Correlation between copy number variation genes and molecular subtypes

Colon/Rectal 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/C1736P2Q

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 75 peak regions and 10 molecular subtypes across 575 patients, 151 significant findings detected with Q value < 0.25.

Amp Peak 1(1q31.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 2(2q33.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 3(5p12) cnvs correlated to 'CN_CNMF'.
Amp Peak 5(6p21.1) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 6(7p21.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 7(8p11.23) cnvs correlated to 'CN_CNMF'.
Amp Peak 8(8p11.21) cnvs correlated to 'CN_CNMF'.
Amp Peak 9(8q12.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 10(8q24.21) cnvs correlated to 'CN_CNMF'.
Amp Peak 12(11p15.5) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 14(13q12.13) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 15(13q12.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 16(13q22.1) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 18(16p11.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 19(17q12) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 20(17q24.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Amp Peak 21(19p13.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 22(19q12) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 23(20p11.23) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 24(20p11.21) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 25(20q11.21) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 26(20q12) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 27(20q13.32) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 28(Xq28) cnvs correlated to 'CN_CNMF'.
Del Peak 1(1p36.11) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 2(1p33) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 3(1p13.2) cnvs correlated to 'CN_CNMF'.
Del Peak 10(4p16.1) cnvs correlated to 'CN_CNMF'.
Del Peak 11(4q22.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 12(4q35.1) cnvs correlated to 'CN_CNMF'.
Del Peak 13(5q11.2) cnvs correlated to 'CN_CNMF'.
Del Peak 14(5q22.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 18(8p23.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Del Peak 19(8p22) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 20(8p11.21) 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 28(12p13.1) cnvs correlated to 'CN_CNMF'.
Del Peak 29(12q21.2) cnvs correlated to 'CN_CNMF'.
Del Peak 30(14q22.1) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 31(15q11.2) cnvs correlated to 'MRNA_CNMF' and 'CN_CNMF'.
Del Peak 32(15q21.1) cnvs correlated to 'CN_CNMF'.
Del Peak 33(15q22.33) cnvs correlated to 'MRNA_CNMF' and 'CN_CNMF'.
Del Peak 36(17p12) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 38(18p11.31) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 39(18q12.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 40(18q21.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 41(18q22.1) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 42(19p13.3) cnvs correlated to 'CN_CNMF'.
Del Peak 43(19q13.43) cnvs correlated to 'CN_CNMF'.
Del Peak 44(20p12.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 45(20p12.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 46(21q11.2) cnvs correlated to 'CN_CNMF'.
Del Peak 47(22q13.32) cnvs correlated to 'CN_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 75 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 151 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 14(13q12 13)	371 (65%)	204	2.09e-08 (1.39e-05)	5.88e-07 (0.000383)	6.42e-44 (4.79e-41)	8.91e-11 (6.1e-08)	0.0105 (1.00)	0.199 (1.00)	8.72e-11 (5.98e-08)	2.25e-11 (1.55e-08)	0.0136 (1.00)	0.237 (1.00)
Amp Peak 15(13q12 2)	366 (64%)	209	6.51e-07 (0.000423)	3.37e-06 (0.00216)	2.2e-45 (1.65e-42)	2.31e-11 (1.59e-08)	0.0256 (1.00)	0.363 (1.00)	6.49e-10 (4.41e-07)	7.11e-11 (4.87e-08)	0.026 (1.00)	0.285 (1.00)
Amp Peak 16(13q22 1)	371 (65%)	204	5.14e-06 (0.00328)	2.28e-05 (0.0143)	7.69e-42 (5.7e-39)	2.99e-09 (2.02e-06)	0.053 (1.00)	0.162 (1.00)	4.34e-09 (2.91e-06)	6.67e-11 (4.58e-08)	0.0301 (1.00)	0.0471 (1.00)
Amp Peak 24(20p11 21)	339 (59%)	236	0.000167 (0.102)	5.11e-06 (0.00327)	8.57e-23 (6.24e-20)	6.98e-06 (0.00444)	0.0154 (1.00)	0.431 (1.00)	3.23e-05 (0.0201)	7.75e-10 (5.25e-07)	0.107 (1.00)	0.188 (1.00)
Amp Peak 25(20q11 21)	439 (76%)	136	2.57e-15 (1.83e-12)	5.25e-13 (3.67e-10)	1.54e-42 (1.14e-39)	2.13e-16 (1.53e-13)	0.00528 (1.00)	0.0284 (1.00)	4.77e-17 (3.44e-14)	4.38e-22 (3.19e-19)	0.124 (1.00)	0.0189 (1.00)
Amp Peak 26(20q12)	441 (77%)	134	2.04e-16 (1.46e-13)	2.78e-14 (1.96e-11)	5.84e-43 (4.34e-40)	3.56e-15 (2.53e-12)	0.00272 (1.00)	0.0139 (1.00)	2.34e-17 (1.68e-14)	5.06e-23 (3.69e-20)	0.065 (1.00)	0.00779 (1.00)
Amp Peak 27(20q13 32)	444 (77%)	131	1.75e-15 (1.25e-12)	9.91e-13 (6.91e-10)	5.66e-43 (4.22e-40)	3.21e-14 (2.27e-11)	0.00469 (1.00)	0.0132 (1.00)	7.61e-18 (5.5e-15)	4.93e-22 (3.58e-19)	0.117 (1.00)	0.033 (1.00)
Del Peak 30(14q22 1)	185 (32%)	390	9.46e-05 (0.0581)	0.000111 (0.068)	1.95e-28 (1.43e-25)	8.14e-06 (0.00515)	9.08e-05 (0.0558)	0.0787 (1.00)	0.000512 (0.306)	2.49e-07 (0.000163)	0.127 (1.00)	0.439 (1.00)
Del Peak 36(17p12)	343 (60%)	232	2.76e-08 (1.84e-05)	2.3e-05 (0.0144)	2.01e-34 (1.48e-31)	6.04e-09 (4.05e-06)	0.00554 (1.00)	0.00441 (1.00)	1.42e-06 (0.000919)	1.46e-07 (9.55e-05)	0.052 (1.00)	0.673 (1.00)
Del Peak 38(18p11 31)	341 (59%)	234	1.7e-13 (1.19e-10)	4.57e-10 (3.11e-07)	1.19e-41 (8.82e-39)	2.31e-15 (1.65e-12)	0.142 (1.00)	0.0173 (1.00)	2.25e-12 (1.56e-09)	3.68e-14 (2.59e-11)	0.0183 (1.00)	0.386 (1.00)
Del Peak 39(18q12 2)	386 (67%)	189	3.41e-10 (2.32e-07)	1.71e-08 (1.14e-05)	1.29e-49 (9.68e-47)	8.06e-18 (5.82e-15)	0.128 (1.00)	0.0286 (1.00)	4.88e-08 (3.23e-05)	3.42e-12 (2.37e-09)	0.00579 (1.00)	0.059 (1.00)
Del Peak 40(18q21 2)	403 (70%)	172	1.39e-10 (9.49e-08)	2.4e-08 (1.6e-05)	1.24e-50 (9.28e-48)	3.43e-15 (2.44e-12)	0.0282 (1.00)	0.0166 (1.00)	2.97e-08 (1.97e-05)	1.04e-11 (7.15e-09)	0.000657 (0.391)	0.126 (1.00)
Del Peak 41(18q22 1)	398 (69%)	177	7.5e-10 (5.09e-07)	5.1e-07 (0.000333)	9.55e-53 (7.16e-50)	1.37e-15 (9.8e-13)	0.0259 (1.00)	0.0204 (1.00)	2.97e-08 (1.97e-05)	1.02e-10 (6.93e-08)	0.00128 (0.747)	0.171 (1.00)
Del Peak 1(1p36 11)	222 (39%)	353	3.22e-05 (0.0201)	0.00256 (1.00)	2.21e-13 (1.54e-10)	2.1e-05 (0.0132)	0.0259 (1.00)	0.225 (1.00)	7.31e-06 (0.00463)	5.89e-05 (0.0364)	0.158 (1.00)	0.0183 (1.00)
Amp Peak 6(7p21 3)	337 (59%)	238	0.000435 (0.26)	0.00497 (1.00)	7.91e-22 (5.75e-19)	7.11e-06 (0.00451)	0.0223 (1.00)	0.00206 (1.00)	4.45e-06 (0.00285)	6.07e-06 (0.00387)	0.0224 (1.00)	0.00259 (1.00)
Amp Peak 12(11p15 5)	129 (22%)	446	3.6e-05 (0.0224)	0.001 (0.59)	1.84e-06 (0.00118)	0.00344 (1.00)	0.389 (1.00)	0.369 (1.00)	2.07e-05 (0.013)	8.56e-06 (0.00541)	0.352 (1.00)	0.00906 (1.00)
Del Peak 19(8p22)	285 (50%)	290	0.00173 (0.998)	0.0275 (1.00)	1.58e-37 (1.17e-34)	1.32e-06 (0.000854)	0.0122 (1.00)	0.00706 (1.00)	5.25e-05 (0.0326)	0.000243 (0.148)	0.763 (1.00)	0.642 (1.00)
Amp Peak 19(17q12)	144 (25%)	431	0.0109 (1.00)	0.0286 (1.00)	3.46e-09 (2.33e-06)	0.00726 (1.00)	0.25 (1.00)	0.103 (1.00)	6.15e-05 (0.038)	0.000367 (0.221)	0.039 (1.00)	0.232 (1.00)
Amp Peak 20(17q24 1)	128 (22%)	447	0.0116 (1.00)	0.00107 (0.627)	1.54e-08 (1.03e-05)	0.00035 (0.211)	0.0938 (1.00)	0.00763 (1.00)	7.98e-05 (0.0492)	0.00237 (1.00)	0.00127 (0.743)	0.0419 (1.00)
Del Peak 18(8p23 2)	272 (47%)	303	0.000891 (0.526)	0.03 (1.00)	2.13e-34 (1.57e-31)	1.96e-06 (0.00126)	0.0192 (1.00)	0.014 (1.00)	3.94e-05 (0.0245)	0.00124 (0.727)	0.802 (1.00)	0.399 (1.00)
Amp Peak 5(6p21 1)	146 (25%)	429	0.0247 (1.00)	0.00145 (0.842)	3.97e-14 (2.79e-11)	0.169 (1.00)	0.482 (1.00)	0.658 (1.00)	0.00094 (0.555)	0.000303 (0.183)	0.531 (1.00)	0.00678 (1.00)
Amp Peak 18(16p11 2)	161 (28%)	414	0.0166 (1.00)	0.00959 (1.00)	1.33e-20 (9.64e-18)	0.00154 (0.891)	0.0235 (1.00)	0.0164 (1.00)	0.0102 (1.00)	0.00022 (0.134)	0.811 (1.00)	0.11 (1.00)
Amp Peak 22(19q12)	122 (21%)	453	0.0191 (1.00)	0.0218 (1.00)	6.23e-08 (4.11e-05)	0.251 (1.00)	0.0723 (1.00)	0.517 (1.00)	0.0108 (1.00)	0.000285 (0.173)	0.71 (1.00)	0.49 (1.00)
Amp Peak 23(20p11 23)	301 (52%)	274	0.00864 (1.00)	0.000777 (0.461)	5.56e-17 (4e-14)	0.0141 (1.00)	0.0171 (1.00)	0.72 (1.00)	0.0106 (1.00)	1.5e-06 (0.000973)	0.353 (1.00)	0.425 (1.00)
Del Peak 2(1p33)	156 (27%)	419	0.00537 (1.00)	0.0646 (1.00)	8.95e-13 (6.25e-10)	0.000371 (0.223)	0.161 (1.00)	0.53 (1.00)	0.0309 (1.00)	0.0935 (1.00)	0.532 (1.00)	0.0159 (1.00)
