.23) WILD-TYPE	114	140	15	0

Figure S5. Get High-res Image Gene #5: 'Amp Peak 5(8p11.23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 6(8p11.21) mutation analysis' versus 'CN_CNMF'

P value = 4.51e-10 (Fisher's exact test), Q value = 2.8e-07

Table S6. Gene #6: 'Amp Peak 6(8p11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 6(8P11.21) MUTATED	75	55	21	22
AMP PEAK 6(8P11.21) WILD-TYPE	95	132	11	2

Figure S6. Get High-res Image Gene #6: 'Amp Peak 6(8p11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 7(8q12.1) mutation analysis' versus 'CN_CNMF'

P value = 9.31e-12 (Fisher's exact test), Q value = 5.9e-09

Table S7. Gene #7: 'Amp Peak 7(8q12.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 7(8Q12.1) MUTATED	106	64	23	22
AMP PEAK 7(8Q12.1) WILD-TYPE	64	123	9	2

Figure S7. Get High-res Image Gene #7: 'Amp Peak 7(8q12.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 7.86e-14 (Fisher's exact test), Q value = 5.1e-11

Table S8. Gene #8: 'Amp Peak 8(8q24.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 8(8Q24.21) MUTATED	119	73	23	24
AMP PEAK 8(8Q24.21) WILD-TYPE	51	114	9	0

Figure S8. Get High-res Image Gene #8: 'Amp Peak 8(8q24.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 9(11p15.5) mutation analysis' versus 'MRNA_CNMF'

P value = 9.39e-06 (Fisher's exact test), Q value = 0.0054

Table S9. Gene #9: 'Amp Peak 9(11p15.5) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	32	30	23
AMP PEAK 9(11P15.5) MUTATED	18	1	3	13
AMP PEAK 9(11P15.5) WILD-TYPE	45	31	27	10

Figure S9. Get High-res Image Gene #9: 'Amp Peak 9(11p15.5) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 9(11p15.5) mutation analysis' versus 'CN_CNMF'

P value = 1.54e-09 (Fisher's exact test), Q value = 9.5e-07

Table S10. Gene #9: 'Amp Peak 9(11p15.5) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 9(11P15.5) MUTATED	54	17	14	1
AMP PEAK 9(11P15.5) WILD-TYPE	116	170	18	23

Figure S10. Get High-res Image Gene #9: 'Amp Peak 9(11p15.5) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 9(11p15.5) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 5.54e-07 (Fisher's exact test), Q value = 0.00033

Table S11. Gene #9: 'Amp Peak 9(11p15.5) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	58	39	20
AMP PEAK 9(11P15.5) MUTATED	27	2	8	9
AMP PEAK 9(11P15.5) WILD-TYPE	40	56	31	11

Figure S11. Get High-res Image Gene #9: 'Amp Peak 9(11p15.5) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 9(11p15.5) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.85e-07 (Fisher's exact test), Q value = 0.00058

Table S12. Gene #9: 'Amp Peak 9(11p15.5) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	18	102
AMP PEAK 9(11P15.5) MUTATED	3	4	39
AMP PEAK 9(11P15.5) WILD-TYPE	61	14	63

Figure S12. Get High-res Image Gene #9: 'Amp Peak 9(11p15.5) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 11(13q12.13) mutation analysis' versus 'MRNA_CNMF'

P value = 1.56e-07 (Fisher's exact test), Q value = 9.2e-05

Table S13. Gene #11: 'Amp Peak 11(13q12.13) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	32	30	23
AMP PEAK 11(13Q12.13) MUTATED	53	14	9	18
AMP PEAK 11(13Q12.13) WILD-TYPE	10	18	21	5

Figure S13. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 11(13q12.13) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 3.33e-07 (Fisher's exact test), Q value = 2e-04

Table S14. Gene #11: 'Amp Peak 11(13q12.13) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	48	13	43
AMP PEAK 11(13Q12.13) MUTATED	15	35	6	38
AMP PEAK 11(13Q12.13) WILD-TYPE	29	13	7	5

Figure S14. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

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

P value = 5.04e-36 (Fisher's exact test), Q value = 3.4e-33

Table S15. Gene #11: 'Amp Peak 11(13q12.13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 11(13Q12.13) MUTATED	158	57	18	17
AMP PEAK 11(13Q12.13) WILD-TYPE	12	130	14	7

Figure S15. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 0.00027 (Fisher's exact test), Q value = 0.15

Table S16. Gene #11: 'Amp Peak 11(13q12.13) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	86	63
AMP PEAK 11(13Q12.13) MUTATED	79	42	33
AMP PEAK 11(13Q12.13) WILD-TYPE	26	44	30

Figure S16. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 11(13q12.13) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 8.19e-09 (Fisher's exact test), Q value = 5e-06

Table S17. Gene #11: 'Amp Peak 11(13q12.13) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	58	39	20
AMP PEAK 11(13Q12.13) MUTATED	56	24	14	17
AMP PEAK 11(13Q12.13) WILD-TYPE	11	34	25	3

Figure S17. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 11(13q12.13) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.17e-07 (Fisher's exact test), Q value = 0.00019

Table S18. Gene #11: 'Amp Peak 11(13q12.13) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	18	102
AMP PEAK 11(13Q12.13) MUTATED	22	11	78
AMP PEAK 11(13Q12.13) WILD-TYPE	42	7	24

Figure S18. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 12(13q22.1) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000106 (Fisher's exact test), Q value = 0.059

Table S19. Gene #12: 'Amp Peak 12(13q22.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	32	30	23
AMP PEAK 12(13Q22.1) MUTATED	50	15	11	17
AMP PEAK 12(13Q22.1) WILD-TYPE	13	17	19	6

Figure S19. Get High-res Image Gene #12: 'Amp Peak 12(13q22.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 12(13q22.1) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.22e-05 (Fisher's exact test), Q value = 0.007

Table S20. Gene #12: 'Amp Peak 12(13q22.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	48	13	43
AMP PEAK 12(13Q22.1) MUTATED	16	35	6	36
AMP PEAK 12(13Q22.1) WILD-TYPE	28	13	7	7

Figure S20. Get High-res Image Gene #12: 'Amp Peak 12(13q22.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 12(13q22.1) mutation analysis' versus 'CN_CNMF'

P value = 7.2e-33 (Fisher's exact test), Q value = 4.8e-30

Table S21. Gene #12: 'Amp Peak 12(13q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 12(13Q22.1) MUTATED	158	63	17	16
AMP PEAK 12(13Q22.1) WILD-TYPE	12	124	15	8

Figure S21. Get High-res Image Gene #12: 'Amp Peak 12(13q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 12(13q22.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 8.12e-07 (Fisher's exact test), Q value = 0.00048

Table S22. Gene #12: 'Amp Peak 12(13q22.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	58	39	20
AMP PEAK 12(13Q22.1) MUTATED	54	26	14	16
AMP PEAK 12(13Q22.1) WILD-TYPE	13	32	25	4

Figure S22. Get High-res Image Gene #12: 'Amp Peak 12(13q22.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 12(13q22.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.85e-06 (Fisher's exact test), Q value = 0.0022

Table S23. Gene #12: 'Amp Peak 12(13q22.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	18	102
AMP PEAK 12(13Q22.1) MUTATED	23	11	76
AMP PEAK 12(13Q22.1) WILD-TYPE	41	7	26

