Correlation between copy number variation genes and molecular subtypes

Overview

Introduction

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

Summary

Testing the association between copy number variation of 75 peak regions and 6 molecular subtypes across 306 patients, 133 significant findings detected with Q value < 0.25.

Amp Peak 1(1p36.22) cnvs correlated to 'CN_CNMF'.
Amp Peak 2(1q21.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 3(1q42.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.
Amp Peak 4(3q26.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 5(5p15.33) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 6(5p13.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 7(6p21.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 8(6q12) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 9(6q21) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 10(7p22.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 11(7p11.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 12(7q21.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 13(8p23.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 14(8q24.21) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 16(9q34.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 17(10q26.13) cnvs correlated to 'CN_CNMF'.
Amp Peak 18(11p13) cnvs correlated to 'CN_CNMF'.
Amp Peak 19(11q13.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 20(12p12.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 21(12q15) cnvs correlated to 'CN_CNMF'.
Amp Peak 22(13q12.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 23(13q22.1) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 24(15q26.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 25(17q12) cnvs correlated to 'CN_CNMF'.
Amp Peak 26(18q11.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 27(19q12) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 28(20q13.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 29(Xq26.2) cnvs correlated to 'CN_CNMF'.
Del Peak 1(1p36.11) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 2(1p13.2) cnvs correlated to 'CN_CNMF'.
Del Peak 4(2q32.1) cnvs correlated to 'CN_CNMF'.
Del Peak 5(2q37.2) cnvs correlated to 'CN_CNMF'.
Del Peak 6(3p26.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 7(3p14.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 8(3q26.31) cnvs correlated to 'CN_CNMF'.
Del Peak 9(4q22.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 10(4q34.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 11(5q11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 12(6p25.3) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 13(6q26) cnvs correlated to 'CN_CNMF'.
Del Peak 14(7q31.1) cnvs correlated to 'CN_CNMF'.
Del Peak 15(7q36.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 16(8p23.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 17(9p23) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 18(9p21.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 19(9q21.11) cnvs correlated to 'CN_CNMF'.
Del Peak 20(10p14) cnvs correlated to 'CN_CNMF'.
Del Peak 21(10q22.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 22(10q23.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 23(11p15.4) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 24(11q23.2) cnvs correlated to 'CN_CNMF'.
Del Peak 25(12p13.31) cnvs correlated to 'CN_CNMF'.
Del Peak 26(13q14.2) cnvs correlated to 'CN_CNMF'.
Del Peak 27(14q21.1) cnvs correlated to 'CN_CNMF'.
Del Peak 28(14q32.33) cnvs correlated to 'CN_CNMF'.
Del Peak 29(15q11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 30(15q15.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 31(16p13.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 32(16q23.1) cnvs correlated to 'CN_CNMF'.
Del Peak 33(17p12) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 34(17q24.3) cnvs correlated to 'CN_CNMF'.
Del Peak 35(18q21.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 36(18q23) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 37(19p13.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 38(19q13.11) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 39(20p12.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 40(20p12.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 41(21q11.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 42(21q22.13) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 43(22q13.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 44(Xp22.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 45(Xp21.1) cnvs correlated to 'CN_CNMF'.
Del Peak 46(Xq21.33) 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 6 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 133 significant findings detected.