Del Peak 11(4q22 1)	198 (34%)	377	0.0186 (1.00)	0.0461 (1.00)	1.25e-14 (8.84e-12)	7.66e-05 (0.0473)	0.354 (1.00)	0.697 (1.00)	0.176 (1.00)	0.00355 (1.00)	0.148 (1.00)	0.409 (1.00)
Del Peak 14(5q22 2)	172 (30%)	403	0.000764 (0.454)	0.0333 (1.00)	2.23e-09 (1.5e-06)	0.114 (1.00)	0.395 (1.00)	0.934 (1.00)	0.00054 (0.322)	0.000238 (0.145)	0.771 (1.00)	0.854 (1.00)
Del Peak 31(15q11 2)	233 (41%)	342	0.000403 (0.242)	0.00282 (1.00)	1.2e-23 (8.82e-21)	0.00572 (1.00)	0.026 (1.00)	0.469 (1.00)	0.0405 (1.00)	0.00984 (1.00)	0.478 (1.00)	0.111 (1.00)
Del Peak 33(15q22 33)	217 (38%)	358	0.000404 (0.242)	0.00175 (1.00)	4.49e-23 (3.28e-20)	0.00084 (0.498)	0.0921 (1.00)	0.497 (1.00)	0.022 (1.00)	0.00184 (1.00)	0.865 (1.00)	0.117 (1.00)
Del Peak 44(20p12 1)	179 (31%)	396	0.0163 (1.00)	0.018 (1.00)	6.5e-15 (4.62e-12)	1.01e-05 (0.00637)	0.87 (1.00)	0.105 (1.00)	0.00454 (1.00)	0.00598 (1.00)	0.223 (1.00)	0.976 (1.00)
Del Peak 45(20p12 1)	179 (31%)	396	0.0163 (1.00)	0.018 (1.00)	6.5e-15 (4.62e-12)	1.01e-05 (0.00637)	0.87 (1.00)	0.105 (1.00)	0.00454 (1.00)	0.00598 (1.00)	0.223 (1.00)	0.976 (1.00)
Amp Peak 1(1q31 1)	134 (23%)	441	0.468 (1.00)	0.56 (1.00)	0.000205 (0.125)	0.722 (1.00)	0.311 (1.00)	0.827 (1.00)	0.0358 (1.00)	0.598 (1.00)	0.765 (1.00)	0.944 (1.00)
Amp Peak 2(2q33 1)	123 (21%)	452	0.0423 (1.00)	0.0188 (1.00)	1.52e-06 (0.000982)	0.00502 (1.00)	0.533 (1.00)	0.298 (1.00)	0.083 (1.00)	0.00518 (1.00)	0.181 (1.00)	0.00129 (0.753)
Amp Peak 3(5p12)	107 (19%)	468	0.109 (1.00)	0.975 (1.00)	6.55e-06 (0.00417)	0.794 (1.00)	0.0423 (1.00)	0.702 (1.00)	0.108 (1.00)	0.0577 (1.00)	0.889 (1.00)	0.347 (1.00)
Amp Peak 7(8p11 23)	196 (34%)	379	0.5 (1.00)	0.339 (1.00)	2.83e-23 (2.07e-20)	0.304 (1.00)	0.981 (1.00)	0.647 (1.00)	0.135 (1.00)	0.36 (1.00)	0.0154 (1.00)	0.0772 (1.00)
Amp Peak 8(8p11 21)	238 (41%)	337	0.255 (1.00)	0.191 (1.00)	3.33e-31 (2.45e-28)	0.237 (1.00)	0.497 (1.00)	0.682 (1.00)	0.0157 (1.00)	0.199 (1.00)	0.0815 (1.00)	0.201 (1.00)
Amp Peak 9(8q12 1)	309 (54%)	266	0.0651 (1.00)	0.0842 (1.00)	1.91e-36 (1.41e-33)	0.0153 (1.00)	0.0252 (1.00)	0.147 (1.00)	0.00115 (0.674)	0.0141 (1.00)	0.102 (1.00)	0.146 (1.00)
Amp Peak 10(8q24 21)	345 (60%)	230	0.211 (1.00)	0.0892 (1.00)	3.18e-35 (2.35e-32)	0.00429 (1.00)	0.0349 (1.00)	0.292 (1.00)	0.00371 (1.00)	0.0416 (1.00)	0.251 (1.00)	0.176 (1.00)
Amp Peak 21(19p13 2)	97 (17%)	478	0.0488 (1.00)	0.612 (1.00)	8.87e-08 (5.85e-05)	0.0317 (1.00)	0.587 (1.00)	0.648 (1.00)	0.0315 (1.00)	0.0102 (1.00)	0.274 (1.00)	0.131 (1.00)
Amp Peak 28(Xq28)	121 (21%)	454	0.526 (1.00)	0.363 (1.00)	1.72e-06 (0.00111)	0.1 (1.00)	0.00337 (1.00)	0.0387 (1.00)	0.241 (1.00)	0.592 (1.00)	0.99 (1.00)	0.783 (1.00)
Del Peak 3(1p13 2)	157 (27%)	418	0.133 (1.00)	0.0908 (1.00)	3.38e-09 (2.28e-06)	0.0153 (1.00)	0.299 (1.00)	0.782 (1.00)	0.0513 (1.00)	0.093 (1.00)	0.756 (1.00)	0.351 (1.00)
Del Peak 10(4p16 1)	182 (32%)	393	0.0324 (1.00)	0.274 (1.00)	1.65e-12 (1.15e-09)	0.00203 (1.00)	0.346 (1.00)	0.722 (1.00)	0.0459 (1.00)	0.0137 (1.00)	0.622 (1.00)	0.117 (1.00)
Del Peak 12(4q35 1)	211 (37%)	364	0.00892 (1.00)	0.177 (1.00)	1.25e-13 (8.75e-11)	0.000642 (0.382)	0.411 (1.00)	0.477 (1.00)	0.0629 (1.00)	0.0142 (1.00)	0.523 (1.00)	0.743 (1.00)
Del Peak 13(5q11 2)	140 (24%)	435	0.00151 (0.875)	0.154 (1.00)	2.13e-12 (1.48e-09)	0.00282 (1.00)	0.111 (1.00)	0.306 (1.00)	0.00226 (1.00)	0.00478 (1.00)	1 (1.00)	0.758 (1.00)
Del Peak 20(8p11 21)	124 (22%)	451	0.013 (1.00)	0.125 (1.00)	4.85e-07 (0.000317)	0.341 (1.00)	0.00557 (1.00)	0.305 (1.00)	0.0251 (1.00)	0.105 (1.00)	0.162 (1.00)	0.4 (1.00)
Del Peak 23(10p15 3)	102 (18%)	473	0.323 (1.00)	0.395 (1.00)	1.38e-07 (9.05e-05)	0.0288 (1.00)	0.08 (1.00)	0.274 (1.00)	0.0757 (1.00)	0.189 (1.00)	0.71 (1.00)	0.302 (1.00)
Del Peak 24(10q21 1)	118 (21%)	457	0.259 (1.00)	0.0703 (1.00)	3.13e-11 (2.16e-08)	0.15 (1.00)	0.0304 (1.00)	0.0559 (1.00)	0.181 (1.00)	0.011 (1.00)	0.691 (1.00)	0.577 (1.00)
Del Peak 25(10q23 31)	145 (25%)	430	0.274 (1.00)	0.245 (1.00)	9.09e-08 (5.98e-05)	0.155 (1.00)	0.127 (1.00)	0.519 (1.00)	0.936 (1.00)	0.033 (1.00)	0.762 (1.00)	0.365 (1.00)
Del Peak 26(10q25 2)	140 (24%)	435	0.382 (1.00)	0.0662 (1.00)	3.06e-12 (2.12e-09)	0.105 (1.00)	0.0108 (1.00)	0.507 (1.00)	0.984 (1.00)	0.00828 (1.00)	0.972 (1.00)	0.779 (1.00)
Del Peak 28(12p13 1)	77 (13%)	498	0.00778 (1.00)	0.019 (1.00)	3.89e-08 (2.58e-05)	0.429 (1.00)	0.921 (1.00)	0.854 (1.00)	0.624 (1.00)	0.00575 (1.00)	0.446 (1.00)	0.919 (1.00)
Del Peak 29(12q21 2)	80 (14%)	495	0.126 (1.00)	0.0201 (1.00)	5.52e-07 (0.00036)	0.348 (1.00)	0.833 (1.00)	0.924 (1.00)	0.689 (1.00)	0.00964 (1.00)	0.521 (1.00)	0.979 (1.00)
Del Peak 32(15q21 1)	227 (39%)	348	0.00161 (0.932)	0.0312 (1.00)	2.43e-21 (1.76e-18)	0.00358 (1.00)	0.0118 (1.00)	0.331 (1.00)	0.116 (1.00)	0.0297 (1.00)	0.742 (1.00)	0.459 (1.00)
Del Peak 42(19p13 3)	92 (16%)	483	0.0923 (1.00)	0.732 (1.00)	1.35e-05 (0.0085)	0.825 (1.00)	0.776 (1.00)	0.461 (1.00)	0.254 (1.00)	0.378 (1.00)	0.579 (1.00)	0.911 (1.00)
Del Peak 43(19q13 43)	68 (12%)	507	0.951 (1.00)	0.414 (1.00)	0.00011 (0.0677)	0.6 (1.00)	0.782 (1.00)	0.915 (1.00)	0.345 (1.00)	0.378 (1.00)	0.255 (1.00)	0.502 (1.00)
Del Peak 46(21q11 2)	195 (34%)	380	0.00121 (0.708)	0.116 (1.00)	4.07e-09 (2.73e-06)	0.0109 (1.00)	0.44 (1.00)	0.364 (1.00)	0.0906 (1.00)	0.0626 (1.00)	0.234 (1.00)	0.0494 (1.00)
Del Peak 47(22q13 32)	204 (35%)	371	0.0215 (1.00)	0.0029 (1.00)	9.83e-15 (6.96e-12)	0.0299 (1.00)	0.397 (1.00)	0.908 (1.00)	0.0827 (1.00)	0.00179 (1.00)	0.696 (1.00)	0.0115 (1.00)
Amp Peak 4(5q22 3)	59 (10%)	516	0.905 (1.00)	0.41 (1.00)	0.0037 (1.00)	0.32 (1.00)	0.351 (1.00)	0.591 (1.00)	0.189 (1.00)	0.0307 (1.00)	0.46 (1.00)	0.894 (1.00)
Amp Peak 11(10q22 3)	35 (6%)	540	0.903 (1.00)	0.224 (1.00)	0.655 (1.00)	0.56 (1.00)	0.634 (1.00)	0.506 (1.00)	0.798 (1.00)	0.18 (1.00)	0.587 (1.00)	0.281 (1.00)
Amp Peak 13(12p13 32)	144 (25%)	431	0.174 (1.00)	0.911 (1.00)	0.252 (1.00)	0.137 (1.00)	0.426 (1.00)	0.997 (1.00)	0.233 (1.00)	0.469 (1.00)	0.676 (1.00)	0.886 (1.00)
Amp Peak 17(15q26 1)	43 (7%)	532	0.858 (1.00)	0.479 (1.00)	0.249 (1.00)	0.842 (1.00)	0.173 (1.00)	0.623 (1.00)	0.849 (1.00)	0.72 (1.00)	0.926 (1.00)	1 (1.00)
Del Peak 4(2p12)	20 (3%)	555	1 (1.00)	0.561 (1.00)	0.00194 (1.00)	0.0111 (1.00)	0.0359 (1.00)	0.975 (1.00)	0.325 (1.00)	0.228 (1.00)	0.0165 (1.00)	0.0215 (1.00)
Del Peak 5(2q22 1)	33 (6%)	542	0.927 (1.00)	0.626 (1.00)	0.146 (1.00)	0.833 (1.00)	0.0164 (1.00)	0.826 (1.00)	0.167 (1.00)	0.167 (1.00)	0.316 (1.00)	0.272 (1.00)
Del Peak 6(2q37 2)	30 (5%)	545	0.924 (1.00)	0.576 (1.00)	0.285 (1.00)	0.833 (1.00)	0.234 (1.00)	0.6 (1.00)	0.666 (1.00)	0.286 (1.00)	0.244 (1.00)	0.364 (1.00)
Del Peak 7(3p26 3)	84 (15%)	491	0.106 (1.00)	0.772 (1.00)	0.163 (1.00)	0.357 (1.00)	0.859 (1.00)	0.518 (1.00)	0.101 (1.00)	0.283 (1.00)	0.277 (1.00)	0.728 (1.00)
Del Peak 8(3p14 2)	104 (18%)	471	0.46 (1.00)	0.88 (1.00)	0.932 (1.00)	0.597 (1.00)	0.341 (1.00)	0.895 (1.00)	0.247 (1.00)	0.0713 (1.00)	0.0595 (1.00)	0.918 (1.00)
Del Peak 9(3q26 31)	56 (10%)	519	0.304 (1.00)	0.837 (1.00)	0.448 (1.00)	0.373 (1.00)	0.163 (1.00)	0.26 (1.00)	0.306 (1.00)	0.88 (1.00)	0.0934 (1.00)	0.123 (1.00)
Del Peak 15(6p25 3)	78 (14%)	497	0.829 (1.00)	0.475 (1.00)	0.0849 (1.00)	0.262 (1.00)	0.184 (1.00)	0.455 (1.00)	0.666 (1.00)	0.196 (1.00)	0.61 (1.00)	0.957 (1.00)
Del Peak 16(6q26)	90 (16%)	485	0.894 (1.00)	0.648 (1.00)	0.0401 (1.00)	0.762 (1.00)	0.0514 (1.00)	0.48 (1.00)	0.312 (1.00)	0.104 (1.00)	0.223 (1.00)	0.507 (1.00)
Del Peak 17(7q31 1)	15 (3%)	560	0.0919 (1.00)	0.502 (1.00)	1 (1.00)	1 (1.00)	0.592 (1.00)	0.411 (1.00)	0.141 (1.00)	0.869 (1.00)	0.235 (1.00)	0.498 (1.00)
Del Peak 21(8q11 1)	44 (8%)	531	0.288 (1.00)	0.923 (1.00)	0.00266 (1.00)	0.661 (1.00)	0.0514 (1.00)	0.494 (1.00)	0.566 (1.00)	0.879 (1.00)	0.0819 (1.00)	0.0193 (1.00)
Del Peak 22(9p24 2)	78 (14%)	497	0.266 (1.00)	0.265 (1.00)	0.00178 (1.00)	0.0506 (1.00)	0.562 (1.00)	0.515 (1.00)	0.147 (1.00)	0.0174 (1.00)	0.296 (1.00)	0.243 (1.00)
Del Peak 27(11q22 3)	104 (18%)	471	0.587 (1.00)	0.895 (1.00)	0.0385 (1.00)	0.125 (1.00)	0.11 (1.00)	0.123 (1.00)	0.144 (1.00)	0.056 (1.00)	0.657 (1.00)	0.363 (1.00)
Del Peak 34(16p13 3)	58 (10%)	517	0.141 (1.00)	0.242 (1.00)	0.215 (1.00)	0.676 (1.00)	0.0654 (1.00)	0.766 (1.00)	0.318 (1.00)	0.369 (1.00)	0.637 (1.00)	0.595 (1.00)
Del Peak 35(16q23 1)	72 (13%)	503	0.0586 (1.00)	0.0022 (1.00)	0.179 (1.00)	0.327 (1.00)	0.287 (1.00)	0.807 (1.00)	0.0074 (1.00)	0.0213 (1.00)	0.805 (1.00)	0.632 (1.00)
Del Peak 37(17q24 3)	84 (15%)	491	0.91 (1.00)	0.722 (1.00)	0.0296 (1.00)	0.528 (1.00)	0.745 (1.00)	0.196 (1.00)	0.663 (1.00)	0.587 (1.00)	0.919 (1.00)	0.425 (1.00)