Figure S23. Get High-res Image Gene #12: 'Amp Peak 12(13q22.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 13(16p11.2) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000402 (Fisher's exact test), Q value = 0.22

Table S24. Gene #13: 'Amp Peak 13(16p11.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	32	30	23
AMP PEAK 13(16P11.2) MUTATED	23	5	3	13
AMP PEAK 13(16P11.2) WILD-TYPE	40	27	27	10

Figure S24. Get High-res Image Gene #13: 'Amp Peak 13(16p11.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 13(16p11.2) mutation analysis' versus 'CN_CNMF'

P value = 8.55e-19 (Fisher's exact test), Q value = 5.7e-16

Table S25. Gene #13: 'Amp Peak 13(16p11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 13(16P11.2) MUTATED	88	18	8	2
AMP PEAK 13(16P11.2) WILD-TYPE	82	169	24	22

Figure S25. Get High-res Image Gene #13: 'Amp Peak 13(16p11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 13(16p11.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.14e-06 (Fisher's exact test), Q value = 0.00067

Table S26. Gene #13: 'Amp Peak 13(16p11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	18	102
AMP PEAK 13(16P11.2) MUTATED	5	10	39
AMP PEAK 13(16P11.2) WILD-TYPE	59	8	63

Figure S26. Get High-res Image Gene #13: 'Amp Peak 13(16p11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 14(16q12.1) mutation analysis' versus 'MRNA_CNMF'

P value = 2.79e-05 (Fisher's exact test), Q value = 0.016

Table S27. Gene #14: 'Amp Peak 14(16q12.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	32	30	23
AMP PEAK 14(16Q12.1) MUTATED	21	3	2	13
AMP PEAK 14(16Q12.1) WILD-TYPE	42	29	28	10

Figure S27. Get High-res Image Gene #14: 'Amp Peak 14(16q12.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 14(16q12.1) mutation analysis' versus 'CN_CNMF'

P value = 1.67e-20 (Fisher's exact test), Q value = 1.1e-17

Table S28. Gene #14: 'Amp Peak 14(16q12.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 14(16Q12.1) MUTATED	82	12	7	1
AMP PEAK 14(16Q12.1) WILD-TYPE	88	175	25	23

Figure S28. Get High-res Image Gene #14: 'Amp Peak 14(16q12.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 14(16q12.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.45e-06 (Fisher's exact test), Q value = 0.00084

Table S29. Gene #14: 'Amp Peak 14(16q12.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	18	102
AMP PEAK 14(16Q12.1) MUTATED	3	7	37
AMP PEAK 14(16Q12.1) WILD-TYPE	61	11	65

Figure S29. Get High-res Image Gene #14: 'Amp Peak 14(16q12.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 15(17q12) mutation analysis' versus 'CN_CNMF'

P value = 7.53e-07 (Fisher's exact test), Q value = 0.00044

Table S30. Gene #15: 'Amp Peak 15(17q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 15(17Q12) MUTATED	62	23	8	8
AMP PEAK 15(17Q12) WILD-TYPE	108	164	24	16

Figure S30. Get High-res Image Gene #15: 'Amp Peak 15(17q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 15(17q12) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000187 (Fisher's exact test), Q value = 0.1

Table S31. Gene #15: 'Amp Peak 15(17q12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	58	39	20
AMP PEAK 15(17Q12) MUTATED	22	8	3	10
AMP PEAK 15(17Q12) WILD-TYPE	45	50	36	10

Figure S31. Get High-res Image Gene #15: 'Amp Peak 15(17q12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 16(17q24.1) mutation analysis' versus 'CN_CNMF'

P value = 1.61e-08 (Fisher's exact test), Q value = 9.6e-06

Table S32. Gene #16: 'Amp Peak 16(17q24.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 16(17Q24.1) MUTATED	59	17	8	8
AMP PEAK 16(17Q24.1) WILD-TYPE	111	170	24	16

Figure S32. Get High-res Image Gene #16: 'Amp Peak 16(17q24.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 17(19p13.2) mutation analysis' versus 'CN_CNMF'

P value = 4.82e-05 (Fisher's exact test), Q value = 0.027

Table S33. Gene #17: 'Amp Peak 17(19p13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 17(19P13.2) MUTATED	39	13	8	5
AMP PEAK 17(19P13.2) WILD-TYPE	131	174	24	19

Figure S33. Get High-res Image Gene #17: 'Amp Peak 17(19p13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 19(20p12.3) mutation analysis' versus 'CN_CNMF'

P value = 1.86e-12 (Fisher's exact test), Q value = 1.2e-09

Table S34. Gene #19: 'Amp Peak 19(20p12.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 19(20P12.3) MUTATED	83	58	31	12
AMP PEAK 19(20P12.3) WILD-TYPE	87	129	1	12

Figure S34. Get High-res Image Gene #19: 'Amp Peak 19(20p12.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 19(20p12.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000181 (Fisher's exact test), Q value = 0.1

Table S35. Gene #19: 'Amp Peak 19(20p12.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	58	39	20
AMP PEAK 19(20P12.3) MUTATED	40	16	17	15
AMP PEAK 19(20P12.3) WILD-TYPE	27	42	22	5

Figure S35. Get High-res Image Gene #19: 'Amp Peak 19(20p12.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 19(20p12.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.53e-06 (Fisher's exact test), Q value = 0.00089

Table S36. Gene #19: 'Amp Peak 19(20p12.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	18	102
AMP PEAK 19(20P12.3) MUTATED	15	8	65
AMP PEAK 19(20P12.3) WILD-TYPE	49	10	37

Figure S36. Get High-res Image Gene #19: 'Amp Peak 19(20p12.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 20(20p11.23) mutation analysis' versus 'CN_CNMF'

P value = 1.26e-16 (Fisher's exact test), Q value = 8.3e-14

Table S37. Gene #20: 'Amp Peak 20(20p11.23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 20(20P11.23) MUTATED	102	58	32	13
AMP PEAK 20(20P11.23) WILD-TYPE	68	129	0	11

Figure S37. Get High-res Image Gene #20: 'Amp Peak 20(20p11.23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 20(20p11.23) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.87e-07 (Fisher's exact test), Q value = 0.00034

Table S38. Gene #20: 'Amp Peak 20(20p11.23) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	18	102
AMP PEAK 20(20P11.23) MUTATED	16	8	68
AMP PEAK 20(20P11.23) WILD-TYPE	48	10	34

Figure S38. Get High-res Image Gene #20: 'Amp Peak 20(20p11.23) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 21(20p11.21) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 7.25e-05 (Fisher's exact test), Q value = 0.041

Table S39. Gene #21: 'Amp Peak 21(20p11.21) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	48	13	43
AMP PEAK 21(20P11.21) MUTATED	12	33	8	30
AMP PEAK 21(20P11.21) WILD-TYPE	32	15	5	13

Figure S39. Get High-res Image Gene #21: 'Amp Peak 21(20p11.21) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 21(20p11.21) mutation analysis' versus 'CN_CNMF'

P value = 4e-23 (Fisher's exact test), Q value = 2.7e-20

Table S40. Gene #21: 'Amp Peak 21(20p11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 21(20P11.21) MUTATED	126	58	32	14
AMP PEAK 21(20P11.21) WILD-TYPE	44	129	0	10