		Molecular subtypes	CN CNMF	METHLYATION CNMF	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
Del Peak 11(5q11 2)	94 (31%)	212	8.3e-27 (3.71e-24)	2.93e-11 (1.19e-08)	0.0452 (1.00)	0.15 (1.00)	2.27e-05 (0.00816)	4.05e-06 (0.00149)
Del Peak 22(10q23 31)	67 (22%)	239	1.17e-18 (5.08e-16)	1.36e-06 (0.000509)	0.00684 (1.00)	0.0899 (1.00)	8.96e-05 (0.0309)	4.69e-05 (0.0166)
Del Peak 37(19p13 3)	91 (30%)	215	2.75e-29 (1.24e-26)	1.98e-12 (8.25e-10)	0.347 (1.00)	0.361 (1.00)	0.000169 (0.0571)	5.79e-09 (2.27e-06)
Amp Peak 3(1q42 3)	95 (31%)	211	6e-18 (2.59e-15)	1.68e-06 (0.000623)	0.755 (1.00)	0.361 (1.00)	9.69e-05 (0.0331)	0.00587 (1.00)
Amp Peak 5(5p15 33)	76 (25%)	230	3.57e-19 (1.56e-16)	1.8e-07 (6.84e-05)	0.51 (1.00)	0.476 (1.00)	0.00824 (1.00)	0.000785 (0.25)
Amp Peak 27(19q12)	82 (27%)	224	7.65e-18 (3.3e-15)	2.2e-08 (8.59e-06)	0.51 (1.00)	0.0604 (1.00)	0.0138 (1.00)	1.13e-05 (0.00412)
Del Peak 9(4q22 1)	120 (39%)	186	1.51e-25 (6.75e-23)	1.3e-07 (4.96e-05)	0.223 (1.00)	0.543 (1.00)	0.00334 (0.993)	0.000205 (0.0684)
Del Peak 10(4q34 3)	111 (36%)	195	9.9e-21 (4.37e-18)	1.78e-06 (0.000659)	0.0305 (1.00)	0.165 (1.00)	0.0138 (1.00)	6.39e-05 (0.0223)
Del Peak 16(8p23 2)	71 (23%)	235	3.78e-18 (1.64e-15)	2.17e-06 (0.000805)	0.51 (1.00)	0.899 (1.00)	0.0474 (1.00)	0.000177 (0.0595)
Del Peak 29(15q11 2)	73 (24%)	233	2.4e-16 (1.02e-13)	2.86e-05 (0.0102)	0.00934 (1.00)	0.011 (1.00)	0.01 (1.00)	0.000107 (0.0362)
Del Peak 30(15q15 1)	75 (25%)	231	3.92e-15 (1.66e-12)	9.19e-05 (0.0315)	0.0452 (1.00)	0.0899 (1.00)	0.0354 (1.00)	5.96e-05 (0.0209)
Del Peak 33(17p12)	103 (34%)	203	8.32e-32 (3.74e-29)	9.36e-08 (3.59e-05)	0.203 (1.00)	0.509 (1.00)	0.00142 (0.442)	2.01e-05 (0.00723)
Del Peak 38(19q13 11)	40 (13%)	266	1.39e-10 (5.61e-08)	0.000142 (0.048)	0.0946 (1.00)	0.23 (1.00)	0.00354 (1.00)	5.22e-05 (0.0184)
Del Peak 43(22q13 31)	91 (30%)	215	1.61e-19 (7.05e-17)	1.05e-06 (0.000396)	1 (1.00)	1 (1.00)	0.00277 (0.829)	0.00019 (0.0637)
Amp Peak 2(1q21 3)	101 (33%)	205	3.9e-22 (1.73e-19)	4.87e-11 (1.98e-08)	0.215 (1.00)	0.0203 (1.00)	0.0008 (0.253)	0.00164 (0.509)
Amp Peak 6(5p13 1)	74 (24%)	232	1.03e-18 (4.47e-16)	9.23e-06 (0.00337)	1 (1.00)	0.561 (1.00)	0.0316 (1.00)	0.00525 (1.00)
Amp Peak 7(6p21 1)	74 (24%)	232	2.54e-17 (1.09e-14)	4.45e-07 (0.000168)	0.332 (1.00)	0.678 (1.00)	0.0368 (1.00)	0.00115 (0.362)
Amp Peak 8(6q12)	56 (18%)	250	2.18e-10 (8.73e-08)	1.77e-05 (0.00642)	0.51 (1.00)	0.899 (1.00)	0.0669 (1.00)	0.0179 (1.00)
Amp Peak 9(6q21)	52 (17%)	254	5.59e-09 (2.2e-06)	0.000295 (0.0972)	0.0883 (1.00)	0.363 (1.00)	0.241 (1.00)	0.0216 (1.00)
Amp Peak 10(7p22 3)	141 (46%)	165	1.63e-22 (7.24e-20)	5.91e-06 (0.00217)	0.763 (1.00)	0.428 (1.00)	0.00811 (1.00)	0.00208 (0.634)
Amp Peak 11(7p11 2)	128 (42%)	178	4.15e-20 (1.83e-17)	0.000402 (0.131)	0.547 (1.00)	0.651 (1.00)	0.00437 (1.00)	0.0208 (1.00)
Amp Peak 14(8q24 21)	186 (61%)	120	5.82e-09 (2.28e-06)	0.000497 (0.161)	0.281 (1.00)	0.464 (1.00)	0.0838 (1.00)	0.0202 (1.00)
Amp Peak 22(13q12 3)	109 (36%)	197	2.59e-12 (1.07e-09)	0.000527 (0.17)	0.223 (1.00)	0.115 (1.00)	0.408 (1.00)	0.151 (1.00)
Amp Peak 23(13q22 1)	118 (39%)	188	2.32e-11 (9.46e-09)	0.0013 (0.407)	0.131 (1.00)	0.652 (1.00)	0.323 (1.00)	0.000777 (0.248)
Amp Peak 24(15q26 1)	65 (21%)	241	5.77e-16 (2.45e-13)	5.42e-05 (0.0191)	1 (1.00)	0.885 (1.00)	0.0241 (1.00)	0.0132 (1.00)
Amp Peak 28(20q13 2)	191 (62%)	115	1.98e-28 (8.85e-26)	4.26e-07 (0.000161)	0.755 (1.00)	0.116 (1.00)	0.0315 (1.00)	0.0239 (1.00)
Del Peak 1(1p36 11)	81 (26%)	225	2.61e-14 (1.09e-11)	0.000391 (0.128)	0.358 (1.00)	0.538 (1.00)	0.0698 (1.00)	0.0118 (1.00)
Del Peak 6(3p26 1)	77 (25%)	229	3.53e-12 (1.46e-09)	0.000596 (0.192)	0.185 (1.00)	0.0899 (1.00)	0.0623 (1.00)	0.00525 (1.00)
Del Peak 7(3p14 2)	97 (32%)	209	4.66e-15 (1.96e-12)	0.000101 (0.0343)	0.488 (1.00)	0.138 (1.00)	0.205 (1.00)	0.0138 (1.00)
Del Peak 12(6p25 3)	66 (22%)	240	7.12e-10 (2.83e-07)	0.0029 (0.865)	0.698 (1.00)	0.424 (1.00)	0.28 (1.00)	0.000293 (0.0967)
Del Peak 15(7q36 3)	55 (18%)	251	3.8e-17 (1.62e-14)	7.87e-06 (0.00288)	0.698 (1.00)	0.499 (1.00)	0.179 (1.00)	0.0017 (0.524)
Del Peak 17(9p23)	110 (36%)	196	1.59e-23 (7.07e-21)	0.000285 (0.0943)	0.124 (1.00)	0.449 (1.00)	0.0331 (1.00)	0.0262 (1.00)
Del Peak 18(9p21 3)	109 (36%)	197	5.65e-23 (2.51e-20)	1.19e-09 (4.69e-07)	0.215 (1.00)	0.839 (1.00)	0.00662 (1.00)	0.00243 (0.739)
Del Peak 21(10q22 3)	46 (15%)	260	4.02e-12 (1.65e-09)	8.92e-05 (0.0309)	0.132 (1.00)	0.15 (1.00)	0.0194 (1.00)	0.00156 (0.485)
Del Peak 23(11p15 4)	56 (18%)	250	1.34e-10 (5.41e-08)	0.000162 (0.0549)	1 (1.00)	1 (1.00)	0.173 (1.00)	0.00269 (0.806)
Del Peak 31(16p13 3)	52 (17%)	254	3.29e-12 (1.36e-09)	0.000676 (0.217)	1 (1.00)	0.641 (1.00)	0.0143 (1.00)	0.181 (1.00)
Del Peak 35(18q21 2)	124 (41%)	182	8.77e-19 (3.83e-16)	8.92e-05 (0.0309)	0.763 (1.00)	0.191 (1.00)	0.112 (1.00)	0.0142 (1.00)
Del Peak 36(18q23)	116 (38%)	190	1.21e-17 (5.2e-15)	1.58e-05 (0.00573)	1 (1.00)	0.917 (1.00)	0.0458 (1.00)	0.00512 (1.00)
Del Peak 39(20p12 1)	50 (16%)	256	1.86e-10 (7.5e-08)	7.73e-05 (0.0269)	1 (1.00)	0.84 (1.00)	0.0244 (1.00)	0.016 (1.00)
Del Peak 40(20p12 1)	50 (16%)	256	1.86e-10 (7.5e-08)	7.73e-05 (0.0269)	1 (1.00)	0.84 (1.00)	0.0244 (1.00)	0.016 (1.00)
Del Peak 41(21q11 2)	97 (32%)	209	2.75e-15 (1.16e-12)	0.00028 (0.0928)	0.51 (1.00)	0.899 (1.00)	0.0115 (1.00)	0.275 (1.00)
Del Peak 42(21q22 13)	102 (33%)	204	6.07e-16 (2.57e-13)	0.000405 (0.131)	0.215 (1.00)	0.58 (1.00)	0.0615 (1.00)	0.143 (1.00)
Del Peak 44(Xp22 2)	52 (17%)	254	2.64e-14 (1.1e-11)	0.000311 (0.102)	0.698 (1.00)	0.732 (1.00)	0.131 (1.00)	0.00839 (1.00)
Amp Peak 1(1p36 22)	34 (11%)	272	5.21e-09 (2.06e-06)	0.00636 (1.00)	0.412 (1.00)	0.557 (1.00)	0.0421 (1.00)	0.181 (1.00)
Amp Peak 4(3q26 2)	91 (30%)	215	6.19e-08 (2.39e-05)	0.00763 (1.00)	0.116 (1.00)	0.142 (1.00)	0.0685 (1.00)	0.378 (1.00)
Amp Peak 12(7q21 2)	124 (41%)	182	3.24e-18 (1.41e-15)	0.00649 (1.00)	0.547 (1.00)	0.433 (1.00)	0.0229 (1.00)	0.0729 (1.00)
Amp Peak 13(8p23 1)	114 (37%)	192	6.18e-05 (0.0216)	0.12 (1.00)	0.364 (1.00)	0.165 (1.00)	0.558 (1.00)	0.623 (1.00)
Amp Peak 16(9q34 3)	67 (22%)	239	1.35e-07 (5.15e-05)	0.0609 (1.00)	0.747 (1.00)	1 (1.00)	0.394 (1.00)	0.313 (1.00)
Amp Peak 17(10q26 13)	55 (18%)	251	2.42e-05 (0.00867)	0.0149 (1.00)	1 (1.00)	1 (1.00)	0.447 (1.00)	0.27 (1.00)
Amp Peak 18(11p13)	48 (16%)	258	0.000705 (0.226)	0.265 (1.00)	0.698 (1.00)	0.293 (1.00)	0.221 (1.00)	0.07 (1.00)
Amp Peak 19(11q13 3)	62 (20%)	244	5.12e-08 (1.98e-05)	0.0899 (1.00)	1 (1.00)	0.264 (1.00)	0.0107 (1.00)	0.05 (1.00)
Amp Peak 20(12p12 1)	76 (25%)	230	1.24e-06 (0.000464)	0.00547 (1.00)	0.412 (1.00)	0.557 (1.00)	0.16 (1.00)	0.799 (1.00)
Amp Peak 21(12q15)	69 (23%)	237	3.03e-05 (0.0108)	0.00484 (1.00)	0.721 (1.00)	1 (1.00)	0.475 (1.00)	0.804 (1.00)
Amp Peak 25(17q12)	83 (27%)	223	3.11e-17 (1.33e-14)	0.00175 (0.538)	0.736 (1.00)	0.162 (1.00)	0.0088 (1.00)	0.00362 (1.00)
Amp Peak 26(18q11 2)	80 (26%)	226	9.1e-09 (3.56e-06)	0.00203 (0.62)	1 (1.00)	0.616 (1.00)	0.338 (1.00)	0.164 (1.00)
Amp Peak 29(Xq26 2)	60 (20%)	246	2.69e-06 (0.000991)	0.385 (1.00)	0.281 (1.00)	0.532 (1.00)	0.0524 (1.00)	0.929 (1.00)
Del Peak 2(1p13 2)	55 (18%)	251	2.42e-12 (1e-09)	0.00674 (1.00)	0.162 (1.00)	0.707 (1.00)	0.0524 (1.00)	0.0308 (1.00)
Del Peak 4(2q32 1)	34 (11%)	272	0.000205 (0.0684)	0.164 (1.00)	0.664 (1.00)	0.73 (1.00)	0.279 (1.00)	0.0614 (1.00)
Del Peak 5(2q37 2)	40 (13%)	266	4.33e-07 (0.000164)	0.00694 (1.00)	0.607 (1.00)	0.643 (1.00)	0.114 (1.00)	0.00889 (1.00)
Del Peak 8(3q26 31)	32 (10%)	274	1.98e-05 (0.00715)	0.00893 (1.00)	0.345 (1.00)	0.356 (1.00)	0.0599 (1.00)	0.00659 (1.00)
Del Peak 13(6q26)	58 (19%)	248	2.71e-07 (0.000103)	0.0185 (1.00)	0.457 (1.00)	0.603 (1.00)	0.223 (1.00)	0.161 (1.00)
Del Peak 14(7q31 1)	41 (13%)	265	3.02e-08 (1.17e-05)	0.00397 (1.00)	0.412 (1.00)	0.557 (1.00)	0.0305 (1.00)	0.0839 (1.00)
Del Peak 19(9q21 11)	68 (22%)	238	1.12e-14 (4.71e-12)	0.00181 (0.554)	0.698 (1.00)	0.641 (1.00)	0.0817 (1.00)	0.00248 (0.749)
Del Peak 20(10p14)	39 (13%)	267	6.64e-08 (2.56e-05)	0.00375 (1.00)	0.721 (1.00)	0.885 (1.00)	0.0167 (1.00)	0.0459 (1.00)
Del Peak 24(11q23 2)	55 (18%)	251	1.18e-06 (0.000444)	0.000872 (0.276)	1 (1.00)	0.215 (1.00)	0.0607 (1.00)	0.221 (1.00)
Del Peak 25(12p13 31)	46 (15%)	260	2.28e-11 (9.35e-09)	0.00244 (0.739)	1 (1.00)	1 (1.00)	0.0802 (1.00)	0.335 (1.00)
Del Peak 26(13q14 2)	40 (13%)	266	3.12e-05 (0.0111)	0.0194 (1.00)	0.412 (1.00)	0.557 (1.00)	0.404 (1.00)	0.879 (1.00)
Del Peak 27(14q21 1)	67 (22%)	239	1.06e-09 (4.2e-07)	0.0412 (1.00)	0.132 (1.00)	0.674 (1.00)	0.0343 (1.00)	0.0177 (1.00)
Del Peak 28(14q32 33)	81 (26%)	225	2.7e-10 (1.08e-07)	0.037 (1.00)	0.0883 (1.00)	0.458 (1.00)	0.251 (1.00)	0.174 (1.00)
Del Peak 32(16q23 1)	104 (34%)	202	1.13e-10 (4.57e-08)	0.0266 (1.00)	0.543 (1.00)	0.915 (1.00)	0.665 (1.00)	0.182 (1.00)
Del Peak 34(17q24 3)	50 (16%)	256	9.38e-12 (3.85e-09)	0.0225 (1.00)	0.0883 (1.00)	0.0551 (1.00)	0.0145 (1.00)	0.00115 (0.362)
Del Peak 45(Xp21 1)	45 (15%)	261	1.54e-13 (6.43e-11)	0.00459 (1.00)	0.281 (1.00)	0.283 (1.00)	0.0208 (1.00)	0.0762 (1.00)
Del Peak 46(Xq21 33)	38 (12%)	268	8.31e-08 (3.2e-05)	0.00261 (0.784)	0.457 (1.00)	0.674 (1.00)	0.0496 (1.00)	0.0108 (1.00)
Amp Peak 15(9p24 1)	45 (15%)	261	0.0752 (1.00)	0.107 (1.00)	0.698 (1.00)	0.159 (1.00)	0.701 (1.00)	0.353 (1.00)
Del Peak 3(1q44)	21 (7%)	285	0.0073 (1.00)	0.0121 (1.00)	0.412 (1.00)	0.84 (1.00)	0.209 (1.00)	0.0617 (1.00)