'Amp Peak 1(1q31.1) mutation analysis' versus 'CN_CNMF'

P value = 0.000205 (Fisher's exact test), Q value = 0.12

Table S1. Gene #1: 'Amp Peak 1(1q31.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 1(1Q31.1) MUTATED	59	34	26	15
AMP PEAK 1(1Q31.1) WILD-TYPE	141	200	74	26

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1q31.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 1.52e-06 (Fisher's exact test), Q value = 0.00098

Table S2. Gene #2: 'Amp Peak 2(2q33.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 2(2Q33.1) MUTATED	59	27	21	16
AMP PEAK 2(2Q33.1) WILD-TYPE	141	207	79	25

Figure S2. Get High-res Image Gene #2: 'Amp Peak 2(2q33.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 3(5p12) mutation analysis' versus 'CN_CNMF'

P value = 6.55e-06 (Fisher's exact test), Q value = 0.0042

Table S3. Gene #3: 'Amp Peak 3(5p12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 3(5P12) MUTATED	51	21	24	11
AMP PEAK 3(5P12) WILD-TYPE	149	213	76	30

Figure S3. Get High-res Image Gene #3: 'Amp Peak 3(5p12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 5(6p21.1) mutation analysis' versus 'CN_CNMF'

P value = 3.97e-14 (Fisher's exact test), Q value = 2.8e-11

Table S4. Gene #5: 'Amp Peak 5(6p21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 5(6P21.1) MUTATED	83	22	27	14
AMP PEAK 5(6P21.1) WILD-TYPE	117	212	73	27

Figure S4. Get High-res Image Gene #5: 'Amp Peak 5(6p21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 5(6p21.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000303 (Fisher's exact test), Q value = 0.18

Table S5. Gene #5: 'Amp Peak 5(6p21.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	154	42
AMP PEAK 5(6P21.1) MUTATED	7	50	4
AMP PEAK 5(6P21.1) WILD-TYPE	52	104	38

Figure S5. Get High-res Image Gene #5: 'Amp Peak 5(6p21.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 6(7p21.3) mutation analysis' versus 'CN_CNMF'

P value = 7.91e-22 (Fisher's exact test), Q value = 5.7e-19

Table S6. Gene #6: 'Amp Peak 6(7p21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 6(7P21.3) MUTATED	157	81	66	33
AMP PEAK 6(7P21.3) WILD-TYPE	43	153	34	8

Figure S6. Get High-res Image Gene #6: 'Amp Peak 6(7p21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 6(7p21.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 7.11e-06 (Fisher's exact test), Q value = 0.0045

Table S7. Gene #6: 'Amp Peak 6(7p21.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
AMP PEAK 6(7P21.3) MUTATED	112	58	51
AMP PEAK 6(7P21.3) WILD-TYPE	31	55	40

Figure S7. Get High-res Image Gene #6: 'Amp Peak 6(7p21.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 6(7p21.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 4.45e-06 (Fisher's exact test), Q value = 0.0029

Table S8. Gene #6: 'Amp Peak 6(7p21.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	94	58	67	36
AMP PEAK 6(7P21.3) MUTATED	66	20	26	24
AMP PEAK 6(7P21.3) WILD-TYPE	28	38	41	12

Figure S8. Get High-res Image Gene #6: 'Amp Peak 6(7p21.3) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 6(7p21.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.07e-06 (Fisher's exact test), Q value = 0.0039

Table S9. Gene #6: 'Amp Peak 6(7p21.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	154	42
AMP PEAK 6(7P21.3) MUTATED	19	101	16
AMP PEAK 6(7P21.3) WILD-TYPE	40	53	26

Figure S9. Get High-res Image Gene #6: 'Amp Peak 6(7p21.3) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 7(8p11.23) mutation analysis' versus 'CN_CNMF'

P value = 2.83e-23 (Fisher's exact test), Q value = 2.1e-20

Table S10. Gene #7: 'Amp Peak 7(8p11.23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 7(8P11.23) MUTATED	56	44	76	20
AMP PEAK 7(8P11.23) WILD-TYPE	144	190	24	21

Figure S10. Get High-res Image Gene #7: 'Amp Peak 7(8p11.23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 3.33e-31 (Fisher's exact test), Q value = 2.5e-28

Table S11. Gene #8: 'Amp Peak 8(8p11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 8(8P11.21) MUTATED	75	51	89	23
AMP PEAK 8(8P11.21) WILD-TYPE	125	183	11	18

Figure S11. Get High-res Image Gene #8: 'Amp Peak 8(8p11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 9(8q12.1) mutation analysis' versus 'CN_CNMF'

P value = 1.91e-36 (Fisher's exact test), Q value = 1.4e-33

Table S12. Gene #9: 'Amp Peak 9(8q12.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 9(8Q12.1) MUTATED	109	69	97	34
AMP PEAK 9(8Q12.1) WILD-TYPE	91	165	3	7

Figure S12. Get High-res Image Gene #9: 'Amp Peak 9(8q12.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 10(8q24.21) mutation analysis' versus 'CN_CNMF'