Figure S40. Get High-res Image Gene #21: 'Amp Peak 21(20p11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 21(20p11.21) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.47e-06 (Fisher's exact test), Q value = 0.0014

Table S41. Gene #21: 'Amp Peak 21(20p11.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	58	39	20
AMP PEAK 21(20P11.21) MUTATED	49	17	19	15
AMP PEAK 21(20P11.21) WILD-TYPE	18	41	20	5

Figure S41. Get High-res Image Gene #21: 'Amp Peak 21(20p11.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 21(20p11.21) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.83e-10 (Fisher's exact test), Q value = 4.9e-07

Table S42. Gene #21: 'Amp Peak 21(20p11.21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	18	102
AMP PEAK 21(20P11.21) MUTATED	16	8	76
AMP PEAK 21(20P11.21) WILD-TYPE	48	10	26

Figure S42. Get High-res Image Gene #21: 'Amp Peak 21(20p11.21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 22(20q11.21) mutation analysis' versus 'MRNA_CNMF'

P value = 1e-10 (Fisher's exact test), Q value = 6.3e-08

Table S43. Gene #22: 'Amp Peak 22(20q11.21) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	32	30	23
AMP PEAK 22(20Q11.21) MUTATED	60	12	15	20
AMP PEAK 22(20Q11.21) WILD-TYPE	3	20	15	3

Figure S43. Get High-res Image Gene #22: 'Amp Peak 22(20q11.21) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 22(20q11.21) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 6.73e-13 (Fisher's exact test), Q value = 4.3e-10

Table S44. Gene #22: 'Amp Peak 22(20q11.21) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	48	13	43
AMP PEAK 22(20Q11.21) MUTATED	14	45	8	40
AMP PEAK 22(20Q11.21) WILD-TYPE	30	3	5	3

Figure S44. Get High-res Image Gene #22: 'Amp Peak 22(20q11.21) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 22(20q11.21) mutation analysis' versus 'CN_CNMF'

P value = 1.54e-43 (Fisher's exact test), Q value = 1e-40

Table S45. Gene #22: 'Amp Peak 22(20q11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 22(20Q11.21) MUTATED	167	74	32	23
AMP PEAK 22(20Q11.21) WILD-TYPE	3	113	0	1

Figure S45. Get High-res Image Gene #22: 'Amp Peak 22(20q11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 22(20q11.21) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.19e-09 (Fisher's exact test), Q value = 1.3e-06

Table S46. Gene #22: 'Amp Peak 22(20q11.21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	86	63
AMP PEAK 22(20Q11.21) MUTATED	96	46	40
AMP PEAK 22(20Q11.21) WILD-TYPE	9	40	23

Figure S46. Get High-res Image Gene #22: 'Amp Peak 22(20q11.21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 22(20q11.21) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1e-15 (Fisher's exact test), Q value = 6.6e-13

Table S47. Gene #22: 'Amp Peak 22(20q11.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	58	39	20
AMP PEAK 22(20Q11.21) MUTATED	66	21	24	18
AMP PEAK 22(20Q11.21) WILD-TYPE	1	37	15	2

Figure S47. Get High-res Image Gene #22: 'Amp Peak 22(20q11.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 22(20q11.21) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.82e-16 (Fisher's exact test), Q value = 1.2e-13

Table S48. Gene #22: 'Amp Peak 22(20q11.21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	18	102
AMP PEAK 22(20Q11.21) MUTATED	21	13	95
AMP PEAK 22(20Q11.21) WILD-TYPE	43	5	7

Figure S48. Get High-res Image Gene #22: 'Amp Peak 22(20q11.21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 23(20q12) mutation analysis' versus 'MRNA_CNMF'

P value = 8.46e-12 (Fisher's exact test), Q value = 5.4e-09

Table S49. Gene #23: 'Amp Peak 23(20q12) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	32	30	23
AMP PEAK 23(20Q12) MUTATED	60	11	14	20
AMP PEAK 23(20Q12) WILD-TYPE	3	21	16	3

Figure S49. Get High-res Image Gene #23: 'Amp Peak 23(20q12) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 23(20q12) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 6.36e-13 (Fisher's exact test), Q value = 4.1e-10

Table S50. Gene #23: 'Amp Peak 23(20q12) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	48	13	43
AMP PEAK 23(20Q12) MUTATED	13	44	8	40
AMP PEAK 23(20Q12) WILD-TYPE	31	4	5	3

Figure S50. Get High-res Image Gene #23: 'Amp Peak 23(20q12) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 23(20q12) mutation analysis' versus 'CN_CNMF'

P value = 6.28e-43 (Fisher's exact test), Q value = 4.2e-40

Table S51. Gene #23: 'Amp Peak 23(20q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 23(20Q12) MUTATED	167	75	32	23
AMP PEAK 23(20Q12) WILD-TYPE	3	112	0	1

Figure S51. Get High-res Image Gene #23: 'Amp Peak 23(20q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 23(20q12) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.58e-08 (Fisher's exact test), Q value = 9.5e-06

Table S52. Gene #23: 'Amp Peak 23(20q12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	86	63
AMP PEAK 23(20Q12) MUTATED	96	48	41
AMP PEAK 23(20Q12) WILD-TYPE	9	38	22

Figure S52. Get High-res Image Gene #23: 'Amp Peak 23(20q12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 23(20q12) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 0.000289 (Fisher's exact test), Q value = 0.16

Table S53. Gene #23: 'Amp Peak 23(20q12) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	142	23	48	51
AMP PEAK 23(20Q12) MUTATED	104	13	25	45
AMP PEAK 23(20Q12) WILD-TYPE	38	10	23	6

Figure S53. Get High-res Image Gene #23: 'Amp Peak 23(20q12) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 23(20q12) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.29e-16 (Fisher's exact test), Q value = 1.5e-13

Table S54. Gene #23: 'Amp Peak 23(20q12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	58	39	20
AMP PEAK 23(20Q12) MUTATED	66	20	24	18
AMP PEAK 23(20Q12) WILD-TYPE	1	38	15	2

Figure S54. Get High-res Image Gene #23: 'Amp Peak 23(20q12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 23(20q12) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.45e-17 (Fisher's exact test), Q value = 1.6e-14

Table S55. Gene #23: 'Amp Peak 23(20q12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	18	102
AMP PEAK 23(20Q12) MUTATED	20	13	95
AMP PEAK 23(20Q12) WILD-TYPE	44	5	7

Figure S55. Get High-res Image Gene #23: 'Amp Peak 23(20q12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 24(20q13.32) mutation analysis' versus 'MRNA_CNMF'

P value = 2.31e-10 (Fisher's exact test), Q value = 1.4e-07

Table S56. Gene #24: 'Amp Peak 24(20q13.32) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	32	30	23
AMP PEAK 24(20Q13.32) MUTATED	60	12	16	20
AMP PEAK 24(20Q13.32) WILD-TYPE	3	20	14	3

Figure S56. Get High-res Image Gene #24: 'Amp Peak 24(20q13.32) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 24(20q13.32) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 8.16e-14 (Fisher's exact test), Q value = 5.3e-11