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

P value = 5.21e-09 (Fisher's exact test), Q value = 2.1e-06

Table S1. Gene #1: 'Amp Peak 1(1p36.22) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
AMP PEAK 1(1P36.22) MUTATED	2	28	4
AMP PEAK 1(1P36.22) WILD-TYPE	151	90	31

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1p36.22) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 3.9e-22 (Fisher's exact test), Q value = 1.7e-19

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
AMP PEAK 2(1Q21.3) MUTATED	12	72	17
AMP PEAK 2(1Q21.3) WILD-TYPE	141	46	18

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

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

P value = 4.87e-11 (Fisher's exact test), Q value = 2e-08

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
AMP PEAK 2(1Q21.3) MUTATED	2	23	11	48
AMP PEAK 2(1Q21.3) WILD-TYPE	35	56	53	30

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

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

P value = 6e-18 (Fisher's exact test), Q value = 2.6e-15

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
AMP PEAK 3(1Q42.3) MUTATED	13	62	20
AMP PEAK 3(1Q42.3) WILD-TYPE	140	56	15

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

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

P value = 1.68e-06 (Fisher's exact test), Q value = 0.00062

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
AMP PEAK 3(1Q42.3) MUTATED	3	21	14	41
AMP PEAK 3(1Q42.3) WILD-TYPE	34	58	50	37

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

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

P value = 9.69e-05 (Fisher's exact test), Q value = 0.033

Table S6. Gene #3: 'Amp Peak 3(1q42.3) mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	55	92
AMP PEAK 3(1Q42.3) MUTATED	19	10	43
AMP PEAK 3(1Q42.3) WILD-TYPE	70	45	49

Figure S6. Get High-res Image Gene #3: 'Amp Peak 3(1q42.3) mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

'Amp Peak 4(3q26.2) mutation analysis' versus 'CN_CNMF'

P value = 6.19e-08 (Fisher's exact test), Q value = 2.4e-05

Table S7. Gene #4: 'Amp Peak 4(3q26.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
AMP PEAK 4(3Q26.2) MUTATED	23	52	16
AMP PEAK 4(3Q26.2) WILD-TYPE	130	66	19

Figure S7. Get High-res Image Gene #4: 'Amp Peak 4(3q26.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 3.57e-19 (Fisher's exact test), Q value = 1.6e-16

Table S8. Gene #5: 'Amp Peak 5(5p15.33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
AMP PEAK 5(5P15.33) MUTATED	8	62	6
AMP PEAK 5(5P15.33) WILD-TYPE	145	56	29

Figure S8. Get High-res Image Gene #5: 'Amp Peak 5(5p15.33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 1.8e-07 (Fisher's exact test), Q value = 6.8e-05

Table S9. Gene #5: 'Amp Peak 5(5p15.33) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
AMP PEAK 5(5P15.33) MUTATED	6	12	7	38
AMP PEAK 5(5P15.33) WILD-TYPE	31	67	57	40

Figure S9. Get High-res Image Gene #5: 'Amp Peak 5(5p15.33) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

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

P value = 0.000785 (Fisher's exact test), Q value = 0.25

Table S10. Gene #5: 'Amp Peak 5(5p15.33) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	104	73
AMP PEAK 5(5P15.33) MUTATED	26	20	13
AMP PEAK 5(5P15.33) WILD-TYPE	33	84	60

Figure S10. Get High-res Image Gene #5: 'Amp Peak 5(5p15.33) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 6(5p13.1) mutation analysis' versus 'CN_CNMF'

P value = 1.03e-18 (Fisher's exact test), Q value = 4.5e-16

Table S11. Gene #6: 'Amp Peak 6(5p13.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
AMP PEAK 6(5P13.1) MUTATED	7	60	7
AMP PEAK 6(5P13.1) WILD-TYPE	146	58	28

Figure S11. Get High-res Image Gene #6: 'Amp Peak 6(5p13.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 6(5p13.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 9.23e-06 (Fisher's exact test), Q value = 0.0034

Table S12. Gene #6: 'Amp Peak 6(5p13.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
AMP PEAK 6(5P13.1) MUTATED	6	12	7	34
AMP PEAK 6(5P13.1) WILD-TYPE	31	67	57	44

Figure S12. Get High-res Image Gene #6: 'Amp Peak 6(5p13.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 7(6p21.1) mutation analysis' versus 'CN_CNMF'

P value = 2.54e-17 (Fisher's exact test), Q value = 1.1e-14

Table S13. Gene #7: 'Amp Peak 7(6p21.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
AMP PEAK 7(6P21.1) MUTATED	7	57	10
AMP PEAK 7(6P21.1) WILD-TYPE	146	61	25

Figure S13. Get High-res Image Gene #7: 'Amp Peak 7(6p21.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 7(6p21.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.45e-07 (Fisher's exact test), Q value = 0.00017

Table S14. Gene #7: 'Amp Peak 7(6p21.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
AMP PEAK 7(6P21.1) MUTATED	2	18	5	33
AMP PEAK 7(6P21.1) WILD-TYPE	35	61	59	45

Figure S14. Get High-res Image Gene #7: 'Amp Peak 7(6p21.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 8(6q12) mutation analysis' versus 'CN_CNMF'

P value = 2.18e-10 (Fisher's exact test), Q value = 8.7e-08

Table S15. Gene #8: 'Amp Peak 8(6q12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
AMP PEAK 8(6Q12) MUTATED	7	41	8
AMP PEAK 8(6Q12) WILD-TYPE	146	77	27

Figure S15. Get High-res Image Gene #8: 'Amp Peak 8(6q12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 8(6q12) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.77e-05 (Fisher's exact test), Q value = 0.0064

Table S16. Gene #8: 'Amp Peak 8(6q12) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
AMP PEAK 8(6Q12) MUTATED	2	14	2	24
AMP PEAK 8(6Q12) WILD-TYPE	35	65	62	54

Figure S16. Get High-res Image Gene #8: 'Amp Peak 8(6q12) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 9(6q21) mutation analysis' versus 'CN_CNMF'

P value = 5.59e-09 (Fisher's exact test), Q value = 2.2e-06

Table S17. Gene #9: 'Amp Peak 9(6q21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
AMP PEAK 9(6Q21) MUTATED	8	39	5
AMP PEAK 9(6Q21) WILD-TYPE	145	79	30

Figure S17. Get High-res Image Gene #9: 'Amp Peak 9(6q21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 9(6q21) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000295 (Fisher's exact test), Q value = 0.097

Table S18. Gene #9: 'Amp Peak 9(6q21) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
AMP PEAK 9(6Q21) MUTATED	1	12	4	22
AMP PEAK 9(6Q21) WILD-TYPE	36	67	60	56

Figure S18. Get High-res Image Gene #9: 'Amp Peak 9(6q21) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 10(7p22.3) mutation analysis' versus 'CN_CNMF'

P value = 1.63e-22 (Fisher's exact test), Q value = 7.2e-20

Table S19. Gene #10: 'Amp Peak 10(7p22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
AMP PEAK 10(7P22.3) MUTATED	29	82	30
AMP PEAK 10(7P22.3) WILD-TYPE	124	36	5