P value = 3.18e-35 (Fisher's exact test), Q value = 2.3e-32

Table S13. Gene #10: 'Amp Peak 10(8q24.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 10(8Q24.21) MUTATED	129	82	99	35
AMP PEAK 10(8Q24.21) WILD-TYPE	71	152	1	6

Figure S13. Get High-res Image Gene #10: 'Amp Peak 10(8q24.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 12(11p15.5) mutation analysis' versus 'MRNA_CNMF'

P value = 3.6e-05 (Fisher's exact test), Q value = 0.022

Table S14. Gene #12: 'Amp Peak 12(11p15.5) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	45	70	39
AMP PEAK 12(11P15.5) MUTATED	21	3	25	3
AMP PEAK 12(11P15.5) WILD-TYPE	42	42	45	36

Figure S14. Get High-res Image Gene #12: 'Amp Peak 12(11p15.5) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 12(11p15.5) mutation analysis' versus 'CN_CNMF'

P value = 1.84e-06 (Fisher's exact test), Q value = 0.0012

Table S15. Gene #12: 'Amp Peak 12(11p15.5) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 12(11P15.5) MUTATED	58	31	21	19
AMP PEAK 12(11P15.5) WILD-TYPE	142	203	79	22

Figure S15. Get High-res Image Gene #12: 'Amp Peak 12(11p15.5) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 12(11p15.5) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.07e-05 (Fisher's exact test), Q value = 0.013

Table S16. Gene #12: 'Amp Peak 12(11p15.5) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	94	58	67	36
AMP PEAK 12(11P15.5) MUTATED	35	5	9	13
AMP PEAK 12(11P15.5) WILD-TYPE	59	53	58	23

Figure S16. Get High-res Image Gene #12: 'Amp Peak 12(11p15.5) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 12(11p15.5) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.56e-06 (Fisher's exact test), Q value = 0.0054

Table S17. Gene #12: 'Amp Peak 12(11p15.5) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	154	42
AMP PEAK 12(11P15.5) MUTATED	3	52	7
AMP PEAK 12(11P15.5) WILD-TYPE	56	102	35

Figure S17. Get High-res Image Gene #12: 'Amp Peak 12(11p15.5) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 14(13q12.13) mutation analysis' versus 'MRNA_CNMF'

P value = 2.09e-08 (Fisher's exact test), Q value = 1.4e-05

Table S18. Gene #14: 'Amp Peak 14(13q12.13) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	45	70	39
AMP PEAK 14(13Q12.13) MUTATED	50	20	58	14
AMP PEAK 14(13Q12.13) WILD-TYPE	13	25	12	25

Figure S18. Get High-res Image Gene #14: 'Amp Peak 14(13q12.13) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 14(13q12.13) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 5.88e-07 (Fisher's exact test), Q value = 0.00038

Table S19. Gene #14: 'Amp Peak 14(13q12.13) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	61	112
AMP PEAK 14(13Q12.13) MUTATED	38	24	80
AMP PEAK 14(13Q12.13) WILD-TYPE	6	37	32

Figure S19. Get High-res Image Gene #14: 'Amp Peak 14(13q12.13) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 14(13q12.13) mutation analysis' versus 'CN_CNMF'

P value = 6.42e-44 (Fisher's exact test), Q value = 4.8e-41

Table S20. Gene #14: 'Amp Peak 14(13q12.13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 14(13Q12.13) MUTATED	194	86	66	25
AMP PEAK 14(13Q12.13) WILD-TYPE	6	148	34	16

Figure S20. Get High-res Image Gene #14: 'Amp Peak 14(13q12.13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 14(13q12.13) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.91e-11 (Fisher's exact test), Q value = 6.1e-08

Table S21. Gene #14: 'Amp Peak 14(13q12.13) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
AMP PEAK 14(13Q12.13) MUTATED	122	55	50
AMP PEAK 14(13Q12.13) WILD-TYPE	21	58	41

Figure S21. Get High-res Image Gene #14: 'Amp Peak 14(13q12.13) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 14(13q12.13) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 8.72e-11 (Fisher's exact test), Q value = 6e-08

Table S22. Gene #14: 'Amp Peak 14(13q12.13) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	94	58	67	36
AMP PEAK 14(13Q12.13) MUTATED	77	23	27	30
AMP PEAK 14(13Q12.13) WILD-TYPE	17	35	40	6

Figure S22. Get High-res Image Gene #14: 'Amp Peak 14(13q12.13) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 14(13q12.13) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.25e-11 (Fisher's exact test), Q value = 1.6e-08

Table S23. Gene #14: 'Amp Peak 14(13q12.13) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	154	42
AMP PEAK 14(13Q12.13) MUTATED	19	121	17
AMP PEAK 14(13Q12.13) WILD-TYPE	40	33	25

Figure S23. Get High-res Image Gene #14: 'Amp Peak 14(13q12.13) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 15(13q12.2) mutation analysis' versus 'MRNA_CNMF'

P value = 6.51e-07 (Fisher's exact test), Q value = 0.00042

Table S24. Gene #15: 'Amp Peak 15(13q12.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	45	70	39
AMP PEAK 15(13Q12.2) MUTATED	49	20	56	15
AMP PEAK 15(13Q12.2) WILD-TYPE	14	25	14	24

Figure S24. Get High-res Image Gene #15: 'Amp Peak 15(13q12.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 15(13q12.2) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 3.37e-06 (Fisher's exact test), Q value = 0.0022

Table S25. Gene #15: 'Amp Peak 15(13q12.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	61	112
AMP PEAK 15(13Q12.2) MUTATED	38	25	77
AMP PEAK 15(13Q12.2) WILD-TYPE	6	36	35

Figure S25. Get High-res Image Gene #15: 'Amp Peak 15(13q12.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 15(13q12.2) mutation analysis' versus 'CN_CNMF'

P value = 2.2e-45 (Fisher's exact test), Q value = 1.6e-42

Table S26. Gene #15: 'Amp Peak 15(13q12.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 15(13Q12.2) MUTATED	194	83	64	25
AMP PEAK 15(13Q12.2) WILD-TYPE	6	151	36	16

Figure S26. Get High-res Image Gene #15: 'Amp Peak 15(13q12.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 15(13q12.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.31e-11 (Fisher's exact test), Q value = 1.6e-08

Table S27. Gene #15: 'Amp Peak 15(13q12.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
AMP PEAK 15(13Q12.2) MUTATED	122	53	50
AMP PEAK 15(13Q12.2) WILD-TYPE	21	60	41

Figure S27. Get High-res Image Gene #15: 'Amp Peak 15(13q12.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 15(13q12.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 6.49e-10 (Fisher's exact test), Q value = 4.4e-07

Table S28. Gene #15: 'Amp Peak 15(13q12.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	94	58	67	36
AMP PEAK 15(13Q12.2) MUTATED	76	23	27	29
AMP PEAK 15(13Q12.2) WILD-TYPE	18	35	40	7

Figure S28. Get High-res Image Gene #15: 'Amp Peak 15(13q12.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 15(13q12.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.11e-11 (Fisher's exact test), Q value = 4.9e-08

Table S29. Gene #15: 'Amp Peak 15(13q12.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	154	42
AMP PEAK 15(13Q12.2) MUTATED	18	119	18
AMP PEAK 15(13Q12.2) WILD-TYPE	41	35	24

Figure S29. Get High-res Image Gene #15: 'Amp Peak 15(13q12.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 16(13q22.1) mutation analysis' versus 'MRNA_CNMF'

P value = 5.14e-06 (Fisher's exact test), Q value = 0.0033

Table S30. Gene #16: 'Amp Peak 16(13q22.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	45	70	39
AMP PEAK 16(13Q22.1) MUTATED	48	21	55	15
AMP PEAK 16(13Q22.1) WILD-TYPE	15	24	15	24

Figure S30. Get High-res Image Gene #16: 'Amp Peak 16(13q22.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 16(13q22.1) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 2.28e-05 (Fisher's exact test), Q value = 0.014

Table S31. Gene #16: 'Amp Peak 16(13q22.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	61	112
AMP PEAK 16(13Q22.1) MUTATED	36	25	78
AMP PEAK 16(13Q22.1) WILD-TYPE	8	36	34

Figure S31. Get High-res Image Gene #16: 'Amp Peak 16(13q22.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 16(13q22.1) mutation analysis' versus 'CN_CNMF'

P value = 7.69e-42 (Fisher's exact test), Q value = 5.7e-39

Table S32. Gene #16: 'Amp Peak 16(13q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 16(13Q22.1) MUTATED	193	88	66	24
AMP PEAK 16(13Q22.1) WILD-TYPE	7	146	34	17

Figure S32. Get High-res Image Gene #16: 'Amp Peak 16(13q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 16(13q22.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.99e-09 (Fisher's exact test), Q value = 2e-06

Table S33. Gene #16: 'Amp Peak 16(13q22.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
AMP PEAK 16(13Q22.1) MUTATED	121	58	51
AMP PEAK 16(13Q22.1) WILD-TYPE	22	55	40

Figure S33. Get High-res Image Gene #16: 'Amp Peak 16(13q22.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 16(13q22.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 4.34e-09 (Fisher's exact test), Q value = 2.9e-06

Table S34. Gene #16: 'Amp Peak 16(13q22.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	94	58	67	36
AMP PEAK 16(13Q22.1) MUTATED	77	26	26	27
AMP PEAK 16(13Q22.1) WILD-TYPE	17	32	41	9

Figure S34. Get High-res Image Gene #16: 'Amp Peak 16(13q22.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 16(13q22.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.67e-11 (Fisher's exact test), Q value = 4.6e-08

Table S35. Gene #16: 'Amp Peak 16(13q22.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	154	42
AMP PEAK 16(13Q22.1) MUTATED	20	120	16
AMP PEAK 16(13Q22.1) WILD-TYPE	39	34	26

Figure S35. Get High-res Image Gene #16: 'Amp Peak 16(13q22.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 18(16p11.2) mutation analysis' versus 'CN_CNMF'

P value = 1.33e-20 (Fisher's exact test), Q value = 9.6e-18

Table S36. Gene #18: 'Amp Peak 18(16p11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 18(16P11.2) MUTATED	101	22	25	13
AMP PEAK 18(16P11.2) WILD-TYPE	99	212	75	28

Figure S36. Get High-res Image Gene #18: 'Amp Peak 18(16p11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 18(16p11.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.13

Table S37. Gene #18: 'Amp Peak 18(16p11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	154	42
AMP PEAK 18(16P11.2) MUTATED	7	58	8
AMP PEAK 18(16P11.2) WILD-TYPE	52	96	34

Figure S37. Get High-res Image Gene #18: 'Amp Peak 18(16p11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 19(17q12) mutation analysis' versus 'CN_CNMF'

P value = 3.46e-09 (Fisher's exact test), Q value = 2.3e-06

Table S38. Gene #19: 'Amp Peak 19(17q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 19(17Q12) MUTATED	69	27	36	12
AMP PEAK 19(17Q12) WILD-TYPE	131	207	64	29