Table S57. Gene #24: 'Amp Peak 24(20q13.32) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	48	13	43
AMP PEAK 24(20Q13.32) MUTATED	14	46	8	40
AMP PEAK 24(20Q13.32) WILD-TYPE	30	2	5	3

Figure S57. Get High-res Image Gene #24: 'Amp Peak 24(20q13.32) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 24(20q13.32) mutation analysis' versus 'CN_CNMF'

P value = 3.18e-43 (Fisher's exact test), Q value = 2.1e-40

Table S58. Gene #24: 'Amp Peak 24(20q13.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 24(20Q13.32) MUTATED	168	77	32	23
AMP PEAK 24(20Q13.32) WILD-TYPE	2	110	0	1

Figure S58. Get High-res Image Gene #24: 'Amp Peak 24(20q13.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 24(20q13.32) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.58e-08 (Fisher's exact test), Q value = 9.5e-06

Table S59. Gene #24: 'Amp Peak 24(20q13.32) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	86	63
AMP PEAK 24(20Q13.32) MUTATED	96	48	41
AMP PEAK 24(20Q13.32) WILD-TYPE	9	38	22

Figure S59. Get High-res Image Gene #24: 'Amp Peak 24(20q13.32) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 24(20q13.32) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 0.000213 (Fisher's exact test), Q value = 0.12

Table S60. Gene #24: 'Amp Peak 24(20q13.32) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	142	23	48	51
AMP PEAK 24(20Q13.32) MUTATED	106	13	25	45
AMP PEAK 24(20Q13.32) WILD-TYPE	36	10	23	6

Figure S60. Get High-res Image Gene #24: 'Amp Peak 24(20q13.32) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 24(20q13.32) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.37e-15 (Fisher's exact test), Q value = 9e-13

Table S61. Gene #24: 'Amp Peak 24(20q13.32) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	58	39	20
AMP PEAK 24(20Q13.32) MUTATED	66	21	25	18
AMP PEAK 24(20Q13.32) WILD-TYPE	1	37	14	2

Figure S61. Get High-res Image Gene #24: 'Amp Peak 24(20q13.32) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 24(20q13.32) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.93e-16 (Fisher's exact test), Q value = 3.9e-13

Table S62. Gene #24: 'Amp Peak 24(20q13.32) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	18	102
AMP PEAK 24(20Q13.32) MUTATED	22	13	95
AMP PEAK 24(20Q13.32) WILD-TYPE	42	5	7

Figure S62. Get High-res Image Gene #24: 'Amp Peak 24(20q13.32) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 2.06e-05 (Fisher's exact test), Q value = 0.012

Table S63. Gene #25: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	32	30	23
DEL PEAK 1(1P36.11) MUTATED	37	9	3	11
DEL PEAK 1(1P36.11) WILD-TYPE	26	23	27	12

Figure S63. Get High-res Image Gene #25: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

P value = 6.32e-17 (Fisher's exact test), Q value = 4.2e-14

Table S64. Gene #25: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 1(1P36.11) MUTATED	91	28	22	9
DEL PEAK 1(1P36.11) WILD-TYPE	79	159	10	15

Figure S64. Get High-res Image Gene #25: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 6.23e-05 (Fisher's exact test), Q value = 0.035

Table S65. Gene #25: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	58	39	20
DEL PEAK 1(1P36.11) MUTATED	40	14	9	9
DEL PEAK 1(1P36.11) WILD-TYPE	27	44	30	11

Figure S65. Get High-res Image Gene #25: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 3.64e-05 (Fisher's exact test), Q value = 0.021

Table S66. Gene #25: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	18	102
DEL PEAK 1(1P36.11) MUTATED	12	6	54
DEL PEAK 1(1P36.11) WILD-TYPE	52	12	48

Figure S66. Get High-res Image Gene #25: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 2(1p33) mutation analysis' versus 'CN_CNMF'

P value = 1.09e-11 (Fisher's exact test), Q value = 6.9e-09

Table S67. Gene #26: 'Del Peak 2(1p33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 2(1P33) MUTATED	69	20	15	3
DEL PEAK 2(1P33) WILD-TYPE	101	167	17	21

Figure S67. Get High-res Image Gene #26: 'Del Peak 2(1p33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 3(1p13.1) mutation analysis' versus 'CN_CNMF'

P value = 6.85e-10 (Fisher's exact test), Q value = 4.3e-07

Table S68. Gene #27: 'Del Peak 3(1p13.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 3(1P13.1) MUTATED	66	23	13	1
DEL PEAK 3(1P13.1) WILD-TYPE	104	164	19	23

Figure S68. Get High-res Image Gene #27: 'Del Peak 3(1p13.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 4(1q43) mutation analysis' versus 'CN_CNMF'

P value = 6.98e-06 (Fisher's exact test), Q value = 0.004

Table S69. Gene #28: 'Del Peak 4(1q43) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 4(1Q43) MUTATED	32	7	5	0
DEL PEAK 4(1Q43) WILD-TYPE	138	180	27	24

Figure S69. Get High-res Image Gene #28: 'Del Peak 4(1q43) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 6(3p26.1) mutation analysis' versus 'CN_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.23

Table S70. Gene #30: 'Del Peak 6(3p26.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 6(3P26.1) MUTATED	36	14	8	2
DEL PEAK 6(3P26.1) WILD-TYPE	134	173	24	22

Figure S70. Get High-res Image Gene #30: 'Del Peak 6(3p26.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 9(4p16.2) mutation analysis' versus 'CN_CNMF'

P value = 1.16e-12 (Fisher's exact test), Q value = 7.4e-10

Table S71. Gene #33: 'Del Peak 9(4p16.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 9(4P16.2) MUTATED	73	23	19	6
DEL PEAK 9(4P16.2) WILD-TYPE	97	164	13	18

Figure S71. Get High-res Image Gene #33: 'Del Peak 9(4p16.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 10(4q22.1) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000453 (Fisher's exact test), Q value = 0.24

Table S72. Gene #34: 'Del Peak 10(4q22.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	32	30	23
DEL PEAK 10(4Q22.1) MUTATED	27	9	2	12
DEL PEAK 10(4Q22.1) WILD-TYPE	36	23	28	11

Figure S72. Get High-res Image Gene #34: 'Del Peak 10(4q22.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 10(4q22.1) mutation analysis' versus 'CN_CNMF'

P value = 8.5e-12 (Fisher's exact test), Q value = 5.4e-09

Table S73. Gene #34: 'Del Peak 10(4q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 10(4Q22.1) MUTATED	77	28	18	3
DEL PEAK 10(4Q22.1) WILD-TYPE	93	159	14	21

Figure S73. Get High-res Image Gene #34: 'Del Peak 10(4q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 11(4q35.1) mutation analysis' versus 'MRNA_CNMF'

P value = 4.76e-05 (Fisher's exact test), Q value = 0.027

Table S74. Gene #35: 'Del Peak 11(4q35.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	32	30	23
DEL PEAK 11(4Q35.1) MUTATED	32	7	3	13
DEL PEAK 11(4Q35.1) WILD-TYPE	31	25	27	10

Figure S74. Get High-res Image Gene #35: 'Del Peak 11(4q35.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 11(4q35.1) mutation analysis' versus 'CN_CNMF'