Figure S19. Get High-res Image Gene #10: 'Amp Peak 10(7p22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 10(7p22.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.91e-06 (Fisher's exact test), Q value = 0.0022

Table S20. Gene #10: 'Amp Peak 10(7p22.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
AMP PEAK 10(7P22.3) MUTATED	14	37	14	50
AMP PEAK 10(7P22.3) WILD-TYPE	23	42	50	28

Figure S20. Get High-res Image Gene #10: 'Amp Peak 10(7p22.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 11(7p11.2) mutation analysis' versus 'CN_CNMF'

P value = 4.15e-20 (Fisher's exact test), Q value = 1.8e-17

Table S21. Gene #11: 'Amp Peak 11(7p11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
AMP PEAK 11(7P11.2) MUTATED	27	70	31
AMP PEAK 11(7P11.2) WILD-TYPE	126	48	4

Figure S21. Get High-res Image Gene #11: 'Amp Peak 11(7p11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 11(7p11.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000402 (Fisher's exact test), Q value = 0.13

Table S22. Gene #11: 'Amp Peak 11(7p11.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
AMP PEAK 11(7P11.2) MUTATED	14	36	13	42
AMP PEAK 11(7P11.2) WILD-TYPE	23	43	51	36

Figure S22. Get High-res Image Gene #11: 'Amp Peak 11(7p11.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 12(7q21.2) mutation analysis' versus 'CN_CNMF'

P value = 3.24e-18 (Fisher's exact test), Q value = 1.4e-15

Table S23. Gene #12: 'Amp Peak 12(7q21.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
AMP PEAK 12(7Q21.2) MUTATED	28	65	31
AMP PEAK 12(7Q21.2) WILD-TYPE	125	53	4

Figure S23. Get High-res Image Gene #12: 'Amp Peak 12(7q21.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 13(8p23.1) mutation analysis' versus 'CN_CNMF'

P value = 6.18e-05 (Fisher's exact test), Q value = 0.022

Table S24. Gene #13: 'Amp Peak 13(8p23.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
AMP PEAK 13(8P23.1) MUTATED	58	32	24
AMP PEAK 13(8P23.1) WILD-TYPE	95	86	11

Figure S24. Get High-res Image Gene #13: 'Amp Peak 13(8p23.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 5.82e-09 (Fisher's exact test), Q value = 2.3e-06

Table S25. Gene #14: 'Amp Peak 14(8q24.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
AMP PEAK 14(8Q24.21) MUTATED	67	91	28
AMP PEAK 14(8Q24.21) WILD-TYPE	86	27	7

Figure S25. Get High-res Image Gene #14: 'Amp Peak 14(8q24.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 0.000497 (Fisher's exact test), Q value = 0.16

Table S26. Gene #14: 'Amp Peak 14(8q24.21) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
AMP PEAK 14(8Q24.21) MUTATED	15	47	29	58
AMP PEAK 14(8Q24.21) WILD-TYPE	22	32	35	20

Figure S26. Get High-res Image Gene #14: 'Amp Peak 14(8q24.21) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 16(9q34.3) mutation analysis' versus 'CN_CNMF'

P value = 1.35e-07 (Fisher's exact test), Q value = 5.2e-05

Table S27. Gene #16: 'Amp Peak 16(9q34.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
AMP PEAK 16(9Q34.3) MUTATED	14	43	10
AMP PEAK 16(9Q34.3) WILD-TYPE	139	75	25

Figure S27. Get High-res Image Gene #16: 'Amp Peak 16(9q34.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 17(10q26.13) mutation analysis' versus 'CN_CNMF'

P value = 2.42e-05 (Fisher's exact test), Q value = 0.0087

Table S28. Gene #17: 'Amp Peak 17(10q26.13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
AMP PEAK 17(10Q26.13) MUTATED	13	35	7
AMP PEAK 17(10Q26.13) WILD-TYPE	140	83	28

Figure S28. Get High-res Image Gene #17: 'Amp Peak 17(10q26.13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 18(11p13) mutation analysis' versus 'CN_CNMF'

P value = 0.000705 (Fisher's exact test), Q value = 0.23

Table S29. Gene #18: 'Amp Peak 18(11p13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
AMP PEAK 18(11P13) MUTATED	13	30	5
AMP PEAK 18(11P13) WILD-TYPE	140	88	30

Figure S29. Get High-res Image Gene #18: 'Amp Peak 18(11p13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 5.12e-08 (Fisher's exact test), Q value = 2e-05

Table S30. Gene #19: 'Amp Peak 19(11q13.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
AMP PEAK 19(11Q13.3) MUTATED	12	42	8
AMP PEAK 19(11Q13.3) WILD-TYPE	141	76	27

Figure S30. Get High-res Image Gene #19: 'Amp Peak 19(11q13.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 20(12p12.1) mutation analysis' versus 'CN_CNMF'

P value = 1.24e-06 (Fisher's exact test), Q value = 0.00046

Table S31. Gene #20: 'Amp Peak 20(12p12.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
AMP PEAK 20(12P12.1) MUTATED	19	46	11
AMP PEAK 20(12P12.1) WILD-TYPE	134	72	24

Figure S31. Get High-res Image Gene #20: 'Amp Peak 20(12p12.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 3.03e-05 (Fisher's exact test), Q value = 0.011

Table S32. Gene #21: 'Amp Peak 21(12q15) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
AMP PEAK 21(12Q15) MUTATED	19	42	8
AMP PEAK 21(12Q15) WILD-TYPE	134	76	27

Figure S32. Get High-res Image Gene #21: 'Amp Peak 21(12q15) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 22(13q12.3) mutation analysis' versus 'CN_CNMF'

P value = 2.59e-12 (Fisher's exact test), Q value = 1.1e-09

Table S33. Gene #22: 'Amp Peak 22(13q12.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
AMP PEAK 22(13Q12.3) MUTATED	25	62	22
AMP PEAK 22(13Q12.3) WILD-TYPE	128	56	13

Figure S33. Get High-res Image Gene #22: 'Amp Peak 22(13q12.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 22(13q12.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000527 (Fisher's exact test), Q value = 0.17

Table S34. Gene #22: 'Amp Peak 22(13q12.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
AMP PEAK 22(13Q12.3) MUTATED	8	22	18	42
AMP PEAK 22(13Q12.3) WILD-TYPE	29	57	46	36

Figure S34. Get High-res Image Gene #22: 'Amp Peak 22(13q12.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 23(13q22.1) mutation analysis' versus 'CN_CNMF'

P value = 2.32e-11 (Fisher's exact test), Q value = 9.5e-09

Table S35. Gene #23: 'Amp Peak 23(13q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
AMP PEAK 23(13Q22.1) MUTATED	30	66	22
AMP PEAK 23(13Q22.1) WILD-TYPE	123	52	13

Figure S35. Get High-res Image Gene #23: 'Amp Peak 23(13q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 23(13q22.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000777 (Fisher's exact test), Q value = 0.25

Table S36. Gene #23: 'Amp Peak 23(13q22.1) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	104	73
AMP PEAK 23(13Q22.1) MUTATED	34	29	25
AMP PEAK 23(13Q22.1) WILD-TYPE	25	75	48

Figure S36. Get High-res Image Gene #23: 'Amp Peak 23(13q22.1) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 24(15q26.1) mutation analysis' versus 'CN_CNMF'

P value = 5.77e-16 (Fisher's exact test), Q value = 2.5e-13

Table S37. Gene #24: 'Amp Peak 24(15q26.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
AMP PEAK 24(15Q26.1) MUTATED	8	54	3
AMP PEAK 24(15Q26.1) WILD-TYPE	145	64	32

Figure S37. Get High-res Image Gene #24: 'Amp Peak 24(15q26.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 24(15q26.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.42e-05 (Fisher's exact test), Q value = 0.019

Table S38. Gene #24: 'Amp Peak 24(15q26.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
AMP PEAK 24(15Q26.1) MUTATED	1	16	9	29
AMP PEAK 24(15Q26.1) WILD-TYPE	36	63	55	49

Figure S38. Get High-res Image Gene #24: 'Amp Peak 24(15q26.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

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

P value = 3.11e-17 (Fisher's exact test), Q value = 1.3e-14

Table S39. Gene #25: 'Amp Peak 25(17q12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
AMP PEAK 25(17Q12) MUTATED	12	64	7
AMP PEAK 25(17Q12) WILD-TYPE	141	54	28

Figure S39. Get High-res Image Gene #25: 'Amp Peak 25(17q12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 9.1e-09 (Fisher's exact test), Q value = 3.6e-06

Table S40. Gene #26: 'Amp Peak 26(18q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
AMP PEAK 26(18Q11.2) MUTATED	19	53	8
AMP PEAK 26(18Q11.2) WILD-TYPE	134	65	27

Figure S40. Get High-res Image Gene #26: 'Amp Peak 26(18q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 7.65e-18 (Fisher's exact test), Q value = 3.3e-15

Table S41. Gene #27: 'Amp Peak 27(19q12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
AMP PEAK 27(19Q12) MUTATED	11	64	7
AMP PEAK 27(19Q12) WILD-TYPE	142	54	28

Figure S41. Get High-res Image Gene #27: 'Amp Peak 27(19q12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 2.2e-08 (Fisher's exact test), Q value = 8.6e-06