Figure S38. Get High-res Image Gene #19: 'Amp Peak 19(17q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 19(17q12) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 6.15e-05 (Fisher's exact test), Q value = 0.038

Table S39. Gene #19: 'Amp Peak 19(17q12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	94	58	67	36
AMP PEAK 19(17Q12) MUTATED	35	10	6	13
AMP PEAK 19(17Q12) WILD-TYPE	59	48	61	23

Figure S39. Get High-res Image Gene #19: 'Amp Peak 19(17q12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 19(17q12) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000367 (Fisher's exact test), Q value = 0.22

Table S40. Gene #19: 'Amp Peak 19(17q12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	154	42
AMP PEAK 19(17Q12) MUTATED	7	52	5
AMP PEAK 19(17Q12) WILD-TYPE	52	102	37

Figure S40. Get High-res Image Gene #19: 'Amp Peak 19(17q12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 20(17q24.1) mutation analysis' versus 'CN_CNMF'

P value = 1.54e-08 (Fisher's exact test), Q value = 1e-05

Table S41. Gene #20: 'Amp Peak 20(17q24.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 20(17Q24.1) MUTATED	67	24	29	8
AMP PEAK 20(17Q24.1) WILD-TYPE	133	210	71	33

Figure S41. Get High-res Image Gene #20: 'Amp Peak 20(17q24.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 20(17q24.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.21

Table S42. Gene #20: 'Amp Peak 20(17q24.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
AMP PEAK 20(17Q24.1) MUTATED	47	20	11
AMP PEAK 20(17Q24.1) WILD-TYPE	96	93	80

Figure S42. Get High-res Image Gene #20: 'Amp Peak 20(17q24.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 20(17q24.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 7.98e-05 (Fisher's exact test), Q value = 0.049

Table S43. Gene #20: 'Amp Peak 20(17q24.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	94	58	67	36
AMP PEAK 20(17Q24.1) MUTATED	31	6	6	12
AMP PEAK 20(17Q24.1) WILD-TYPE	63	52	61	24

Figure S43. Get High-res Image Gene #20: 'Amp Peak 20(17q24.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 21(19p13.2) mutation analysis' versus 'CN_CNMF'

P value = 8.87e-08 (Fisher's exact test), Q value = 5.8e-05

Table S44. Gene #21: 'Amp Peak 21(19p13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 21(19P13.2) MUTATED	54	16	17	10
AMP PEAK 21(19P13.2) WILD-TYPE	146	218	83	31

Figure S44. Get High-res Image Gene #21: 'Amp Peak 21(19p13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 22(19q12) mutation analysis' versus 'CN_CNMF'

P value = 6.23e-08 (Fisher's exact test), Q value = 4.1e-05

Table S45. Gene #22: 'Amp Peak 22(19q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 22(19Q12) MUTATED	68	25	19	10
AMP PEAK 22(19Q12) WILD-TYPE	132	209	81	31

Figure S45. Get High-res Image Gene #22: 'Amp Peak 22(19q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 22(19q12) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000285 (Fisher's exact test), Q value = 0.17

Table S46. Gene #22: 'Amp Peak 22(19q12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	154	42
AMP PEAK 22(19Q12) MUTATED	2	38	11
AMP PEAK 22(19Q12) WILD-TYPE	57	116	31

Figure S46. Get High-res Image Gene #22: 'Amp Peak 22(19q12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 5.56e-17 (Fisher's exact test), Q value = 4e-14

Table S47. Gene #23: 'Amp Peak 23(20p11.23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 23(20P11.23) MUTATED	120	85	55	41
AMP PEAK 23(20P11.23) WILD-TYPE	80	149	45	0

Figure S47. Get High-res Image Gene #23: 'Amp Peak 23(20p11.23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 1.5e-06 (Fisher's exact test), Q value = 0.00097

Table S48. Gene #23: 'Amp Peak 23(20p11.23) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	154	42
AMP PEAK 23(20P11.23) MUTATED	13	94	21
AMP PEAK 23(20P11.23) WILD-TYPE	46	60	21

Figure S48. Get High-res Image Gene #23: 'Amp Peak 23(20p11.23) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 24(20p11.21) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000167 (Fisher's exact test), Q value = 0.1

Table S49. Gene #24: 'Amp Peak 24(20p11.21) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	45	70	39
AMP PEAK 24(20P11.21) MUTATED	43	17	50	16
AMP PEAK 24(20P11.21) WILD-TYPE	20	28	20	23

Figure S49. Get High-res Image Gene #24: 'Amp Peak 24(20p11.21) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 24(20p11.21) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 5.11e-06 (Fisher's exact test), Q value = 0.0033

Table S50. Gene #24: 'Amp Peak 24(20p11.21) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	61	112
AMP PEAK 24(20P11.21) MUTATED	34	20	72
AMP PEAK 24(20P11.21) WILD-TYPE	10	41	40

Figure S50. Get High-res Image Gene #24: 'Amp Peak 24(20p11.21) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 24(20p11.21) mutation analysis' versus 'CN_CNMF'

P value = 8.57e-23 (Fisher's exact test), Q value = 6.2e-20

Table S51. Gene #24: 'Amp Peak 24(20p11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 24(20P11.21) MUTATED	150	88	60	41
AMP PEAK 24(20P11.21) WILD-TYPE	50	146	40	0

Figure S51. Get High-res Image Gene #24: 'Amp Peak 24(20p11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 24(20p11.21) mutation analysis' versus 'METHLYATION_CNMF'

P value = 6.98e-06 (Fisher's exact test), Q value = 0.0044

Table S52. Gene #24: 'Amp Peak 24(20p11.21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
AMP PEAK 24(20P11.21) MUTATED	107	55	45
AMP PEAK 24(20P11.21) WILD-TYPE	36	58	46

Figure S52. Get High-res Image Gene #24: 'Amp Peak 24(20p11.21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 24(20p11.21) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.23e-05 (Fisher's exact test), Q value = 0.02

Table S53. Gene #24: 'Amp Peak 24(20p11.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	94	58	67	36
AMP PEAK 24(20P11.21) MUTATED	68	22	29	23
AMP PEAK 24(20P11.21) WILD-TYPE	26	36	38	13

Figure S53. Get High-res Image Gene #24: 'Amp Peak 24(20p11.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 24(20p11.21) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.75e-10 (Fisher's exact test), Q value = 5.2e-07

Table S54. Gene #24: 'Amp Peak 24(20p11.21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	154	42
AMP PEAK 24(20P11.21) MUTATED	13	108	21
AMP PEAK 24(20P11.21) WILD-TYPE	46	46	21

Figure S54. Get High-res Image Gene #24: 'Amp Peak 24(20p11.21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 25(20q11.21) mutation analysis' versus 'MRNA_CNMF'

P value = 2.57e-15 (Fisher's exact test), Q value = 1.8e-12

Table S55. Gene #25: 'Amp Peak 25(20q11.21) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	45	70	39
AMP PEAK 25(20Q11.21) MUTATED	62	19	64	21
AMP PEAK 25(20Q11.21) WILD-TYPE	1	26	6	18

Figure S55. Get High-res Image Gene #25: 'Amp Peak 25(20q11.21) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 25(20q11.21) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 5.25e-13 (Fisher's exact test), Q value = 3.7e-10

Table S56. Gene #25: 'Amp Peak 25(20q11.21) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	61	112
AMP PEAK 25(20Q11.21) MUTATED	41	25	100
AMP PEAK 25(20Q11.21) WILD-TYPE	3	36	12

Figure S56. Get High-res Image Gene #25: 'Amp Peak 25(20q11.21) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 25(20q11.21) mutation analysis' versus 'CN_CNMF'

P value = 1.54e-42 (Fisher's exact test), Q value = 1.1e-39

Table S57. Gene #25: 'Amp Peak 25(20q11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 25(20Q11.21) MUTATED	199	116	83	41
AMP PEAK 25(20Q11.21) WILD-TYPE	1	118	17	0

Figure S57. Get High-res Image Gene #25: 'Amp Peak 25(20q11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 25(20q11.21) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.13e-16 (Fisher's exact test), Q value = 1.5e-13

Table S58. Gene #25: 'Amp Peak 25(20q11.21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
AMP PEAK 25(20Q11.21) MUTATED	139	65	62
AMP PEAK 25(20Q11.21) WILD-TYPE	4	48	29

Figure S58. Get High-res Image Gene #25: 'Amp Peak 25(20q11.21) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 25(20q11.21) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 4.77e-17 (Fisher's exact test), Q value = 3.4e-14

Table S59. Gene #25: 'Amp Peak 25(20q11.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	94	58	67	36
AMP PEAK 25(20Q11.21) MUTATED	91	25	39	34
AMP PEAK 25(20Q11.21) WILD-TYPE	3	33	28	2

Figure S59. Get High-res Image Gene #25: 'Amp Peak 25(20q11.21) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 25(20q11.21) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.38e-22 (Fisher's exact test), Q value = 3.2e-19

Table S60. Gene #25: 'Amp Peak 25(20q11.21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	154	42
AMP PEAK 25(20Q11.21) MUTATED	17	145	27
AMP PEAK 25(20Q11.21) WILD-TYPE	42	9	15

Figure S60. Get High-res Image Gene #25: 'Amp Peak 25(20q11.21) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 26(20q12) mutation analysis' versus 'MRNA_CNMF'

P value = 2.04e-16 (Fisher's exact test), Q value = 1.5e-13

Table S61. Gene #26: 'Amp Peak 26(20q12) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	45	70	39
AMP PEAK 26(20Q12) MUTATED	62	18	64	20
AMP PEAK 26(20Q12) WILD-TYPE	1	27	6	19

Figure S61. Get High-res Image Gene #26: 'Amp Peak 26(20q12) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 26(20q12) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 2.78e-14 (Fisher's exact test), Q value = 2e-11

Table S62. Gene #26: 'Amp Peak 26(20q12) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	61	112
AMP PEAK 26(20Q12) MUTATED	41	23	100
AMP PEAK 26(20Q12) WILD-TYPE	3	38	12

Figure S62. Get High-res Image Gene #26: 'Amp Peak 26(20q12) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 26(20q12) mutation analysis' versus 'CN_CNMF'

P value = 5.84e-43 (Fisher's exact test), Q value = 4.3e-40

Table S63. Gene #26: 'Amp Peak 26(20q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 26(20Q12) MUTATED	199	116	85	41
AMP PEAK 26(20Q12) WILD-TYPE	1	118	15	0

Figure S63. Get High-res Image Gene #26: 'Amp Peak 26(20q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 26(20q12) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.56e-15 (Fisher's exact test), Q value = 2.5e-12

Table S64. Gene #26: 'Amp Peak 26(20q12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
AMP PEAK 26(20Q12) MUTATED	139	68	63
AMP PEAK 26(20Q12) WILD-TYPE	4	45	28