P value = 1.05e-13 (Fisher's exact test), Q value = 6.8e-11

Table S75. Gene #35: 'Del Peak 11(4q35.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 11(4Q35.1) MUTATED	88	28	16	5
DEL PEAK 11(4Q35.1) WILD-TYPE	82	159	16	19

Figure S75. Get High-res Image Gene #35: 'Del Peak 11(4q35.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 11(4q35.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 7.69e-05 (Fisher's exact test), Q value = 0.043

Table S76. Gene #35: 'Del Peak 11(4q35.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	86	63
DEL PEAK 11(4Q35.1) MUTATED	46	13	20
DEL PEAK 11(4Q35.1) WILD-TYPE	59	73	43

Figure S76. Get High-res Image Gene #35: 'Del Peak 11(4q35.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 12(5q11.2) mutation analysis' versus 'CN_CNMF'

P value = 4.94e-09 (Fisher's exact test), Q value = 3e-06

Table S77. Gene #36: 'Del Peak 12(5q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 12(5Q11.2) MUTATED	60	16	9	6
DEL PEAK 12(5Q11.2) WILD-TYPE	110	171	23	18

Figure S77. Get High-res Image Gene #36: 'Del Peak 12(5q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 13(5q21.3) mutation analysis' versus 'CN_CNMF'

P value = 1.14e-09 (Fisher's exact test), Q value = 7.1e-07

Table S78. Gene #37: 'Del Peak 13(5q21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 13(5Q21.3) MUTATED	71	24	14	8
DEL PEAK 13(5Q21.3) WILD-TYPE	99	163	18	16

Figure S78. Get High-res Image Gene #37: 'Del Peak 13(5q21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 14(5q23.1) mutation analysis' versus 'CN_CNMF'

P value = 1.57e-08 (Fisher's exact test), Q value = 9.4e-06

Table S79. Gene #38: 'Del Peak 14(5q23.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 14(5Q23.1) MUTATED	64	22	13	8
DEL PEAK 14(5Q23.1) WILD-TYPE	106	165	19	16

Figure S79. Get High-res Image Gene #38: 'Del Peak 14(5q23.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 0.000102 (Fisher's exact test), Q value = 0.057

Table S80. Gene #39: 'Del Peak 15(6p25.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 15(6P25.3) MUTATED	13	23	9	9
DEL PEAK 15(6P25.3) WILD-TYPE	157	164	23	15

Figure S80. Get High-res Image Gene #39: 'Del Peak 15(6p25.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 18(8p23.3) mutation analysis' versus 'CN_CNMF'

P value = 6.84e-26 (Fisher's exact test), Q value = 4.6e-23

Table S81. Gene #42: 'Del Peak 18(8p23.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 18(8P23.3) MUTATED	119	32	6	14
DEL PEAK 18(8P23.3) WILD-TYPE	51	155	26	10

Figure S81. Get High-res Image Gene #42: 'Del Peak 18(8p23.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 18(8p23.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.61e-06 (Fisher's exact test), Q value = 0.0021

Table S82. Gene #42: 'Del Peak 18(8p23.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	86	63
DEL PEAK 18(8P23.3) MUTATED	62	21	22
DEL PEAK 18(8P23.3) WILD-TYPE	43	65	41

Figure S82. Get High-res Image Gene #42: 'Del Peak 18(8p23.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 19(8p22) mutation analysis' versus 'CN_CNMF'

P value = 2.41e-30 (Fisher's exact test), Q value = 1.6e-27

Table S83. Gene #43: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 19(8P22) MUTATED	129	33	8	15
DEL PEAK 19(8P22) WILD-TYPE	41	154	24	9

Figure S83. Get High-res Image Gene #43: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 19(8p22) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.46e-07 (Fisher's exact test), Q value = 2e-04

Table S84. Gene #43: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	86	63
DEL PEAK 19(8P22) MUTATED	69	24	24
DEL PEAK 19(8P22) WILD-TYPE	36	62	39

Figure S84. Get High-res Image Gene #43: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 19(8p22) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 0.000139 (Fisher's exact test), Q value = 0.077

Table S85. Gene #43: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	142	23	48	51
DEL PEAK 19(8P22) MUTATED	69	5	12	32
DEL PEAK 19(8P22) WILD-TYPE	73	18	36	19

Figure S85. Get High-res Image Gene #43: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 19(8p22) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000387 (Fisher's exact test), Q value = 0.21

Table S86. Gene #43: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	58	39	20
DEL PEAK 19(8P22) MUTATED	39	14	14	12
DEL PEAK 19(8P22) WILD-TYPE	28	44	25	8

Figure S86. Get High-res Image Gene #43: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 19(8p22) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000323 (Fisher's exact test), Q value = 0.18

Table S87. Gene #43: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	18	102
DEL PEAK 19(8P22) MUTATED	15	9	55
DEL PEAK 19(8P22) WILD-TYPE	49	9	47

Figure S87. Get High-res Image Gene #43: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 20(8p11.22) mutation analysis' versus 'CN_CNMF'

P value = 8.88e-09 (Fisher's exact test), Q value = 5.4e-06

Table S88. Gene #44: 'Del Peak 20(8p11.22) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 20(8P11.22) MUTATED	58	18	3	1
DEL PEAK 20(8P11.22) WILD-TYPE	112	169	29	23

Figure S88. Get High-res Image Gene #44: 'Del Peak 20(8p11.22) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 5.81e-07 (Fisher's exact test), Q value = 0.00034

Table S89. Gene #45: 'Del Peak 21(8p11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 21(8P11.21) MUTATED	35	7	1	0
DEL PEAK 21(8P11.21) WILD-TYPE	135	180	31	24

Figure S89. Get High-res Image Gene #45: 'Del Peak 21(8p11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 22(9p21.3) mutation analysis' versus 'CN_CNMF'

P value = 4.51e-05 (Fisher's exact test), Q value = 0.025

Table S90. Gene #46: 'Del Peak 22(9p21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 22(9P21.3) MUTATED	35	10	7	4
DEL PEAK 22(9P21.3) WILD-TYPE	135	177	25	20

Figure S90. Get High-res Image Gene #46: 'Del Peak 22(9p21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 2.25e-08 (Fisher's exact test), Q value = 1.3e-05

Table S91. Gene #47: 'Del Peak 23(10p15.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 23(10P15.3) MUTATED	38	12	15	3
DEL PEAK 23(10P15.3) WILD-TYPE	132	175	17	21

Figure S91. Get High-res Image Gene #47: 'Del Peak 23(10p15.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 24(10q21.1) mutation analysis' versus 'CN_CNMF'

P value = 2.24e-11 (Fisher's exact test), Q value = 1.4e-08

Table S92. Gene #48: 'Del Peak 24(10q21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 24(10Q21.1) MUTATED	48	12	17	5
DEL PEAK 24(10Q21.1) WILD-TYPE	122	175	15	19

Figure S92. Get High-res Image Gene #48: 'Del Peak 24(10q21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 25(10q23.31) mutation analysis' versus 'CN_CNMF'

P value = 3.46e-07 (Fisher's exact test), Q value = 2e-04

Table S93. Gene #49: 'Del Peak 25(10q23.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 25(10Q23.31) MUTATED	53	21	15	5
DEL PEAK 25(10Q23.31) WILD-TYPE	117	166	17	19