Table S42. Gene #27: 'Amp Peak 27(19q12) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
AMP PEAK 27(19Q12) MUTATED	7	12	9	42
AMP PEAK 27(19Q12) WILD-TYPE	30	67	55	36

Figure S42. Get High-res Image Gene #27: 'Amp Peak 27(19q12) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

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

P value = 1.13e-05 (Fisher's exact test), Q value = 0.0041

Table S43. Gene #27: 'Amp Peak 27(19q12) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	104	73
AMP PEAK 27(19Q12) MUTATED	29	21	10
AMP PEAK 27(19Q12) WILD-TYPE	30	83	63

Figure S43. Get High-res Image Gene #27: 'Amp Peak 27(19q12) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 28(20q13.2) mutation analysis' versus 'CN_CNMF'

P value = 1.98e-28 (Fisher's exact test), Q value = 8.8e-26

Table S44. Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
AMP PEAK 28(20Q13.2) MUTATED	50	108	33
AMP PEAK 28(20Q13.2) WILD-TYPE	103	10	2

Figure S44. Get High-res Image Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 28(20q13.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.26e-07 (Fisher's exact test), Q value = 0.00016

Table S45. Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
AMP PEAK 28(20Q13.2) MUTATED	25	42	27	66
AMP PEAK 28(20Q13.2) WILD-TYPE	12	37	37	12

Figure S45. Get High-res Image Gene #28: 'Amp Peak 28(20q13.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 29(Xq26.2) mutation analysis' versus 'CN_CNMF'

P value = 2.69e-06 (Fisher's exact test), Q value = 0.00099

Table S46. Gene #29: 'Amp Peak 29(Xq26.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
AMP PEAK 29(XQ26.2) MUTATED	13	36	11
AMP PEAK 29(XQ26.2) WILD-TYPE	140	82	24

Figure S46. Get High-res Image Gene #29: 'Amp Peak 29(Xq26.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 2.61e-14 (Fisher's exact test), Q value = 1.1e-11

Table S47. Gene #30: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 1(1P36.11) MUTATED	12	58	11
DEL PEAK 1(1P36.11) WILD-TYPE	141	60	24

Figure S47. Get High-res Image Gene #30: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 0.000391 (Fisher's exact test), Q value = 0.13

Table S48. Gene #30: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 1(1P36.11) MUTATED	2	20	11	30
DEL PEAK 1(1P36.11) WILD-TYPE	35	59	53	48

Figure S48. Get High-res Image Gene #30: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

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

P value = 2.42e-12 (Fisher's exact test), Q value = 1e-09

Table S49. Gene #31: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 2(1P13.2) MUTATED	6	44	5
DEL PEAK 2(1P13.2) WILD-TYPE	147	74	30

Figure S49. Get High-res Image Gene #31: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 4(2q32.1) mutation analysis' versus 'CN_CNMF'

P value = 0.000205 (Fisher's exact test), Q value = 0.068

Table S50. Gene #33: 'Del Peak 4(2q32.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 4(2Q32.1) MUTATED	7	24	3
DEL PEAK 4(2Q32.1) WILD-TYPE	146	94	32

Figure S50. Get High-res Image Gene #33: 'Del Peak 4(2q32.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 4.33e-07 (Fisher's exact test), Q value = 0.00016

Table S51. Gene #34: 'Del Peak 5(2q37.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 5(2Q37.2) MUTATED	5	27	8
DEL PEAK 5(2Q37.2) WILD-TYPE	148	91	27

Figure S51. Get High-res Image Gene #34: 'Del Peak 5(2q37.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 3.53e-12 (Fisher's exact test), Q value = 1.5e-09

Table S52. Gene #35: 'Del Peak 6(3p26.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 6(3P26.1) MUTATED	12	50	15
DEL PEAK 6(3P26.1) WILD-TYPE	141	68	20

Figure S52. Get High-res Image Gene #35: 'Del Peak 6(3p26.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 0.000596 (Fisher's exact test), Q value = 0.19

Table S53. Gene #35: 'Del Peak 6(3p26.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 6(3P26.1) MUTATED	7	20	6	30
DEL PEAK 6(3P26.1) WILD-TYPE	30	59	58	48

Figure S53. Get High-res Image Gene #35: 'Del Peak 6(3p26.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

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

P value = 4.66e-15 (Fisher's exact test), Q value = 2e-12

Table S54. Gene #36: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 7(3P14.2) MUTATED	17	65	15
DEL PEAK 7(3P14.2) WILD-TYPE	136	53	20

Figure S54. Get High-res Image Gene #36: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 0.000101 (Fisher's exact test), Q value = 0.034

Table S55. Gene #36: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 7(3P14.2) MUTATED	13	26	8	37
DEL PEAK 7(3P14.2) WILD-TYPE	24	53	56	41

Figure S55. Get High-res Image Gene #36: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 8(3q26.31) mutation analysis' versus 'CN_CNMF'

P value = 1.98e-05 (Fisher's exact test), Q value = 0.0072

Table S56. Gene #37: 'Del Peak 8(3q26.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 8(3Q26.31) MUTATED	5	24	3
DEL PEAK 8(3Q26.31) WILD-TYPE	148	94	32

Figure S56. Get High-res Image Gene #37: 'Del Peak 8(3q26.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 9(4q22.1) mutation analysis' versus 'CN_CNMF'

P value = 1.51e-25 (Fisher's exact test), Q value = 6.7e-23

Table S57. Gene #38: 'Del Peak 9(4q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 9(4Q22.1) MUTATED	17	84	19
DEL PEAK 9(4Q22.1) WILD-TYPE	136	34	16

Figure S57. Get High-res Image Gene #38: 'Del Peak 9(4q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 9(4q22.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.3e-07 (Fisher's exact test), Q value = 5e-05

Table S58. Gene #38: 'Del Peak 9(4q22.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 9(4Q22.1) MUTATED	5	29	16	49
DEL PEAK 9(4Q22.1) WILD-TYPE	32	50	48	29

Figure S58. Get High-res Image Gene #38: 'Del Peak 9(4q22.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 9(4q22.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000205 (Fisher's exact test), Q value = 0.068

Table S59. Gene #38: 'Del Peak 9(4q22.1) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	104	73
DEL PEAK 9(4Q22.1) MUTATED	36	31	23
DEL PEAK 9(4Q22.1) WILD-TYPE	23	73	50

Figure S59. Get High-res Image Gene #38: 'Del Peak 9(4q22.1) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 10(4q34.3) mutation analysis' versus 'CN_CNMF'

P value = 9.9e-21 (Fisher's exact test), Q value = 4.4e-18

Table S60. Gene #39: 'Del Peak 10(4q34.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 10(4Q34.3) MUTATED	18	78	15
DEL PEAK 10(4Q34.3) WILD-TYPE	135	40	20

Figure S60. Get High-res Image Gene #39: 'Del Peak 10(4q34.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 10(4q34.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.78e-06 (Fisher's exact test), Q value = 0.00066

Table S61. Gene #39: 'Del Peak 10(4q34.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 10(4Q34.3) MUTATED	3	25	20	44
DEL PEAK 10(4Q34.3) WILD-TYPE	34	54	44	34

Figure S61. Get High-res Image Gene #39: 'Del Peak 10(4q34.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 10(4q34.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.39e-05 (Fisher's exact test), Q value = 0.022

Table S62. Gene #39: 'Del Peak 10(4q34.3) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	104	73
DEL PEAK 10(4Q34.3) MUTATED	35	28	20
DEL PEAK 10(4Q34.3) WILD-TYPE	24	76	53

Figure S62. Get High-res Image Gene #39: 'Del Peak 10(4q34.3) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 11(5q11.2) mutation analysis' versus 'CN_CNMF'

P value = 8.3e-27 (Fisher's exact test), Q value = 3.7e-24

Table S63. Gene #40: 'Del Peak 11(5q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 11(5Q11.2) MUTATED	8	76	10
DEL PEAK 11(5Q11.2) WILD-TYPE	145	42	25

Figure S63. Get High-res Image Gene #40: 'Del Peak 11(5q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 11(5q11.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.93e-11 (Fisher's exact test), Q value = 1.2e-08

Table S64. Gene #40: 'Del Peak 11(5q11.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 11(5Q11.2) MUTATED	2	24	8	46
DEL PEAK 11(5Q11.2) WILD-TYPE	35	55	56	32

Figure S64. Get High-res Image Gene #40: 'Del Peak 11(5q11.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 11(5q11.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.27e-05 (Fisher's exact test), Q value = 0.0082

Table S65. Gene #40: 'Del Peak 11(5q11.2) mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	55	92
DEL PEAK 11(5Q11.2) MUTATED	24	5	40
DEL PEAK 11(5Q11.2) WILD-TYPE	65	50	52

Figure S65. Get High-res Image Gene #40: 'Del Peak 11(5q11.2) mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

'Del Peak 11(5q11.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.05e-06 (Fisher's exact test), Q value = 0.0015

Table S66. Gene #40: 'Del Peak 11(5q11.2) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	104	73
DEL PEAK 11(5Q11.2) MUTATED	32	26	11
DEL PEAK 11(5Q11.2) WILD-TYPE	27	78	62

Figure S66. Get High-res Image Gene #40: 'Del Peak 11(5q11.2) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 12(6p25.3) mutation analysis' versus 'CN_CNMF'