Figure S64. Get High-res Image Gene #26: 'Amp Peak 26(20q12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 26(20q12) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.34e-17 (Fisher's exact test), Q value = 1.7e-14

Table S65. Gene #26: 'Amp Peak 26(20q12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	94	58	67	36
AMP PEAK 26(20Q12) MUTATED	91	25	38	34
AMP PEAK 26(20Q12) WILD-TYPE	3	33	29	2

Figure S65. Get High-res Image Gene #26: 'Amp Peak 26(20q12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 26(20q12) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.06e-23 (Fisher's exact test), Q value = 3.7e-20

Table S66. Gene #26: 'Amp Peak 26(20q12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	154	42
AMP PEAK 26(20Q12) MUTATED	16	145	27
AMP PEAK 26(20Q12) WILD-TYPE	43	9	15

Figure S66. Get High-res Image Gene #26: 'Amp Peak 26(20q12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 27(20q13.32) mutation analysis' versus 'MRNA_CNMF'

P value = 1.75e-15 (Fisher's exact test), Q value = 1.3e-12

Table S67. Gene #27: 'Amp Peak 27(20q13.32) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	45	70	39
AMP PEAK 27(20Q13.32) MUTATED	62	19	65	22
AMP PEAK 27(20Q13.32) WILD-TYPE	1	26	5	17

Figure S67. Get High-res Image Gene #27: 'Amp Peak 27(20q13.32) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Amp Peak 27(20q13.32) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 9.91e-13 (Fisher's exact test), Q value = 6.9e-10

Table S68. Gene #27: 'Amp Peak 27(20q13.32) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	61	112
AMP PEAK 27(20Q13.32) MUTATED	41	26	101
AMP PEAK 27(20Q13.32) WILD-TYPE	3	35	11

Figure S68. Get High-res Image Gene #27: 'Amp Peak 27(20q13.32) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 27(20q13.32) mutation analysis' versus 'CN_CNMF'

P value = 5.66e-43 (Fisher's exact test), Q value = 4.2e-40

Table S69. Gene #27: 'Amp Peak 27(20q13.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 27(20Q13.32) MUTATED	199	117	87	41
AMP PEAK 27(20Q13.32) WILD-TYPE	1	117	13	0

Figure S69. Get High-res Image Gene #27: 'Amp Peak 27(20q13.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Amp Peak 27(20q13.32) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.21e-14 (Fisher's exact test), Q value = 2.3e-11

Table S70. Gene #27: 'Amp Peak 27(20q13.32) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
AMP PEAK 27(20Q13.32) MUTATED	138	68	63
AMP PEAK 27(20Q13.32) WILD-TYPE	5	45	28

Figure S70. Get High-res Image Gene #27: 'Amp Peak 27(20q13.32) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Amp Peak 27(20q13.32) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 7.61e-18 (Fisher's exact test), Q value = 5.5e-15

Table S71. Gene #27: 'Amp Peak 27(20q13.32) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	94	58	67	36
AMP PEAK 27(20Q13.32) MUTATED	92	25	40	34
AMP PEAK 27(20Q13.32) WILD-TYPE	2	33	27	2

Figure S71. Get High-res Image Gene #27: 'Amp Peak 27(20q13.32) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Amp Peak 27(20q13.32) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.93e-22 (Fisher's exact test), Q value = 3.6e-19

Table S72. Gene #27: 'Amp Peak 27(20q13.32) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	154	42
AMP PEAK 27(20Q13.32) MUTATED	18	146	27
AMP PEAK 27(20Q13.32) WILD-TYPE	41	8	15

Figure S72. Get High-res Image Gene #27: 'Amp Peak 27(20q13.32) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 28(Xq28) mutation analysis' versus 'CN_CNMF'

P value = 1.72e-06 (Fisher's exact test), Q value = 0.0011

Table S73. Gene #28: 'Amp Peak 28(Xq28) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
AMP PEAK 28(XQ28) MUTATED	51	25	32	13
AMP PEAK 28(XQ28) WILD-TYPE	149	209	68	28

Figure S73. Get High-res Image Gene #28: 'Amp Peak 28(Xq28) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 3.22e-05 (Fisher's exact test), Q value = 0.02

Table S74. Gene #29: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	45	70	39
DEL PEAK 1(1P36.11) MUTATED	38	15	34	6
DEL PEAK 1(1P36.11) WILD-TYPE	25	30	36	33

Figure S74. Get High-res Image Gene #29: '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 = 2.21e-13 (Fisher's exact test), Q value = 1.5e-10

Table S75. Gene #29: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 1(1P36.11) MUTATED	110	52	34	26
DEL PEAK 1(1P36.11) WILD-TYPE	90	182	66	15

Figure S75. Get High-res Image Gene #29: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 2.1e-05 (Fisher's exact test), Q value = 0.013

Table S76. Gene #29: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
DEL PEAK 1(1P36.11) MUTATED	72	26	29
DEL PEAK 1(1P36.11) WILD-TYPE	71	87	62

Figure S76. Get High-res Image Gene #29: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 7.31e-06 (Fisher's exact test), Q value = 0.0046

Table S77. Gene #29: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	94	58	67	36
DEL PEAK 1(1P36.11) MUTATED	57	19	15	16
DEL PEAK 1(1P36.11) WILD-TYPE	37	39	52	20

Figure S77. Get High-res Image Gene #29: '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 = 5.89e-05 (Fisher's exact test), Q value = 0.036

Table S78. Gene #29: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	154	42
DEL PEAK 1(1P36.11) MUTATED	13	81	13
DEL PEAK 1(1P36.11) WILD-TYPE	46	73	29

Figure S78. Get High-res Image Gene #29: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 8.95e-13 (Fisher's exact test), Q value = 6.2e-10

Table S79. Gene #30: 'Del Peak 2(1p33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 2(1P33) MUTATED	83	37	14	22
DEL PEAK 2(1P33) WILD-TYPE	117	197	86	19

Figure S79. Get High-res Image Gene #30: 'Del Peak 2(1p33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 0.000371 (Fisher's exact test), Q value = 0.22

Table S80. Gene #30: 'Del Peak 2(1p33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
DEL PEAK 2(1P33) MUTATED	53	17	25
DEL PEAK 2(1P33) WILD-TYPE	90	96	66

Figure S80. Get High-res Image Gene #30: 'Del Peak 2(1p33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 3(1p13.2) mutation analysis' versus 'CN_CNMF'

P value = 3.38e-09 (Fisher's exact test), Q value = 2.3e-06

Table S81. Gene #31: 'Del Peak 3(1p13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 3(1P13.2) MUTATED	82	39	18	18
DEL PEAK 3(1P13.2) WILD-TYPE	118	195	82	23

Figure S81. Get High-res Image Gene #31: 'Del Peak 3(1p13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 10(4p16.1) mutation analysis' versus 'CN_CNMF'

P value = 1.65e-12 (Fisher's exact test), Q value = 1.1e-09

Table S82. Gene #38: 'Del Peak 10(4p16.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 10(4P16.1) MUTATED	92	40	26	24
DEL PEAK 10(4P16.1) WILD-TYPE	108	194	74	17

Figure S82. Get High-res Image Gene #38: 'Del Peak 10(4p16.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 1.25e-14 (Fisher's exact test), Q value = 8.8e-12

Table S83. Gene #39: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 11(4Q22.1) MUTATED	101	43	28	26
DEL PEAK 11(4Q22.1) WILD-TYPE	99	191	72	15

Figure S83. Get High-res Image Gene #39: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 7.66e-05 (Fisher's exact test), Q value = 0.047

Table S84. Gene #39: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
DEL PEAK 11(4Q22.1) MUTATED	64	22	34
DEL PEAK 11(4Q22.1) WILD-TYPE	79	91	57

Figure S84. Get High-res Image Gene #39: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 12(4q35.1) mutation analysis' versus 'CN_CNMF'

P value = 1.25e-13 (Fisher's exact test), Q value = 8.7e-11

Table S85. Gene #40: 'Del Peak 12(4q35.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 12(4Q35.1) MUTATED	105	46	35	25
DEL PEAK 12(4Q35.1) WILD-TYPE	95	188	65	16

Figure S85. Get High-res Image Gene #40: 'Del Peak 12(4q35.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 2.13e-12 (Fisher's exact test), Q value = 1.5e-09

Table S86. Gene #41: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 13(5Q11.2) MUTATED	69	23	27	21
DEL PEAK 13(5Q11.2) WILD-TYPE	131	211	73	20

Figure S86. Get High-res Image Gene #41: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 14(5q22.2) mutation analysis' versus 'CN_CNMF'

P value = 2.23e-09 (Fisher's exact test), Q value = 1.5e-06

Table S87. Gene #42: 'Del Peak 14(5q22.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 14(5Q22.2) MUTATED	80	38	32	22
DEL PEAK 14(5Q22.2) WILD-TYPE	120	196	68	19

Figure S87. Get High-res Image Gene #42: 'Del Peak 14(5q22.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 14(5q22.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000238 (Fisher's exact test), Q value = 0.14

Table S88. Gene #42: 'Del Peak 14(5q22.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	154	42
DEL PEAK 14(5Q22.2) MUTATED	9	61	7
DEL PEAK 14(5Q22.2) WILD-TYPE	50	93	35

Figure S88. Get High-res Image Gene #42: 'Del Peak 14(5q22.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 2.13e-34 (Fisher's exact test), Q value = 1.6e-31

Table S89. Gene #46: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 18(8P23.2) MUTATED	135	42	77	18
DEL PEAK 18(8P23.2) WILD-TYPE	65	192	23	23

Figure S89. Get High-res Image Gene #46: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 1.96e-06 (Fisher's exact test), Q value = 0.0013

Table S90. Gene #46: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
DEL PEAK 18(8P23.2) MUTATED	89	35	38
DEL PEAK 18(8P23.2) WILD-TYPE	54	78	53

Figure S90. Get High-res Image Gene #46: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 3.94e-05 (Fisher's exact test), Q value = 0.024

Table S91. Gene #46: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	94	58	67	36
DEL PEAK 18(8P23.2) MUTATED	61	22	20	20
DEL PEAK 18(8P23.2) WILD-TYPE	33	36	47	16

Figure S91. Get High-res Image Gene #46: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 1.58e-37 (Fisher's exact test), Q value = 1.2e-34

Table S92. Gene #47: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 19(8P22) MUTATED	142	44	80	19
DEL PEAK 19(8P22) WILD-TYPE	58	190	20	22

Figure S92. Get High-res Image Gene #47: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 1.32e-06 (Fisher's exact test), Q value = 0.00085

Table S93. Gene #47: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
DEL PEAK 19(8P22) MUTATED	94	39	39
DEL PEAK 19(8P22) WILD-TYPE	49	74	52

Figure S93. Get High-res Image Gene #47: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

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

P value = 5.25e-05 (Fisher's exact test), Q value = 0.033

Table S94. Gene #47: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	94	58	67	36
DEL PEAK 19(8P22) MUTATED	61	20	23	22
DEL PEAK 19(8P22) WILD-TYPE	33	38	44	14