Figure S93. Get High-res Image Gene #49: 'Del Peak 25(10q23.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 26(10q25.2) mutation analysis' versus 'CN_CNMF'

P value = 1.91e-11 (Fisher's exact test), Q value = 1.2e-08

Table S94. Gene #50: 'Del Peak 26(10q25.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 26(10Q25.2) MUTATED	57	16	17	3
DEL PEAK 26(10Q25.2) WILD-TYPE	113	171	15	21

Figure S94. Get High-res Image Gene #50: 'Del Peak 26(10q25.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 27(12p13.2) mutation analysis' versus 'CN_CNMF'

P value = 9.87e-08 (Fisher's exact test), Q value = 5.9e-05

Table S95. Gene #51: 'Del Peak 27(12p13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 27(12P13.2) MUTATED	34	4	5	1
DEL PEAK 27(12P13.2) WILD-TYPE	136	183	27	23

Figure S95. Get High-res Image Gene #51: 'Del Peak 27(12p13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 28(13q14.13) mutation analysis' versus 'CN_CNMF'

P value = 0.000128 (Fisher's exact test), Q value = 0.071

Table S96. Gene #52: 'Del Peak 28(13q14.13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 28(13Q14.13) MUTATED	1	9	6	2
DEL PEAK 28(13Q14.13) WILD-TYPE	169	178	26	22

Figure S96. Get High-res Image Gene #52: 'Del Peak 28(13q14.13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 29(14q32.11) mutation analysis' versus 'MRNA_CNMF'

P value = 1.14e-05 (Fisher's exact test), Q value = 0.0066

Table S97. Gene #53: 'Del Peak 29(14q32.11) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	32	30	23
DEL PEAK 29(14Q32.11) MUTATED	36	7	3	11
DEL PEAK 29(14Q32.11) WILD-TYPE	27	25	27	12

Figure S97. Get High-res Image Gene #53: 'Del Peak 29(14q32.11) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 29(14q32.11) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000242 (Fisher's exact test), Q value = 0.13

Table S98. Gene #53: 'Del Peak 29(14q32.11) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	48	13	43
DEL PEAK 29(14Q32.11) MUTATED	7	19	5	26
DEL PEAK 29(14Q32.11) WILD-TYPE	37	29	8	17

Figure S98. Get High-res Image Gene #53: 'Del Peak 29(14q32.11) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 29(14q32.11) mutation analysis' versus 'CN_CNMF'

P value = 1.61e-20 (Fisher's exact test), Q value = 1.1e-17

Table S99. Gene #53: 'Del Peak 29(14q32.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 29(14Q32.11) MUTATED	98	22	10	3
DEL PEAK 29(14Q32.11) WILD-TYPE	72	165	22	21

Figure S99. Get High-res Image Gene #53: 'Del Peak 29(14q32.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 29(14q32.11) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 7.25e-05 (Fisher's exact test), Q value = 0.041

Table S100. Gene #53: 'Del Peak 29(14q32.11) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	58	39	20
DEL PEAK 29(14Q32.11) MUTATED	38	12	9	9
DEL PEAK 29(14Q32.11) WILD-TYPE	29	46	30	11

Figure S100. Get High-res Image Gene #53: 'Del Peak 29(14q32.11) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 29(14q32.11) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.35e-05 (Fisher's exact test), Q value = 0.025

Table S101. Gene #53: 'Del Peak 29(14q32.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	18	102
DEL PEAK 29(14Q32.11) MUTATED	12	4	52
DEL PEAK 29(14Q32.11) WILD-TYPE	52	14	50

Figure S101. Get High-res Image Gene #53: 'Del Peak 29(14q32.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 30(15q11.2) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000129 (Fisher's exact test), Q value = 0.071

Table S102. Gene #54: 'Del Peak 30(15q11.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	32	30	23
DEL PEAK 30(15Q11.2) MUTATED	37	8	5	12
DEL PEAK 30(15Q11.2) WILD-TYPE	26	24	25	11

Figure S102. Get High-res Image Gene #54: 'Del Peak 30(15q11.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 30(15q11.2) mutation analysis' versus 'CN_CNMF'

P value = 1.2e-21 (Fisher's exact test), Q value = 8e-19

Table S103. Gene #54: 'Del Peak 30(15q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 30(15Q11.2) MUTATED	104	29	22	5
DEL PEAK 30(15Q11.2) WILD-TYPE	66	158	10	19

Figure S103. Get High-res Image Gene #54: 'Del Peak 30(15q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 31(15q21.1) mutation analysis' versus 'CN_CNMF'

P value = 8.15e-18 (Fisher's exact test), Q value = 5.4e-15

Table S104. Gene #55: 'Del Peak 31(15q21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 31(15Q21.1) MUTATED	97	30	20	4
DEL PEAK 31(15Q21.1) WILD-TYPE	73	157	12	20

Figure S104. Get High-res Image Gene #55: 'Del Peak 31(15q21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 32(15q22.33) mutation analysis' versus 'MRNA_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.15

Table S105. Gene #56: 'Del Peak 32(15q22.33) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	32	30	23
DEL PEAK 32(15Q22.33) MUTATED	32	8	3	11
DEL PEAK 32(15Q22.33) WILD-TYPE	31	24	27	12

Figure S105. Get High-res Image Gene #56: 'Del Peak 32(15q22.33) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 32(15q22.33) mutation analysis' versus 'CN_CNMF'

P value = 2.48e-21 (Fisher's exact test), Q value = 1.7e-18

Table S106. Gene #56: 'Del Peak 32(15q22.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 32(15Q22.33) MUTATED	96	23	21	5
DEL PEAK 32(15Q22.33) WILD-TYPE	74	164	11	19

Figure S106. Get High-res Image Gene #56: 'Del Peak 32(15q22.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 32(15q22.33) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000435 (Fisher's exact test), Q value = 0.23

Table S107. Gene #56: 'Del Peak 32(15q22.33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	86	63
DEL PEAK 32(15Q22.33) MUTATED	49	17	22
DEL PEAK 32(15Q22.33) WILD-TYPE	56	69	41

Figure S107. Get High-res Image Gene #56: 'Del Peak 32(15q22.33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 32(15q22.33) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S108. Gene #56: 'Del Peak 32(15q22.33) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	18	102
DEL PEAK 32(15Q22.33) MUTATED	10	9	49
DEL PEAK 32(15Q22.33) WILD-TYPE	54	9	53

Figure S108. Get High-res Image Gene #56: 'Del Peak 32(15q22.33) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 35(17p12) mutation analysis' versus 'MRNA_CNMF'

P value = 9.32e-09 (Fisher's exact test), Q value = 5.6e-06

Table S109. Gene #59: 'Del Peak 35(17p12) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	32	30	23
DEL PEAK 35(17P12) MUTATED	51	10	7	16
DEL PEAK 35(17P12) WILD-TYPE	12	22	23	7

Figure S109. Get High-res Image Gene #59: 'Del Peak 35(17p12) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 35(17p12) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.22e-06 (Fisher's exact test), Q value = 0.00071

Table S110. Gene #59: 'Del Peak 35(17p12) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	48	13	43
DEL PEAK 35(17P12) MUTATED	11	35	6	32
DEL PEAK 35(17P12) WILD-TYPE	33	13	7	11