P value = 7.12e-10 (Fisher's exact test), Q value = 2.8e-07

Table S67. Gene #41: 'Del Peak 12(6p25.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 12(6P25.3) MUTATED	13	48	5
DEL PEAK 12(6P25.3) WILD-TYPE	140	70	30

Figure S67. Get High-res Image Gene #41: 'Del Peak 12(6p25.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 12(6p25.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000293 (Fisher's exact test), Q value = 0.097

Table S68. Gene #41: 'Del Peak 12(6p25.3) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	104	73
DEL PEAK 12(6P25.3) MUTATED	23	17	8
DEL PEAK 12(6P25.3) WILD-TYPE	36	87	65

Figure S68. Get High-res Image Gene #41: 'Del Peak 12(6p25.3) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 13(6q26) mutation analysis' versus 'CN_CNMF'

P value = 2.71e-07 (Fisher's exact test), Q value = 1e-04

Table S69. Gene #42: 'Del Peak 13(6q26) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 13(6Q26) MUTATED	11	38	9
DEL PEAK 13(6Q26) WILD-TYPE	142	80	26

Figure S69. Get High-res Image Gene #42: 'Del Peak 13(6q26) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 14(7q31.1) mutation analysis' versus 'CN_CNMF'

P value = 3.02e-08 (Fisher's exact test), Q value = 1.2e-05

Table S70. Gene #43: 'Del Peak 14(7q31.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 14(7Q31.1) MUTATED	6	33	2
DEL PEAK 14(7Q31.1) WILD-TYPE	147	85	33

Figure S70. Get High-res Image Gene #43: 'Del Peak 14(7q31.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 15(7q36.3) mutation analysis' versus 'CN_CNMF'

P value = 3.8e-17 (Fisher's exact test), Q value = 1.6e-14

Table S71. Gene #44: 'Del Peak 15(7q36.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 15(7Q36.3) MUTATED	4	49	2
DEL PEAK 15(7Q36.3) WILD-TYPE	149	69	33

Figure S71. Get High-res Image Gene #44: 'Del Peak 15(7q36.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 15(7q36.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 7.87e-06 (Fisher's exact test), Q value = 0.0029

Table S72. Gene #44: 'Del Peak 15(7q36.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 15(7Q36.3) MUTATED	0	16	5	25
DEL PEAK 15(7Q36.3) WILD-TYPE	37	63	59	53

Figure S72. Get High-res Image Gene #44: 'Del Peak 15(7q36.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 16(8p23.2) mutation analysis' versus 'CN_CNMF'

P value = 3.78e-18 (Fisher's exact test), Q value = 1.6e-15

Table S73. Gene #45: 'Del Peak 16(8p23.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 16(8P23.2) MUTATED	8	59	4
DEL PEAK 16(8P23.2) WILD-TYPE	145	59	31

Figure S73. Get High-res Image Gene #45: 'Del Peak 16(8p23.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 16(8p23.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.17e-06 (Fisher's exact test), Q value = 8e-04

Table S74. Gene #45: 'Del Peak 16(8p23.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 16(8P23.2) MUTATED	1	16	9	33
DEL PEAK 16(8P23.2) WILD-TYPE	36	63	55	45

Figure S74. Get High-res Image Gene #45: 'Del Peak 16(8p23.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 16(8p23.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000177 (Fisher's exact test), Q value = 0.06

Table S75. Gene #45: 'Del Peak 16(8p23.2) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	104	73
DEL PEAK 16(8P23.2) MUTATED	26	18	11
DEL PEAK 16(8P23.2) WILD-TYPE	33	86	62

Figure S75. Get High-res Image Gene #45: 'Del Peak 16(8p23.2) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 17(9p23) mutation analysis' versus 'CN_CNMF'

P value = 1.59e-23 (Fisher's exact test), Q value = 7.1e-21

Table S76. Gene #46: 'Del Peak 17(9p23) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 17(9P23) MUTATED	17	82	11
DEL PEAK 17(9P23) WILD-TYPE	136	36	24

Figure S76. Get High-res Image Gene #46: 'Del Peak 17(9p23) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 17(9p23) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000285 (Fisher's exact test), Q value = 0.094

Table S77. Gene #46: 'Del Peak 17(9p23) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 17(9P23) MUTATED	7	26	16	42
DEL PEAK 17(9P23) WILD-TYPE	30	53	48	36

Figure S77. Get High-res Image Gene #46: 'Del Peak 17(9p23) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 18(9p21.3) mutation analysis' versus 'CN_CNMF'

P value = 5.65e-23 (Fisher's exact test), Q value = 2.5e-20

Table S78. Gene #47: 'Del Peak 18(9p21.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 18(9P21.3) MUTATED	17	81	11
DEL PEAK 18(9P21.3) WILD-TYPE	136	37	24

Figure S78. Get High-res Image Gene #47: 'Del Peak 18(9p21.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 18(9p21.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.19e-09 (Fisher's exact test), Q value = 4.7e-07

Table S79. Gene #47: 'Del Peak 18(9p21.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 18(9P21.3) MUTATED	2	26	15	48
DEL PEAK 18(9P21.3) WILD-TYPE	35	53	49	30

Figure S79. Get High-res Image Gene #47: 'Del Peak 18(9p21.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 19(9q21.11) mutation analysis' versus 'CN_CNMF'

P value = 1.12e-14 (Fisher's exact test), Q value = 4.7e-12

Table S80. Gene #48: 'Del Peak 19(9q21.11) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 19(9Q21.11) MUTATED	8	53	7
DEL PEAK 19(9Q21.11) WILD-TYPE	145	65	28

Figure S80. Get High-res Image Gene #48: 'Del Peak 19(9q21.11) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 20(10p14) mutation analysis' versus 'CN_CNMF'

P value = 6.64e-08 (Fisher's exact test), Q value = 2.6e-05

Table S81. Gene #49: 'Del Peak 20(10p14) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 20(10P14) MUTATED	5	31	3
DEL PEAK 20(10P14) WILD-TYPE	148	87	32

Figure S81. Get High-res Image Gene #49: 'Del Peak 20(10p14) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 21(10q22.3) mutation analysis' versus 'CN_CNMF'

P value = 4.02e-12 (Fisher's exact test), Q value = 1.7e-09

Table S82. Gene #50: 'Del Peak 21(10q22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 21(10Q22.3) MUTATED	3	38	5
DEL PEAK 21(10Q22.3) WILD-TYPE	150	80	30

Figure S82. Get High-res Image Gene #50: 'Del Peak 21(10q22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 21(10q22.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.92e-05 (Fisher's exact test), Q value = 0.031

Table S83. Gene #50: 'Del Peak 21(10q22.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 21(10Q22.3) MUTATED	2	11	2	22
DEL PEAK 21(10Q22.3) WILD-TYPE	35	68	62	56

Figure S83. Get High-res Image Gene #50: 'Del Peak 21(10q22.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 22(10q23.31) mutation analysis' versus 'CN_CNMF'

P value = 1.17e-18 (Fisher's exact test), Q value = 5.1e-16

Table S84. Gene #51: 'Del Peak 22(10q23.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 22(10Q23.31) MUTATED	5	56	6
DEL PEAK 22(10Q23.31) WILD-TYPE	148	62	29

Figure S84. Get High-res Image Gene #51: 'Del Peak 22(10q23.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 22(10q23.31) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.36e-06 (Fisher's exact test), Q value = 0.00051

Table S85. Gene #51: 'Del Peak 22(10q23.31) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 22(10Q23.31) MUTATED	4	13	4	32
DEL PEAK 22(10Q23.31) WILD-TYPE	33	66	60	46

Figure S85. Get High-res Image Gene #51: 'Del Peak 22(10q23.31) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 22(10q23.31) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 8.96e-05 (Fisher's exact test), Q value = 0.031

Table S86. Gene #51: 'Del Peak 22(10q23.31) mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	55	92
DEL PEAK 22(10Q23.31) MUTATED	24	2	28
DEL PEAK 22(10Q23.31) WILD-TYPE	65	53	64

Figure S86. Get High-res Image Gene #51: 'Del Peak 22(10q23.31) mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

'Del Peak 22(10q23.31) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.69e-05 (Fisher's exact test), Q value = 0.017

Table S87. Gene #51: 'Del Peak 22(10q23.31) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	104	73
DEL PEAK 22(10Q23.31) MUTATED	22	27	5
DEL PEAK 22(10Q23.31) WILD-TYPE	37	77	68

Figure S87. Get High-res Image Gene #51: 'Del Peak 22(10q23.31) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 23(11p15.4) mutation analysis' versus 'CN_CNMF'

P value = 1.34e-10 (Fisher's exact test), Q value = 5.4e-08

Table S88. Gene #52: 'Del Peak 23(11p15.4) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 23(11P15.4) MUTATED	10	44	2
DEL PEAK 23(11P15.4) WILD-TYPE	143	74	33

Figure S88. Get High-res Image Gene #52: 'Del Peak 23(11p15.4) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 23(11p15.4) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000162 (Fisher's exact test), Q value = 0.055

Table S89. Gene #52: 'Del Peak 23(11p15.4) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 23(11P15.4) MUTATED	2	10	5	25
DEL PEAK 23(11P15.4) WILD-TYPE	35	69	59	53