Figure S94. Get High-res Image Gene #47: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

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

P value = 0.000243 (Fisher's exact test), Q value = 0.15

Table S95. Gene #47: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	154	42
DEL PEAK 19(8P22) MUTATED	17	91	18
DEL PEAK 19(8P22) WILD-TYPE	42	63	24

Figure S95. Get High-res Image Gene #47: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 20(8p11.21) mutation analysis' versus 'CN_CNMF'

P value = 4.85e-07 (Fisher's exact test), Q value = 0.00032

Table S96. Gene #48: 'Del Peak 20(8p11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 20(8P11.21) MUTATED	68	28	18	10
DEL PEAK 20(8P11.21) WILD-TYPE	132	206	82	31

Figure S96. Get High-res Image Gene #48: 'Del Peak 20(8p11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 1.38e-07 (Fisher's exact test), Q value = 9.1e-05

Table S97. Gene #51: 'Del Peak 23(10p15.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 23(10P15.3) MUTATED	41	21	21	19
DEL PEAK 23(10P15.3) WILD-TYPE	159	213	79	22

Figure S97. Get High-res Image Gene #51: '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 = 3.13e-11 (Fisher's exact test), Q value = 2.2e-08

Table S98. Gene #52: 'Del Peak 24(10q21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 24(10Q21.1) MUTATED	49	20	27	22
DEL PEAK 24(10Q21.1) WILD-TYPE	151	214	73	19

Figure S98. Get High-res Image Gene #52: '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 = 9.09e-08 (Fisher's exact test), Q value = 6e-05

Table S99. Gene #53: 'Del Peak 25(10q23.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 25(10Q23.31) MUTATED	55	35	32	23
DEL PEAK 25(10Q23.31) WILD-TYPE	145	199	68	18

Figure S99. Get High-res Image Gene #53: '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 = 3.06e-12 (Fisher's exact test), Q value = 2.1e-09

Table S100. Gene #54: 'Del Peak 26(10q25.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 26(10Q25.2) MUTATED	56	30	26	28
DEL PEAK 26(10Q25.2) WILD-TYPE	144	204	74	13

Figure S100. Get High-res Image Gene #54: 'Del Peak 26(10q25.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 28(12p13.1) mutation analysis' versus 'CN_CNMF'

P value = 3.89e-08 (Fisher's exact test), Q value = 2.6e-05

Table S101. Gene #56: 'Del Peak 28(12p13.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 28(12P13.1) MUTATED	44	10	13	10
DEL PEAK 28(12P13.1) WILD-TYPE	156	224	87	31

Figure S101. Get High-res Image Gene #56: 'Del Peak 28(12p13.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 29(12q21.2) mutation analysis' versus 'CN_CNMF'

P value = 5.52e-07 (Fisher's exact test), Q value = 0.00036

Table S102. Gene #57: 'Del Peak 29(12q21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 29(12Q21.2) MUTATED	45	13	12	10
DEL PEAK 29(12Q21.2) WILD-TYPE	155	221	88	31

Figure S102. Get High-res Image Gene #57: 'Del Peak 29(12q21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 30(14q22.1) mutation analysis' versus 'MRNA_CNMF'

P value = 9.46e-05 (Fisher's exact test), Q value = 0.058

Table S103. Gene #58: 'Del Peak 30(14q22.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	45	70	39
DEL PEAK 30(14Q22.1) MUTATED	32	10	30	5
DEL PEAK 30(14Q22.1) WILD-TYPE	31	35	40	34

Figure S103. Get High-res Image Gene #58: 'Del Peak 30(14q22.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 30(14q22.1) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000111 (Fisher's exact test), Q value = 0.068

Table S104. Gene #58: 'Del Peak 30(14q22.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	61	112
DEL PEAK 30(14Q22.1) MUTATED	22	9	46
DEL PEAK 30(14Q22.1) WILD-TYPE	22	52	66

Figure S104. Get High-res Image Gene #58: 'Del Peak 30(14q22.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 30(14q22.1) mutation analysis' versus 'CN_CNMF'

P value = 1.95e-28 (Fisher's exact test), Q value = 1.4e-25

Table S105. Gene #58: 'Del Peak 30(14q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 30(14Q22.1) MUTATED	124	31	17	13
DEL PEAK 30(14Q22.1) WILD-TYPE	76	203	83	28

Figure S105. Get High-res Image Gene #58: 'Del Peak 30(14q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 30(14q22.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.14e-06 (Fisher's exact test), Q value = 0.0052

Table S106. Gene #58: 'Del Peak 30(14q22.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
DEL PEAK 30(14Q22.1) MUTATED	63	19	24
DEL PEAK 30(14Q22.1) WILD-TYPE	80	94	67

Figure S106. Get High-res Image Gene #58: 'Del Peak 30(14q22.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 30(14q22.1) mutation analysis' versus 'RPPA_CNMF'

P value = 9.08e-05 (Fisher's exact test), Q value = 0.056

Table S107. Gene #58: 'Del Peak 30(14q22.1) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	94	158	18	120
DEL PEAK 30(14Q22.1) MUTATED	34	70	3	24
DEL PEAK 30(14Q22.1) WILD-TYPE	60	88	15	96

Figure S107. Get High-res Image Gene #58: 'Del Peak 30(14q22.1) mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'Del Peak 30(14q22.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.49e-07 (Fisher's exact test), Q value = 0.00016

Table S108. Gene #58: 'Del Peak 30(14q22.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	154	42
DEL PEAK 30(14Q22.1) MUTATED	7	71	7
DEL PEAK 30(14Q22.1) WILD-TYPE	52	83	35

Figure S108. Get High-res Image Gene #58: 'Del Peak 30(14q22.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 31(15q11.2) mutation analysis' versus 'MRNA_CNMF'

P value = 0.000403 (Fisher's exact test), Q value = 0.24

Table S109. Gene #59: 'Del Peak 31(15q11.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	45	70	39
DEL PEAK 31(15Q11.2) MUTATED	35	13	36	8
DEL PEAK 31(15Q11.2) WILD-TYPE	28	32	34	31

Figure S109. Get High-res Image Gene #59: 'Del Peak 31(15q11.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 31(15q11.2) mutation analysis' versus 'CN_CNMF'

P value = 1.2e-23 (Fisher's exact test), Q value = 8.8e-21

Table S110. Gene #59: 'Del Peak 31(15q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 31(15Q11.2) MUTATED	122	41	40	30
DEL PEAK 31(15Q11.2) WILD-TYPE	78	193	60	11

Figure S110. Get High-res Image Gene #59: 'Del Peak 31(15q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 32(15q21.1) mutation analysis' versus 'CN_CNMF'

P value = 2.43e-21 (Fisher's exact test), Q value = 1.8e-18

Table S111. Gene #60: 'Del Peak 32(15q21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 32(15Q21.1) MUTATED	117	41	40	29
DEL PEAK 32(15Q21.1) WILD-TYPE	83	193	60	12

Figure S111. Get High-res Image Gene #60: 'Del Peak 32(15q21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 0.000404 (Fisher's exact test), Q value = 0.24

Table S112. Gene #61: 'Del Peak 33(15q22.33) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	45	70	39
DEL PEAK 33(15Q22.33) MUTATED	32	13	34	6
DEL PEAK 33(15Q22.33) WILD-TYPE	31	32	36	33

Figure S112. Get High-res Image Gene #61: 'Del Peak 33(15q22.33) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

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

P value = 4.49e-23 (Fisher's exact test), Q value = 3.3e-20

Table S113. Gene #61: 'Del Peak 33(15q22.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 33(15Q22.33) MUTATED	113	35	40	29
DEL PEAK 33(15Q22.33) WILD-TYPE	87	199	60	12

Figure S113. Get High-res Image Gene #61: 'Del Peak 33(15q22.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 36(17p12) mutation analysis' versus 'MRNA_CNMF'

P value = 2.76e-08 (Fisher's exact test), Q value = 1.8e-05

Table S114. Gene #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	45	70	39
DEL PEAK 36(17P12) MUTATED	52	18	51	13
DEL PEAK 36(17P12) WILD-TYPE	11	27	19	26

Figure S114. Get High-res Image Gene #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 36(17p12) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 2.3e-05 (Fisher's exact test), Q value = 0.014

Table S115. Gene #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	61	112
DEL PEAK 36(17P12) MUTATED	34	23	77
DEL PEAK 36(17P12) WILD-TYPE	10	38	35

Figure S115. Get High-res Image Gene #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 36(17p12) mutation analysis' versus 'CN_CNMF'

P value = 2.01e-34 (Fisher's exact test), Q value = 1.5e-31

Table S116. Gene #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 36(17P12) MUTATED	169	69	75	30
DEL PEAK 36(17P12) WILD-TYPE	31	165	25	11

Figure S116. Get High-res Image Gene #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 36(17p12) mutation analysis' versus 'METHLYATION_CNMF'

P value = 6.04e-09 (Fisher's exact test), Q value = 4e-06

Table S117. Gene #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
DEL PEAK 36(17P12) MUTATED	112	50	44
DEL PEAK 36(17P12) WILD-TYPE	31	63	47

Figure S117. Get High-res Image Gene #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 36(17p12) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.42e-06 (Fisher's exact test), Q value = 0.00092

Table S118. Gene #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	94	58	67	36
DEL PEAK 36(17P12) MUTATED	71	27	28	29
DEL PEAK 36(17P12) WILD-TYPE	23	31	39	7

Figure S118. Get High-res Image Gene #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 36(17p12) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.46e-07 (Fisher's exact test), Q value = 9.5e-05

Table S119. Gene #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	154	42
DEL PEAK 36(17P12) MUTATED	20	114	21
DEL PEAK 36(17P12) WILD-TYPE	39	40	21

Figure S119. Get High-res Image Gene #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 38(18p11.31) mutation analysis' versus 'MRNA_CNMF'

P value = 1.7e-13 (Fisher's exact test), Q value = 1.2e-10

Table S120. Gene #66: 'Del Peak 38(18p11.31) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	45	70	39
DEL PEAK 38(18P11.31) MUTATED	54	12	52	11
DEL PEAK 38(18P11.31) WILD-TYPE	9	33	18	28

Figure S120. Get High-res Image Gene #66: 'Del Peak 38(18p11.31) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 38(18p11.31) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 4.57e-10 (Fisher's exact test), Q value = 3.1e-07

Table S121. Gene #66: 'Del Peak 38(18p11.31) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	61	112
DEL PEAK 38(18P11.31) MUTATED	37	16	76
DEL PEAK 38(18P11.31) WILD-TYPE	7	45	36

Figure S121. Get High-res Image Gene #66: 'Del Peak 38(18p11.31) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 38(18p11.31) mutation analysis' versus 'CN_CNMF'