Figure S110. Get High-res Image Gene #59: 'Del Peak 35(17p12) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 35(17p12) mutation analysis' versus 'CN_CNMF'

P value = 2.81e-35 (Fisher's exact test), Q value = 1.9e-32

Table S111. Gene #59: 'Del Peak 35(17p12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 35(17P12) MUTATED	146	43	24	16
DEL PEAK 35(17P12) WILD-TYPE	24	144	8	8

Figure S111. Get High-res Image Gene #59: 'Del Peak 35(17p12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 35(17p12) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.8e-09 (Fisher's exact test), Q value = 1.1e-06

Table S112. Gene #59: 'Del Peak 35(17p12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	86	63
DEL PEAK 35(17P12) MUTATED	82	30	29
DEL PEAK 35(17P12) WILD-TYPE	23	56	34

Figure S112. Get High-res Image Gene #59: 'Del Peak 35(17p12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 35(17p12) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 4.89e-05 (Fisher's exact test), Q value = 0.027

Table S113. Gene #59: 'Del Peak 35(17p12) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	142	23	48	51
DEL PEAK 35(17P12) MUTATED	85	7	16	37
DEL PEAK 35(17P12) WILD-TYPE	57	16	32	14

Figure S113. Get High-res Image Gene #59: 'Del Peak 35(17p12) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'Del Peak 35(17p12) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.04e-07 (Fisher's exact test), Q value = 6.2e-05

Table S114. Gene #59: 'Del Peak 35(17p12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	58	39	20
DEL PEAK 35(17P12) MUTATED	52	20	16	17
DEL PEAK 35(17P12) WILD-TYPE	15	38	23	3

Figure S114. Get High-res Image Gene #59: 'Del Peak 35(17p12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 35(17p12) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.35e-08 (Fisher's exact test), Q value = 8.2e-06

Table S115. Gene #59: 'Del Peak 35(17p12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	18	102
DEL PEAK 35(17P12) MUTATED	18	11	76
DEL PEAK 35(17P12) WILD-TYPE	46	7	26

Figure S115. Get High-res Image Gene #59: 'Del Peak 35(17p12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 37(18p11.31) mutation analysis' versus 'MRNA_CNMF'

P value = 2.86e-12 (Fisher's exact test), Q value = 1.8e-09

Table S116. Gene #61: 'Del Peak 37(18p11.31) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	32	30	23
DEL PEAK 37(18P11.31) MUTATED	52	6	6	16
DEL PEAK 37(18P11.31) WILD-TYPE	11	26	24	7

Figure S116. Get High-res Image Gene #61: 'Del Peak 37(18p11.31) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 37(18p11.31) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 7.25e-09 (Fisher's exact test), Q value = 4.4e-06

Table S117. Gene #61: 'Del Peak 37(18p11.31) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	48	13	43
DEL PEAK 37(18P11.31) MUTATED	7	32	8	33
DEL PEAK 37(18P11.31) WILD-TYPE	37	16	5	10

Figure S117. Get High-res Image Gene #61: 'Del Peak 37(18p11.31) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 37(18p11.31) mutation analysis' versus 'CN_CNMF'

P value = 1.93e-42 (Fisher's exact test), Q value = 1.3e-39

Table S118. Gene #61: 'Del Peak 37(18p11.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 37(18P11.31) MUTATED	145	34	28	13
DEL PEAK 37(18P11.31) WILD-TYPE	25	153	4	11

Figure S118. Get High-res Image Gene #61: 'Del Peak 37(18p11.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 37(18p11.31) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.11e-13 (Fisher's exact test), Q value = 2e-10

Table S119. Gene #61: 'Del Peak 37(18p11.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	86	63
DEL PEAK 37(18P11.31) MUTATED	83	22	31
DEL PEAK 37(18P11.31) WILD-TYPE	22	64	32

Figure S119. Get High-res Image Gene #61: 'Del Peak 37(18p11.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 37(18p11.31) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.82e-11 (Fisher's exact test), Q value = 1.1e-08

Table S120. Gene #61: 'Del Peak 37(18p11.31) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	58	39	20
DEL PEAK 37(18P11.31) MUTATED	57	15	16	14
DEL PEAK 37(18P11.31) WILD-TYPE	10	43	23	6

Figure S120. Get High-res Image Gene #61: 'Del Peak 37(18p11.31) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 37(18p11.31) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.97e-13 (Fisher's exact test), Q value = 5.1e-10

Table S121. Gene #61: 'Del Peak 37(18p11.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	18	102
DEL PEAK 37(18P11.31) MUTATED	13	10	79
DEL PEAK 37(18P11.31) WILD-TYPE	51	8	23

Figure S121. Get High-res Image Gene #61: 'Del Peak 37(18p11.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 38(18q12.2) mutation analysis' versus 'MRNA_CNMF'

P value = 6.79e-12 (Fisher's exact test), Q value = 4.3e-09

Table S122. Gene #62: 'Del Peak 38(18q12.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	32	30	23
DEL PEAK 38(18Q12.2) MUTATED	55	8	8	17
DEL PEAK 38(18Q12.2) WILD-TYPE	8	24	22	6

Figure S122. Get High-res Image Gene #62: 'Del Peak 38(18q12.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 38(18q12.2) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 3.95e-09 (Fisher's exact test), Q value = 2.4e-06

Table S123. Gene #62: 'Del Peak 38(18q12.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	48	13	43
DEL PEAK 38(18Q12.2) MUTATED	9	35	9	35
DEL PEAK 38(18Q12.2) WILD-TYPE	35	13	4	8

Figure S123. Get High-res Image Gene #62: 'Del Peak 38(18q12.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 38(18q12.2) mutation analysis' versus 'CN_CNMF'

P value = 1.87e-45 (Fisher's exact test), Q value = 1.3e-42

Table S124. Gene #62: 'Del Peak 38(18q12.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 38(18Q12.2) MUTATED	157	44	27	19
DEL PEAK 38(18Q12.2) WILD-TYPE	13	143	5	5

Figure S124. Get High-res Image Gene #62: 'Del Peak 38(18q12.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 38(18q12.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.98e-16 (Fisher's exact test), Q value = 5.9e-13

Table S125. Gene #62: 'Del Peak 38(18q12.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	86	63
DEL PEAK 38(18Q12.2) MUTATED	93	29	31
DEL PEAK 38(18Q12.2) WILD-TYPE	12	57	32

Figure S125. Get High-res Image Gene #62: 'Del Peak 38(18q12.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 38(18q12.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.07e-09 (Fisher's exact test), Q value = 6.6e-07

Table S126. Gene #62: 'Del Peak 38(18q12.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	58	39	20
DEL PEAK 38(18Q12.2) MUTATED	57	18	20	16
DEL PEAK 38(18Q12.2) WILD-TYPE	10	40	19	4

Figure S126. Get High-res Image Gene #62: 'Del Peak 38(18q12.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 38(18q12.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.63e-14 (Fisher's exact test), Q value = 1.7e-11

Table S127. Gene #62: 'Del Peak 38(18q12.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	18	102
DEL PEAK 38(18Q12.2) MUTATED	15	11	85
DEL PEAK 38(18Q12.2) WILD-TYPE	49	7	17