Figure S89. Get High-res Image Gene #52: 'Del Peak 23(11p15.4) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 24(11q23.2) mutation analysis' versus 'CN_CNMF'

P value = 1.18e-06 (Fisher's exact test), Q value = 0.00044

Table S90. Gene #53: 'Del Peak 24(11q23.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 24(11Q23.2) MUTATED	12	38	5
DEL PEAK 24(11Q23.2) WILD-TYPE	141	80	30

Figure S90. Get High-res Image Gene #53: 'Del Peak 24(11q23.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 25(12p13.31) mutation analysis' versus 'CN_CNMF'

P value = 2.28e-11 (Fisher's exact test), Q value = 9.3e-09

Table S91. Gene #54: 'Del Peak 25(12p13.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 25(12P13.31) MUTATED	4	38	4
DEL PEAK 25(12P13.31) WILD-TYPE	149	80	31

Figure S91. Get High-res Image Gene #54: 'Del Peak 25(12p13.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 26(13q14.2) mutation analysis' versus 'CN_CNMF'

P value = 3.12e-05 (Fisher's exact test), Q value = 0.011

Table S92. Gene #55: 'Del Peak 26(13q14.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 26(13Q14.2) MUTATED	8	28	4
DEL PEAK 26(13Q14.2) WILD-TYPE	145	90	31

Figure S92. Get High-res Image Gene #55: 'Del Peak 26(13q14.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 27(14q21.1) mutation analysis' versus 'CN_CNMF'

P value = 1.06e-09 (Fisher's exact test), Q value = 4.2e-07

Table S93. Gene #56: 'Del Peak 27(14q21.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 27(14Q21.1) MUTATED	12	47	8
DEL PEAK 27(14Q21.1) WILD-TYPE	141	71	27

Figure S93. Get High-res Image Gene #56: 'Del Peak 27(14q21.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 28(14q32.33) mutation analysis' versus 'CN_CNMF'

P value = 2.7e-10 (Fisher's exact test), Q value = 1.1e-07

Table S94. Gene #57: 'Del Peak 28(14q32.33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 28(14Q32.33) MUTATED	16	53	12
DEL PEAK 28(14Q32.33) WILD-TYPE	137	65	23

Figure S94. Get High-res Image Gene #57: 'Del Peak 28(14q32.33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 29(15q11.2) mutation analysis' versus 'CN_CNMF'

P value = 2.4e-16 (Fisher's exact test), Q value = 1e-13

Table S95. Gene #58: 'Del Peak 29(15q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 29(15Q11.2) MUTATED	7	54	12
DEL PEAK 29(15Q11.2) WILD-TYPE	146	64	23

Figure S95. Get High-res Image Gene #58: 'Del Peak 29(15q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 29(15q11.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.86e-05 (Fisher's exact test), Q value = 0.01

Table S96. Gene #58: 'Del Peak 29(15q11.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 29(15Q11.2) MUTATED	5	17	7	34
DEL PEAK 29(15Q11.2) WILD-TYPE	32	62	57	44

Figure S96. Get High-res Image Gene #58: 'Del Peak 29(15q11.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 29(15q11.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000107 (Fisher's exact test), Q value = 0.036

Table S97. Gene #58: 'Del Peak 29(15q11.2) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	104	73
DEL PEAK 29(15Q11.2) MUTATED	26	21	9
DEL PEAK 29(15Q11.2) WILD-TYPE	33	83	64

Figure S97. Get High-res Image Gene #58: 'Del Peak 29(15q11.2) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 30(15q15.1) mutation analysis' versus 'CN_CNMF'

P value = 3.92e-15 (Fisher's exact test), Q value = 1.7e-12

Table S98. Gene #59: 'Del Peak 30(15q15.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 30(15Q15.1) MUTATED	9	55	11
DEL PEAK 30(15Q15.1) WILD-TYPE	144	63	24

Figure S98. Get High-res Image Gene #59: 'Del Peak 30(15q15.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 30(15q15.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 9.19e-05 (Fisher's exact test), Q value = 0.032

Table S99. Gene #59: 'Del Peak 30(15q15.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 30(15Q15.1) MUTATED	6	16	7	33
DEL PEAK 30(15Q15.1) WILD-TYPE	31	63	57	45

Figure S99. Get High-res Image Gene #59: 'Del Peak 30(15q15.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 30(15q15.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.96e-05 (Fisher's exact test), Q value = 0.021

Table S100. Gene #59: 'Del Peak 30(15q15.1) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	104	73
DEL PEAK 30(15Q15.1) MUTATED	26	23	8
DEL PEAK 30(15Q15.1) WILD-TYPE	33	81	65

Figure S100. Get High-res Image Gene #59: 'Del Peak 30(15q15.1) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 31(16p13.3) mutation analysis' versus 'CN_CNMF'

P value = 3.29e-12 (Fisher's exact test), Q value = 1.4e-09

Table S101. Gene #60: 'Del Peak 31(16p13.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 31(16P13.3) MUTATED	6	43	3
DEL PEAK 31(16P13.3) WILD-TYPE	147	75	32

Figure S101. Get High-res Image Gene #60: 'Del Peak 31(16p13.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 31(16p13.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000676 (Fisher's exact test), Q value = 0.22

Table S102. Gene #60: 'Del Peak 31(16p13.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 31(16P13.3) MUTATED	1	13	6	23
DEL PEAK 31(16P13.3) WILD-TYPE	36	66	58	55

Figure S102. Get High-res Image Gene #60: 'Del Peak 31(16p13.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 32(16q23.1) mutation analysis' versus 'CN_CNMF'

P value = 1.13e-10 (Fisher's exact test), Q value = 4.6e-08

Table S103. Gene #61: 'Del Peak 32(16q23.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 32(16Q23.1) MUTATED	25	64	15
DEL PEAK 32(16Q23.1) WILD-TYPE	128	54	20

Figure S103. Get High-res Image Gene #61: 'Del Peak 32(16q23.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 33(17p12) mutation analysis' versus 'CN_CNMF'

P value = 8.32e-32 (Fisher's exact test), Q value = 3.7e-29

Table S104. Gene #62: 'Del Peak 33(17p12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 33(17P12) MUTATED	7	82	14
DEL PEAK 33(17P12) WILD-TYPE	146	36	21

Figure S104. Get High-res Image Gene #62: 'Del Peak 33(17p12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 33(17p12) mutation analysis' versus 'METHLYATION_CNMF'

P value = 9.36e-08 (Fisher's exact test), Q value = 3.6e-05

Table S105. Gene #62: 'Del Peak 33(17p12) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 33(17P12) MUTATED	5	24	12	46
DEL PEAK 33(17P12) WILD-TYPE	32	55	52	32

Figure S105. Get High-res Image Gene #62: 'Del Peak 33(17p12) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 33(17p12) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.01e-05 (Fisher's exact test), Q value = 0.0072

Table S106. Gene #62: 'Del Peak 33(17p12) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	104	73
DEL PEAK 33(17P12) MUTATED	33	32	13
DEL PEAK 33(17P12) WILD-TYPE	26	72	60

Figure S106. Get High-res Image Gene #62: 'Del Peak 33(17p12) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 34(17q24.3) mutation analysis' versus 'CN_CNMF'

P value = 9.38e-12 (Fisher's exact test), Q value = 3.8e-09

Table S107. Gene #63: 'Del Peak 34(17q24.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 34(17Q24.3) MUTATED	4	39	7
DEL PEAK 34(17Q24.3) WILD-TYPE	149	79	28

Figure S107. Get High-res Image Gene #63: 'Del Peak 34(17q24.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 35(18q21.2) mutation analysis' versus 'CN_CNMF'

P value = 8.77e-19 (Fisher's exact test), Q value = 3.8e-16

Table S108. Gene #64: 'Del Peak 35(18q21.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 35(18Q21.2) MUTATED	26	83	15
DEL PEAK 35(18Q21.2) WILD-TYPE	127	35	20

Figure S108. Get High-res Image Gene #64: 'Del Peak 35(18q21.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 35(18q21.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.92e-05 (Fisher's exact test), Q value = 0.031

Table S109. Gene #64: 'Del Peak 35(18q21.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 35(18Q21.2) MUTATED	15	29	13	45
DEL PEAK 35(18Q21.2) WILD-TYPE	22	50	51	33

Figure S109. Get High-res Image Gene #64: 'Del Peak 35(18q21.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 36(18q23) mutation analysis' versus 'CN_CNMF'

P value = 1.21e-17 (Fisher's exact test), Q value = 5.2e-15

Table S110. Gene #65: 'Del Peak 36(18q23) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 36(18Q23) MUTATED	24	79	13
DEL PEAK 36(18Q23) WILD-TYPE	129	39	22

Figure S110. Get High-res Image Gene #65: 'Del Peak 36(18q23) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 36(18q23) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.58e-05 (Fisher's exact test), Q value = 0.0057

Table S111. Gene #65: 'Del Peak 36(18q23) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 36(18Q23) MUTATED	14	25	11	44
DEL PEAK 36(18Q23) WILD-TYPE	23	54	53	34

Figure S111. Get High-res Image Gene #65: 'Del Peak 36(18q23) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 37(19p13.3) mutation analysis' versus 'CN_CNMF'