P value = 1.19e-41 (Fisher's exact test), Q value = 8.8e-39

Table S122. Gene #66: 'Del Peak 38(18p11.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 38(18P11.31) MUTATED	176	65	64	36
DEL PEAK 38(18P11.31) WILD-TYPE	24	169	36	5

Figure S122. Get High-res Image Gene #66: 'Del Peak 38(18p11.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 38(18p11.31) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.31e-15 (Fisher's exact test), Q value = 1.7e-12

Table S123. Gene #66: 'Del Peak 38(18p11.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
DEL PEAK 38(18P11.31) MUTATED	120	40	49
DEL PEAK 38(18P11.31) WILD-TYPE	23	73	42

Figure S123. Get High-res Image Gene #66: 'Del Peak 38(18p11.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 38(18p11.31) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.25e-12 (Fisher's exact test), Q value = 1.6e-09

Table S124. Gene #66: 'Del Peak 38(18p11.31) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	94	58	67	36
DEL PEAK 38(18P11.31) MUTATED	77	19	26	29
DEL PEAK 38(18P11.31) WILD-TYPE	17	39	41	7

Figure S124. Get High-res Image Gene #66: 'Del Peak 38(18p11.31) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 38(18p11.31) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.68e-14 (Fisher's exact test), Q value = 2.6e-11

Table S125. Gene #66: 'Del Peak 38(18p11.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	154	42
DEL PEAK 38(18P11.31) MUTATED	12	119	20
DEL PEAK 38(18P11.31) WILD-TYPE	47	35	22

Figure S125. Get High-res Image Gene #66: 'Del Peak 38(18p11.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 39(18q12.2) mutation analysis' versus 'MRNA_CNMF'

P value = 3.41e-10 (Fisher's exact test), Q value = 2.3e-07

Table S126. Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	45	70	39
DEL PEAK 39(18Q12.2) MUTATED	56	19	56	15
DEL PEAK 39(18Q12.2) WILD-TYPE	7	26	14	24

Figure S126. Get High-res Image Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 39(18q12.2) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.71e-08 (Fisher's exact test), Q value = 1.1e-05

Table S127. Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	61	112
DEL PEAK 39(18Q12.2) MUTATED	39	23	84
DEL PEAK 39(18Q12.2) WILD-TYPE	5	38	28

Figure S127. Get High-res Image Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 39(18q12.2) mutation analysis' versus 'CN_CNMF'

P value = 1.29e-49 (Fisher's exact test), Q value = 9.7e-47

Table S128. Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 39(18Q12.2) MUTATED	187	76	86	37
DEL PEAK 39(18Q12.2) WILD-TYPE	13	158	14	4

Figure S128. Get High-res Image Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 39(18q12.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.06e-18 (Fisher's exact test), Q value = 5.8e-15

Table S129. Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
DEL PEAK 39(18Q12.2) MUTATED	132	51	52
DEL PEAK 39(18Q12.2) WILD-TYPE	11	62	39

Figure S129. Get High-res Image Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 39(18q12.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 4.88e-08 (Fisher's exact test), Q value = 3.2e-05

Table S130. Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	94	58	67	36
DEL PEAK 39(18Q12.2) MUTATED	79	26	35	30
DEL PEAK 39(18Q12.2) WILD-TYPE	15	32	32	6

Figure S130. Get High-res Image Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 39(18q12.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.42e-12 (Fisher's exact test), Q value = 2.4e-09

Table S131. Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	154	42
DEL PEAK 39(18Q12.2) MUTATED	18	127	25
DEL PEAK 39(18Q12.2) WILD-TYPE	41	27	17

Figure S131. Get High-res Image Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 40(18q21.2) mutation analysis' versus 'MRNA_CNMF'

P value = 1.39e-10 (Fisher's exact test), Q value = 9.5e-08

Table S132. Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	45	70	39
DEL PEAK 40(18Q21.2) MUTATED	57	19	57	16
DEL PEAK 40(18Q21.2) WILD-TYPE	6	26	13	23

Figure S132. Get High-res Image Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 40(18q21.2) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 2.4e-08 (Fisher's exact test), Q value = 1.6e-05

Table S133. Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	61	112
DEL PEAK 40(18Q21.2) MUTATED	39	24	86
DEL PEAK 40(18Q21.2) WILD-TYPE	5	37	26

Figure S133. Get High-res Image Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 40(18q21.2) mutation analysis' versus 'CN_CNMF'

P value = 1.24e-50 (Fisher's exact test), Q value = 9.3e-48

Table S134. Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 40(18Q21.2) MUTATED	190	84	91	38
DEL PEAK 40(18Q21.2) WILD-TYPE	10	150	9	3

Figure S134. Get High-res Image Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 40(18q21.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.43e-15 (Fisher's exact test), Q value = 2.4e-12

Table S135. Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
DEL PEAK 40(18Q21.2) MUTATED	134	61	54
DEL PEAK 40(18Q21.2) WILD-TYPE	9	52	37

Figure S135. Get High-res Image Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 40(18q21.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.97e-08 (Fisher's exact test), Q value = 2e-05

Table S136. Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	94	58	67	36
DEL PEAK 40(18Q21.2) MUTATED	81	27	36	30
DEL PEAK 40(18Q21.2) WILD-TYPE	13	31	31	6

Figure S136. Get High-res Image Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 40(18q21.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.04e-11 (Fisher's exact test), Q value = 7.2e-09

Table S137. Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	154	42
DEL PEAK 40(18Q21.2) MUTATED	20	129	25
DEL PEAK 40(18Q21.2) WILD-TYPE	39	25	17

Figure S137. Get High-res Image Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 41(18q22.1) mutation analysis' versus 'MRNA_CNMF'

P value = 7.5e-10 (Fisher's exact test), Q value = 5.1e-07

Table S138. Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	45	70	39
DEL PEAK 41(18Q22.1) MUTATED	57	19	56	17
DEL PEAK 41(18Q22.1) WILD-TYPE	6	26	14	22

Figure S138. Get High-res Image Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'Del Peak 41(18q22.1) mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 5.1e-07 (Fisher's exact test), Q value = 0.00033

Table S139. Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	61	112
DEL PEAK 41(18Q22.1) MUTATED	39	26	84
DEL PEAK 41(18Q22.1) WILD-TYPE	5	35	28

Figure S139. Get High-res Image Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'Del Peak 41(18q22.1) mutation analysis' versus 'CN_CNMF'

P value = 9.55e-53 (Fisher's exact test), Q value = 7.2e-50

Table S140. Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 41(18Q22.1) MUTATED	190	80	89	39
DEL PEAK 41(18Q22.1) WILD-TYPE	10	154	11	2

Figure S140. Get High-res Image Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 41(18q22.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.37e-15 (Fisher's exact test), Q value = 9.8e-13

Table S141. Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
DEL PEAK 41(18Q22.1) MUTATED	133	59	52
DEL PEAK 41(18Q22.1) WILD-TYPE	10	54	39

Figure S141. Get High-res Image Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 41(18q22.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.97e-08 (Fisher's exact test), Q value = 2e-05

Table S142. Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	94	58	67	36
DEL PEAK 41(18Q22.1) MUTATED	81	27	36	30
DEL PEAK 41(18Q22.1) WILD-TYPE	13	31	31	6

Figure S142. Get High-res Image Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'Del Peak 41(18q22.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.02e-10 (Fisher's exact test), Q value = 6.9e-08

Table S143. Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	154	42
DEL PEAK 41(18Q22.1) MUTATED	21	128	25
DEL PEAK 41(18Q22.1) WILD-TYPE	38	26	17

Figure S143. Get High-res Image Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 42(19p13.3) mutation analysis' versus 'CN_CNMF'

P value = 1.35e-05 (Fisher's exact test), Q value = 0.0085

Table S144. Gene #70: 'Del Peak 42(19p13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 42(19P13.3) MUTATED	44	17	21	10
DEL PEAK 42(19P13.3) WILD-TYPE	156	217	79	31

Figure S144. Get High-res Image Gene #70: 'Del Peak 42(19p13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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

P value = 0.00011 (Fisher's exact test), Q value = 0.068

Table S145. Gene #71: 'Del Peak 43(19q13.43) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 43(19Q13.43) MUTATED	28	13	16	11
DEL PEAK 43(19Q13.43) WILD-TYPE	172	221	84	30

Figure S145. Get High-res Image Gene #71: 'Del Peak 43(19q13.43) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 44(20p12.1) mutation analysis' versus 'CN_CNMF'

P value = 6.5e-15 (Fisher's exact test), Q value = 4.6e-12

Table S146. Gene #72: 'Del Peak 44(20p12.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 44(20P12.1) MUTATED	96	46	37	0
DEL PEAK 44(20P12.1) WILD-TYPE	104	188	63	41

Figure S146. Get High-res Image Gene #72: 'Del Peak 44(20p12.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 44(20p12.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.01e-05 (Fisher's exact test), Q value = 0.0064

Table S147. Gene #72: 'Del Peak 44(20p12.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
DEL PEAK 44(20P12.1) MUTATED	63	21	20
DEL PEAK 44(20P12.1) WILD-TYPE	80	92	71

Figure S147. Get High-res Image Gene #72: 'Del Peak 44(20p12.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 45(20p12.1) mutation analysis' versus 'CN_CNMF'

P value = 6.5e-15 (Fisher's exact test), Q value = 4.6e-12

Table S148. Gene #73: 'Del Peak 45(20p12.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 45(20P12.1) MUTATED	96	46	37	0
DEL PEAK 45(20P12.1) WILD-TYPE	104	188	63	41

Figure S148. Get High-res Image Gene #73: 'Del Peak 45(20p12.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 45(20p12.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.01e-05 (Fisher's exact test), Q value = 0.0064

Table S149. Gene #73: 'Del Peak 45(20p12.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	143	113	91
DEL PEAK 45(20P12.1) MUTATED	63	21	20
DEL PEAK 45(20P12.1) WILD-TYPE	80	92	71

Figure S149. Get High-res Image Gene #73: 'Del Peak 45(20p12.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Del Peak 46(21q11.2) mutation analysis' versus 'CN_CNMF'

P value = 4.07e-09 (Fisher's exact test), Q value = 2.7e-06

Table S150. Gene #74: 'Del Peak 46(21q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 46(21Q11.2) MUTATED	95	50	28	22
DEL PEAK 46(21Q11.2) WILD-TYPE	105	184	72	19

Figure S150. Get High-res Image Gene #74: 'Del Peak 46(21q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'Del Peak 47(22q13.32) mutation analysis' versus 'CN_CNMF'

P value = 9.83e-15 (Fisher's exact test), Q value = 7e-12

Table S151. Gene #75: 'Del Peak 47(22q13.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	200	234	100	41
DEL PEAK 47(22Q13.32) MUTATED	108	45	28	23
DEL PEAK 47(22Q13.32) WILD-TYPE	92	189	72	18

Figure S151. Get High-res Image Gene #75: 'Del Peak 47(22q13.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

Methods & Data

Input

Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
Molecular subtype file = COADREAD-TP.transferedmergedcluster.txt
Number of patients = 575
Number of copy number variation regions = 75
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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