Figure S127. Get High-res Image Gene #62: 'Del Peak 38(18q12.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 39(18q21.2) mutation analysis' versus 'MRNA_CNMF'

P value = 2.46e-11 (Fisher's exact test), Q value = 1.5e-08

Table S128. Gene #63: 'Del Peak 39(18q21.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	32	30	23
DEL PEAK 39(18Q21.2) MUTATED	55	8	9	17
DEL PEAK 39(18Q21.2) WILD-TYPE	8	24	21	6

Figure S128. Get High-res Image Gene #63: 'Del Peak 39(18q21.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 39(18q21.2) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 2.09e-09 (Fisher's exact test), Q value = 1.3e-06

Table S129. Gene #63: 'Del Peak 39(18q21.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	48	13	43
DEL PEAK 39(18Q21.2) MUTATED	9	36	9	35
DEL PEAK 39(18Q21.2) WILD-TYPE	35	12	4	8

Figure S129. Get High-res Image Gene #63: 'Del Peak 39(18q21.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 39(18q21.2) mutation analysis' versus 'CN_CNMF'

P value = 1.51e-45 (Fisher's exact test), Q value = 1e-42

Table S130. Gene #63: 'Del Peak 39(18q21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 39(18Q21.2) MUTATED	161	51	28	20
DEL PEAK 39(18Q21.2) WILD-TYPE	9	136	4	4

Figure S130. Get High-res Image Gene #63: 'Del Peak 39(18q21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 39(18q21.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.29e-12 (Fisher's exact test), Q value = 2.1e-09

Table S131. Gene #63: 'Del Peak 39(18q21.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	86	63
DEL PEAK 39(18Q21.2) MUTATED	94	38	33
DEL PEAK 39(18Q21.2) WILD-TYPE	11	48	30

Figure S131. Get High-res Image Gene #63: 'Del Peak 39(18q21.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 39(18q21.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 5.07e-09 (Fisher's exact test), Q value = 3.1e-06

Table S132. Gene #63: 'Del Peak 39(18q21.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	58	39	20
DEL PEAK 39(18Q21.2) MUTATED	57	19	21	16
DEL PEAK 39(18Q21.2) WILD-TYPE	10	39	18	4

Figure S132. Get High-res Image Gene #63: 'Del Peak 39(18q21.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 39(18q21.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.12e-13 (Fisher's exact test), Q value = 3.9e-10

Table S133. Gene #63: 'Del Peak 39(18q21.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	18	102
DEL PEAK 39(18Q21.2) MUTATED	17	11	85
DEL PEAK 39(18Q21.2) WILD-TYPE	47	7	17

Figure S133. Get High-res Image Gene #63: 'Del Peak 39(18q21.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 40(18q22.1) mutation analysis' versus 'MRNA_CNMF'

P value = 8.41e-11 (Fisher's exact test), Q value = 5.3e-08

Table S134. Gene #64: 'Del Peak 40(18q22.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	32	30	23
DEL PEAK 40(18Q22.1) MUTATED	55	8	10	17
DEL PEAK 40(18Q22.1) WILD-TYPE	8	24	20	6

Figure S134. Get High-res Image Gene #64: 'Del Peak 40(18q22.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 40(18q22.1) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.12e-08 (Fisher's exact test), Q value = 6.7e-06

Table S135. Gene #64: 'Del Peak 40(18q22.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	48	13	43
DEL PEAK 40(18Q22.1) MUTATED	10	36	9	35
DEL PEAK 40(18Q22.1) WILD-TYPE	34	12	4	8

Figure S135. Get High-res Image Gene #64: 'Del Peak 40(18q22.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 40(18q22.1) mutation analysis' versus 'CN_CNMF'

P value = 1.58e-47 (Fisher's exact test), Q value = 1.1e-44

Table S136. Gene #64: 'Del Peak 40(18q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 40(18Q22.1) MUTATED	162	50	29	19
DEL PEAK 40(18Q22.1) WILD-TYPE	8	137	3	5

Figure S136. Get High-res Image Gene #64: 'Del Peak 40(18q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 40(18q22.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.02e-12 (Fisher's exact test), Q value = 1.3e-09

Table S137. Gene #64: 'Del Peak 40(18q22.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	86	63
DEL PEAK 40(18Q22.1) MUTATED	94	38	32
DEL PEAK 40(18Q22.1) WILD-TYPE	11	48	31

Figure S137. Get High-res Image Gene #64: 'Del Peak 40(18q22.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 40(18q22.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.52e-08 (Fisher's exact test), Q value = 9.2e-06

Table S138. Gene #64: 'Del Peak 40(18q22.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	58	39	20
DEL PEAK 40(18Q22.1) MUTATED	57	20	21	16
DEL PEAK 40(18Q22.1) WILD-TYPE	10	38	18	4

Figure S138. Get High-res Image Gene #64: 'Del Peak 40(18q22.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 40(18q22.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.77e-12 (Fisher's exact test), Q value = 4.3e-09

Table S139. Gene #64: 'Del Peak 40(18q22.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	18	102
DEL PEAK 40(18Q22.1) MUTATED	18	12	84
DEL PEAK 40(18Q22.1) WILD-TYPE	46	6	18

Figure S139. Get High-res Image Gene #64: 'Del Peak 40(18q22.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 42(20p12.1) mutation analysis' versus 'CN_CNMF'

P value = 1.38e-13 (Fisher's exact test), Q value = 8.9e-11

Table S140. Gene #66: 'Del Peak 42(20p12.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 42(20P12.1) MUTATED	61	12	0	6
DEL PEAK 42(20P12.1) WILD-TYPE	109	175	32	18

Figure S140. Get High-res Image Gene #66: 'Del Peak 42(20p12.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 43(21q11.2) mutation analysis' versus 'CN_CNMF'

P value = 3.37e-09 (Fisher's exact test), Q value = 2.1e-06

Table S141. Gene #67: 'Del Peak 43(21q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 43(21Q11.2) MUTATED	72	30	18	5
DEL PEAK 43(21Q11.2) WILD-TYPE	98	157	14	19

Figure S141. Get High-res Image Gene #67: 'Del Peak 43(21q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 44(22q13.32) mutation analysis' versus 'CN_CNMF'

P value = 9.76e-13 (Fisher's exact test), Q value = 6.3e-10

Table S142. Gene #68: 'Del Peak 44(22q13.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 44(22Q13.32) MUTATED	85	28	17	8
DEL PEAK 44(22Q13.32) WILD-TYPE	85	159	15	16

Figure S142. Get High-res Image Gene #68: 'Del Peak 44(22q13.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 44(22q13.32) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.99e-05 (Fisher's exact test), Q value = 0.011

Table S143. Gene #68: 'Del Peak 44(22q13.32) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	18	102
DEL PEAK 44(22Q13.32) MUTATED	10	9	50
DEL PEAK 44(22Q13.32) WILD-TYPE	54	9	52

Figure S143. Get High-res Image Gene #68: 'Del Peak 44(22q13.32) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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 = COAD-TP.transferedmergedcluster.txt
Number of patients = 413
Number of copy number variation regions = 68
Number of molecular subtypes = 10
Exclude regions that fewer than K tumors have alterations, K = 3

Fisher's exact test

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

Q value calculation

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

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References

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

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

[3] GISTIC_version2

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