P value = 2.75e-29 (Fisher's exact test), Q value = 1.2e-26

Table S112. Gene #66: 'Del Peak 37(19p13.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 37(19P13.3) MUTATED	5	75	11
DEL PEAK 37(19P13.3) WILD-TYPE	148	43	24

Figure S112. Get High-res Image Gene #66: 'Del Peak 37(19p13.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 37(19p13.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.98e-12 (Fisher's exact test), Q value = 8.3e-10

Table S113. Gene #66: 'Del Peak 37(19p13.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 37(19P13.3) MUTATED	3	20	5	46
DEL PEAK 37(19P13.3) WILD-TYPE	34	59	59	32

Figure S113. Get High-res Image Gene #66: 'Del Peak 37(19p13.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 37(19p13.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000169 (Fisher's exact test), Q value = 0.057

Table S114. Gene #66: 'Del Peak 37(19p13.3) mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	55	92
DEL PEAK 37(19P13.3) MUTATED	22	7	40
DEL PEAK 37(19P13.3) WILD-TYPE	67	48	52

Figure S114. Get High-res Image Gene #66: 'Del Peak 37(19p13.3) mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

'Del Peak 37(19p13.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.79e-09 (Fisher's exact test), Q value = 2.3e-06

Table S115. Gene #66: 'Del Peak 37(19p13.3) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	104	73
DEL PEAK 37(19P13.3) MUTATED	36	23	10
DEL PEAK 37(19P13.3) WILD-TYPE	23	81	63

Figure S115. Get High-res Image Gene #66: 'Del Peak 37(19p13.3) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 38(19q13.11) mutation analysis' versus 'CN_CNMF'

P value = 1.39e-10 (Fisher's exact test), Q value = 5.6e-08

Table S116. Gene #67: 'Del Peak 38(19q13.11) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 38(19Q13.11) MUTATED	2	31	7
DEL PEAK 38(19Q13.11) WILD-TYPE	151	87	28

Figure S116. Get High-res Image Gene #67: 'Del Peak 38(19q13.11) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 38(19q13.11) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000142 (Fisher's exact test), Q value = 0.048

Table S117. Gene #67: 'Del Peak 38(19q13.11) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 38(19Q13.11) MUTATED	0	13	2	17
DEL PEAK 38(19Q13.11) WILD-TYPE	37	66	62	61

Figure S117. Get High-res Image Gene #67: 'Del Peak 38(19q13.11) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 38(19q13.11) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.22e-05 (Fisher's exact test), Q value = 0.018

Table S118. Gene #67: 'Del Peak 38(19q13.11) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	104	73
DEL PEAK 38(19Q13.11) MUTATED	18	7	5
DEL PEAK 38(19Q13.11) WILD-TYPE	41	97	68

Figure S118. Get High-res Image Gene #67: 'Del Peak 38(19q13.11) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 39(20p12.1) mutation analysis' versus 'CN_CNMF'

P value = 1.86e-10 (Fisher's exact test), Q value = 7.5e-08

Table S119. Gene #68: 'Del Peak 39(20p12.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 39(20P12.1) MUTATED	10	40	0
DEL PEAK 39(20P12.1) WILD-TYPE	143	78	35

Figure S119. Get High-res Image Gene #68: 'Del Peak 39(20p12.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 39(20p12.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 7.73e-05 (Fisher's exact test), Q value = 0.027

Table S120. Gene #68: 'Del Peak 39(20p12.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 39(20P12.1) MUTATED	4	14	2	24
DEL PEAK 39(20P12.1) WILD-TYPE	33	65	62	54

Figure S120. Get High-res Image Gene #68: 'Del Peak 39(20p12.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 40(20p12.1) mutation analysis' versus 'CN_CNMF'

P value = 1.86e-10 (Fisher's exact test), Q value = 7.5e-08

Table S121. Gene #69: 'Del Peak 40(20p12.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 40(20P12.1) MUTATED	10	40	0
DEL PEAK 40(20P12.1) WILD-TYPE	143	78	35

Figure S121. Get High-res Image Gene #69: 'Del Peak 40(20p12.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 40(20p12.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 7.73e-05 (Fisher's exact test), Q value = 0.027

Table S122. Gene #69: 'Del Peak 40(20p12.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 40(20P12.1) MUTATED	4	14	2	24
DEL PEAK 40(20P12.1) WILD-TYPE	33	65	62	54

Figure S122. Get High-res Image Gene #69: 'Del Peak 40(20p12.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 41(21q11.2) mutation analysis' versus 'CN_CNMF'

P value = 2.75e-15 (Fisher's exact test), Q value = 1.2e-12

Table S123. Gene #70: 'Del Peak 41(21q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 41(21Q11.2) MUTATED	17	66	14
DEL PEAK 41(21Q11.2) WILD-TYPE	136	52	21

Figure S123. Get High-res Image Gene #70: 'Del Peak 41(21q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 41(21q11.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.093

Table S124. Gene #70: 'Del Peak 41(21q11.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 41(21Q11.2) MUTATED	4	26	15	37
DEL PEAK 41(21Q11.2) WILD-TYPE	33	53	49	41

Figure S124. Get High-res Image Gene #70: 'Del Peak 41(21q11.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 42(21q22.13) mutation analysis' versus 'CN_CNMF'

P value = 6.07e-16 (Fisher's exact test), Q value = 2.6e-13

Table S125. Gene #71: 'Del Peak 42(21q22.13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 42(21Q22.13) MUTATED	18	68	16
DEL PEAK 42(21Q22.13) WILD-TYPE	135	50	19

Figure S125. Get High-res Image Gene #71: 'Del Peak 42(21q22.13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 42(21q22.13) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000405 (Fisher's exact test), Q value = 0.13

Table S126. Gene #71: 'Del Peak 42(21q22.13) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 42(21Q22.13) MUTATED	4	26	16	37
DEL PEAK 42(21Q22.13) WILD-TYPE	33	53	48	41

Figure S126. Get High-res Image Gene #71: 'Del Peak 42(21q22.13) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 43(22q13.31) mutation analysis' versus 'CN_CNMF'

P value = 1.61e-19 (Fisher's exact test), Q value = 7.1e-17

Table S127. Gene #72: 'Del Peak 43(22q13.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 43(22Q13.31) MUTATED	12	69	10
DEL PEAK 43(22Q13.31) WILD-TYPE	141	49	25

Figure S127. Get High-res Image Gene #72: 'Del Peak 43(22q13.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 43(22q13.31) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.05e-06 (Fisher's exact test), Q value = 4e-04

Table S128. Gene #72: 'Del Peak 43(22q13.31) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 43(22Q13.31) MUTATED	2	23	11	38
DEL PEAK 43(22Q13.31) WILD-TYPE	35	56	53	40

Figure S128. Get High-res Image Gene #72: 'Del Peak 43(22q13.31) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 43(22q13.31) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.064

Table S129. Gene #72: 'Del Peak 43(22q13.31) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	104	73
DEL PEAK 43(22Q13.31) MUTATED	29	27	12
DEL PEAK 43(22Q13.31) WILD-TYPE	30	77	61

Figure S129. Get High-res Image Gene #72: 'Del Peak 43(22q13.31) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 44(Xp22.2) mutation analysis' versus 'CN_CNMF'

P value = 2.64e-14 (Fisher's exact test), Q value = 1.1e-11

Table S130. Gene #73: 'Del Peak 44(Xp22.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 44(XP22.2) MUTATED	7	45	0
DEL PEAK 44(XP22.2) WILD-TYPE	146	73	35

Figure S130. Get High-res Image Gene #73: 'Del Peak 44(Xp22.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 44(Xp22.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000311 (Fisher's exact test), Q value = 0.1

Table S131. Gene #73: 'Del Peak 44(Xp22.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 44(XP22.2) MUTATED	0	13	9	23
DEL PEAK 44(XP22.2) WILD-TYPE	37	66	55	55

Figure S131. Get High-res Image Gene #73: 'Del Peak 44(Xp22.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 45(Xp21.1) mutation analysis' versus 'CN_CNMF'

P value = 1.54e-13 (Fisher's exact test), Q value = 6.4e-11

Table S132. Gene #74: 'Del Peak 45(Xp21.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 45(XP21.1) MUTATED	3	40	2
DEL PEAK 45(XP21.1) WILD-TYPE	150	78	33

Figure S132. Get High-res Image Gene #74: 'Del Peak 45(Xp21.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 46(Xq21.33) mutation analysis' versus 'CN_CNMF'

P value = 8.31e-08 (Fisher's exact test), Q value = 3.2e-05

Table S133. Gene #75: 'Del Peak 46(Xq21.33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	153	118	35
DEL PEAK 46(XQ21.33) MUTATED	4	29	5
DEL PEAK 46(XQ21.33) WILD-TYPE	149	89	30

Figure S133. Get High-res Image Gene #75: 'Del Peak 46(Xq21.33) mutation analysis' versus Clinical Feature #1: '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 = STAD-TP.transferedmergedcluster.txt
Number of patients = 306
Number of copy number variation regions = 75
Number of molecular subtypes = 6
Exclude regions that fewer than K tumors have alterations, K = 3

Fisher's exact test

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

Q value calculation

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

References

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

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

[3] GISTIC_version2

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